HC's Corporate Magazine Voyager

I N S T I T U T I O N
A Hwa Chong Institution Research Publication
ISSUE : 03/2014
ABOUT
VOYAGER
ABOUT
VOYAGER
Voyager, the brainchild of members from the Science

Voyager,
Students
the brainchild
ResearchofCouncil,
members
was
from
established
the Science Studen
in 2010. The theme varies from year to year and ininthis
2010.
third
The
issue
theme
of Voyager,
varies from
we year
explore
to year
the theme
and in this third is
Discover: Forging Ahead Together for the next
Discover:
Milestone.
Forging
This publication
Ahead Together
aims tofor
serve
the as
next
a Milestone
microcosm of the many facets of research andmicrocosm
seeks to reveal
of thethe
many
research
facets experiences
of research and
and seeks to
extensive support network of Hwa Chong Institutions
extensive
research
support
community.
network of Hwa Chong Institutions resea
Editor-in-Chief
Editor-in-Chief
Chiang Yan Xin 14S7F
Chiang Yan Xin 14S7F
Publication Team
Publication Team
Chiang Yan Li 13S7B
Chiang Yan Li 13S7B
Poh Yong Rui 13S7J
Poh Yong Rui 13S7J
Ng Jun Xuan 13S7G
Ng Jun Xuan 13S7G
Kwan Jing Ling 14S79
Kwan Jing Ling 14S79
Lee Zhi Rui 14S79
Lee Zhi Rui 14S79
Zhou Pei Yu 14S6A
Zhou Pei Yu 14S6A
Teacher Advisor
Teacher Advisor
Dr Kelvin Tan Yong Leng
Dr Kelvin Tan Yong Leng
Education Consultant/ Research
Education Consultant/ Research
www. hc i.e d u. s g
We maintain a culture of continuous transformation. This year, Voyager has evolved to

include Foundations for the Future, which feature articles with a personal and distinct
focus on the research experiences of Hwa Chongs alumni who have embarked on their
various endeavours after graduating from Hwa Chong. Our team has had the privilege of
sharing their insights on their research experiences as well as the potent driving force
behind their choices to embark on their present disciplines with you. We believe that by
sharing both the experiences of our present students as well as our alumni, we can impart
profound meaning to the relevance of Hwa Chongs research experience to the present
and the future.
We hope that this issue of Voyager will be an invigorating and insightful read that serves
as a harbinger of Hwa Chongs distinctive research culture and close-knitted research
community. We also hope that future Voyager editorial committees will continue to
present the best of our students work to you.
Yours sincerely,
Chiang Yan Xin
Editor-in-Chief
On behalf of the Voyager Editorial Committee 2014
VOYAGER 2014
The advent of 2014 marks new beginnings for Voyager. Featuring a plethora of
research-centered articles, we remain committed to bringing to you the finest of Hwa
Chongs research work.
Editorial
EDITORIAL
03
CONTENTS
06
07
SPOTLIGHT:
Nurturing Bright Sparks
09
14
FALL DETECTION SYSTEM BASED ON

KINECT SENSOR USING NOVEL DETECTION
AND POSTURE RECOGNITION ALGORITHM
INVESTIGATION INTO THE RELATIONSHIP

BETWEEN VIOLIN STRING TIMBRE AND
ITS HARMONIC STRUCTURE
57
63
GREEN SYNTHESIS OF SILVER

NANOPARTICLES USING
LALANG EXTRACT
DETERMINING THE AMINO ACIDS

INVOLVED IN INHIBITION OF PDE4B BY
STRUCTURALLY-DIVERSE COMPOUNDS
45
51
USE OF RECYCLED CLAM SHELLS

IN WATER PURIFICATION
QUORUM SENSING INHIBITION

ACTIVITY OF SELECTED TRADITIONAL
CHINESE MEDICINAL (TCM) HERBS TO
INHIBIT BIOFILM FORMATION
32
37
FOUNDATIONS FOR
THE FUTURE
STUDENTS VOICES
17
24
FOREWORD
HISTORIC VENUS TRANSIT 2012

AND INSTRUMENTATION
ACKNOWLEDGEMENTS
This research provides a method to

build a database of different
instrumental timbre. Findings in this
studycan be used in computer
generated music to create more
variance in instrumental timbre.
Yang Liuyi and Wang Jia
Investigation into the relationship between violin string

timbre and its harmonic structure
Our fall detection system is capable of processing

incoming sensor information and displaying of
results concurrently without a loss in processing
speed or performance degradation.
Lee Choon Kiat
Fall Detection System based on Kinect Sensor using Novel Detection and
Posture Recognition Algorithm
Cai Anni
Determining the amino acids involved in inhibition of PDE4B by

structurally-diverse compounds
Four versions of prototype were constructed using lala clam

and blood cockle shells. With each version, improvement
was made to enhance the feasibility of the prototype.
Ong Yinn Jaye, Yeo Kang Le and Gong Wei Jin
Use of recycled clam shells in water purification
VOYAGER 2014
05
Excerpts
The different frequency of stained colonies

for different buffers may be correlated to
the rate and type of mutagenesis that the 6
buffers confer. High rates of mutagenesis
may lead to changes in the essential amino
acids of the catalytic domain, thus
rendering the PDE product non-functional.
FOREWORD
Now in its third issue, Voyager highlights some of our students
exemplary research projects. It is heartening to see the next
generation of scientific talents eager to contribute positively to
the world around them.
Indeed, such passion has been the driving force behind humanitys
efforts to overcome barriers and expand our boundaries. In
todays complex and uncertain world, the challenges are
multifaceted and immense. However, the faith scientists have in
the transformative power of research remains strong. It is research
that will enable us to not just survive, but thrive in the future.
Dr Hon Chiew Weng

Principal
Hwa Chong Institution
Foreword
VOYAGER 2014
06
This year, our students continue to work under the mentorship of

esteemed research institutions and industry partners, such as the
Agency for Science, Technology and Research (A*STAR), National
University of Singapore (NUS), Nanyang Technological University
(NTU), and Singapore University of Technology and Design
(SUTD). Our partners demonstrate the extensive breadth and
depth of cutting-edge research that Singapore has been lauded
for. In addition, our own School Scientist Programme, started in
2012, has shown much promise. The school scientists have taken
students under their wing, proffering their wealth of experience
and knowledge. Under their mentors auspices, our students have
been inspired to think creatively and critically, and to always direct
research for the benefit of mankind. We are thus grateful for their
dedication and guidance.
In this issue of Voyager, you will read about how our students have
striven to help society and the world-at-large overcome critical
obstacles. Under the mentorship of Dr Lee Vwen Yen, from the
Institute for Infocomm Research, A*STAR, Lee Choon Kiat (12S68)
invented a fall detection system for the elderly who live alone. The
system can automatically recognise falls and notify healthcare
services to provide timely assistance, a boon to the elderly in
ageing societies all around the world. Ong Yinn Jaye (13S75), Yeo
Kang Le (13S79) and Gong Wei Jin (13S67) meanwhile explored
the use of clam shells to remove heavy metal ions from water, and
constructed a low-cost water filter. Their project is a significant
breakthrough that might significantly aid developing countries in
their critical quest for clean water. These projects and the other
equally impressive studies all have the potential to shape the
worlds future in a revolutionary manner.
Learn from yesterday, live for today, hope for tomorrow. The
important thing is to not stop questioning. Albert Einsteins quote
encapsulates what we hope to develop our budding scientists into
inquisitive scientific leaders who constantly seek to find new
hopes for the future. After all, science will remain a constructive
and guiding force only if its leaders are driven by two important
values passion and compassion, the very values that we nurture
in our students.
Spotlight:
NURTURING
BRIGHT
SPARKS
think what nobody has thought. Nobel laureate
and the Defence Science and Technology Agency
Albert
great
(DSTA). Similarly, the Nanyang Research Program
scientists, made groundbreaking discoveries in the
(NRP) helmed by Nanyang Technological University
most unsuspecting of circumstances. Hwa Chong too
(NTU) provides a platform for our students to explore
hopes to lay the foundations for such discoveries by
their
developing our students critical, creative and caring
sciences and social sciences. In addition, Hwa Chong
minds, grooming them to become leaders in the
has formed firm partnerships with local research
scientific community of tomorrow.
institutes such as the Agency for Science, Technology
Szent
Gyorgyi,
alongside
many
and
research
Research
interests
(A*STAR)
in
as
engineering,
well
as
natural
overseas
Hwa Chongs own internal research programme, the
universities such as University of Glasgow, Scotland.
Centre for Talent Development in Science (CenTaD),
These strong alliances provide a vibrant hub for
aims to promote a strong culture and passion for
scientific discoveries and opinions where the passion
research amongst its students. Under the guidance of
and curiosity of Hwa Chong students are cultivated.
experienced mentors and laboratory staff, Hwa

Chong students engage in authentic problem-solving
and gain in-depth knowledge beyond the walls of the
classroom. Equipped with specialised laboratories
with the ability to support projects in the fields of
environmental science, synthetic chemistry, biology
Hwa Chongs own internal research

programme, the Centre for Talent
Development in Science (CenTaD), aims
to promote a strong culture and passion
for research amongst its students.
and photonics, Hwa Chongs Science Research Center

(SRC) is a dynamic nexus for the exchange of
Hwa Chong provides many platforms, such as the
scientific ideas and a facility to promote innovation.
annual CenTaD Research Conference, for budding

student researchers to communicate their research
jointly
projects and receive valuable feedback from their
organised by the Ministry of Education and the
peers as well as mentors. The Singapore Science
National University of Singapore (NUS), provides
Engineering Fair (SSEF) allows for outstanding
opportunities for students to delve into research
student researchers to represent the school in
fields as diverse as robotics and engineering,
showcasing
computer science, microbiology and pharmaceutical
presenting their projects to experts hailing from the
The
Science
Research
Program
(SRP),
their
work
on
the
national
stage,
07
VOYAGER 2014
sciences under the mentorship of scientists from NUS
Spotlight: Nurturing Bright Sparks
Research is to see what everyone has seen, and to
Spotlight: Nurturing Bright Sparks
VOYAGER 2014
08
academia, research institutes and industry. Moreover,
important. Students embark on rigorous learning
Hwa Chong also hosts the annual International
journeys and they end up gaining more than just their
Science Youth Forum (ISYF), where our top science
research findings: they are empowered with the
research students are joined by like-minded peers
ability to think creatively, solve problems and
from across the globe. With activities ranging from
persevere. They see problems in a new light, think out
master classes with Nobel Laureates and Fields
of the box and by applying the valuable skills that
Medallists, to understanding Singapores research
they have learnt, offer refreshing perspectives.
landscape through visits, to dialogue sessions where

ideas are exchanged and experiences shared, ISYF
sets the stage for close interaction between these top
science talents from all over the world, enabling them
to forge valuable friendships and gain new insights
into the global research culture.
Any research student will ascertain the fact that
research is far from a bed of roses. It is rigorous and
the demanding nature of research can be at times
overwhelming, but the process of gaining new
insights and perspectives make research an enjoyable
and exhilarating experience. As Tricia Teo Wei Tian
from 14S7D shared with us, Research is really about
keeping an open mind. There is always a chance for
experimental
results
to
deviate
from
your
expectations so you cannot maintain a fixed mindset.

You have to be able to learn from each attempt, and
be willing to consider and try different ways of
approaching the same problem.
Ultimately, in research, the focus is not solely on the
end-product, as the process is equally if not more
Students embark on rigorous learning

journeys and they end up gaining more
than just their research findings: they
are empowered with the ability to think
creatively,
solve
problems
and
persevere.
FOUNDATIONS
FOR THE FUTURE
The Voyager Editorial Team had the privilege of speaking to three of our distinguished
alumni: Dr Vincent Tan Yan Fu (98S34), Dr Guo Huili (00S73) and Mr Sng Jie Han Timothy
(09S79). Leveraging on the solid foundations built during their time in Hwa Chong, Dr Tan
and Dr Guo, who are married to each other, continued to pursue their passion for research
in their present careers while Mr Sng is currently a Dentistry undergraduate at the
National University of Singapore. They share with us their research experiences and what
influenced them to embark on their present fields and disciplines
ocean and yet barnacles can still stick so sturdily to
rocks and surfaces of ships etc. Interestingly, one of
our team mates was on orthodontic treatment and
somehow we drew parallels between the barnacle
and the orthodontic brackets (braces) that were
adhered to his teeth.
the
reason
for
such
phenomenon.
This
protein-based glue, commonly termed as barnacle

cement, secreted by barnacles was found to be a
bane to the shipping industry and many material
scientists, one of whom was our co-mentor, Dr Gary
H. Dickinson, were exploring ways to develop
anti-fouling surfaces to weaken this robust adhesion
between barnacles and ships.
Could you tell us more about your research project?

My research team was investigating the potential of
With guidance from our 2 mentors (from different
barnacle cement in dentistry, more specifically as a
fields), we continued researching on how we may
form of dental material.
utilise this material for clinical dentistry,
We understand that your initial research topic was
Reflecting on your time as a student, what forms of
not directly related to the application of barnacles in
research exposure did you have and what forms of
the dentistry sector. Your team came up with the
support did you receive from the school?
ingenious idea of applying what was previously
In year 3 and 4 at High School, I was trained under the
undesirable for the shipping industry to dentistry.
Science & Math Research Programme (SMRP). Via
What was your teams inspiration for delving into
SMRP, students learnt about the basics of scientific
this cross-disciplinary research topic and how was
research from guest scientists, teachers & our seniors.
this idea developed?
We
All of us in the team had experiences with dental
projects, eventually presenting and defending our
restorations (fillings) and orthodontic treatment
research paper in the presence of teacher assessors. I
where the dental material used plays a very crucial
believe that the HCI Integrated programme has
role in determining the longevity and success of the
offered me much more liberty to participate actively
specific treatment.
in research projects and research-related activities
then
proceeded
to
conduct
experimental
such as the research collaboration cum exchange

What inspired us was a meeting with our project
programme with the Academy of Science-Virginia,
mentor, A/P Stephen Hsu. He mentioned how the
International Science Youth Forum (ISYF) and various
harsh environment of our oral cavity is akin to the
science fairs. These opportunities to learn beyond the
09
VOYAGER 2014
From there, we were very intrigued and read up on
Foundations For The Future
Our alumnus, Mr Sng Jie Han Timothy

(09S79) was part of a team of 3 HCI
students who undertook a project under
the Science Research Program, which was
co-mentored by a faculty member from the
Faculty of Dentistry as well as a marine
biology expert from the Tropical Marine
Science Institute. This project was awarded
the Gold Award at the 2010 Singapore
Science and Engineering Fair (SSEF), and
the team was selected to represent
Singapore at the 2010 International
Science and Engineering Fair (ISEF).
Timothy is currently an undergraduate at
the Faculty of Dentistry at NUS.
designated O level science syllabus has seeded in me
There were other fun-filled ISEF-organised events
the academic curiosity and drive to apply knowledge
throughout that entire week at San Jose, including
in experimental research.
the pin-exchange, Nobel panel discussion as well as

an exhibition of GOOGLEs technology (robotics and
In addition, the helpful and patient laboratory staff at
satellite technology).
Hwa Chongs Science Research Centre, especially the

laboratory manager, Madam Lim Cheng Fui, have
What challenges did your team face during your
always been pillars of support from the time I was
research and how did you overcome them?
doing experimental research in year 3 till my final year
This project has been a fruitful learning journey as I
in college. I am very grateful for their guidance and
have not only acquired a deeper understanding of the
they are certainly assets to HCI.
multi-faceted aspects of dental research but have

also grown in terms of character. The first bottleneck
came when my group spent one month brainstorming
medallists in the Singapore Science and Engineering
for a research topic but remained undecided on any.
Fair (SSEF) and represented Singapore in the
Nevertheless, with the motivation of our mentors, my
International Science and Engineering Fair (ISEF).
team persevered on and finally chanced upon a
When you first started your research, were you
unique topic that we were all excited about. Despite
expecting such an outcome?
having a slow start, the passion we had for our novel
Personally, I was hoping that our research was, as
and well thought-out project was the very source of
much as possible, conducted to a certain degree of
our motivation. Thus, while we often faced challenges
completion (that we agreed upon before we started
in the experimental phase of our research, we were
on our experiments). Receiving awards in such
always determined to overcome them as a team.
on the cake. Still, I felt that they serve as a form of
Any words of encouragement or advice for your
VOYAGER 2014
science fairs are often stated to be a bonus or icing

recognition and approval of the standards of ones
juniors?
research project. I was certainly exhilarated when we
Take ownership of your project. Be proud of it.
10
We understand that your team emerged as gold
Could
were given this opportunity to participate in ISEF. I

Work on a topic that you are really very keen on and
would say that it is indeed by Gods grace!
this passion will likely be your source of fuel in times

you
share
with
us
more
about
your
experiences at ISEF?
of stress and fatigue as you face various challenges in

your project.
The public viewing day was certainly memorable. As

ISEF finalists, we had the chance to explain our work
If you are unexcited in your research, it is hard to
to the general public and even to one another. The
expect others (be it your peers or judges) to be
depth and scope of the projects at ISEF were
interested in it.
incredible and it was an eye opener to witness how

peers of our age can actually come up with such
Thank you very much and we wish you the very best
detailed methodologies and creative ideas to tackle
in your future endeavours!
scientific problems.
Timothy (right) with fellow Hwa Chong team members Joseph Ang (09S7A) and Clement Lee (09S6K) at the Intel ISEF 2010.
FOUNDATIONS
FOR THE FUTURE
Dr Guo Huili
Dr Vincent Tan Yan Fu

Dr Vincent Tan (98S34) graduated from the
University of Cambridge with an undergraduate
degree in Electrical Engineering as well as a Ph.D.
degree in Electrical Engineering and Computer
Science from MIT. He was a recipient of the Public
Service Commission and A*STAR scholarships.
After working at the Institute for Infocomm
Research at A*STAR, Dr Tan joined NUS as an
Assistant Professor, where he currently holds a
joint appointment at both the departments of
Electrical and Computer Engineering as well as
Mathematics.
Dr Vincent Tan
VOYAGER 2014
11
Dr Guo Huili
A recipient of National Science Scholarships from

the Agency for Science, Technology and Research
(A*STAR), Dr Guo (00S73) graduated from the
University of Cambridge in 2005 with a B.A.
degree in Natural Sciences. In 2011, she received
her Ph.D. degree in Biology from the
Massachusetts Institute of Technology (MIT). Dr
Guo was awarded an Institute of Molecular and Cell
Biology Independent Fellowship in 2012. She is
currently an Adjunct Assistant Professor with the
Department of Biological Sciences at the National
University of Singapore (NUS), as well as the Lee
Kong Chian School of Medicine at Nanyang
Technological University. Dr Guo was recently
selected to be one of the ambassadors for the UN
Women STEM (Science, Technology, Engineering
and Mathematics) program.
Dr Guo and Dr Tan, please tell us more about your
combine my love for teaching and mentoring with the
current research field and direction.
discovery of new ideas and theorems.
Dr Guo (HG): I use molecular biology and genomics

to study how protein synthesis regulates cellular
Could you kindly share with us some insights from
differentiation. This may sound abstract but is
your research experience?
actually not: people are familiar with the idea that
HG: I learnt from my professor at MIT to never ignore
genes get turned on and off to make different types
the small details/blips/weird result that come out of
of cells; I am doing essentially that, just that I am
an experiment you never know when that blip could
focusing on a downstream step When a gene is
be telling you something important that has yet to be
turned on, messenger molecule known as the
discovered. Do not be afraid of trying out new
messenger RNA gets made, but this does not
fields/testing out new ideas; you never know when
necessarily lead to the synthesis of a protein. I am
you might find your passion/discover something
studying how this step is regulated, and how it in
because you bothered testing out your ideas (lots of
turns controls the differentiation of different cell
people dont they just say, but dont do. And thats a
types. This is important because proteins are the foot
mistake.)
soldiers that carry out most of the work in our cells.

VT: The main lesson I learned from my professor is to
deciphering how they work will impact upon many
think hard rather than do too much. I remembered
different biological processes and human diseases.
a meeting with him early on my PhD. I told him that I
Gaining insight into these mechanisms, and the
did A, B and C over the past week. He said great but
potential to come up with novel therapeutic avenues,
added that the important thing in research is to think
is what drives my interest in life science research.
deeply rather than be too mired in the details of

advise interested Hwa Chong students to be involved
VOYAGER 2014
doing, which I guess is very Singaporean. I would

Dr Tan (VT): My research is in the area of information
theory. Just as biology is the science behind modern
in research as soon as possible so that you know
medicine, information theory is the science behind
whether this is the right thing for you. To be a
communication systems. It forms the mathematical
successful researcher or academic, you need a certain
basis of why your mobile phones work and why we can
type of personality. You need to be really driven and
compress large files using g-zip efficiently. I establish
have initiative. You cant wait for things to happen.
12
Because these pathways are so basic to a cell,
the fundamental performance limits of transmitting

information through noisy environments. Much of my
What do you find most enjoyable in doing research
work is mathematical in nature and involves using
and what do you find most challenging?
theories
in
HG: Most enjoyable: When you logically plan out an
mathematical statistics and optimization. You can learn
experiment after a lot of troubleshooting, deduce
much more about my work from my homepage.
what you expect to see, and then see the fruits of your
www.ece.nus.edu.sg/stfpage/vtan/
labour (i.e. the results are not uninterpretable
from
and
develop
new
theories
uninterpretable results are worse than negative

What motivated you to embark on research as a
results), that is extremely rewarding. The nature of
career?
research is such that 99% of the time, you are
HG: I have always liked to find out the reason behind
disappointed by what you see, but in that 1% of the
phenomena and explain how things work. When the
time when things work out, the joy is so addictive that
library couldnt answer all the why questions that I
you keep going back for more .
had, I decided that I would go into science to have a
Most challenging: In life science experiments, you
shot at finding things out myself. Growing up, I had
often need to do quite a bit of optimisation and
pretty severe eczema, and wanting to know the
troubleshooting. Knowing when to keep going, and
reason behind my condition was also why I decided
when to let go and try a new approach is not easy, and
to go into the life sciences.
is still something Im learning to do now.
VT: I was motivated to embark on research due to my
VT: The most enjoyable aspect of my job is the
inspirational teachers in school and professors in
discovery of a new result and the proof of a difficult
Cambridge where I did my undergraduate studies. In
theorem. The realization that youre the first to
particular, in the latter part of my studies in
demonstrate
Cambridge, I knew I wanted to be a professor, to
satisfying. It means youre contributed to mankinds
non-trivial
result
is
immensely
knowledge. Future references to your result would

bear your name. Isnt that cool?
The most challenging aspect is the knowledge that
when you try to prove something difficult, you know
that generations of brilliant people have tried and
probably failed so it is hard to imagine that you can
do it. I try not to be affected by this too much and to
persevere or in some cases, work on a completely
new and relatively unexplored area to break new
ground.
In your opinion, what are some qualities that a
researcher should embody?
HG: (i) perseverance, (ii) working smart, (iii) always
thinking of new angles to attack a problem, (iv)
being aware of what is going on in your field, so that
you can do point (iii).
VT: A certain naivety is sometimes crucial and can
prove the difference between success and failure. If
you dont know too much about a certain field,
youre able to bring in tools and techniques from
mathematics in my case is imperative.

