Quantitative understanding of biosystems: An introduction to biophysics

Quantitative Understanding of Biosystems: An Introduction to Biophysics

Volumn , Issue , 2011, Pages 1-549

  Nordlund, Thomas M ^a  

^a UNIVERSITY OF ALABAMA AT BIRMINGHAM   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CALCULATIONS; CHEMICAL ANALYSIS; COMPUTATIONAL CHEMISTRY; DIFFERENTIAL EQUATIONS; DIFFERENTIATION (CALCULUS); ENERGY TRANSFER; QUANTUM THEORY; STATISTICAL MECHANICS;

BIOLOGICAL PHYSICS; BIOLOGICAL STRUCTURES; COMPUTATIONAL TOOLS; MICROSCOPIC STRUCTURES; PROJECT EXPERIENCES; SPECTROSCOPIC CHARACTERIZATION; SUBCELLULAR STRUCTURE; VISUALIZATION TOOLS;

BIOLOGICAL SYSTEMS;

EID: 85059294721     PISSN: None     EISSN: None     Source Type: Book    
DOI: None     Document Type: Book

References (289)

1. Nobel Foundation, The Nobel Prize in Physiology or Medicine. 1962. Francis Crick, James Watson, Maurice Wilkins, Nobelprize.org, http://nobelprize.org/nobel_ prizes/medicine/laureates/1962/index.html.
2. Nobel Foundation, The Nobel Prize in Chemistry. 1962. Max F. Perutz, John C. Kendrew, Nobelprize.org, http://nobelprize.org/nobel_prizes/chemistry/laureates/ 1962/index.html.
3. Nobel Foundation, The Nobel Prize in Physiology or Medicine. 1969. Max Delbrück, Alfred D. Hershey, Salvador E. Luria, Nobelprize.org, http://nobelprize.org/nobel_ prizes/medicine/laureates/1969/delbruck-bio.html.
4. Nobel Foundation, The Nobel Prize in Chemistry. 1980. Paul Berg, Walter Gilbert, Frederick Sanger, Nobelprize.org, http://nobelprize.org/nobel_prizes/chemistry/ laureates/1980/index.html.
5. Nobel Foundation, The Nobel Prize in Chemistry. 1988. Johann Deisenhofer, Robert Huber, Hartmut Michel, Nobelprize.org, http://nobelprize.org/nobel_ prizes/chemistry/ laureates/1988/index.html.
6. Nobel Foundation, The Nobel Prize in Physiology or Medicine. 1991. Erwin Neher, Bert Sakmann, Nobelprize.org, http://nobelprize.org/nobel_prizes/medicine/laureates/ 1991/index.html.
7. Nobel Foundation, The Nobel Prize in Physiology or Medicine. 2003. Paul C. Lauterbur, Sir Peter Mansfield, Nobelprize.org, http://nobelprize.org/nobel_ prizes/medicine/laureates/2003/index.html.
8. McMasters, J. H. 1989. The flight of the bumblebee and related myths of entomological engineering. Am Sci 77:164-168.
9. Brown, R. 1828. A brief account of microscopical observations made in the months of June, July and August, 1827, on the particles contained in the pollen of plants. Philos Mag 4:161-173.
10. Kendrew, J. C., G. Bodo, H. M. Dintzis, R. G. Parrish, H. Wyckoff, and D. C. Phillips. 1958. A three-dimensional model of the myoglobin molecule obtained by x-ray analysis. Nature 181:662-666.
11. Muirhead, H., and M. F. Perutz. 1963. Structure of haemoglobin. A three-dimensional Fourier synthesis of reduced human haemoglobin at 5-5 A resolution. Nature 199:633-638.
12. Watson, J. D., and F. H. C. Crick. 1953. Molecular structure of nucleic acids: A structure for deoxyribose nucleic acid. Nature 171:737-738.
13. Watson, J. D., and F. H. C. Crick. 1953. Genetical implications of the structure of deoxyribonucleic acid. Nature 171:964-967.
14. Savageau, M. A. 1995. Michaelis-Menten mechanism reconsidered: Implications of fractal kinetics. J Theor Biol 176:115-124.
15. Xu, F., and H. Ding. 2007. A new kinetic model for heterogeneous (or spatially confined) enzymatic catalysis: Contributions from the fractal and jamming (overcrowding) effects. Appl Catal A Gen 317:70-81.
16. Franks, F. 1983. Polywater. Cambridge, MA: The MIT Press.
17. Valkanov, A. 1968. Das Neuston. Limnologica Berlin 6:381-403.
18. Atlas, R. M., and R. Bartha. 1998. Microbial Ecology. Upper Saddle River, NJ: Benjamin Cummings, 342-342.
19. Fleming, G. R., and M. A. Ratner. 2008. Grand challenges in basic energy sciences. Physics Today 61:28-33.
20. Alon, U. 2006. An Introduction to Systems Biology: Design Principles of Biological Circuits. Boca Raton, FL: Chapman & Hall/CRC.
21. Klafter, J., M. F. Shlesinger, and G. Zumofen. 1996. Beyond Brownian motion. Physics Today 49:33-39.
22. West, G. B., and J. H. Brown. 2004. Life's universal scaling laws. Physics Today 57:36-42.
23. Reif, F. 1967. Statistical Physics. New York, NY: McGraw-Hill, 350-357.
24. Voet, D., and J. G. Voet, 2004. Biochemistry, 39. New York, NY: John Wiley & Sons.
25. Catling, D. C., et al., 2005. Martian vistas (Editor's summary and following articles). Nature 436:42-69.
26. Franks, F., ed. 1972-1982. Water, A Comprehensive Treatise. New York, NY: Plenum Press, 7 vols.
27. Franks, F., ed. 2009. Water Science Reviews 5: Volume 5: The Molecules of Life. (Reissue edition). Cambridge, UK: Cambridge University Press.
28. Hasted, J. B. 1973. Aqueous Dielectrics. London: Chapman and Hall.
29. Eisenberg, D., and W. Kauzmann. 1969. The Structure and Properties of Water. London: Oxford University Press.
30. Finney, J. L., A. Halibrucker, I. Kohl, A. K. Soper, and D. T. Bowron. 2002. Structures of high and low density amorphous ice by neutron diffraction. Phys. Rev. Lett. 88:225503-225506.
31. Wermet, P., D. Nordlund, U. Bergmann, M. Cavalleri, M. Odelius, H. Ogasawara, L. Å. Näslund et al. 2004. The structure of the first coordination shell in liquid water. Science 304:995-999.
32. Morgan, J., and B. E. Warren. 1938. X-ray analysis of the structure of water. J. Chem. Phys. 6:666-673.
33. Soper, A. K. 2000. The radial distribution functions of water and ice from 200 to 673 K and at pressures up to 400 MPa. Chem. Phys. 258:121-137.
34. Franks, F. 2000. Water: A Matrix of Life. Cambridge, Great Britain: Royal Society of Chemistry, 27-28.
35. Debye, P. J. W. 1912. Polar molecules. Phys. Z. 13:97
36. Onsager, L. 1936. Electric moments of molecules in liquids. J. Am. Chem. Soc. 58:1486-1493.
37. Fröhlich, H. 1987. Theory of Dielectrics (2nd Ed.). Oxford: Oxford University Press, 1-200.
38. Sheinerman, F. B., R. Norel, and B. Honig. 2000. Electrostatic aspects of protein-protein interactions. Curr. Opin. Struct. Biol. 10:153-159.
