Single-molecule experiments in biological physics: Methods and applications

Journal of Physics Condensed Matter

Volumn 18, Issue 32, 2006, Pages

  Ritort, F ^a  

^a UNIVERSITY OF BARCELONA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

BIOASSAY; FLUORESCENCE; LASER OPTICS; MICROSCOPIC EXAMINATION; MOLECULAR PHYSICS; NUCLEIC ACIDS; PROTEINS; SENSITIVITY ANALYSIS; THEOREM PROVING; THERMODYNAMICS;

ATOMIC-FORCE MICROSCOPY (AFM); BIOLOGICAL PHYSICS; BIOMOLECULAR REACTIONS; SINGLE-MOLECULE EXPERIMENTS (SMES);

MOLECULAR BIOLOGY;

EID: 33746675190     PISSN: 09538984     EISSN: 1361648X     Source Type: Journal    
DOI: 10.1088/0953-8984/18/32/R01     Document Type: Article

References (458)

1. Alberts B, Bray D, Johnson A, Lewis J, Raff M, Roberts K and Walter P 1998 Essential Cell Biology (New York: Garland)
2. Lang MJ and Block SM 2003 Resource letter: Lbot-1: Laser-based optical tweezers Am. J. Phys. 71 201-15
3. Bai C, Wang C, Xie XS and Wolynes PG 1999 Single molecule physics and chemistry Proc. Natl Acad. Sci. 96 11075-6
4. Fisher TE, Oberhausser A F, Carrion-Vazquez M, Marszalek PE and Fernandez JM 1999 The study of protein mechanics with the atomic force microscope Trends Biochem. Sci. 24 379-84
5. Strick T, Allemand J F, Croquette V and Bensimon D 2001 The manipulation of single biomolecules Phys. Today 54 46-51
6. Bustamante C, Macosko JC and Wuite GJL 2000 Grabbing the cat by the tail: manipulating molecules one by one Nat. Rev. Mol. Cell Biol. 1 130-6
7. Bustamante C, Smith S B, Liphardt J and Smith D 2000 Single-molecule studies of DNA mechanics Curr. Opin. Struct. Biol. 10 279-85
8. Bao G 2002 Mechanics of biomolecules J. Mech. Phys. Solids 50 2237-74
9. Cocco S, Marko J and Monasson R 2002 Theoretical models for single-molecule DNA and RNA experiments: from elasticity to unzipping C. R. Phys. 3 569-84
10. Strick TR, Dessinges M N, Charvin G, Dekker N H, Allemand J K, Bensimon D and Croquette V 2003 Stretching of macromolecules and proteins Rep. Prog. Phys. 66 1-45
11. Bryant Z, Smith SB and Bustamante C 2003 Ten years of tension: single-molecule DNA mechanics Nature 421 423-7
12. Wang K, Forbes JG and Jin AJ 2001 Single molecule measurements of titin elasticity Prog. Biophys. Mol. Biol. 77 1-44
13. Carrion-Vazquez M, Oberhausser A F, Fisher T E, Marszalek P E, Li H and Fernandez JM 2000 Mechanical design of proteins studies by single-molecule force spectroscopy and protein engineering Prog. Biophys. Mol. Biol. 74 63-91
14. Carrion-Vazquez M, Oberhausser A F, Diez H, Hervas R, Oroz J, Fernandez J and Martínez-Martín D 2006 Protein nanomechanics as studied by AFM single-molecule force spectroscopy Advanced Techniques in Biophysics vol 10 ed JLR Arrondo and A Alonso (Heidelberg: Springer) pp163-245
15. Bustamante C, Chemla Y R, Forde NR and Izhaky D 2004 Mechanical processes in biochemistry Annu. Rev. Biochem. 73 705-48
16. Weiss S 1999 Fluorescence spectrocopy of single biomolecules Science 283 1676-83
17. Ha T 2001 Single-molecule fluorescence methods for the study of nucleic acids Curr. Opin. Struct. Biol. 11 287-92
18. Haran G 2003 Single-molecule fluorescence spectroscopy of biomolecular folding J. Phys.: Condens. Matter 15 R1291-317
19. Neumann KC and Block SM 2004 Optical trapping Rev. Sci. Instrum. 75 2787-809
20. Williams M C 2006 Optical tweezers: measuring piconewton forces volume http://www.biophysics.org/education/williams.pdf Biophysical Society Textbook Online
21. Leuva SH and Zlatanova J 2001 Biology at the Single Molecule Level (Oxford: Pergamon)
22. 1999 Science 283 1593-804 (Frontiers in Chemistry: Single Molecules)
23. Flyvbjerg H, Jülicher F, Ormos P and David F (ed) 2002 Physics of Biomolecules and Cells vol LXXV (Berlin: Springer)
24. Chatenay D, Cocco S, Monasson R, Thieffry D and Dalibard J (ed) 2004 Multiple Aspects of DNA and RNA: from Biophysics to Bioinformatics vol LXXXII (Berlin: Springer)
25. Optical tweezers list and resources pages 2006 http://www.st-andrews.ac. uk/∼atomtrap/Resources.htm
26. Curr. Opin. Struct. Biol. http://www.current-opinion.com/jstb/about.htm? jcode ≤ jstb
27. Ritort F 2003 Work fluctuations, transient violations of the second law and free-energy recovery methods Semin. Poincaré 2 193-226
28. Bustamante C, Liphardt J and Ritort F 2005 The nonequilibrium thermodynamics of small systems Phys. Today 58 43-8
29. Ritort F 2006 Nonequilibrium fluctuations in small systems: from physics to biology Adv. Chem. Phys. (Preprint)
30. Fraunfelder H, Wolynes P G and Austin R H 1999 Biological physics Rev. Mod. Phys. 71 S419-30
31. Rhoades E, Cohen M, Schuler B and Haran G 2004 Two-state folding observed in individual protein molecules J. Am. Chem. Soc. 126 14686-7
32. Rhoades E, Gussakovsky E and Haran G 2003 Watching proteins fold one at a time Proc. Natl Acad. Sci. 100 3197-202
33. Rubinstein M and Colby R 2003 Polymer Physics (New York: Oxford University Press)
34. Finzi L, Smith SB and Bustamante C 1992 Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads Science 258 1122-4
35. Bustamante C, Marko J, Siggia E and Smith S B 1994 Entropic elasticity of λ-phage DNA Science 265 1599-600
36. Frey E and Kroy K 2005 Brownian motion: a paradigm of soft matter and biological physics Ann. Phys., Lpz 14 20-50
37. Hill TL 1994 Thermodynamics of Small Systems (New York: Dover)
38. Binnig G and Rohrer H 1987 Scanning tunneling microscopy: from birth to adolescence Rev. Mod. Phys. 59 615-25
39. Binnig G, Quate CF and Berger CH 1986 Atomic force microscope Phys. Rev. Lett. 56 930-3
40. Moreno-Herrero F, Colchero J, Gomez-Herrero J and Baro AM 2004 Atomic force microscopy contact, tapping, and jumping modes for imaging biological samples in liquids Phys. Rev. E 69 031915
41. Horber JKH and Miles MJ 2003 Scanning probe evolution in biology Science 302 1002-5
42. Bustamante C, Rivetti C and Keller DJ 1997 Scanning force microscopy under aqueous solutions Curr. Opin. Struct. Biol. 7 709-16
43. Czajkowsky D M and Shao Z 1998 Submolecular resolution of single macromolecules with atomic force microscopy FEBS Lett. 430 51-4
44. Smith B L 2000 The importance of molecular structure and conformation: learning with scaning force microscopy Prog. Biophys. Mol. Biol. 74 93-113
45. Hafner JH, Cheung C-L, Woolley AT and Lieber CM 2000 Structural and functional imaging with carbon nanotube AFM probes Prog. Biophys. Mol. Biol. 77 73-110
46. Engel A and Müller DJ 2000 Observing single biomolecules at work with the atomic force microscope Nat. Struct. Mol. Biol. 7 715-8
47. Müller DJ and Anderson K 2002 Biomolecular imaging using atomic force microscopy Trends Biotechnol. 20 S45-9
48. Kellermayer M S K 2005 Visualizing and manipulating individual protein molecules Physiol. Meas. 26 R119-53
49. Ashkin A 1970 Acceleration and trapping of particles by radiation pressure Phys. Rev. Lett. 24 156-9
50. Ashkin A 1970 Atomic-beam deflection by resonance-radiation pressure Phys. Rev. Lett. 25 1321-4
51. Ashkin A, Dziedzic J M, Bjorkholm JE and Chu S 1986 Observation of a single beam gradient force optical trap for dielectric particles Opt. Lett. 11 288-90
52. Phillips WD 1998 Laser cooling and trapping of neutral atoms Rev. Mod. Phys. 70 721-41
53. Ashkin A, Dziedzic JM and Yamane T 1987 Optical trapping and manipulation of single cells using infrared laser beams Nature 330 769-71
54. Ashkin A and Dziedzic JM 1987 Optical trapping and manipulation of viruses and bacteria Science 235 1517-20
55. Ashkin A 1997 Optical trapping and manipulation of neutral particles using lasers Proc. Natl Acad. Sci. 94 4853-60
56. Smith SB, Cui Y and Bustamante C 2003 An optical-trap force transducer that operates by direct measurement of light momentum Methods Enzymol. 361 134-62
57. Visscher K and Block SM 1998 Versatile optical traps with feedback control Methods Enzymol. 298 460-89
58. Lang MJ, Asbury C L, Shaevitz JW and Block S M 2002 An automated two-dimensional optical force clamp for single molecule studies Biophys. J. 83 491-501
59. Gosse C and Croquette V 2002 Magnetic tweezers: micromanipulation and force measurement at the molecular level Biophys. J. 82 3314-29
60. Bryant Z, Stone M D, Gore J, Smith S B, Cozzarelli N and Bustamante C 2003 Structural transitions and elasticity from torque measurements on DNA Nature 424 338-441
