BIOL/PHYS 319 – Syllabus Winter 2016

Introduction to Biophysics: Syllabus BIOL/PHYS 319 – Winter 2016

Course Description: Introduction to Biophysics is designed to give you critical knowledge, hands-on training in mathematical and computational tools, as well as perspective on modern biophysics research so that you can quantitatively describe and understand a wide range of biological systems. Throughout this course, we will develop a picture of what’s going on inside living cells. We will develop quantitative physical reasoning skills to describe biological systems. We will perform predictions and simulations of molecular processes to integrate physical concepts with biological phenomena. Further, we will develop perspective on cutting edge tools and gain an appreciation of how biological discoveries rely upon emerging physical techniques. Throughout the course you will meet students from a range of disciplines including , , mechanical , , , , etc. united by a common interest in and passion for biophysics. Our course has graduate TAs that work in biophysics labs with whom you will interact often. This is a fantastic way to learn about cutting edge biophysics as well as quantitative biology research. We will also have an opportunity to tour labs at the end of the semester, where you will be able to meet other students and professors at McGill in this interdisciplinary field.

Grading Scheme

6x5%=30% Assignments: Assignments will contain analytic as well as programming (MATLAB) problems, for which you will receive training in programming tools. The assignments are designed to be fun and at the same time provide you with a deep insight into the topic. The goal of the programming questions is to give you a flavor of how to model biophysical systems. The Matlab problems directly visualize results (e.g. images, particle trajectories) and thus complement analytic expressions. We will model ion channels, microscopy experiments and random walks, for example. The analytic problems will be representative of the final and midterm examinations. 15% Student Presentation: Students will present a biophysical technique in direct connection with course content (e.g. , DNA Sequencing, Microscopy etc.). You will be graded on your presentation as well as the participation in others’ presentations (attendance and asking questions). You will get to meet with the Professor on your material prior to your in- class presentation and thus receive detailed feedback before and after the presentation. Typically we pair students together from different disciplines, facilitating exchange of perspective, approaches and ideas.

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20% Midterm: The midterm will contain problems similar to the assignments (analytical). The midterm is held sufficiently late in the course (after reading break) to provide time for mastery and to allow bridges to be developed between concepts. Review and practice problems will be provided. 35% Final: The final is cumulative and will consist of analytical problems similar to the assignments. Review and practice problems will be provided.

Weekly Schedule Week / Lecture Details Readings Student Presentations / Assignments Date MATLAB Tutorials 1 / Jan 12th 1: Introduction to the Course PBC Ch 1.3, 1.4 Questionnaire Quantitatively modeling biological PMLS Ch 1 A01: MATLAB and Calculus systems. The role of new biophysical Warm-Up measurements and instruments in biology 1 / Jan 14th 2: Introduction to Brownian BP pg 114-121 (to Probability tutorial (by TA Motion. Steps towards computer check) Simon; Piano room; time simulation and visualization of PBC Ch13 TBA) particle trajectories. 2 / Jan 19th 3,4: Diffusion Equation. PBC Ch13 Mathematical theory; application to nutrient delivery 2 / Jan 21st 5,6: Diffusion continued; Stokes PBC 3.4.2 Einstein Relation Optional: PBC 12.4 3 / Jan 26th Matlab training: Introduction, PBC 3.4.2 In class Matlab training Loops and Logic Optional: PBC 12.4 (MT1 MT2) 3 / Jan 28th Matlab Training Continued: In class: Matlab training Symmetric Random Walks, ‘Vectorized’ Operations 4 / Feb 2nd 7: Stokes Einstein Law for A01 Due Diffusion; Diffusion-limited A02: Diffusion and Random reaction rates Walks Posted

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4 / Feb 4th 8: Microscopy and Introduction to single- Seeing in solution and in microscopy cells. 5 / Feb 9th 9: Models for Reactions PBC Ch 15.2 PMLS Ch 9.4 5 / Feb 11th 10: Fluorescence Correlation Schwille review article; A02 Due Spectroscopy. Theory; measuring Classical FCS articles A03: FCS and Image molecular diffusion and reactions from 1972/1974 Processing Posted by Feb 15 6 / Feb 16th 11: Michaelis-Menten Model of BP pg 433-437 Biochemical Processes 6 / Feb 18th 12: DNA Structure PBC Ch 15.2 A04: Molecular Interactions Random walks in space PMLS Ch 9.4 Posted on Feb 22 7 / Feb 23rd 13: DNA Structure BP pg 433-437 Self-avoiding role of applied confinement 7 / Feb 25th Practice Questions on the board! Posting more Midterm (Midterm style & overview) Practice Questions 8 / Mar 1st READING WEEK 8 / Mar 3rd READING WEEK 9 / Mar 8th Single-photon sensitivity in human A03 due in class vision. Guest Lecture by Philip Nelson (author of 2 texts we are using! Visiting McGill this day) 9 / Mar 10th Student Presentations 1-3 PBC 10.2.2, PBC 10.2.3 SP1: DNA Dynamics under A04 due in class extreme confinement SP2: In vivo FCS applied to molecular interactions SP3: DNA topology and its influence on transcription

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10 / Mar 14: “A Travels to Lilliput” 15th (Steve Michnick guest lecture)

10 / Mar MIDTERM 17th 11 / Mar DNA Sequencing methodologies SP4: Overview of DNA A05: DNA Structure Posted 22nd (Student presentations) sequencing / mapping SP4a: Approaches to DNA Sequencing – Sanger SP4b: Approaches to DNA sequencing – Illumina SP4c: Approaches to DNA sequencing – Pac Bio 11 / Mar 15: Introduction to the A06: Cytoskeleton Dynamics 24th cytoskeleton and its dynamics. posted Actin dynamics, myosin motors and actin tread milling 12 / Mar 16: Brownian Ratchet Model for Movements Ch 4 29th Force Generation. PBC Ch 16 12 / Mar 16+: Brownian Ratchet Model SP5: Super Resolution A05 Due 31st continued; + Super Resolution Imaging applied to resolving Imaging Presentation components of the cytoskeleton 13 / Apr 5th Tours of DNA-imaging laboratory Meet at green couches, (Leslie) and Genome Quebec Rutherford 2nd floor, 1pm 13 / Apr 7th 17: How to measure small forces SP6: in the biological world: tweezers SP7: and atomic force microscopy Guest: Atomic Force Microscopy & 14 / Apr 12th 18: Entropically mediated forces PBC 14.2.3 & 14.2.4 (Optional)

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14 / Apr 14th Last day of class (TBA) A06 Due

Additional laboratory tours will be announced via a Doodle Poll