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Perspective: Reaches of chemical physics in biology
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1.
1. B. Alberts, A. Johnson, J. Lewis, and M. Raff, Molecular Biology of the Cell (Taylor & Francis, New York, 2007).
2.
2. A. M. Turing, Philos. Trans. R. Soc. London, Ser. B 237, 37 (1952).
http://dx.doi.org/10.1098/rstb.1952.0012
3.
3. L. Pauling, H. A. Itano, S. J. Singer, and I. C. Wells, Science 110, 543 (1949).
http://dx.doi.org/10.1126/science.110.2865.543
4.
4. M. Delbrück, Trans. Conn. Acad. Arts Sci. 38, 173 (1949)
4.[reprinted in J. Cairns, G. S. Stent, and J. D. Watson, Phage and the Origins of Molecular Biology, expanded edition (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1992)].
5.
5. J. D. Watson and F. H. C. Crick, Nature (London) 171, 737 (1953).
http://dx.doi.org/10.1038/171737a0
6.
6. L. Pauling, R. B. Corey, and H. R. Branson, Proc. Natl. Acad. Sci. U.S.A. 37, 205 (1951).
http://dx.doi.org/10.1073/pnas.37.4.205
7.
7. F. H. C. Crick, Nature (London) 227, 561 (1970).
http://dx.doi.org/10.1038/227561a0
8.
8. F. H. C. Crick, Symp. Soc. Exp. Biol. XII, 139 (1958).
9.
9. J. C. Kendrew, G. Bodo, H. M. Dintzis, R. G. Parrish, H. Wyckoff, and D. C. Phillips, Nature (London) 181, 662 (1958).
http://dx.doi.org/10.1038/181662a0
10.
10. M. F. Perutz, W. Bolton, R. Diamond, H. Muirhead, and H. Watson, Nature (London) 203, 687 (1964).
http://dx.doi.org/10.1038/203687a0
11.
11. C. B. Afinsen, Science 181, 223 (1973).
http://dx.doi.org/10.1126/science.181.4096.223
12.
12. F. A. Jacob and J. Monod, J. Mol. Biol. 3, 318 (1961).
http://dx.doi.org/10.1016/S0022-2836(61)80072-7
13.
13. J. Monod, J. Wyman, and J. P. Changeus, J. Mol. Biol. 12, 88 (1965).
http://dx.doi.org/10.1016/S0022-2836(65)80285-6
14.
14. F. H. C. Crick, What Mad Pursuit (Basic Books, New York, 1990).
15.
15. W. A. Eaton and R. M. Hochstrasser, J. Chem. Phys. 49, 985 (1968).
http://dx.doi.org/10.1063/1.1670263
16.
16. M. Eigen, G. Maass, and D. Porschke, Angew. Chem., Int. Ed. 6, 459 (1967).
http://dx.doi.org/10.1002/anie.196704591
17.
17. W. E. Moerner, J. Phys. Chem. B 106, 910 (2002).
http://dx.doi.org/10.1021/jp012992g
18.
18. A. Szabo and M. Karplus, J. Mol. Biol. 72, 163 (1972).
http://dx.doi.org/10.1016/0022-2836(72)90077-0
19.
19. M. Levitt and A. Warshel, Nature (London) 253, 694 (1975).
http://dx.doi.org/10.1038/253694a0
20.
20. S. J. Benkovic and S. Hammes-Schiffer, Science 312, 208 (2006).
http://dx.doi.org/10.1126/science.1127654
21.
21. M. Garcia-Vilaco, J. Gao, M. Karplus, and D. G. Truhlar, Science 303, 186 (2004).
http://dx.doi.org/10.1126/science.1088172
22.
22. H. Frauenfelder, S. Sligar, and P. G. Wolynes, Science 254, 1598 (1991).
http://dx.doi.org/10.1126/science.1749933
23.
23. Y. S. Kim, L. Liu, P. H. Axelsen, and R. M. Hochstrasser, Proc. Natl. Acad. Sci. U.S.A. 106, 17751 (2009).
http://dx.doi.org/10.1073/pnas.0909888106
24.
24. D. T. Gillespie, J. Chem. Phys. 81, 2340 (1977).
http://dx.doi.org/10.1021/j100540a008
25.
25. J. D. Bryngelson and P. G. Wolynes, Proc. Natl. Acad. Sci. U.S.A. 84, 7524 (1987).
http://dx.doi.org/10.1073/pnas.84.21.7524
26.
