May 2008
Introduction to biophysics
809 ‫ חדר‬,9782 '‫ טל‬,‫ארז בראון‬
1. Biological Macromolecules and Interfaces:
(a) Intermolecular forces.
(b) Proteins: protein folding, helix-coil transition, cooperativity.
(c) DNA molecules: supercoiling, information storage and access, duplication
and transcription-the genetic code and gene expression mechanisms, errorcorrection and proofreading mechanisms.
(d) Membranes: biological versus physical membranes, elastic properties and
shape of vesicles, fluctuations.
(e) Enzymes and kinetics; Feedback mechanisms, feedback
inhibition.
2. Transport:
(a) Diffusion processes in biological systems.
(b) The escape from a potential well-Kramers problem.
(c) Transport through membranes; channels, exchangers and pumps, cell
signaling receptors and signal trunsduction.
3. Molecular machines:
(a) Energy transduction at the molecular level, motor proteins, thermal ratchets
and Maxwell demons.
(b) Muscle contraction.
(c) The swimming bacteria-life at low Reynolds number.
4. Pattern formation:
(a) Morphogenesis- the Turing mechanism.
5. Electrical Processes:
(a) Electrodiffusion across membranes and their resting potential.
(b) Action potential generation, the Hodgkin-Huxley model and voltage-gated
ion-channels.
(c) Neurons, synapses and neural networks.
:‫הערה‬
‫הציון בקורס יקבע לפי מבחן בית‬
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May 2008
Introduction to biophysics/ some references
General references:
M. Delbruck, A physicist look at biology, reprinted from the Transactions of the Connecticut Academy of
Arts and Sciences, Vol 38, Dec. 1949, pp. 173-190.
General Biology:
B. Alberts et al, Molecular Biology of the Cell, fourth edition, Gerland Publishing Inc., 2004.
J. Gerhart & M. Kirschner, Cells, embryos, and evolution, Blackwell Science, 1997.
J. Maynard Smith & E. Szathmary, The major transitions in evolution, Oxford Univ. Press, 1995.
History of molecular biology:
H.F. Judson, The Eight Day of Creation, expanded edition, Cold Spring Harbor Laboratory Press, 1996.
Introductory books:
J.D. Murray, Mathematical Biology, third edition, Springer-Verlag, 2002.
P. Nelson, Biological physics: Energy, Information , Life, 2004.
P.M. Chaikin and T.C. Lubensky, Principles of Condensed Matter Physics, Cambridge
University Press (1995).
J. Israelachvili, Intermolecular & surface forces, Academic Press, second edition (1992).
R. Nossal and H. Lecar, Molecular&Cell Biophysics, Addison-Wesley Publishing
Company (1991).
S.A. Safran, Statistical Thermodynamics of Surfaces, Interfaces and Membranes,
Addison-Wesley Publishing Company (1994).
Biological macromolecules and membranes:
C.R. Cantor and P.R. Schimmel, Biophysical Chemistry Vol III, The behavior of
biological macromolecules, W.H. Freeman and Company, N.Y. (1980).
S. Leibler, Equilibrium statistical mechanics of fluctuating films and membranes, in the
Jerusalem Winter School for theoretical Physics, statistical Mechanics of Membranes and
Surfaces, Vol 5, p. 45, eds. D. Nelson, T. Piran and S. Weinberg (1988).
Transport:
T.F. Weiss, Cellular Biophysics, Vol I, The MIT Press, Cambridge Massachusetts (1996).
Purcell, Life at low Reynolds number, American Journal of Physics, 45 p.3 (1977).
Error Corrections:
J. Von Neuman, Probabilistic logics and the synthesis of reliable organisms from
unreliable components, a paper based on the notes taken by Dr. S. Pierce on five lectures
given by the author at Caltech in January 1952, Von Neuman collected works, Vol. V, p. 329.
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A.R. Fersht, Enzymic editing mechanisms and the genetic code, Proc. R. Soc. Lond. B212,
351-379 (1981).
Molecular machines:
A. Libchaber, Genome stability, cell motility and force generation, Progress of Theoretical
Physics Supplement, No 130, p. 1, 1998.
D. Kuchnir et al, Mechanical forces in the biological world, the case of tubulin, actomyosin and Brownian particles, T. Riste and D. Sherrington (eds.), Physics of Biomaterials:
Fluctuations, Selfassembly and Evolution, 153-171 (1996).
D. Bray, Protein molecules as computational elements in living cells, Nature 376, 307-312
(1995).
H. Leff and A.F. Rex, Maxwell’s Demon: Entropy, Information, Computing, Princeton
Univ. Press (1990); Szilard; Brillouin.
F. Julicher et al., Modeling molecular motors, Rev. Mod. Phys. 69, 1269, 1997.
DNA:
J.F. Marko and E.D. Siggia, Statistical mechanics of supercoiled DNA, Phys. Rev. E 52,
2912-2938 (1995).
Computation:
R.P. Feynman, Feynman lectures on computation, eds. A.J.G. Hey and R.W. Allen,
Addison-Wesley Publishing Co., Inc. (1996).
J. Von Neuman, The general and logical theory of automata, edited version of a lecture
given in 1948 at the Hixon symposium, Pasadena, California, Von Neuman collected works,
Vol. V, p. 288.
Chemotaxis and Morphogenesis:
A.M. Turing, The chemical basis of morphogenesis, Phil. Trans. Roy. Soc. (London), B237,
37, 1952.
E.O. Burdene and H.C. Berg, Dynamics of formation of symmetrical patterns by
chemotactic bacteria, Lett. To Nature, 376, 49-53 (1995).
E. Ben-Jacob, I. Cohen and H. Levine, Cooperative self-organization of microorganisms,
Advances in Physics, vol 49, No 4, p. 395, 2000.
Brownian motion:
H.A. Kramers, Brownian motion in a field of force and the diffusion model of chemical
reactions, Physica VII no 4, 284-341 (1940).
H. Berg, Random walks in Biology.
Protein folding:
F.M. Richards, The Protein Folding Problem, Scientific American, Jan 1991, p. 34-41.
E.I. Shakhnovich and A.M. Gutin, Implications of Thermodynamics of Protein Folding for Evolution
of Primary Sequences, Nature, 346, 773-775, 1990.
H. Frauenfelder and P.G. Wolynes, Biomolecules: Where the Physics of Complexity and Simplicity
Meet, Physics Today, Feb. 1994, p. 58-64.
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J.D. Bryngelson et al, Funnels, Pathways, and the Energy Landscape of Protein Folding: A
Synthesis, in the Physics of Biological Systems: From Molecules to Species, European-Nordic Summer
School and Workshop-Krogerup Hojskole, Humlebaek, denemark Aug. 1995.
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