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Protein Simulations

Protein Simulations. Prof. Corey S. O’Hern Department of Mechanical Engineering Department of Physics. Coarse-grained descriptions. All-atom descriptions. Your model is oversimplified and has nothing to do with biology!. Your model is too complicated and has no predictive power!.

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Protein Simulations

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  1. Protein Simulations Prof. Corey S. O’Hern Department of Mechanical Engineering Department of Physics Coarse-grained descriptions All-atom descriptions

  2. Your model is oversimplified and has nothing to do with biology! Your model is too complicated and has no predictive power! Molecular biologist Biological Physicist

  3. Topics • Protein Folding • Protein Misfolding and Aggregation

  4. Journal Articles 1. J. D. Honeycutt and D. Thirumalai, “The nature of folded states of globular proteins,” Biopolymers32 (1992) 695. 2. W. C. Swope and J. W. Pitera, “Describing protein folding kinetics By molecular dynamics simulations. 1. Theory,” J. Phys. Chem. B108 (2004) 6571. 3. D. Bratko, T. Cellmer, J. M. Prausnitz, and H. W. Blanch, “Molecular Simulation of protein aggregation,” Biotechnology and Bioengineering96 (2007) 1.

  5. Methods I Coarse-grained Brownian dynamics simulations of proteins

  6. Methods II …energy minimization, simulated annealing, Markov models, Master-equation approaches, Monte Carlo simulations, advanced sampling techniques…

  7. Cell and Immunology Simulations Prof. Steven Kleinstein Department of Pathology • Modeling cell mutation, division and death • Population dynamics using ODEs • Viral dynamics and immunological response • Optimization and matching experimental data

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