61. Merkel R, Nassoy P, Leung A, Ritchie K and Evans E 1999 Energy landscapes of receptor-ligand bonds explored with dynamic force spectroscopy Nature 397 50-3
62. Evans E and Williams P 2002 Dynamic force spectroscopy Physics of Bomolecules and Cells vol LXXV ed H Flyvbjerg, F Jüulicher, P Ormos and F David (Berlin: Springer) pp145-204
63. Gelles J, Schnapp BJ and Sheetz MP 1988 Tracking kinesin-driven movements with nanometre-scale precision Nature 331 450-3
64. Gordon M P, Ha T and Selvin PR 2004 Single-molecule high resolution imaging with photobleaching Proc. Natl Acad. Sci. 101 6462-5
65. Qu X, Wu D, Mets L and Scherer NF 2004 Nanometer-localized multiple single molecule fluorescence microscopy Proc. Natl Acad. Sci. 101 11298-303
66. Forkey JN, Quinian M E, Shaw M A, Corrie J ET and Goldman YE 2003 Three-dimensional structure dynamics of myosin V by single molecule fluorescence polarization Nature 422 399-404
67. Yildiz A, Forkey J N, McKinney S A, Ha T, Goldman YE and Selvin PR 2003 Myosin V walks hand-over-hand: single fluorophore imaging with 1.5 nm localization Science 300 2061-5
68. 1974 Nature 248 765-88 (Molecular Biology)
69. 2003 Nature 421 396-453 (Fifty years of the Double Helix)
70. Watson JD and Crick FH 1953 Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid Nature 171 737-8
71. Frank-Kamentskii MD 1997 Biophysics of the DNA molecule Phys. Rep. 288 13-60
72. Tinoco I Jr 1996 Nucleic acid structures, energetics and dynamics J. Phys. Chem. 100 13311-22
73. Marko J 1997 Twist and shout (and pull): molecular chiropractors undo DNA Proc. Natl Acad. Sci. 94 11770-2
74. Cluzel P, Lebrun A, Heller C, Lavery R, Viovy J-L, Chatenaly D and Caron F 1995 DNA: an extensible molecule Science 271 792-4
75. Cui Y, Smith SB and Bustamante C 1995 Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules Science 271 795-9
76. Strick TR, Allemand J-F, Bensimon D, Bensimon A and Croquette V 1996 The elasticity of a single supercoiled DNA molecule Science 271 1835-7
77. Rief M, Clausen-Schaumann H and Gaub HE 1999 Sequence-dependent mechanics of single DNA molecules Nat. Struct. Mol. Biol. 6 346-9
78. Vologodskii A 1994 DNA extension under the action of an external force Macromolecules 27 5623-5
79. Marko JF and Siggia ED 1995 Stretching DNA Macromolecules 28 209-12
80. Wang MD, Yin H, Landick R, Gelles J and Block SM 1997 Stretching DNA with optical tweezers Biophys. J. 72 1335-46
81. Bouchiat C, Wang M D, Allemand J-F, Strick T, Block SM and Croquette V 1999 Estimating the persistence length of a worm-like chain molecule from force-extension measurements Biophys. J. 76 409-13
82. McGurn AR and Scalapino DJ 1975 One-dimensional ferromagnetic classical-spin-field model Phys. Rev. B 11 2552-8
83. Wilkins M H F, Gosling RG and Seeds WE 1951 Nucleic acid: an extensible molecule? Nature 167 759-60
84. Rouzina I and Bloomfield VA 2001 Force-induced melting of the DNA double helix. 1. Thermodynamic analysis Biophys. J. 80 882-93
85. Rouzina I and Bloomfield VA 2001 Force-induced melting of the DNA double helix. 2. Effect of solution conditions Biophys. J. 80 894-900
86. Williams MC, Rouzina I and Bloomfield VA 2002 Thermodynamics of DNA interactions from single molecule stretching experiments Acc. Chem. Res. 35 159-66
87. Wenner JR, Williams M C, Rouzina I and Bloomfield VA 2002 Salt dependence of the elasticity and overstretching transition of single DNA molecules Biophys. J. 82 3160-9
88. Poland D and Sheraga HA 1966 Phase transitions in one dimension and the helix-coil transition in polyamino acids J. Chem. Phys. 45 1456-63
89. Poland D and Sheraga HA 1966 Ocurrence of a phase transition in nucleic acid models J. Chem. Phys. 45 1464-9
90. Wartell RM and Benight AS 1985 Thermal denaturation of DNA molecules: a comparison of theory with experiment Phys. Rep. 126 67-107
91. Peyrard M and Bishop AR 1989 Statistical mechanics of a nonlinear model for DNA denaturation Phys. Rev. Lett. 62 2755-8
92. Cule D and Hwa T 1997 Denaturation of heterogeneous DNA Phys. Rev. Lett. 79 2375-8
93. Kafri Y, Mukamel D and Peliti L 2000 Why is the DNA denaturation transition first order? Phys. Rev. Lett. 85 4988-91
94. Causo MS, Coluzzi B and Grassberger P 2000 Simple model for the DNA denaturation transition Phys. Rev. E 62 3958-73
95. Sales-Pardo M, Guimera R, Moreira A A, Widom J and Amaral LAN 2005 Mesoscopic modeling for nucleic acid chain dynamics Phys. Rev. E 71 051902
96. Cuesta-Lopez S, Peyrard M and Graham DJ 2005 Model for DNA hairpin denaturation Eur. Phys. J. E 16 235-46
97. Cocco S and Monasson R 1999 Statistical mechanics of torque induced denaturation Phys. Rev. Lett. 83 5178-81
98. Cocco S and Monasson R 2000 Theoretical study of collective modes in DNA at amnbient temperature J. Chem. Phys. 112 10017-33
99. Hwa T, Marinari E, Sneppen K and Tang L-H 2003 Localization of denaturation bubbles in random DNA sequences Proc. Natl Acad. Sci. 100 4411-6
100. Hanke A and Metzler R 2003 Buble dynamics in DNA J. Phys. A: Math. Gen. 36 L473-80
101. Konrad MW and Bolonick JI 1996 Molecular dynamics simulation of DNA stretching is consistent with the tension observed for extension and strand separation and predicts a novel ladder structure J. Am. Chem. Soc. 118 10989-94
102. Ahsan A, Rudnick J and Bruinsma R 1998 Elasticity theory of the B-DNA to S-DNA transition Biophys. J. 74 132-7
103. Kosikov KM, Gorin A A, Zhurkin VB and Olson WK 1999 DNA stretching and compression: large-scale simulations of double helical structures J. Mol. Biol. 289 1301-26
104. Storm C and Nelson P 2003 Theory of high-force DNA stretching and overstretching Phys. Rev. E 67 051906
105. Mergell B, Ejtehadi MR and Everaers R 2003 Modeling DNA structure, elasticity and deformations at the base-pair level Phys. Rev. E 68 021911
106. Cocco S, Yan J, Léger J F, Chatenay D and Marko JF 2004 Overstretching and force-driven strand separation of double-helix DNA Phys. Rev. E 70 011910
107. Rief M, Oesterhelt F, Heymann B and Gaub HE 1997 Single molecule force spectroscopy on polysaccharides by atomic force microscopy Science 275 1295-7
108. Marszalek PE, Oberhauser A F, Pang YP and Fernandez JM 1998 Polysaccharide elasticity governed by chair-boat transitions of the glucopyranose ring Nature 396 661-4
109. Marszalek PE, Li H, Oberhauser AF and Fernandez JM 2002 Chair-boat transitions in single polysaccharide molecules obserbed with force-ramp AFM Proc. Natl Acad. Sci. 99 4278-83
110. Kawakami M, Byrne K, Khatri B, McLeish T C B, Radford SE and Smith DA 2004 Viscoelastic properties of single polysaccharide molecules determined by analysis of thermally driven oscillations of an atomic force microscope cantilever Langmuir 20 9299-303
111. Hugel T, Rief M, Seitz M, Gaub H and Netz R 2005 Highly stretched single polymers: atomic-force-microscope experiments versus ab initio theory Phys. Rev. Lett. 94 048301
112. Léger JF, Romano G, Sarkar A, Robert J, Bourdieu L, Chatenay D and Marko JF 1999 Structural transitions of a twisted and stretched DNA molecule Phys. Rev. Lett. 83 1066-9
113. Sarkar A, Léger J F, Chatenay D and Marko JF 2001 Structural transitions in DNA driven by external force and torque Phys. Rev. E 63 051903
114. Allemand JF, Bensimon D, Lavery R and Croquette V 1998 Stretched and overwound DNA forms a Pauling-like structure with exposed bases Proc. Natl Acad. Sci. 95 14152-7
115. Pauling L and Corey RB 1953 A proposed structure for the nucleic acids Proc. Natl Acad. Sci. 39 84-97
116. Lebrun A and Lavery R 1996 Modelling extreme stretching of DNA Nucleic Acids Res. 24 2260-7
117. Fain B, Rudnick J and stlund S 1997 Conformations of linear DNA Phys. Rev. E 55 7364-8
118. Marko J 1998 DNA under high tension: overstretching, undertwisting, and relaxation dynamics Phys. Rev. E 57 2134-49
119. Bouchiat C and Mézard M 1998 Elasticity model of a supercoiled DNA molecule Phys. Rev. Lett. 80 1556-9
120. Zhou H, Zhang Y and Ou-Yang Z-C 2000 Elastic property of single double-stranded DNA molecules: theoretical study and comparison with experiments Phys. Rev. E 62 1045-58
121. Neukirch S 2004 Extracting DNA twist rigidity from experimental supercoiling data Phys. Rev. Lett. 93 198107