Any words of advice for your Hwa Chong juniors
intending to pursue a career in research?
HG:
Have more confidence in your abilities. One
thing that was immediately apparent doing a PhD in

the US is that Americans are very confident.
Conversely, Singaporeans tend to be more reserved
and afraid of voicing out, and in so doing, often
shortchange ourselves.
VT: The training required to be a researcher is a very
long journey. It is important to continually discover
your interests along the way and not to be afraid of
learning new things but if you do choose to do
research, it is important to know the fundamentals
well.
Thank you very much and we wish the both of you
all the best for your careers and family life!
13
VOYAGER 2014
problems. Of course, having a strong background in
some other field youre more familiar in to solve
STUDENTS VOICES
Research is formalized curiosity. It is poking and prying with a purpose
- Zora Neale Hurston
Students Voices
VOYAGER 2014
14
Every year, more than a hundred Hwa Chong Students embark on a new journey to satisfy
their curiosity through the various research programmes such as CenTaD, NRP and SRP.
These programmes provide students with the valuable opportunity to discover the
unknown and embark on an unforgettable learning journey in the realm of research.
As the saying goes, If you want to build a ship, dont drum up people to collect wood and
dont assign them tasks and work, but rather teach them to long for the endless
immensity of the sea. Through their respective research projects, students enrich their
learning experiences and enhance their understanding of their chosen area of study,
going beyond the boundary of textbooks and school curriculum. In the process, students
mature into innovative, independent and resilient individuals with acute and analytical
minds.
Each students research experience is unique and each of them has a different story to tell.
The following are but some of the responses we have collected from students who have
taken their first exploratory steps into the invigorating realm of research.
What have you learnt from your research
experience?
In your opinion, what is the most enjoyable

part of research?
You need to be very patient when conducting the
The most enjoyable part of research is to be able to
experiments, and have to be very persistent and not
learn from your mentor and peers, as well as
give up. You will also need to think out of the box,
interacting with them. When you face problems in
because
or
your experiment, they will come to encourage you
straightforward. It is more than just carrying out
and similarly, when they face problems, you are able
processes and redoing things. You can use the
to help them. This is what makes research enjoyable.
methods others have used before and modify them
It is also exciting when you learn new and interesting
to formulate a better method or simply improve on
things or when your mentor shows you how to handle
those methods.
or solve problems in a different way. It can really
research
is
not
methodological
show you the practicality of science outside of

textbooks and the rest of your academic subjects.
Rachel Ng Li En 12S70
The process of the scientific

method is a meticulous and noble
oneit seems almost too easy to
overlook the fact that mundane
processes contribute significantly
to humanity.
Students Voices
VOYAGER 2014
16
What has your research experience in Hwa

Chong Institution taught you?
Why do you enjoy research?

One of my favourite aspects of research is finding
relationships
and
unlocking
new
possibilities.
Something that seems as predictable as the path of a

shuttlecock
in
badminton
can
hold
hidden
complexities that can be exploited. Simple factors

such as speed and the terminal velocity of a
shuttlecock can dramatically change the shape of its
trajectory and these can be exploited by athletes and
shuttlecock manufacturers in their designs.
Being in Hwa Chong has allowed me to be exposed

to a plethora of research opportunities. I was very
Research is also about adapting to unforeseen
fortunate that Hwa Chong was able to provide me
circumstances.
with the environment as well as the guidance.
conducting our experiments due to unfavourable
Throughre search, I have been able to acquire a
environmental circumstances such as poor lighting
whole range of skills. Last year, I had the privilege of
and bad weather, and had to continuously adapt to
presenting my project at the annual Singapore
these situations. These variables often affected our
Science and Engineering Fair. I had to learn to
sensitive measurements and caused erratic results
present my research in the most succinct manner to
that required us to redo our experiments many times.
my fellow peers as well as the general public. After
Finding solutions to these problems and minimizing
all, what is science if we cant communicate it well?
inaccuracies is a key part of research and is one of

the most valuable skills I have learnt throughout my
research journey.
Furthermore, the process allowed me to crystallize

many of my ideas and the comments from the
experts were invaluable. They provided me with
many extensions and intriguing perspectives for me
We
faced
many
difficulties
in
Ho Kai Lun 14S6G
to further my research. I realised that research was

indeed appealing to me. I felt reinvigorated every
time I entered the laboratory. Research has become a
passion. This year, I decided take up a project with
the Institute of Materials Research and Engineering.
Together with the guidance from my mentors and
support from the school, I believe that I am able to
continue doing what I love.
Han Kai Zhong Terence 14S7F
I had to learn to present my

research in the most succinct
manner to my fellow peers as well
as the general public. After all, what
is science if we cant communicate
it well?
USE OF RECYCLED CLAM

SHELLS IN WATER PURIFICATION
INTRODUCTION
First prize in Singapore Junior Water

Prize Competition 2013
Represented Singapore at the
Stockholm Junior Water Prize
Competition 2013, Sweden
Water is critical to food production. While the

majority of agriculture is rain-fed, irrigated agriculture
provides some 40 per cent of the worlds food and
consumes 75 per cent of worlds freshwater resources
(The Gender and Water Development Report, 2003).
Supplies of freshwater are increasingly threatened by
population growth, changing lifestyles (use of more
water per capita) and pollution. A lack of water has
driven up the use of wastewater for agricultural
production in poor urban and rural communities. More
than 10% of people worldwide consume foods
irrigated by wastewater that can contain chemicals or
disease-causing organisms. Also, current rapid
industrialization in developing countries has caused
levels of heavy metals and pollutants to significantly
increase in the last couple of decades, especially
those from aquatic ecosystems. For example,
according to an investigation conducted by the State
Environmental Protection Administration, much of the
Pearl River Delta in China has been polluted by heavy
metals and that 40 per cent of farms and vegetable
plots in the region had been polluted by these heavy
metals (Wade, 2011).
Heavy metals pose a threat to the environment as
they cannot be degraded and would remain in the soil
and water for a long period of time. They produce
their toxicity by forming complexes with proteins, in
17
VOYAGER 2014
Research Mentor
Mrs Sow-Peh Yoke Keow
Access to clean water is a universal human right.

Unfortunately, around 1.1 billion people globally do not
have access to improved water supply sources
whereas 2.4 billion people do not have access to any
type of improved sanitation facility (WHO-UNICEF,
2000). The most affected are the populations in
developing countries, living in extreme conditions of
poverty, normally peri-urban dwellers or rural
inhabitants. The people from these countries have to
travel great distances to collect water every day, from
water sources that are often polluted. The time spent
on the collection of water could have been spent on
more productive work for them to earn a living.
According to the United Nations Development
Programme (2006), 443 million school days are lost
each year due to water-related diseases. Falling ill due
to water related diseases also further reduces
peoples ability to do work and completing education.
According to WHO-UNICEF (2000), about 2 million
people die every year due to diarrhoeal diseases and
most of them are children less than 5 years of age.
88% of the diarrhoeal diseases are due to a lack of
access to sanitation facilities, together with
inadequate availability of water for hygiene and
unsafe drinking water. Globally, the problem is
deteriorating as cities and populations grow, and the
need for water increase in agriculture, industry and
households.
Use Of Recycled Clam Shells In Water Purification
Ong Yinn Jaye 13S75

Yeo Kang Le 13S79
Gong Wei Jin 13S67
which carboxylic (-COOH), amine (-NH2), and thiol

(-SH) groups are involved. These modified biological
molecules lose their ability to function properly and
result in the malfunction or death of the cells. When
metals bind to these groups, they inactivate important
enzyme systems or affect protein structure, which is
linked to the catalytic properties of enzymes
(Adepoju-Bello and Alabi, 2005).
Many industries such as mining, electroplating and
piping discharge waste which contains high levels of
metal ions. For example, copper is widely present in
metal-bearing industrial discharges, and if not treated
can cause damage to a variety of aquatic fauna such
as fish and invertebrates (Ng et al, 2002).
VOYAGER 2014
18
The presence of metal ions in domestic drinking water

is also a problem in many countries. Lead
accumulation causes major health problems such as
immune disorders and lead-induced intelligence
impairment, while iron contamination results in poor
tasting and unattractive water with a distinctive
reddish-brown colour (World Health Organisation,
1996). In fact, there was a case in 2009 where
residents in Singapore had reported seeing iron
contaminated reddish-brown coloured water coming
out from taps (Kreamer, 2009). Thus, it can be seen
that contamination of drinking water by corroded
pipes can indeed be a cumbersome problem.
Various kinds of methods have been developed to
purify contaminated water around the world, such as
the invention of desalination plants and sedimentation
(Lalov et al., 2000). However, such methods are not
cost effective. Developing countries cannot afford
expensive filtration systems to treat wastewater it is
difficult for them (and other developing countries) to
obtain pure drinking water.
Hence, scientists have explored alternatives which are
more cost effective. One popular alternative is the
biosorption of metal ions by metabolically inactive
non-living biomass of microbial or plant origin. Due to
their unique chemical composition, metabolically
inactive dead biomass sequesters metal ions, by
forming metal complexes from a solution and
removing the necessity to maintain special
growthsupporting conditions (Ahluwalia and Goyal,
2006).
Another group of researchers found that shells of
crustaceans such as crabs and shrimp can be used to
remove heavy metals. This is mainly because their
shells are made up of the material chitin which has the
ability to adsorb toxic metals (Karthikeyan et al.,
2005). Seashells have also been tested for their
ability to remove zinc, lead, cadmium and iron (Reilly,
2009). Researchers found that flooding ground shells
with highly contaminated water would cause the
metals to be removed by the shell. Shells consist of
aragonite, a mineral that is found to swap its calcium
ions in exchange for heavy metal ions. The metals
trapped are in a solid state and are harmless towards
the environment.
This study explores the feasibility of constructing a

filter from low cost and easily available material which
can be used to remove heavy metal ions. The ability of
three types of clam shell (mussel, lala clam and blood
cockles) in removing copper(II), iron(III) and lead(II)
ion was investigated and the most effective shell was
used to construct the prototype. If successful, such a
filter can be used in developing countries to help
alleviate the problem of access to clean water caused
by heavy metal pollution.
HYPOTHESES
1) All three types of shells are able to remove metal ions.
2) The prototype constructed using clam shell is effective in removing metal ions from contaminated water.
MATERIALS AND METHODS

Materials
Shells of lala clam, blood cockles and mussels were

collected. The shells were washed with deionised
water and dried in an oven at 70C for 24 hours. The
solutions containing various concentrations of
copper(II) ion, lead(II) ion and iron(III) ion were
prepared from copper(II) sulfate, lead(II) nitrate and
iron(III) nitrate respectively.
Preliminary studies:
1) To investigate effectiveness of removing metal ions
with shells:
0.5g of each type of shell was added to 50ml of
50ppm metal ion solution. The mixture was stirred on
a magnetic stirrer for 60 min, after which it was
filtered. The filtrate was analysed for the
concentration of metal ion remaining using a AA
spectrophotometer (AA 6300 Shimadzu) for lead (II)
and a colorimeter (HACH, DR/890) for copper (II) and
iron(III) ion. A control containing same volume of
metal ion solution but without shell was subjected to
the same experimental conditions.
2) Effect of pH on removal of metal ions
The pH of metal ion solution was adjusted to 2 or 5
using Nitric acid (HNO3) or Sodium hydroxide
(NaOH). pH above 5 was not studied as the metal ions
were observed to precipitate out as metal hydroxide
at pH greater than 5.
50ml of the solution with the desired pH was stirred
with 0.5g of shell for 60min. After 60 min, the mixture
was filtered and the metal ion remaining in the filtrate
determined.
Results and discussion
Analysis for removal of Copper (II) ions at pH 2

As shown in figure 1, all three types of shell are able to
remove Cu2+ ions, blood cockles being the most
effective (87.2%), followed closely by lala clam (80.6%)
then by mussels (33.4%). No significant difference is
seen between the effectiveness of removal by lala and
blood cockles.
Analysis for removal of iron (III) ion at pH 2

All 3 types of shells are effective in removing iron(III)
ions, with percentage removal of at least 95% for all
types of shell. The percentage removal is the highest
for mussel (98.9%), followed by blood cockles (98.6%)
and lala clam (97.7%).
Analysis for removal of Copper (II) ions at pH 5

At pH 5 however, all three types of shell show similar
effectiveness in the removal of Cu2+ ions, with mussel
shells showing the highest percentage of removal
(97.8%), followed very closely by blood cockles (97.4%)
and lala clam shells (95.3%). Unlike pH 2, there is no
significant difference among the effectiveness of
removal by the 3 types of shell at pH 5. The removal of
copper (II) ion is more effective at pH 5 than at pH 2.
Analysis for removal of iron (III) ion at pH 5

Lala clam showed the greatest percentage removal
(96.7%), followed by blood cockles (95.8%), and finally
by mussel shells (92.1%). The trend observed here is
similar to that observed for the removal of lead(II) at
pH 5, where mussel shells is least effective.
Discussion:
Lala clam and blood cockle shells are effective in

removing all three types of metal ions at both pH
studied. Mussel shell on the other hand is not as
effective in removing copper(II) ion and lead(II) ion at
pH 2, and not as effective in removing iron(III) ion at pH
5.
Clam shells are able to remove metal ions effectively
due to the presence of aragonite, a biogenic form of
calcium carbonate, which is able to readily swap its
calcium ions in exchange for heavy metal ions. The
equation is:
MCO3 + Ca2+
CaCO3 + M2+
Figure 2: Removal of lead (II) ion at different pH
Analysis for removal of lead (II) ion at pH 2

As figure 2 shows, all three types of shell are able to
remove Pb2+ ions, blood cockles showing the greatest
% removal (99.5%), followed closely by lala clam
(99.4%) then by mussels (95.4%).
Analysis for removal of lead (II) ion at pH 5
Figure 2 shows that the removal of Pb2+ ions by all 3
types of shell at pH 5 is very effective, with the
percentage removed being close to 100%. Blood
cockles showed the greatest % removal (99.3%),
followed by clam shells (99.2%), and finally by mussel
shells (99.0%). No significant difference is seen among
the effectiveness of removal of the three types of shells
as the error bars overlap.
The difference in the ability of different shells in

removing metal ions is likely due to the difference in
the composition of the shell as the amount of calcium
carbonate may vary in different types of shell. To
ascertain whether the ability to remove metal ions is
related to the amount of calcium carbonate,
experiments were carried out to compare the calcium
carbonate content in each type of shell. This was
carried out by first reacting a fixed mass of shell with
excess hydrochloric acid and titrating the unreacted
acid with standard sodium hydroxide. Results show
that mussel shell has the lowest percentage of calcium
carbonate (84.3%), followed by blood cockles (94.4%)
and lala clam (95.2%). Hence it is likely that mussel
shell was less effective as it contains a lower
percentage of calcium carbonate than the other two
types of shell.
To further validate the aforementioned hypothesis,
tests were also carried out with pure calcium carbonate
19
VOYAGER 2014
Figure 3: Removal of iron(III) ion by clam shells at different pH
Figure 1: Removal of copper (II) ion by clam shells at different pH
at pH 5 under the same conditions as that conducted

with the shell. Results are shown in figure 4
Figure 4: Comparing clam shells with pure calcium carbonate in the

removal of metal ions
Figure 4 shows that the effectiveness of pure calcium

carbonate is comparable to that of lala and blood
cockle shells, both of which contain more than 90%
calcium carbonate. This further suggests that calcium
carbonate is the primary agent in the removal of metal
ions.
Version 2:
Figure 7: Version 2 of
prototype
Version 3:
CONSTRUCTION OF PROTOTYPE
VOYAGER 2014
20
4 different versions of prototype were created, with

each version aiming to improve on its effectiveness
and efficiency. Lala clams and blood cockles were
selected because they generally outperformed
mussels at the 2 pH values studied. As this prototype
was developed with third world countries in mind, the
emphasis was on simplicity and ease of construction. A
recycled plastic water bottle was used to contain clam
shell, with sand at the base to prevent turbidity, and a
piece of cloth at the mouth of the bottle to prevent the
shell from flowing out. To test the effectiveness of our
prototype, 100ml of water spiked with Cu2+, Fe3+ and
Pb2+ was poured through the filter. The initial
concentrations of the metal ions were within the range
of 10-40 ppm. The filtrate was then collected and
analysed for the concentration of Cu2+, Fe3+ and Pb2+.
This process was then repeated until more than 90% of
the metal ion was removed, and the number of times to
filter this 100ml of polluted water was then recorded.
Thus, the opening was enlarged

for the second version. However,
though it was again effective with
close to 90% of metal ion being
removed after the first cycle, flow
rate improved only slightly to
10ml/hour. It was then realised
that the slow flow rate was not
due to the opening of the bottle,
but in fact due to the small
particle size of the shells that
were added, which blocked the
flow of water.
prototype
For the 3rd version, only pounded

but not blended shells were
used. This increased the particle
size of the shells, and thus a
much more practical flow rate of
20ml/min
was
obtained
compared to previous models.
Also, this version was more
eco-friendly as compared to
previous models, only half the
amount of shells was used while
treating the same volume of
water. However, due to this
decrease in the mass of shells,
the water must be passed
through the filter several times
before the metal ions can be
removed.
Figure 9 shows that after the first cycle, the percentage

of metal ion which remains in the filtrate dropped
tremendously. At the end of fourth cycle, percentage
of metal ion has dropped to almost 0% for both
copper(II) and iron(III) and 1.13% for lead(II). Four
cycles of treatment are required before more than 90%
of each metal ion can be removed using version 3 of
prototype.
Version 1:
Finely blended lala

clam and blood
cockle shells in a
mass ratio of 1 : 1
(Total mass: 120g)
Sand
prototype
Figure 6: Schematic diagram of

Version 1 of prototype
Version 1 of our prototype was able to remove close to

90% of each of the metal ion after the first cycle but it
was impractical as it had a very slow flow rate of
6ml/hour, and it was hypothesized that the slow flow
rate was due to the small opening at the bottom of the
bottle.
Figure 9: Percentage of metal ion remaining after each cycle of filtration

using version 3 of prototype
Charcoal
(10 g)
Clam shell
(300 g)
Sand
(20 g)
Figure 10: Version

4 of prototype
The major shortcoming of

version 3 of prototype is that
water needs to be passed
through the filter 4 times
before more than 90% of the
three types of metal ions can
be removed. This makes the
purification process time
consuming and laborious. To
overcome this problem, 4th
version of prototype was
constructed. The 4th version
of
prototype
adopts
a
modular design. Such a
design has two notable
advantages:
1) Increased interaction time between metal ion

pollutants and the prototype components.
2) Easy and convenient replacement of individual
prototype component. In addition, a layer of charcoal
was introduced to the prototype to further improve its
effectiveness in removing water pollutants as charcoal
is known to adsorb several types of pollutants
including metal ions and organic pollutants.
The mass of shell was also increased from 60 g in
version 3 to 300 g in version 4 to improve its
effectiveness. Lastly sand in the 3rd bottle filters out
big solid particles in water and ensures that the water
after filtration is clear and not turbid.
flow rate of version 4 was 19 ml/min, which was

comparable to the flow rate of version 3. Hence
effectiveness of removing metal ions was enhanced
without compromising the flow rate.
2) Determining the maximum volume of water which
can be purified
100 ml of aliquot of polluted water containing about 5
ppm of each metal ion was poured through the
prototype. Concentration of 5 ppm is a realistic
concentration to investigate as several studies have
reported the concentration of metal ions in
groundwater to be within or less than a few ppm
(Iqbal et al., 2009; Tombul et al., 2005; Minnesota
Pollution Control Agency, 2009). Filtrate was
analysed for the remaining levels of metal ions. The
process was repeated until the metal ion exceeds the
MCL (maximum contaminant level) set by United
States Environmental Protection Agency. An MCL is
the maximum allowable amount of a contaminant in
drinking water which is delivered to the consumer. The
maximum number of 100 ml of aliquots which can be
effectively and safely purified was then determined.
Results are shown in figure 12 and 13
Original 1st
2nd
3rd
4th
5th
6th
7th
8th
21
Figure 12: Contrast between the polluted water and the water filtered
through the prototype, from 1st to 8th aliquot.
Several studies were conducted on the 4th prototype.

Results are as follows
1) Effectiveness of prototype in removing metal ions
of three different concentrations
Water containing 3 different concentrations of metal
ions (15 ppm, 10 ppm and 5 ppm) was filtered
separately using the prototype.
Figure 13: Concentration of metal ions remaining in the filtrate after

passing through version 4 of prototype.
Figure 11: Removal of metal ions of 3 different con centrations using

4 thversion of prototype
Figure 11 shows that the prototype was able to

remove at least 85% of all three metal ions of all three
concentrations after first cycle of filtration. This was a
marked improvement as compared to version 3
which requires 4 cycles of treatment. In addition, the
VOYAGER 2014
Version 4
The MCL of copper and lead are 1.3 ppm and 0.015
ppm respectively. MCL does not apply to iron as it is
regarded as a secondary contaminant which affects
the aesthetics of water such as taste, colour and
odour. Secondary contaminants are not health
threatening (United States Environmental Protection
Agency, 2012).
Figure 12 shows that all the eight 100 ml aliquots that
were filtered using version 4 of prototype was clear
and colourless - a stark contrast to the polluted water
which was yellow due to the presence of iron(III) ion.

