BIOREPS

BIOphysical REsearch Problem Sets:
a database of problem sets based on biophysics research articles,
a free resource for educators and students

HeLa cells stained with the actin binding toxin phalloidin (red), microtubules (cyan) and cell nuclei (blue). Source: NIH [public domain]

Overview

The BIOREPS database is an initiative of the Biotheory Group in the Physics Department of Case Western Reserve University, in collaboration with students from PHYS 320/420, "Introduction to Biological Physics", taught every fall semester. As a final project, groups of students from the course create entirely new problem sets based on recent biophysical research articles. Each set consists of a brief background essay describing the context of the problem, followed by a series of questions that reconstruct some of the analytical and/or numerical calculations in the paper (or perform an analysis of data).

The sets are made openly available in the BIOREPS online database, in both PDF form and as ZIP files containing LaTeX source code. The latter can be freely re-used and modified by educators in other institutions under a Creative Commons CC BY-NC 4.0 license. Future students of PHYS 320/420 also use the sets as actual homework, thus ensuring that the course materials remain up-to-date, reflecting the latest advances in the field. For those using the sets in teaching similar courses, or for self-study, solutions are available by contacting the project administrator.

Project support:
National Science Foundation grant BIO/MCB #1651560  
Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

Problem Set Database

Creative Commons License
The PDFs and LaTeX source code for the BIOREPS problem sets are licensed under a Creative Commons Attribution-NonCommercial 4.0 International License. Solutions are available upon request.

1. Switching dimensions: beating the diffusion speed limit

PDF TeX
Author: M. Hinczewski
Based on: L. Mirny et al., "How a protein searches for its site on DNA: the mechanism of facilitated diffusion", J. Phys. A: Math. Theor. 42, 434013 (2009). DOI

2. The perils of prions: mad cows and cannibals

PDF TeX
Author: M. Hinczewski
Based on: Knowles, T.P. et al., "An analytical solution to the kinetics of breakable filament assembly", Science 326, 1533 (2009). DOI

3. Chaperones to the rescue

PDF TeX
Author: M. Hinczewski
Based on: M.J. Todd, G.H. Lorimer, D. Thirumalai, "Chaperonin-facilitated protein folding: Optimization of rate and yield by an iterative annealing mechanism", Proc. Natl. Acad. Sci. USA 93, 4030 (1996). DOI

4. Adaptation and cooperation

PDF TeX
Author: M. Hinczewski
Based on: C.H. Hansen, R.G. Endres, N.S. Wingreen, "Chemotaxis in Escherichia coli: a molecular model for robust precise adaptation", PLoS Comput. Biol. 4, e1 (2008). DOI

5. A tale of two scallops

PDF TeX
Author: M. Hinczewski
Based on: E. Lauga, D. Bartolo, "No many-scallop theorem: Collective locomotion of reciprocal swimmers", Phys. Rev. E 78, 030901R (2008). DOI

6. Cost and precision of Brownian clocks

PDF TeX
Authors: N. Kodama, B. Kuznets-Speck, J. Moran, S. Musilli, N. Ramey, C. Weisenberger
Based on: A.C. Barato, U. Seifert "Cost and Precision of Brownian Clocks" Phys. Rev. X 6, 041053 (2016). DOI

7. Models of tumor progression: two-type branching processes

PDF TeX
Authors: M. Beem, B. Eck, M. Kang, A. Krajewski, L. Marcich, C. Reed, B. Shultes, A. Smerglia
Based on: T. Antal, P.L. Krapivsky, "Exact solution of a two-type branching process: models of tumor progression", J. Stat. Mech. P08018 (2011). DOI

8. Hamsters, cows, and infectious dimers: the secret life of prions

PDF TeX
Authors: J. Carlen, E. Larkin, E. Shanley, B. Sunday, L. Thompson, P. Turner, T. Wang
Based on: A.S. Ferreira, M.A. Silva, J.C. Cressoni, "Stochastic Modeling Approach to the Incu- bation Time of Prionic Diseases", Phys. Rev. Lett. 90, 19 (2003). DOI

9. The physics of chemoreception

PDF TeX
Authors: R. Adkins, K. Darrah, A. Ferris, G. Santiago, G. Schumacher, J. Ziegler
Based on: H.C. Berg, E.M. Purcell, "Physics of Chemoreception", Biophys. J. 20, 193 (1977). DOI

10. Of protein carts and DNA railroads: helicase unwinding of DNA

PDF TeX
Authors: M. Blachman, M. Conley, K. Crowley, S. Iram, J. Osborne, K. Premasiri
Based on: M.D. Betterton, F. Jülicher, "A Motor that Makes Its Own Track: Helicase Unwinding of DNA", Phys. Rev. Lett. 25, 81031 (2003). DOI

11. The evolution of DNA strands

PDF TeX
Authors: N. Barendregt, J. Broderick, A. Gross, M. Korman, C. Pozderac, N. Starkman
Based on: C. Arnold, "Evolution Runs Faster on Shorter Timescales", Quanta (2017). Link

12. Signal transduction via protein kinase

PDF TeX
Authors: B. Andrews, R. Bhatt, G. Hildebrandt, N. Shaffer, J. Wang
Based on: R. Heinrich, B.G. Neel, T.A. Rapoport, "Mathematical models of protein kinase signal transduction", Molec. Cell 9, 957 (2002). DOI

13. How a well-adapted immune system is organized

PDF TeX
Authors: C. Cai, Y. Han, G. Hessler, P. Thompson
Based on: A. Mayer, V. Balasubramanian, T. Mora, A.M. Walczak, "How a well-adapted immune system is organized", Proc. Natl. Acad. Sci. USA 112, 5950 (2015). DOI

14. Are bacteria more efficient than us?

PDF TeX
Authors: N. Abuyazid, J. Kishbaugh-Maish, B. Schissel, E. Schnittman, G. Singh
Based on: A. Maitra, K.A. Dill, "Bacterial growth laws reflect the evolutionary importance of energy efficiency", Proc. Natl. Acad. Sci. USA 112, 406 (2014). DOI

Get in touch

If you have any questions about the BIOREPS database, individual problem sets, or requests for solutions, please write the site administrator Michael Hinczewski at: mxh605@case.edu.