122. Leger JF, Robert J, Bourdieu L, Chatenay D and Marko JF 1998 RecA binding to a single double-stranded DNA molecule: a possible role of DNA conformational fluctuations Proc. Natl Acad. Sci. 95 12295-9
123. Pant K, Karpel RL and Williams MC 2004 Kinetic regulation of single DNA molecule denaturation by T4 gener 32 protein structural domains J. Mol. Biol. 327 571-8
124. Dekker NH, Rybenkov V V, Duguet M, Crisona N J, Cozzarelli N R, Bensimon D and Croquette V 2002 The mechanism of type IA topoisomerases Proc. Natl Acad. Sci. 99 12126-31
125. Essevaz-Roulet B, Bockelmann U and Heslot F 1997 Mechanical separation of the complementary strands of DNA Proc. Natl Acad. Sci. 94 11935-40
126. Bockelmann U, Essevaz-Roulet B and Heslot F 1998 DNA strand separation studied by single molecule force measurements Phys. Rev. E 58 2386-94
127. Clausen-Schaumann H, Rief M, Tolksdorf C and Gaub HE 2000 Mechanical stability of single DNA molecules Biophys. J. 78 1997-2007
128. Danilowicz C, Coljee V W, Bouzigues C, Lubensky D K, Nelson DR and Prentiss M 2003 DNA unzipped under a constant force exhibits multiple metastable intermediates Proc. Natl Acad. Sci. 100 1694-9
129. Bhattacharjee SM and Marenduzzo D 2001 DNA sequence from the unzipping force?: one mutation problem J. Phys. A: Math. Gen. 35 L349-56
130. Cocco S, Monasson R and Marko J 2001 Force and kinetic barriers to unzipping of the DNA double helix Proc. Natl Acad. Sci. 98 8608-13
131. Cocco S, Monasson R and Marko J 2002 Force and kinetic barriers to initiation of DNA unzipping Phys. Rev. E 65 041907
132. Baldazzi V, Cocco S, Marinari E and Monasson R 2006 Inferring DNA sequences from mechanical unzipping: an ideal-case study Phys. Rev. Lett. 96 128102
133. Lubensky DK and Nelson DR 2002 Single molecule statistics and the polynucleotide unzipping transition Phys. Rev. E 65 031917
134. Chen JZY 2002 Unzipping double-stranded DNA with a force: scaling theory Phys. Rev. E 66 031912
135. Kafri Y, Mukamel D and Peliti L 2002 Melting and unzipping of DNA Eur. Phys. J. B 27 135-46
136. Allahverdyan A, Gevorkian Zh S, Hu CK and Wu MC 2004 Unzipping of DNA with correlated base sequence Phys. Rev. E 69 061908
137. Mukamel EA and Shaknovich EI 2002 Phase diagram for unzipping DNA with long-range interactions Phys. Rev. E 66 032901
138. Orlandini E, Bhattacharjee S M, Marenduzzo D, Maritan A and Seno F 2001 Mechanical denaturation of DNA: existence of a low-temperature denaturation J. Phys. A: Math. Gen. 34 L751-8
139. Marenduzzo D, Bhattacharjee S M, Maritan A, Orlandini E and Seno F 2002 Dynamical scaling of the DNA unzipping transition Phys. Rev. Lett. 88 028102
140. Braslavsky I, Hebert B, Kartalov E and Qualke SR 2003 Sequence information can be obtained from single DNA molecules Proc. Natl Acad. Sci. 100 3960-4
141. De Duve C 1995 Vital Dust: The Origin and Evolution of Life on Earth (New York: Perseus Books Group)
142. Gestland RF and Atkins JF 1993 The RNA World (Cold Spring Harbor) (New York: Cold Spring Harbor Laboratory Press)
143. Abels JA, Moreno-Herrero F, Van der Heijden T, Dekker C and Dekker NH 2005 Single-molecule measurements of the persistence length of double-stranded RNA Biophys. J. 88 2737-44
144. Tinoco I Jr and Bustamante C 2002 The effect of force on thermodynamics and kinetics of single molecule reactions Biophys. Chem. 102 513-33
145. Tinoco I Jr 2004 Force as a useful variable in reactions: unfolding RNA Annu. Rev. Biophys. Biomol. Struct. 33 363-85
146. Onoa B and Tinoco I Jr 2004 RNA folding and unfolding Curr. Opin. Struct. Biol. 14 374-9
147. Herschlag D 1995 RNA chaperones and the RNA folding problem J. Biol. Chem. 270 20871-4
148. Tinoco I Jr and Bustamante C 1999 How RNA folds J. Mol. Biol. 293 271-81
149. Schroeder R, Barta A and Semrad K 2004 Strategies for RNA folding Nat. Rev. Mol. Cell Biol. 5 908-19
150. Higgs PG 1996 Overlaps between RNA secondary structures Phys. Rev. Lett. 76 704-7
151. Pagnani A, Parisi G and Ricci-Tersenghi F 2000 Glassy transition in a disordered model for the RNA secondary structure Phys. Rev. Lett. 84 2026-9
152. Orland H and Zee A 2002 RNA folding and large N matrix theory Nucl. Phys. B 620 456-76
153. Bundschuh R and Hwa T 2002 Statistical mechanics of secondary structures formed by random RNA sequences Phys. Rev. E 62 031903
154. Müller M 2003 Statistical physics of RNA folding Phys. Rev. E 67 021914
155. Müller M, Krzakala F and Mézard M 2002 The secondary structure of RNA under tension Eur. Phys. J. B 9 67-77
156. Liphardt J, Onoa B, Smith S B, Tinoco I Jr and Bustamante C 2001 Reversible unfolding of single RNA molecules by mechanical force Science 292 733-7
157. Zuker M 1989 On finding all suboptimal foldings of an RNA molecule Science 244 45-82
158. Mathews DH, Sabina J, Zuker M and Turner DH 1999 Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure J. Mol. Biol. 288 911-40
159. Manosas M, Collin D and Ritort F 2006 Force dependent fragility in RNA hairpins Phys. Rev. Lett. 96 218301
160. Green NH, Williams P M, Wahab O, Davies M C, Roberts C J, Tendler S JB and Allen S 2004 Single-molecule investigations of RNA dissociation Biophys. J. 86 3811-21
161. Altan-Bonnet G, Krichevsky O and Libchaber A 1998 Kinetics of conformational fluctuations in DNA hairpin-loops Proc. Natl Acad. Sci. 95 8602-6
162. Altan-Bonnet G, Libchaber A and Krichevsky O 2003 Bubble dynamics in double-stranded DNA Phys. Rev. Lett. 90 138101
163. Lee G U, Chrisey LA and Colton RJ 1994 Direct measurement of the forces between complentary strands of DNA Science 266 771-3
164. Noy A, Vezenov D V, Kayyem J F, Meade TJ and Lieber CM 1997 Stretching and breaking duplex DNA by chemical force Chem. Biol. 4 519-27
165. Strunz T, Oroszlan K, Schäfer R and Güntherodt H-J 1999 Dynamic force spectroscopy of single DNA molecules Proc. Natl Acad. Sci. 96 11277-82
166. Grange W, Strunz T, Schumakovitch I and Güntherodt H-J 2001 Molecular recognition and adhesion of individual DNA strands studied by dynamic force spectroscopy Single Mol. 2 75-8
167. Schumakovitch I, Grange W, Strunz T, Bertoncini P and Güntherodt H-J 2002 Temperature dependence of unbinding forces between complementary DNA strands Biophys. J. 82 517-21
168. Nelson DR 2003 Statistical physics of unzipping DNA Preprint cond-mat/0309559
169. Gerland U, Bundschuh R and Hwa T 2004 Translocation of structured polynucleotides through nanopores Phys. Biol. 1 19-26
170. Montanari A and Mezard M 2001 Hairpin formation and elongation of biomolecules Phys. Rev. Lett. 86 2178-81
171. Gerland U, Bundschuh R and Hwa T 2001 Force-induced denaturation of RNA Biophys. J. 81 1324-32
172. Dessinges MN, Maier B, Zhang Y, Peliti M, Bensimon D and Croquette V 2002 Stretching single stranded DNA, a model polyelectrolyte Phys. Rev. Lett. 89 248102
173. Imparato A and Peliti L 2004 Kinetic barriers in RNA unzipping Eur. Phys. J. B 39 357-63
174. Hyeon C and Thirumalai D 2005 Mechanical unfolding of RNA hairpins Proc. Natl Acad. Sci. 102 6789-94
175. Liu F and Ou-Yang Z-C 2004 Monte carlo simulation for single RNA unfolding by force Biophys. J. 88 76-84
176. Liu F, Tong H and Ou-Yang Z-C 2006 Force unfolding single RNAs Biophys. J. 90 1895-902
177. Hyeon C and Thirumalai D 2006 Force-unfolding and force-quench refolding of RNA hairpins Biophys. J. 90 3410-27
178. Fernandez JM, Chu S and Oberhauser AF 2001 Pulling on hair(pins) Science 292 653-4
179. Cocco S, Monasson R and Marko J 2003 Slow nucleic acid unzipping from sequence-defined barriers Eur. Phys. J. E 10 153-61
180. Gerland U, Bundschuh R and Hwa T 2003 Mechanically probing the folding pathway of single RNA molecules Biophys. J. 84 2831-40
181. Manosas M and Ritort F 2005 Thermodynamic and kinetic aspects of RNA pulling experiments Biophys. J. 88 3224-42
182. Wen J D, Manosas M, Li P T X, Smith S B, Bustamante C, Ritort F and Tinoco I Jr 2006 Force unfolding kinetics of RNA using laser tweezers. I. effect of experimental variables on measured results submitted
183. Manosas M, Wen J D, Li P T X, Smith S B, Bustamante C, Tinoco I Jr and Ritort F 2006 Force unfolding kinetics of RNA using laser tweezers. II. Modeling experiments submitted
184. Greenleaf WJ, Woodside M T, Abbondazieri EA and Block SM 2005 Passive all-optical force-clamp for high resolution laser trapping Phys. Rev. Lett. 95 208102