39. Dix, J. A., and A. S. Verkman. 2008. Crowding effects on diffusion in solutions and cells. Annu. Rev. Biophys. 37:247-263.
40. Takashima, S., A. Casaleggio, F. Giuliano, M. Morando, P. Arrigo, and S. Ridella. 1986. Study of bound water of poly-adenine using high frequency dielectric measurements. Biophys. J. 49:1003-1008.
41. Kendrew, J. C., R. E. Dickerson, B. E. Strandberg, R. G. Hart, D. R. Davies, D. C. Phillips, and V. C. Shore. 1960. Structure of myoglobin: A three-dimensional Fourier synthesis at 2 Å resolution. Nature 185:422-427.
42. Perutz, M. F., M. G. Rossman, A. F. Cullis, H. Muirhead, G. Will, and A. C. T. North. 1960. Structure of hæmoglobin: A three-dimensional Fourier synthesis at 5.5-Å resolution, obtained by X-ray analysis. Nature 185:416-422.
43. Richardson, J. S. 1981. The anatomy and taxonomy of protein structure. In Advances in Protein Chemistry, ed. C. B. Anfinsen, J. T. Edsall, and F. M. Richards, 34:168-364. New York, NY: Academic Press.
44. Reilly, C. 2004. The Nutritional Trace Metals. Oxford, UK: Wiley-Blackwell.
45. Richardson, J. S., and Richardson, D. C. 1989. In Prediction of Protein Structure and the Principles of Protein Conformation, ed. G. D. Fasman. New York, NY: Plenum Press.
46. Rost, B., G. Yachdav, and J. Liu. 2004. PredictProtein: The PredictProtein Server. Nucleic Acids Res. 32:W321-W326.
47. Voet, D., and J. G. Voet. 2004. Biochemistry, 224. New York, NY: John Wiley & Sons.
48. Pace, C., and S. JM. 1998. A helix propensity scale based on experimental studies of peptides and proteins. Biophys. J. 75:422-427.
49. Arora, N., and B. Jayaram. 1997. Strength of hydrogen bonds in a helices. J. Comput. Chem. 18:1245-1252.
50. Engelman, D. M., T. A. Steitz, and A. Goldman. 1986. Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins. Annu. Rev. Biophys. Biophys. Chem. 15:321-353.
51. Kyte, J., and R. Doolittle. 1982. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157:105-132.
52. Chaplin, M. 2009. Water Structure and Science. London: Creative Commons, www .lsbu.ac.uk/water/.
53. Eckert, R. L. 1988. Sequence of the human 40-kDa keratin reveals an unusual structure with very high sequence identity to the corresponding bovine keratin. Proc. Natl. Acad. Sci. U S A 85:1114-1118.
54. Barnard, K., N. D. Light, T. J. Sims, and A. J. Bailey. 1987. Chemistry of the collagen cross-links. Origin and partial characterization of a putative mature cross-link of collagen. Biochem. J. 244:303-309.
55. Robinson, C. R., Y. Liu, J. A. Thomson, J. M. Sturtevant, and S. G. Sligar. 1997. Energetics of heme binding to native and denatured states of cytochrome b562. Biochemistry 36:16141-16146.
56. Lin, L., R. J. Pinker, K. Forde, G. D. Rose, and N. R. Kallenbach. 1994. Molten globular characteristics of the native state of apomyoglobin. Nat. Struct. Biol. 1:447-452.
57. Kitahara, R., H. Yamada, K. Akasaka, and P. E. Wright. 2002. High pressure NMR reveals that apomyoglobin is an equilibrium mixture from the native to the unfolded. J. Mol. Biol. 320:311-319.
58. Frauenfelder, H., F. Parak, and R. D. Young. 1988. Conformational substates in proteins. Annu. Rev. Biophys. Biophys. Chem. 17:451-479.
59. Frauenfelder, H., G. A. Petsko, and D. Tsernoglou. 1979. Temperature-dependent X-ray diffraction as a probe of protein structural dynamics. Nature 425, 21 (04 September 2003); doi:10.1038/425021a 280:558-563.
60. Davis, R. C., and I. J. Tinoco. 1968. Temperature-dependent properties of dinucleoside phosphates. Biopolymers 6:223-242.
61. Ke, C., M. Humeniuk, H. S-Gracz, and P. E. Marszalek. 2007. Direct measurements of base stacking interactions in DNA by single-molecule atomic-force spectroscopy. Phys. Rev. Lett. 99:018302.
62. Voet, D., and J. G. Voet. 2004. Biochemistry, 1122. New York, NY: John Wiley & Sons.
63. Gesteland, R. F., T. R. Cech, and J. F. Atkins, eds. 2005. The RNA World. 3rd ed. New York, NY: Cold Spring Harbor Laboratory Press.
64. Johnston, W. K., P. J. Unrau, M. S. Lawrence, M. E. Glasner, and D. P. Bartel. 2001. RNA-catalyzed RNA polymerization: Accurate and general RNA-templated primer extension. Science 292:1319-1325.
65. Breaker, R. R., and G. F. Joyce. 1994. A DNA enzyme that cleaves RNA. Chem. Biol. 9(4):403-415.
66. Schlosser, K., and Y. Li. 2009. Biologically inspired synthetic enzymes made from DNA. Chem. Biol. 16:311-322.
67. Huebner, J. S., E. Jakobsson, H. G. Dam, V. A. Parsegian, and R. H. Austin. 1997. Harness the hubris: Useful things physicists could do in biology. Phys. Today 50:11-14.
68. Brush, M. 1999. Sugars and splice. Glycobiology: The next frontier. Scientist 13:22-23.
69. Voet, D., and J. G. Voet. 2004. Biochemistry (Chapter 12). New York, NY: John Wiley & Sons.
70. Phillips, R., J. Kondev, and J. Theriot. 2009. Physical Biology of the Cell (Chapter 11). New York, NY: Garland Science.
71. GE Healthcare. 2007. Affinity Chromatography: Principles and Methods. Uppsala: GE Healthcare Bio-sciences. Download at www.gelifesciences.com/protein-purification.
72. Invitrogen, Staff. Molecular Probes: The Handbook. Life Technologies. www.invitrogen .com/site/us/en/home/References/Molecular-Probes-The-Handbook. Accessed 30 Aug, 2010.
73. Alberding, N., S. S. Chan, L. Eisenstein, H. Frauenfelder, D. Good, I. C. Gunsalus, T. M. Nordlund, M. F. Perutz, A. H. Reynolds, and L. B. Sorensen. 1978. Binding of carbon monoxide to isolated hemoglobin chains. Biochemistry 17:43-51.
74. Emerson, J. 2008. The Color of Blood: A Study in Scarlet. Web blog, http:// blogs.suntimes.com/scanners/2008/07/the_color_of_blood_a_study_in.html. Accessed 14 July, 2009.