Figure 13 shows that the concentrations of copper(II)
and lead(II) ions in all the 100 ml of filtered aliquots
were below the MCL. Although the prototype was
able to filter at least 800 ml of polluted water, it was
observed that the flow rate decreases after each
aliquot was filtered. At the 8th filtration, the flow rate
has decreased from the initial 19 ml/min to 4 ml/min.
The decrease in flow rate was due to clogging of cloth
filter by solid particles which obstruct the flow of
water. It is likely that more water could be purified if
the cloth filter is being replaced. Further investigation
is needed to determine the absolute maximum
volume of polluted water which the prototype can
filter.
3)Comparing 4th version of prototype with
commercial filter
Tests were conducted to compare the effectiveness of
the clam shell filter in removing the three metal ions
with a commercial filter. Results are shown in figure 14.
Table 1: Breakdown of the cost of 1 unit of

version 4 of prototype
Cost (in USD)
Fabric
$0.12
Charcoal
$0.010
Clam shell
Recycled
Bottle
Recycled
Sand
$0.064
Total
$0.194
Another feature of the filter is that it is easy to

construct, portable and can be assembled within
minutes anywhere, any time. In addition, clam shells
can be reused by washing it with 1% (W/V) aqueous
NaCl without apparent loss of effectiveness in
removing metal ions as the washed shell was still able
to remove close to 95% of each metal ion.
CONCLUSION
VOYAGER 2014
22
Figure 14: Comparing the effectiveness of version 4 of prototype

with commercial filter. Initial concentration of metal ion is 15 ppm.
Figure 14 shows that the 4th version of prototype is

comparable to the commercial filter in removing all the
three metal ions, with the percentage removal being at
least 95%. The commercial filter is made of commercial
adsorbents such as activated carbon and zeolite. The
clam shell filter on the other hand is made of easily
available and low cost materials charcoal, clam shell,
sand and recycled bottles.
Table 1 reveals the cost of the individual component of
the filter. The cost of the clam shell prototype is very
affordable, with a total cost of less than USD 0.20 per
unit. The low cost of the prototype can be attributed to
the fact that two of the components (clam shell and
bottle) are recyclable materials. Clam shells play a
similar role as zeolite of commercial filter as both serve
to remove metal ions via ion exchange mechanism.
However zeolite costs about USD 76.70 per 100 g while
clam shells are recycled materials with practically no
cost. Also, low cost charcoal is used in place of the
more costly activated carbon which is commonly used
in commercial filters, thus further reducing the cost
without compromising its effectiveness in removing
metal ions.
All 3 types of shells (lala clam, blood cockles, and

mussels) are able to remove metal ions. Lala clam and
blood cockle shells are effective in removing all three
types of metal ions at both pH studied, with the
percentage of removal being above 80%. Mussel shell
on the other hand is not as effective in removing
copper(II) ion and lead(II) at pH 2, and not as effective
in removing iron(III) ion at pH 5. Four versions of
prototype were constructed using lala clam and blood
cockle shell. With each version, improvement was
made to enhance the feasibility of the prototype. The
version 4 of the clam shell prototype was able to
effectively remove metal ions with the following
features:
1) It is eco-friendly as its main components - clam shell
and bottles, are recycled materials.
2) It has zero carbon emission as it utilizes adsorption
(by charcoal), ion exchange (by clam shell) and
filtration (by sand) in purifying the water.
3) It is portable and easy to construct as it makes use
of the modular concept.
4) It is highly effective due to the multi-mechanism
approach.
5) It is cost effective and affordable.
Further studies of the prototype include investigating
whether it can purify more than 800 ml of water by
replacing the cloth filter after it is being clogged and
carrying out on-site studies with the prototype, testing
its effectiveness with real polluted water. In addition,
studies can be carried out to find out whether the
prototype can remove other types of pollutants such
as organic dyes. Finally the flow rate can be further
improved.
REFERENCES
Adepoju-Bello, A.A. and. Alabi, (2005). Heavy metals: A
review. The Nig. J. Pharm., 37, 41-45.
Ahluwalia, S., Goyal, D., (2006). Microbial and plant
derived biomass for removal of heavy metals from
wastewater. Biosource Technology, 98, 2243-225.
Iqbal, M. A., Gupta, S.G (2009). Studies on Heavy Metal
Ion Pollution of Ground Water Sources as an Effect of
Municipal Solid Waste Dumping. African Journal of
Basic & Applied Sciences1 (5-6), 117-122,
Karthikeyan, G, Mandal, N., Anbalagan, K. (2005).
Adsorption studies of iron(III) on chitin. J. Chem. Sci.,
117, 6, 663-672.
Kreamer, J. (2009, July 15). Tap water's clean, but are
the pipes? Straits Times
Nuisance Chemicals. Retrieved April 10, 2013 from

http://water.epa.gov/drink/contaminants/secondarysta
ndards.cfm
Wade, S.(2011). Dangerous elements: Heavy metal
pollution in China. China Digital Times. Retrieved
March 4, 2013 from
http://chinadigitaltimes.net/2011/07/dangerous-eleme
nts-heavy-metal-pollution-in-china/
WHO-UNICEF (2000). Global water supply and
sanitation assessment 2000 Report. World Health
Organisation, 1-2. Retrieved March 4, 2013 from
http://www.who.int/water_sanitation_health/monitorin
g/jmp2000.pdf
World Health Organisation (1996). Iron in drinking
water. Guidelines for drinking-water quality, World
Health Organisation, 1-4. Retrieved March 4, 2013 from
http://www.who.int/water_sanitation_health/dwq/che
micals/iron.pdf
Lalov, I.G, Guerginov, I.I., Krysteva, M. A., and Fartsov,

K.(2000). Treatment of waste water from distilleries
with chitosan. Water Research. 34, 5, 1503-1506.
Reilly, M. (2009). Sea shells used to clean up heavy

metals. Discovery News. Retrieved March 4, 2013 from
http://dsc.discovery.com/news/2009/04/27/shells-met
als-water.html.
The Gender and Water Development Report (2003).
Gender Perspectives on Policies in the Water Sector.
Loughborough, United Kingdom, Water, Engineering
and Development Centre, Gender and Water Alliance.
Retrieved March 4, 2013 from
http://www.genderandwateralliance.org/reports/GWA
Annual Report.pdf.
Tombul, M., Koparal, A.S., Ogutveren, U.B. (2005).
Transport modelling of copper contamination in
groundwater caused by a wood preservation plant.
Water Qual. Res. J. Canada, 40, 4, 469-475.
United Nations Development Programme (2006).
Beyond Scarcity: Power, Poverty and the Global Water
Crisis. Human Development Report. Retrieved March 5,
2013 from
http://hdr.undp.org/en/reports/global/hdr2006/
United States Environmental Protection Agency (2012).
Secondary Drinking Water Regulations: Guidance for
VOYAGER 2014
Ng, J. C. Y., Cheung, W. H., McKay, G. (2002).

Equilibrium Studies of the Sorption of Cu(II) Ions onto
Chitosan. Journal of Colloid and Interface Science. 255,
6474.
23
Minnesota Pollution Control Agency (2009). Cadmium,

Lead and Mercury in Minnesotas Ground Water.
Environmental Outcomes Division, Ground Water
Monitoring & Assessment Program. Retrieved April 10,
2013 from
http://www.pca.state.mn.us/index.php/view-document
.html?gid=6312
QUORUM SENSING INHIBITION

ACTIVITY OF SELECTED
TRADITIONAL CHINESE MEDICINAL (TCM)
HERBS TO INHIBIT BIOFILM FORMATION
INTRODUCTION
Chua Jia Jie 13S7G
Ng Jun Xuan 13S7G
Ng Wei Hao 13S7J
Research Mentor
Dr Ng Tze Chiang Albert
Singapore Science and Engineering Fair,
Silver Award
Understanding of biofilms, first reported more than 60

years ago (Zobell, 1943), has increased tremendously.
Biofilms are structured communities of bacterial cells
living on the interface of a solid-liquid or liquid-liquid
media, enclosed in a self-produced polymeric matrix.
Such biofilm formation naturally occurs due to the
many survival advantages conferred to individual
bacterium when living in a community. Moreover,
bacteria thrive on synergistic cooperation within the
biofilm environment. As such, bacteria evolved ways to
form communities as layers of biofilm (Simes et al.,
2010).
Biofilm formation is a process that begins from the
adsorption
Quorum Sensing Inhibition Activity Of Selected

Traditional Chinese Medicinal (TCM) Herbs To Inhibit Biofilm Formation
VOYAGER 2014
24
of
molecules
such
as
proteins
and
polysaccharides onto the substratum. After initial

conditioning of the surface with biopolymers, motile
bacteria swim towards the surface and adhere to it.
Such movements occur especially since there is a
greater concentration of nutrients near the surface of
the substratum. Bacterial adherence is followed by the
secretion of extracellular polymeric substances (EPS).
Subsequently colonisation of the surface by the
primary bacteria begins. As the biofilm begins to
swarm along the surface, secondary bacteria are
attracted towards the matrix. Once a mature biofilm is
established, it will actively propagate. Upon reaching a
threshold, where the biofilm becomes overcrowded,
dispersal occurs such that bacteria released are able to
colonise other areas (Lewandowski and Boltz, 2011;
Annous et al., 2008).
Despite the ubiquitous nature of biofilms, this state of
living creates numerous problems. The presence of
biofilms is particularly problematic in food, medical
and environmental related fields. Biofilm contamination
of food products is a serious hygiene issue that will
lead food spoilage and equipment impairment (Simes
et al., 2010). Biofilms found on medical devices and
implants have serious implications. Such internal
biofilms are the cause of 65% of all microbial infections.
Common
infections
like
urinary
tract
infections,
catheter infection, and even common dental plague are

difficult to treat due to the antimicrobial resistance
conferred to bacteria by the structure of the biofilm
(Lewis, 2001). In an industrial setting, biofilms cause
metal corrosion in pipeline and tanks. Microorganisms
Advanced
in biofilms reduce metals and metal alloys as sources of
research fields have shown that biofilm formation could
energy, leading to an accelerated rate of corrosion
be
(Lewandowski and Boltz, 2011). Biofilms found on
Quenchers (QQ), which inhibit bacterial cross-talk or
filtration membranes used in water and wastewater
cell-to-cell communication. This inhibition process is
treatment systems must be periodically removed as
known as Quorum Sensing Inhibition (QSI). QSI may
they cause physical blockage of membrane pores,
proceed in 3 main ways, namely (i) inhibition of
thereby increasing resistance towards water flow
receptors to signal molecules; (ii) inhibition of signal
through the membrane. Biofilms may also release
biosynthesis or inhibition of activity of autoinducer
chemical compounds which subsequently adversely
acyl-homoserine lactone (AHL)-producing enzymes
affects permeate quality (Mafirad et al., 2011). All
and (iii) signal degredation (Khan et al., 2009). The first
biofilm
associated
problems
eventually
lead
biotechnological
controlled
by
techniques
compounds
in
called
other
Quorum
to
method can be carried out by antagonising the binding
economic losses as practitioners have to constantly
of AHL at receptors that resemble those of competitive
combat and remove the bacterial film.
inhibitors in enzymatic activity. Signalling molecule

production is currently undeveloped and only a few
inhibiting microbial growth. The most common method
biosythesis in Pseudomonas aeruginosa. The approach
is primarily based on introducing antibiotics or
to destruction of signalling molecules, however, is
antimicrobial agents to kill bacteria cells. However,
accomplished via controlling local pH or by specific
rampant and indiscriminate use of such compounds led
enzymes (Kociolek, 2009), such as AHL lactonase and
to increased resistance by bacteria through the
AHL acylase (Decho et al., 2009). Studies have shown
evolution of new resistance mechanisms and pathways
that plants, such as pea plants, are able to secrete
(Huerta et al., 2008). Even with introducing stronger
AHL-signal mimic compounds that overwhelm the
agents, bacterial cells are advantaged by the physical
effects of the actual QS mechanism in plant-associated
architecture of the biofilm environment (Flemming,
bacteria (Teplitski et al., 2000).
2009). Therefore, there is a need to develop strategies

that control the very basis of biofilm formation.
Traditional Chinese Medicine (TCM) is characterised as

a potent combination multiple compounds that work
Quorum Sensing (QS) is the process that is believed to
synergistically. It has been used, up till today, to treat a
cause biofilm formation. Occurring in many species
variety of diseases. Studies have shown that some
across gram-negative and gram-positive bacteria, it is a
herbs possess antimicrobial and antifungal properties,
mechanism
for example, cinnamon (Prabuseenivasan et al., 2006).
for
intra-species.
cross-talk
Microbial
between
inter-
communities
and
utilise
As
different
herbs
express
varying
quenching
extracellular signalling molecules called autoinducers,
compounds,
as the main mode of communication. As population
significant QSI properties that can be harnessed. QSI
density of a microbe increases, concentration of
achieved using TCM plant compounds, is expected to
autoinducers increases up to a given threshold in the
be a more ideal solution in controlling biofouling as it is
surrounding
environment
(Kociolek,
there
may
be
herbs
that
possess
2009).
inexpensive and environmentally friendly. Such natural
Autoinducers are detected by, and binds to receptors
products already being consumed as food or medicinal
on neighbouring bacteria, transmitting signals, which
herbs are expected to create less downstream
are transduced by receiving molecules into intracellular
problems should they be used in water treatment or
biochemical signal, stimulating a series of physiological
medical industries. Specifically towards membrane
adaptations, such as the formation of a biofilm layer
bioreactors (MBR) for water reclamation, this method
(Raffa et al., 2004). Autoinducers serve as precursors
will reduce reliance on physical and chemical control
to biofilm formation, by acting as chemical signals
strategies that are largely inefficient and laborious,
communicated between bacteria. These compounds
providing an effective method to control biofouling as
are actively transmitted throughout the stages of
well as a pathway to a continued supply of freshwater.
biofilm formation, including bacterial motilities such as
As most herbs are found to have bactericidal
movement in a medium or a solid surface, or
properties, they will be able to destroy bacteria and
agglomeration. By quenching the signals produced by
prevent biofilm formation (Koh and Tham, 2009).
the molecules, information cannot be passed between
However, in order to co-opt this treatment into
bacterial cells, inhibiting motility and the initiation of
biofouling control in MBRs, only herbs with QSI
biofilm formation.
properties are required.
25
VOYAGER 2014
QQs have been identified for use in targeting signal

Current methods of biofilm control are based on
The objectives of the research were to investigate the
Antibacterial Assay
QSI activity of various TCM herb extracts for reducing
Bacteria cultures were each inoculated across the
biofilm formation on membranes in an MBR. This was
surface of the agar. 9-mm diameter wells were bored
done by incorporating bacteria, membrane as well as
into the agar of each plate using a glass borer. 50 L of
extracts in a suspension. This study further determined
the sterile herb extracts solutions were added into the
the inhibition process on various bacterial motilities,
wells of each plate with different bacteria. Sterile water
since the motilities, complimented by autoinducers,
and bleach were also added into the wells of each plate
serve as the basis of biofilm formation. By targeting the
with different bacteria as the negative and positive
different aspects of biofilm formation separately, the
control,
different
appropriate temperatures overnight and diameter of
extracts
were
then
assessed
for
their
effectiveness in greater depth.
respectively.
Plates
were
incubated
at
the zones of inhibition measured after the incubation

period.

Modified Microtitre Plate Assay

VOYAGER 2014
26
Plant Material and Extraction Method
Sodium alginate solution was prepared and mixed with
The extraction methods used in this experiment were
the herb extracts to obtain a 3% alginate solution at a
adapted from Yeo and Tham (2012). 6 TCM herbs were
final concentration of 30 mg/mL of herb extract. The
chosen for their potential QSI ability (Table 1). 5 g each
solution was then added drop-wise to 2% calcium
of the TCM herb was ground into small pieces with
chloride solution to produce alginate beads containing
mortar and pestle. Dried ground plant material was
extracts.
soaked in 50% acetone at a ratio of 1:6 (wt:vol) on a
incorporated with a 10 x 5 mm Millipore polyvinylidene
shaker overnight. The mixtures were filtered with filter
difluoride (PVDF) membrane and 2 calcium alginate
paper, of nominal pore size of 5
beads
m, to remove
in
mL
of
each
bacterial
micro-centrifuge
culture
tube.
Tubes
was
were
particulate matter. Filtrates were vacuum-dried and
incubated and shaken for 5 d, before biofilms on the
stored at 4oC. Extracts were reconstituted in deionized
membrane were stained with 1% crystal violet solution
water to obtain final working concentrations of 25, 50,
and its absorbance value read at 600 nm.
and 75 mg/mL. Extracts were filter-sterilized using 0.22

m (pore size) Iwaki filter disks before application.
Swimming Motility
Sterile herb extracts were individually mixed with 10
Bacterial Strains and Culture Conditions
mL of 0.3% LB agar to final concentrations of 25, 50
Both Gram positive and Gram negative bacteria were
and 75 mg/mL, and poured immediately over an agar
used as model strains in this study. Gram negative
plate. Bacteria cultures were stab inoculated at the
bacteria used were Escherichia coli (ATCC 25922), and
centre of the agar after solidification. Plates were
Agrobacterium tumefaciens (ATCC 33970). Gram
incubated at appropriate temperatures for 3 d.
positive bacterial strain used was Staphylococcus
Swimming
epidermidis
(ATCC
12228).
Each
bacterium
migration
distance
was
assayed
by
was
following the colony fronts of the bacterial cells.
cultured in 10 mL of DifcoTM LuriaBertani (LB) media,
Swimming assays were performed in eighteen identical
and incubated overnight on a shaker spinning at 200
plates on three independent occasions. Measurements
rpm at 28 C. Bacterial cultures were diluted with LB
were taken every 24-h throughout the course of 3 d.
broth to an absorbance value of 0.1 at 600 nm before
Bacterial cultures used for swimming motility tests
being used in subsequent studies.
included E. coli and A. tumefaciens.
Table 1. Traditional Chinese Medicinal herbs used.
Name (Scientific)
Angelicae Sinensis Radix
Asini Corii Colla
Panax notoginseng
Persicae Semen
Rhizoma Curcumae Longae
Salviae Miltiorrhizae Radix
Swarming Motility
Sterile herb extracts were individually mixed with 10
Name
Name
(Chinese Characters)
(Hanyu Pinyin)
mL of 0.75% molten LB agar to final concentrations of
Dang Gui
E Jiao
Tian Qi
Tao Ren
Jiang Huang
Dan Shen
25, 50 and 75 mg/mL and poured immediately over an

agar plate. 1 L of E. coli culture was point inoculated
onto the surface at the centre of the agar plate after
solidification, and the surface was air-dried for 10 min
and incubated at 35oC. Extent of swarming was
determined by measuring the area of the colony in
square millimetre. Swarming assays were performed in
eighteen identical plates on three independent occasions,
with measurements taken every 24-h throughout the
Modified Microtitre Plate Assay
course of 3d.
Extracts immobilised into alginate beads were added

into a bacterial broth containing membrane pieces for
RESULTS AND DISCUSSIONS
delivering QQ in a controlled manner into the broth

culture. The modified microtitre plate assay tested the
Antibacterial Assay
effectiveness of the various extracts on an actual
Preliminary tests were conducted to identify herb
membrane. Bacteria were allowed to form biofilms on
extracts containing antibacterial compounds after the
membrane surfaces under the influence of the extracts.
extraction process. Table 2 shows results of the
A lower absorbance value recorded signified an
well-diffusion tests, with sterile water and bleach as the
inhibition of the bacteria to form extensive biofilms on
negative and positive controls, respectively. None of
membrane surfaces.
the TCM extracts exhibited any antibacterial activity

A.
Figure 1a shows the effect of herbs on E. coli biofilm
tumefaciens. However, herb extracts Angelicae Sinensis
Gram-negative
formation on PVDF membrane slices. With the
Radix and Salviae Miltiorrhizae Radix were seen to be
exception of Persicae Semen, all extracts showed
antibacterial
varying effectiveness in biofilm control. In order of
against
bacteria,
E.
Gram-positive
coli
and
bacterium,
S.
epidermidis.
increasing efficacy, Panax notoginseng, Angelicae

Sinensis Radix, Asini Corii Colla, Salviae Miltiorrhizae
Table 2. Zones of inhibition recorded for antibacterial assay.
Radix, and Rhizoma Curcumae Longae were found to
Zones of Inhibition (mm)
inhibit biofilm concentration as evident from the lower
E. coli
9.0 0.0
9.0 0.0
9.0 0.0
9.0 0.0
9.0 0.0
9.0 0.0
9.0 0.0
17.0 0.0
absorbance values compared to the control. Both
* Well diameter = 9.0 mm. Antibacterial property was

not observed when a value of 9.0 was recorded.
tumefaciens. Surprisingly, less extracts were now
Panax notoginseng and Angelicae Sinensis Radix were

able to marginally suppress bacterial attachment and
agglomeration of E. coli on the membrane surface by
approximately 17%. Salviae Miltiorrhizae Radii and
Rhizoma Curcumae Longae were able to inhibit and
restrict biofilm formation of E. coli by 46% and 57%,
respectively.
Figure 1b shows the effect of herb extracts on A.
effective in preventing biofilm formation even though
both E. coli and A. tumefaciens were Gram negative
Bacteria present within MBRs function to break down
bacteria. This was likely due to different autoinducers
waste in wastewater influent. The metabolic processes
being expressed in each bacterial strain. Among Gram
of bacteria are responsible for the biodegradation of
negative bacteria, two main types of AIs have been
bioorganic
in
classified: AI-1 and AI-2 (Niu et al., 2006). E. coli
wastewater, leading to the overall purification effect
expresses AI-2 autoinducers while A. tumefaciens
(Gallert and Winter, 2005). Therefore, TCM extracts
secrete
possessing antibacterial compounds are discouraged
highlights the different abilities of the extracts in
from use due to its bactericidal effects on such useful
targeting a wide range of autoinducers. Panax
bacteria, which can possibly lead to a reduction in
notoginseng and Angelicae Sinensis Radix were found
treatment
compounds
to be ineffective, to the extent the biofilm growth was
exhibiting strong antibacterial activity, any reduction in
promoted by 15% in the latter. Asini Corii Colla and
biofilm formation or motilities as described may not be
Persicae
attributed
especially
concentration by up to 20%. Salviae Miltiorrhizae Radii
important since the effect of biofilm reduction may be
and Rhizoma Curcumae Longae were the most
attributed to the toxicity of the extracts to the
effective herbs in controlling A. tumefacians biofilm
bacterium tested, as such Modified Microtitre Plate
growth where bacterial growth on membranes was
Assay results for herb extracts of Angelicae Sinensis
restricted by 50% as compared to the control.
and
organic
efficacy.
to
QSI.
compounds
Moreover,
This
present
for
distinction
is
AI-1
autoinducers,
Semen
were
able
and
to
this
discrepancy
control
bacterial
Radix and Salviae Miltiorrhizae Radix on S. epidermidis

should not be treated as QSI effect.
In preventing biofilm formation of S. epidermidis

(Figure 1c), only Salviae Miltiorrhizae Radix and
27
VOYAGER 2014
S. epidermidis A. tumefaciens
9.0 0.0
9.0 0.0
9.0 0.0
9.0 0.0
9.0 0.0
9.0 0.0
11.3 3.2
9.0 0.0
32.0 1.0
9.0 0.0
9.0 0.0
9.0 0.0
Sterile water
9.0 0.0
9.0 0.0
Bleach
23.7 1.2
18.3 0.6

against
Persicae Semen were effective. Both herbs were able to

control the amount of biofilm formed on the membrane
by 20% on average. However, as compared to the
previous results, the other herbs were unable to inhibit
bacterial agglomeration of S. epidermidis. This could
again be due to the difference in autoinducers utilised
by the bacteria. Gram positive S. epidermidis expresses
autoinducer oligopeptides (AIPs), and effectiveness
against preventing biofilm formation of S. epidermidis
on membranes correlated to the ability of the extracts
in preventing cell communication via AIPs.
(a)
However, Salviae Miltiorrhizae Radix was found to
possess an antibacterial effect against S. epidermidis.
Therefore, results of relating to the effect of biofilm
inhibition by Salviae Miltiorrhizae Radix may not be due
to QSI but due to its toxicity towards the bacterium. In
contrast, Persicae Semen has not been found to be
antibacterial against S. epidermidis, thus the QSI
properties of this herb extract can be ascertained in the
Modified Microtitre Plate Assays since it was not found
to be toxic towards the bacterium.

