Lab 10/20 |
Setup, UNIX, Molecular Graphics
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Assigned Reading |
UNIX overview HTML |
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Lecture 10/25 |
Molecular dynamics simulations
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Lab 10/27 |
Molecular dynamics simulations of water
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Assigned Reading |
Feig M: Molecular Simulation Methods: Standard Practices and Modern Challenges in Computational Modeling in Lignocellulosic Biofuel Production, eds. Mark R. Nimlos, Michael Crowley, ACS (2010) PDF |
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Lecture 11/1 |
Biomolecular simulations
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Lab 11/3 |
Molecular dynamics simulations of biomolecules
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Assigned Reading |
A. D. MacKerell jr.: Empirical Force Fields for Biological Macromolecules: Overview and Issues, J. Comp. Chem. (2004) 25, 1584-1604 PDF |
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W. F. van Gunsteren, A. E. Mark: Validation of molecular dyanmics simulation, J. Chem. Phys. (1998) 108, 6109-6116 PDF |
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Lecture 11/8 |
Biological solvent environments
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Lab 11/10 |
Implicit solvent treatments
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Assigned Reading |
V. Makarov, B. M. Pettitt, M. Feig: Solvation and Hydration of Proteins and Nucleic Acids: A Theoretical View of Simulation and Experiment, Accounts of Chemical Research (2002) 35, 376-384 PDF |
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M. Feig: Biomolecular Solvation in Theory and Experiment in: Modeling Solvent Environments: Applications to Simulations of Biomolecules, ed. M. Feig, Wiley-VCH (2010) PDF |
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B. Roux, T. Simonson: Implicit solvent models, Biophysical Chemistry (1999) 78, 1-20 PDF |
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Lecture 11/15 |
Free energy calculations
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Lab 11/17 |
Free energy calculations
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Assigned Reading |
D. L. Beveridge and F. M. DiCapua: Free Energy via Molecular Simulation: Applications to Chemical and Biomolecular Systems. Annual Review of Biophyics and Biophysical Chemistry (1989) 18, 431-492 PDF |
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P. Kollman: Free Energy Calculations: Applications to Chemical and Biochemical Phenomena. Chemical Reviews (1993) 93, 2395-2417 PDF |
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Lecture 11/22 |
Coarse graining
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Assigned Reading |
Choon-Peng Chng, Lee-Wei Yang: Coarse-Grained Models Functional Dynamics - II. Molecular Dynamics Simulation at the Coarse-Grained Level - Theories and Biological Applications. Bioinformatics and Biology Insights (2008) 2, 171-185 PDF |
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Lecture 11/29 |
Dynamic mode analysis
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Lab 12/1 |
Mode analysis
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Assigned Reading |
A. W. van Wynsberghe, Q. Cui: Comparison of Mode Analyses at Different Resolutions Applied to Nucleic Acid Systems. Biophysical Journal (2005) 89, 2939-2949 PDF |
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AJ Rader. Chakra Chennubhotla, Lee-Wei Yang, and Ivet Bahar: The Gaussian Network Model: Theory and Applications.in "Normal Mode Analysis. Theory and Applications to Biological and Chemical Systems" Eds Qiang Cui and I Bahar, Chapman & Hall / CRC Mathematical and Computational Biology Series, CRC Press, Taylor & Francis Group, 41-64, 2006. PDF |
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Lab 12/8 |
Project presentations
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Finals 12/16 |
Project write-up is due |
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