185. Woodside MT, Behne-Parks W M, Larizadeh K, Travers K, Herschlag D and Block SM 2006 Nanomechanical measurements of the sequence-dependent folding landscapes of single nucleic acid hairpins Proc. Natl Acad. Sci. 103 6190-5
186. Ritort F, Bustamante C and Tinoco I Jr 2002 A two-state kinetic model for the unfolding of single molecules by mechanical force Proc. Natl Acad. Sci. 99 13544-8
187. Zhuang X, Bartley L E, Babcock H P, Russell R, Ha T, Herschlag D and Chu S 2000 A single-molecule study of RNA catalysis and folding Science 288 2048-51
188. Onoa B, Dumont S, Liphardt J, Smith S B, Tinoco I Jr and Bustamante C 2003 Identifying kinetic barriers to mechanical unfolding of the T. thermophila ribozyme Science 299 1892-5
189. Harlepp S, Marchal T, Robert J, Leger J-F, Xayaphoummine A, Isambert H and Chatenay D 2003 Probing complex RNA structures by mechanical force Eur. Phys. J. E 12 605-15
190. Li P T X, Collin D, Smith S B, Bustamante C and Tinoco I Jr 2006 Probing the mechanical folding kinetics of TAR RNA by hopping, force-jump, and force-ramp methods Biophys. J. 90 250-60
191. Ha T, Zhuang X, Kim H D, Orr J W, Williamson JR and Chu S 1999 Ligand-induced conformational changes observed in single RNA molecules Proc. Natl Acad. Sci. 96 9077-82
192. 2+-dependent conformational change of RNA studied by fluorescence correlation and FRET on immobilized single molecules Proc. Natl Acad. Sci. 99 4284-9
193. Collin D, Ritort F, Jarzynski C, Smith S B, Tinoco I Jr and Bustamante C 2005 Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies Nature 437 231-4
194. Zarrinkar P and Williamson J 1994 Kinetic intermediates in RNA folding Science 265 918-23
195. Pan J, Thirumalai D and Woodson SA 1997 Folding of RNA involves parallel pathways J. Mol. Biol. 273 7-13
196. Treiber DK and Williamson JR 1999 Exposing the kinetic traps in RNA folding Curr. Opin. Struct. Biol. 9 339-45
197. Treiber DK and Williamson JR 2001 Beyond kinetic traps in RNA folding Curr. Opin. Struct. Biol. 11 309-14
198. Li P T X, Bustamante C and Tinoco I Jr 2006 Misfolding and rescue of RNA molecules by force submitted
199. Chen S-J and Dill KA 2000 RNA folding energy ladscapes Proc. Natl Acad. Sci. 97 646-51
200. Hyeon C and Thirumalai D 2003 Can energy landscape roughness mof proteins and RNA be measured by using mechanical unfolding experiments Proc. Natl Acad. Sci. 100 10249-53
201. Thirumalai D and Hyeon C 2005 RNA and protein folding: common themes and variations Biochemistry 44 4957-70
202. Watson JD, Baker T A, Bell S P, Gann A, Levine M and Losick R 2004 Molecular Biology of the Gene (New York: Benjamin Cummings)
203. Calladine CR and Drew HR 1997 Understanding DNA: The Molecule & How It Works (London: Academic)
204. Bloomfield VA 1996 DNA condensation Curr. Opin. Struct. Biol. 6 334-41
205. Yager TD, McMurray CT and van Holde KE 1989 Salt-induced release of DNA from nucleosome core particles Biochemistry 28 2271-81
206. Hansen JC 2002 Conformational dynamics of the chromatin fiber in solution: determinants, mechanisms, and functions Annu. Rev. Biophys. Biomol. Struct. 31 361-92
207. Widom J 1998 Structure, dynamics and function of chromatin in vitro Annu. Rev. Biophys. Biomol. Struct. 27 285-327
208. Daban JR 2003 High concentration of DNA in condensed chromatin Biochem. Cell Biol. 81 91-9
209. Schiessel H 2003 The physics of chromatin J. Phys.: Condens. Matter 15 R699-774
210. Cui Y and Bustamante C 2000 Pulling a single chromatin fiber reveals the forces that maintain its higher-order structure Proc. Natl Acad. Sci. 97 127-32
211. Ladoux B, Quivy J-P, Doyle P, duRoure O, Almouzni G and Viovy J-L 2000 Fast kinetics of chromatin assembly revealed by single-molecule videomicroscopy and scanning force microscopy Proc. Natl Acad. Sci. 97 14251-6
212. Bennink ML, Leuba S H, Leno G H, Zlatanova J, deGrooth BG and Greve J 2001 Unfolding individual nucleosomes by stretching single chromatin fibers with optical tweezers Nat. Struct. Mol. Biol. 8 606-10
213. Bennink ML, Pope L H, Leuba S H, deGrooth B G and Greve J 2001 Single chromatin fiber assembly using optical tweezers Single Mol. 2 91-7
214. Leuba SH, Karymov M A, Tomschik M, Ramjit R, Smith P and Zlatanova J 2003 Assembly of single chromatin fibers depends on tension in the DNA molecule: magnetic tweezers study Proc. Natl Acad. Sci. 100 495-500
215. Brower-Toland BD, Smith C L, Yeh R C, Lis J T, Peterson CL and Wang MD 2002 Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA Proc. Natl Acad. Sci. 99 1960-5
216. Poirier MG and Marko JF 2002 Mitotic chromosomes are chromatin networks without a mechanically contiguous protein scaffold Proc. Natl Acad. Sci. 99 15393-7
217. Ritort F, Mihardja S, Smith SB and Bustamante C 2006 Condensation transition in DNA-PAMAM dendrimer fibers studied using optical tweezers Phys. Rev. Lett. 96 118301
218. Thurmond KB II, Remsen E E, Kowalewski T and Wooley KL 1999 Packaging of DNA by shell crosslinked nanoparticles Nucleic Acids Res. 27 2966-71
219. Kukowska-Latallo JF, Bielinska A U, Johnson J, Spindler R, Tomalia DA and Baker JR Jr 1996 Efficient transfer of genetic material into mammalian cells using starburst polyamidoamine dendrimers Proc. Natl Acad. Sci. 93 4897-902
220. Fréchet JMJ and Tomalia DA 2001 Dendrimers and Other Dendritic Polymers (New York: Wiley)
221. Frechet JM 2002 Dendrimers and supramolecular chemistry Proc. Natl Acad. Sci. 99 4782-7
222. Baumann CG, Smith S B, Bloomfield VA and Bustamante C 1997 Ionic effects on the elasticity of single DNA molecules Proc. Natl Acad. Sci. 94 6185-90
223. Deng H and Bloomfield VA 1999 Structural effects of cobalt-amine compounds on DNA condensation Biophys. J. 77 1556-61
224. Baumann CG, Bloomfield V A, Smith S B, Bustamante C, Wang MD and Block SM 2000 Stretching of single collapsed DNA molecules Biophys. J. 78 1965-78
225. Woodcock CL, Grigoryev S A, Horowitz RA and Whitaker N 1993 A chromatin folding model that incorporates linker variability generates fibers resembling the native structures Proc. Natl Acad. Sci. 90 9021-5
226. Kunze K-K and Netz R 2000 Salt-induced DNA-histone complexation Phys. Rev. Lett. 85 4389-92
227. Katritch V, Bustamante C and Olson WK 2000 Pulling chromatin fibers: computer simulations of direct physical micromanipulations J. Mol. Biol. 295 29-40
228. Nguyen TT, Grossberg AY and Shklovskii BI 2001 Lateral correlations of multivalent counterions is the universal mechanism of charge inversion Electrostatic Effects in Soft Matter and Biophysics: Proc. NATO Advanced Study Institute (Les Houches, France, Oct. 2000) (NATO Science Series II: Mathematics, Physics & Chemistry) ed C Holm, P Kekicheff and R Podgornik (Dordrecht: Kluwer-Academic)
229. Nguyen TT and Shklovskii BI 2001 Complexation of a polyelectrolyte with oppositely charged spherical macroions: giant inversion of charge J. Chem. Phys. 114 5905-16
230. Schiessel H, Widom J, Bruinsma RF and Gelbart WM 2001 Polymer reptation and nucleosome repositioning Phys. Rev. Lett. 86 4414-7
231. Schiessel H, Gelbart WM and Bruinsma R 2001 DNA folding: structural and mechanical properties of the two angle model for chromatin Biophys. J. 80 1940-56
232. Nguyen TT, Grossberg AYu and Shklovskii IB 2002 Colloquium: the physics of charge inversion in chemical and biological systems Rev. Mod. Phys. 74 329-45
233. Kunze K-K and Netz R 2002 Complexes of semiflexible polyelectrolytes and charged spheres as models for salt-modulated nucleosomal structures Phys. Rev. E 66 011918
234. Boroudjerdi H and Netz R 2003 Interactions between polyelectrolyte- macroion complexes Europhys. Lett. 64 413-9
235. Kulic IM and Schiessel H 2004 DNA spools under tension Phys. Rev. Lett. 92 228101
236. Wada H, Murayama Y and Sano M 2005 Nonlinear elasticity of single collapsed polyelectrolytes Phys. Rev. E 72 041803
237. Sun J, Zhang Q and Schlik T 2005 Electrostatic mechanism of nucleosomal array folding revealed by computer simulation Proc. Natl Acad. Sci. 102 8180-5
238. Ros R, Eckel R, Bartels F, Sischka A, Baumgarth B, Wilkin S D, Pühler A, Sewald N, Becker A and Anselmetti D 2004 Single molecule force spectroscopy on ligand-DNA complexes: from molecular binding mechanisms to biosensor applications J. Biotechnol. 112 5-12