75. Tanaka, H., K. Kato, E. Yamashita, T. Sumizawa, Y. Zhou, M. Yao, K. Iwasaki, M. Yoshimura, and T. Tsukihara. 2009. The structure of rat liver vault at 3.5 angstrom resolution. Science 323:384-388.
76. Weixlbaumer, A., S. Petry, C. M. Dunham, M. Selmer, A. C. Kelley, and V. Ramakrishnan. 2007. Crystal structure of the ribosome recycling factor bound to the ribosome. Nat. Struct. Mol. Biol. 14:733-737.
77. Hernández, F., and J. Avila. 2008. The role of glycogen synthase kinase 3 in the early stages of Alzheimers' disease. FEBS Lett. 582:3848-3854.
78. Carpita, N. C., and D. M. Gibeaut 1993. Structural models of primary cell walls in flowering plants: consistency of molecular structure with the physical properties of the walls during growth. Plant J. 3:1-30.
79. Briggs, D. E. G. 1999. Molecular taphonomy of animal and plant cuticles: selective preservation and diagenesis. Philos. Trans. R. Soc. B Biol. Sci. 354:7-17.
80. Round, F. E., and R. M. Crawford. 2007. The Diatoms. Biology and Morphology of the Genera. Cambridge: Cambridge University Press.
81. Drum, R. W., and R. Gordon. 2003. Star Trek replicators and diatom nanotechnology. Trends Biotechnol. 21:325-328.
82. Kröger, N., and N. Poulsen. 2008. Diatoms-from cell wall biogenesis to nanotechnology. Annu. Rev. Genet. 42:83-107.
83. Karttunen, M. 2009. Membrane Molecular Dynamics. www.apmaths.uwo.ca/ ~mkarttu/pope-5ns.mpg. Accessed 11 July, 2009.
84. Lakowicz, J. R. 1999. Principles of Fluorescence Spectroscopy. New York, NY: Kluwer Academic/Plenum Publishers.
85. Martí, J., and F. S. Csajka. 2003. Flip-flop dynamics in a model lipid bilayer membrane. Europhys. Lett. 61:409-414.
86. Tieleman, D. P., and S.-J. Marrink. 2006. Lipids out of equilibrium: Energetics of desorption and pore mediated flip-flop. J. Am. Chem. Soc. 128:12462-12467.
87. Bhattacharya, A. A., T. Grune, and S. Curry. 2000. Crystallographic analysis reveals common modes of binding of medium and long-chain fatty acids to human serum albumin. J. Mol. Biol. 303:721-732.
88. Sapaya, N., W. F. D. Bennetta, and D. P. Tielemana. 2009. Lipid flip-flop: influence of the bilayer composition and the presence of peptides. Biophys. J. 96:349.
89. Blatt, M. R., editor. 2004. Membrane Transport in Plants Annual Plant Reviews. London: Blackwell.
90. Forster, A. C., and G. M. Church. 2006. Towards synthesis of a minimal cell. Mol. Syst. Biol. 2:45. www.nature.com/msb/journal/v2/n1/full/msb4100090.html.
91. Gribaldo, S., and C. Brochier-Armanet. 2006. The origin and evolution of Archaea: A state of the art. Philos. Trans. R. Soc. Lond. B Biol. Sci. 361:1007-1022.
92. Cavalier-Smith, T. 2004. Only six kingdoms of life. Proc. R. Soc. 271:1251-1262.
93. Norris, V., and R. Root-Bernstein. 2009. The eukaryotic cell originated in the integration and redistribution of hyperstructures from communities of prokaryotic cells based on molecular complementarity. Int. J. Mol. Sci. 10:2611-2632.
94. Voet, D., and J. G. Voet. 2004. Biochemistry, 7. New York, NY: John Wiley & Sons.
95. Rucinsky, T. E., and E. H. Cota-Robles. 1974. Mesosome structure in Chromobacterium violaceum. J. Bacteriol. 118:717-724.
96. Courties, C., A. Vaquer, M. Troussellier, J. Lautier, M. J. Chrétiennot-Dinet, J. Neveux, C. Machado, and H. Claustre. 1994. Smallest eukaryotic organism. Nature 370:255.
97. Törnroth-Horsefield, S., and R. Neutze. 2008. Opening and closing the metabolite gate. Proc. Natl. Acad. Sci. U S A. 105:19565-19566.
98. Beck, M., F. Förster, M. Ecke, J. M. Plitzko, F. Melchior, G. Gerisch, W. Baumeister, and O. Medalia. 2004. Nuclear pore complex structure and dynamics revealed by cryoelectron tomography. Science 306:1387-1390.
99. Vollmar, F., C. Hacker, R. P. Zahedi, A. Sickmann, A. Ewald, U. Scheer, and M. C. Dabauvalle. 2009. Assembly of nuclear pore complexes mediated by major vault protein. J. Cell Sci. 5:780-786.
100. Howard, J. 2009. Mechanical signaling in networks of motor and cytoskeletal proteins. Annu. Rev. Biophys. Biomol. Struct. 38:217-234.
101. Krueger, A. P., B. B. Brown, and E. J. Scribner. 1941. The effect of sonic vibrations on phage, phage precursor and the bacterial substrate. J. Gen. Physiol. 24:691-698.
102. Norris, V., T. den Blaauwen, R. H. Doi, R. M. Harshey, L. Janniere, A. Jiménez-Sánchez, D. J. Jin, P. A. Levin, E. Mileykovskaya, A. Minsky, G. Misevic, C. Ripoll, M. Saier Jr., K. Skarstad, and M. Thellier. 2007. Toward a hyperstructure taxonomy. Annu. Rev. Microbiol. 61:309-329.
103. Singleton, K., N. Parvaze, K. R. Dama, K. S. Chen, P. Jennings, B. Purtic, M. D. Sjaastad, C. Gilpin, M. M. Davis, and C. Wülfing. 2006. A large T cell invagination with CD2 enrichment resets receptor engagement in the immunological synapse. J. Immunol. 177:4402-4413.
104. Hopfield, J. J. 1974. Electron transfer between biological molecules by thermally activated tunneling. Proc. Natl. Acad. Sci. U S A 71:3640-3644.
105. Valiev, M., R. Kawai, J. A. Adams, and J. H. Weare. 2003. The role of the putative catalytic base in the phosphoryl transfer reaction in a protein kinase: first principles calculations. J. Am. Chem. Soc. 125:9926-9927.
106. Olson, J. S., E. W. Foley, D. H. Maillett, and E. V. Paster. 2003. Measurement of rate constants for reactions of O2, CO, and NO with hemoglobin. In Hemoglobin Disorders. Molecular Methods and Protocols, ed. R. L. Nagel. Totowa, NJ: Humana Press, p. 74.
107. Barth, A., and C. Zscherp. 2002. What vibrations tell us about proteins. Q. Rev. Biophys. 35:369-430.
108. Pelton, J. T., and L. R. McLean. 2000. Spectroscopic methods for analysis of protein secondary structure. Anal. Biochem. 277:167-176.
109. Matthäus, C., B. Bird, M. Miljkovic, T. Chernenko, M. Romeo, and M. Diem. 2008. Chapter 10: Infrared and Raman microscopy in cell biology. Methods Cell Biol. 89:275-308.
