Multiscale Modeling of Biomolecular Systems
MAE 207

Lectures: Sept 25-December 4: Weekly lectures on Tue and Thu at 3:30-4.50 PM in Room 4050A YORK

Instructor: Dr. Gaurav Arya
Contact Information: EBU II 261; 858-822-5542; garya@ucsd.edu
Office hours: 5pm Fridays

Grading Scheme: Homework (50%) and computer (50%) assignments. Assignments will be posted every Thursday on the course website and submissions are due the next Thursday.

Covered Topics:
  1. Introduction to biomolecular systems: Central dogma of biology; proteins, DNA, RNA, lipids, carbohydrates, and water; multiple length and time scales in biology

  2. Intra/intermolecular interactions: ionic, covalent, and metallic bonding; van der Waals, charge-charge, charge-dipole, and dipole-dipole interactions, hydrogen bonding, pi-pi stacking, and hydrophobic interactions

  3. Molecular mechanics: mathematical description of molecules and their interactions (force fields), energy minimization methods

  4. Statistical mechanics: Boltzmann distribution, microcanonical and canonical ensembles, partition functions, entropy and free energy, computing thermodynamic properties, molecular simulations

  5. Molecular dynamics: Newton's equations of motion, periodic boundary conditions, thermostats, integrators, ensembles, multiple timestep schemes, neighbor lists, constrained molecular dynamics

  6. Monte Carlo: Monte Carlo integration, importance sampling, ensembles, Markov chains, detailed balance conditions, advanced methods involving biasing

  7. Computing transport, thermodynamic, and structural properties: radial distribution functions, potential of mean forces, free energy computation, autocorrelation functions

  8. Continuum modeling of solvent/electrolyte: Langevin dynamics, Brownian dynamics and hydrodynamics, Poisson-Boltzmann equation, Debye-Huckel approximation

  9. Mesoscale modeling: lattice models of polymers/proteins, normal mode analysis, elastic network models

Reference Material:
  1. B. Alberts et al, "Molecular Biology of the Cell", 4th Edition, Garland Science, New York (2002)

  2. A. R. Leach, "Molecular Modeling: Principles and Applications", Addison Wesley Longman, Essex, England (2001)

  3. D. Frenkel and B. Smit, "Understanding Molecular Simulations: From Algorithms to Applications", Academic Press, San Diego, California (1996)

  4. M. P. Allen and D. J. Tildesley, "Computer Simulation of Liquids", Clarendon Press, Oxford (1990)

  5. D. Chandler, "Introduction to Modern Statistical Mechanics", Oxford University Press, Oxford (1987)

  6. G. D. J. Phillies, "Elementary Lectures in Statistical Mechanics", Springer- Verlag, New York (2000)

  7. K. A. Dill and S. Bromberg, "Molecular Driving Forces", Garland Science, New York (2002)

  8. J. Israelachvili, "Interfacial and Surface Forces", Academic Press, London (1991)

Lecture Material:
  1. Lecture1.pdf

  2. Lecture2+3.pdf

  3. Lecture4.pdf

  4. Lecture5.pdf

  5. Lecture6.pdf

  6. Lecture7.pdf

  7. Lecture8.pdf

  8. Lecture9.pdf

  9. Lecture10.pdf

  10. Lecture11.pdf

  11. Lecture12.pdf

  12. Lecture13-14.pdf

  13. Lecture15.pdf

  14. Lecture16.pdf

  15. Lecture17.pdf

Homework Assignments:
  1. Homework1.pdf [Solution]

  2. Homework2.pdf [download simplex.f] [Solution]

  3. Homework3.pdf [Solution]

  4. Homework4.pdf [Solution]

  5. Homework5.pdf [download Moldyn.zip] [Solution]

  6. Homework6.pdf [download MC.zip]