PHY7097 – Selected Topics in Biological Physics

Fall 2020, course number PHY7097-0919 (27206), also as PHY4095-762B (27904)

Classes:

Tuesday & Thursday, 1:55 – 3:25 PM (Period 7 – 8.5)
Classes will be delivered online at the zoom link: https://ufl.zoom.us/j/95342437256 (passcode will be sent separately)

Instructors:

Prof. BingKan Xue (primary)

  • Email: b.xue@ufl.edu
  • Phone: 2-6973
  • Office: NPB 2328
  • Office Hour: Tuesday & Thursday, 5:10 – 6:00 PM

Prof. Purushottam Dixit
Prof. Juan Guan
Prof. Stephen Hagen

Objectives:

The goal of this course is to provide students with a broad overview of important topics in biological physics. The field of biological physics has grown from a few classic applications of physics methods to biological systems to a diverse collection of emerging topics that bring new perspectives on both biology and physics. This course will help students to familiarize with the wide range of classic and new topics (see Schedule). We will learn about these topics through reading the original research articles that had major influences on the field, so that the students can see and appreciate biophysics research at its best.

Prerequisites:

This course should be accessible to graduate students from a broad background. It is recommended for early-year graduate students who are considering or have chosen to work on biological physics. It can also be appreciated by senior undergraduate students (with permission from the instructor) or graduate students from other fields who are interested in learning about the scope of biophysics research. Basic knowledge and quantitative skills of undergraduate physics would be useful; no training in biology is required, though some exposure to the subject would be helpful.

Textbooks:

No textbook is required. We will read research articles from scientific journals, which can be accessed online (through subscription provided by UF Libraries, may require VPN) and will also be uploaded to our Canvas website.

Description:

The course will be taught jointly by multiple biophysics faculty, each covering a few selected topics within their expertise. We will generally learn about one topic every week and read one paper per class. The topics are organized according to “themes” that appeal to a physics style, i.e., common patterns and general principles found in various biological systems.

We will meet twice a week, about 1.5h each time. The class time is divided into a lecture (~50min) and a discussion (~30min), with a short break in between. During the lecture, the instructor will go over the background of the topic, the main idea of the particular paper and its impact, and more recent developments of the subject. In the discussion, the students will answer questions from the instructor and other students on the details of the paper.

Assignments:

The papers to read each week are listed in the Schedule below. The students are expected to have read the paper before the class (should take 1~2 hours) and to come with questions. We will let the students take turns to lead the discussion for each class. The leader will invite questions and elicit answers from other students, so that everyone understands the paper. After the discussion, there will be a quiz (10 min) containing questions on the paper that all students have to take (on Canvas).

At the end of the semester, every student will finish a small project related to one of the topics covered in the course. The project can be, for example, a follow-up on one of the topics to find and summarize new developments or address a simple question that was not answered before. Some projects will be suggested by the instructors during the semester, but the students are welcome to find their own projects. Each student should discuss the choice of project with one of the instructors two weeks before classes end (by Thanksgiving). As the final exam, every student will write a report (~2 pages) on the project and give a short presentation (~12 min) to the class.

Schedule:

Please check back periodically as the schedule may be adjusted. (download list or table)

