{"id":227,"date":"2020-07-17T23:39:27","date_gmt":"2020-07-18T03:39:27","guid":{"rendered":"http:\/\/people.clas.ufl.edu\/b-xue\/?page_id=227"},"modified":"2026-09-14T10:26:33","modified_gmt":"2026-09-14T14:26:33","slug":"phy7097-selected-topics-in-biological-physics-fall-2020","status":"publish","type":"page","link":"https:\/\/people.clas.ufl.edu\/b-xue\/courses\/phy7097-selected-topics-in-biological-physics-fall-2020\/","title":{"rendered":"PHY7097 &#8211; Selected Topics in Biological Physics, Fall 2020"},"content":{"rendered":"\n<section class=\"fullwidth-text-block\"><div class=\"container px-0\"><div class=\"row align-items-start\"><div class=\"col-12\">\n<h1 class=\"wp-block-heading\">PHY7097 \u2013 Selected Topics in Biological Physics, Fall 2020<\/h1>\n\n\n\n<p class=\"wp-block-paragraph\">Fall 2020, course number PHY7097-<span id=\"UF_CAN_CRSE_EMP_DESCR254$1\" class=\"PSEDITBOX_DISPONLY\" aria-disabled=\"true\">0919 (27206), <\/span>also as PHY4095-762B (27904)<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Classes:<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">Tuesday &amp; Thursday, 1:55 &#8211; 3:25 PM (Period 7 &#8211; 8.5)<br>\nClasses will be delivered online at the zoom link: <a href=\"https:\/\/ufl.zoom.us\/j\/95342437256\" target=\"_blank\" rel=\"noopener\">https:\/\/ufl.zoom.us\/j\/95342437256<\/a> (passcode will be sent separately)<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Instructors:<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\"><a href=\"https:\/\/www.phys.ufl.edu\/wp\/index.php\/people\/faculty\/BingKan-Xue\/\">Prof. BingKan Xue<\/a> (primary)<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Email: b.xue@ufl.edu<\/li>\n\n\n\n<li>Phone: 2-6973<\/li>\n\n\n\n<li>Office: NPB 2328<\/li>\n\n\n\n<li>Office Hour: Tuesday &amp; Thursday, 5:10 &#8211; 6:00 PM<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><a href=\"https:\/\/www.phys.ufl.edu\/wp\/index.php\/people\/faculty\/purushottam-dixit\/\">Prof. Purushottam Dixit<\/a><br>\n<a href=\"https:\/\/www.phys.ufl.edu\/wp\/index.php\/people\/faculty\/juan-guan\/\">Prof. Juan Guan<\/a><br>\n<a href=\"https:\/\/www.phys.ufl.edu\/wp\/index.php\/people\/faculty\/stephen-hagen\/\">Prof. Stephen Hagen<\/a><\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Objectives:<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">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 <a href=\"#Schedule\">Schedule<\/a>). 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.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Prerequisites:<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">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.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Textbooks:<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">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 <a href=\"https:\/\/ufl.instructure.com\/courses\/404876\" target=\"_blank\" rel=\"noopener\">Canvas website<\/a>.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Description:<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">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 &#8220;themes&#8221; that appeal to a physics style, i.e., common patterns and general principles found in various biological systems.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">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.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Assignments:<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">The papers to read each week are listed in the <a href=\"#Schedule\">Schedule<\/a> 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 <a href=\"https:\/\/ufl.instructure.com\/courses\/404876\" target=\"_blank\" rel=\"noopener\">Canvas<\/a>).<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">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.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\" id=\"schedule\">Schedule:<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">Please check back periodically as the schedule may be adjusted. (download <a href=\"https:\/\/docs.google.com\/document\/d\/1Yz7UQygaqvjxQSJ8hExJsxMqcSFpG-jieha3BNhaiJU\/export?format=pdf\" target=\"_blank\" rel=\"noopener\">list<\/a> or <a href=\"https:\/\/docs.google.com\/spreadsheets\/d\/e\/2PACX-1vRkvRAA9sHSK5dhX5JNzCdtKw6o5QR7fU8ZgUj9S5FQZSWQlx9OVD2SqLFo_3tcAdvkifKIFkeDxgtl\/pub?gid=1726749001&amp;single=true&amp;output=pdf\" target=\"_blank\" rel=\"noopener\">table<\/a>)<\/p>\n\n\n\n<table class=\" aligncenter\" style=\"border-color: #000000\">\n<tbody>\n<tr>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000;width: 80px\">Date<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000;width: 80px\">Instructor<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000;width: 260px\">Topic<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Reading<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Tue 09\/01<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Xue<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000;padding: 5px\">Genetic and Phenotypic Variations:<br>\nMutation and resistance<\/td>\n<td style=\"text-align: left;vertical-align: middle;border: 1px solid #000000;padding: 5px\">SE Luria &amp; M Delbruck, Mutations of bacteria from virus sensitivity to virus resistance, <a href=\"https:\/\/www.genetics.org\/content\/28\/6\/491\" target=\"_blank\" rel=\"noopener\">Genetics 28, 491-511 (1943)<\/a>.