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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)