### “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 Physics*, **81**: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 Physics*, **84**: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:

CalcDfromTrackResults, ProcessTrackResults, GetRidofBlanks

**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

**Modern Laboratory Blog**

Somewhere in my first year as a professor I realized I was running my laboratory all wrong! The undergraduates couldn’t follow the chicken scratch in the lab notebook that detailed how to make samples, the external hard drives we were using to store data kept breaking, and preparation for lab meetings was taking over my student’s week. This is in addition to the normal woes of the ever increasing load of administrative tasks and teaching requirements. So to procrastinate, I started searching for a way to get things done faster, make things simpler, or do things better using technology. And to my surprise, solutions did exist. The Modern Laboratory is my “captain’s log” of those solutions in blog format. Of course, this is not a real blog since I only post things here when I get a chance. Also take a look at my editorial in AJP that details some of my fumbles and fixes. Check out the blog here.

**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 S2021**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

**ALPhA**

**•**Advanced Laboratory Physics Association