<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Thu 09\/03<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Xue<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000;padding: 5px\">Genetic and Phenotypic Variations:<br>\nBacterial persistence<\/td>\n<td style=\"text-align: left;vertical-align: middle;border: 1px solid #000000;padding: 5px\">NQ Balaban, J Merrin, R Chait, L Kowalik &amp; S Leibler, Bacterial persistence as a phenotypic switch, <a href=\"https:\/\/doi.org\/10.1126\/science.1099390\" target=\"_blank\" rel=\"noopener\">Science 305, 1622-1625 (2004)<\/a>.<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Tue 09\/08<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Xue<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000;padding: 5px\">Phenomenological Models:<br>\nBacterial growth laws<\/td>\n<td style=\"text-align: left;vertical-align: middle;border: 1px solid #000000;padding: 5px\">M Scott, CW Gunderson, EM Mateescu, Z Zhang &amp; T Hwa, Interdependence of cell growth and gene expression: origins and consequences, <a href=\"https:\/\/doi.org\/10.1126\/science.1192588\" target=\"_blank\" rel=\"noopener\">Science 330, 1099-1102 (2010)<\/a>.<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Thu 09\/10<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Xue<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000;padding: 5px\">Phenomenological Models:<br>\nCell-size maintenance<\/td>\n<td style=\"text-align: left;vertical-align: middle;border: 1px solid #000000;padding: 5px\">S Jun &amp; S Taheri-Araghi, Cell-size maintenance: universal strategy revealed, <a href=\"https:\/\/doi.org\/10.1016\/j.tim.2014.12.001\" target=\"_blank\" rel=\"noopener\">Trends Microbiol 23(1), 4\u20136 (2015)<\/a>.<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Tue 09\/15<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Xue<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000;padding: 5px\">Dimensional Reduction:<br>\nBehavioral dynamics<\/td>\n<td style=\"text-align: left;vertical-align: middle;border: 1px solid #000000;padding: 5px\">GJ Stephens, B Johnson-Kerner, W Bialek &amp; WS Ryu, Dimensionality and dynamics in the behavior of C. elegans, <a href=\"https:\/\/doi.org\/10.1371\/journal.pcbi.1000028\" target=\"_blank\" rel=\"noopener\">PLoS Comput Biol 4, e1000028 (2008)<\/a>.<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Thu 09\/17<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Dixit<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000;padding: 5px\">Dimensional Reduction:<br>\nGene expression<\/td>\n<td style=\"text-align: left;vertical-align: middle;border: 1px solid #000000;padding: 5px\">L Haghverdi, F Buettner &amp; FJ Theis, Diffusion maps for high-dimensional single-cell analysis of differentiation data, <a href=\"https:\/\/doi.org\/10.1093\/bioinformatics\/btv325\" target=\"_blank\" rel=\"noopener\">Bioinformatics 31(18), 2989\u20132998 (2015)<\/a>.<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Tue 09\/22<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">guest<br>\n(Xue)<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000;padding: 5px\">Dynamical Systems and Networks:<br>\nEcological stoichiometry<\/td>\n<td style=\"text-align: left;vertical-align: middle;border: 1px solid #000000;padding: 5px\">T Andersen, JJ Elser &amp; DO Hessen, Stoichiometry and population dynamics. <a href=\"https:\/\/doi.org\/10.1111\/j.1461-0248.2004.00646.x\" target=\"_blank\" rel=\"noopener\">Ecol Lett 7(9), 884\u2013900 (2004)<\/a>.<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Thu 09\/24<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Dixit<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000;padding: 5px\">Dynamical Systems and Networks:<br>\nGenetic circuits<\/td>\n<td style=\"text-align: left;vertical-align: middle;border: 1px solid #000000;padding: 5px\">MB Elowitz &amp; S Leibler, A synthetic oscillatory network of transcriptional regulators, <a href=\"https:\/\/doi.org\/10.1038\/35002125\" target=\"_blank\" rel=\"noopener\">Nature 403, 335-338 (2000)<\/a>.<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Tue 09\/29<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Dixit<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000;padding: 5px\">Material and Energy Balance:<br>\nFlux Balance Analysis<\/td>\n<td style=\"text-align: left;vertical-align: middle;border: 1px solid #000000;padding: 5px\">JS Edwards, RU Ibarra &amp; BO Palsson, In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data, <a href=\"https:\/\/doi.org\/10.1038\/84379\" target=\"_blank\" rel=\"noopener\">Nat Biotechnol 19, 125\u2013130 (2001)<\/a>.