April 2004
‫ מקורות‬/‫מבוא לביופיסיקה‬
1.
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.
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.
2.
DNA single molecule measuremants and supercoiling
J.F. Marko and E.D. Siggia, Statistical mechanics of supercoiled DNA, Phys. Rev. E52, 2912
(1995).
D. Bensimon, http://www.msri.org/publications/ln/msri/2000/molbio/bensimon/1/
3.
Error correction in DNA and protein worlds:
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, Vol.5, 329-379.
A.R. Fersht, Enzymic editing mechanisms and the genetic code, Proc. R. Soc. Lond. B212, 351-379 (1981).
Kinetic Proofreading Hopfield.pdf
4.
Shape of vesicles:
S. Leibler, Equilibrium statistical mechanics of fluctuating films and membranes, in the Jerusalem Winter
School for theoretical Physics, statistical Mechanics of Membranes and Surfaces, 5th, p. 45, eds. D. Nelson, T.
Piran and S. Weinberg (1988).
S. Safran, Statistical Thermodynamics of Surfaces, Interfaces and Membranes.
5.
Maxwell demons:
H. Leff and A.F. Rex, Maxwell’s Demon: Entropy, Information, Computing, Princeton Univ. Press (1990);
Szilard; Brillouin.
6.
Receptors and pumps:
T.F. Weiss, Cellular Biophysics, Vol I, The MIT Press, Cambridge Massachusetts (1996).
7.
Feedback mechanisms, feedback inhibition:
J.D. Murray, Mathematical Biology, second edition (1993).
8.
Optical tweezers and their use in biophysical experiments:
K. Svoboda et al, Direct observation of kinesin stepping by optical trapping interferometry, Nature, 365, p.
721 (1993).
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H. Yin et al , Transcription against an applied force, Science 270, p. 1653 (1995).
D.A. Schafer et al, Transcription by single molecules of RNA polymerase observed by light microscopy,
Nature, 352, p. 444 (1991).
A. Simon, Princeton University thesis (have a copy of it).
9.
Biological motors:
D. Kuchnir et al, Mechanical forces in the biological world, the case of tubulin, acto-myosin 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.
T.A. McMahon, Muscles, Reflexes, and Locomotion (1984).
S.M. Block, Real engines of creation, Nature, 386, p. 217 (1997).
J.A. Spudich, How molecular motors work, Nature, 372, 515 (1994).
Kramers paper on escape from a potential well (two parts due to its size): Kramers-I.pdf Kramers-II.pdf
Modeling molecular motors; Frank Ju¨ licher, Armand Ajdari, and Jacques Prost, Reviews of Modern Physics,
Vol. 69, No. 4, October 1997
10.
The swimming bacteria and other swimmers at low Reynolds:
Purcell E.M., Life at low reynolds number, American J. of Physics, 45 p. 3 (1977).
H. Berg, Random walks in Biology.
11.
Chemotaxis:
E. Ben-Jacob, I. Cohen and H. Levine, Cooperative self-organization of microorganisms, Advances in
Physics, 49, 395 (2000).
E.O. Burdene and H.C. Berg, Dynamics of formation of symmetrical patterns by chemotactic bacteria, Lett.
To Nature, 376, 49-53 (1995).
J.D. Murray, Mathematical Biology, second edition (1993).
Frontiers in Biology: Development, special issue of Science vol 266, p. 561 (1994).
12.
Pattern formation in biological systems:
J.D. Murray, Mathematical Biology, second edition (1993).
A.M. Turing, The chemical basis of morphogenesis, Trans.R.Soc.Ser.B, 1952, 237, 37-73.
A.J. Koch and H. MeinhardtProject No.12\Koch.pdf, Biological pattern formation: from basic mechanisms to
complex structures, Rev. of Mod. Phys., 66, p. 1481 (1994).
D. Thompson, On Growth and Form.
13.
Nerve impulse propagation (inc. neural networks):
B. Hille, Ionic channels of Excitable membranes, second edition (1992).
Kandel, Schwartz and Jessel, Principles of Neuroscience, Third edition.
J.J. Jack, D. Noble and R.W. Tsein, Electric current flow in excitable cells, (1975).
R. FitzHugh, Mathematical models of excitation and propagation in nerve, in Biological Engineering, H.P.
Schwaned, p.1-85.
M. Abeles, Corticonics.
F. Rieke et al, Spikes.
D. J. Amit, Modeling Brain Function.
G.M. Shepard, Neurobiology.
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14.
Electrical transport in cells (inc. Muscle contraction):
D.J. Aidley, The Physiology of Excitable Cells, third edition (1996).
T.F. Weiss, Cellular Biophysics, Vol I, The MIT Press, Cambridge Massachusetts (1996).
B. Hille, Ionic channels of Excitable membranes, second edition (1992).
15.
Energy transduction-photosynthesis and mitochondria:
G.R. Fleming and R. V. Grondelle, the primary steps of photosynthesis, Physics Today, Feb. 1994 p. 48.
16.
Oscillators and switches in biology:
J.D. Murray, Mathematical Biology, second edition (1993).
17.
Transmembrane transport:
T.F. Weiss, Cellular Biophysics.
B. Hille, Ionic channels of Excitable membranes, second edition (1992).
18.
Reaction rate theories and stochastic resonance:
P. Hanggi, Reaction-rate theory: fifty years after Kramers, Rev. Mod. Physics, 62, 2 p. 251 (1990).
S. Chandrasekhar, Stochastic problems in physics and astronomy, Rev. Mod. Phys., 15, P.1 (1943).
K. Wiesenfeld and F. Moss, Stochastic resonance and the benefits of noise: from ice ages to crayfish and
SQUIDs, Nature, 373, 33 (1995).
M.O. Magnesco, Forced Thermal Ratchets, Phys. Rev. Lett., 71, 1477 (1993).
J. Rousselet et al, Directional motion of brownian particles induced by a periodic asymmetric potential,
Nature, 370, 446 (1994).
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