Instructor: Dr. Jianhua Xing, Assistant Professor, Dept. of Biological Sciences

Time and location: Tues/Thu at 9:30-10:45, Randolph 121, Spring Semester, 2008

Contact Info: 5100 Derring Hall, phone: 231-1359, email: jxing@vt.edu

Office Hours: by appointment

Course Description: There is a general consensus that the future of biological research requires cross talk among people from various backgrounds. This is NOT a course emphasizing specialized knowledge, experimental, mathematical and numerical techniques, etc. Rather the course's goal is to break down the cultural barriers between researchers in physical and life sciences. I will help students to understand some basic ideas in modeling by repeatedly applying them to real biological problems.

Your learning objectives for this course are:

1. To be familiar with some basic concepts in physical chemistry (including statistical thermodynamics and dynamics) and their applications to biological problems.
2. To understand how to cast a complex biological problem into simple mathematical models, and to understand the physics behind a model.
3. To write/run simple computer code, and to study simple problems numerically.

Grading: Homework (85%), presentation (15%).

Textbook:

Primary: R. Phillips, J. Kondev & J. Theriot, Physical Biology of the Cell (Garland, soon to be in press). We are authorized to use the electronic copy preprint.

Suggested reference books:

Philip Nelson, Biological Physics: Energy, Information & Life (Freeman, 2003)

Ken Dill, Sarina Bromberg, Molecular Driving Forces: Stat Thermo in Chem & Biol (Routledge, 2002)

Jonathon Howard, Mechanics of Motor Proteins and the Cytoskeleton (Sinauer, 2001)

Prerequisite Courses:

This course is open to both advanced upper level undergraduates and graduates. Basic knowledge in Molecular Biology and Cell Biology, Calculus are expected.

Honor system: You are expected to abide by the Virginia Tech honor system (see http://www.honorsystemvt.edu). You are encouraged to discuss homework assignments with other students in the class, but should finish all by yourself.

Special Needs: If you need adaptations or accommodations because of a disability (learning disability, attention deficit disorder, psychological, physical, etc.), if you have emergency medical information to share, or if you need special arrangements in case the building must be evacuated, please make an appointment with me as soon as possible. I will respect your privacy and do everything I can to provide a supportive, comfortable learning environment.

Tentative schedule

Class	Month	Date	Day	Topic
1	January	15	T	Introduction to quantitative modeling
2		17	Th	Spring models and applications
3		22	T	Using XPP
4		24	Th	Spring models and applications
5		29	T	Thermodynamics and Biology
6		31	Th	No class
7	February	5	T
8		7	Th
9		12	T
10		14	Th	Statistical mechanics of simple systems
11		19	T
12		21	Th
13		26	T	Random walk: polymer
14		28	Th
	March	4	T	Spring Break
		6	Th	Spring Break
15		11	T	Rate equation formalisms
16		13	Th
17		18	T	Protein interaction networks
18		20	Th
19		25	T	Metabolic networks
20		27	Th
21	April	1	T	Gene regulatory networks
22		3	Th	Random walk: diffusion, transport
23		8	T
24		10	Th	cytoskeleton
25		15	T
26		17	Th	Protein motors
27		22	T
28		24	Th	Student presentation
29		29	T