## Course Meeting Times

Lectures: 2 sessions / week, 1.5 hours / session

## Recommended Textbooks

Schlick, T. *Molecular Modeling and Simulation: An Interdisciplinary Guide*. New York, NY: Springer, 2002. ISBN: 9780387954042.

Allen, M. P., and D. J. Tildesley. *Computer Simulation of Liquids*. New York, NY: Oxford University Press, 1989. ISBN: 9780198556459.

Trefethen, L. N., and D. Bau, III. *Numerical Linear Algebra*. Philadelphia, PA: SIAM, 1997. ISBN: 9780898713619.

Branden, C.-I., and J. Tooze. *Introduction to Protein Structure*. 2nd ed. New York, NY: Routledge, 1999. ISBN: 9780815323051.

Bertero, M., and P. Boccacci. *Introduction to Inverse Problems in Imaging*. New York, NY: Taylor & Francis, 1998. ISBN: 9780750304399.

## Grading

ACTIVITIES | PERCENTAGES |
---|---|

Homework | 80% |

Class Participation | 20% |

## Calendar

LEC # | TOPICS | KEY DATES |
---|---|---|

Protein Modeling |
||

1 | Introduction and Protein Modeling Questions | |

2 | Models of Proteins | |

3 | Discrete Conformational Search | |

4 | Binding and Docking | |

5 | Molecular Dynamics Simulation | Homework 1 due |

6 | Molecular Dynamics and Electrostatics | |

7 | Continuum Electrostatic Modeling I | |

8 | Continuum Electrostatic Modeling II | |

9 | Electrostatic Optimization and Design | Homework 2 due |

10 | Electrostatics Modeling | |

11 | Statistical Mechanics | |

Network Modeling |
||

12 | Statistical Mechanics (cont.) | |

13 | Formulating and Simulating Network Models in Biology | Homework 3 due |

14 | Formulating Models | |

15 | Nonlinear Dynamics and Stability | Homework 4 due |

16 | Steady-State Problems | |

17 | Parameter Fitting and Estimation | |

18 | Parameter Estimation; Robustness, Fragility, Control | Homework 5 due |

Image Modeling |
||

19 | 2-D and 3-D Light Microscopy; Image Reconstruction | |

20 | Deconvolution | |

21 | Deconvolution II | |

22 | Blind Deconvolution | Homework 6 due |

23 | Optical Flow | |

24 | High-Throughput Data and its Analysis | |

25 | Inference and Statistics | |

26 | Roundup | Homework 7 due |