VOYAGER 2014
28
Results from the Modified Microtitre Plate Assays

(b)
indicated that specific herbs were effective to only

specific autoinducers. This indicated that while each of
the extracted contained QQ, in order to eliminate
environmental biofilms, which contain a mix of
Gram-negative and Gram positive bacteria, a cocktail
of extracts should be used. Understanding the
mechanism to which each of the extracts prevented
biofilm formation could yield more insights towards
producing such a cocktail. Motility studies were
conducted to determine which stages of the biofilm
process were the autoinducers inhibited.
(c)
Inhibition of Swimming Motility

Figure 1. Effect of herb extracts on biofilm formation on PVDF
membrane slices. Error bars represent standard error of data; (a) E.
coli; (b) A. tumefaciens; (c) S. epidermidis.
Swimming motility refers to the ability of bacteria to

travel
through
liquid
medium.
In
biofilm
developmental mechanism, swimming motility was

postulated to be the first course of action wherein
bacteria swim towards a solid stratum, which will be
the membrane surface in an MBR. Such actions were
thought to be due to a higher concentration of solutes
near the solid stratum. Effects of herb extracts and
their concentrations on swimming motilities of E. coli
and A. tumefaciens are shown in Figures 2 and 3,
respectively.
(a)
(a)
(b)
(b)
(c)
(c)
Figure 2. Effects of herbs on swimming of E. coli. Error bars represent
Figure 3. Effects of herbs on swimming of A. tumefaciens. Error bars
standard error of data; (a) Day 1, (b) Day 2, (c) Day 3.
represent standard error of data; (a) Day 1, (b) Day 2, (c) Day 3.
Rhizoma Curcumae Longae and Persicae Semen at all
Figure 3 shows the effect of TCM herb extracts on
concentrations inhibited the swimming motility of E.
swimming motility of A. tumefaciens. Similarly, it was
coli throughout the 3 days (Figure 2). Their inhibitory
observed that Rhizoma Curcumae Longae, Persicae
properties were further enhanced in Days 2 and 3,
Semen and Asini Corii Colla inhibited swimming
where there was a significant difference in the
motility of A. tumefaciens throughout the 3 days. The
swimming radii of E. coli in the negative control plate
properties were further enhanced in Days 2 and 3.
and in the plates with Rhizoma Curcumae Longae and
However, Persicae Semen was the most effective
Persicae Semen added. This difference in swimming
amongst these 3 herbs, showing up to 90% inhibition of
motility of E. coli was approximately 80% on Day 3.
the swimming motility of A. tumefaciens by Day 3.
Panax notoginseng at low concentrations was also

effective in inhibiting the swimming motility of E. coli
Both sets of results showed that Rhizoma Curcumae
throughout
Panax
Longae and Persicae Semen were effective against
notoginseng at high concentrations only revealed its
swimming motility of E. coli and A. tumefaciens. These
swimming inhibitory abilities on Day 3.
results reflected that compounds in both extracts
the
days.
Interestingly,
possessed the ability to restrict bacterial movement

VOYAGER 2014
29
through semi-solid or aqueous mediums. Presence of

inhibition decreases probability of bacterial adhesion
onto membrane surfaces in MBRs as was observed in
the modified microtitre plate assays, reducing bacterial
concentration on membrane surfaces to less than that
of biofilm formation threshold.
Consequently, since membrane biofouling consitututes
of the formation of a biofilm on the surface, in which
(a)
pores become blocked, thereby restricting the smooth

flow of water, the use of QQ into an MBR will prove to
be beneficial in reducing such fouling occurences
(Yeon et al., 2009). As biofilm initiated fouling
dominates at sub-critical flux conditions in an MBR (Ng
and Ng, 2010), the aid of QQ to inhibit swimming
motilities of bacteria, will allow the bacteria to remain
suspended within the mixed liquor.
Inhibition of Swarming Motility
The swarming motility of bacteria is the ability of the
(b)
bacteria to congregate and grow to reach a certain

concentration upon adhesion onto a liquid-liquid

VOYAGER 2014
30
interface or solid-liquid interface. At this stage, QS

occurs at its peak and EPS is secreted, forming the
basis of the biofilm.
From Figure 4, Rhizoma Curcumae Longae was able to
inhibit the swarming motility of E. coli only at Day 1, but
this effect could not be sustained through Days 2 and
3.
While the effectiveness of Asini Corii Colla was
(c)
marginally ineffective, given adequate time, on Day 2
Figure 4. Effects of herbs on swarming of E. coli. Error bars represent
and Day 3, Asini Corii Colla was able to inhibit the
standard error of data; (a) Day 1, (b) Day 2, (c) Day 3.
swarming motility of E. coli of up to 15%. As for the

remaining herbs, they showed to be ineffective in
CONCLUSIONS
preventing bacterial swarming, evident by the increase

of area of bacterial colony. The promotion of bacterial
All TCM herb extracts tested in this research exhibited
swarming in E. coli could be due to the compounds
varying abilities in targeting the issue of biofouling.
exhibiting effects that amplifies the production of
Most evidently, Rhizoma Curcumae Longae, Asini Corii
autoinducers, or increases bacterial movement along
Colla and Persicae semen showed potential in the
the interface by acting as an energy source for the
combating and prevention of biofilms in Gram positive
bacteria.
and Gram negative bacteria on a whole. Time-based

analysis, however, showed discrepancies in the effects
Swarming motility comes as the second yet most
of the various extracts over time, and have to be
crucial step in biofilm formation. Antagonising the
analysed further. Different herb extracts displays
process of swarming prevents the basic structure of
varying effectiveness against membrane biofouling, as
biofilm from forming, as well as succeeding expansions
shown by the membrane titre assay. By analysing the
of the biofilm layer. Extracts of Rhizoma Curcumae
in-depth processes in which biofilm prevention occurs,
Longae and Asini Corii Colla both display varying
the individual effectiveness of each herb can be
effectiveness of swarming inhibition over time. By
deduced and more accurately justified. A combination
inhibiting swarming motility of E. coli, bacteria is
of extracts can also be derived, maximising the
unable to communicate via signalling molecules at high
potential of each herb against the various motilities, to
threshold values, preventing a series of physiological
further combat the issue of membrane biofouling to its
chain reactions and subsequent biofilm formations.
best ability.
REFERENCES
Annous B. A., Fratamico P. M. and Smith J. L. 2008
Quorum sensing in biofilms: why bacteria behave the
way they do. Journal of Food Science, 74(1), pp. R24-R37.
Decho A. W., Norman R. S. and Visscher P. T. 2009
Quorum sensing in natural environments: emerging
views from microbial mats. Trends in Microbiology,
18(2), pp. 73-80.
Flemming H. C. 2009 Why microorganisms live in
Mafirad S., Mehrnia M. R., Azami H. and Sarrafzadeh M.

H. 2011 Effects of biofilm formation on membrane
performance in submerged membrane bioreactors.
Biofouling: The Journal of Bioadhesion and Biofilm
Research, 27(5), pp. 477-485.
Ng T. C. A. and Ng H. Y. 2010 Characterisation of initial
fouling in aerobic submerged membrane bioreactors
in relation to physico-chemical characteristics under
different flux conditions. Water Research, 44(7), pp.
2336-2348.
industrial biofouling, H. C. Flemming, P. S. Murthy, R.
Niu C., Afre S. and Gilbert E. S. 2006 Subinhibitory

concentrations of cinnamaldehyde interfere with
quorum sensing. Letters in Applied Microbiology,
Venkatesan and K. Cooksey (eds.), Springer, Berlin
43(5), pp. 489-494.
biofilms and the problem of biofouling. In: Marine and
Heidelberg, pp. 3-12.
Biotechnology: Concepts and Applications, Jrdening

H. J. and Winter J. (eds.), Wiley-VCH Verlag,
Weinheim, Germany, pp. 1-48.
Huerta V., Mihalik K., Crixell S. H. and Vattem D. A.
2008 Herbs, spices and medicinal plants used in
Hispanic traditional medicine can decrease quorum
sensing
dependent
virulence
in
Pseudomonas
aeruginosa. International Journal of Applied Research

in Natural Products, 1(2), pp. 9-15.
Khan M. S. A., Zahin M., Hassan S., Husain F. M. and
Ahmad
I.
2009
Inhibition
of
quorum
with specific reference to clove oil. Letters in Applied

Microbiology, 49(3), pp. 354-360.
Kociolek M. G. 2009 Quorum-sensing inhibitors and
biofilms. Anti-Infective Agents in Medicinal Chemistry,
8(4), pp. 315-326.
Koh K. H. and Tham F. 2009 Screening of traditional
medicinal
inhibitors
activity.
plants
Journal
for
quorum-sensing
of
Simes M., Simes L. C. and Vieira M. J. 2010 A review

of current and emergent biofilm control strategies.
LWT Food Science and Technology, 43(4), pp.
573-583.
sensing
regulated bacterial functions by plant essential oils
chinese
Raffa R. B., Iannuzzo J. R., Levine D. R., Saeid K. K.,

Schwartz R. C., Sucic N. T., Terleckyj O. D. and Young J.
M. 2004 Bacterial communication (quorum sensing)
via ligands and receptors: a novel pharmacologic
target for the design of antibiotic drugs. Perspectives
in Pharmacology, 312(2), pp. 417-423.
Microbiology,
Immunology and Infection, 44(2), pp. 144-148.

Lewandowski Z. and Boltz J. P. 2011 Biofilms in water
and wastewater treatment. In: Treatise on water
science, Wilderer P. A. (ed.), Elsevier Science, Oxford,
pp. 529-570.
Lewis K. 2001 Riddle of biofilm resistance. Antimicrobial
Agents and Chemotherapy, 45(4), pp. 999-1007.
Teplitski M., Robinson J. B. and Bauer W. D. 2000

Plants secrete substances that mimic bacterial N-Acyl
Homoserine Lactone signal activities and affect
population density-dependent behaviors in associated
bacteria. The American Phytopathological Society,
13(6), pp. 637-648.
Yeo S. S. M. and Tham F. 2012 Anti-quorum sensing and
antimicrobial activities of some traditional Chinese
medicinal plants commonly used in South-East Asia.
Malaysian Journal of Microbiology, 8(1), pp. 11-20.
Yeon K. M., Cheong W. S., Oh H. S., Lee W. N., Hwang B.
K., Lee C. H., Beyenal H. and Lewandowski Z. 2009
Quorum sensing: a new befouling control paradigm in
a membrane bioreactor for advanced wastewater
treatment. Environmental Science and Technology,
43(2), pp. 380-385.
Zobell C. E. 1943 The effect of solid surfaces upon
bacterial activity. Journal of Bacteriology, 46(1), pp.
39-56.
31
VOYAGER 2014
wastewater treatment systems. In Environmental
Prabuseenisvasan S., Jayakumar M. and Ignacimuthu S.

2006 In vitro antibacterial activity of some plant
essential oils. BMC Complementary and Alternative
Medicine, 6(39).

Gallert C. and Winter J. 2005 Bacterial metabolism in
What is an important quality you think

research students should possess?
passionate will they be dedicated, putting in effort

constantly, and seeing the project through to
completion, and this will build up to some discovery,
be it small or large. This discovery may not have a
significant impact on the world as we know it, but if
they pursue their passion in the future, this initial
research experience will definitely be beneficial, and
they will continue to push the boundaries of science.
Some might see spending countless hours in a lab as
dry and dull, but for those who have a passion for
What inspired you to take up research?

My research project involved the study of the
metabolic pathways of FAT10, a ubiquitin-like protein
which was found by the National Cancer Centre
Laboratories to be involved in the disruption of
cellular checkpoints of cell division. This was a topic
that extended what I learnt as a biology student in
class about cancer, and therefore brought real-life
implications and applications of cancer studies into
my experiences. Through the course of the project I
was inspired by how the seemingly mundane tasks of
research, they see meaning in what they do.
transferring extremely small amounts of substances
In what ways have Hwa Chong supported

you?
results leading to the contribution to potentially
I would like to thank Hwa Chong for its amazing

teachers, as without my mentor's help, my research
team would not have had the opportunities we have
had, and grown so much as researchers and as
people. The laboratory staff would also tirelessly help
all
the
research
groups
refine
our
laboratory
techniques. Hwa Chong has invested intelligently into

grooming young student researchers, by having a
well-equipped Science Research Centre, and by
providing us with the opportunities for participating
in science fairs and international competitions. Hwa
Chong is the wind beneath our wings.
with a micropipette was vital in obtaining accurate

groundbreaking fields for my mentors and other
researchers. The process of the scientific method is a
meticulous and noble oneit seems almost too easy
to overlook the fact that mundane processes
contribute significantly to humanity.
Chiang Yan Li 13S7B

Research not only broadens our knowledge in
science and bolsters our confidence in this subject; it
trains our resilience as well. I did a research project at
the Weizmann Institute in Israel as part of the
International Summer Science Institute Programme. I
met
instrumental,
empirical,
and
theoretical
challenges at almost every step of the journey. Words
Tan Jiefeng 14S7B
of encouragement by my mentor kept me going and

provided me with the courage to present my project
Hwa Chong has invested

intelligently into grooming young
student researchers, by having a
well-equipped Science Research
Centre, and by providing us with the
opportunities for participating in
science fairs and international
competitions. Hwa Chong is the
wind beneath our wings.
in front of my peers. I hope that my newfound spirit

of resilience will act as the vital scaffold for my
eventual success. I believe that scientific research is
just like the inexplicable black-holeit is mysterious,
elusive, and we never know what we will pick up and
learn from it. But one thing is for certain: it is certainly
attractive!
Yi Kui Shuai 14S7B
15
VOYAGER 2014
students should possess is passion. Only if they are
Students Voices
I think that the one important quality research
GREEN SYNTHESIS OF
SILVER NANOPARTICLES
USING LALANG EXTRACT
1. INTRODUCTION
Lee Wei Hao, Joel 13S7C
Phua Yue Jun 13S6F
Tan Kwan Wei Kevin 13A16
The application of nanoparticles, usually ranging from 1

to 100 nanometers (nm), is an emerging area of
nanoscience
and
nanotechnology.
Nanoparticles
exhibit completely new or improved properties based

on specific characteristics such as size, distribution and
morphology. Silver nanoparticles have been widely
Research Mentor
Mrs Sow-Peh Yoke Keow
used in the field of catalysis, micro-electronics (Jain et

al, 2009), biological systems (Roy & Barik, 2010) and
medicine due to their antimicrobial and antibacterial
effects (Kamal et al, 2010).
Silver nanoparticles are synthesized by the reduction
Gold Award
of silver ions from Ag+ to Ag0 (Roy & Barik,
2010)
using reducing agents. The current methods of

synthesizing silver nanoparticles include chemical and
Green Synthesis Of Silver Nanoparticles Using Lalang Extract
VOYAGER 2014
32
National representative at the

Intel International Science and
Engineering Fair
photochemical reactions in reverse micelles, thermal

decomposition of silver compounds
in organic
solvents (Jain et al, 2009; Singh et al, 2010), radiation

chemical reduction and the chemical reduction of
silver ions in aqueous metal salt solutions (Forough &
Farhadi, 2010) with different external reducing agents
(Kamal et al, 2010). However, these chemical routes
can be extremely expensive and require the use of
toxic chemicals (Kamal et al, 2010). Hence there is a
need to explore alternative green chemistry routes,
where natural products are used for the synthesis of
silver nanoparticles.
The use of environmentally benign and organic
materials for the synthesis of silver nanoparticles
offers
several
benefits
of
eco-friendliness
and
compatibility for pharmaceutical and other biomedical

applications as they do not use toxic chemicals.
Chemical synthesis methods lead to the presence of
some toxic chemical adsorbed on the surface that may
have adverse effect in the medical applications (Jain et
al, 2009). Green synthesis, on the other hand, is
environment friendly, cost effective, easily scaled up
for large scale synthesis and does not require the use
of high pressure, energy, temperature and toxic
chemicals.
These
biologically
synthesized
silver
nanoparticles are also toxic against multi drug resistant

human pathogens (Kamal et al, 2010; Jain et al, 2009),
so they can be effectively used in the medical industry.
Chemical and physical methods are replaced with
green alternatives, using microorganisms, enzymes,
fungus and plants or plant extracts (Forough &
3 hours. The colloidal silver nanoparticles obtained
Farhadi,
was characterised using a UV-VIS spectrophotometer
2010)
for
the
biological
methods
of
synthesizing nanoparticles. Among these possible
(Shimadzu UV-1800). Triplicates were performed.
natural products, plants or plant extracts are preferred

over the microorganism routes as there is no need to
maintain
microbial
cultures,
which
can
be
2.2.3 Purification of silver nanoparticles
troublesome and arduous (Kamal et al, 2010).

The reaction mixture was centrifuged at 8000 rpm to
Thus this project aims to make use of organic
obtain the solid silver nanoparticles. Excess extract
extracts derived from lalang (Imperata cylindrical),
was decanted and the silver nanoparticles were
a weed, to synthesize silver nanoparticles. Lalang is
purified by repeated centrifugation at 8000 rpm with
a weed found commonly in tropical countries such
deionised water. The silver nanoparticles were dried
as Singapore and Malaysia. It is a novel weed to study
with a vacuum concentrator (Christ, RVC 2-25 CD).
as thus far, there have been no reports on the use of
The size of the solid silver nanoparticles was
this weed to synthesize silver nanoparticles. The silver
determined by a JEOL JSM-5200 Scanning Electron
nanoparticles synthesized were characterized using
Microscope (SEM).
UV-VIS Spectroscopy and its size determined by SEM

(Scanning electron microscope). Its anti-bacterial
2.2.4 Antibacterial Activity
property against Staphylococcus epidermidis (S.

Escherichia.
Coli
(E.coli)
and
The antibacterial properties of both the colloidal and
antifungal property against Aspergillus niger (A.niger)
solid
were also studied.
S.epidermidis, a common gram positive bacterium
silver
nanoparticles
were
studied
against
commonly found on human skin and mucosa and

E.coli, a common gram negative bacteria commonly
Hypothesis
The
solid
synthesized
and
colloidal
silver
lalang
extract
using
nanoparticles
will
exhibit
found in intestinal and digestive tracks of mammal

were tested.
antibacterial property against S. epidermidis and E.

coli and antifungal property against A. niger.
2.2.4.1 Colloidal silver nanoparticles
2. MATERIALS AND METHOD
Well diffusion test was carried out. The bacteria were

first grown in a nutrient broth for 24 hours/37C
before use. The overnight culture was swabbed onto
2.1 Materials
the Mueller-Hinton agar plates. 4 wells of 0.6cm in

Lalang
Road
diameter were created on each plate and they were
(Singapore). S.epidermidis and E.coli were obtained
was
obtained
from
Sembawang
labeled A (which contained the lalang colloidal silver
from Microbiologics while A.niger was obtained from
nanoparticles), B (which contained the lalang extract),
Carolina. Silver nitrate was obtained from GCE
+ve control (which contained 10% bleach solution)
Laboratory Chemicals.
and ve control (which contained sterile water). They

were all filled with 75l of respective extracts or
2.2 Methods
control. After 24 hours of incubation at 37C, the
2.2.1 Preparation of extracts
zones of inhibition around each plate were measured.
Lalang leaves were cut into small pieces. 25 g of
2.2.4.2 Solid silver nanoparticles
leaves were boiled in 100 ml of deionised water for 15

minutes. The mixture was centrifuged and filtered to
Total plate count method was carried out. The
obtain aqueous extract. The extract was stored at 4C.
bacteria were first grown in a nutrient broth for 24

hours/37C before use. The absorbance of the
2.2.2 Synthesis of silver nanoparticles
overnight culture was measured at 600nm. 100l of

the overnight culture was transferred to 10ml of
2.5 ml of lalang extract and 2.5 ml of deionised water
Nutrient Broth tubes. The tubes were labelled as
were added to 45 ml of 1mM aqueous silver nitrate. A
sample and control respectively. 0.01 g of solid silver
control was set up using 47.5ml of deionised water
nanoparticles was washed twice with 70% ethanol
with 2.5ml of lalang extract. The flasks were shaken for
followed by sterile water (2 times) and dried. The
33
VOYAGER 2014
and
epidermidis)
1.6
broth and sonicated to obtain a homogeneous
1.4
mixture. To the sample tubes was added 1 ml of silver

nanoparticle suspension while to the control tubes
was added the same volume of nutrient broth. The
tubes were incubated at an incubator shaker for 24hr.
After 24 hr, the overnight broth culture was diluted
and 100l was spread onto the Nutrient Agar plates by
using
an
L-shaped
spreader.
The
plates
Absorbance
nanoparticles were then suspended in 5 ml of nutrient
1.2
1
0.8
0.6
0.4
0.2
were
incubated at 37C in an incubator for 24 hr. The
400
colonies were counted.