26. P. G. Wolynes, J. N. Onuchic, and D. Thirumalai, Science 267, 1619 (1995).
http://dx.doi.org/10.1126/science.7886447
27.
27. E. Shaknovich, Chem. Rev. 106, 1559 (2006).
http://dx.doi.org/10.1021/cr040425u
28.
28. K. A. Dill and H.-S. Chan, Nat. Struct. Biol. 4, 10 (1997).
http://dx.doi.org/10.1038/nsb0197-10
29.
29. J. N. Onuchic and P. G. Wolynes, Curr. Opin. Struct. Biol. 14, 70 (2004).
http://dx.doi.org/10.1016/j.sbi.2004.01.009
30.
30. K. A. Dill, S. B. Ozkan, M. S. Shell, and T. R. Weikl, Annu. Rev. Biophys. 37, 289 (2008).
http://dx.doi.org/10.1146/annurev.biophys.37.092707.153558
31.
31. D. Thirumalai, E. P. O’Brien, G. Morrison, and C. Hyeon, Annu. Rev. Biophys. 39, 159 (2010).
http://dx.doi.org/10.1146/annurev-biophys-051309-103835
32.
32. D. Thirumalai, Z. Liu, E. P. O’Brien, and G. Reddy, Curr. Opin. Struct. Biol. 23, 22 (2013).
http://dx.doi.org/10.1016/j.sbi.2012.11.010
33.
33. C. Hyeon and J. N. Onuchic, Proc. Natl. Acad. Sci. U.S.A. 104, 2175 (2007).
http://dx.doi.org/10.1073/pnas.0610939104
34.
34. J. Chen, S. Darst, and D. Thirumalai, Proc. Natl. Acad. Sci. U.S.A. 107, 12523 (2010).
http://dx.doi.org/10.1073/pnas.1003533107
35.
35. L. Lu, J. F. Dama, and G. A. Voth, J. Chem. Phys. 139, 121906 (2013).
http://dx.doi.org/10.1063/1.4811667
36.
36. M. Gur, E. Zomot, and I. Bahar, J. Chem. Phys. 139, 121912 (2013).
http://dx.doi.org/10.1063/1.4816375
37.
37. H. H. Truong, B. L. Kim, N. P. Schafer, and P. G. Wolynes, J. Chem. Phys. 139, 121908 (2013).
http://dx.doi.org/10.1063/1.4813504
38.
38. P. Wright and J. Dyson, Nat. Rev. Mol. Cell Biol. 6, 197 (2005).
http://dx.doi.org/10.1038/nrm1589
39.
39. N. Lyle, R. K. Das, and R. V. Pappu, J. Chem. Phys. 139, 121907 (2013).
http://dx.doi.org/10.1063/1.4812791
40.
40. K. A. Merchant, R. B. Best, J. M. Louis, I. V. Gopich, and W. A. Eaton, Proc. Natl. Acad. Sci. U.S.A. 104, 1528 (2007).
http://dx.doi.org/10.1073/pnas.0607097104
41.
41. S. M. Kreuzer and R. Elber, J. Chem. Phys. 139, 121902 (2013).
http://dx.doi.org/10.1063/1.4811366
42.
42. O. Kononova, L. Jones, and V. Barsegov, J. Chem. Phys. 139, 121913 (2013).
http://dx.doi.org/10.1063/1.4816104
43.
43. V. A. Voelz, M. Jager, S. Yao, Y. Chen, L. Zhu, S. A. Waldauer, G. R. Bowman, M. Friedrichs, O. Bakajin, L. J. Lapidus, S. Weiss, and V. S. Pande, J. Am. Chem. Soc. 134, 12565 (2012).
http://dx.doi.org/10.1021/ja302528z
44.
44. J. Yao, H. J. Dyson, and P. E. Wright, FEBS Lett. 419, 285 (1997).
http://dx.doi.org/10.1016/S0014-5793(97)01474-9
45.
45. F. Chiti and C. M. Dobson, Annu. Rev. Biochem. 75, 333 (2006).
http://dx.doi.org/10.1146/annurev.biochem.75.101304.123901
46.
46. M. A. Ketchum, K. N. Olafson, E. V. Petrova, J. D. Rimer, and P. G. Vekilov, J. Chem. Phys. 139, 121911 (2013).
http://dx.doi.org/10.1063/1.4816106
47.
