MB&B 435/635 - MATHEMATICAL METHODS IN BIOPHYSICS - Syllabus Time: 10:30a-11:20a, Bass 405.

Monday-Wednesday-Friday, Fall 2011

Instructors: Elizabeth Rhoades, elizabeth.rhoades@yale.edu (in charge) Yong Xiong, yong.xiong@yale.edu Corey OHern, corey.ohern@yale.edu Alice Zhou (teaching assistant), alice.zhou@yale.edu Textbooks (not required for use as a reference; both are on hold at Kline library): Mathematical Methods in the Physical Sciences (3rd edition), Mary L. Boas; Matlab Guide (1st Edition), Desmond J. Higham and Nicholas J. Higham Grading: The course grade will be determined by homework assignments (~75%) and a final project (~25%) which will have both analytical and numerical parts and will involved data analysis. There will be two homework assignments per mathematical topic, assigned and collected as noted in the schedule. Who should take this class?: This course is aimed at students who have taken mathematics through multivariable calculus, but have not had courses in linear algebra, differential equations, or fourier analysis. The goal of this one-credit course is to provide first year graduate students (and junior/senior level undergraduates) with practical understanding and hands-on experience with the mathematical methods needed to analyze and interpret biochemical and biophysical data. Students will learn from real-world projects to develop models to describe experimental observations and test the models. More information: The course format will consist of three 50 minute lectures per week. Analytical approaches to topics will be covered on Monday and Wednesday, whereas numerical and computational approaches to the same topics will be covered on Friday. There will be an optional 1 hour recitation section with the TA once a week, at a time to be determined. All students should plan to bring their personal laptop with Matlab installed on it to class on Friday, 2 September. Instructions on how to install Matlab will be posted on the classes server.

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day W F M W F M W F M W F M W F M W F M W F M W F M W F M W F M W F M W F M W F

date/lecturer/topic 31 Aug (ER) Math Review 2 Sept (AZ) Matlab Intro 5 Sept (ER) Prob, Stat, Error Analysis 7 Sept (ER) Prob, Stat, Error Analysis (HW1 assigned) 9 Sept (CO) Prob, Stat, Error Analysis 12 Sept (ER) Prob, Stat, Error Analysis 14 Sept (ER) Prob, Stat, Error Analysis 16 Sept (CO) Prob, Stat, Error Analysis (HW1 due; HW2 assigned) 19 Sept (ER) Prob, Stat, Error Analysis 21 Sept (ER) Prob, Stat, Error Analysis 23 Sept (CO) Prob, Stat, Error Analysis 26 Sept (YX) Fourier Analysis 28 Sept (YX) Fourier Analysis (HW2 due; HW 3 assigned) 30 Oct (CO) Fourier Analysis 3 Oct (YX) Fourier Analysis 5 Oct (YX) Fourier Analysis 7 Oct (CO) Fourier Analysis (HW3 due; HW4 assigned) 10 Oct (YX) Fourier Analysis 12 Oct (YX) Fourier Analysis 14 Oct (CO) Fourier Analysis 17 Oct (ER) Diff Eq 19 Oct (ER) Diff Eq (HW4 due; HW5 assigned) 21 Oct (CO) Diff Eq 24 Oct (ER) Diff Eq 26 Oct (ER) Diff Eq 28 Oct (CO) Diff Eq (HW5 due; HW6 assigned) 31 Oct (ER) Diff Eq 2 Nov (ER) Diff Eq 4 Nov (CO) Diff Eq 7 Nov (YX) Linear Algebra 9 Nov (YX) Linear Algebra (HW6 due; HW7 assigned) 11 Nov (CO) Linear Algebra 14 Nov (YX) Linear Algebra 16 Nov (YX) Linear Algebra 18 Nov (YX) Linear Algebra (HW7 due; HW8 assigned) 28 Nov (YX) Linear Algebra 30 Nov (CO) Linear Algebra 2 Dec (CO) Linear Algebra (HW8 due)

Review Introduction to the course Review of differentiation, integration, vector calculus and complex numbers Introduction to Matlab Probability & Statistics & Error Analysis motivation why probability, statistics, and error analysis are important for biophysics and biochemistry probability; sample and parent distributions probability theorems and Bayesian probability special distributions: binomial, Poisson, and Gaussian (normal) Monte Carlo techniques Regression Analysis: linear and nonlinear Maximum likelihood Least squares Goodness of fits: 2, students T-test Transform Methods Overview of the history and application of transforms methods Fourier Transforms: why and how Fourier Transforms: basics and properties Fourier Transforms: relationship of phase and amplitude Fast Fourier Transforms (FFT) Other transforms: Laplace, Wavelet Differential Equations Classification of differential equations First order ODEs Second Order ODEs Series Solutions and Difference Equation Partial Differential Equations Greens Functions Linear Algebra Basics of vector and matrix operations Applications in biological sciences Solving coupled equations Linear transforms Eigenvalue, eingenvector and eingensapce General caseSingular value decomposition