2.2.5
Antifungal
Assay
of
colloidal
500
600
700
800
Wavelength/nm
Figure 2. UV-VIS spectrum of colloidal lalang silver nanoparticles
silver
Figure 2 shows the UV-VIS spectrum of colloidal silver
nanoparticles
nanoparticles synthesized. A peak was observed at

silver
around 450 nm, which is typical of absorption for
nanoparticles was tested on the fungus, A. niger.
metallic silver nanoparticles, due to the Surface
Culture media was prepared using Potato Dextrose
Plasmon Resonance (SPR), confirming that silver
Agar. The agar was cooled at a 50C water-bath for at
nanoparticles have been successfully synthesized.
The
antifungal
property
of
the
colloidal
least 15 minutes and 5 ml of colloidal silver

nanoparticles were added and mixed. The agar was
poured onto petri dishes. A.niger was grown in Potato
VOYAGER 2014
34
Dextrose Broth at room temperature for 24 hours. A

loopful of overnight culture was placed onto the
Figure 3. SEM image of
middle of the agar and the plate incubated at room
lalang silver nanoparticles
temperature for 5 days. The diameter of growth of the

fungus was measured on the 3rd and 5th day.
3. RESULTS AND DISCUSSION

Figure 3 shows the SEM image of the silver
nanoparticles synthesized by lalang extract. The size
3.1 Synthesis of silver nanoparticles
of silver nanoparticles ranges from 40 to 50nm. The

On shaking for three hours, the flask which contains
silver nanoparticles synthesized are spherical in
lalang extract and aqueous silver nitrate turned brown
shape. The size of the silver nanoparticles is smaller
(Figure 1), indicating the reduction of Ag(I) to Ag(0).
than that synthesized from weeds from India which
The formation of brown colouration is due to the
have a size ranging from 100-400 nm (Roy et al, 2010)
excitation of surface plasmon vibrations in the silver
and similar to that synthesized from aloe vera (Zhang
metal nanoparticles.
et al, 2010).
Silver
3.2
nitrate
Antibacterial
+
lalang
extract
Control
(without silver
of
colloidal
silver
(+) 10% Bleach solution
( - ) Sterilized water
(A) Colloidal lalang silver nano
(B) Lalang extract
nitrate)
Figure 1. Colour change of extract before and after
adding silver nitrate
Activity
nanoparticles
A
Figure 4. Zone of inhibition for
S.epidermidis
Figure 5. Zone of inhibition for

E.coli
Figures 4 and 5 show the presence of zones of
Figures 6 and Figure 7 show that the lalang solid silver
inhibition for both S.epidermidis and E.coli in the well
nanoparticles exhibit antibacterial properties against
filled
nanoparticles,
the two bacteria tested upon. For S.epidermidis,
indicating that the colloidal silver nanoparticles have
with
colloidal
lalang
silver
the lalang solid silver nanoparticles result in a drastic
antibacterial property against both bacteria. The
drop in the bacteria colonies, from 5 x 107 colonies in
inhibition zone for S.epidermidis was 1.25 cm while
control plate to 1 x 104 colonies in the plate containing
that for E.coli was 1.33 cm. In contrast, sterile water
silver nanoparticles, amounting to close to 100%
and lalang extract show no zone of inhibition. Lalang
reduction of bacteria colonies.
extract was tested to confirm that the antibacterial
reduction of bacteria colonies was around 48%, with
properties were in fact from the silver nanoparticles
the reduction of bacteria colonies from 84 x 106
synthesized from lalang extract and not from the
colonies in control plate to 43.5 x 106 colonies in the
lalang extract itself.
plate containing silver nanoparticles.
According to Marambio-Jones and Hoek (2010), silver

nanoparticles
exert
bactericidal
bind to the negatively charged cell membrane. Also

the silver nanoparticles could bind to thiol containing
by
permeability.
chelation,
This
in
which
turn
enhances
results
in
3.4 Antifungal Activity
activity
predominantly through the release of silver ions which
protein
For E.coli, the
Lalang
extract
Lalang
Silver nano
Control
cell
efflux
of
phosphate, leakage of cellular contents, disruption of

DNA replication and eventually cell death.
properties
of
solid
35
silver
nanoparticles
Figure 8. Photograph showing diameter of growth of A.niger in different
media on 3rd day
50
10
40
99.99%
30
20
10
0
control
Silver nano
Figure 6. Total plate count for S.epidermidis
Diameter of gowth/cm
Bacterial count x106/(CFU/ml)
60
7.9
5.6
6
4
2.5
2
0
7.7
2.5
0.5
No. of days
3rd Day
Control
Lalang silver nano
5th Day
Lalang extract
Figure 9. Diameter of growth of A.niger for a period of 5 days
Bacterial count x 106/ (CFU/ml)
From figure 8 and 9, it can be deduced that the lalang

100
84
silver nanoparticles are able to slow down the growth
90
of A.niger. As can be seen from Figure 8, there is little
80
48.2%
70
60
43.5
50
growth for the plate with the silver nanoparticles

added on the 3rd day, and this is in stark contrast with
the significant growth observed for the control plate
and the plate with lalang extract. Figure 9 shows that
40
on the 5th day, the diameter of growth for the plate
30
containing lalang silver nanoparticles was still smaller
20
than both the control plate and the plate containing
10
lalang extract.
control
Silver nano
Figure 7. Total plate count for E.coli
VOYAGER 2014
Antibacterial
3.3
4. CONCLUSIONS AND RECOMMENDATIONS
International
Journal
of
Nanotechnology
and
Applications, 4, 95-101. Retrieved February 22, 2011 from

Silver nanoparticles can be synthesized from lalang
http://www.ripublication.com/ijna/ijnav4n2_4.pdf
extract. The presence of silver nanoparticles was

confirmed by UV-VIS spectrophotometry whereby a
Singh, A., Jain, D., Upadhyay, M.K., Khandelwal, N. &
peak was observed at 450 nm. The particle size of the
Verma,
silver nanoparticles synthesized range from 40 nm to
nanoparticles using argemone mexicana leaf extract
50nm. Silver nanoparticles synthesized from lalang
and evaluation of their anti microbial activities. Digest
extract were found to be effective against the bacteria
Journal
Staphylococcus epidermidis and Escherichia coli as
483-489.
well as against the fungus Aspergillus niger. As lalang
http://www.chalcogen.infim.ro/483_Singh.pdf
H.N.
of
(2010).
Green
Nanomaterials
Retrieved
synthesis
and
of
silver
Biostructures,
February
22,
2011
5,
from
is a common and fast growing weed in Singapore

which is unexploited, the use of it as a starting
Zhang, Y., Yang, D., Kong Y., Wang X., Pandoli, O., Gao.,
material for the large scale synthesis of silver
G. (2010). Synergetic antibacterial effects of silver
nanoparticles is viable, economical, eco- friendly and
nanoparticles@ aloe vera prepared via a green
sustainable.
method. Nano Biomed Eng, 267-274
This scope of this study can be widened by

investigating more types of bacteria. The lalang silver
nanoparticles can also be incorporated into everyday
products such as soap, cosmetics or socks and the
antibacterial properties of these products can be
evaluated.
VOYAGER 2014
36
REFERENCES
Forough, Mehrdad & Farhadi, Khalil (2010). Biological
and green synthesis of silver nanoparticles. Turkish J.
Eng. Env. Sci., 34, 1-7. Retrieved February 22, 2011 from
http://journals.tubitak.gov.tr/engineering/issues/muh10-34-4/muh-34-4-7-1005-30.pdf
Jain, D., Diama, H. Kumar, Kachhwaha, S. & Kothari,
S.L.
(2009).
nanoparticles
Synthesis
using
of
plant-mediated
papaya
fruit
silver
extract
and
evaluation of their anti microbial activities. Digest

Journal
of
Nanomaterials
and
Biostructures,
4,
557-563. Retrieved February 22, 2011 from

http://www.chalcogen.infim.ro/557_Jain.pdf
Kamal, S.S.K., Sahoo, P.K., Vimala, J., Premkumar, M.,
Ram, S. & Durai, L. (2010). A Novel Green Chemical
Route for Synthesis of Silver Nanoparticles Using
Camellia Sinensis. Acta Chim. Slov., 57, 808-812.
Retrieved February 22, 2011 from
http://acta.chem-soc.si/57/57-4-808.pdf
Marambio-Jones, C., Hoek, E. M.V. A review of the
antibacterial effects of silver nanomaterials and
potential implications for human health and the
environment, J Nanopart Res. 2010;12:1531-1551
Roy, N. & Barik, A. (2010). Green Synthesis of Silver
nanoparticles from the Unexploited Weed Resources.
DETERMINING THE AMINO ACIDS

INVOLVED IN INHIBITION OF
PDE4B BY STRUCTURALLY-DIVERSE
COMPOUNDS
1 INTRODUCTION
Cai Anni 11S7B
External Research Mentor
Professor Charles S. Hoffman
Boston College
Centre for Excellence in Education,
Research Science Institute, MIT, USA
Top prize for written report and oral
presentation
Phosphodiesterases (PDEs) are a class of related

enzymes
that
degrade
adenosine
35-cyclic
monophosphate (cAMP) by selectively catalyzing the

hydrolysis of the 3 cyclic phosphate bond of
cAMP[4].
Figure 1 : PDE Action On cAMP.
PDEs catalyze the hydrolysis of 3 cyclic phosphate
bond (shown in bond), thereby converting cAMP to
AMP.

Silver Award
transduction
pathways,
including
production
of
cortisol and metabolism of lipids. Spontaneous

degradation
of
cAMP
by
PDEs
allows
cAMP-mediated cellular transduction pathway to be

quickly
terminated
once
the
initial
chemical
messenger is no longer present, so that the cell may

respond to a fresh or repeated signal. This feedback
loop forms a basis for the tight regulation of
metabolic pathways in response to a fluctuating
environment [5].
Human PDEs are categorized into 11 families based on
substrate
specificity,
regulatory
properties,
and
homologies in primary sequence. The various PDEs

are encoded by 21 genes, which is transcribed into
more than 100 isoforms of the enzyme via alternative
splicing. In the official PDE nomenclature, the Arabic
numeral specifies the PDE family to which the enzyme
belongs, while the capitalized letter represents the
gene as reported in Genbank (NIH genetic sequence
database) [4]. Each family has unique substrate
selectivity: only the PDE4, PDE7, and PDE8 families
act specifically on cAMP; others act on both cGMP (a
second messenger similar to cAMP), or on cGMP and
cAMP [11].
It has been postulated that some PDEs function solely
to prevent
clouds of cyclic nucleotides from
spreading to inappropriate regions of the cell while
37
VOYAGER 2014
key second messenger involvedin many cellular signal
Determining The Amino Acids Involved In Inhibition Of

PDE4B By Structurally-diverse Compoundseditorial
PDEs are physiologically important because cAMP is a
others regulate local access to specific cAMP/cGMP
functions.
receptors.
unique
family-specific, but isoform-specific. As such, drugs
distributions of PDE isoforms, and the nature and
can be made to target specific disease pathways by
localization of these PDEs are likely to be a major
selectively
regulator of the local concentration of cAMP/cGMP in
involved. This can potentially minimize side-effects.
Different
cell
types
express
Some
pathways
inhibiting
the
are
not
specific
PDE
merely
isoform
the cell [4]. Tissue-specific expression of various PDEs

is
physiological
To this end, PDE inhibitor drugs have gained
functions. For example, PDE1B is implicated in allergic
intimately
mainstream acceptance. The erectile dys- function
reactions
for
drug, sildenafil (Viagra), is a selective PDE5 inhibitor
regulating IL-13 in PHA or anti-CD3/CD28-activated
which prevents cGMP from being degraded, thereby
human T-lymphocytes. PDE6, predominantly found in
prolonging the signal for smooth muscle relaxation.
rod cells of the photo-receptor layer of the retina,
The
functions in photo-transduction by reducing the
cavernosum optimizes physiological conditions for
steady-state concentration of cGMP in response to
penile erection [24]. Sildenafil is also used to treat
light stimulus, thereby leading to the closure of cyclic
pulmonary arterial hypertension [16] and altitude
nucleotide-gated
ion
sickness
channels.
consequent
as
linked
PDE1B
The
to
different
mRNA
is
channel
responsible
(CNG)
cell
cationic
membrane
consequent
[19]
vasodilation
based
on
the
in
the
same
corpus
mechanism
(vasodilation).
hyper-polarization sends an electric signal through

optical nerves to the brain, which is interpreted as a
Inspired by the pharmacological success of sildenafil,
visual stimulus [18].
drug companies are increasingly looking towards

archetypal PDE4 inhibitor, was originally created by
38
recent years as it was found to influence a number of
Schering AG as a potential antidepressant and also
autoimmune diseases. One of the earliest to be
shows promise for treating inflammatory diseases
characterized, the PDE4 family was originally named
associated with PDE4B activity, ranging from chronic
for its selective resistance to rolipram (see Appendix
obstructive pulmonary disease to asthma, arthritis
for structure) and is characterized by cAMP substrate
and psoriasis. However, rolipram induces emetic
selectivity and low Km values. It comprises 4 isoforms
side-effects which are thought to be
which are sub-categorized into >20 variants that
non-specific inhibition of PDE4D in the brain [15]. Our
differ in their N-termini, where the PDE4 regulatory
current research is focused on understanding PDE4B
domains and phosphorylation sites are located [4].
inhibitor-specificity by determining the amino acids
Studies in knockout mice indicate that each individual
involved in inhibition of PDE4B through a novel
PDE4 gene plays a non-redundant regulatory role that
screening strategy outlined below.

Much interest has been focused on the PDE4 family in
VOYAGER 2014
PDE4 inhibitors as drug candidates. Rolipram, the
caused
by
cannot be supplanted by the other 3 PDE4 transcripts

[12, 20], which agrees with the isoform-specific nature
of many PDE-related diseases. One region of the

PDE4D gene is linked to heightened risk of ischemic
2.1
stroke[21], and absence of PDE4D3 led to progressive
PCR was carried out on plasmid pK63-N21 containing
cardiomyopathy
and accelerated heart failure in
the human PDE4B gene using the FailSafe PCR Kit
knockout mice possibly by increasing PKA-mediated
(Epicentre Biotechnologies, Madison, WI). Premix
phosphorylation of the cardiac ryanodine receptor
buffers A, B, E, F, K, L (Integrated DNA Technologies,
which rendered the ion channels leaky [14]. PDE4B,
Coralville, IA) containing 100mM Tris-HCl (pH 8.3),
the focus of this study, regulates inflammatory
100mM
responses by controlling the the production of TNF-
concentrations of MgCl2 (3-7mM) and PCR Enhancer
in both monocytes [12] and macrophages [13] in
(0-8X) were used with primers Cgs2-PCRmut-3 (3 to
response
open reading frame) 5AAA GTG TCC GAT GAG AAA
to
bacterial
lipopolysaccharide
(LPS)
stimulation.
Random mutagenesis via PCR
KCl,
400M
of
each
dNTP,
varying
AGC GTG 3 and Cgs2-PCRmut-5 (5 to ORF) 5 TCA

TAG CAT ACT TCT TCA CCA AGC 3. 30 cycles of PCR
The diversity and specificity of PDEs make them
were performed (each cycle consisted of 30s at 95C
excellent pharmacological targets. Unlike similarly
to denature DNA, 30s at 55C to anneal primers to the
ubiquitous cellular enzymes such as PKA that show no
template DNA, and 2.5 minutes at 72C for extension),
structural variance, each of the structurally different 11
after
PDE families is involved in different physiological
which
the
mutated
gene
products
were
2.2
Screening for inhibitor resistant PDE4B alleles
Schizosaccharomyces
(h leu1-32ade6-17216
pombe
was
cell culture was mixed with 10l of DMSO, BC27-5,
SP578
BC35 and BC58 respectively at 4M concentration in
transformed
DMSO. 5l of each mixture was plated on agar
following a gap-repair DMSO transformation protocol
containing YELleu medium and incubated at 30C
[2]. Yeast cells were cultured in Yeast Extract Liquid
for 2 days. Colonies were stained with iodine to
(YEL) medium [9] overnight, then subcultured into
identify colonies resistant to inhibitors.
90
cgs2-2)
strain
Edinburgh Minimal Medium (EMM)(MP Biomedicals,

Solon, OH) to target for 107 cells/ml. Cells were then
2.3 Phenotypic characterization of transformants
washed with 1X LiOAc/TE buffer ((10LiAc: 1M lithium
expressing candidate mutant PDE4B alleles
acetate, adjusted to pH 7.5 with diluted acetic acid;
Selected colonies were transferred to liquid YELleu
10TE: 0.1M Tris-HCl, 0.01M EDTA, pH7.5) [2] and
medium and incubated at 37C for 1 day. The cell
brought to a final concentration of 2109cells/ml in
cultures were then diluted to a concentration of
this buffer. Either 200ng (first transformation) or
1107cells/ml. 10l of cell culture was mixed with 90l
50ng
StuI-linearized
of DMSO, and 40 M of compounds BC27-5, BC35 and
plasmid pKG3-N21 together with an excess of PCR
(second
transformation)
BC58, respectively to yield 100l of mixture, which is
product from each of the 6 PCR reactions and 20g
incubated at 30C for 1 day. Sample solutions from
boiled carrier DNA (Sigma Corporation, St. Louis, MO)
each cell culture were then inspected under the
were mixed with 100l of the prepared yeast cells. The
hemocytometer to determine the number of asci,
DNA-cell mixtures were incubated for 10 minutes at
zygotes and stationary phase cells. Mating efficiency
room
was calculated using the formula
temperature,
after
which
of
260l
of
40%
PEG/LiOAc/TE was added. The mixture was then
2(a + z) + s
2(a + z) + s + p
heat shocked for 5 minutes at 42C. Following

pelleting of cells (centrifugation at 16000 g for 5s),
where a = No. of asci, z = No. of zygotes, s = No. of
removal of supernatant and re-suspension in water,
spores and p = No. of stationary phase cells.
the cell solution was spread onto EMM plates

containing 3% glucose, adenine, histidine and uracil,
2.4
Plasmid rescue and DNA sequencing
but lacking leucine to select for transformed cells.
Plasmid rescue from yeast to E. coli was done using
Plates were incubated at 30C for five to seven days.
the Smash and Grab method [10]. The PDE4B2 alleles

on the plasmids were PCR-amplified as performed for
was
the initial gap-repair transformations using pre-mix
performed on colonies to identify candidates that
buffer G, purified on a Qiagen spin-column to remove
have successfully expressed the human PDE4B gene.
excess PCR primers and sent out to Eurofins MWG
Stained colonies were picked and transferred to a
Operon (Huntsville, Alabama) for DNA sequencing
384-well microtiter dish and incubated at 37C
to
using custom DNA primers Cgs2-PCRmut-5 (5 TCA
enrich for vegetative growth relative to mating and
TAG CAT ACT TCT TCA CCA AGC 3), PDE4B2-505F
meiosis.
(5TTC CTC CAT GAT GCG GTC TGT C 3), and
An
iodine-staining
assay
(see
Appendix)
PDE4B2-1165F (5CAC TGT GCA GAC CTG AGC AAC

Cells were then transferred to 50 l cultures of
3).
EMM-leucine medium in each of 4 plates: 1 control

plate containing 0.5% DMSO solution, the other 3
2.5
Structural Analysis of PDE4B
containing compounds 40 M BC27-5, BC35 and BC58
PDE4B structure (ID: 2QYL) was downloaded from
(see Appendix) dissolved in DMSO, respectively. The
RCSB PDB (http://www.pdb.org/pdb/home/home.do).
cultures from each of the compound-containing
The protein viewing software Chimera from UCSF
dishes were screened for ascus formation in the
(http://www.cgl.ucsf.edu/chimera/) was used to analyse
presence of inhibitor compounds, after which the
the mutant PDE4B enzyme. Residues flanking the
candidates were purified for plasmid rescue.
pocket were labeled, and the location of hydrophobic

and charged residues was determined relative to the
Purified single colonies were then transferred to liquid
pocket to assess its likelihood of being a ligand-binding
YELleu medium. Cell density was estimated using a
domain.
cytometer. Cell cultures were diluted to approximately

the same order of concentration (~ 107cells/ml). 10l of
39
VOYAGER 2014
mating efficiency =
addition of 43l of DMSO solution, the mixture was

incubated for 30-60 minutes at 30C. Following
RESULTS
transformants yielded sparser colonies, allowing

colonies to be picked with greater accuracy.
3.1
Generating PDE4B mutant alleles via PCR
We generated PCR products using 6 different buffers
Frequency of stained colonies in each plate vary
designed to confer different rates and types of
among the different PCR buffers used for generating
mutations.
product
the mutant PDE4B allele. Based on visual inspection,
samples showed that the gene product was 2.1kb in
the percentage of colonies stained in each plate was
size, corresponding to that of PDE4B2. All bands were
estimated. Notwithstanding the limited precision of
distinct, which shows a large amount of product
this type of measurement, it is clear that buffers B and
formed.
E generated a much higher frequency of stained
Gel
electrophoresis
of
PCR
colonies than buffers K and L.
Figure 2: Gel Electrophoresis Image of PCR Products

a. PCR products generated using 6 different buffers were all 2.1kb in size,
corresponding to that of PDE4B. b. The plasmid cut with StuI is 21kb in
size, and smaller than the uncut circular plasmid.
The band corresponding to the cut plasmid travelled a
PCR buffer
A
B
E
F
K
L
Percentage of colonies stained

40%
60%
60%
20%
5%
10%
Table 1 : Frequency of stained colonies for different PCR buffers used
smaller distance than that of the uncut plasmid,

showing successful linearization by StuI.

