Multiscale Modeling of Biological Systems
Instructor: Ravi Radhakrishnan, Bioengineering
BE 559 Spring 2007
Tuesdays, Thursdays 1.30 to 3.00 pm

Class Lectures and in-class 
lab sessions: Moore 100, time will be during regular class hours
pre-requisites: none

Course description: This course aims to provide theoretical, conceptual, and hands-on
modeling experience on three different length and time scales that are crucial to
biochemical phenomena in cells and to nanotechnology applications. 60% lectures, 40% computational laboratory

No programming skills required. Undergraduates who have taken BE324 need no permission. Others, email instructor rradhak@seas.upenn.edu for permission

Special Emphasis will be on cellular signal transduction

Course Syllabus
* Motivation for Computational Biology (1 lecture)
* Interactions (1 lecture)
* Master Equation, Markov Models, Monte Carlo, Kinetic Monte Carlo (2 lectures)
* Applications (student presentations) (1 lecture)
* Monte Carlo Lab (lab+assignment)
* Systems Biology Lab (lab+demos)
	Protein and Nucleic Acid Interaction
	Cellular Signals, Second Messengers
	Receptor Signaling
	Nuclear Signaling
	Cell Cycle
	Cell Cycle Deregulation and Cancer
* Equilibrium and Stability (2 lectures)
* Molecular Dynamics (1-2 lecture)
* Forcefields, long-range interactions (1-2 lecture)
* Student Presentations (Ewald Summation, Nose-Hoover, Nose-Hoover Chain)
* Biomolecular Dynamics (Lab+ Assignment)
Multiscale Modeling Techniques
* Free Energy Methods
* Applications (Student Presentations): protein-ligand design, protein folding
* Transition Path Sampling
* Applications: Protein conformational changes
* Linear response and Fluctuation Dissipation Theorem
* Applications (Student Presentations)
* Integrating Molecular dynamics and Continuum Mechanics
* Application Wetting of drop on a surface, endocytosis, biological adhesion

Grading: 60% Homework assignments;
30% Course project (15% write-up, 15% presentation);
10% Class participation

Textbook: Course notes, online manuals, journal articles, review articles (all provided)

Reference Textbooks: These are in reserve in the Engineering Library
1. Molecular Modeling and Simulation:An Interdisciplinary Guide, T. Schlick, Springer
Series : Interdisciplinary Applied Mathematics , Vol. 21, 2002
2. Understanding Molecular Simulation: From Algorithms to Applications, second
edition, Daan Frenkel and Berend Smit, Academic Press, 2001.