110. Harz, M., P. Rösch, and J. Popp. 2009. Vibrational spectroscopy-A powerful tool for the rapid identification of microbial cells at the single-cell level. Cytometry A 75:104-113.
111. Zhuang, W., T. Hayashi, and S. Mukamel. 2009. Coherent multidimensional vibrational spectroscopy of biomolecules: concepts, simulations, and challenges. Angew. Chem. Int. Ed. Engl. 48:3750-3781.
112. Schwesyg, J. R., T. Beckmann, A. S. Zimmermann, K. Buse, and D. Haertle. 2009. Fabrication and characterization of whispering-gallery-mode resonators made of polymers. Opt. Express 17:2573-2578.
113. Bate, A. E. 1938. Note on the whispering gallery of St. Paul's Cathedral, London. Proc. Phys. Soc. 50:293-297.
114. Astratov, V. N., and S. P. Ashili. 2007. Percolation of light through whispering gallery modes in 3D lattices of coupled microspheres. Opt. Express 15:17351-17361.
115. Vollmer, F., S. Arnold, and D. Keng. 2008. Single virus detection from the reactive shift of a whispering-gallery mode. Proc. Natl. Acad. Sci. U. S. A. 105:20701-20704.
116. Clement-sengewald, A., K. Schütze, A. Ashkin, G. A. Palma, G. Kerlen, and G. Brem. 1996. Fertilization of bovine oocytes induced solely with combined laser microbeam and optical tweezers. J. Assist. Reprod. Gen. 13:259-265.
117. Seeger, S., S. Monajembashi, K.-J. Hutter, G. Futterman, J. Wolfrum, and K. O. Greulich. 1991. Application of laser optical tweezers in immunology and molecular genetics. Cytometry 12:497-504.
118. Yin, H., M. D. Wang, K. Svoboda, R. Landick, S. M. Block, and J. Gelles. 1995. Transcription against an applied force. Science 270:1653-1657.
119. Green, L., C. H. Kim, C. Bustamante, and I. Tinoco Jr. 2008. Characterization of the mechanical unfolding of RNA pseudoknots. J. Mol. Biol. 375:511-528.
120. Avery, N. C., T. J. Sims, and A. J. Bailey. 2009. Quantitative determination of collagen cross-links. Methods Mol. Biol. 522:103-121.
121. Lakowicz, J. R. 2006. Principles of Fluorescence Spectroscopy. 3rd ed. New York, NY: Springer.
122. Huang, B., M. Bates, and X. Zhuang. 2009. Super-resolution fluorescence microscopy. Annu. Rev. Biochem. 78:993-1016.
123. Resch-Genger, U., M. Grabolle, S. Cavaliere-Jaricot, R. Nitschke, and T. Nann. 2008. Quantum dots versus organic dyes as fluorescent labels. Nat. Methods 5:763-775.
124. Molecular Probes-The Handbook. 2009. Carlsbad, CA: Invitrogen (Molecular Probes). http://www.invitrogen.com/site/us/en/home/References/Molecular-Probes-The-Handbook.html.
125. Levi, V., and E. Gratton. 2007. Exploring dynamics in living cells by tracking single particles. Cell Biochem. Biophys. 48:1-15.
126. Demchenko, A. P., Y. Mély, G. Duportail, and A. S. Klymchenko. 2009. Monitoring biophysical properties of lipid membranes by environment-sensitive fluorescent probes. Biophys. J. 96:3461-3470.
127. Lee, J. S., Y. K. Kim, M. Vendrell, and Y. T. Chang. 2009. Diversity-oriented fluorescence library approach for the discovery of sensors and probes. Mol. Biosyst. 5:411-421.
128. Thornton, S. T., and A. Rex. 2006. Modern Physics for Scientists and Engineers, 315. Belmont, CA: Thomson (Brooks/Cole).
129. Hoshino, A., N. Manabe, K. Fujioka, K. Suzuki, M. Yasuhara, and K. Yamamoto. 2007. Use of fluorescent quantum dot bioconjugates for cellular imaging of immune cells, cell organelle labeling, and nanomedicine: surface modification regulates biological function, including cytotoxicity. J. Artif. Organs 10:149-157.
130. Helland, A., P. Wick, A. Koehler, K. Schmid, and C. Som. 2007. Reviewing the environmental and human health knowledge base of carbon nanotubes. Environ. Health Perspect. 115:1125-1131.
131. Einstein, A. 1917. Zur Quantentheorie der Strahlung (On the quantum mechanics of radiation). Phys. Z. 18:121-128.
132. Strickler, S. J., and R. A. Berg. 1962. Relationship between absorption intensity and fluorescence lifetime of molecules. J. Chem. Phys. 37:814-822.
133. Clegg, R. M. 1996. Fluorescence resonance energy transfer. In Fluorescence Imaging Spectroscopy and Microscopy, ed. X. F. Wang, and B. Herman, 179-252. New York, NY: John Wiley & Sons.
134. Photosynthesis and the Web: 2008, www.life.illinois.edu/govindjee/photoweb/index.html or http:// photoscience.la.asu.edu/photosyn/photoweb/, accessed 18 August, 2009.
135. U.S. Energy Information Administration report, released June-December 2008, http://www.eia.doe.gov/emeu/iea/Notes%20for%20Table%201_8.html, accessed August 10, 2009.
136. Buick, R. 2008. When did oxygenic photosynthesis evolve? Philos. Trans. R. Soc. Lond., B, Biol. Sci. 363:2731-2743.
137. Ke, B. 2001. Photosynthesis: Photochemistry and Photobiophysics. Dordrecht: Kluwer Academic Publishing.
138. Parson, W. W. 1978. Thermodynamics of the primary reactions in photosynthesis. Photochem. Photobiol. 28:389-393.
139. Voet, D., and J. G. Voet. 2004. Biochemistry, 3rd ed. New York, NY: John Wiley & Sons, p. 896.
140. Emerson, R., and W. Arnold. 1932. The photochemical reaction in photosynthesis. J. Gen. Physiol. 16:191-205.
141. D. Krogmann. 2005. Discoveries in oxygenic photosynthesis (1727-2003): A perspective. In Discoveries in Photosynthesis, ed. Govindjee, J. T. Beatty, H. Gest, and J. F. Allen, 63-105. New York, NY: Springer.
142. Duysens, L. N. M. 1952. Transfer of excitation energy in photosynthesis. PhD thesis, State University at Utrecht, Utrecht.
143. Parson, W. W. 2006. Electron donors and acceptors in the initial steps of photosynthesis in purple bacteria: A personal account. In Advances in Photosynthesis and Respiration, ed. Govindjee, J. T. Beatty, H. Gest, and J. F. Allen, 213-224. Dordrecht: Springer.
144. Ke, B. 2001. Chapter 1: Photosynthesis: An Overview. In Photosynthesis: Photochemistry and Photobiophysics. New York, NY: Kluwer Academic Publishing.
145. Emerson, R., R. Chalmers, and C. Cederstrand. 1957. Some factors influencing the long-wave limit of photosynthesis. Proc. Natl. Acad. Sci. U. S. A., 43:133-143.