VOYAGER 2014
40
3.2
Transformation of S. pombe
Transformation of the first batch of S. pombe using

200ng of plasmid vector yielded a lawn of colonies
after 48 hours, making the process of picking
individual colonies difficult. To decrease colony
density, the second batch of cells were transformed
using only 50ng of plasmid vector. Number of
colonies was reduced 10-fold, resulting in increased
Figure 4 : Different frequency of stained colonies for different PCR

buffers
a. Left plate showed colonies expressing PCR product from buffer E, where
more than 60% of colonies were stained. b. Right plate showed PCR
products from buffer K, where less than 5% of colonies were stained.
colony separation.
3.3.2 Selecting candidates resistant to inhibitor
Mutants of interest have PDEs that function in the
presence of inhibitors and can regulate the glucose
sensing pathway. Such cells enter into a quiescent
state readily in glucose-deficient medium, presenting
with a short, shiny morphology, unlike cells that lack
PDE activity and fail to enter stationary phase [7].
Figure 3 : Comparison of colony density of Batch 1 and Batch 2
There should also be increased mating as reflected by
transformants
an abundance of zygotes, asci and spores, as cells
a. Left plate was transformed using 200ng of plasmid vector, and yielded
a dense mesh of small colonies which impeded later efforts to pick
lacking PDE activity display a severe mating defect
individual stained colonies. b. Right plate was transformed using 50ng of
[7].
plasmid vector, and yielded larger colonies with distinct separation.
3.3
3.3.1
Preliminary screening eliminated colonies showing
Screening for candidate mutants
little mating in the control plate. The remaining
Iodine Staining
The iodine staining assay identified 318 colonies from
candidates were screened for mating or quiescent
the first batch and 257 colonies from the second
cells in the inhibitor dishes. Out of 257 preliminary
batch expressing functional (though not necessarily
candidates, colonies we named A5, A6, A13, A17, A18,
wild-type) PDE genes. However, the first batch
A23, B11, B21, B29, D11, D19, D21, G4, G10, G13, G14, G17,
yielded
G18 were selected after the second screening.
dense
colonies
with
poor
separation,
compromising the accuracy with which stained

colonies
were
picked.
The
second
batch
of
Following
single-cell
purification
to
eliminate
contamination of strains, these 18 colonies underwent

iodine staining, which identified colonies A18, A23,
B21, D19, D21 as clearly inhibitor-resistant.
3.5 DNA Sequencing

To investigate the underlying molecular mechanism
for inhibition, sequencing was performed on D19.
Similar analyses are being performed for the
remaining colonies.
Sequencing analysis showed that the mutant PDE4B
recovered from colony D19 had an A to G transition
mutation at base pair 1403 of the open reading frame,
resulting in an aspartic acid to glycine substitution at
the position 468 in the primary sequence (NCBI
Reference Sequence: NM-001037339.1).
Figure 6
shows the location of the amino acid substitution in
the 3D conformation of PDE4B, obtained via
comparison of the primary sequence with the known
crystal structure of PDE4B.
Figure 5 : Result of iodine staining of 18 colonies selected after second

screening
DMSO plate generally showed dark staining. In the compound plates,
DISCUSSION
colonies A18, A23, B21, D19, D21 also showed significant staining,
compound plates.
However, D19 showed darker
staining in the BC35 plate than in the DMSO plate.

BC58 appears to be the most potent inhibitor in this
assay since, the staining was appreciably lighter for
most colonies in the BC58 plate as compared to the
DMSO plate. Inspection under the microscope also
showed that the dish containing BC58 contained the
fewest number of asci after an incubation period of
24h.
3.4
Phenotypic characterisation: quantitative
mating assay
Results of the quantitative mating assay performed on
colonies A18, A23, B21, D19, D21 is shown in Figure 6.
4.2 Mating assay

The results of the mating assay differed significantly
from those obtained via the iodine staining assay.
Random error may be a factor compromising both
assays, but each approach has its advantages and
drawbacks.
The mating assay here is done under more controlled
conditions with the yeast cell concentration fixed
across all colonies, as opposed to the solid medium
iodine staining assay, which concentrations of yeast
cells may vary 10-fold. However, the lack of distinct
morpho-logical difference between a spore and a
stationary phase cell means that counting of cells is
liable to human error.
Figure 6 : Results of mating assay

Colonies in DMSO plates generally showed the highest mating efficiency,
consistent with our prediction. A18 was an exception, as it should higher
mating efficiency in the BC35 plate than in the DMSO plate.
The results obtained from the mating assay differed

from those of the iodine staining assay. Colonies
generally showed highest mating in the DMSO plate,
with the exception of A18, which showed higher
mating in the BC35 plate. BC58 showed most potent
inhibition only for 2 of the 5 plates, while BC35 did not
show potent inhibition for most plates.
41
VOYAGER 2014
DMSO plates generally showed darker staining than
4.1 Generation of PDE4B mutants and

transformation
The different frequency of stained colonies for
different buffers may be correlated to the rate and
type of mutagenesis that the 6 buffers confer. High
rates of mutagenesis may lead to changes in the
essential amino acids of the catalytic domain, thus
rendering the PDE product non-functional. Future
research may be done to confirm whether this result is
reproducible to ascertain if the buffer delivers
consistent rates of mutation.

suggesting that they express inhibitor-resistant mutant PDE4B alleles.
to interesting possibilities. Firstly, this D468G

mutation removes negative charge from the region,
altering the electrostatic interactions of that region
and possibly affecting binding affinities for charged
ligands. This may have caused BC35 to bind in a
different orientation, such that it becomes an
activator rather than an inhibitor of PDE4B.
Furthermore, glycine, by virtue of its small size, breaks
the local secondary structure, which may cause
drastic conformational changes in the entire pocket.
Much of the uncertainty regarding the precise effect
of this D468G mutation arises from our interpretation
of the PDE4B protein crystal structure. protein crystal
structures are inherently static, however, and cannot
Figure 7 : Model of PDE4B enzymatic structure
(Pink: Amino acid residues flanking the pocket. Orange: substituted
Gly-468. Yellow: hydrophobic residues.) a. Pocket is flanked by 3 -helices
ological conditions. Nevertheless, all the evidence
and lined with hydrophobic residues, which provides a hydrophobic
discussed above suggest strongly that we have
environment for bound ligands. b. A close-up view of the pocket. A

disordered loop shields the entrance to the pocket, and may function as a
VOYAGER 2014
identified a ligand binding pocket in PDE4B that
gate. The two fused rings of tryptophan protrudes and blocks entry to the
functions as an allosteric regulatory site, and is
pocket. c. Top view of the pocket. Tryptophan is located right in the center,
therefore a possible target for PDE4B inhibitor drugs.
and its bulkiness prevents access by binding ligands.
42
accurately depict enzyme interactions under physi-
The iodine staining assay is a more robust screening

test as high levels of mating must be present in a
colony for it to be stained. Results are representative
of the entire colony, unlike the mating assay which is
limited by the field of vision of the microscope.
Nevertheless, BC58 appears to be a potent inhibitor in

both the mating assay and iodine staining test, having
equal or sometimes greater effect than either BC27-5
or BC35. This contrasts with the results of in vitro
assays [6] which showed that BC58 is 10-fold less
potent than BC27-5 and BC35. It is possible that BC58
is more readily uptaken by the cells and thus show
greater effect in vivo.
transformed PDE- deficient S. pombe hosts with
4.3 Structural Analysis of PDE4B D468G Mutation

Analysis of PDE4B enzymatic structure reveals that
the substituted glycine lies at the periphery of a
pocket flanked by 3 - helices and partially covered by
a disordered loop. The presence of the disordered
loop in between highly ordered -helices meets the
requirements for a gated binding site, separate from
the substrate binding/catalytic site. This notion is
further supported by the presence of a large
tryptophan residue in the center of the pocket, which
likely regulates access to the putative allosteric
binding site by ligands. The core of the pocket is lined
with hydrophobic residues, providing a hydrophobic
environment for binding ligands. The periphery of the
pocket, however, contains several charged residues
that can form electrostatic interactions with
charged/polar groups of binding ligands.
The observation that the mutated PDE4B appears to
be activated rather than inhibited by BC35 gives rise
CONCLUSION
This study used a classic chemical genetics approach to

determine the amino acids involved in PDE4B inhibition.
We generated random mutant alleles of PDE4B,
mutated alleles and used the iodine staining assay to
screen
for
inhibitor-resistant
candidates.
DNA
sequencing of PDE4B2 mutant alleles recovered from

candidates
of
interest
revealed
an
amino
acid
substitution from aspartic acid to glycine near a pocket

directly opposite to the active site. Analysis of the
mutant PDE4B enzyme revealed strong evidence that
the pocket is a ligand-binding domain and functions as
an allosteric regulatory site. This information may be
useful in rational drug design when creating a PDE4B
specific inhibitor.
ACKNOWLEDGMENTS
I would like to express my profound gratitude to my

mentor, Professor Charles S. Hoffman of Boston College
for
his
invaluable
guidance
and
encouragement
throughout the course of this research project. In

addition, I would also like to thank Mr. Vinay Tripuraneni
for his insightful comments and suggestions for
improvement. Last but not least, I would like to thank
the Center for Excellence in Education for offering me
this opportunity, MIT for hosting this program, and the
Ministry of Education, Singapore for its generous
funding.
REFERENCES
[12] S.L. Jin & M. Conti. (2002). Induction of the cyclic

nucleotide phosphodiesterase PDE4B is essential for
[1] J. Atienza & J. Colicelli. (1998). Yeast model system
LPS-activated TNF- responses. Proc Natl Acad Sci
for study of mammalian phosphodiesterases. Methods:
USA. 99: 7628-7633.
A Companion to Methods in Enzymology. 14:35-42.

[13] S.L. Jin, L. Lan, M. Zoudilova & M. Conti. (2005a).
[2] J. Bahler, J.Q. Wu, M.S. Longtine, N.G. Shah, A.
Specific
McKenzie 3rd, A.B. Steever, A. Wach, P. Philippsen, J.R.
lipopolysaccharide-induced
Pringle. (1998). Heterologous modules for efficient and
macrophages. J Immunol. 175: 1523-1531.
versatile
PCR-based
gene
targeting
role
of
phosphodiesterase
signaling
4B
in
in
mouse
in
[14] S.E. Lehnart, X.H. Wehrens, S. Reiken, S. Warrier,
Schizosaccharomyces pombe. Yeast. 14(10):943-51.
A.E. Belevych, R.D. Harvey, W. Richter, S.L. Jin, M. Conti,

[3] J.A. Beavo, R.S. Hansen, S.A. Harrison, R.L. Hurwitz, T.J.
& A.R. Marks. (2005). Phosphodiesterase 4D deficiency
Martins, M.C. Mumby.(1982). Identification and properties
in the ryanodine-receptor complex promotes heart
of cyclic nucleotide phosphodiesterases. Mol Cell
failure and arrhythmias Cell. 123:25-35
Endocrinol. 46:399-405
[15]
B.J.
Lipworth.
for
(2005).
asthma
and
Phosphodiesterase-4
[4] A.T. Bender, J.A. Beavo. (2006). Cyclic nucleotide
inhibitors
chronic
phosphodiesterases: molecular regulation to clinical
pulmonary disease.Lancet. 365: 167-175.
obstructive
use. Pharmacological Reviews 58:488-520.

[16] Pfizer, Inc. (2005). FDA Approves Pfizers Revatio
2005 News Releases. Pfizer. Retrieved December 27,
2005.
[6] D. Demirbas, O. Ceyhan, A.R. Wyman, C.S. Hoffman.
for
[17] R. Pillai, K. Kytle, A. Reyes, & J. Colicelli.(1993). Use
Phosphodiesterase Inhibitor HTSs and Analyses of
of a yeast expression system for the isolation and
Phosphodiesterase Activity. Handbook of experimental
analysis of drug-resistant mutants of a mammalian
pharmocology. 204:135-49
phosphodiesterase. Biochemistry. 90:11970-11974.
[7] J. DeVoti, G. Seydoux, D. Beach, M. McLeod. (1991).
[18]
Interaction between ran1+ protein kinase and cAMP
Phototransduction in vertebrate rods and cones:
dependent protein kinase as negative regulators of
molecular mechanism of amplification, recovery and
fission yeast meiosis.EMBO J. 10(12):3759-68.
light adaptation. Molecular Mechanisms in Visual
(2011).
Fission
Yeast-Based
Platform
E.N.
Pugh
Jr.
&
T.D.
Lamb
(2000).
Transduction. 18:32-55
[8] S.L. Forsburg. (2001). The art and design of genetic
[19] J.P. Richalet, P. Gratadour, P. Robach, et al. (2005).
screens: yeast. Nature Reviews: Genetics. 2:659-668.
Sildenafil inhibits altitude-induced hypoxemia and

[9] H. Gutz, H. Heslot, U. Leupold and N. Loprieno.
pulmonary hypertension. Am. J. Respir. Crit. Care Med.
(1974). Schizosaccharomyces pombe. pp399-446 in
171 (3): 275-281.
Handbook of Genetics. 395-446. Edited by R. C. King.

[20] W. Richter, S.L. Jin & M. Conti. (2005). Splice
Pienum Press, New York.
variants of the cyclic nucleotide phosphodiesterase

[10] C.S. Hoffman & F. Winston. (1987). A ten-minute
PDE4D are differentially expressed and regulated in rat
DNA
tissue. Biochem J 388. (Pt 3): 803-811.
preparation
autonomous
from
yeast
plasmids
for
efficiently
releases
transformation
of
[21] D. Saleheen, S. Bukhari, S.R. Haider, A. Nazir, S.
Escherichia coli. Gene. 57:267-272
Khanum, S. Shafqat, M.K. Anis, and P. Frossard.(2005).

[11] F.D. Ivey, L. Wang, D. Demirbas, C. Allain, & C.S.
Association of phosphodiesterase 4D gene with
Hoffman. (2008). Development of a fission yeast-based
ischemic stroke in a Pakistani population. Stroke.
high-thoroughput
36:2275-2277
screen
to
identify
chemical
regulators of cAMP phosphodiesterases. Journal of

Biomedical Screening. 13:62-71
43
VOYAGER 2014
as Treatment for Pulmonary Arterial Hypertension.
edition. Redwood City, Calif.: Benjamin Cummings.

[5] N.A. Campbell, &J.B. Reece. (2008). Biology 8th
[22] W.J. Thompson, W.L. Terasaki, P.M. Epstein, and

S.G.
Strada.
(1979).
Assay
of
cyclic
A.3 Results of mating assay
nucleotide
phosphodiesterase adn resolution of multiple molecular

forms of the enzyme. Adv Cyclic Nucleotide
Res.
10:69-92
[23] R.X. Xu, W.J. Rocque, M.H. Lambert, W.D. Holmes,
M.A. Luther, W.J. Rocque, M.V. Milburn, Y. Zhao, H. Ke, et
al. (2000). Atomic structure of PDE4: insights into
phosphodiesterase mechanism and specificity. Science
(Wash DC). 288:1822-1825
[24] D.J. Webb, S. Freestone, M.J. Allen, G.J. Muirhead.
(1999). Sildenafil citrate and bloodpressure-lowering
Table 2: Mating efficiencies of colonies in different compound plates
drugs: results of drug interaction studies with an
A.4
PDE4B enzymatic structure
organic nitrate and a calcium antagonist. Am. J. Cardiol.

83 (5A): 21C-28C
A APPENDIX
A.1 Inhibitor compounds

VOYAGER 2014
44
Figure 8 : Known Inhibitors of Rolipram

Rolipram is the archetypal PDE4 inhibitor, for which the family was initially
named. BC27-5, BC35 and BC58 were previously identified by the
Hoffman lab in an in vitro assay as potent PDE4 inhibitors.
A.2
Iodine staining assay
This assay is used to identify colonies expressing a

functional PDE. Small iodine crystals are spread on a
plate. Each colony plate is inverted and placed on top of
the iodine plate, covering the latter. Following 2 minutes
of iodine vapor staining, the colony plate is removed.
Colonies with high rates of mating are stained.
The basis for this assay lies in a cAMP-mediated
glucose sensing pathway that controls mating. In a
glucose-deficient
environment,
no
new
cAMP
is
Figure 9: Additional PDE4B enzymatic structures

Different views of the PDE4B enzyme. Pink: Residues flanking the pocket
are colored pink. Orange: Substituted Gly-468. Different panels show the
ribbon structure (left), ribbon structure (right).
synthesized, so cells with functional PDE will have low

cAMP levels, which induces mating. Cells undergoing
mating have high levels of glycogen, which stains with
iodine. In contrast, dysfunctional PDE cannot degrade
cAMP, and cellular cAMP levels is persistently high in
the absence of glucose, so no mating occurs.
Figure 10: Additional PDE4B enzymatic structures

Yellow: Hydrophobic residues Different panels show the ribbon structure
(left), ribbon structure and stick structure (center) and stick structure
only (right).
Fall Detection System based on

Kinect Sensor using Novel Detection
and Posture Recognition Algorithm
1 INTRODUCTION
Lee Choon Kiat 12S68
The progressive aging of population has become a

major social challenge for countries around the world.
As more elderly begin living with health problems and

Lee Vwen Yen
Institute for Infocomm Research, Agency
for Science, Technology and Research
are home-alone, they require increasing assistive

support in daily activities. For the elderly, involuntary
falls are frequent. A visit to Lee Ah Mooi Old Folks
Home showed that among the 100 elderly residing in
the home, about 3 fall cases occur in every quarter of
the year, while annual statistics show that one in every
three adults age 65 and older in the USA have recently
suffered a fall [1]. Falls cause a loss in quality of life for
the fallen elderly and can be more dangerous due to
the fact that the victim can easily lose consciousness
and thus become unable to seek help if they are home
alone, which is detrimental to their long-term health if
order to avoid this scenario, fall detection systems
that
are
capable
of
identifying
and
notifying
caregivers when the elderly fall are very much

essential in the bid to provide assistive services to the
elderly.
Current fall detection systems have fall detection rates
of 70% to 80% [3], which might be unconvincing to
some
consumers
when
making
decisions
on
purchasing such systems. There are privacy concerns

when vision-based fall detection systems are used,
although there are situations where it is acceptable
for visual sensors to be deployed, where the risk of
falls being undetected heavily outweighs the loss of
privacy.
Furthermore,
detection
systems
current
with
vision-based
heavy
dependence
fall
on
complex video processing also limit the systems

effectiveness when deployed in real time [3].
We aim to develop and test a fall detection system
that utilizes the Microsoft Kinect sensor [4] and our
novel
fall
detection
algorithm
to
determine
automatically if a fall has occurred. The Kinect sensor

has an RGB camera and depth sensor which provides
full-body 3D motion capture and facial recognition
[5]. When compared to other commercially available
depth sensors, Kinects low cost makes it a good
choice for developing inexpensive, vision-based fall
detection systems that appeals to the consumer
market and industry. Relative lack of research into
45
VOYAGER 2014
the accident is serious and undetected [2]. Thus, in
Fall Detection System based on Kinect Sensor using Novel

Detection and Posture Recognition Algorithm
This research was presented at the 2013

International Conference On Smart homes
and health Telematics (ICOST)
Kinect-based fall detection systems also provides us

with
much
room
in
conducting
research
and
development within this field.

We propose our fall detection system which is
optimized using current preliminary datasets and
when used in conjunction with our novel posture
recognition
algorithm,
help
us
to
achieve
significantly higher specificity rate of fall detection, up

to 90% accuracy rate in an actual test with a real
human subject.
2 FALL DETECTION SYSTEM

In this project, we aim to create a fall detection system
Fig. 2: Block diagram of our fall detection system
(Fig. 1 & 2) for use in confined areas like the bedrooms

or washrooms in single room apartments. This
3 FALL DETECTION ALGORITHM

3.1 Control Algorithm
who normally live in such apartments. In order to
Many other current fall detection algorithms are
avoid privacy concerns over the use of our system in
based on the concept that during a fall, the person will
these settings [6], the fall detection system only
experience a large initial downward velocity, ending
46
utilises the Kinects depth camera and displays only a
with the persons centre of mass on or near the floor
stickman model of the user, and eliminates the usage
[8]. Though it has been successfully used by other fall
of any actual footage, thus making it suitable to be
detection systems, this algorithm has a few flaws,
used in such regions. In addition, our system is also
chiefly among which is its sub-optimal specificity and
able to operate in situations with little or no light [7],
sensitivity, which still have not been addressed by
therefore making it possible for the Kinect to track
current research. We adopted this algorithm as a
human activity both in the day and night, something
starting point for our own fall detection algorithm
that conventional stereo video camera systems are
with modifications to address the flaws of this main
unable to do. This makes it especially useful as most
algorithm. We then implemented this fall detection
falls by the elderly happen at night when visibility is
algorithm
poor and this also improves the effectiveness of our
effectiveness of our own novel algorithm

towards the detection of falls for home-alone elderly
VOYAGER 2014
constraint is in place as the project is targeted
as
control
so
as
to
assess
the
fall detection system.

