Physics 171.310: Spring 2013

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 Tuesday in Bloomberg 278
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 1st Edition by Philip Nelson (Paperback: ISBN-10: 0716798972 or ISBN-13:978-0716798972)
    Recommended:       Intermediate Physics for Medicine and Biology, 4th 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 (25%), lab 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. Students are expected to attend all lectures, labs, and sections, and to complete all assignments and exams. 

 

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.

 

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. 28

Basics of probability, statistical physics

Nelson 1-3

Feb. 4

Boltzmann distribution, Brownian motion

Nelson 3-4

Feb. 11

Friction and Diffusion

Nelson 4

Feb. 18

Life at low Reynolds number

Nelson 5, First lab

Feb. 25

Low-R applications

Nelson 5

March 4

Statistical physics: entropy, temperature and free energy

Nelson 6, Second lab, FIRST MIDTERM

March 11

Statistical physics continued

Nelson 6

March 18

SPRING BREAK

 

March 25

Entropic forces

Nelson 7

April 1

Chemical forces

Nelson 7-8, third lab

April 8

Chemical reactions

Nelson 8

April 15

Membrane Transport

Nelson 11, SECOND MIDTERM

April 22

Ion pumping, nerve impulses

Nelson 11-12

April 29

Nerve conduction: Hodgkin-Huxley model

Nelson 12

May 14

Final Exam  2 PM 

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.