239. Kramers HA 1940 Brownian motion in a field of force and the diffusion model of chemical reactions Physica A 7 284-304
240. Hanggi P, Talkner P and Borkovec M 1990 Reaction-rate theory: fifty years after kramers Rev. Mod. Phys. 62 251-341
241. Melnikov VI 1991 The kramers problem: fifty years of development Phys. Rep. 209 1-71
242. Bell GI 1978 Models for the specific adhesion of cells to cells Science 200 618-27
243. Evans E and Ritchie K 1997 Dynamic strength of molecular adhesion bonds Biophys. J. 72 1541-55
244. Evans E and Ritchie K 1999 Strength of a weak bond connecting flexible polymer chains Biophys. J. 76 2439-47
245. Evans E 2001 Probing the relationship between force-lifetime-and chemistry in single molecular bonds Annu. Rev. Biophys. Biomol. Struct. 30 105-28
246. Lee GU, Kidwell DA and Colton RJ 1993 Sensing discrete streptavidin-biotin interactions with atomic force microscopy Langmuir 10 354-7
247. Florin EL, Moy VT and Gaub HE 1994 Adhesion forces between individual ligand-receptor pairs Science 264 415-7
248. Moy VT, Florin EL and Gaub HE 1994 Intermolecular forces and energies between ligands and receptors Science 266 257-9
249. Dammer U, Hegner M, Anselmetti D, Wagner P, Dreier M, Huber W and Güntherodt HJ 1996 Specific antigen/antibody reactions measured by force microscopy Biophys. J. 70 2437-41
250. Hinterdorfer P, Baumgartner W, Gruber H J, Schilcher K and Schindler H 1996 Detection and localization of individual antibody-antigen recognition events by atomic force microscopy Proc. Natl Acad. Sci. 93 3477-81
251. Schwesinger F, Ros R, Strunz T, Anselmetti D, Güntherodt H J, Honegger A, Jermutus L, Tiefenauer L and Plückthun A 2000 Unbinding forces of single antibody-antigen complexes correlate with their thermal dissociation rates Proc. Natl Acad. Sci. 97 9972-7
252. Fritz J, Katopodis A G, Kolbinger F and Anselmetti D 1998 Force-mediated kinetics of single p-selectin/ligand complexes observed by atomic force microscopy Proc. Natl Acad. Sci. 95 11283-8
253. Hanley W, McCarty O, JadhavDagger S, TsengDagger Y, WirtzDagger D and Konstantopoulos K 2003 Single molecule characterization of P-selectin/ligand binding Biochemistry 278 10556-61
254. Garcia-Manyes S, Oncins G and Sanz F 2005 Effect of temperature on the nanomechanics of lipid bilayers studied by force spectroscopy Biophys. J. 89 4261-74
255. Gergely C, Voegel J-C, Schaaf P, Senger B, Maaloum J M, Hörber J KH and Hemmerlé J 2000 Unbinding process of adsorbed proteins under external stress studied by atomic force spectroscopy Proc. Natl Acad. Sci. 97 10802-7
256. Perret E, Benoliel A M, Nassoy P, Pierres A, Delmas V, Thiery J P, Bongrand P and Feracci H 2002 Fast dissociation kinetics between individual E-cadherin fragments revealed by flow chamber analysis EMBO J. 21 2537-46
257. Perret E, Leung A, Feracci H and Evans E 2004 Trans-bonded pairs of E-cadherin exhibit a remarkable hierarchy of mechanical strengths Proc. Natl Acad. Sci. 101 16472-7
258. Evans E, Leung A, Hammer D and Simon S 2001 Chemically distinct transition states govern rapid dissociation of single L-selectin bonds under force Proc. Natl Acad. Sci. 98 3784-9
259. Dammer U, Popescu O, Wagner P, Anselmetti D, Dreier M, Huber W and Güntherodt HJ 1995 Binding strength between cell adhesion proteoglycans measured by atomic force microscopy Science 267 1173-5
260. Garcia-Manyes S, Bucior I, Ros R, Anselmetti D, Sanz F, Burger MM and Fernndez-Busquets X 2006 Proteoglycan mechanics studied by single molecule force spectroscopy of allotypic cell adhesion glycans J. Biol. Chem. 281 5992-9
261. Suchek TA, Friddle R W, Langry K, Lau E Y, Albrecht H, Ratto T V, DeNardo S J, Colvin ME and Noy A 2005 Dynamic force spectroscopy of parallel individual Mucin1-antibody bonds Proc. Natl Acad. Sci. 102 16638-43
262. Bartolo D, Derényi I and Adjari A 2002 Dynamic response of adhesion complexes: beyond the single-path picture Phys. Rev. E 65 051910
263. Williams PM 2002 Analytical descriptions of dynamic force spectroscopy: behaviour of multiple connections Anal. Chim. Acta 479 107-15
264. Rief M, Gautel M, Oesterhelt F, Fernandez JM and Gaub HE 1997 Reversible unfolding of individual titin inmunoglobulin domains by AFM Science 276 1109-12
265. Kellermayer MS, Smith S B, Granzier HL and Bustamante C 1997 Folding-unfolding transitions in single titin molecules characterized with laser tweezers Science 276 1112-6
266. Rief M, Gautel M, Schemmel A and Gaub HE 1998 The mechanical stability of immunoglobulin and fibronectin III domains in the muscle protein titin measured by atomic force microscopy Biophys. J. 75 3008-14
267. Carrion-Vazquez M, Oberhauser A F, Fowler S B, Marszalek P E, Broedel S E, Clarke J and Fernandez JM 1999 Mechanical and chemical unfolding of a single protein: a comparison Proc. Natl Acad. Sci. 96 3694-9
268. Carrion-Vazquez M, Marszalek P E, Oberhauser AF and Fernandez JM 1999 Atomic force microscopy captures length phenotypes in single proteins Proc. Natl Acad. Sci. 96 11288-92
269. Yang G, Cecconi C, Baase W A, Vetter I R, Breyer W A, Haack J A, Matthews B W, Dahlquist FW and Bustamante C 2000 Solid-state synthesis and mechanical unfolding of polymers of T4 lysozyme Proc. Natl Acad. Sci. 97 139-44
270. Oberhauser AF, Marszalek P E, Erickson HP and Fernandez JM 1998 The molecular elasticity of tensacin, an extracellular matrix protein Nature 393 181-5
271. Rief M, Pascual J, Saraste M and Gaub HE 1999 Single molecule force spectroscopy of spectrin repeats: low unfolding forces in helix bundles J. Mol. Biol. 286 553-61
272. Muller DJ, Kessler M, Oesterhelt F, Møller C, Oesterhelt D and Gaub H 2002 Stability of bacteriorhodopsin α-helices and loops analyzed by single-molecule force spectroscopy Biophys. J. 83 3578-88
273. Carl P, Kwok C H, Manderson G, Speicher DW and Discher DE 2001 Forced unfolding modulated by disulfide bonds in the Ig domains of a cell adhesion molecule Proc. Natl Acad. Sci. 98 1565-70
274. Rief M, Fernandez JM and Gaub HE 1998 Elastically coupled two-level systems as a model for biopolymer extensibility Phys. Rev. Lett. 81 4764-7
275. Kühner F, Friedsam C, Wehle A K and Gaub HE 2003 Dynamic single-molecule force spectroscopy: bond rupture analysis with variable spacer lengths J. Phys.: Condens. Matter 15 S1709-23
276. Munoz V, Thomson A P, Hofrichter J and Eaton WA 1997 Folding dynamics and mechanisms of beta-hairpin formation Nature 390 196-9
277. Bhasin N, Carl P, Harper S, Feng G, Lu H, Speicher DW and Discher DE 2004 Chemistry on a single protein, vascular cell adhesion molecule-1, during forced unfolding J. Biol. Chem. 279 45865-74
278. Wiita AP, Ainavarapu S R K, Huang HH and Fernandez JM 2006 Force-dependent chemical kinetics of disulfide bond reduction observed with single-molecule techniques Proc. Natl Acad. Sci. 103 7222-7
279. Discher DE, Bhasin N and Johnson CP 2006 Covalent chemistry on distended proteins Proc. Natl Acad. Sci. 103 7533-4
280. Klimov DK and Thirumalai D 1999 Stretching single-domain proteins: phase diagram and kinetics of forced-induced unfolding Proc. Natl Acad. Sci. 96 6166-70
281. Paci E and Karplus M 2000 Unfolding proteins by external forces and temperature: the importance of topology and energetics Proc. Natl Acad. Sci. 97 6521-6
282. Shen T, Canino LS and McCammon JA 2002 Unfolding proteins under external forces: a solvable model under the self-consistent pair contact probability approximation Phys. Rev. Lett. 89 068103
283. Valpuesta JM, Martín-Benito J, Gømez-Puertas P, Carrascosa JL and Willison KR 2002 Structure and function of a protein folding machine: the eukaryotic cytosolic chaperonin CCT FEBS Lett. 529 11-6
284. Schlierf M, Li H and Fernandez JM 2004 The unfolding kinetics of ubiquitin captured with single-molecule force-clamp techniques Proc. Natl Acad. Sci. 101 7299-304
285. Fernandez JM and Li H 2004 Force-clamp spectroscopy monitors the folding trajectory of a single protein Science 303 1674-8
286. Brujic J, Hermans Z R I, Walther KA and Fernandez JM 2006 Single-molecule force spectroscopy reveals signatures of glassy dynamics in the energy landscape of ubiquitin Nat. Phys. 2 282-6
287. Sosnick TR 2004 Comment on 'Force-clamp spectroscopy monitors the folding trajectory of a single protein' Science 306 411b