<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Thu 10\/01<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Dixit<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000;padding: 5px\">Material and Energy Balance:<br>\nThermodynamic constraints<\/td>\n<td style=\"text-align: left;vertical-align: middle;border: 1px solid #000000;padding: 5px\">DA Beard, SD Liang &amp; H Qian, Energy balance for analysis of complex metabolic networks, <a href=\"https:\/\/doi.org\/10.1016\/S0006-3495(02)75150-3\" target=\"_blank\" rel=\"noopener\">Biophys J 83(1), 79\u201386 (2002)<\/a>.<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Tue 10\/06<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Dixit<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000;padding: 5px\">Statistical Descriptions:<br>\nProtein sequences<\/td>\n<td style=\"text-align: left;vertical-align: middle;border: 1px solid #000000;padding: 5px\">F Morcos, A Pagnani, B Lunt, A Bertolino, DS Marks, C Sander, R Zecchina, JN Onuchic, T Hwa &amp; M Weigt, Direct-coupling analysis of residue coevolution captures native contacts across many protein families, <a href=\"https:\/\/doi.org\/10.1073\/pnas.1111471108\" target=\"_blank\" rel=\"noopener\">Proc Natl Acad Sci USA 108 (49), E1293 (2011)<\/a>.<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Thu 10\/08<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Dixit<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000;padding: 5px\">Statistical Descriptions:<br>\nNeural activity<\/td>\n<td style=\"text-align: left;vertical-align: middle;border: 1px solid #000000;padding: 5px\">L Meshulam, JL Gauthier, CD Brody, DW Tank &amp; W Bialek, Coarse graining, fixed points, and scaling in a large population of neurons, <a href=\"https:\/\/doi.org\/10.1103\/PhysRevLett.123.178103\" target=\"_blank\" rel=\"noopener\">Phys Rev Lett 123, 178103 (2019)<\/a>.<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Tue 10\/13<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Xue<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000;padding: 5px\">Representation and Encoding:<br>\nAssociative memory<\/td>\n<td style=\"text-align: left;vertical-align: middle;border: 1px solid #000000;padding: 5px\">JJ Hopfield, Neural networks and physical systems with emergent collective computational abilities, <a href=\"https:\/\/doi.org\/10.1073\/pnas.79.8.2554\" target=\"_blank\" rel=\"noopener\">Proc Natl Acad Sci USA 79, 2554 (1982)<\/a>.<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Thu 10\/15<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Hagen<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000;padding: 5px\">Representation and Encoding:<br>\nOlfaction codes<\/td>\n<td style=\"text-align: left;vertical-align: middle;border: 1px solid #000000;padding: 5px\">B Malnic, J Hirono, T Sato &amp; LB Buck, Combinatorial receptor codes for odors, <a href=\"https:\/\/doi.org\/10.1016\/S0092-8674(00)80581-4\" target=\"_blank\" rel=\"noopener\">Cell 96(5), 713-723 (1999)<\/a>.<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Tue 10\/20<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Hagen<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000;padding: 5px\">Sensing and Navigation:<br>\nConcentration sensing<\/td>\n<td style=\"text-align: left;vertical-align: middle;border: 1px solid #000000;padding: 5px\">HC Berg &amp; EM Purcell, Physics of chemoreception, <a href=\"https:\/\/doi.org\/10.1016\/S0006-3495(77)85544-6\" target=\"_blank\" rel=\"noopener\">Biophys J 20, 193 (1977)<\/a>.<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Thu 10\/22<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Hagen<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000;padding: 5px\">Sensing and Navigation:<br>\nBacterial chemotaxis<\/td>\n<td style=\"text-align: left;vertical-align: middle;border: 1px solid #000000;padding: 5px\">HC Berg &amp; DA Brown, Chemotaxis in Escherichia coli analysed by three-dimensional tracking, <a href=\"https:\/\/doi.org\/10.1038\/239500a0\" target=\"_blank\" rel=\"noopener\">Nature 239, 500\u2013504 (1972)<\/a>.<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Tue 10\/27<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Hagen<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000;padding: 5px\">Stochastic Fluctuations:<br>\nStochastic gene expression<\/td>\n<td style=\"text-align: left;vertical-align: middle;border: 1px solid #000000;padding: 5px\">MB Elowitz, AJ Levine, ED Siggia &amp; PS Swain, Stochastic gene expression in a single cell, <a href=\"https:\/\/doi.org\/10.1126\/science.1070919\" target=\"_blank\" rel=\"noopener\">Science 297, 1183 (2002)<\/a>.