Meets Monday,Wednesday 17:30-18:45 Physics Room 5
Instructor: Prof. Keith Lidke
Room 1140, Physics and Astronomye-mail: klidke@unm.edu
phone: (505)277-0302
Text
There is no required text, but the following are recommended. These will be supplemented by many other sources.
Syllabus
Flyer about Course Content: Phys480_Biophysics FlyerGrading
Using this grading scale, grades will be assigned based on the following:Homework Assignments (30%)
All homework assignments and due dates will be posted here on this website. Since we will often have discussions about homework problem results, no late homework will be accepted.Lab reports (30%)
This course will include approximately eight mini-laboratories intended to familiarize the student with common techniques employed in a biophysics lab. For each laboratory, each lab group will submit a lab write up of no more than 2 pages.Quizes(20%)
Quizes will cover basic cell and molecular biology concepts and terminology.Final Exam (20%)
Homework Assignments, Labs and Quizes
Homework #1. Due August 29. Homework #1 Solutions m-file. Due August 29. HW/HW1Solutions.png
Lab one is due September 9. Your group must submit one PDF file. The report is limited to two pages. Include a short derivation of the equilibrium concentration of the beads as a function of height. Show a combined plot of the c(z) vs z for the five different beads. Give concentration in units of Molar. The beads were 2.0, 1.0, 0.5, 0.2 and 0.1 microns in diameter. Assume they were each contained in a cylinder with radius 2.5 mm, that the total volume was 500 microliters, and that the total bead volume was 0.2% of the total volume. Relate your calculation to your observation in the microscope.
Lab two is due September 21. Your group must submit one PDF file. The report is limited to two pages. Include a calculation of the initial pH (after adding Tris) and how much volume of 1M HCl was needed to reach pH 8.0. Compare your calculations to your observations. At pH 8.0, calculate the ratio [TrisH+]/([Tris]+[TrisH+]).
BioChem1 BioChem Quiz #1 will be Wednesday, September 21.
Homework #2. Due September 28. Solutions: HW2_Solutions HW2_1.m PB_ShootingMethod_Plane.m PB_ShootingMethod_Sphere.m
Lab three is due October 5. Your group must submit one PDF file. The report is limited to two pages. Identify and quantify the samples that you measured. Include a derivation of the Beer-Lambert law. spectroscopy lab.xlsx
Lab four is due November 2. Your group must submit one PDF file. The report is limited to two pages. Analyze at least one single particle trajectory that is 100 frames or longer. Your report must include a figure showing the trajectory, a mean square displacement plot, and a description of the mathematics used in your analysis.
Anonymous-2011-10-19-18-58.mat
Anonymous-2011-10-19-19-0.mat
GroupAwesome2-2011-10-19-18-38.mat
GroupAwesome-2011-10-19-18-37.mat
LosRenegados-2011-10-19-19-26.mat
LosRenegados-2011-10-19-19-27.mat
Homework #3. Due November 9. HW3_Solutions HW3_2.m
Lab five is due November 21. Your group must submit one PDF file. The report is limited to two pages. Analyze at least one movie and make an estimate of the filtration coefficient. State all your assumptions. Place upper and lower bounds on the value. Clearly state your reasoning.
Group1Cell1-2011-11-7-17-57.mat
Group1Cell2-2011-11-7-18-4.mat
Group1Cell3-2011-11-7-18-7.mat
Group2Cell1-2011-11-7-18-24.mat
Group2Cell2-2011-11-7-18-31.mat
Group2Cell3-2011-11-7-18-37.mat
Group3Cell1-2011-11-7-18-48.mat
Group3Cell2-2011-11-7-18-54.mat
Group3Cell3-2011-11-7-18-58.mat
BioChem2 BioChem Quiz #2 will be Wednesday, November 30.
Homework #4. Due December 5.
Reference Material
Lecture PDFs
PDF1: DNAPDF2: RNA and Proteins
Protein Structure
Polymers
Lipids
Links
Fluorescence Correlation Spectroscopy:An Introduction to its Concepts and ApplicationsKochLab 1064 Optical tweezers
real-life Tetris under a microscope
PhET interactive Optical Tweezers
DipImage Example startup.m
Link to a short MATLAB class that has examples posted
YouTube:DNA to Protein
UNM Matlab Download/Install
Online Searching of "Molecular Biology of the Cell"
MBOC: The Shape and Stucture of Proteins
Laminar Flow Video
Fluorescence Super-Resolution
MATLAB
PSFfit.m BlobMLE_Fast.mEntropy.m
Diffusion2DExample.m
PlottingPDFandHistogram.m
DiffusionInGravity.m
FitExample.m
LSQfunc.m
SPTexample.m
DiffusionInPotentialWell.m
GenTestVector.m