288. Fernandez JM, Li H and Brujic J 2004 Response to Comment on 'Force-clamp spectroscopy monitors the folding trajectory of a single protein' Science 306 411c
289. Best RB and Hummer G 2005 Comment on 'Force-clamp spectroscopy monitors the folding trajectory of a single protein' Science 308 498b
290. Fernandez JM and Li H 2005 Response to Comment on 'Force-clamp spectroscopy monitors the folding trajectory of a single protein' Science 308 498c
291. Lu H, Isralewitz B, Krammer A, Vogel V and Schulten K 1998 Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation Biophys. J. 75 662-71
292. Marszalek PE, Lu H, Li H, Carrion-Vazquez M, Oberhauser A F, Schulten K and Fernandez JM 1999 Mechanical unfolding intermediates in titin modules Nature 402 100-3
293. Williams PM, Fowler S B, Best R B, Toca-Herrera J L, Scott K A, Steward A and Clarke J 2003 Hidden complexity in the mechanical unfolding of titin Nature 422 446-9
294. Cecconi C, Shank E A, Bustamante C and Marqusee S 2005 Direct observation of the three-state folding of a single protein molecule Science 309 2057-60
295. Onuchic JN, Luthey-Schulten Z and Wolynes PG 1997 Theory of protein folding: the energy landscape perspective Annu. Rev. Phys. Chem. 48 545-600
296. Finkelstein AV 2004 Proteins: structural, thermodynamic and kinetic aspects Slow Relaxations and Nonequilibrium Dynamics ed JL Barrat and J Kurchan (Berlin: Springer) pp650-703
297. Junier I and Ritort F 2006 Single-domain protein folding: a multi-faceted problem to be published
298. Xie Z, Srividya N, Sosnick T R, Pan T and Scherer NF 2004 Single-molecule studies highlight conformational heterogeneity in the early folding steps of a large ribozyme Proc. Natl Acad. Sci. 101 534-9
299. Spudich A 2002 How molecular motors work Nature 372 515-8
300. Jeruzalmi D, O'Donell M and Kuriyan J 2002 Clamp loaders and sliding clamps Curr. Opin. Struct. Biol. 12 217-24
301. Bustamante C, Keller D and Oster G 2001 The physics of molecular motors Acc. Chem. Res. 34 412-20
302. Hugel T, Holland N B, Cattani A, Moroder L, Seitz M and Gaub HE 2002 Single-molecule optomechanical cycle Science 296 1103-6
303. Howard J 2001 Mechanics of Motor Proteins and the Cytoskeleton (Sunderland, MA: Sinauer)
304. Cross RA 2004 The kinetic mechanism of kinesin Trends Biochem. Sci. 29 301-9
305. Carter NJ and Cross RA 2006 Kinesin's moonwalk Curr. Opin. Struct. Biol. 18 61-7
306. Svoboda K, Schmidt C F, Schnapp BJ and Block SM 1993 Direct observation of kinesin stepping by optical trapping interferometry Nature 365 721-7
307. Yildiz A, Tomishige M, Vale RD and Selvin PR 2004 Kinesin walks hand-over-hand Science 303 676-8
308. Uemura S and Ishiwata S 2003 Loading direction regulates the affinity of ADP for kinesin Nat. Struct. Mol. Biol. 10 308-11
309. Block SM, Asbury C L, Shaevitz JW and Lang MJ 2003 Probing the kinesin reaction cycle with a 2D optical force clamp Proc. Natl Acad. Sci. 100 2351-6
310. Block SM, Goldstein L SB and Schnapp BJ 1990 Bead movement by single kinesin molecules studied with optical tweezers Nature 348 348-52
311. Carter NJ and Cross RA 2005 Mechanics of the kinesin step Nature 435 308-12
312. Nayashima M, Higuchi H and Yanagida T 2002 Chemomechanical coupling of the forward and backward steps of single kinesin molecules Nat. Cell Biol. 4 790-7
313. Helenius J, Brouhard G, Kalaidzidis Y, Diez S and Howard J 2006 The depolymerizing kinesin MCAK uses lattice diffusion to rapidly target microtubule ends Nature 441 115-9
314. Leduc C, Campas O, Zeldovich K B, Roux A, Jolimaitre P, Bourel-Bonnet L, Goud B, Joanny J-F, Bassereau P and Prost J 2004 Cooperative extraction of membrane nanotubes by molecular motors Proc. Natl Acad. Sci. 101 17096-101
315. Mallik R, Carter B C, Lex S A, King SJ and Gross SP 2004 Cytoplasmic dynein functions as a gear in response to load Nature 427 649-52
316. Burgess SA, Walker M L, Sakakibara H, Knight PJ and Oiwa K 2003 Dynein structure and power stroke Nature 421 715-8
317. Sellers JR 1999 Myosins (Oxford: Oxford University Press)
318. Veigel C, Coluccio L M, Jontes J D, Sparrow J C, Milligan RA and Molloy JE 1999 The motor protein myosin-I produces its working stroke in two steps Nature 398 530-3
319. Kitamura K, Tokunaga M, Iwane AH and Yanagida T 1999 A single myosin head moves along an actin filament with regular steps of 5.3 nanometers Nature 397 129-34
320. Inoue A, Saito J, Ikebe R and Ikebe M 2002 Myosin IXb is a single-headed minus-end-directed processive motor Nat. Cell Biol. 4 302-6
321. Veigel C, Wang F, Bartoo M L, Sellers JR and Molloy JE 2002 The gated gait of the processive molecular motor, myosin V Nat. Cell Biol. 4 59-65
322. Tanaka H, Homma K, Iwane A H, Katayama E, Ikebe R, Saito J, Yanagida T and Ikebe M 2002 The motor domain determines the large step of myosin-V Nature 415 192-5
323. Finer JT, Simmons RM and Spudich JA 1994 Single myosin molecule mechanics: piconewton forces and nanometre steps Nature 368 113-9
324. Molloy JE, Burns J E, Kendrick-Jones J, Tregear RT and White DCS 1995 Movement and force produced by a single myosin head Nature 378 209-12
325. Noji H, Yasuda R, Yoshida M and Kinosita K Jr 1997 Direct observation of the rotation of F1-ATPase Nature 386 299-302
326. Yasuda R, Noji H, Kinosita K Jr and Yoshida M 1998 F1-ATPase is a highly efficient molecular motor that rotates with discrete 120° steps Cell 93 1117-24
327. Adachi K, Yasuda R, Noji H, Itoh H, Harada Y, Yoshida M and Kinosita K Jr 2000 Stepping rotation of F1-ATPase visualized through angle-resolved single-fluorescence imaging Proc. Natl Acad. Sci. 97 7243-7
328. Masaike T, Mitome N, Noji H, Muneyuki E, Yasuda R, Kinosita K Jr and Yoshida M 2000 Rotation of F1-ATPase and the hinge residues of the β-subunit J. Exp. Biol. 203 1-8
329. Yasuda R, Noji H, Yoshida M, Kinosita K Jr and Itoh H 2001 Resolution of distinct rotational substeps by submillisecond kinetic analysis of F1-ATPase Nature 410 898-904
330. Soong RK, Bachand G D, Neves H P, Olkhovets A G, Craighead H G and Montemagno CD 2000 Powering an inorganic device with a biomolecular motor Science 290 1555-8
331. Wuite GJ L, Smith S B, Young M, Keller D and Bustamante C 2000 Single-molecule studies of the effect of template tension on T7 DNA polymerase activity Nature 404 103-6
332. Maier B, Bensimon D and Croquette V 2000 Replication by a single DNA polymerase of a stretched single-stranded DNA Proc. Natl Acad. Sci. 97 12002-7
333. Goel A, Frank-Kamenetskii M D, Ellenberger T and Herschbach D 2001 Tuning DNA 'strings': modulating the rate of DNA replication with mechanical tension Proc. Natl Acad. Sci. 98 8485-9
334. Goel A, Astumian RD and Herschbach D 2003 Tuning and switching a DNA polymerase motor with mechanical tension Proc. Natl Acad. Sci. 100 9699-704
335. Saleh OA, Bigot S, Barre F X and Allemand JF 2005 Analysis of DNA supercoil induction by FtsK indicates translocation without groove-tracking Nat. Struct. Mol. Biol. 12 436-40
336. Pease P J, Levy O, Cost G J, Gore J, Ptacin J L, Sherratt D, Bustamante C and Cozzarelli NR 2005 Sequence-directed DNA translocation by purified FtsK Science 307 586-90
337. Forde NR, Izhaky D, Woodcock G R, Wuite G JL and Bustamante C 2002 Using mechanical force to probe the mechanism of pausing and arrest during continuous elongation by Escherichia coli RNA polymerase Proc. Natl Acad. Sci. 99 11682-7
338. Abbondanzieri EA, Greenleaf W J, Shaevitz J W, Landick R and Block SM 2005 Direct observation of base-pair stepping by RNA polymerase Nature 438 460-5
339. Gelles J and Landick R 1998 RNA polymerase as a molecular motor Cell 93 13-6
340. Klug A 2001 A marvelous machine for making messages Science 292 1844-6
341. Uptain SM, Kane CM and Chamberlin MJ 1997 Basic mechanisms of transcript elongation and its regulation Annu. Rev. Biochem. 66 117-72
342. Yin H, Wang M D, Svoboda K, Landick R, Block SM and Gelles J 1995 Transcription against an applied force Science 270 1653-7
343. Wang MD, Schnitzer M J, Yin H, Landick R, Gelles J and Block SM 1998 Force and velocity measured for single molecules of RNA polymerase Science 282 902-7
344. Davenport RJ, Wuite G J, Landick R and Bustamante C 2000 Single-molecule study of transcriptional pausing and arrest by E. coli RNA polymerase Science 287 2497-500