146. Greenbaum, E., J. W. Lee, C. V. Trevault, S. L. Blankinship, and L. J. Mets. 1995. CO2 fixation and photoevolution of H2 and O2 in a mutant of Chlamydomonas lacking photosystem I. Nature 376:438-441.
147. Amunts, A., O. Drory, and N. Nelson. 2007. The structure of a plant photosystem I supercomplex at 3.4 A resolution. Nature 447:58-63.
148. Sener, M. K., C. Jolley, A. Ben-Shem, P. Fromme, N. Nelson, R. Croce, and K. Schulten. 2005. Comparison of the light harvesting networks of plant and cyanobacterial photosystem I. Biophys. J. 89:1630-1642.
149. Sener, M. K., S. Park, D. Lu, A. Damjanovic, T. Ritz, P. Fromme, and K. Schulten. 2004. Excitation migration in trimeric cyanobacterial photosystem I. J. Chem. Phys. 120:11183-11195.
150. Allen, J. P., G. Feher, T. O. Yeates, D. C. Rees, J. Deisenhofer, H. Michel, and R. Huber. 1986. Structural homology of reaction centers from Rhodopseudomanas sphaeroides and Rhodopseudomonas viridis as determined by x-ray diffraction. Proc. Natl. Acad. Sci. U. S. A. 83:8589-8593.
151. Hu, X., A. Damjanovic, T. Ritz, and K. Schulten. 1997. Architecture and function of the light harvesting apparatus or purple bacteria. In Theoretical Biophysics Technical Reports, 1-28. Urbana, IL: University of Illinois at Urbana-Champaign.
152. Förster, T. 1948. Zwischenmoleckulare energiewanderung und fluoreszenz (Intermolecular energy transfer and fluorescence). Ann. Physik (ser. 6) 437:55-77.
153. Cory, M. G., M. C. Zerner, X. Hu, and K. Schulten. 1998. Electronic excitations in aggregates of bacteriochlorophylls. J. Phys. Chem. B 102:7640-7650.
154. Knox, R. S., and H. van Amerongen. 2002. Refractive index dependence of the Förster resonance excitation transfer rate. J. Phys. Chem. B 106:5289-5293.
155. Hu, X., A. Damjanovic, T. Ritz, and K. Schulten. 1998. Architecture and mechanism of the light-harvesting apparatus of purple bacteria. Proc. Natl. Acad. Sci. U. S. A. 95:5935-5941.
156. Borisov, A. Y. 2000. Why is electron transport in the reaction centers of purple bacteria unidirectional? Biochemistry (Moscow) 65:1429-1434.
157. Goldstein, R. A., L. Takiff, and S. G. Boxer. 1988. Energetics of initial charge separation in bacterial photosynthesis: The triplet decay rate in very high magnetic fields. Biochim. Biophys. Acta Bioenerg. 934:253-263.
158. Ferreira, K. N., T. M. Iverson, K. Maghlaoui, J. Barber, and S. Iwata. 2004. Architecture of the photosynthetic oxygen-evolving center. Science 303:1831-1838.
159. Woodward, J., M. Orr, K. Cordray, and E. Greenbaum. 2000. Biotechnology: Enzymatic production of biohydrogen. Nature 405:1014-1015.
160. Zhang, Y.-H. P. 2009. A sweet out-of-the-box solution to the hydrogen economy: Is the sugar-powered car science fiction? Energy Environ. Sci. 2:272-282.
161. Hambourger, M., A. Brune, D. Gust, A. L. Moore, and T. A. Moore. 2005. Enzyme-assisted reforming of glucose to hydrogen in a photoelectrochemical cell. Photochem. Photobiol. 81:1015-1020.
162. Takeuchi, Y., and Y. Amao. 2004. Photo-operated glucose-O2 biofuel cell based on the visible-light photosensitization of chlorophyll derivatives adsorbed on nanocrystalline TiO2 film. J. Japan Petrol. Inst. 47:355-358.
163. Kanan, M. W., and D. G. Nocera. 2008. In situ formation of an oxygen-evolving catalyst in neutral water containing phosphate and Co2+. Science 321:1072-1075.
164. Brimblecombe, R., G. F. Swiegers, G. C. Dismukes, and L. Spiccia. 2008. Sustained water oxidation photocatalysis by a bioinspired manganese cluster. Angew. Chem. (Int. Ed.) 47:7335-7338.
165. Brimblecombe, R., D. R. J. Kolling, A. M. Bond, G. C. Dismukes, G. F. Swiegers, and L. Spiccia. 2009. Sustained water oxidation by [Mn4O4]7+ core complexes inspired by oxygenic photosynthesis. Inorg. Chem. 48:7269-7279.
166. Nocera, D. Fall meeting of the American Chemical Society, Philadelphia, quoted by Katharine Sanderson in Chemistry for the climate, Nature Reports (online), October, 2008, pp. 124-125, doi:10.1038/climate.2008.96.
167. Fischer, A. 2009. Quantum wells boost solar efficiency. In Photonics Spectra, 32. Pittsfield, MA: Laurin Publishing.
168. Vass, I., A. Szilard, and C. Sicora. 2005. Adverse effects of UV-B light on the structure and function of the photosynthetic apparatus (Chapter 43). In Handbook of Photosynthesis, ed. M. Pessarakli, 827-842. Baton Rouge, LA: CRC Press.
169. RCA Corporation. 1974. Electro-Optics Handbook. Technical Series EOH-11. Lancaster, PA: RCA Corp.
170. Koller, L. R. 1952. Ultraviolet Radiation, 3. New York, NY: John Wiley & Sons.
171. Allamandola, L. J., S. A. Sandford, and B. Wopenka. 1987. Interstellar polycyclic aromatic hydrocarbons and carbon in interplanetary dust particles and meteorites. Science 237:56-59.
172. Shock, E. L., and M. D. Schulte. 1990. Amino-acid synthesis in carbonaceous meteorites by aqueous alteration of polycyclic aromatic hydrocarbons. Nature 343:728-731.
173. Greenberg, J. M., O. M. Shalabiea, C. X. Mendoza-Gomez, W. Schutte, and P. A. Gerakines. 1995. Origin of organic matter in the protosolar nebula and in comets. Adv. Space Res. 16:9-16.
174. Arnoult, K. M., T. J. Wdowiak, and L. W. Beegle. 2000. Laboratory investigation of the contribution of complex aromatic/aliphatic polycyclic hybrid molecular structures to interstellar ultraviolet extinction and infrared emission. Astrophys. J. 535:815-822.
175. Sandford, S. A. et al. 2006. Organics captured from comet 81P/Wild 2 by the Stardust spacecraft. Science 314:1720-1724.
176. Thornton, S. T., and A. Rex. 2006. Modern Physics for Scientists and Engineers, 114-118. Belmont, CA: Thomson (Brooks/Cole).
177. Ozone Commission. 1991. Guidance for the use of new ozone absorption coefficients in processing Dobson and Brewer spectrophotometer total ozone data beginning 1 January 1992. International Ozone Commission Report, Geneva, www.esrl.noaa.gov/gmd/ozwv/dobson/papers/coeffs.html.
