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Com Sci 221 Numerical Methods in Computational Molecular Biology

Fall. 3 credits. Prerequisites: At least one course in calculus such as Math 106, 111, or 191 and a course in linear algebra such as Math 221 or 294 or Biometry 417. No particular course in programming is required, but the student should have some familiarity with iteration, arrays, and procedures. Limited to 25 students.

An introduction to numerical computing using Matlab organized around five applications: the analysis of protein shapes, dynamics, protein folding, score functions, and field equations. Students become adept at plotting, linear equation solving, least squares fitting, and cubic spline interpolation. More advanced problem-solving techniques that involve eigenvalue analysis, the solution of ordinary and partial differential equations, linear programming, and nonlinear minimization will also be treated. The goal of the course is to develop a practical computational expertise with Matlab and to build mathematical intuition for the problems of molecular biology.

There will be two lectures and one problem-solving recitation per week. The course grade will be based on five Matlab assignments, a more involved project, two prelims and a final exam.