345. Shaevitz JW, Abbondanzieri E A, Landick R and Block SM 2003 Backtracking by single RNA polymerase molecules observed at near-base-pair resolution Nature 426 684-7
346. Adelman K, La Porta A, Santangelo T J, Lis J T, Roberts JW and Wang MD 2002 Single molecule analysis of RNA polymerase elongation reveals uniform kinetic behaviour Proc. Natl Acad. Sci. 99 13538-43
347. Orphanides G and Reinberg D 2002 A unified theory of gene expression Cell 108 439-51
348. Smith DE, Tans S J, Smith S B, Grimes S, Anderson DL and Bustamante C 2001 The bacteriophage 29 portal motor can package DNA against a large internal force Nature 413 748-52
349. Purohit PK, Kondev J and Phillips R 2003 Mechanics of DNA packaging in viruses Proc. Natl Acad. Sci. 100 3173-8
350. Kindt J, Tzlil S, Ben-Shaul A and Gelbart WM 2001 DNA packaging and ejection forces in bacteriophage Proc. Natl Acad. Sci. 98 13671-4
351. Zandi R, Reguera D, Rudnick J and Geldbart WM 2003 What drives the translocation of stiff chains? Proc. Natl Acad. Sci. 100 8649-53
352. Strick TR, Croquette V and Bensimon D 2000 Single-molecule analysis of DNA uncoiling by a type II topoisomerase Nature 404 901-4
353. Charvin G, Bensimon D and Croquette V 2003 Single-molecule study of DNA unlinking by eukaryotic and prokaryotic type-II topoisomerases Proc. Natl Acad. Sci. 100 9820-5
354. Koster DA, Croquette V, Dekker C, Shuman S and Dekker NH 2005 Friction and torque govern the relaxation of DNA supercoils by eukaryotic topoisomerase IB Nature 434 671-4
355. Gore J, Bryant Z, Stone M D, Nöllmann M, Cozzarelli NR and Bustamante C 2006 Mechanochemical analysis of DNA gyrase using rotor bead tracking Nature 439 100-4
356. Charvin G, Strick T R, Bensimon D and Croquette V 2005 Topoisomerase IV bends and overtwists DNA upon binding Biophys. J. 89 384-92
357. Bensimon D, Dessinges MN, Lionnet T, Xi X G and Croquette V 2004 Single-molecule assay reveals strand switching and enhanced processivity of UvrD Proc. Natl Acad. Sci. 101 6439-44
358. Dohoney KM and Gelles J 2001 χ-sequence recognition and DNA translocation by single RecBCD enzyme molecules Nature 409 370-4
359. Gelles J, Perkins TT, Li H W, Dalal R W and Block SM 2004 Forward and reverse motion of single RecBCD molecules on DNA Biophys. J. 86 1640-8
360. Ha T, Rasnik I, Cheng W, Babcock H P, Gauss G H, Lohman TM and Chu S 2002 Initiation and re-initiation of DNA unwinding by the Escherichia Coli Rep helicase Nature 419 638-41
361. Dumont S, Cheng W, Serebrov V, Beran R K, Tinoco I Jr, Pyle AM and Bustamante C 2006 RNA translocation and unwinding mechanism of HCV NS3 helicase and its coordination by ATP Nature 439 105-8
362. Vanzi F, Vladimirov S, Knudsen C R, Goldman YE and Cooperman BS 2003 Protein synthesis by single ribosomes RNA 9 1174-9
363. Blanchard SC, Kim H D, Gonzalez R L, Puglisi JD and Chu S 2004 tRNA dynamics on the ribosome during translation Proc. Natl Acad. Sci. 101 12893-8
364. Vanzi F, Takagi Y, Shuman H, Cooperman BS and Goldman YE 2005 Mechanical studies of single ribosome/mRNA complexes Biophys. J. 89 1909-19
365. Hill TL 1975 Free-energy and the kinetics of biochemical diagrams, including active transport Biochemistry 14 2127-37
366. Eisenberg E and Hill TL 1985 Muscle contraction and free energy transduction in biological systems Science 277 999-1006
367. Córdova NJ, Ermentrout B and Oster GF 1992 Dynamics of single-motor molecules: the thermal ratchet model Proc. Natl Acad. Sci. 89 339-43
368. Astumian RD 1997 Thermodynamics and kinetics of a Brownian motor Science 276 917-22
369. Jülicher F, Adjari A and Prost J 1998 Modeling molecular motors Rev. Mod. Phys. 69 1269-81
370. Fisher ME and Kolomeisky AB 1999 The force exerted by a molecular motor Proc. Natl Acad. Sci. 96 6597-602
371. Keller D and Bustamante C 2000 The mechanochemistry of molecular motors Biophys. J. 78 541-56
372. Lipowsky R, Klumpp S and Nieuwenhuizen ThM 2001 Random walks of cytoskeletal motors in open and closed compartments Phys. Rev. Lett. 87 108101
373. Reimann P 2002 Brownian motors: noisy transport far from equilibrium Phys. Rep. 361 57-265
374. Betterton MD and Jülicher F 2005 Opening of DNA double strands by helicases: active verus passive opening Phys. Rev. E 71 011904
375. Bhattacharjee SM 2003 Helicase activity on DNA as a propagating front Europhys. Lett. 65 574-80
376. Kolomeisky AB, Stukalin EB and Popov AA 2005 Understanding mechanochemical coupling in kinesins using first-passage-time processes Phys. Rev. E 71 031902
377. Keller D, Swigon D and Bustamante C 2003 Relating single-molecule measurements to thermodynamics Biophys. J. 84 733-8
378. Gross DHE 2001 Microcanonical Thermodynamics, Phase Transitions in 'Small systems' (World Scientific Lecture Notes in Physics) (Singapore: World scientific)
379. Tsallis C 1988 Possible generalization of Boltzmann-Gibbs statistics J. Stat. Phys. 52 479-87
380. Beck C 2001 Dynamical foundations of nonextensive statistical mechanics Phys. Rev. Lett. 87 180601
381. Cohen EGD 2002 Some recent advances in classical statistical mechanics Dynamics of Dissipation vol 597 ed P Garbaczewski and R Olkiewicz (Berlin: Springer) p7
382. Evans DJ and Searles D 2002 The fluctuation theorem Adv. Phys. 51 1529-85
383. Maes C 2003 On the origin and use of fluctuation relations on the entropy Semin. Poincaré 2 145-91
384. Cohen EGD and Mauzerall D 2004 A note on the Jarzynski equality J. Stat. Mech. (Theor. Exp.) P07006
385. Jarzynski C 2004 Nonequilibrium work theorem for a system strongly coupled to a thermal environment J. Stat. Mech. P09005
386. Astumian RD 2006 The unreasonable effectiveness of equilibrium-like theory for interpreting nonequilibrium experiments Am. J. Phys. (Preprint cond-mat/0512024)
387. Evans DJ and Searles DJ 1994 Equilibrium microstates which generate second law violating steady-states Phys. Rev. E 50 1645-8
388. Crooks GE 1999 Entropy production fluctuation theorem and the nonequilibrium work relation for free-energy differences Phys. Rev. E 60 2721-6
389. Cohen EG D, Evans DJ and Morriss GP 1993 Probability of second law violations in shearing steady states Phys. Rev. Lett. 71 2401-4
390. Gallavotti G and Cohen EGD 1995 Dynamical ensembles in nonequilibrium statistical mechanics Phys. Rev. Lett. 74 2694-7
391. Kurchan J 1998 Fluctuation theorem for stochastic dynamics J. Phys. A: Math. Gen. 31 3719-29
392. Lebowitz JL and Spohn H 1999 A Gallavotti-Cohen type symmetry in the large deviation functional for stochastic dynamics J. Stat. Phys. 95 333-65
393. Maes C 1999 The fluctuation theorem as a gibbs property J. Stat. Phys. 95 367-92
394. Oono Y and Paniconi M 1998 Steady state thermodynamics Prog. Theor. Phys. Suppl. 130 29-44
395. Hatano T and Sasa S 2001 Steady-state thermodynamics of Langevin systems Phys. Rev. Lett. 86 3463-6
396. Speck T and Seifert U 2005 Integral fluctuation theorem for the housekeeping heat J. Phys. A: Math. Gen. 38 L581-8
397. Ciliberto S and Laroche C 1998 An experimental test of the Gallavotti-Cohen fluctuation theorem J. Physique IV 8 215-20
398. Ciliberto S, Garnier N, Hernandez S, Lacpatia C, Pinton JF and Ruiz-Chavarria G 2004 Experimental test of the Gallavotti-Cohen fluctuation theorem in turbulent flows Physica A 340 240-50
399. Wang GM, Sevick E M, Mittag E, Searles DJ and Evans DJ 2002 Experimental demonstration of violations of the second law of thermodynamics for small systems and short timescales Phys. Rev. Lett. 89 050601
400. Carberry DM, Reid J C, Wang G M, Sevick E M, Searles DJ and Evans DJ 2004 Fluctuations and irreversibility: an experimental demonstration of a second-law-like theorem using a colloidal particle held in an optical trap Phys. Rev. Lett. 92 140601
401. Trepagnier EH, Jarzynski C, Ritort F, Crooks G E, Bustamante C and Liphardt J 2004 Experimental test of Hatano and Sasa's nonequilibrium steady state equality Proc. Natl Acad. Sci. 101 15038-41
402. Blickle V, Speck T, Helden L, Seifert U and Bechinger C 2005 Thermodynamics of a colloidal particle in a time-dependent non-harmonic potential Phys. Rev. Lett. 93 158105
403. Crooks GE 2000 Path-ensemble averages in systems driven far from equilibrium Phys. Rev. E 61 2361-6
