Physics 171.310: Spring 2012

Biological Physics

Page Contents:

1. Important Messages From the Instructor
2. Instructor 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 Instructor

THIS PAGE IS DESIGNED TO PROVIDE ONLY A BASIC INTRODUCTION TO THE COURSE. THE MAIN WEB PAGE CAN BE FOUND ON BLACKBOARD.

Contact Information

Instructor	Teaching Assistant
Robert Leheny	Daniel Allan
leheny at pha.jhu.edu	dallan at jhu.edu
410-516-6442	410-516-8501
Bloomberg 353	349
Office Hours: Tueday, 2:30-4:30	TBD

Class:
11-12 AM Monday, Wednesday and Friday in Bloomberg 361
Section: 1:30-2:20PM Thursday in Bloomberg 361
Labs: The course will hold 3-4 labs during the semester, at times that overlap with the section meeting time.

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, Updated 1^st Edition by Philip Nelson (Paperback: ISBN-10: 0716798972 or ISBN-13:978-0716798972)
Recommended: Intermediate Physics for Medicine and Biology, 4^th Edition by R. K. Hobbie and B. J. Roth (ISBN-10: 0-387-30942-X, ISBN-13: 978-0-387-30942-2)
Used Math by C. E. Swartz (ISBN-10: 0139397361, ISBN-13: 9780917853500)

Grading:
The grading will be based on homework (20%), labs (5%), class participation (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 lower 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 Friday 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.

Preliminary Syllabus: The syllabus is subject to change and will be updated as the course progresses.

Week of	Subject Matter	Reading/ Lab
Jan. 30	Basics of probability, statistical physics	Nelson 1-3
Feb. 6	Boltzmann distribution, Brownian motion	Nelson 3-4
Feb. 13	Friction and Diffusion	Nelson 4
Feb. 20	Life at low Reynolds number	Nelson 5, First lab
Feb. 27	Low-R applications	Nelson 5
March 5	Statistical physics: entropy, temperature and free energy	Nelson 6, Second lab, FIRST MIDTERM
March 12	Statistical physics continued	Nelson 6
March 19	SPRING BREAK
March 26	Entropic forces	Nelson 7
April 2	Chemical forces	Nelson 7-8, third lab
April 9	Chemical reactions	Nelson 8
April 16	Membrane Transport	Nelson 11, SECOND MIDTERM
April 23	Ion pumping, nerve impulses	Nelson 11-12
April 30	Nerve conduction: Hodgkin-Huxley model	Nelson 12
May 16	Final Exam 9 AM	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.