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Physics 420

Introduction to Biophysics – Fall 2018

Time: Tue, Fri 9:10-11:00 AM Place: 1311 HN
Instructor:
Associate Professor Hyungsik Lim
Email: Hyungsik.Lim@hunter.cuny.edu
Office: 1237 Hunter North, 695 Park Avenue
Office hours: by appointment

Pre-requisites or Co-requisites: Permission of instructor
Description: The goal of this course is two-fold; 1) to learn how to build a simple physical model to produce testable predictions for diverse living systems from gene expression to neural networks and 2) to understand modern techniques that opened the fields of molecular biophysics.
Recommended texts:
"Physical Biology of the Cell", Rob Philips, Jane Kondev, and Julie Theriot
"Molecular Driving Forces", Ken Dill and Sarina Bromberg
"Biological Physics: Energy, Information, Life", Philip Nelson
Grading: Homework 20%: Midterms 40%: Final 40%.

Preliminary Class Schedule:

Week 1 8/28 Biology in Numbers 8/31 Random Walk Model
Week 2 9/4 Random Walk I: DNA 9/7 Random Walk II: Protein
Week 3 9/11 No class 9/14 Two-state System I HW#1
Week 4 9/18 No class 9/21 Two-state System II
Week 5 9/25 Chemical Reaction I 9/28 Chemical Reaction II
Week 6 10/2 Midterm #2 10/5 Cooperativity I HW#2
Week 7 10/9 Cooperativity II 10/12 Allostery I
Week 8 10/16 Allostery II 10/19 Network I
Week 9 10/23 Network II 10/26 Kinetics of Two-state System HW#3
Week 10 10/30 Random Telegraph Model 11/2 Bursting I: Ion Channel
Week 11 11/6 Bursting II: Transcription 11/9 Midterm #2
Week 12 11/13 Excitable Membrane I 11/16 Excitable Membrane II HW#4
Week 13 11/20 Hodgkin-Huxley Model I 11/23 No class
Week 14 11/27 Hodgkin-Huxley Model II 11/30 Biophysics of Computation
Week 15 12/4 Biotechniques I 12/7 Biotechniques II HW#5
Week 16 12/11 Biotechniques III 12/14 Final Exam

Final Exam: 12/14/2018 9:10 ‐ 11:00 AM

Policy:
Hunter College regards acts of academic dishonesty (e.g. plagiarism, cheating on examinations, obtaining unfair advantage, and falsification of records or official documentations) as serious offenses against the values of intellectual honesty. The college is committed to enforcing the CUNY Policy on Academic Integrity and will pursue cases of academic dishonesty according to the Hunter College Academic Integrity Procedures.
http://www.hunter.cuny.edu/studentservices/advising/policies-sub/policies-academic-integrity

Table of Contents
Introduction - Biology in Numbers
Random Walk Model
  Random Walk Model I: Brownian Motion and Diffusion
  Random Walk Model II: Conformation of Linear Biomolecules
  *Random Walk Model III: Motility in Low Reynolds Number
Two-State System: Adding Energy to Random Walk Model
  Two-State System I: Modulating Equilibrium by Temperature and Energy
  Two-State System II: Diffusion of Molecular Motors under Force
  Two-State System III: Conformation of Linear Biomolecules under Force
Actuation of Two-State Systems by Ligand Binding
  Laws of Chemical Reaction
  Cooperative Binding: Pauling Model
  Allostery: Monod-Wyman-Changeux Model
  Ion Channels and Transcription Factors
Two-State System with Feedback: Bistability and Oscillation
*Network of Two-State Systems with Interaction: Ising Model
Nonlinear Membrane: Hodgkin-Huxley Model
  Electrical Properties of Excitable Membranes
  Generation of Action Potentials
  Conduction of Action Potentials
Fluctuating Single Molecules
  Kinetics of Two-State System: Poisson Process
  Bistable Neuron and Information Coding
  *Two-State System with Dark State: Bursting Process
Biotechniques
  Optical Tweezer (Single-molecule Force Spectroscopy)
  Förster Resonance Energy Transfer (FRET)
  Fluorescence Correlation Spectroscopy (FCS)

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