404. Jarzynski C 1997 Nonequilibrium equality for free-energy differences Phys. Rev. Lett. 78 2690-3
405. Jarzynski C 2002 What is the microscopic response of a system driven far from equilibrium Dynamics of Dissipation vol 597 ed P Garbaczewski and R Olkiewicz (Berlin: Springer) pp63-82
406. Zwanzig RW 1954 High-temperature equation of state by a perturbation method. I. Nonpolar gases J. Chem. Phys. 22 1420-6
407. Bochkov GN and Kuzovlev YE 1981 Non-linear fluctuation relations and stochastic models in nonequilibrium thermodynamics. I. Generalized fluctuation-dissipation theorem Physica A 106 443-79
408. Hummer G and Szabo A 2001 Free-energy reconstruction from nonequilibrium single-molecule experiments Proc. Natl Acad. Sci. 98 3658-61
409. Jarzynski C 2001 How does a system respond when driven away from thermal equilibrium? Proc. Natl Acad. Sci. 98 3636-8
410. Hummer G and Szabo A 2005 Free-energy surfaces from single-molecule force spectroscopy Acc. Chem. Res. 38 504-13
411. Liphardt J, Dumont S, Smith S B, Tinoco I Jr and Bustamante C 2002 Equilibrium information from nonequilibrium measurements in an experimental test of the jarzynski equality Science 296 1833-5
412. Schuler S, Speck T, Tierz C, Wrachtrup J and Seifert U 2005 Experimental test of the fluctuation theorem for a driven two-level system with time-dependent rates Phys. Rev. Lett. 94 180602
413. Douarche F, Ciliberto S and Petrosyan A 2005 An experimental test of the Jarzynski equality in a mechanical experiment Europhys. Lett. 70 593-8
414. Douarche F, Ciliberto S and Petrosyan A 2005 Estimate of the free energy difference in mechanical systems from work fluctuations: experiments and models J. Stat. Mech. P09011
415. Van Zon R and Cohen EGD 2003 Extension of the fluctuation theorem Phys. Rev. Lett. 91 110601
416. Van Zon R and Cohen EGD 2003 Stationary and transient work-fluctuation theorems for a dragged Brownian particle Phys. Rev. E 67 046102
417. Seifert U 2004 Fluctuation theorem for birth-death or chemical master equations with time-dependent rates J. Phys. A: Math. Gen. 37 L517-21
418. Jarzynski C and Wojcik DK 2004 Classical and quantum fluctuation theorems for heat exchange Phys. Rev. Lett. 92 230602
419. Seifert U 2005 Entropy production along a stochastic trajectory and an integral fluctuation theorem Phys. Rev. Lett. 95 040602
420. Reid JC, Sevick EM and Evans DJ 2005 A unified description of two theorems in non-equilibrium statistical mechanics: the fluctuation theorem and the work relation Europhys. Lett. 72 726-30
421. Hummer G 2001 Fast-growth thermodynamic integration: error and efficiency analysis J. Chem. Phys. 114 7330-7
422. Isralewitz B, Gao M and Schulten K 2001 Steered molecular dynamics and mechanical functions of proteins Curr. Opin. Struct. Biol. 11 224-30
423. Jensen MO, Park S, Tajkhorshid E and Schulten K 2002 Energetics of glycerol conduction through aquaglyceroporin Glpf Proc. Natl Acad. Sci. 99 6731-6
424. Park S, Khalili-Araghi F, Tajkhorshid E and Schulten K 2003 Free-energy calculation from steered molecular dynamics simulations using Jarzynski's equality J. Phys. Chem. B 119 3559-66
425. Andriocioaei I, Dinner AR and Karplus M 2003 Self-guided enhanced sampling methods for thermodynamic averages J. Chem. Phys. 118 1074-84
426. Park S and Schulten K 2004 Calculating potentials of mean force from steered molecular dynamics simulation J. Chem. Phys. 13 5946-61
427. Bennett CH 1976 Efficient estimation of free-energy differences from Monte Carlo data J. Comput. Phys. 22 245-68
428. Wood RH, Mühlbauer W CF and Thompson PT 1991 Systematic errors in free energy perturbation calculations due to a finite sample of configuration space: sample-size hysteresis J. Phys. Chem. 95 6670-5
429. Hendrix DA and Jarzynski C 2001 A 'fast growth' method of computing free-energy differences J. Chem. Phys. 114 5974-81
430. Zuckermann DM and Woolf TB 2002 Overcoming finite-sampling errors in fast-switching free-energy estimates: extrapolative analysis of a molecular system Chem. Phys. Lett. 351 445-53
431. Zuckermann DM and Woolf TB 2002 Theory of systematic computational error in free energy differences Phys. Rev. Lett. 89 180602
432. Gore J, Ritort F and Bustamante C 2003 Bias and error in estimates of equilibrium free-energy differences from nonequilibrium measurements Proc. Natl Acad. Sci. 100 12564-9
433. Shirts M R, Bair E, Hooker G and Pande VS 2003 Equilibrium free energies from nonequilibrium measurements using maximum-likelihood methods Phys. Rev. Lett. 91 140601
434. Schurr J M and Fujimoto B S 2003 Equalities for the nonequilibrium work transferred from an external potential to a molecular system: analysis of single-molecule extension experiments J. Phys. Chem. B 107 14007-19
435. Braun O, Hanke A and Seifert U 2004 Probing molecular free energy landscapes by periodic loading Phys. Rev. Lett. 93 158105
436. Qian H 2005 Cycle kinetics, steady state thermodynamics and motors-a paradigm for living matter physics J. Phys.: Condens. Matter 17 S3783-94
437. Min W, Jiang L, Yu J, Kou S C, Qian H and Xie XS 2005 Nonequilibrium steady state of a nanometric biochemical system: determining the thermodynamic driving force from single enzyme turnover time traces Nanoletters 5 2373-8
438. Mazonka O and Jarzynski C 1999 Exactly solvable model illustrating far-from-equilibrium predictions Preprint cond-mat/9912121
439. Lhua RC and Grossberg AY 2005 Practical applicability of the Jarzynski relation in statistical mechanics: a pedagogical example J. Phys. Chem. B 109 6805-11
440. Bena I, Van den Broeck C and Kawai R 2005 Jarzynski equality for the Jepsen gas Europhys. Lett. 71 879-85
441. Seifert U 2005 Fluctuation theorem for a single enzyme or molecular motor Europhys. Lett. 70 36-41
442. Speck T and Seifert U 2005 Dissipated work in driven harmonic diffusive systems: general solution and application to stretching rouse polymers Eur. Phys. J. B 43 521-7
443. Cleuren B, Van den Broeck C and Kawai R 2006 Fluctuation and sissipation of work in a Joule experiment Phys. Rev. Lett. 96 050601
444. Van Zon R and Cohen EGD 2004 Extended heat-fluctuation theorems for a system with deterministic and stochastic forces Phys. Rev. E 69 056121
445. Ritort F 2004 Work and heat fluctuations in two-state systems: a trajectory thermodynamics formalism J. Stat. Mech. P10016
446. Imparato A and Peliti L 2005 Work distribution and path integrals in mean-field systems Europhys. Lett. 70 740-6
447. Imparato A and Peliti L 2005 Work probability distribution in systems driven out of equilibrium Phys. Rev. E 72 046114
448. Garnier N and Ciliberto S 2005 Nonequilibrium fluctuations in a resistor Phys. Rev. E 71 060101(R)
449. Feitosa K and Menon N 2004 Fluidized granular medium as an instance of the fluctuation theorem Phys. Rev. Lett. 92 164301
450. Kosztin I, Barz B and Janosi L 2006 Calculating potentials of mean force and diffusion coefficients from nonequilibrium processes without Jarzynski equality J. Chem. Phys. 124 064106
451. Moffitt JR, Chemla Y R, Izhaky D and Bustamante C 2006 Differential detection of dual traps improves the spatial resolution of optical tweezers Proc. Natl Acad. Sci. 103 9006-11
452. Lang MJ, Fordyce PM and Block SM 2003 Combined optical trapping and single-molecule fluorescence J. Biol. 2 6
453. Sarkar A, Robertson RB and Fernandez JM 2004 Simultanoeus atomic force microscope and fluorescence measurements of protein unfolding using a calibrated evanescent wave Proc. Natl Acad. Sci. 101 12882-6
454. Williams MC, Wenner J R, Rouzina I and Bloomfield VA 2001 Entropy and heat capacity of DNA melting from temperature dependence of single molecule stretching Biophys. J. 80 1932-9
455. Law R, Liao G, Harper S, Yang G, Speicher DW and Discher DE 2003 Pathway shifts and thermal softening in temperature-coupled force unfolding of spectrin domains Biophys. J. 85 3286-93
456. Tinoco I Jr, Mao H, Arias-Gonzalez J R, Smith S B and Bustamante C 2005 Temperature control methods in a laser-tweezers system Biophys. J. 89 1308-16
457. Garces-Chavez V, McGloin D, Melville H, Sibbett W and Dholakia K 2002 Simultaneous micromanipulation in multiple planes using a self-reconstructed light beam Nature 419 145-7
458. Grier DG 2003 A revolution in optical manipulation Nature 424 810-6