Teaching

dna

“Plug and Play” Experiments in Biophysics

Interdisciplinary training is becoming more important as diverse fields intersect and researchers investigate the boundaries between disciplines. Here we develop experiments that can be “plugged” into many different courses and “played” on a single day or over several weeks. These experiments must meet many different theoretical, computational, and experimental goals, which allow instructors to tailor the experiment to their needs. The laboratories we propose introduce a biophysical concept, measure a biophysical quantity, and require students to use equipment relevant to modern research laboratories. These requirements ensure that the laboratories are rich enough to meet multiple experimental, computational, and theoretical goals.

1. Plug and Play, 3D Experiments
Read this publication about creating laboratory courses with plug and play experiments that are also 3D. That is they have 3 different types of goals: theoretical, computational, and experimental.
Publication:A. R. Carter, “Case study on how to develop 3D labs with theoretical, experimental, and computational goals.” Proceedings of BFY. (2018). PDF
Resources: 
Presentation at BFY III
Example Waves Laboratory Manual
Goals and Practices BLANK
Goals and Practices EXAMPLE
Course Evaluation

2. Measuring the Brownian Motion of Particles in Water
Biophysical concept: Brownian motion
Biophysical quantity: viscosity of water
Equipment: microscopy
Publication: M. A. Catipovic, P. M. Tyler, J. G. Trapani, and A. R. Carter, “Improving the quantification of Brownian motion.” American Journal of Physics81:485 (2013). PDF
Talks and Demonstrations: Beyond First Year Labs Conference 2012, AAPT summer meeting 2014, Gordon Research Conference 2014
Resources: Brownian Motion Simulator in IGOR

3. Using an AFM to Image Cells, Microtubules, and DNA
Biophysical concept: basic polymer physics and models of DNA (freely jointed chain, worm-like chain), membrane dynamics
Biophysical quantities: persistence length, contour length, radius of gyration, membrane tension, stretching force
Equipment: AFM
Publication: L. M. Devenica, C. Contee, R. Cabrejo, E. F. Deveney, and A. R. Carter, “Biophysical Measurements of Cells, Microtubules, and DNA with an Atomic Force Microscope.” American Journal of Physics84:301 (2016). PDF
Talks and Demonstrations: Beyond First Year Labs Conference 2015, AAPT summer meeting 2015, ALPhA Immersion 2016

4. Training Module in Optics
Biophysical concept: optics and optical alignment
Biophysical quantities: magnification and resolution limits
Equipment: lenses, mirrors, irises, optomechanical components, optical breadboard
Publication:
Talks and Demonstrations: AAPT summer meeting 2017
Resources:
Presentation at AAPT
Optics Rules to Live By document on best practices for optical alignment

ezLectures

ezLectures are online lectures located on YouTube that students can watch independently. Typically, these lectures supplement the material taught in class, and are therefore designed to stand alone. If you are an instructor, feel free to use any of these lectures in your courses. If you would like more information, please contact me.

Series on Data Analysis in IGOR Pro
Being able to manipulate and graph data in a powerful data analysis tool like IGOR is a must when doing research. To learn how to use this tool, open the tutorial and complete the tasks laid out for you. The tutorial will ask you to watch a series of ezLectures on IGOR Pro, which are listed here.

Data Analysis TUTORIAL
ezLecture Loading Data in IGOR
ezLecture Graphing with IGOR
ezLecture Command line in IGOR
ezLecture IGOR procedures

Series on Tracking using ImageJ
There are all sorts of reasons you might want to track an object in a video. Perhaps you are watching the motion of a particle in a fluid to determine the properties of the fluid, such as viscosity, flow, or elasticity. Perhaps you are tracking the motion of fly larva or zebrafish as they execute a complicated behavior. Or perhaps you are watching the motion of a projectile to determine air resistance and lift. In all of these cases, you need to track an object in a video, which can get quite complicated. A quick and easy method is to use the MTrack2 Plug-in available in the free software program ImageJ. In this tutorial, we will walk you through how to track fluorescent particles in water to determine their diffusion coefficient.

Tracking using ImageJ TUTORIAL
ezLecture Tracking using ImageJ
     Brownian motion data available as a Zip.
     Igor Procedures for analyzing Brownian motion:
CalcDfromTrackResultsProcessTrackResultsGetRidofBlanks

Series on Concepts in Intermediate Mechanics
Many physics students take intermediate mechanics. This is a popular course where students learn about Lagrangians, drag, orbital motion, and oscillations. In the version of the course at Amherst, we use Taylor’s Classical Mechanics. This is a great text, but there is too much material for a one semester course. In this lecture series, we go through some of the main math and physics concepts that students need to learn to be successful in intermediate mechanics. These ezLectures are designed as a supplement to the in-class lectures. They are not comprehensive and are just used to introduce some concepts before the week of class begins.

ezLecture Non-Cartesian Coordinate Systems
Non-Cartesian Coordinate Systems NOTES
Non-Cartesian Coordinate Systems TUTORIAL

ezLecture Drag
Drag NOTES
Drag TUTORIAL

ezLecture Differential Equations Part 1
Differential Equations Part 1 NOTES
Differential Equations Part 1 TUTORIAL

ezLecture Differential Equations Part 2
Differential Equations Part 2 NOTES
Differential Equations Part 2 TUTORIAL

ezLecture Calculus of Variations
Calculus of Variations NOTES
Calculus of Variations TUTORIAL

ezLecture Orbital Motion
Orbital Motion TUTORIAL

Amherst Class Websites

PHYS 112 • Electronics (general lab course for non-majors) • F2018
PHYS 116 • Introductory Physics I – Mechanics (with calculus for non-majors) • F2010 S2011 S2020 F2020
PHYS 117 • Introductory Physics II – E&M (with calculus for nonmajors) • F2015 S2016 F2016 F2017
PHYS 124 • Maxwellian Synthesis (intro electricity and magnetism for majors) • S2012 S2013 S2014
PHYS 125 • Waves (waves, acoustics and optics for majors) • F2018
PHYS 147 • Maker Optics (general lab course for science majors) • S2018
PHYS 343 • Dynamics (intermediate mechanics for majors) • F2011 F2012 F2013
BCBP 400 • Molecular and Cellular Biophysics (capstone course for majors) • F2011 F2012 F2013 S2016 S2018

Teaching Resources

JAUPLI • Journal of Advanced Undergraduate Physics Laboratory Investigation
ComPADRE •  Database of physics instructional material.