Introduction to Biophysics: Syllabus

Transcription

1 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 microscopy 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 physics, biology, mechanical engineering, pharmacology, chemistry, biochemistry, computer science 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. Atomic Force Microscopy, DNA Sequencing, Fluorescence 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 inclass 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. 1

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

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

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

5 14 / Apr 14 th Last day of class (TBA) A06 Due Additional laboratory tours will be announced via a Doodle Poll 5