178. Solov'ev, A. A., Z. K. Makhneva, and Y. Erokhin. 2001. UV-Induced destruction of light-harvesting complexes from purple bacterium Chromatium minutissimum. Membr. Cell Biol. 14:463-474.
179. Smith, K. C., and P. C. Hanawalt. 1969. Molecular Photobiology, 87-88. New York, NY: Academic Press.
180. Xu, D., and T. M. Nordlund. 2000. Sequence dependence of energy transfer in DNA oligonucleotides. Biophys. J. 78:1042-1058.
181. Gueron, M., J. Eisinger, and A. A. Lamola. 1974. Excited states of nucleic acids. In Basic Principles in Nucleic Acid Chemistry, ed. P. O. P. T'so, 311-398. New York, NY: Academic Press.
182. Aida, M., F. Inoue, M. Kaneko, and M. Dupuis. 1997. An ab initio MO study on fragmentation reaction mechanism of thymine dimer radical cation. J. Am. Chem. Soc. 119:12274-12279.
183. Zheng, X., J. Garcia, and A. A. Stuchebrukhov. 2008. Theoretical study of excitation energy transfer in DNA photolyase. J. Phys. Chem. B 112:8724-8729.
184. Klar, T., G. Kaiser, U. Hennecke, T. Carell, A. Batschauer, and L.-O. Essen. 2006. Natural and non-natural antenna chromophores in the DNA photolyase from Thermus thermophilus. Chembiochem 7(11):1798-1806.
185. Tian, W. D., R. Gillies, L. Brancaleon, and N. Kollias. 2001. Aging and effects of ultraviolet A exposure may be quantified by fluorescence excitation spectroscopy in vivo. J. Invest. Dermatol. 116:840-845.
186. Uitto, J. 2008. The role of elastin and collagen in cutaneous aging: Intrinsic aging versus photoexposure. J. Drugs Dermatol. 7:s12-s16.
187. Zeise, L., M. R. Chedekel, and T. B. Fitzpatrick, eds. 1995. Melanin: Its Role in Human Photoprotection, 299. Overland Park, KS: American Society for nknown. Rodolfo Alessandro Nicolaus. http://www.tightrope.it/nicolaus/index .htm (accessed 15 September 2009).Photobiology/Valdenmar Publishing Co.
188. Diffey, B. L. 2001. When should sunscreen be reapplied? J. Am. Acad. Dermatol. 45:882-885.
189. Hayden, C. G., M. S. Roberts, and H. A. Benson. 1997. Systemic absorption of sunscreen after topical application. Lancet 350:863-864.
190. Morgan, T. M., B. L. Reed, and B. C. Finnin. 1998. Enhanced skin permeation of sex hormones with novel topical spray vehicles. J. Pharm. Sci. 87:1213-1218.
191. Diffey, B., and P. Farr. 1991. Sunscreen protection against UVB, UVA and blue light: An in vivo and in vitro comparison. Br. J. Dermatol. 124:258-263.
192. McKinlay, A. F., and B. L. Diffey. 1987. A reference action spectrum for ultra-violet induced erythema in human skin. In Human Exposure to Ultraviolet Radiation: Risks and Regulations. W. F. Passchier, and B. F. M. Bosnjakovich, editors. New York, NY: Excerpta Medica Division, Elsevier Science Publisher. pp. 83-87.
193. Krishnan, R., and T. M. Nordlund. 2008. Fluorescence dynamics of three UV-B sunscreens. J. Fluoresc. 18:203-217.
194. Allen, J. M., C. J. Gossett, and S. F. Allen. 1996. Photochemical formation of singlet molecular oxygen (1O2) in illuminated aqueous solutions of p-aminobenzoic acid (PABA). J. Photochem. Photobiol. B Biol. 32:33-37.
195. Allen, J. M., C. J. Gossett, and S. K. Allen. 1996. Photochemical formation of singlet molecular oxygen in illuminated aqueous solutions of several commercially available sunscreen active ingredients. Chem. Res. Toxicol. 9:605-609.
196. Hanson, K. M., E. Gratton, and C. J. Bardeen. 2006. Sunscreen enhancement of UV-induced reactive oxygen species in the skin. Free Radic. Biol. Med. 41:1205-1212.
197. Krishnan, R., S. Pradhan, L. Timares, S. K. Katiyar, C. A. Elmets, and T. M. Nordlund. 2006. Fluorescence of sunscreens adsorbed to dielectric nanospheres: Parallels to optical behavior on HaCat cells and skin. Photochem. Photobiol. 82:1557-1565.
198. Henry, E. R., W. A. Eaton, and R. M. Hochstrasser. 1986. Molecular dynamics simulations of cooling in laser-excited heme proteins. Proc. Natl. Acad. Sci. U. S. A. 83:8982-8986.
199. Schreier, W. J., T. E. Schrader, F. O. Koller, P. Gilch, C. E. Crespo-Hernández, V. N. Swaminathan, T. Carell, W. Zinth, and B. Kohler. 2007. Thymine dimerization in DNA is an ultrafast photoreaction. Science 315:625-629.
200. Mo, Y., K. T. Turner, and I. Szlufarska. 2009. Friction laws at the nanoscale. Nature 425, 21 (04 September 2003); doi:10.1038/425021a 457:1116-1119.
201. Hay, S., R. M. Evans, C. Levy, E. J. Loveridge, X. Wang, D. Leys, R. K. Allemann, and N. S. Scrutton. 2009. Are the catalytic properties of enzymes from piezophilic organisms pressure adapted? Chembiochem 6(8), 1419-1422
202. von Arx, W. S. 1962. An Introduction to Physical Oceanography. Reading, MA: Addison-Wesley.
203. Keller, E. http://www.extremescience.com/zoom/index.php/life-in-the-deep-ocean/39-viperfish-fangtooth, accessed 5 Sept., 2010.
204. Zahn, K., R. Lenke, and G. Maret. 1994. Friction coefficient of rod-like chains of spheres at very low Reynolds numbers: I. Experiment. J. Phys. II 4:555-560.
205. Serdyuk, I. N., N. R. Zaccai, and J. Zaccai. 2007. Methods in Molecular Biophysics, 272-290. Cambridge: Cambridge University Press.
206. Levinthal, C. 1969. How to fold graciously. In Mössbauer Spectroscopy in Biological Systems, Ed. P. Debrunner, J. C. M. Tsibris, and E. Münck, 22-24. Monticello: University of Illinois, Allerton House.
207. Levinthal, C. 1968. Are there pathways for protein folding? Journal de Chimie Physique et de Physico-Chimie Biologique 65:44-45.
208. Zwanzig, R., A. Szabo, and B. Bagchi. 1992. Levinthal's paradox. Proc. Natl. Acad. Sci. USA 89:20-22.
209. A. Einstein, 1905. "über die von der molekularkinetischen Theorie der Wärme geforderte Bewegung von in ruhenden Flüssigkeiten suspendierten Teilchen," Annalen der Physik 17:549-560.
210. Reif, F. 1967. Statistical Physics. New York: McGraw-Hill, 73.
211. Nelson, P. 2004. Biological Physics. New York: W. H. Freeman, 117-118.
212. Dauty, E., and A. S. Verkman. 2005. Actin cytoskeleton as the principal determinant of size-dependent DNA mobility in cytoplasm. J. Biol. Chem. 280:7823-7828.
