Physics 171.310: Spring 2009

Biological Physics

Page Contents:

1. Important Messages From the Professor
2. Professor Contact Information
3. Class Meeting Times
4. Course Description
5. Textbooks
6. Grading, Homework and Labs
7. Syllabus
8. University Policies on Ethics and Disabilities

Messages from the Professor

The final exam is May 13 from 2 to 5PM. The final will cover the entire course, but emphasize material since the second midterm. A review will be held on Sunday, May 10, 2009 at 7PM in Room 278 (where section was held). Be sure to bring questions. This page is the official web page and syllabus. The WEBCT page has assignments, reading, solutions, etc..

Contact Information

Professor	Teaching Assistant
Mark Robbins	Hongyu Guo
mr at jhu.edu	hguo5 at jhu.edu
410-516-7204	410-516-7832
Bloomberg 317	335
Office Hours: Tu 12:30-1:30, W 3:45-4:45	Tu 4-5, Th 1-3

Class:
11-12 AM Monday, Wednesday and Friday in Bloomberg 361
Section: 1:30-2:20PM Thursday in Bloomberg 278. For labs, section will probably be extended.

Course Description:
This course introduces topics of classical statistical mechanics through the study of biological systems. Additional topics include low-Reynolds number hydrodynamics and ionic solutions, via biologically relevant examples such as diffusion, entropic forces, self-assembly, membrane physics and nerve conduction. It is intended for students with an interest in biological inspired physics or the biophysical or biological sciences.

Prerequisite: Physics 171:101-102, 171:103-104 or 171.105-106; Calculus II 110.109.

Textbooks:
Required: Biological Physics: Energy, Information, Life, 2^nd Edition by Philip Nelson
Recommended: Intermediate Physics for Medicine and Biology, 4^th Edition by R. K. Hobbie
Used Math by C. E. Swartz.

Grading:
The grading will be based on homework (25%), labs (5%), two midterms (15% each) and the final exam (40%). If a student's grade on the Final exam is higher than his or her average on the midterm exams, the final exam will be counted for 55% of the grade, and the student¹s worst midterm exam score will be dropped. It is expected that students will attend all lectures, labs, and sections, and complete all assignments, and exams. “Senior Option” is not an option.

Homework:
Solving problems is the only way to learn physics. For this reason, the problem sets are probably the most important part of the course. To get the greatest benefit from the problems sets you should work on every problem yourself before discussing it with others. Subsequent collaboration can be useful and constructive, provided all parties put in equal efforts. While such collaboration is not discouraged, the final writeup must be your own.

Problem sets are due on the Wednesday the week after they are assigned. Late homework will be given reduced credit. No credit will be given for homework more than one week late without prior approval for a compelling reason.

Some exercises require the use of a computer. Computers and software are available in the Physics Undergraduate Computer (PUC) lab in Bloomberg. As a student in Physics 310, you are welcome to use this lab. Please see Brian Schriver in Bloomberg 366G (Dept. Office) for an application form. Mathematica will be the software of choice and you may wish to install it on your own machine. A free temporary license will be available, or a permanent license may be purchased through HITS.

Labs:

There will be periodic laboratory exercises. These will be scheduled at mutually agreed upon times. These will be of an informal nature, but they are instructive and perhaps even fun. Attendance and participation is mandatory, but extensive lab write-ups etc will not be required. A tentative schedule of the labs is given below. We may have to shift the dates of one or more lab.

Syllabus: The syllabus will be updated as the course progresses.

Week of	Subject Matter	Reading/ Lab
Jan. 26	Basics of probability, statistical physics	Nelson 1,2,3
Feb. 2	Boltzmann distribution, Brownian motion	Nelson 3,4
Feb. 9	Friction and Diffusion	Nelson 4, First lab starts
Feb. 16	Life at low Reynolds number	Nelson 5, End of first lab
Feb. 23	Low-R applications	Nelson 5, Start 2nd lab
March 2	Statistical physics: entropy, temperature and free energy	Nelson 6, FIRST MIDTERM March 6
March 9	Statistical physics continued	Nelson 6, Second lab finishes March 12
March 16	Spring Break
March 23	Entropic forces	Nelson 7
March 30	Chemical forces	Nelson 7,8
April 6	Chemical reactions	Nelson 8, SECOND MIDTERM
April 13	Membrane Transport	Nelson 11
April 20	Ion pumping, nerve impulses	Nelson 11-12
April 27	Nerve conduction: Hodgkin-Huxley model	Nelson 12
May 13	Final Exam 2:00-5:00PM	Final Exam

Official University Policies on Ethics and Disabilities

University-wide statement on Academic Ethics

The strength of the university depends on academic and personal integrity. In this course, you must be honest and truthful. Ethical violations include cheating on exams, plagiarism, reuse of assignments, improper use of the Internet and electronic devices, unauthorized collaboration, alteration of graded assignments, forgery and falsification, lying, facilitating academic dishonesty, and unfair competition. As noted above, collaboration on homework sets is encouraged. However, you should attempt problems independently before collaborating and must write up your homework independently.

Report any violations you witness to the instructor. You may consult the associate dean of students and/or the chairman of the Ethics Board beforehand. See the guide on "Academic Ethics for Undergraduates" and the Ethics Board web site (http://ethics.jhu.edu/ ) or http://www.advising.jhu.edu/ethics.html for more information.

Homewood-wide statement on Disabilities

If you are a student with a disability or believe you might have a disability that requires accommodations, please contact Dr. Richard Sanders, Homewood Undergraduate Disability Services Coordinator, in the Office of Academic Advising, Garland Suite 3A, (410) 516-8216, sanders@jhu.edu , to discuss reasonable and appropriate accommodations.