<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Thu 10\/29<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Guan<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000;padding: 5px\">Stochastic Fluctuations:<br>\nTranscriptional burst<\/td>\n<td style=\"text-align: left;vertical-align: middle;border: 1px solid #000000;padding: 5px\">I Golding, J Paulsson, SM Zawilski &amp; EC Cox, Real-time kinetics of gene activity in individual bacteria, <a href=\"https:\/\/doi.org\/10.1016\/j.cell.2005.09.031\" target=\"_blank\" rel=\"noopener\">Cell 123(6), 1025 (2005)<\/a>.<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Tue 11\/03<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Guan<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000;padding: 5px\">Nonequilibrium Dynamics:<br>\nActive matter<\/td>\n<td style=\"text-align: left;vertical-align: middle;border: 1px solid #000000;padding: 5px\">A Yildiz, JN Forkey, SA McKinney, T Ha, YE Goldman &amp; PR Selvin, Myosin V walks hand-over-hand: Single fluorophore imaging with 1.5-nm localization, <a href=\"https:\/\/doi.org\/10.1126\/science.1084398\" target=\"_blank\" rel=\"noopener\">Science 300, 2061 (2003)<\/a>.<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Thu 11\/05<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Hagen<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000;padding: 5px\">Nonequilibrium Dynamics:<br>\nKinetic proofreading<\/td>\n<td style=\"text-align: left;vertical-align: middle;border: 1px solid #000000;padding: 5px\">JJ Hopfield, Kinetic proofreading: A new mechanism for reducing errors in biosynthetic processes requiring high specificity, <a href=\"https:\/\/doi.org\/10.1073\/pnas.71.10.4135\" target=\"_blank\" rel=\"noopener\">Proc Nat Acad Sci USA 71, 4135 (1974)<\/a>.<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Tue 11\/10<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Hagen<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000;padding: 5px\">Pattern Formation:<br>\nTuring pattern<\/td>\n<td style=\"text-align: left;vertical-align: middle;border: 1px solid #000000;padding: 5px\">AM Turing, The chemical basis of morphogenesis, <a href=\"https:\/\/doi.org\/10.1098\/rstb.1952.0012\" target=\"_blank\" rel=\"noopener\">Phil Trans R Soc Lond B237, 37 (1952)<\/a>.<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Thu 11\/12<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Guan<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000;padding: 5px\">Pattern Formation:<br>\nEmbryonic development<\/td>\n<td style=\"text-align: left;vertical-align: middle;border: 1px solid #000000;padding: 5px\">CP Brangwynne, CR Eckmann, DS Courson, A Rybarska, C Hoege, J Gharakhani, F Julicher &amp; AA Hyman, Germline P granules are liquid droplets that localize by controlled dissolution\/condensation, <a href=\"https:\/\/doi.org\/10.1126\/science.1172046\" target=\"_blank\" rel=\"noopener\">Science 324, 1729 (2009)<\/a>.<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Tue 11\/17<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Guan<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000;padding: 5px\">Novel Phases of Matter:<br>\nPhase separation<\/td>\n<td style=\"text-align: left;vertical-align: middle;border: 1px solid #000000;padding: 5px\">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 &amp; MK Rosen, Phase transitions in the assembly of multivalent signalling proteins, <a href=\"https:\/\/doi.org\/10.1038\/nature10879\" target=\"_blank\" rel=\"noopener\">Nature 483, 336 (2012)<\/a>.<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Thu 11\/19<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Xue<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000;padding: 5px\">Novel Phases of Matter:<br>\nCollective behavior<\/td>\n<td style=\"text-align: left;vertical-align: middle;border: 1px solid #000000;padding: 5px\">T Vicsek, A Czirok, E Ben-Jacob, I Cohen &amp; O Shochet, Novel type of phase transition in a system of self-driven particles, <a href=\"https:\/\/doi.org\/10.1103\/PhysRevLett.75.1226\" target=\"_blank\" rel=\"noopener\">Phys Rev Lett 75, 1226 (1995)<\/a>.<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Tue 11\/24<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\"><\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000;padding: 5px\"><strong>choice of final project<\/strong><\/td>\n<td style=\"text-align: left;vertical-align: middle;border: 1px solid #000000;padding: 5px\"><\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Tue 12\/01<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Guan<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000;padding: 5px\">Optical Limit and Imaging:<br>\nSingle-molecule detection<\/td>\n<td style=\"text-align: left;vertical-align: middle;border: 1px solid #000000;padding: 5px\">J Elf, GW Li &amp; XS Xie, Probing transcription factor dynamics at the single-molecule level in a living cell, <a href=\"https:\/\/doi.org\/10.1126\/science.1141967\" target=\"_blank\" rel=\"noopener\">Science 316, 1191 (2007)<\/a>.