213. Volkmuth W. D., and R. H. Austin. 1992. DNA electrophoresis in microlithographic arrays. Nature 358:600-602.
214. Morton, K. J., K. Loutherback, D. W. Inglis, O. K. Tsui, J. C. Sturm, S. Y. Chou, and R. H. Austin. 2008. Hydrodynamic metamaterials: microfabricated arrays to steer, refract, and focus streams of biomaterials. Proc. Natl. Acad. Sci. USA 105:7434-7438.
215. Nordlund, T. M., and W. H. Knox. 1981. Lifetime of fluorescence from light-harvesting chlorophyll a/b proteins: excitation intensity dependence. Biophys. J. 35:193-201;
216. Greene, B. I., and R. R. Millard. 1985. Singlet-exciton fusion in molecular solids: a direct subpicosecond determination of time-dependent annihilation rates. Phys. Rev. Lett. 55:1331-1333.
217. Gillbro, T., Å. Sandström, M. Spangfort, V. Sundström, and R. van Grondelle. 1988. Excitation energy annihilation in aggregates of chlorophyll a/bC, Biochim. Biophys. Acta 934:369-374.
218. Tanford, C. 1961. Physical Chemistry of Macromolecules. New York: John Wiley.
219. Friddle, R. W., J. E. Klare, S. S. Martin, M. Corzett, R. Balhorn, E. P. Baldwin, R. J. Baskin, and A. Noy. 2004. Mechanism of DNA Compaction by Yeast Mitochondrial Protein Abf2p. Biophys. J. 86:1632-1639.
220. Ramstein, J., and R. Lavery. 1988. Energetic coupling between DNA bending and base pair opening. Proc. Natl. Acad. Sci. USA 85:7231-7235.
221. Hogan M. E., and R. H. Austin. 1987. Importance of DNA stiffness in protein-DNA binding specificity. Nature 329:263-266.
222. Nordlund, T. M., S. Andersson, L. Nilsson, R. Rigler, A. Graslund, and L. W. McLaughlin. 1989. Structure and dynamics of a fluorescent DNA oligomer containing the EcoRI recognition sequence: fluorescence, molecular dynamics, and NMR studies. Biochemistry 28:9095-9103.
223. Yuan, C., H. Chen, X. W. Lou, and L. A. Archer. 2008. DNA bending stiffness on small length scales. Phys. Rev. Lett. 100:018102.
224. Serway, R. A. 1990. Physics for Scientists and Engineers. Philadelphia: Saunders, 574-578.
225. Landau, L. D., and E. M. Lifshitz. 1969. Statistical Physics. Reading, Mass.: Addison-Wesley.
226. Moore, W. J. 1972. Physical Chemistry. Englewood Cliffs, N.J.: Prentice-Hall. 4. Moore, Physical Chemistry, p. 195.
227. Wikipedia, "Sackur-Tetrode Equation," Wikipedia. http://en.wikipedia.org/wiki/ Sackur-Tetrode (accessed 19 November 2009).
228. Serdyuk, I. N., N. R. Zaccai, and J. Zaccai. 2007. Methods in Molecular Biophysics. New York: Cambridge University Press, 641-657.
229. Rechendorff, K., G. Witz, J. Adamcik, and G. Dietler. Persistence length and scaling properties of single-stranded DNA adsorbed on modified graphite. J. Chem. Phys. 131 (2009):095103.
230. Wall, F. T., L. A. J. Hiller, and D. J. Wheeler. 1954. Statistical computation of mean dimensions of macromolecules. I. J. Chem. Phys. 22:1036-1041.
231. Berg. H. C. 1993. Random Walks in Biology. Princeton, N.J.: Princeton University Press.
232. Perkins, T. T., D. E. Smith, and S. Chu. 1994. Direct observation of tube-like of a single polymer chain. Science 264:819-822.
233. Bao, X., H. J. Lee, and S. R. Quake. 2003. Behavior of complex knots in single DNA molecules. Phys. Rev. Lett. 91:265506.
234. Sundin, O., and A. Varshavsky. 1981. Arrest of segregation leads to accumulation of highly intertwined catenated dimers: dissection of the final stages of SV40 DNA replication. Cell 25:659-669.
235. Dean, F. B., A. Stasiak, T. Koller, and N. R. Cozzarelli. 1985. Duplex DNA knots produced by Escherichia coli topoisomerase I. Structure and requirements for formation. J. Biol. Chem. 260:4975-4983.
236. Voet, D., J. G. Voet, and C. W. Pratt. 1999. Fundamentals of Biochemistry. New York: John Wiley, 732-738.
237. Gebe, J. A., S. A. Allison, J. B. Clendenning, and J. M. Schurr. 1995. Monte Carlo simulations of supercoiling free energies for unknotted and trefoil knotted DNAs. Biophys. J. 68:619-633.
238. Vologodskii, A. 2009. Theoretical Models of DNA Topology Simplification by Type IIA DNA Topoisomerases. Nucleic Acids Res. 37:3135-3133.
239. Katritch, V., W. K. Olson, A. Vologodskii, J. Dubochet, and A. Stasiak. 2000. Tightness of random knotting. Phys. Rev. E 61:5545-5549.
240. Quake, S. R. 1995. Fast Monte Carlo algorithms for knotted polymers. Phys. Rev. E 52:1176-1180.
241. Nureki, O., M. Shirouzu, K. Hashimoto, R. Ishitani, T. Terada, M. Tamakoshi, T. Oshima, et al. 2002. An Enzyme with a Deep Trefoil Knot for the Active-Site Architecture, Acta Cryst. D 58:1129-1137.
242. Stryer, L. 1988. Biochemistry, 3rd ed., New York: W. H. Freeman, 319.
243. Privalov, P. L., and N. N. Khechinashvili. 1974. A thermodynamic approach to the problem of stabilization of globular protein structure: a calorimetric study. J. Mol. Biol. 86:665-684.
244. Welch, G. R., ed. 1986. New York: John Wiley. The Fluctuating Enzyme.
245. Austin, R. H., K. W. Beeson, L. Eisenstein, H. Frauenfelder, and I. C. Gunsalus. 1975. Dynamics of Ligand Binding to Myoglobin. Biochemistry 14:5355-5373.
246. Wikipedia, "Triosephosphate Isomerase," http://en.wikipedia.org/wiki/Triose_ phosphate_isomerase (accessed 4 December 2009).
247. Radzicka, A., and R. Wolfenden. 1995. A proficient enzyme. Science 267:90-93.
248. Weston, Jr., R. E., and H. E. Schwarz. 1972. Chemical Kinetics. Englewood Cliffs, N.J.: Prentice-Hall, 155-158.
249. Austin, R. H., K. W. Beeson, S. S. Chan, P. G. Debrunner, R. Downing, L. Eisenstein, H. Frauenfelder, and T. M. Nordlund. 1976. Transient analyzer with logarithmic time base. Review of Scientific Instrumentation 47:445-447.
