BP205 Molecular Dynamics of the Cell

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Documents/Textbooks

• Recommended Textbooks
• Stephen Strogatz, Nonlinear Dynamics and Chaos: With Applications to Physics, Biology, Chemistry and Engineering - @amazon.com
• Ken Dill, Molecular Driving Forces (Chapter 18) - @amazon.com
• Meyer B. Jackson, Molecular and Cellular Biophysics (Chapter 4 and Chapter 5) - @amazon.com
• David Katz, Transport Phenomena in Biological Systems - @amazon.com


• Molecular Motions in the Cell
• Einstein's Explanation of Brownian Motion Applet - @galileoandeinstein.physics.virginia.edu
• Robert Brown's 1828 Manuscript - Brownian.pdf
• English translation of Einstein's investigation into Brownian motion - Einstein_brownian.pdf
• Vale RD, et al. One-Dimensional Diffusion of Microtubules Bound to Flagellar Dynein - Vale_dynein.pdf
• Wang YM, et al. Single Molecue Measurements of Repressor Protein 1D Diffusion on DNA - Wang_lacR.pdf
• Papadopoulos S, et al. Protein Diffusion in Living Skeletal Muscle Fibers: Dependence on Protein Size, Fiber Type, and Contraction - Gros_muscle.pdf
• Elowitz MB, et al. Protein Mobility in the Cytoplasm of Escherichia coli - Elowitz_diffusion.pdf
• Berg HC, et al. Physics of Chemoreception - Berg.pdf
• Saffman, et al. Brownian motion in biological membranes - Delbruck_membranediffusion.pdf
• Peskin, et al. Cellular Motions and Thermal Fluctuations: The Brownian Ratchet - Simple_brownian.pdf


• Fluid Flow on the Scale of a Cell
• Purcell EM. Life at low Reynolds number - LowReNumber.pdf
• Short MB, et al. Flows driven by flagella of multicellular organisms enhance long-range molecular transport - Convection_differentiation.pdf
• Okada Y, et al. Mechanism of Nodal Flow: A Conserved Symmetry Breaking Event in Left-Right Axis Determination - Cilia_flow.pdf


• Single Molecule Kinetics


• Reaction Kinetics


• Stability and Simple Bifurcations


• Kinetics of Gene Regulation
• Ackers GK, et al. Quantitative model for gene regulation by lambda phage repressor - shea_lambda.pdf
• Brenowitz M, et al. "Footprint" titrations yield valid thermodynamic isotherms - shea_isotherms.pdf
• Becskei A, et al. Engineering stability in gene networks by autoregulation - serrana_negative.pdf


• Numerical Methods


• Bifurcations of 2-Dimensional Systems


• Multistability


• Oscillations


• Reaction-Diffusion


• Metabolic Flux Analysis
• Ibarra RU, et al. Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth - mfa1.pdf
• Edwards JS, et al. In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data - mfa2.pdf

Contact:: [david.h.burkhardt@gmail.com] [monica.tremont@ucsf.edu]

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