Date Instructor Topic Reading
Tue 09/01 Xue Genetic and Phenotypic Variations:
Mutation and resistance
SE Luria & M Delbruck, Mutations of bacteria from virus sensitivity to virus resistance, Genetics 28, 491-511 (1943).
Thu 09/03 Xue Genetic and Phenotypic Variations:
Bacterial persistence
NQ Balaban, J Merrin, R Chait, L Kowalik & S Leibler, Bacterial persistence as a phenotypic switch, Science 305, 1622-1625 (2004).
Tue 09/08 Xue Phenomenological Models:
Bacterial growth laws
M Scott, CW Gunderson, EM Mateescu, Z Zhang & T Hwa, Interdependence of cell growth and gene expression: origins and consequences, Science 330, 1099-1102 (2010).
Thu 09/10 Xue Phenomenological Models:
Cell-size maintenance
S Jun & S Taheri-Araghi, Cell-size maintenance: universal strategy revealed, Trends Microbiol 23(1), 4–6 (2015).
Tue 09/15 Xue Dimensional Reduction:
Behavioral dynamics
GJ Stephens, B Johnson-Kerner, W Bialek & WS Ryu, Dimensionality and dynamics in the behavior of C. elegans, PLoS Comput Biol 4, e1000028 (2008).
Thu 09/17 Dixit Dimensional Reduction:
Gene expression
L Haghverdi, F Buettner & FJ Theis, Diffusion maps for high-dimensional single-cell analysis of differentiation data, Bioinformatics 31(18), 2989–2998 (2015).
Tue 09/22 Xue Dynamical Systems and Networks:
Ecological stoichiometry
T Andersen, JJ Elser & DO Hessen, Stoichiometry and population dynamics. Ecol Lett 7(9), 884–900 (2004).
Thu 09/24 Dixit Dynamical Systems and Networks:
Genetic circuits
MB Elowitz & S Leibler, A synthetic oscillatory network of transcriptional regulators, Nature 403, 335-338 (2000).
Tue 09/29 Dixit Material and Energy Balance:
Flux Balance Analysis
JS Edwards, RU Ibarra & BO Palsson, In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data, Nat Biotechnol 19, 125–130 (2001).
Thu 10/01 Dixit Material and Energy Balance:
Thermodynamic constraints
DA Beard, SD Liang & H Qian, Energy balance for analysis of complex metabolic networks, Biophys J 83(1), 79–86 (2002).
Tue 10/06 Dixit Statistical Descriptions:
Protein sequences
F Morcos, A Pagnani, B Lunt, A Bertolino, DS Marks, C Sander, R Zecchina, JN Onuchic, T Hwa & M Weigt, Direct-coupling analysis of residue coevolution captures native contacts across many protein families, Proc Natl Acad Sci USA 108 (49), E1293 (2011).
Thu 10/08 Dixit Statistical Descriptions:
Neural activity
L Meshulam, JL Gauthier, CD Brody, DW Tank & W Bialek, Coarse graining, fixed points, and scaling in a large population of neurons, Phys Rev Lett 123, 178103 (2019).
Tue 10/13 Xue Representation and Encoding:
Associative memory
JJ Hopfield, Neural networks and physical systems with emergent collective computational abilities, Proc Natl Acad Sci USA 79, 2554 (1982).
Thu 10/15 Hagen Representation and Encoding:
Olfaction codes
B Malnic, J Hirono, T Sato & LB Buck, Combinatorial receptor codes for odors, Cell 96(5), 713-723 (1999).
Tue 10/20 Hagen Sensing and Navigation:
Concentration sensing
HC Berg & EM Purcell, Physics of chemoreception, Biophys J 20, 193 (1977).
Thu 10/22 Hagen Sensing and Navigation:
Bacterial chemotaxis
HC Berg & DA Brown, Chemotaxis in Escherichia coli analysed by three-dimensional tracking, Nature 239, 500–504 (1972).
Tue 10/27 Hagen Stochastic Fluctuations:
Stochastic gene expression
MB Elowitz, AJ Levine, ED Siggia & PS Swain, Stochastic gene expression in a single cell, Science 297, 1183 (2002).
Thu 10/29 Guan Stochastic Fluctuations:
Transcriptional burst
I Golding, J Paulsson, SM Zawilski & EC Cox, Real-time kinetics of gene activity in individual bacteria, Cell 123(6), 1025 (2005).
Tue 11/03 Guan Nonequilibrium Dynamics:
Active matter
A Yildiz, JN Forkey, SA McKinney, T Ha, YE Goldman & PR Selvin, Myosin V walks hand-over-hand: Single fluorophore imaging with 1.5-nm localization, Science 300, 2061 (2003).
Thu 11/05 Hagen Nonequilibrium Dynamics:
Kinetic proofreading
JJ Hopfield, Kinetic proofreading: A new mechanism for reducing errors in biosynthetic processes requiring high specificity, Proc Nat Acad Sci USA 71, 4135 (1974).
Tue 11/10 Hagen Pattern Formation:
Turing pattern
AM Turing, The chemical basis of morphogenesis, Phil Trans R Soc Lond B237, 37 (1952).
Thu 11/12 Guan Pattern Formation:
Embryonic development
CP Brangwynne, CR Eckmann, DS Courson, A Rybarska, C Hoege, J Gharakhani, F Julicher & AA Hyman, Germline P granules are liquid droplets that localize by controlled dissolution/condensation, Science 324, 1729 (2009).
Tue 11/17 Guan Novel Phases of Matter:
Phase separation
P Li, S Banjade, HC Cheng, S Kim, B Chen, L Guo, M Llaguno, JV Hollingsworth, DS King, SF Banani, PS Russo, QX Jiang, BT Nixon & MK Rosen, Phase transitions in the assembly of multivalent signalling proteins, Nature 483, 336 (2012).
Thu 11/19 Xue Novel Phases of Matter:
Collective behavior
T Vicsek, A Czirok, E Ben-Jacob, I Cohen & O Shochet, Novel type of phase transition in a system of self-driven particles, Phys Rev Lett 75, 1226 (1995).
Tue 11/24 choice of final project
Tue 12/01 Guan Optical Limit and Imaging:
Single-molecule detection
J Elf, GW Li & XS Xie, Probing transcription factor dynamics at the single-molecule level in a living cell, Science 316, 1191 (2007).
Thu 12/03 Guan Optical Limit and Imaging:
Super-resolution techniques
M Bates, B Huang, GT Dempsey & X Zhuang, Multicolor super-resolution imaging with photo-switchable fluorescent probes, Science 317, 1749 (2007).
Tue 12/08 preparation for final project
Thu 12/17 10-12PM presentation of final project