250. Wilson, M. C., and A. K. Galwey. 1973. Compensation effect in heterogeneous catalytic reactions including hydrocarbon formation on clays. Nature 243:402-404.
251. Hopfield, J. J. Electron transfer between biological molecules by thermally activated tunneling. Proc. Natl. Acad. Sci. U S A 71 (1974):3640-3644.
252. D. DeVault. 1989. Tunneling enters biology. Photosynthesis Res. 22:3-10.
253. Alberding, N., R. H. Austin, K. W. Beeson, S. S. Chan, L. Eisenstein, H. Frauenfelder, and T. M. Nordlund. 1976. Tunneling in ligand binding to heme proteins. Science 192:1002-1004.
254. Meyer, M. P., D. R. Tomchick, and J. P. Klinman. Enzyme structure and dynamics affect hydrogen tunneling: the impact of a remote side chain (I553) in soybean lipoxygenase-1. Proc. Natl. Acad. Sci. U S A 105 (2008):1146-1151.
255. Oppenländer, A., A. C. Rambaud, H. P. Trommsdorff, and J. C. Vial. 1989. Translational tunneling of protons in benzoic-acid crystals. Phys. Rev. Lett. 63:1432-1435.
256. http://hyper textbook.com/facts/2001/JacquelineLing.shtml.
257. Nelson, P., 2008. Biological Physics (New York: W. H. Freeman), 572.
258. N. Serdyuk, N. R. Zaccai, and J. Zaccai. Methods in Molecular Biophysics. 2007. New York: Cambridge University Press.
259. Höök, P., X. Li, J. Sleep, S. Hughes, and L. Larsson, 1999. In vitro motility speed of slow myosin extracted from single soleus fibres from young and old rats. J. Physiol. 520:463-471.
260. Fehr, A. N., B. Gutiérrez-Medina, C. L. Asbury, and S. M. Block. 2009. On the origin of kinesin limping. Biophys. J. 97:1663-1670.
261. Ng, S. Y., B. Chaban, and K. F. Jarrell. 2006. Archaeal flagella, bacterial flagella and type IV pili: a comparison of genes and posttranslational modifications. J. Mol. Microbiol. Biotechnol. 11:167-191.
262. Berg, H. C. 1993. Chapter 6 in Random Walks in Biology. Princeton, N.J.: Princeton University Press.
263. Lang, E. R., and C. Rha. 1982. Apparent shear viscosity of native egg white. Int. J. Food Sci. Tech. 17:595-606.
264. Visscher, K., M. J. Schnitzer, and S. M. Block. 1999. Single kinesin molecules studied with a molecular force clamp. Nature 400:184-189.
265. Asbury, C. L. 2005. Kinesin: world's tiniest biped. Curr. Opin. Cell Biol. 17:89-97.
266. Bustamante, C., Z. Bryant, and S. B. Smith. 2003. Ten years of tension: singlemolecule DNA mechanics. Nature 421:423-427.
267. Nawroth, J. C., C. A. Greer, W. R. Chen, S. B. Laughlin, and G. M. Shepherd. 2007. An energy budget for the olfactory glomerulus. J. Neurosci. 27:9790-9800;
268. Kooijman, B. 2009. Dynamic Energy Budget Theory for Metabolic Organisation. New York, Cambridge University Press.
269. Smith, S. B., L. Finzi, and C. Bustamante. 1992. Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads. Science 258:1122-1126.
270. Schultz, S. C., G. C. Shields, and T. A. Steitz. 1991. Crystal structure of a CAP-DNA complex: the DNA is bent by 90°. Science 253:1001-1007.
271. Hogan, M. E., and R. H. Austin. 1987. Importance of DNA stiffness in protein-DNA binding specificity. Nature 329:263-266.
272. Steitz, T. A. 1990. Structural studies of protein-nucleic acid interaction: the sources of sequence-specific binding. Q. Rev. Biophys. 23:205-280.
273. Smith, D. E., S. J. Tans, S. B. Smith, S. Grimes, D. L. Anderson, and C. Bustamante. 2001. The bacteriophage straight 29 portal motor can package DNA against a large internal force. Nature 413:748-752.
274. Nierhaus, K. H., and D. N. Wilson, eds. 2004. Protein Synthesis and Ribosome Structure: Translating the Genome. Weinheim, Germany: Wiley-VCH Verlag.
275. Spirin, A. S. 2000. Ribosomes. New York: Springer.
276. Garrett, R. A., ed. 2000. The Ribosome: Structure, Function, Antibiotics, and Cellular Interactions. Washington, D.C.: AMS Press.
277. Cambre, K., Ribosomes, from the album, The Guy You Cheer For (Kinder Gentler Records, 2006).
278. Hayashi, T., and A. G. Szent-Gyorgyi, eds. 1966. Molecular Architecture in Cell Physiology. Englewood Cliffs, N.J.: Prentice-Hall.
279. Booth, C. R., A. S. Meyer, Y. Cong, M. Topf, A. Sali, S. J. Ludtke, W. Chiu, and J. Frydman. 2008. Mechanism of lid closure in the eukaryotic chaperonin TRiC/CCT. Nat. Struct. Mol. Biol. 15:746-753.
280. Böker, A., Y. Lin, K. Chiapperini, R. Horowitz, M. Thompson, V. Carreon, T. Xu, et al. 2004. Hierarchical nanoparticle assemblies formed by decorating breath figures. Nat. Mater. 3:302-306.
281. Nguyen, T. T., and B. I. Shklovskii. 2001. Complexation of DNA with positive spheres: phase diagram of charge inversion and reentrant condensation. J. Chem. Phys. 115:7298-7308.
282. Cherstvy, A. G. 2009. Positively charged residues in DNA-binding domains of structural proteins follow sequence-specific positions of DNA phosphate groups. J. Phys. Chem. B 113:4242-4247.
283. Yang, Y., A. P. Lyubartsev, N. Korolev, and L. Nordenskio. 2009. Computer modeling reveals that modifications of the histone tail charges define salt-dependent interaction of the nucleosome core particles. Biophys. J. 96:2082-2094.
284. Ren, Q., and M. A. Gorovsky. 2001. Histone H2A.Z acetylation modulates an essential charge patch. Mol. Cell 7:1329-1335.
285. Henikoff, S. 2005. Histone modifications: combinatorial complexity or cumulative simplicity? Proc. Natl. Acad. Sci. USA 102:5308-5309.
286. Pennings, S., S. Muyldermans, G. Meersseman, and L. Wyns. 1989. Formation, stability and core histone positioning of nucleosomes reassembled on bent and other nucleosome-derived DNA, J. Mol. Biol. 207:183-192.
287. Fu, Y., M. Sinha, C. L. Peterson, and Z. Weng. 2008. The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome. PLoS Genetics 4:e1000138.
288. Matulis, D., I. Rouzina, and V. A. Bloomfield. 2000. Thermodynamics of DNA binding and condensation: isothermal titration calorimetry and electrostatic mechanism. J. Mol. Biol. 296:1053-1063.
289. Krishnan, R., T. Jaleel, and T. Nordlund. "Imaging of DNA/Nanosphere Condensates" (paper presented at March Meeting of the American Physical Society, Los Angeles, Calif., 2005).