Course Outline Phys-Biol 319_W2020 PDF

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Course outline for PHYS319 or BIOL319 (Biophysics) at McGill Univeristy...

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Phys/Biol 319 Introduction to Biophysics Winter Term 2020 Course Information

Calendar Description: Phys/Biol 319 Introduction to Biophysics (3 credits) Emerging physical approaches and quantitative measurement techniques are providing new insights into longstanding biological questions. This course will present underlying physical theory, quantitative measurement techniques, and significant findings in molecular and cellular biophysics. Principles covered include Brownian motion, low Reynolds-number environments, forces relevant to cells and molecules, chemical potentials, and free energies. These principles are applied to enzymes as molecular machines, membranes, DNA, and RNA. Prerequisites: Prerequisites: BIOL 200; MATH 222; PHYS 230 and (PHYS 232 or PHYS 253), or permission of the instructor. Restriction: Physics: Not open to students who have taken or are taking BIOL 319 Biology: Not open to students who have taken or are taking PHYS 319 Instructor:

Prof. Paul W. Wiseman

Course Website: Via McGill MyCourses: https://mycourses2.mcgill.ca/d2l/loginh/ Classroom ERB Physics 114 Offices:

Chemistry Office: Otto Maass Rm. 218 phone: 514-398-5354 (more often here) Physics Office: ERB Rm. 410

e-mail: [email protected] Timetable:

Tuesday/Thursday 2:35-3:55 PM in ERB 114 (Physics) No classes during “Study Week” March 2 - 6 Special Guest lectures TBA Intro to Matlab tutorials Wong 0190 (not ERB 114) classtime Tues. Jan. 14, Thurs Jan. 16 (half the class alphabetically on Tues. other half on Thurs.)

Textbook: Physical Biology of the Cell 2nd Edition by Rob Phillips, Jane Kondev, Julie Theriot, Hernan Garcia (copies at the McGill Bookstore or through online distributors) Garland Science; 2nd edition (October 29, 2012) ISBN-10: 0815344503

Phys/Biol 319 Winter 2020

Evaluation: Assignments* 1st Test in class 2nd Test in class Final exam

30% 15% 15% 40%

Tues. Feb. 25, ERB 114 during class Tues. Mar. 31, ERB 114 during class (scheduled during official exam period by McGill)

*Some assignment questions will make use of Matlab programming. "In the event of extraordinary circumstances beyond the University’s control, the evaluation scheme in a course is subject to change, provided that there be timely communications to the students regarding the change." Office Hours: OMC 218 Fridays 1:30-3 PM or by appointment Topics (The detail & total number of topics presented will depend on time available) Introduction to biophysics/physical biology and quantitative modeling. Brownian motion and diffusion. Stokes-Einstein relation and applications. Gibbs free energy and Entropy. Diffusion-limited reaction rates, and dynamics in the cell. Mechanical and chemical equilibrium in the living cell. Chemical binding kinetics, membrane receptors Random walks and Biopolymer structures Electrostatics in salty solutions, osmotic pressure, Poisson-Boltzmann equation, Debye length Cellular membranes and membrane potential Cytoskeleton and dynamics. Biophysics applications of fluorescence and super-resolution optical microscopy Research asides will be woven into some sections I will try to arrange a few guest lectures on Biophysics research (e.g. Biophysics theory) Two lectures will involve an interactive Matlab tutorial with the TA Goals: To provide an introduction to fundamental concepts of Molecular Biophysics and the physical concepts needed for quantitative modeling in cell biology Other Useful Textbooks Biological Physics (Energy, Information, Life) By: Philip Nelson Physical Chemistry for the Chemical and Biological Sciences By: Raymond Chang Molecular Driving Forces: Statistical Thermodynamics in Biology, Chemistry, Physics, and Nanoscience, 2nd Edition By: Ken A. Dill and Sarina Bromberg See Course Website for announcements, course notes, weblinks of interest

Phys/Biol 319 Winter 2020

TA Information Félix Proulx-Giraldeau [email protected] Cynthia Shaheen [email protected] Baljyot Parmar [email protected] Information on tutorials to be announced in class and on WebCT Tomlinson Engagement Mentor: Gloria Lau [email protected] McGill Policy Statements Required Course Outline Statements [in keeping with Senate resolutions] Language of Submission: “In accord with McGill University’s Charter of Students’ Rights, students in this course have the right to submit in English or in French any written work that is to be graded. This does not apply to courses in which acquiring proficiency in a language is one of the objectives.” « Conformément à la Charte des droits de l’étudiant de l’Université McGill, chaque étudiant a le droit de soumettre en français ou en anglais tout travail écrit devant être noté (sauf dans le cas des cours dont l’un des objets est la maîtrise d’une langue). » Academic Integrity: “McGill University values academic integrity. Therefore, all students must understand the meaning and consequences of cheating, plagiarism and other academic offences under the Code of Student Conduct and Disciplinary Procedures” (see www.mcgill.ca/students/srr/honest/ for more information). (Approved by Senate on 29 January 2003) « L'université McGill attache une haute importance à l’honnêteté académique. Il incombe par conséquent à tous les étudiants de comprendre ce que l'on entend par tricherie, plagiat et autres infractions académiques, ainsi que les conséquences que peuvent avoir de telles actions, selon le Code de conduite de l'étudiant et des procédures disciplinaires (pour de plus amples renseignements, veuillez consulter le site www.mcgill.ca/students/srr/honest/).»

Phys/Biol 319 Winter 2020...