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