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Journal of Chemical Physics

Volumn 130, Issue 20, 2009, Pages

Density-dependent analysis of nonequilibrium paths improves free energy estimates

(1) Minh, David D L a

a NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY AND PRECISION; DENSITY-DEPENDENT; ENERGY ESTIMATES; EQUILIBRIUM DENSITY; FREE-ENERGY DIFFERENCE; NON EQUILIBRIUM; NONEQUILIBRIUM WORK; OUT OF EQUILIBRIUM; RELATIVE ENTROPY; TEST CASE; TIME-DEPENDENT;

FREE ENERGY;

ALGORITHM; ARTICLE; CHEMICAL MODEL; COMPUTER SIMULATION; DIAGNOSIS, MEASUREMENT AND ANALYSIS; ENTROPY; METHODOLOGY; PHYSICAL PHENOMENA; PROTEIN CONFORMATION; THERMODYNAMICS;

ALGORITHMS; COMPUTER SIMULATION; ENTROPY; LABORATORY TECHNIQUES AND PROCEDURES; MODELS, CHEMICAL; PHYSICAL PROCESSES; PROTEIN CONFORMATION; RESEARCH DESIGN; THERMODYNAMICS;

EID: 66749162015 PISSN: 00219606 EISSN: None Source Type: Journal
DOI: 10.1063/1.3139189 Document Type: Article

Times cited : (7)

References (36)

1
- 4243754128
- 0031-9007,. 10.1103/PhysRevLett.78.2690
- C. Jarzynski, Phys. Rev. Lett. 0031-9007 78, 2690 (1997). 10.1103/PhysRevLett.78.2690
- (1997) Phys. Rev. Lett. , vol.78 , pp. 2690
- Jarzynski, C.¹

2
- 4244116139
- 1063-651X,. 10.1103/PhysRevE.56.5018
- C. Jarzynski, Phys. Rev. E 1063-651X 56, 5018 (1997). 10.1103/PhysRevE.56.5018
- (1997) Phys. Rev. e , vol.56 , pp. 5018
- Jarzynski, C.¹

3
- 0032023968
- 0022-4715,. 10.1023/A:1023208217925
- G. E. Crooks, J. Stat. Phys. 0022-4715 90, 1481 (1998). 10.1023/A:1023208217925
- (1998) J. Stat. Phys. , vol.90 , pp. 1481
- Crooks, G.E.¹

4
- 0000765761
- 1063-651X,. 10.1103/PhysRevE.60.2721
- G. E. Crooks, Phys. Rev. E 1063-651X 60, 2721 (1999). 10.1103/PhysRevE.60.2721
- (1999) Phys. Rev. e , vol.60 , pp. 2721
- Crooks, G.E.¹

5
- 0000186593
- 1063-651X,. 10.1103/PhysRevE.61.2361
- G. E. Crooks, Phys. Rev. E 1063-651X 61, 2361 (2000). 10.1103/PhysRevE.61.2361
- (2000) Phys. Rev. e , vol.61 , pp. 2361
- Crooks, G.E.¹

6
- 0037036070
- 0036-8075,. 10.1126/science.1071152
- J. Liphardt, S. Dumont, S. B. Smith, I. Tinoco, Jr., and C. Bustamante, Science 0036-8075 296, 1832 (2002). 10.1126/science.1071152
- (2002) Science , vol.296 , pp. 1832
- Liphardt, J.¹ Dumont, S.² Smith, S.B.³ Tinoco Jr., I.⁴ Bustamante, C.⁵

7
- 24644450199
- 0028-0836,. 10.1038/nature04061
- D. Collin, F. Ritort, C. Jarzynski, S. B. Smith, I. Tinoco, and C. Bustamante, Nature (London) 0028-0836 437, 231 (2005). 10.1038/nature04061
- (2005) Nature (London) , vol.437 , pp. 231
- Collin, D.¹ Ritort, F.² Jarzynski, C.³ Smith, S.B.⁴ Tinoco, I.⁵ Bustamante, C.⁶

8
- 0035333627
- 0021-9606,. 10.1063/1.1363668
- G. Hummer, J. Chem. Phys. 0021-9606 114, 7330 (2001). 10.1063/1.1363668
- (2001) J. Chem. Phys. , vol.114 , pp. 7330
- Hummer, G.¹

9
- 18744379822
- 0031-9007,. 10.1103/PhysRevLett.89.180602
- D. M. Zuckerman and T. B. Woolf, Phys. Rev. Lett. 0031-9007 89, 180602 (2002). 10.1103/PhysRevLett.89.180602
- (2002) Phys. Rev. Lett. , vol.89 , pp. 180602
- Zuckerman, D.M.¹ Woolf, T.B.²