3.2 Our Novel Fall Detection Algorithm
The Kinect depth camera captures a depth image of
The control fall detection algorithm described earlier
the surroundings. The raw data streams are then
was then applied to a preliminary dataset of 10,479
processed by the Microsoft Kinect SDK to return a
frames of skeletal data from the Kinect comprising 34
pipeline of information that provides our fall detection
fall and non-fall events, with the results used to
system with skeletal data of the user. The skeletal data
optimise our enhanced fall detection algorithm. The
of the user is then transmitted to our fall detection
results of this experiment are described in greater
software and subsequently passed to our algorithm as
detail in the Results section (section 4) of this paper.
described in section 3 for further processing. If a fall is
Our enhanced fall detection algorithm is based on a
detected, we would relay a signal to an alarm system
modular system with skeletal data received from the
to sound an alert.
Kinect sensor and processed by two functions
Fig. 1: Setup of our fall detection

system
(function 1 and 2). If both functions return a positive

result, a fall is tentatively indicated. After that, our
novel postural recognition algorithm is then applied to
reduce the amount of false positives returned by our
fall detection algorithm, resulting in a fall detection
algorithm that manages to achieve relatively high
sensitivity and specificity.
3.2.1 Function 1 (Checking position of users centre

of mass)
The real world coordinates of the persons hip centre
ds y (t )
dt
(roughly representative of the persons centre of
v(t )
(1)
sh (t )
sx (t ) 2 sz (t ) 2
dsh (t )
dt
vh (t )
(2)
mass), are obtained by the fall detection algorithm

after processing of the raw data from the Kinect by
our fall detection system. Our algorithm checks if the
users hip centre is within a certain threshold distance
from the floor returns a positive result if found to be
true.
4.2.2 Function 2 (Checking velocity of users centre
of mass)
Many current algorithms that make use of the centre
of mass are unable to accurately detect slow falls.
This is because the measured vertical velocity in slow
falls tends to be relatively lower than that measured
into its horizontal and vertical components
not detected. Figure 3 shows the different velocities
The different velocities of the users hip centre are
of the users hip centre joint where the vertical
given different scores for the vertical and horizontal
velocity of the slow fall did not exceed the threshold,
velocities as shown below in Table 1. Our fall
resulting in no falls being detected.
detection algorithm checks if the combined scores

for both the vertical and horizontal component
exceed our pre-set overall threshold score. As the
vertical velocity of the users hip centre was deemed
to be an important factor in determining a fall, we
weighted the algorithm accordingly. The overall
threshold score was then optimized such that a large
vertical velocity typically indicative of a fall would be
able to trigger an alert, but a large horizontal velocity
which could signify a subject moving at fast speeds
would not trigger a fall alert, thus enhancing the
specificity of our fall detection algorithm.
The table of scores shown in Table 1 was optimized
manually by studying the preliminary dataset of falls
and tweaking the parameters until a maximum fall
Fig. 3: Graph showing different velocities of the users hip centre joint for
detection rate was obtained.
both the slow fall (solid lines) and the vertical fall (dotted line).
Table 1 Table showing how the scoring system was applied for vertical
Our algorithm separates the velocity of the users hip

centre into two components. The first component is
the vertical velocity of the hip centre (Equation 1),
while the second component is the velocity of the hip
velocities
Vertical velocity
Score of users hip centre, Remarks
VV / m s-1
VV > -0.9
-0.9> VV > -1.4
Representative of a small vertical velocity that

is typical of a slow horizontal fall, but not low
enough to be triggered by everyday activities
-1.4> VV > -1.6
Representative of a moderate vertical velocity

typical of a fast horizontal fall
VV < -1.6
centre with respect to the vector sum of the

displacement of the hip centre in both the x and z
directions, thus giving us the horizontal component
of the hip centres velocity, as illustrated in Fig. 4 and
(Equation 2).
Representative of negligible vertical velocity

typical of everyday activities
Representative of a large vertical velocity

typical of a vertical fall
47
VOYAGER 2014
values are normally not exceeded and the slow fall is
Fig. 4: Diagram showing how the actual overall velocity of a joint is split

during a normal fall. Therefore pre-set threshold
This new method of fall detection provides two main
In order for our postural recognition system to
benefits:
1. It is more sensitive to falls in any direction than
correctly identify these postures, two main defining
conventional fall detection systems as both the
features were identified in order to separate fallen

postures from other possible postures.
horizontal and vertical components of velocity of

the users hip centre are taken into account,
1. Feature 1: Users ankles have to be below the users
reducing the impact of the reduced vertical
hip centre.
velocity of the persons hip centre during a
!$!')!/1.! ,+/01.!/#%*/0,+/01.!/
horizontal fall.
and 3 listed in Table 2 as we observed from skeletal

data that all three postures exhibit this feature.
2. It is less prone to false positives generated by large

horizontal
movements
by
the
user
than
2. Feature 2: One of the users legs is either folded
conventional fall detection systems that determine
below his body or one knee being significantly higher
falls based on the total velocity of the users
than the other.
centroid.
!$!')!/1.! ,+/01.!/#%*/0,+/01.!%*
Table 2 for users that bend down to perform actions
such as wearing of shoes or tying of shoelaces.
4.2.3 Postural Recognition Algorithm

We observed that the starting adopted control

VOYAGER 2014
48
algorithm has a high rate of false positives. Due to the
These two features were refined and checked against
multiple similarities between falls that are classified as
previously obtained skeletal data of postures to
false positive and actual real falls, most current fall
ensure their specificity.
detection
systems
between
these
have
two
difficulty
differentiating
classifications
[9].
Table 2: List of false positive postures considered
We
demonstrate this similarity with results in Figure 5

using our own data, where the monitored subjects
Posture
Classified
Fall /
Non-Fall using rule no.
Non-fall
1
Sitting on the floor

both legs folded behind
Kneeling on the floor
Non-fall
the false positives from actual real falls by checking
Squatting
Non-fall
the users posture to determine the likelihood that the
Non-fall
4 Bending down
(to wear shoes or tie shoelaces)
velocity is similar for an actual fall and an action of just

bending down. To resolve this problem, we developed
a novel postural recognition algorithm that separates
user has been involved in a fall when previous

functions 1 and 2 return positive results.
4 RESULTS
In order to test the actual effectiveness of our system,
we conducted a trial experiment that was simulated
as closely to the actual conditions where our fall
detection system would be deployed. We want to test
the robustness of our fall detection system by
conducting tests within a setting that is previously
unknown to the system. A nursing ward was recreated
within our laboratory to provide a realistic setting that
is similar to wards found in the previously mentioned
Ah Mooi Old Folks Home. A hospital bed was placed
in the corner of our ward, with PVC pipes representing
the walls of the ward and the Kinect sensor was
deployed at the top corner of our ward.
Fig. 5: Graph showing different velocities of the users hip centre joint
The nurses and caregivers at Ah Mooi Old Folks Home
for bending down (solid lines) and the an actual fall (dotted line).
have provided us with domain knowledge regarding

elderly falls and the common locations of such falls.
There are mainly three kinds of falls that frequently
occur within the Home, mainly falling after getting out
of the bed, falling after getting out of the wheelchair,
Our fall detection system is capable of processing
and a normal fall in any direction in open space. These
incoming sensor information and displaying of results
different kinds of falls were then simulated by our
concurrently without a loss in processing speed or
volunteers to replicate the kind of conditions that our
performance degradation. By connecting an SMS
fall detection system will face when deployed at the
gateway or alert module to the system, we can detect
Home. Our test volunteer was given the freedom and
falls within half a second of the fall and subsequently
not restricted in the way that he could fall. A video
alert the caregivers. The system automatically starts
camera was placed to capture his movements and
when someone enters the field of vision of the Kinect
also to provide ground truth which we could then
sensor. By producing a stickman display (Fig. 6.2) for
compare against our logged results. Fig. 6.1 shows our
display purposes which users can choose to hide, we
experimental setup, while Fig. 6.2 shows a screenshot
also managed to preserve the users privacy.
of our fall detection system user interface during the

Initial results show that most falls that include falling
experiment.
from the bed or in open spaces were accurately

identified by our fall detection system. Multiple other
kinds of non-fall events were also accurately detected
by
our
fall
detection
algorithm
and
correctly
classified, mainly due to the assistance from our novel

posture
recognition
algorithm
that
points
out
abnormalities in the data obtained through the

sensors. From our results, this recognition algorithm is
able to point out 62.5% of all non-fall events and helps
of our system and help in preventing more false

positives from being classified, thus demonstrating
the usefulness of our posture recognition algorithm in
recognizing and differentiating falls. Our system is
able to achieve an overall specificity rate of up to 90%
and our algorithms helped improve the fall detection
rate such that we could detect all falls (100%) in
Fig. 6.1 Picture showing experimental setup
certain situations, where conditions are optimal. This

includes situations where more sensor information
allows us to perform inference in order to provide a
more accurate assessment.
However, further analysis also showed that there were
occasions where the system was not able to classify
actual falls. For example, a user might fall off the chair
and the fall is undetected, due to the fall taking place
in a low position, and reduced time required by the
system to measure a significant increase in users
velocity while he is falling, hence resulting in the
system not being able to correctly detect the fall. We
have detailed data and information regarding this kind
of misclassification and also have a solution for this
problem and are currently working on correcting this
issue so as to ensure that it does not occur again in
subsequent modifications.
Fig. 6.2 Screenshot of fall detection system user interface running on

laptop
49
VOYAGER 2014
other non-fall events are then detected by other parts

us in classification of the majority of actual falls. The
5 CONCLUSIONS
Manuscript submitted for publication
Our fall detection system is able to detect and identify
[9] Gadre, K. R. (2012). Fall Detection System Using
falls using the Kinect sensor within confined spaces at

a relatively high specificity rate when compared to
usage of control algorithms. The system also uses our
novel posture recognition algorithm to enhance our
detection
rate
deployment.
and
ensures
Overall,
with
robustness
during
sufficient
sensor
information while maintaining users privacy, our fall

detection system is able to automatically recognise
falls and notify healthcare services to provide timely
assistance to elderly who have fallen.
REFERENCES
[1] George, F. F. (2000). Falls in the elderly. Am Fam
Physician, 61(7), (pp. 2159-2168.)
[2] Wild, D., Nayak, U. S., & Isaacs, B. (1981). How
dangerous are falls in old people at home?. British
medical journal (Clinical research ed.), 282(6260), 266

VOYAGER 2014
50
[3] Perry, J. T., Kellog, S., Vaidya, S. M., Youn, J. H., Ali,
H., & Sharif, H. (2009, December). Survey and
evaluation of real-time fall detection approaches. In
High-Capacity
Technologies
Optical
Networks
(HONET),
2009
and
6th
Enabling
International
Symposium on (pp. 158-164). IEEE.

[4] C. Rougier, J. Meunier, A. St-Arnaud and J.
Rousseau, (2007). Fall Detection from Human Shape
and Motion History using Video Surveillance, 21st IEEE
International Conference on Advanced Information
Networking
and
Applications
Workshops
(AINAW'07),875-880.
[5]
Totilo,
Stephen
(January
7,
2010).
"Natal
Recognizes 31 Body Parts, Uses Tenth of Xbox 360

"Computing Resources"". Kotaku, Gawker Media.
Retrieved November 25, 2010.
[6] Yongli, G., Yin, O. S., & Han, P. Y. State of the Art: A
Study on Fall Detection.
[7] Stone, E. E., & Skubic, M. (2011, May). Evaluation of
an inexpensive depth camera for passive in-home fall
risk assessment. In Pervasive Computing Technologies
for
Healthcare
(Pervasive
Health),
2011
5th
International Conference on (pp. 71-77). IEEE.

[8] Kawatsul, C., Lil, J., Chung CJ. (2012) Development
of a Fall Detection System with Microsoft Kinect,
Low
Cost
Computing
University of Missouri).
(Doctoral
dissertation,
INVESTIGATION INTO THE RELATIONSHIP

BETWEEN VIOLIN STRING TIMBRE AND
ITS HARMONIC STRUCTURE
INTRODUCTION AND HYPOTHESIS

Gold Award
Hypothesis and Assumption

We hypothesize that sound waves produced by violin
open E strings with different timbres can be matched
to different, distinctive patterns of harmonic structure.
Assumptions in this study include: sound samples
played by professional players are stable period
waves; bow stokes applied for sound samples are the
same throughout the recording process; strings in
each timbre group are most representative of that
timbre.
BACKGROUND THEORIES
Violin and Timbre
The violin is a bowed string instrument. Drawing a
bow across the string correctly causes the violin body
to resonate due to a complex system of different
couplings. (Crosmer, 2011) Its timbre or tone color can
be affected by factors including the string
composition, the instrument used, vibrations from
other strings, bow speed, bow pressure and sounding
point where the bow intersects the string. (Charles,
2010) Physically, change in technical factors will
affect the amplitude of individual component
frequencies in a complex tone, resulting in a distinct
shaped frequency spectrum that characterizes a
specific timbre.(Crosmer, 2011) As sound waves
entering human ears are interpreted by the brain,
people usually use words like rich nasal or
brilliant to describe their feeling. Different English
51
VOYAGER 2014

Professor Chan Aik Hui, Phil
Mr Tan Peng Kian
National University of Singapore
Introduction
Music is part of all cultures and traditions. Amidst the
evolution from early church hymns to modern
electronic music, people have worked towards a
deeper
understanding
of
musical
sound
characteristics so as to reproduce pleasant music.
With todays advanced signal processing technology,
much work has been done on the physical aspects
that distinguish different musical instruments.
However, the complete timbre space of a single string
instrument with distinctive rich sound the violin - is
not as well understood. Violin timbre depends on
many factors including the wood material of the violin,
bow strokes, etc. This research focuses on the
variance of violin timbre due to different violin strings
and investigates the relationship between violin
timbre descriptors and the harmonic content of
various open E string samples.
Investigation Into The Relationship Between Violin String Timbre And

Its Harmonic Structure
Yang Liuyi 12S7D

Wang Jia 12S7F
descriptors for violin are mapped systematically by

the following coordinate constructed by Acoustical
Society of America (Friz, et al., 2011) (see figure 1). The
area under the dotted line represents descriptions for
pleasant violin sound, which can be further split into
3 regions in the order of harshness: rich/warm,
bright/open and penetrating/projecting. This way of
classifying string timbre will be used for later
discussion of experiment results.
At a point of discontinuity, the Fourier series

converges to the average of the two function values at
either side of the discontinuity.
In the experiment, data was Fourier analyzed by
oscilloscope software. Nonetheless, understanding
the mathematical foundation enabled us to use the
software with greater confidence.
HARMONICS
In the periodic waves produced by musical
instruments, the periodic frequencies of all
component waves are called harmonics. The first
harmonic is also called the fundamental (f0), while the
frequencies of higher harmonics (overtones fi) are
multiples of that of fundamental. (Oldham,et al.,2011)
In the trigonometric series of equations [1],
fundamental while
is
the
function
of
is
the first overtone and so on.
SPECTRAL PLOT

VOYAGER 2014
52
Figure 1: Acoustical Society of Americas A-MDS map of timbre descriptors

for overall violin sound quality
Fourier Analysis
Joseph Fourier showed that any complex wave can be
described as the sum of a series of simple sinusoidal
waves called partials (Campbell, 1987). (See figure 2)
When a wave is Fourier analyzed, the results can be

shown in a spectral plot. The wave spectrum is a
2-dimensional
representation
manifesting
the
amplitudes of sinusoidal waves of different frequencies
that comprise the wave. Different spikes of energy in the
spectral plot are partials. (See figure 3)
Fourier Analysis
Figure 2: Fourier analysis can break a complex wave which is the

ummation of two sine waves of different amplitude, frequencies and
phases into their components
If f(t) is a periodic function with period 2L and

fundamental angular frequency
, the
Fourier-series representation of f(t) is given by

n
[1]
The coefficients (called the Fourier coefficients of f(t)

a0, an and bn are to be evaluated and given by the
expressions
;
an
1
L
f (t ) cos n tdt
for n=1,2,;
for n=1,2,;
Figure 3: Spectral plot of the sound wave of Pirast ro Olive Gold E
NOISE CONTROL AND MINIMIZATION

Due to the high sensitivity of the microphone, it is
assumed that all sound waves are recorded. Hence, it is
pertinent to discuss sources of noise that cause errors in
recording before proceeding into data analysis. Below
are three main sources of noise involved and respective
ways to minimize their influence:
a) Initial noise is caused by the condition of recording
room, including the noise of air conditioner, human
breathing and noise outside the room. It is minimized by
using a music recording room with air conditioner off
when outside the room the noise is minimal. (See figure 5)
b) Cable noise is due to the radio waves picked up by
the conducting wire. We shortened the length of the
cable by winding up the wire.
c) Machine noise is due to the running of laptop hard
drive and oscilloscope, as well as possible radio waves
picked up by the hardware. A silent audio was played to
record machine noise A0 /dB, and amplitude of samples
without machine noise Ai/dB is calculated by the
following equation:
Ai '
Figure 4: Material used for recording of E string sound samples
Recording
The violin and microphone were placed 50 cm apart
and fixed at the same position in the room. Each E string
was tuned to 663.0 Hz and then bowed by a team
member who is an experienced violinist for recording.
Each sample includes 3 consecutive legato bows of 2
seconds as 3 trials. The bow is controlled at 2 cm away
from the bridge and maintained at a relatively constant
bow angle and speed so as to prevent variance in
timbre caused by bow strokes. (Chen, 2007) While
playing, the other 3 violin strings A, D, G were muted to
1
lg 10 Ai 10 A0
10
Figure 5: The negligible initial noise in recording
53
VOYAGER 2014
Materials
To investigate the sound quality of violin strings, we
used ten violin E strings with different composition and
the identical diameter 0.265 mm. As the sounding
frequency of a string tends to fall after it is first tuned steel stabilizes within a few minutes, synthetic strings
about 8 hours and gut strings 48 hours (Fletcher et al.,
1998), 2 days were allowed for each string to settle in a
violin from the China Conservatory of Music.
Throughout the process all materials were kept in the
same room under 25C and humidity from 30% - 50%.
Recording of open E strings took place in a music
recording room with laminated glass window and
acoustic panels to prevent excessive reverberation;
hence the sound can disperse approximately equally
throughout the room without minimal distortion.
(Campbell et al., 1987) A Neumann U87AI condenser
microphone was used due to its excellent response for
frontal sound incidence and high fidelity. Software for
sound analysis includes LeCroyWaveRunner Xi-A /
MXi-A Oscilloscope, Microsoft Excel and SciDavis, which
enable us to plot the waveform of samples and Fourier
analyze the resultant data.
prevent their influence on the timbre of E string. The

samples were saved in audio files, which were later run
through oscilloscope and computer software for
Fourier analysis.

METHODOLOGY
Penetrating
Projecting
1k
4k
7k
10k
13k
16k
19k
21k Freq/Hz
Figure 9: Comparison of strings with penetrating tone colour and good

projection
Discussion of Results
After grouping, patterns are observed from 3 aspects:
the strength of harmonics, the fluctuation of partials
and , the level of scattering of the amplitude data.
Figure 6: The waveform and FFT diagram of machine noise
RESULTS AND DISCUSSION

VOYAGER 2014
54
Interpretation of Data
After removing the effects of machine noise, we
tabulated the amplitude of various partials against
frequency for all 3 trials of each string. The average
data of 3 trials was taken to plot graphs for
comparison.
The 10 strings with varying timbres are grouped in 3
categories based on timbre descriptors provided by
string producers: rich/warm, bright/open and
projection/penetrating. The spectral diagrams of 3
groups are provided below.
Samples with a rich and warm tone colour have

relatively even distribution of energy across the
spectrum with constant fluctuations throughout the
spectrum. (See figure 7). The level scattering of
amplitude of partials is the greatest among 3 groups,
with standard deviation w from 16.5 to 16.8 (see Table
1). The brilliant tone of bright/open and
penetrating/projecting groups is likely to be
associated with high energy distributed on high
harmonics with sustained strength, which can be seen
from the plateau of spectral diagrams from 10,000
Hz to 19,000 Hz with amplitude between -50 dB to
-60 dB (see figure 8, 9). The harsh penetrating
property can be attributed to greater scattering of
amplitude as well as more fluctuations (see figure 8,
9), as P bears a slightly higher range than B.
Table 1: The standard deviation of amplitude data of different strings
Rich
Warm
1k
4k
7k
10k
13k
16k
19k
21k Freq/Hz
Figure 7: Comparison of strings with rich, warm tone colour
Bright
Open
1k
4k
7k
10k
13k
16k
19k
21k Freq/Hz
Figure 8: Comparison of strings with bright and open tone colour
Rich/Warm
<EvahP Au>
<Pir Oliv>
<D'Light>
Std Dv w
16.765
16.673
16.549
Range
16.5 16.8
Bright/Open <Chromcor> <D'heavy>
<Infd Tn>
<Lenzner>
Std Dv B
14.318
15.459
15.281
14.951
Penetrating
<Vision>
<EP Ag>
<Infd Pt>
Std Dv P
16.208
16.295
16.363
14.3 15.5
16.3 16.4
CONCLUSION AND EXTENSION

Our study has proven the hypothesis to be true, and at
the same time provided a deeper insight into patterns
of different string tone colours.
This research provides a method to build a database
of different instrumental timbre. Findings in this study,
although limited to a rather small scale, can be used in
computer generated music to create more variance in
instrumental timbre. This allows electronic music
producers to add life to music produced by
machines, which is of great practical use in
entertainment industry such as synthesis of pop music
and movie making.
We are highly indebted to our mentors Professor Chan

Aik Hui, Phil and Mr Tan Peng Kian for their inspiring
guidance and supervision throughout the project. We
would also like to express our gratitude towards our
Supervising Tutor, Dr Lim Jit Ning for his constant help
and guidance. Special thanks also go to Dr Tan
Wee-Hsin and Ms Lillian Wang for their suggestions
and feedback as professional musicians. Last but not
least, we would like to thank Hwa Chong Institution
Science Research Centre Lab staff Ms Chua and Ms
Tan for their help and facilitation for our experiments.
REFERENCES
[1] Campbell. M., Greated.C. (1987). The Musician's Guide
to Acoustics. New York: Schirmer Books. Pg 545.
[2] Chen. C.W. (2007). The Physical Modeling ofthe
Bowing Techniques for Violin. Tatung University,Taiwan.
https://docs.google.com/viewer?a=v&q=cache:clnyUna
kDC4J:ethesys.library.ttu.edu.tw/ETD-db/ETD-search/g
etfile%3FURN%3Detd-0214107-181852%26filename%3D
etd-0214107-181852.pdf+&hl=en&gl=sg&pid=bl&srcid=A
DGEESiGJvwU9YNxWDErxcGp6f20zQ7NRjuu-OW1h2
YuroJFPrSvLpTjjKXB2s1tVkYj4Nw9jbWDmMDE4JxL72
UxovPPuO9IM4v1JP-yQKiARMuoV0xU0c06soPq1ehAL
N9kzSFAs3Sf&sig=AHIEtbSAq2Z8W9F14_mgT2-kdOu
GjHaKgQ [last access 2013/01/04]
[3] Fletcher. N. H., Rossing. T. D. (1998). The Physics of
Musical Instruments, 2nd edition. New York: Springer
Science+Business Media, Inc.
[4] Fritz. C., Blackwell. A.F., Cross. I., Woodhouse. J.,
Moore. B.C. (2011). Exploring violin sound quality:
Investigating
English
timbre
descriptors
and
correlating resynthesized acoustical modifications
with perceptual properties. Universit Pierre et Marie
Curie, UMR CNRS 7190, Institut Jean Le Rond
d'Alember. 2012 Acoustical Society of America.
http://www.ncbi.nlm.nih.gov/pubmed/22280701 [last
access 2012/12/31]
[5] Charles. J. (2010). Playing Technique and Violin
Timbre: Detecting Bad Playing. Dublin Institute of
Technology.
School
of
Engineering.
http://arrow.dit.ie/cgi/viewcontent.cgi?article=1030&c
ontext=engdoc [last access 2012/12/31]
[7] Oldham, Guy, et al. 2011. Harmonics. In Grove