<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Thu 12\/03<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Guan<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000;padding: 5px\">Optical Limit and Imaging:<br>\nSuper-resolution techniques<\/td>\n<td style=\"text-align: left;vertical-align: middle;border: 1px solid #000000;padding: 5px\">M Bates, B Huang, GT Dempsey &amp; X Zhuang, Multicolor super-resolution imaging with photo-switchable fluorescent probes, <a href=\"https:\/\/doi.org\/10.1126\/science.1146598\" target=\"_blank\" rel=\"noopener\">Science 317, 1749 (2007)<\/a>.<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Tue 12\/08<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\"><\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000;padding: 5px\">preparation for final project<\/td>\n<td style=\"text-align: left;vertical-align: middle;border: 1px solid #000000;padding: 5px\"><\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">Thu 12\/17<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000\">10-12PM<\/td>\n<td style=\"text-align: center;vertical-align: middle;border: 1px solid #000000;padding: 5px\"><strong>presentation of final project<\/strong><\/td>\n<td style=\"text-align: left;vertical-align: middle;border: 1px solid #000000;padding: 5px\"><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n\n\n\n<p class=\"wp-block-paragraph\"><\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Grading:<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">The final grade will consist of both the class quizzes (50%) and the final project (50%):<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>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.<\/li>\n\n\n\n<li>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.<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\">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.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">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:<br>\n<a href=\"https:\/\/catalog.ufl.edu\/UGRD\/academic-regulations\/attendance-policies\/\">https:\/\/catalog.ufl.edu\/UGRD\/academic-regulations\/attendance-policies\/<\/a><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Students with disabilities who experience learning barriers and would like to request academic accommodations should connect with the disability Resource Center by visiting:<br>\n<a href=\"https:\/\/disability.ufl.edu\/students\/get-started\/\">https:\/\/disability.ufl.edu\/students\/get-started\/<\/a><br>\nIt is important for students to share their accommodation letter with their instructor and discuss their access needs, as early as possible in the semester.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Information on current UF grading policies for assigning grade points may be found at:<br>\n<a href=\"https:\/\/catalog.ufl.edu\/UGRD\/academic-regulations\/grades-grading-policies\/\">https:\/\/catalog.ufl.edu\/UGRD\/academic-regulations\/grades-grading-policies\/<\/a><\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Evaluation:<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">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:<br>\n<a href=\"https:\/\/gatorevals.aa.ufl.edu\/students\/\">https:\/\/gatorevals.aa.ufl.edu\/students\/<\/a><br>\nStudents 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:<br>\n<a href=\"https:\/\/gatorevals.aa.ufl.edu\/public-results\/\">https:\/\/gatorevals.aa.ufl.edu\/public-results\/<\/a><\/p>\n<\/div><\/div><\/div><\/section>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":1086,"featured_media":0,"parent":8,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"featured_post":"","footnotes":"","_links_to":"","_links_to_target":""},"class_list":["post-227","page","type-page","status-publish","hentry"],"acf":[],"_links":{"self":[{"href":"https:\/\/people.clas.ufl.edu\/b-xue\/wp-json\/wp\/v2\/pages\/227","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/people.clas.ufl.edu\/b-xue\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/people.clas.ufl.edu\/b-xue\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/people.clas.ufl.edu\/b-xue\/wp-json\/wp\/v2\/users\/1086"}],"replies":[{"embeddable":true,"href":"https:\/\/people.clas.ufl.edu\/b-xue\/wp-json\/wp\/v2\/comments?post=227"}],"version-history":[{"count":9,"href":"https:\/\/people.clas.ufl.edu\/b-xue\/wp-json\/wp\/v2\/pages\/227\/revisions"}],"predecessor-version":[{"id":617,"href":"https:\/\/people.clas.ufl.edu\/b-xue\/wp-json\/wp\/v2\/pages\/227\/revisions\/617"}],"up":[{"embeddable":true,"href":"https:\/\/people.clas.ufl.edu\/b-xue\/wp-json\/wp\/v2\/pages\/8"}],"wp:attachment":[{"href":"https:\/\/people.clas.ufl.edu\/b-xue\/wp-json\/wp\/v2\/media?parent=227"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}