47. Y. Wang, A. Lomakin, R. F. Latypov, J. P. Laubach, T. Hideshima, P. G. Richardson, N. C. Munshi, K. C. Anderson, and G. B. Benedek, J. Chem. Phys. 139, 121904 (2013).
http://dx.doi.org/10.1063/1.4811345
48.
48. D. Thirumalai, R. Dima, and D. K. Lkimov, Curr. Opin. Struct. Biol. 13, 146 (2003).
http://dx.doi.org/10.1016/S0959-440X(03)00032-0
49.
49. J. K. Weber and V. S. Pande, J. Chem. Phys. 139, 121917 (2013).
http://dx.doi.org/10.1063/1.4816633
50.
50. K. E. Theisen, N. J. Desai, A. M. Volski, and R. I. Dima, J. Chem. Phys. 139, 121926 (2013).
http://dx.doi.org/10.1063/1.4819817
51.
51. T. Mitchison and M. Kirschner, Nature (London) 312, 237 (1984).
http://dx.doi.org/10.1038/312237a0
52.
52. A. Robinson and A. M. van Oijen, Nat. Rev. Microbiol. 11, 303 (2013).
http://dx.doi.org/10.1038/nrmicro2994
53.
53. P. Vivas, Y. Velmurugu, S. V. Kuznetsov, P. A. Rice, and A. Ansari, J. Chem. Phys. 139, 121927 (2013).
http://dx.doi.org/10.1063/1.4818596
54.
54. D. Thirumalai, N. Lee, S. A. Woodson, and D. K. Klimov, Annu. Rev. Phys. Chem. 52, 751 (2001).
http://dx.doi.org/10.1146/annurev.physchem.52.1.751
55.
55. I. Tinoco and C. Bustamante, J. Mol. Biol. 293, 271 (1999).
http://dx.doi.org/10.1006/jmbi.1999.3001
56.
56. S. J. Chen and K. A. Dill, Proc. Natl. Acad. Sci. U.S.A. 97, 646 (2000).
http://dx.doi.org/10.1073/pnas.97.2.646
57.
57. C. Hyeon and D. Thirumalai, J. Chem. Phys. 139, 121924 (2013).
http://dx.doi.org/10.1063/1.4818594
58.
58. M. Sarikaya, C. Tamerler, A. K. Y. Jen, K. Schulten, and F. Baneyx, Nature Mater. 2, 577 (2003).
http://dx.doi.org/10.1038/nmat964
59.
59. J. Helbing, H. Bregy, J. Bredenbeck, R. Pfister, P. Hamm, R. Huber, J. Wachtveitl, L. De Vico, and M. Olivucci, J. Am. Chem. Soc. 126, 8823 (2004).
http://dx.doi.org/10.1021/ja049227a
60.
60. S. Deechongkit, H. Nguyen, E. T. Powers, P. E. Dawson, M. Gruebele, and J. W. Kelly, Nature (London) 430, 101 (2004).
http://dx.doi.org/10.1038/nature02611
61.
61. M. Wang, T. E. Wales, and M. C. Fitzgerald, Proc. Natl. Acad. Sci. U.S.A. 103, 2600 (2006).
http://dx.doi.org/10.1073/pnas.0508121103
62.
62. B. K. Pandey, M. S. Smith, C. Torgerson, P. B. Lawrence, S. S. Matthews, E. Watkins, M. L. Groves, M. B. Prigozhin, and J. L. Price, Bioconjugate Chem. 24, 796 (2013).
http://dx.doi.org/10.1021/bc3006122
63.
63. M. Egholm, P. E. Nielsen, O. Buchardt, and R. H. Berg, J. Am. Chem. Soc. 114, 9677 (1992).
http://dx.doi.org/10.1021/ja00050a068
64.
64. G. Swiegers, Bioinspiration and Biomimicry in Chemistry (Wiley-VCH, Hoboken, NJ, 2012).
65.
65. N. M. Kocherginsky, M. G. Goldfeld, and I. S. Osak, J. Membr. Sci. 45, 85 (1989).
http://dx.doi.org/10.1016/S0376-7388(00)80847-9
66.
66. A. Lejardi, A. E. López, J. R. Sarasua, U. B. Sleytr, and J. L. Toca-Herrera, J. Chem. Phys. 139, 121903 (2013).
http://dx.doi.org/10.1063/1.4811778
67.
67. J. Y. Fang and S. Hammes-Schiffer, J. Chem. Phys. 106, 8442 (1997).
http://dx.doi.org/10.1063/1.473903
68.