10
- 0242268467
- 0027-8424,. 10.1073/pnas.1635159100
- J. Gore, F. Ritort, and C. Bustamante, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 100, 12564 (2003). 10.1073/pnas.1635159100
- (2003) Proc. Natl. Acad. Sci. U.S.A. , vol.100 , pp. 12564
- Gore, J.¹ Ritort, F.² Bustamante, C.³

11
- 3142740709
- 0022-4715,. 10.1023/B:JOSS.0000013961.84860.5b
- D. M. Zuckerman and T. B. Woolf, J. Stat. Phys. 0022-4715 114, 1303 (2004). 10.1023/B:JOSS.0000013961.84860.5b
- (2004) J. Stat. Phys. , vol.114 , pp. 1303
- Zuckerman, D.M.¹ Woolf, T.B.²

12
- 33645666178
- 1063-651X,. 10.1103/PhysRevE.73.046105
- C. Jarzynski, Phys. Rev. E 1063-651X 73, 046105 (2006). 10.1103/PhysRevE.73.046105
- (2006) Phys. Rev. e , vol.73 , pp. 046105
- Jarzynski, C.¹

13
- 47249092172
- 0021-9606,. 10.1063/1.2937892
- P. Maragakis, F. Ritort, C. Bustamante, M. Karplus, and G. E. Crooks, J. Chem. Phys. 0021-9606 129, 024102 (2008). 10.1063/1.2937892
- (2008) J. Chem. Phys. , vol.129 , pp. 024102
- Maragakis, P.¹ Ritort, F.² Bustamante, C.³ Karplus, M.⁴ Crooks, G.E.⁵

14
- 0000318631
- 10.1063/1.459753
- A. E. Mark, W. F. van Gunsteren, and H. J. C. Berendsen, J. Chem. Phys. 94, 3808 (1991). 10.1063/1.459753
- (1991) J. Chem. Phys. , vol.94 , pp. 3808
- Mark, A.E.¹ Van Gunsteren, W.F.² Berendsen, H.J.C.³

15
- 0000464094
- 0021-9606,. 10.1063/1.463235
- W. P. Reinhardt and J. E. Hunter, J. Chem. Phys. 0021-9606 97, 1599 (1992). 10.1063/1.463235
- (1992) J. Chem. Phys. , vol.97 , pp. 1599
- Reinhardt, W.P.¹ Hunter, J.E.²

16
- 0001541834
- 0021-9606,. 10.1063/1.465830
- J. E. Hunter, W. P. Reinhardt, and T. F. Davis, J. Chem. Phys. 0021-9606 99, 6856 (1993). 10.1063/1.465830
- (1993) J. Chem. Phys. , vol.99 , pp. 6856
- Hunter, J.E.¹ Reinhardt, W.P.² Davis, T.F.³

17
- 0001464311
- 0021-9606,. 10.1063/1.472836
- J. C. Schon, J. Chem. Phys. 0021-9606 105, 10072 (1996). 10.1063/1.472836
- (1996) J. Chem. Phys. , vol.105 , pp. 10072
- Schon, J.C.¹

18
- 0031556559
- 1089-5647,. 10.1021/jp9716795
- C. Jarque and B. Tidor, J. Phys. Chem. B 1089-5647 101, 9402 (1997). 10.1021/jp9716795
- (1997) J. Phys. Chem. B , vol.101 , pp. 9402
- Jarque, C.¹ Tidor, B.²

19
- 33847786887
- 0031-9007,. 10.1103/PhysRevLett.98.108301
- T. Schmiedl and U. Seifert, Phys. Rev. Lett. 0031-9007 98, 108301 (2007). 10.1103/PhysRevLett.98.108301
- (2007) Phys. Rev. Lett. , vol.98 , pp. 108301
- Schmiedl, T.¹ Seifert, U.²

20
- 41949096684
- 1063-651X,. 10.1103/PhysRevE.77.041105
- H. Then and A. Engel, Phys. Rev. E 1063-651X 77, 041105 (2008). 10.1103/PhysRevE.77.041105
- (2008) Phys. Rev. e , vol.77 , pp. 041105
- Then, H.¹ Engel, A.²

21
- 47249155183
- 0021-9606,. 10.1063/1.2948948
- A. Gomez-Marin, T. Schmiedl, and U. Seifert, J. Chem. Phys. 0021-9606 129, 024114 (2008). 10.1063/1.2948948
- (2008) J. Chem. Phys. , vol.129 , pp. 024114
- Gomez-Marin, A.¹ Schmiedl, T.² Seifert, U.³

22
- 34548080273
- 0021-9606,. 10.1063/1.1906209
- D. Wu and D. A. Kofke, J. Chem. Phys. 0021-9606 122, 204104 (2005). 10.1063/1.1906209
- (2005) J. Chem. Phys. , vol.122 , pp. 204104
- Wu, D.¹ Kofke, D.A.²

