• Lecture 1 (Jan 22)  Overview and organizational matters.
• Read: "Seven Pillars of Life", First chapter of Stryer.
• Watch: DNA replication

• Lecture 2 (Jan 27) Which, where and how many molecules make a cell
• Read: First chapter of Stryer.
• Read: Chapter 2 pp. 50-80 of “Essential Cell Biology”

• Lecture 3 (Jan 29) Nucleic acids and Central Dogma
• Read: Chapter 2, pp. 50-80 of Essential Cell Biology
• Read: Chapter 2 and 3 of "Physical Biology of the Cell"
• Watch: DNA wrapping in chromosomes, Transciption, Bacterial translation
• Watch: Transcription and translation in details

• Lecture 4 (Feb 3)  Cell architecture
• Read: Chapter 2, pp. 50-80 of  Essential Cell Biology
• Read: Chapters 2 and 3 of "Physical Biology of the Cell"
• Watch: Protein folding movie; more information here.
• Watch: DNA sequence analysis method
• Try: Protein folding puzzles

• Self-Study (Feb 5)  Looking at cell's machinary using VMD
• Download: VMD
• Do: Using VMD tutorial. Required part:"Working with single molecules". Also helptul "Scripting in VMD". 

• Lecture 5 (Feb 12)  Molecular forces and partition function
• Supplementary notes (blackboard)
• Read: Chapter 6.3, 6.4 and 15.2 of "Physical Biology of the Cell"
• Watch: Hexokinase enzyme
• Watch: Induced fit mechanism

• Lecture 6 (Feb 17)  Reactions, enzymes and ATP
• Supplementary notes (blackboard)
• Read: Chapter 6.3, 6.4 and 15.2 of "Physical Biology of the Cell"
• Watch: Hexokinase enzyme
• Watch: Induced fit mechanism
• Watch: Kinesin movie

• Lecture 7 (Feb 19)  Imaging cell machinery: ATP Synthase
• Watch: Molecular mechanism of ATP synthase
• Animation of F1 motor
• Amination of Fo motor
• More animations
• Read: Yasuda, R. et al., Nature 410:898 (2001)
• Read: Noji, H. et al., Nature 386, 299-302 (1997)

• Lecture 8 (Feb 24)  Random walk and diffusion
• Read: Chapter 8 of "Physical Biology of the Cell"
• Read: "Random walks in Biology" by H. Berg
• Read: Reverse Engineering of Biological Complexity
• Read: From the microworld to King Kong
• Read: Life at low Reynolds number

• Lecture 9 (Feb 26) Bacterial motility and diffusion

• Blackboard: Reynolds number
• Blackboard: More on diffusion
• Read: Molecular motors: Theory
• Watch: Chemotaxis, Cytoskeleton

• Lecture 10 (Mar 3) Polymerization and flashing rachets
• Watch: Polymerization ratchet
• Watch: Brownian ratchet
• Explore: Flashing ratchet Java applet
• Read: "French Ratchet" paper
• Read: "Fluctuation driven ratchets"
• Read:  Molecular motors: Theory

• Lecture 11 (March 5) Langevin vesus Smoluchowski
• Read: "Thermodynamics and Kinetics of a Brownian Motor", Science 1997
• Read: Molecular motors: Theory

• Lecture 12 (March 10)  Coupling chemistry to mechanical motion
• Blackboard notes
• Read: "The Physics of Molecular Motors", Acc. Chem Res. 2001
• Read: "Energy transduction in ATP synthase", Nature 1998
• Explore: Langevin Java applet of the Fo motor
• Explore: Smoluchowski Java applet of the Fo motor

• Lecture 13 (March 12)  Myosin, kinesin and Fiona.
• Blackboard notes
• Read: Myosin V Walks Hand-Over-Hand
• Read: Single molecule approaches to biophysics

• Lecture 14 (March 17)  Magnetic tweezers
• Read: Relaxation of DNA supercoils by topoisomerase
• Read: Jumping supercoils
• Watch: supercoil relaxation by topoisomerases
• Watch: supercoil relaxation techno version

• Lecture 15 (March 19)  DNA elasticity
• Read: DNA wind-up motor.

Spring Break

March 24-28

• Lecture 16 (March 30)  Ion channels
• Blackboard notes
• Read: Stochastic resonance in membrane channels
• Watch:  ion transport through selectivity filter
• Watch:  structural fluctuations in an ion channel

• Lecture 17 (April 2)  Action potential 
• Blackboard notes
• Read: Optimizing passive transport through binding
• Read: Adiabatic pumping accross a bilayer
• Read and watch: ion channel opens up

• Lecture 18 (April 7) Vision
• Read: Visual sensitivity
• Watch: Isomerization reaction
• Watch: Visual phototransduction
• Watch: G-protein receptors

• Lecture 19 (April 9)  Mitochondria: a cell's battery.
• Read: Turning back time: ageing reversed in mice. More
• Read (for Quiz 8 on April 14) Bioelecrochemical propulsion
• Read (for Quiz 8 on April 14) Spinach batteries
• Watch: Mitochondion, the movie. 3D reconstruction.
• Watch: Electron transfer chain

• Lecture 20 (April 14) DNA nanotechnology
• Read: (for quiz 9 on April 21) Syntheic biology for nanotechnology
• Read: (for quiz 9 on April 21) The "right" size in nanobiotechnology

• Lecture 21 (April 16) Experimental ecology

• Lecture 22 (April 21) Biological motors in man-made devices

• Lecture 23 (April 23) Single molecule biophysics using nanopores

• Lecture 24 (April 28). Optical traps

• Lecture 25 (April 30). Modeling life: from atoms to cells.

• Lecture 26 (May 5) Synthetic life

• Lecture 27 (May 7) Sinescence and death