Links to other pages in this course website: HOME PAGE Project assignment Project grading rubric	BIOEN 599M, Spring 2007 Quantitative Molecular Biomechanics
	Class Schedule Instructor: Wendy Thomas Office: Foege Hall (BIOE) N430P Office Hours: TBA e-mail: wendyt@u.washington.edu Phone: (206)616-3947 Class Meeting Times and Location: Lecture: MWF 2:30-3:20 FTR 034
	Class Schedule Subject to change during the quarter. Class 1: Mon, March 26 Topic: Overview of Class Structure and Introduction to Material Reading assignment: course web site. Class 2: Wed, March 28 Topic: Nanoscale Mechanical Forces Lecture notes from this year, handwritten Lecture notes from last year, powerpoint Review of linear mechanical elements and imortance of nanoscale Reading: Howard, Ch 2 "Mechanical Forces", p 9-26 Homework HW 1 assigned: Mechanical Forces & Mechanical Properties of Proteins Class 3: Fri, March 30 Topic: Properties of Proteins Lecture notes for this year, powerpoint. Elasticity and Young’s modulus Reading: Howard , Ch. 3: “Mass, Stiffness, and Damping of Proteins”, p. 29 - 45 Class 4: Mon, April 2 Topic: Boltzmann's Law and Thermal Forces notes will be posted late today, so I'll bring hardcopies to class. Reading assignment: Howard , Ch. 4: “Thermal Forces and Diffusion”, p. 49-55 Probability Distributions in Nanomechanics (Wendy's notes) Class 5: Wed, April 4 Topic: Diffusion and Fluctuations Focker-Planck Equation Mean First Passage Times Reading: Howard , Ch. 4: “Thermal Forces and Diffusion”, p. 55-63 Homework HW 1 due: Mechanical Forces & Mechanical Properties of Proteins. HW 2 assigned: Thermal forces and Diffusion hw2 requires files; beadsettling.csv and opticaltrap.csv Class 6: Fri, April 6 Topic: Fluctuations and Correlation Times. Langevin Equation Time correlations Reading: Howard , Ch. 4: Correlation Times , p. 63-71 Class 7: Mon, April 9 Topic: Protein Conformations, Chemical Equilibria, and Forces Reading assignment: Howard , Ch. 5: “Chemical Forces”, p. 75-82 Class 8: Wed, April 11 Topic: Force and Chemical Rates Reading assignment: Howard , Ch. 5: “Chemical Forces”, p. 83-98 Homework HW 2 due: Thermal forces and diffusion HW 3 assigned: chemical forces Class 9: Fri, April 13 Topic: Rates, continued Steered Molecular Dynamics Simulations Equilibrium and nonequilibrium processes Reading: Class 10: Mon, April 16 Topic: Rigid Polymer Mechanics Reading assingment: Howard , Ch. 6: “Polymer Mechanics”, p. 99-112 Class 11: Wed, April 18 Topic: Thermal Forces and Polymer Mechanics Reading assignment: Howard , Ch. 6: “Polymer Mechanics”, p. 112-116 Homework HW 3 due. Chemical forces HW 4 assigned: Polymer Mechanics Class 12: Fri, April 20 Topic: Flexible Polymer Mechanics Reading: Wikipedia Freely-Jointed Chain Worm-like chain (Short Bustamante paper) Wikipedia WLC Class 13: Mon, April 23 Review of Basic Principles Class 14: Wed, April 25 Synthesis, Examples Homework: HW 4: Polymer Mechanics due on Friday April 27, unlike what it says on the assignment itself. Fri, April 27 Cancelled for COE Open House Class 15: Mon, April 1 topic 1: Polymerization (Wendy) Howard Ch. 9 and 10 Class 16: Wed, May 2 Mid-Term Exam Class 17: Fri, May 4 topic 2: Multiscale adhesion (Wendy) powerpoint slides lecture notes Reading: Reliability Theory for Receptor-Ligand Bond Dissociation Tees, ... Hammer, 2001 Rupture of Multiple Parallel Bonds under Dynamic Loading by Seifert, 2000. Class 18: Mon, May 7 topic 3: Iintroduction to linear motors(Wendy) Reading Molecular Motors: a theorist's perspective by Kolomeisky and Fisher, 2007 Phosphorylation Energy Hypothesis: Open Chemical Systems and their Biological Functions, by Hong Qian 2007 Class 19: Wed, May 9 topic 4: Myosin II (Wendy or Mike R.) Reading: ATP Analogs and Muscle Contraction: Mechanics and Kinetics of Nucleoside Triphosphate Binding and Hydrolysis, Regnier et al 1998 The Effect of ATP Analogs on Posthydrolytic and Force Development Steps in Skinned Skeletal Muscle Fibers, Regnier and Homsher 1998 Class 20: Fri, May 11 topic 5: ATP synthase rotary motor or Dynein (Wendy) Reading: Direct observation of rotation of F1-ATPase by Noji et al, Nature 1997 Step sizes by Yasuda et al 2001 High ADP concentrations and mutant ATPase by Muneyuki 2007 Class 21: Mon, May 14 topic 6: MT polymerization dynamics (Andrew) Reading: Force Generation by Microtubule Assembly/Disassembly in Mitosis and Related Movements Inoue & Salmon (1995) Molecular Biology of the Cell Vol. 6, 1619-1640 Microtubule Polymerization Dynamics Desai & Mitchell Annu. Rev. Cell Dev. Biol. (1997). 13:83–117 Class 22: Wed, 16 topic 7: Catch Bond mechanisms: (Olga) Class 23: Fri, May 18 topic 8: Bacterial adhesion (Shraddha) Class 24: Mon, May 21 topic 9: Shear-enhanced platelet adhesion (Gianluca) Class 25: Wed, May 23 topic 10: Structural Simulations and Catch bond Mechanisms (Bridget) Class 26: Fri, May 25 topic 11: Kinesin (Chip) No Class on Memorial Day, Mon, May 28 Class 27: Wed, May 30 topic 12: Myosin V (Lauren) Class 28: Fri, June 1 topic 13: Cardiac Actin (Justin) <-- RETURN TO TOP
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