Computational Biophysics and Systems Biology

CSE 60531/40531

Course Assignments Spring 2006

This document is an outline for your reference. The final assignment specifications can be found by clicking the highlighted assignment headers. Students will have approximately two weeks to complete each assignment

Assignment 1 – Introduction to Molecular Dynamics, Simulation, and Visualization

Due: Tues Feb 7

1. Short Answer

   1. 5 questions based on the primary papers from each lecture

2. Theory

3. Implementation/Computation

   1. Perform simulation in NAMD and RMSD analysis in VMD

   2. Write Python script in PMV to manipulate the visualization

4. Project

   1. Review recommended course project ideas, discuss high level details with instructor/TA, write a paragraph explaining your project and indicate at least three initial references.

Tutorial(s): (1) NAMD and VMD -week 1

(2) PMV and Python -week 2

Assignment 2 – Protein Protein Interactions and Equilibration

Due: Thur Feb 23

1. Short Answer

   1. 5 questions based on the primary papers from each lecture

2. Theory

3. Implementation/Computation

   1. Protein protein interaction analysis

   2. Perform equilibration in NAMD

   3. Compare Langevin and RMT methods in MDL (Molecular Dynamics Language)

4. Project

   1. Outline project's experimental hypothesis and scientific/academic goal

   2. Provide a two page summary of recent literature relevant to your project

Tutorial(s): (1) CytoScape -week 3

(2) MDL -week 4

Project Progress Review – Tues Feb 14

• 15 minute meeting with Instructor and TA

Assignment 3 – Minimization and Distributed Simulations

Due: TBA

1. Short Answer

   1. 5 questions based on the primary papers from each lecture

2. Theory

3. Implementation/Computation

   1. Implement a minimization routine in MDL

   2. Implement a REM exchange pattern in ProtoMol, utilize cluster for simulation, perform post analysis, submit results using GEMS

4. Project

   1. First draft of your project conference/journal paper.

Tutorial(s): (1) ProtoMol and MPI -week 6

(2) Distributed Systems (Clusters, Condor, GEMS) -week 7

Midterm – Take Home (Mon Mar 6^th - Fri Mar 10^th )

Assignment 4 – Free Energy and Efficient Electrostatics

Due: TBA

1. Short Answer

   1. 5 questions based on the primary papers from each lecture

2. Theory

3. Implementation/Computation

   1. Free energy analysis in MDL

   2. Run ABF (Adaptive Biasing Force) in NAMD

   3. Given trajectory files, perform GNM (Gaussian Network Model) analysis

4. Project

   1. Summary of Experimental Results

Tutorial(s): (1) GNM/ANM (Anisotropic Network Model) - week 9

(2) ABF - week 10

Project Progress Review – Tues April 18

• Second draft of your project conference/journal paper.

• 15 minute meeting with Instructor and TA

Project Final Presentation – Tues May 2

• 10 minute oral presentation

• 5 to 7 page paper in conference or journal format