68. M. Muthukumar and R. Nossal, J. Chem. Phys. 139, 121928 (2013).
http://dx.doi.org/10.1063/1.4816634
69.
69. B. M. F. Pearse, Proc. Natl. Acad. Sci. U.S.A. 73, 1255 (1976).
http://dx.doi.org/10.1073/pnas.73.4.1255
70.
70. C. Lagaudriere-Gesbert, S. L. Newmyer, T. F. Gregers, O. Bakke, and H. L. Ploegh, Proc. Natl. Acad. Sci. U.S.A. 99, 1515 (2002).
http://dx.doi.org/10.1073/pnas.042688099
71.
71. J. Foley, S. E. Hill, T. Miti, M. Mulai, M. Ciesla, R. Robeel, C. Persichilli, R. Raynes, S. Westerdeide, and M. Muschol, J. Chem. Phys. 139, 121901 (2013).
http://dx.doi.org/10.1063/1.4811343
72.
72. M. R. D’Orsogna, B. Zhao, B. Berenji, and T. Chou, J. Chem. Phys. 139, 121918 (2013).
http://dx.doi.org/10.1063/1.4817202
73.
73. A. Nordsieck, W. E. Lamb, and G. E. Uhlenbeck, Physica 7, 344 (1940).
http://dx.doi.org/10.1016/S0031-8914(40)90102-1
74.
74. W. Pauli and M. Fierz, Z. Phys. 106, 572 (1937).
http://dx.doi.org/10.1007/BF01339897
75.
75. I. Teo and K. Schulten, J. Chem. Phys. 139, 121929 (2013).
http://dx.doi.org/10.1063/1.4820876
76.
76. A. M. Berezhkovskii and A. Szabo, J. Chem. Phys. 139, 121910 (2013).
http://dx.doi.org/10.1063/1.4816105
77.
77. G. R. Bowman, L. Meng, and X. Huang, J. Chem. Phys. 139, 121905 (2013).
http://dx.doi.org/10.1063/1.4812768
78.
78. A. N. Kravats, S. Toddast-Navaei, R. J. Bucher, and G. Stan, J. Chem. Phys. 139, 121921 (2013).
http://dx.doi.org/10.1063/1.4817410
79.
79. T. Ando, E. Chow, and J. Skolnick, J. Chem. Phys. 139, 121922 (2013).
http://dx.doi.org/10.1063/1.4817660
80.
80. S. R. McGuffee and A. H. Elcock, PLOS Comput. Biol. 6, e1000694 (2010).
http://dx.doi.org/10.1371/journal.pcbi.1000694
81.
81. E. Roberts, J. E. Stone, and Z. Luthey-Schulten, J. Comput. Chem. 34, 245 (2013).
http://dx.doi.org/10.1002/jcc.23130
82.
82. A. Dhar, K. Girdhar, D. Singh, H. Gelman, S. Ebbinghaus, and M. Gruebele, Biophys. J. 101, 421 (2011).
http://dx.doi.org/10.1016/j.bpj.2011.05.071
83.
83. K. Xu, G. S. Zhong, and X. W. Zhuang, Science 339, 452 (2013).
http://dx.doi.org/10.1126/science.1232251
84.
84. Y. Ishitsuka, Y. M. Li, R. Fischer, N. Takeshita, and G. U. Nienhaus, Biophys. J. 104, 652A (2013).
http://dx.doi.org/10.1016/j.bpj.2012.11.3599
85.
85. B. H. Blehm, T. A. Schroer, K. M. Trybus, Y. R. Chemla, and P. R. Selvin, Proc. Natl. Acad. Sci. U.S.A. 110, 3381 (2013).
http://dx.doi.org/10.1073/pnas.1219961110
86.
86. G. P. Zhao, J. R. Perilla, E. L. Yufenyuy, X. Meng, B. Chen, J. Y. Ning, J. Ahn, A. M. Gronenborn, K. Schulten, C. Aiken, and P. J. Zhang, Nature (London) 497, 643 (2013).
http://dx.doi.org/10.1038/nature12162
87.
87. K. Y. Chan, L. G. Trabuco, E. Schreiner, and K. Schulten, Biopolymers 97, 678 (2012).
http://dx.doi.org/10.1002/bip.22042
88.
88. P. C. Whitford and K. Sanbonmatsu, J. Chem. Phys. 139, 121919 (2013).
http://dx.doi.org/10.1063/1.4817212
89.