23
- 43949083060
- 0031-9007,. 10.1103/PhysRevLett.100.190601
- S. Vaikuntanathan and C. Jarzynski, Phys. Rev. Lett. 0031-9007 100, 190601 (2008). 10.1103/PhysRevLett.100.190601
- (2008) Phys. Rev. Lett. , vol.100 , pp. 190601
- Vaikuntanathan, S.¹ Jarzynski, C.²

24
- 0037398346
- 0021-9606,. 10.1063/1.1555845
- S. X. Sun, J. Chem. Phys. 0021-9606 118, 5769 (2003). 10.1063/1.1555845
- (2003) J. Chem. Phys. , vol.118 , pp. 5769
- Sun, S.X.¹

25
- 10844282657
- 0021-9606,. 10.1063/1.1813434
- E. Atilgan and S. X. Sun, J. Chem. Phys. 0021-9606 121, 10392 (2004). 10.1063/1.1813434
- (2004) J. Chem. Phys. , vol.121 , pp. 10392
- Atilgan, E.¹ Sun, S.X.²

26
- 3042688939
- 0021-9606,. 10.1063/1.1760511
- F. M. Ytreberg and D. M. Zuckerman, J. Chem. Phys. 0021-9606 120, 10876 (2004). 10.1063/1.1760511
- (2004) J. Chem. Phys. , vol.120 , pp. 10876
- Ytreberg, F.M.¹ Zuckerman, D.M.²

27
- 17444372741
- 1089-5647,. 10.1021/jp044556a
- H. Oberhofer, C. Dellago, and P. Geissler, J. Phys. Chem. B 1089-5647 109, 6902 (2005). 10.1021/jp044556a
- (2005) J. Phys. Chem. B , vol.109 , pp. 6902
- Oberhofer, H.¹ Dellago, C.² Geissler, P.³

28
- 44649134762
- 0010-4655,. 10.1016/j.cpc.2008.01.017
- H. Oberhofer and C. Dellago, Comput. Phys. Commun. 0010-4655 179, 41 (2008). 10.1016/j.cpc.2008.01.017
- (2008) Comput. Phys. Commun. , vol.179 , pp. 41
- Oberhofer, H.¹ Dellago, C.²

29
- 3042660129
- 0021-9606,. 10.1063/1.451695
- L. Pratt, J. Chem. Phys. 0021-9606 85, 5045 (1986). 10.1063/1.451695
- (1986) J. Chem. Phys. , vol.85 , pp. 5045
- Pratt, L.¹

30
- 0000729781
- 0021-9606,. 10.1063/1.475562
- C. Dellago, P. G. Bolhuis, F. S. Csajka, and D. Chandler, J. Chem. Phys. 0021-9606 108, 1964 (1998). 10.1063/1.475562
- (1998) J. Chem. Phys. , vol.108 , pp. 1964
- Dellago, C.¹ Bolhuis, P.G.² Csajka, F.S.³ Chandler, D.⁴

31
- 66749152822
- e-print arXiv:cond-mat/9912121.
- O. Mazonka and C. Jarzynski, e-print arXiv:cond-mat/9912121.
- Mazonka, O.¹ Jarzynski, C.²

32
- 62449091284
- 1063-651X,. 10.1103/PhysRevE.79.021122
- D. D. L. Minh and A. B. Adib, Phys. Rev. E 1063-651X 79, 021122 (2009). 10.1103/PhysRevE.79.021122
- (2009) Phys. Rev. e , vol.79 , pp. 021122
- Minh, D.D.L.¹ Adib, A.B.²

33
- 66749134290
- See EPAPS Document No. E-JCPSA6-130-042921 for asymptotic variance expressions in unidirectional and bidirectional protocol postprocessing. For more information on EPAPS, see.
- See EPAPS Document No. E-JCPSA6-130-042921 for asymptotic variance expressions in unidirectional and bidirectional protocol postprocessing. For more information on EPAPS, see http://www.aip.org/pubservs/epaps.html.

34
- 36549009223
- 0006-3495,. 10.1529/biophysj.107.111658
- J. Nummela and I. Andricioaei, Biophys. J. 0006-3495 93, 3373 (2007). 10.1529/biophysj.107.111658
- (2007) Biophys. J. , vol.93 , pp. 3373
- Nummela, J.¹ Andricioaei, I.²

35
- 0035334524
- 10.1063/1.1359181
- N. D. Lu and D. A. Kofke, J. Chem. Phys. 114, 7303 (2001). 10.1063/1.1359181
- (2001) J. Chem. Phys. , vol.114 , pp. 7303
- Lu, N.D.¹ Kofke, D.A.²

36
- 0035957434
- 0027-8424,. 10.1073/pnas.071034098
- G. Hummer and A. Szabo, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 98, 3658 (2001). 10.1073/pnas.071034098
- (2001) Proc. Natl. Acad. Sci. U.S.A. , vol.98 , pp. 3658
- Hummer, G.¹ Szabo, A.²

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