SI2008 Molecular Electrostatics and Diffusion

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General Information

This track will cover the electrostatics and molecular diffusion theories and applications in molecular interactions and the supramolecular complexes.

Time: 1 pm to 5 pm

Location: EBU2 - 239'

Prerequisites Basic UNIX knowledge required. Some scripting (Python, Perl, bash, etc.) background helpful. Math background important (at least calculus, ideally differential equations). As far as suggested reading - any advanced undergraduate or graduate physical chemistry textbook would be a good start. An excellent textbook is Berry/Rice/Ross Physical Chemistry or more biology oriented texts as Dill's Statistical Thermodynamics in Chemistry & Biology and Nelson's Biological Physics.

Software Requirements

Study Materials

Lab Information

  • To initialize the necessary software environment execute the following in your terminal window before starting the lab:
    . /home/linux/ieng6/nbcr08/public/Track5_Electrostatics/
  • On-line version of pdb2pqr application
  • Opal dashboard:


  • Tuesday, Aug 5, Computational electrostatics for biomolecular systems
    Instructor: Robert Konecny
    Users will be introduced to the basics of using continuum methods to systematically integrate atomic details simulations into macroscopic simulations, the limitation of the methods, and case studies of electrostatics and solvation in systems such as ribosomes, microtubules and computational alanine scanning (online tutorial).
    Class lecture
  • Wednesday, Aug 6, Continuum diffusion modeling using the SMOL package
    Instructor: Yuhui Cheng
    Users will learn the basics of diffusion-controlled diffusion reactions and how to use the SMOL package to model both steady-state and time-dependent diffusion equations, using mouse acetylcholine esterase and the neuromuscular junction in case studies.
  • Thursday, Aug 7, Brownian dynamics and coarse-grained modeling
    Users will be introduced to the new UCSD Brownian Dynamics (BrownDye) package for coarse-grained simulations of biomolecular systems.
    Instructor: Gary Huber
  • Friday, Aug 8, Advanced Studies
    Instructor: Robert Konecny
    Hands on exercises for the various tools covered in this track (online tutorial)

Related Materials from previous SI sessions

SI2007 Molecular Electrostatics and Diffusion

Back to SI2008 program

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