## 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 Flyer### Grading

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.pngLab 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