PH475 Intro Biophysics I (Fall, 2020)

Last modified on August 27, 2020

Messages from Instructor:

  • [8/17] Class will meet on Aug 25 at 9:30am in ZOOM.

Course Format: Remote
This course is based on the mixture of prereorded video lectures and online live meetings. There is no in-person component.

Study cycle

  1. Read a lecture note and corresponding sections of the textbook
  2. Watch the corresponding video lecture.
  3. Attend the corresponding Q&A session.
  4. Solve homework problems.
  5. Work on your project.


Video Lectures: Asynchronous
All lectures are prerecorded video streamed from the course web site. Go to course schedule and click the topics of a lecture. Then, you will find videos. Students are required to watch each video lecture before the date given in the course schedule.


Q&A session, Exercise, and Discussion: Online Live Meeting
Students are required to attend live online session in ZOOM held during the regular class hours (Tue. & Thu. 9:30am -- 10:45am). Topics of the discussion are listed in the course schedule. The discussion will be recorded and the videos are available if you should have missed the sessions. Please try to attend the live meeting as much as possible.


Required Textbook


Physical Biology of the Cell
by R. Phillips et al.
Garland Science, 2012
ISBN: 978-0815344506

Links

Course Description:
Through this course students will learn how the laws of physics play important roles in biological processes in living cells through examples.


Learning Objectives:

Biophysical processes involved in the following biological processes

  • Diffusion of macromolecules
  • Motor proteins and Brownian motors
  • Entropic force
  • Electrostatics in biological cell
  • Chemical oscillations (neurons, β cell, ...)
  • Wave phenomena (potential waves, chemical waves)
  • Allostery coupling
  • Protein Folding
  • Self-Assembly (polymerization, micell, ...)
  • Neuron and network of newurons
  • Synchronization (neural network, insulin secretion, ...)
  • Pattern formation

Homework

Ten homework problems will be given. Homework must be turned in electronically by email.  Allowed formats are PDF (.pdf), MATLAB script file (.m), Mathematica notebook (.nb). Hand written pages should be scanned in PDF. Do not send picture taken by a cellphone camera app. Use scanner app instead. Microsoft Office Lens (a free app for Android and iPhone) is recommended.


Projects

There is no paper exam in this course. Students must complete either a theoretical or a computational project and write a term paper. Proposal, abstract, drafts, and final paper must be submitted as scheduled in the project page. Late submission will result in the substantial loss of points.


Grading

Homework carries 50 pts and the term paper 50 pts.

Grade Total Score
A 85 or above
B 75 or above
C 65 or above
D 55 or above
F Otherwise

Where the university can, it is providing a Pass/Fail option in case there are circumstances and/or challenges students are encountering related to the ongoing pandemic that might make a Pass/Fail option a better option. If students are not remaining with the default letter grade method for any of their courses, they must select the Pass/Fail grading method for each course individually. This selection is made toward the end of the semester. Once a student selects the option for a Pass/Fail grading method for a particular course, that decision is not reversible regardless of their performance on remaining assignments or final exams.


MATLAB

MATLAB is used in all lectures. The use of MATLAB is required in this course. UAB has a site license and students are elligible to install MATLAB on their computer. Installation instruction is given at https://docs.uabgrid.uab.edu/wiki/Matlab_site_license


Python

Python is another popular computer language. Although we use MATLAB as main language in the lectures, Phython 3 is also supported. If you wish to use Python, Anadonda package is recommended for Microsoft Windows and Mac. (Linux is also supported by Anaconda but it is better to use the python package included in yourLinux distros.) The instructor uses Python 3 (Not Python 2). Download Anaconda for Python 3.7 at https://www.anaconda.com/download/. Every Linux distribution inlucdes Python 3. Use a software installer in your Liux system.

About Instructor

I am available to meet with you virtually via Zoom by appointment during my virtual office hours shown below. Please make an appointment via email.


Dr. Ryoichi Kawai

Virtual Office Hour: Tue. 1-2pm, Thu. 3-4pm
Tel: (205) 934-3931
Fax: (205) 934-8042
Email: kawai@uab.edu
(My PGP public key)

Address

Campbell Hall 309
Department of Physics
University of Alabama at Birmingham
1300 University Blvd.
Birmingham, AL 35294

© Dr. Ryoichi Kawai, 2020 All Rights Reserved. No part of this website or any of its contents may be reproduced, copied, modified or adapted, without the prior written consent of the author, unless otherwise indicated for stand-alone materials.

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