 

Grading:

The final grade will consist of both the class quizzes (50%) and the final project (50%):

  • The quiz will be taken right after each class (3:25-3:35PM). Each quiz will be graded on a 0-5 scale. There are 26 quizzes in total but your lowest one will be dropped when calculating the average score.
  • The project will serve as the final exam (due Thu 12/17 at noon). It will be graded by all instructors on both the presentation (25%) and the report (25%); the average score among instructors will be used.

Attendance at all class meetings is expected. A student who seeks a makeup for missed work should contact the instructor as soon as practical and be prepared to document any excuse. See detailed policies below.


Requirements for class attendance and make-up exams, assignments, and other work in this course are consistent with university policies that can be found at:
https://catalog.ufl.edu/UGRD/academic-regulations/attendance-policies/

Students with disabilities who experience learning barriers and would like to request academic accommodations should connect with the disability Resource Center by visiting:
https://disability.ufl.edu/students/get-started/
It is important for students to share their accommodation letter with their instructor and discuss their access needs, as early as possible in the semester.

Information on current UF grading policies for assigning grade points may be found at:
https://catalog.ufl.edu/UGRD/academic-regulations/grades-grading-policies/

Evaluation:

Students are expected to provide professional and respectful feedback on the quality of instruction in this course by completing course evaluations online via GatorEvals. Guidance on how to give feedback in a professional and respectful manner is available at:
https://gatorevals.aa.ufl.edu/students/
Students will be notified when the evaluation period opens, and can complete evaluations through the email they receive from GatorEvals, in their Canvas course menu under GatorEvals, or via ufl.bluera.com/ufl/. Summaries of course evaluation results are available to students at:
https://gatorevals.aa.ufl.edu/public-results/