Course description
The goal of this course is to equip students of a variety of
backgrounds with the basic skills necessary to design and carry out
molecular simulations:
- formulation of both atomistically detailed and
simplified molecular models
- basic and advanced algorithms for computing
thermodynamic and kinetic behavior
- modern analysis techniques and visualization
packages
- physical intuition for developing and
interpreting new simulation “experiments”
- knowledge of computational issues and methods
for improving efficiency
Topics discussed in the course include: ab initio methods, classical
semi-empirical force fields, energy minimization, molecular dynamics
techniques, Monte Carlo methods, free energy algorithms, advanced
sampling strategies, coarse-graining and multiscale methods, and rare
events algorithms. Case studies in soft condensed
matter, materials, and biophysics will be presented throughout the
lecture material.
This course focuses more on concepts, algorithms, and tools than on
specific programming styles and languages, although enrolling students
should have had at least minimal exposure to coding or mathematical
software (e.g., have used any of Matlab, Mathematica, C, C++, Visual
Basic, or Fortran). From early in the course, a strong
emphasis will be placed on students performing and visualizing their
own simulation projects.
Coursework consists of a series of exercises in which students
write their own small simulation programs based on methodologies
discussed in lecture, run these, and provide analysis of
results. At the end of the course, students will complete a
project in which they simulate a system of interest, based on current
topics in the literature, using methodologies discussed in
class. The course will present Python as
a particularly powerful and freely available programming platform for
scientific
computing and highly encourage its use.
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Course information
| instructors |
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Professor M. Scott Shell
shell (at) engineering.ucsb.edu
Engineering II 3321
office hours: Tuesday 3-4pm, or drop by if my office door is open, or
by
appointment
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| schedule |
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TR
9:30-10:45am, Engineering II 3301
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| textbook |
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Molecular Modelling: Principles
and Applications (2nd edition)
Andrew R. Leach, Prentice-Hall (2001)
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| grading |
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70%
simulation exercises, 30% final project
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Course syllabus and
schedule
Download
here.
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