Lab 9/3 |
Setup, UNIX, Molecular Graphics
Feig |
Assigned Reading |
UNIX overview PDF |
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Lecture 9/8 |
Basic data analysis under UNIX
Feig |
Lab 9/10 |
Basic UNIX scripting
Feig |
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Lecture 9/15 |
Molecular dynamics and Monte Carlo simulations
Mukherjee |
Lab 9/17 |
Molecular dynamics simulations of simple liquids
Mukherjee |
Assigned Reading |
Feig M: Molecular Simulation Methods: Standard Practices and Modern Challenges (2009) in press PDF |
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Hu, J. et. al.: Monte Carlo Simulations of Biomolecules: The MC Module in CHARMM. J. Comp. Chem. (2006) 27, 203-216 PDF |
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Lecture 9/22 |
Force fields and molecular dynamics simulations of biomolecules
Mukherjee |
Lab 9/24 |
First molecular dynamics simulations of biomolecules
Mukherjee |
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 9/29 |
Biological solvent environments
Feig |
Lab 10/1 |
Explicit solvent simulations
Feig |
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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Lecture 10/6 |
Implicit solvent models
Feig |
Lab 10/8 |
Implicit solvent simulations
Feig |
Assigned Reading |
B. Roux, T. Simonson: Implicit solvent models, Biophysical Chemistry (1999) 78, 1-20 PDF |
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Lecture 10/13 |
Enhanced sampling
Feig |
Lab 10/15 |
Umbrella sampling and Steered Molecular Dynamics
Feig
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Assigned Reading |
M. Souaille and B. Roux: Extension to the weighted histogram analysis method: Combining umbrella sampling with free energy calculations. Computer Physics Communications (2001), 135, 40-57 PDF |
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S.Izrailev,S.Stepaniants,B.Isralewitz,D.Kosztin,H.Lu, F.Molnar,W.Wriggers,and K.Schulten: Steered Molecular Dynamics PDF |
| TBD |
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Lecture 10/20 |
Replica exchange simulations
Feig |
Lab 10/22 |
Replica exchange simulations
Feig |
Assigned Reading |
A. Mitsutake, Y. Sugita, and Y. Okamoto: Generalized-ensemble algorithms for molecular simulations of biopolymers. Biopolymers (Peptide Science) (2001) 60, 96-123 PDF |
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A. Okur, D. R. Roe, G. L. Cui, V. Hornak, C. Simmerling: Improving convergence of replica-exchange simulations through coupling to a high-temperature structure reservoir. Journal of Chemical Theory and Computation (2007) 3, 557-568 PDF |
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Lecture 10/27 |
Free energy calculations
Mukherjee |
Lab 10/29 |
MMPB/SA analysis
Mukherjee |
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 11/3 |
Coarse graining
Feig |
Lab 11/5 |
Coarse grained simulations
Feig |
Assigned Reading |
Choon-Peng Chng, Lee-Wei Yang: Coarse-Grained Models Functional Dynamics - II. Molecular Dynamics Simulation at the Coarse-Graned Level - Theories and Biological Applications. Bioinformatics and Biology Insights (2008) 2, 171-185 PDF
MD projects
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Lecture 11/10 |
Dynamic mode analysis
Mukherjee |
Lab 11/12 |
Mode analysis
Mukherjee |
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 work 11/17 |
Class project
Feig/Mukherjee |
Lab work 11/19 |
Class project
Feig/Mukherjee |
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Lab work 11/24 |
Class project Feig/Mukherjee |
Thanksgiving 11/26 |
Holiday |
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Presentations 12/1 |
Rahul Banerjee, Langhua Hu, Qiong Zheng 3 pm - 4:30 pm ! |
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Presentations 12/8 |
Leann Buhrow, Abu Hassan, Patrick Ochieng, Xiaowei Lu 2:30 pm - 4:30 pm ! |
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Finals 12/18 |
Project write-up is due |