Music Online. Oxford MusicOnline,
http://0-www.oxfordmusiconline.com.library.unl.edu/
subscriber/article/grove/music/ 50023 [last access
2012/12/31]
APPENDIX
Appendix A: Information of E strings
Brand
Description of string timbre
Category
Thomastik
Pure, rapid settling and
Rich/warm
Vision
rich, complex2
Pi Infield
Perfect blend of power and
Platinum
elegance, brightness and warmth, power
Projection/
brilliant projection3
Pi Infield Tin
Full sound enhances the brighter
Bright/open
overtones
Pirastro Oliv
Complex tone with warm balance5 Rich/warm
Pirastro
Bright, loud sound with easy
Chromcor
response
Lenzner
Open and bright tone
Bright/open
DAddario
Traditional sound, rich and
Rich/warm
Kaplan Light
expressive6
Bright/open
Goldbrokat
Non-whistling Traditional sound, brilliant
Projection/
DAddario
projection, volume projection7
power
Evah Pirazzi
Nuanced rich response,
Rich/warm
Gold
and tonal complexity
Evah Pirazza
Brilliant, focused projection
Projection/
Silver
and complex overtones9
power
Kaplan Heavy
8
Thomastik-Infield Vision Titanium. http://www.thomastik-infeld.com/

strings/index.html
http://www.violinist.com/discussion/response.cfm?ID=17252
Thomastik Infield http://www.thomastik-infeld.com/strings/index.html
Pirastro Oliv http://www.pirastro.com/homeset.html
DAddario Kaplan Light http://www.daddariobowed.com/Bowed

ProductDetail.Page?ActiveID=4495&productid=173
DAddario Kaplan Heavy http://www.daddariobowed.com/Bowed

ProductDetail.Page?ActiveID=4495&productid=174
Pirastro Evah Pirazzi Gold http://www.pirastro.com/homeset.html
Pirastro Evah Pirazzi Silver http://www.pirastro.com/homeset.html
55
VOYAGER 2014
ACKNOWLEDGEMENTS
[6] Crosmer. J.P. (2011). A Comparison of Viola Strings

with Harmonic Frequency Analysis. University of
Nebraska-Lincoln.
Student
Research,
Creative
Activity, and Performance - School of Music.
http://digitalcommons.unl.edu/cgi/viewcontent.cgi?a
rticle=1032&context=musicstudent
[last
access
2012/12/31]

In further research, we can extend this method to the

rest of violin timbre space to study how other
technical factors affect the violin timbre.
Appendix B: Data obtained from oscilloscope to plot

graph
B1: Rich/warm
Rich/Warm
Mean
Freq/Hz
StdDv w
663
f0
1326
f1
1989
f2
2652
f3
3315
f4
3979
f5
4642
f6
5305
f7
5968
f8
6631
f9
7294
f10
7958
f11
8621
f12
9284
f13
9947
f14
10610
f15
11273
f16
11937
f17
12600
f18
13263
f19
13926
f20
14589
56
f22
VOYAGER 2014
f24

f21
f31
15252
15916
f23
16579
17242
f25
17905
f26
18568
f27
19232
f28
19895
f29
20558
f30
21216
<EvahP Au>
<Pir Oliv>
<D'Light>
-48.9178
-52.3219
-50.2751
16.76548
16.57306
16.54861
-24.3219
-21.3164
-26.0006
-23.9871
-27.9636
-31.1955
-39.1947
-30.6193
-39.9081
-16.6909
-27.1948
-22.9255
-41.1532
-22.8385
-19.9669
-50.6977
-29.7998
-32.5611
-23.8760
-43.0134
-32.6399
-38.7424
-51.1825
-39.0466
-30.2138
-38.0432
-31.6149
-32.7347
-35.9622
-52.8383
-34.2789
-44.5197
-39.8154
-56.4396
-50.5843
-42.3778
-46.3108
-52.8896
-46.2920
-38.8692
-52.8439
-44.4274
-43.8915
-48.3091
-58.0537
-44.2106
-55.1661
-44.0552
-47.2058
-57.6363
-46.6112
-57.7746
-60.3264
-51.4791
-53.0100
-52.6583
-50.2692
-48.0239
-54.9492
-58.2125
-46.7055
-58.2345
-64.9922
-60.2342
-72.3065
-49.9887
-55.5799
-62.8681
-58.096
-57.6032
-55.7024
-60.7513
-57.3036
-59.8076
-73.7595
-50.1053
-63.1419
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<Infd Tn>
<Lenzner>
-46.9796
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663
-23.2034
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1326
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1989
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4642
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5305
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B3: Penetratin/Projecting
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f13
f14
f15
f16
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f21
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f23
f24
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<Chromcor>
Mean
StdDv B
f25
f25
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Rich/
Warm
B2: Bright/Open
f27
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Freq/Hz
663
1326
1989
2652
3315
3979
4642
5305
5968
6631
7294
7958
8621
9284
9947
10610
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19895
20558
21216
HISTORIC VENUS TRANSIT 2012

AND INSTRUMENTATION
BACKGROUND AND OBJECTIVES

Professor Chan Aik Hui, Phil
National University of Singapore
Venus Transit is a rare astronomical event
whereby Venus, Earth and the Sun line up
in a straight line. Historically, the size of the
Solar System was accurately determined
for the first time in 1771 based on the Venus
Transit data. This research is noteworthy
because it was the last observation in this
century. The next Venus Transit will occur
about a hundred years from now in 2117. In
this project, a formula based on Kepler's
Laws and trigonometry was derived to
determine the Astronomical Unit; the
obtained results agreed with modern
methods to within 4 percent.
Aims and objectives

Our group aims to provide a comprehensive way to
calculate the value of AU through following steps:
i. Venus transit observation: Determine the visibility
graph to select a suitable observing location.
Observe the transit and measure the four essential
contact times of Venus transit.
ii. Calculation of AU: Use trigonometry and Keplers law
to calculate Sun- Earth distance.
Estimate the degree of accuracy based on errors
involved in instrumentation and calculation.
VENUS TRANSIT INSTRUMENTATION

Determine the world visibility graph
During Venus transit, not all parts of the world can
witness this extraordinary event. Hence, it is important to
determine the function that defines the world visibility
zone. Since the diameter of the Earth is relatively
insignificant compared to the Sun-Earth distance and
the apparent diameter of the sun is much larger than
that of Venus, places that can see the sun at the time of
transit can see Venus. During the transit, the earth is near
its summer solstice and its axis is tilted around 23.5 to
the ecliptic plane. During the 6-hour transit, the transit is
visible in any parts of the world that rotated to face the
Sun.
For clearer explanation, we put the earth in a 3D
coordinate system. The rotational axis is altered to be in
the z-direction. The line AB separates the region facing
57
VOYAGER 2014
Research Mentor
Dr Lim Jit Ning
Background
Venus Transit is a rare astronomical event that happens a
total of four times every 243 years (8, 121.5, 8, 105.5). It
occurs when Venus and Earth meet up at the orbital
nodes, resulting in a solar eclipse of a kind. Since the 18th
century, Venus transit has been studied by scientists to
calculate the size of solar system. In 1716, Sir Edmund
Halley proposed more accurate calculations using the
contact times of the transit based on the principle of
parallax. However, his detailed workings and
corresponding accuracy are unavailable. Therefore, our
project takes the challenge to come up with a more
comprehensive method to calculate the value of AU
based on data collected from our own observation while
restricting the method to what was known and available
in terms of astronomy and mathematics at the time of
Halley.
Historic Venus Transit 2012 And Instrumentation
Vanessa Lim Yu 12S60

Yang Shuo 12S7D
Zhang Lanqiong 12S7D
and opposite to the Sun. Let R represent the radius of

the Earth, a and o represents latitude and longitude
respectively. (Detailed working can be found in the
Appendix)
VENUS TRANSIT OBSERVATION

Equipment
Figure 2.1 Earth in a

2D coordinate system
! 1.
! 3.
! 4.
x2
y2 z2
z
a
VOYAGER 2014
58
a
sin
a
sin
1
sin
z
R
sin
tan
sin 2 66.5
sin 66.5
tan o sin 66.5
tan 2
(2.2)
x
y
tan 66.5 tan

R
tan 66.5 tan

1
(2.1)
tan 66.5 x
z
sin 1
R
R2
1. Telescope (Vixen SS08V)

2. iOptron GOTONOVA controller
(2.3)
3. Eyepieces (Vixen PL 17mm MULTI-COATED, PLSSL

32mm FULLY MULTI-COATED)
(2.4)
4. Solar filter (Thousand Oaks Optical Type 2)

Procedure
1. Assemble the telescope according to the instructions.
y
sin 2
! 2.
2. Align the SOUTH mark to face the south.

a
(2.5)
cos 2 66.5
By using the software MathCai, we managed to obtain

the graph.
3. Level the mount using the bubble at the side by

adjusting the tripod.
4. Switch on the controller. The built-in GPS would have
ascertained the location and time.
5. Select SUN as target. The telescope will automatically
rotate to the Sun and track it.
6. At intervals of 10 minutes, a video camera on a tripod
is placed at the eyepiece of the telescope to record the
transit for 2 minutes. The telescope is manually adjusted
before the recording to account for the error.
Figure 2.2 World Visibility graph
According to the graph, Singapore (1.23N, 103.92E) lies

in the region where transit starts earlier than sunrise. To
overcome this limitation, two of our group members
traveled to Shenyang, China (41.630N 123.404E) where
entire transit is visible while our international
collaborator observed in Chongqing where the entire
transit is also visible.
Distance between the trajectories
Figure 2.4 Pictures of Venus transit

Figure 3.1 Flight trajectories
Observer 1 (our group)
Observer 2 (collaborator)
Shenyang, China
Chongqing,
41.63N 123.40E
China 29.57N 106.57E
Timing of 2nd contact
06:27
06:29
Timing of 3rd contact
12:32
12:32
Duration between the
6h 5min = 365min (1min)
6h 3min = 363min (1min)
location
2nd and 3rd contact
Table 3.1 Experimental data
Hence, take the mid points of the two chords

; let be the angle between OM
andOM
PRELIMINARY CALCULATIONS
Assumptions
In our calculation, there are a few assumptions made.
(1) The distance of the observers to the sun is constant.
(2) Earth and Venus move in straight lines relative to the
Sun during the transit. (3) The orbit of Venus around the
Sun lies in the ecliptic plane.
d a2
360
Tsyn
syn
2
b
bb '
2
(3.4)
R = the apparent radius of the Sun - the apparent radius

of Venus = 32' 60.3' '
2
M aMb
The apparent velocity of Venus relative to the Sun

Relative to a rotating coordinate system, in which the
line Earth-Sun is fixed, Venus cover an orbit of in one
synodic orbit, with an angular velocity of
aa '
2
R2
Ma, Mb
2
d b sin
or 0.0000132 in radians
15.5'
2
d b cos
da
0.04538
(3.5)
Calculating the baseline
(3.1)
The synodic orbital velocity of Venus relative to the

rotating coordinate system is
vsyn
syn
d vs
(3.2)
Hence, the corresponding velocity of Venus as seen from

the Earth equals to the required apparent velocity
relative to the Sun
Vsyn
vs
d ev
syn
d vs
d ev
0.0672' ' / s
(3.3)
Figure 3.2 Earth in a 3D

coordinate system
59
VOYAGER 2014
Experimental data
Due to the movement of the observer, most transit

trajectories are curves instead of straight lines, nor are
their chords parallel. This makes it hard to obtain the
distance between the two trajectories, since it is no
longer a constant. However, the distance between the
center-points of the two chords changes only little with
the angle between them, while for all other dividing
points of the chords, the difference is larger.
RESULT ANALYSIS
The baseline is defined as the length of projection of the

line connecting the two observers onto the plane normal
to the Earth-Sun viewing line. To calculate the baseline,
we set up a three-dimensional coordinate system, with
the x-y plane on the equator and the x-axis pointing
towards the Sun.
e is the unit vector perpendicular to the plane of ecliptic
sin sin
0.0338
sin cos
0.385
cos
Computing the AU through solar parallax
Figure 3.3 Relative positions of Earth, Venus and the Sun
(3.6)
0.922
Parallax of Venus ( v ) and the parallax of the Sun (

can be computed by
Where and are the right ascension of the Sun and

obliquity of the ecliptic respectively. Points P and Q
represent the two observers,
cos
R cos
OP
cos H p
sin H p
sin p
Px
Py
Pz
PQ
VOYAGER 2014
60
OQ
cos
cos H q
qx
R cos
sin H q
qy
sin
OQ OP
px
qx
py
qy
pz
qz
(3.7)
PQ1
PQ 2
(3.9)
0.171
px )ex (qy
py )ey (qz
pz )ez
635.9km
b2
PQ 2 e (qx
px )ex (q y
p y )ey (qz
pz )ez
844.5km
Finding the ratio
d vs
d ev
740.2km
(3.10)
(3.11)
(3.12)
by Keplers Third Law
Keplers Third Law states that, the square of the orbital

period of a planet is directly proportional to the cube of
the semi-major axis of its orbit; or simply, T 2
r3
d es
d vs
d vs
d ev
Te
Tv
2
3
d vs
d es d vs
365.256
224.701
1
d es
d vs
2
3
b
d es
b
A
1.35968
1
2.78025
1 1.35968 1
(3.15)
(3.13)
d es
d ev
1
A
d vs
d ev
d vs
d ev
(3.16)
Sub in the quantities we have obtained from the

previous calculations, Sun-Earth distance becomes
d es
740.2
2.78025 1.56 108 km
0.0000132
(3.17)
Estimation of errors
Error of the computed AU comes mainly from the
measured duration of Venus transit, the distance
between trajectories and the accuracy of baseline.
Based on we have derived earlier, defining q as
d vs
b
b
Hence,
d
q
es
PQ1 e (qx
b1 b2
2
(3.8)
b1
d es
qz
0.134
R 0.077
b
d ev
A and
B are angular distances of the chords seen by
observers A and B respectively. By geometry,
Due to the non-linear movement of the observers, the

length of the baseline changes throughout the entire
transit. Hence, a good choice would be the arithmetic
mean of the lengths of the baseline at the start and the
end of the transit. Let R represent the radius of the
Earth= 6371km
0.231
R 0.130
0.171
d d es
b d q
d ev
q d b
bq
d q
d b
dvs
des
(4.1)
b
d q
(4.2)
Length of transit trajectory
The Length
of transit trajectory in front of the solar
disk can be determined by
t
(4.3)
Where is the apparent velocity of Venus relative to the
sun and is the duration of Venus transit.
The absolute error is
(4.4)
d
wdt td
tdt
Distance between trajectories

The apparent distance
of the trajectory to the center
of the solar disk with apparent radius R is calculated
with length of transit trajectory
R2
(3.14)
d
d
RdR
RdR
)2
d
4
d
4
(4.5)
Error of the ratio q

By Keplers Third Law, let k
d es
d ev
d es
d es d ev
1
d es
1
d vs
d (k )
k
2 1
d (Te )
3 Te
dq
1 k
2
3
d (Te )
Te
d es
d vs
1
k 1
Te
Tv
2
3
8. Moar, E. (2004). Venus in Transit. Princeton, US:

Princeton University Press.
Hence,
(4.6)
1
d (Tv )
Tv
(4.7)
d (Tv )
Tv
(4.8)
9. Roberts, C., & Cooper, M. (2010, April 13). The Scale of

the Solar System: Re-enacting the Transit of Venus
Observations 5 - 6 June 2012. Retrieved 3rd March, 2012, from
http://www.fig.net/pub/fig2010/papers/ts05f/ts05f_roberts
_cooper_3851.pdf
10. Sim, C. (2010) Chapter 6 Energy and Matter
Retrieved. 12th July, 2012, from
http://www.physicalgeography.net/fundamentals/6h.ht
ml
CONCLUSION
12. Van Roode, S. (2012) Venus curved trajectory.

Retrieved 3rd March, 2012, from
https://docs.google.com/document/d/1iWm8hFB9oeL
GETh07GhHWBcoozBGskpJLlyfu3uVqSg/edit
REFERENCES
A1. Physical quantities
1. Adam and Michael Fremont High School (1996) Right

Ascension and Declination. Retrieved 3rd March, 2012, from
http://library.thinkquest.org/2595/reference/ra.html
The radius of the Earth

Sideral period (T)
Earth
6371km
365.256 days
Venus
224.701 days
Table 2.3
2. Anonymous (2012) Solar Time. Retrieved 12th July, 2012,
from http://en.wikipedia.org/wiki/Solar_time
3. The Astronomical Society of Singapore (2012). TASOS
Transit of Venus Observation at Science Center Singapore
on 6th June 2012. Retrieved 8th August, 2012 from
http://tasos.org.sg/
The apparent diameter of the Sun
32
The apparent diameter of Venus
60.3
Right ascension of the Sun on 6th, June, 2012 ( )
5059
Obliquity of the ecliptic on 6th, June, 2012 ( )
224436
A2. Detailed derivation of the World Visibility curve

At the time of transit, the earth is near its summer solstice.
Hence, the earth is tilted in such a way that the northern
4. Blatter, H. (2003) Venus Transit 2004. Retrieved 3rd

March, 2012, from
http://eclipse.astroinfo.org/transit/venus/project2004/pu
b/Blatter.etal.eng.200306.pdf
5. Google Maps (2012) Google Maps. Retrieved 10th Nov,
2012, from https://maps.google.com/maps?hl=en&tab=wl
6. Hoffmann, S. (2006) A beginners Guide to Computer
Imaging and Printing Using Digital Cameras, Scanners and
Home Photo printers Retrieved 3rd March, 2012, from
http://www.sphoto.com/homedd/pixels&imagesize.html
7. Krisciunas, K. (2012) Right ascension and declination of
the
Sun.
Retrieved
3rd
March,
2012,
from
http://people.physics.tamu.edu/krisciunas/ra_dec_sun.ht
ml
hemisphere experiences polar day. As shown in figure 1, the

shaded region is covered in sunlight. Hence, during the 6-hour
transit, any parts of the world that enters the shaded region due
to earths self-rotation can see Venus traveling across the sun.
N66.5
!
Sun
Sunshine
VOYAGER 2014
61
APPENDIX
In conclusion, this project gives us an invaluable learning

opportunity to observe the last Venus transit of the
century and further our understanding on calculation of
the AU in the earlier days. In preparation, the world
visibility curve that we derived, enabled us to determine
desirable location for observation. We also managed to
figure out a simple yet comprehensive way to calculate
the value of AU from Venus transit. Based on the data
from our observation and our collaborators, we
obtained a result within an error of 4.28%.
11. Teets, D. A. (December 2003). Transits of Venus and

the Astronomical Unit. Mathematics Magazine, Vol. 76,
No. 5, p. 335-348
For clearer explanation, we put the earth in a 3D

coordinate system. The rotational axis is altered to be in
the z-direction. The shaded area is the plane that
separates visible and not visible zone of the sun.
x2
y2 z2
R2
sin
z
R
tan 66.5 tan
R
sin 1 ( tan 66.5 tan
sin
66.5
B
In a 2D x-z plane, the shaded area can be represented by
the line AB. Since the rotational axis tilts 23.5 from the
vertical during the orbit, the angle between line AB and
x-axis is 66.5.
62
tan 66.5 x
(A2.2)
From (A2.1) and (A2.2)
y 2 sec 2 66.5 x 2
z
sin 1
a
R
R2
(A2.3)
(A2.4)
where a represents latitude.

From (A2.2) and (A2.3)
R
sin
tan 66.5
(A2.5)
From (A2.3) and (A2.5),
y
From (A2.5) and (A2.6),
x
Since o tan 1 , where
R 1
(sin a ) 2
sin 2 66.5
(A2.6)
represents longitude
y tan
(A2.7)
From (A2.2),
tan 66.5 tan
(A2.8)
tan 66.5 tan
tan 2
sin
tan
tan 2
) 1
sin 2 a
sin 2 66.5
sin 2 66.5
sin 66.5
sin 2 a )
(sin 2 66.5
1
VOYAGER 2014
(A2.1)
where R is the radius of the earth.
sin
o
o
sin 66.5
cos 2 66.5
sin 2
cos 2 66.5 sin 2
ACKNOWLEDGEMENTS
We are deeply grateful to our principal, Dr. Hon Chiew Weng and deputy principals
Mrs. Chin-Leow Bee Kuan and Mr. Chan Kwok Leong for their strong support in our
students science research programmes. We would also like to give special thanks to
our Dean of Research Studies, Mrs. Tan-Tiang Ai Chin, who has given us her strong
support throughout the production.
The extent to which science research has been developed at Hwa Chong has been
possible due to the support of our external research mentors and teacher mentors.
They teach, guide and provide resources for our learning journeys.
We are also indebted to the schools laboratory staff for staying back in school late
during crucial periods; offering their invaluable support and giving our students the
extra time required to complete their research projects.

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I N S T I T U T I O N

A Hwa Chong Institution Research Publication

Voyager, the brainchild of members from the Science

Chiang Yan Xin 14S7F

Chiang Yan Xin 14S7F

Chiang Yan Li 13S7B

Chiang Yan Li 13S7B

Poh Yong Rui 13S7J

Poh Yong Rui 13S7J

Ng Jun Xuan 13S7G

Ng Jun Xuan 13S7G

Kwan Jing Ling 14S79

Kwan Jing Ling 14S79

Lee Zhi Rui 14S79

Lee Zhi Rui 14S79

Zhou Pei Yu 14S6A

Zhou Pei Yu 14S6A

Dr Kelvin Tan Yong Leng

Dr Kelvin Tan Yong Leng

Education Consultant/ Research

Education Consultant/ Research

We maintain a culture of continuous transformation. This year, Voyager has evolved to

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HISTORIC VENUS TRANSIT 2012

This research provides a method to

Investigation into the relationship between violin string

Our fall detection system is capable of processing

Lee Choon Kiat

Determining the amino acids involved in inhibition of PDE4B by

Four versions of prototype were constructed using lala clam

The different frequency of stained colonies

Dr Hon Chiew Weng

This year, our students continue to work under the mentorship of

and the Defence Science and Technology Agency

(DSTA). Similarly, the Nanyang Research Program

scientists, made groundbreaking discoveries in the

(NRP) helmed by Nanyang Technological University

most unsuspecting of circumstances. Hwa Chong too

(NTU) provides a platform for our students to explore

hopes to lay the foundations for such discoveries by

developing our students critical, creative and caring

sciences and social sciences. In addition, Hwa Chong

minds, grooming them to become leaders in the

has formed firm partnerships with local research

scientific community of tomorrow.

institutes such as the Agency for Science, Technology

Hwa Chongs own internal research programme, the

universities such as University of Glasgow, Scotland.

Centre for Talent Development in Science (CenTaD),

These strong alliances provide a vibrant hub for

aims to promote a strong culture and passion for

scientific discoveries and opinions where the passion

research amongst its students. Under the guidance of

and curiosity of Hwa Chong students are cultivated.

experienced mentors and laboratory staff, Hwa

Hwa Chongs own internal research

and photonics, Hwa Chongs Science Research Center

Hwa Chong provides many platforms, such as the

scientific ideas and a facility to promote innovation.

HC's Corporate Magazine Voyager

HC's Corporate Magazine Voyager