89. J. Yu, J. Xiao, X. J. Ren, K. Q. Lao, and X. S. Xie, Science 311, 1600 (2006).
http://dx.doi.org/10.1126/science.1119623
90.
90. M. Coelho, N. Maghelli, and I. M. Tolic-Norrelykke, Integr. Biol. 5, 748 (2013).
http://dx.doi.org/10.1039/c3ib40018b
91.
91. P. Lenz, S. S. Cho, and P. G. Wolynes, Chem. Phys. Lett. 471, 310 (2009).
http://dx.doi.org/10.1016/j.cplett.2009.02.054
92.
92. J. S. Cao, Chem. Phys. Lett. 327, 38 (2000).
http://dx.doi.org/10.1016/S0009-2614(00)00809-5
93.
93. T. Firman and K. Ghosh, J. Chem. Phys. 139, 121915 (2013).
http://dx.doi.org/10.1063/1.4816527
94.
94. W. Wu and J. Wang, J. Chem. Phys. 139, 121920 (2013).
http://dx.doi.org/10.1063/1.4816376
95.
95. T. Butler and N. Goldenfeld, Phys. Rev. E 80, 030902(R) (2009).
http://dx.doi.org/10.1103/PhysRevE.80.030902
96.
96. J.-H. Jeon, E. Barkai, and R. Metzler, J. Chem. Phys. 139, 121916 (2013).
http://dx.doi.org/10.1063/1.4816635
97.
97. K. R. Haas, H. Yang, and J.-W. Chu, J. Chem. Phys. 139, 121931 (2013).
http://dx.doi.org/10.1063/1.4820491
98.
98. G. Scott and M. Gruebele, J. Comput. Chem. 31, 2428 (2010).
http://dx.doi.org/10.1002/jcc.21535
99.
99. O. M. Becker and M. Karplus, J. Chem. Phys. 106, 1495 (1997).
http://dx.doi.org/10.1063/1.473299
100.
100. E. Schrödinger, What is Life? The Physical Aspect of the Living Cell (Cambridge University Press, Cambridge, 1944).
101.
101. J. England, J. Chem. Phys. 139, 121923 (2013).
http://dx.doi.org/10.1063/1.4818538
102.
102. E. V. Koonin, Annu. Rev. Genomics Hum. Genet. 1, 99 (2000).
http://dx.doi.org/10.1146/annurev.genom.1.1.99
103.
103. C. M. Fraser, J. D. Gocayne, O. White, M. D. Adams, R. A. Clayton, R. D. Fleischmann, C. J. Bult, A. R. Kerlavage, G. Sutton, J. M. Kelley, R. D. Fritchman, J. F. Weidman, K. V. Small, M. Sandusky, J. Fuhrmann, D. Nguyen, T. R. Utterback, D. M. Saudek, C. A. Phillips, J. M. Merrick, J. F. Tomb, B. A. Dougherty, K. F. Bott, P. C. Hu, T. S. Lucier, S. N. Peterson, H. O. Smith, C. A. I. Hutchison, and J. C. Venter, Science 270, 397 (1995).
http://dx.doi.org/10.1126/science.270.5235.397
104.
104. S. Rasmussen, L. H. Chen, M. Nilsson, and S. Abe, Artif. Life 9, 269 (2003).
http://dx.doi.org/10.1162/106454603322392479
105.
105. C. C. Mello, Cell Death Differ. 14, 2013 (2007).
http://dx.doi.org/10.1038/sj.cdd.4402252
106.
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2013-09-25
2014-07-22

Abstract

Chemical physics as a discipline contributes many experimental tools, algorithms, and fundamental theoretical models that can be applied to biological problems. This is especially true now as the molecular level and the systems level descriptions begin to connect, and multi-scale approaches are being developed to solve cutting edge problems in biology. In some cases, the concepts and tools got their start in non-biological fields, and migrated over, such as the idea of glassy landscapes, fluorescence spectroscopy, or master equation approaches. In other cases, the tools were specifically developed with biological physics applications in mind, such as modeling of single molecule trajectories or super-resolution laser techniques. In this introduction to the special topic section on chemical physics of biological systems, we consider a wide range of contributions, all the way from the molecular level, to molecular assemblies, chemical physics of the cell, and finally systems-level approaches, based on the contributions to this special issue. Chemical physicists can look forward to an exciting future where computational tools, analytical models, and new instrumentation will push the boundaries of biological inquiry.

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