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Volumn 131, Issue 15, 2009, Pages

Separating forward and backward pathways in nonequilibrium umbrella sampling

Author keywords

[No Author keywords available]

Indexed keywords

ARBITRARY NUMBER; CIRCADIAN OSCILLATIONS; IN-PHASE; LIMIT CYCLE; NON EQUILIBRIUM; NON-EQUILIBRIUM PROCESS; ORDER PARAMETER; OSCILLATION PERIODS; STEADY-STATE DISTRIBUTIONS; TRANSITION PATHS; UMBRELLA SAMPLING; UNIFORM SAMPLING;

EID: 70449369638     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3244561     Document Type: Article
Times cited : (71)

References (40)
  • 4
    • 0342929614 scopus 로고
    • 0021-9991, 10.1016/0021-9991(77)90121-8
    • G. M. Torrie and J. P. Valleau, J. Comput. Phys. 0021-9991 23, 187 (1977). 10.1016/0021-9991(77)90121-8
    • (1977) J. Comput. Phys. , vol.23 , pp. 187
    • Torrie, G.M.1    Valleau, J.P.2
  • 8
    • 33746187786 scopus 로고    scopus 로고
    • Transition pathways in complex systems: Application of the finite-temperature string method to the alanine dipeptide
    • DOI 10.1063/1.2013256, 134109
    • W. Ren, E. Vanden-Eijnden, P. Maragakis, and W. E, J. Chem. Phys. 0021-9606 123, 134109 (2005). 10.1063/1.2013256 (Pubitemid 41435113)
    • (2005) Journal of Chemical Physics , vol.123 , Issue.13 , pp. 1-12
    • Ren, W.1    Vanden-Eijnden, E.2    Maragakis, P.3    Weinan, E.4
  • 9
    • 24344467850 scopus 로고    scopus 로고
    • Transition pathways in complex systems: Reaction coordinates, isocommittor surfaces, and transition tubes
    • DOI 10.1016/j.cplett.2005.07.084, PII S0009261405011176
    • W. E, W. Ren, and E. Vanden-Eijnden, Chem. Phys. Lett. 0009-2614 413, 242 (2005). 10.1016/j.cplett.2005.07.084 (Pubitemid 41252399)
    • (2005) Chemical Physics Letters , vol.413 , Issue.1-3 , pp. 242-247
    • Weinan, E.1    Ren, W.2    Vanden-Eijnden, E.3
  • 14
    • 3042545299 scopus 로고    scopus 로고
    • 0021-9606, 10.1063/1.1738640
    • A. K. Faradjian and R. Elber, J. Chem. Phys. 0021-9606 120, 10880 (2004). 10.1063/1.1738640
    • (2004) J. Chem. Phys. , vol.120 , pp. 10880
    • Faradjian, A.K.1    Elber, R.2
  • 15
    • 32044445540 scopus 로고    scopus 로고
    • Efficient computation of the first passage time distribution of the generalized master equation by steady-state relaxation
    • DOI 10.1063/1.2161211, 054112
    • D. Shalloway and A. K. Faradjian, J. Chem. Phys. 0021-9606 124, 054112 (2006). 10.1063/1.2161211 (Pubitemid 43202674)
    • (2006) Journal of Chemical Physics , vol.124 , Issue.5 , pp. 1-8
    • Shalloway, D.1    Faradjian, A.K.2
  • 16
    • 34247210226 scopus 로고    scopus 로고
    • Extending molecular dynamics time scales with milestoning: Example of complex kinetics in a solvated peptide
    • DOI 10.1063/1.2716389
    • A. M. A. West, R. Elber, and D. Shalloway, J. Chem. Phys. 0021-9606 126, 145104 (2007). 10.1063/1.2716389 (Pubitemid 46610034)
    • (2007) Journal of Chemical Physics , vol.126 , Issue.14 , pp. 145104
    • West, A.M.A.1    Elber, R.2    Shalloway, D.3
  • 19
    • 30744470375 scopus 로고    scopus 로고
    • Simulating rare events in equilibrium or nonequilibrium stochastic systems
    • DOI 10.1063/1.2140273, 024102
    • R. J. Allen, D. Frenkel, and P. R. ten Wolde, J. Chem. Phys. 0021-9606 124, 024102 (2006). 10.1063/1.2140273 (Pubitemid 43100174)
    • (2006) Journal of Chemical Physics , vol.124 , Issue.2 , pp. 1-16
    • Allen, R.J.1    Frenkel, D.2    Ten Wolde, P.R.3
  • 20
    • 34547648612 scopus 로고    scopus 로고
    • Forward flux sampling-type schemes for simulating rare events: Efficiency analysis
    • DOI 10.1063/1.2198827
    • R. J. Allen, D. Frenkel, and P. R. ten Wolde, J. Chem. Phys. 0021-9606 124, 194111 (2006). 10.1063/1.2198827 (Pubitemid 43782006)
    • (2006) Journal of Chemical Physics , vol.124 , Issue.19 , pp. 194111
    • Allen, R.J.1    Frenkel, D.2    Ten Wolde, P.R.3
  • 25
    • 16844362197 scopus 로고    scopus 로고
    • 0021-9991, 10.1016/j.jc2004.11.003
    • T. S. van Erp and P. G. Bolhuis, J. Comput. Phys. 0021-9991 205, 157 (2005). 10.1016/j.jcp.2004.11.003
    • (2005) J. Comput. Phys. , vol.205 , pp. 157
    • Van Erp, T.S.1    Bolhuis, P.G.2
  • 26
    • 17544374740 scopus 로고    scopus 로고
    • Automatic method for identifying reaction coordinates in complex systems
    • DOI 10.1021/jp045546c
    • A. Ma and A. R. Dinner, J. Phys. Chem. B 1089-5647 109, 6769 (2005). 10.1021/jp045546c (Pubitemid 40552537)
    • (2005) Journal of Physical Chemistry B , vol.109 , Issue.14 , pp. 6769-6779
    • Ma, A.1    Dinner, A.R.2
  • 27
    • 0036957459 scopus 로고    scopus 로고
    • Deterministic versus stochastic models for circadian rhythms
    • DOI 10.1023/A:1021286607354
    • D. Gonze, J. Halloy, and A. Goldbeter, J. Biol. Phys. 0092-0606 28, 637 (2002). 10.1023/A:1021286607354 (Pubitemid 36083523)
    • (2002) Journal of Biological Physics , vol.28 , Issue.4 , pp. 637-653
    • Gonze, D.1    Halloy, J.2    Goldbeter, A.3
  • 30
    • 77951683382 scopus 로고    scopus 로고
    • Enhanced sampling of nonequilibrium steady states
    • 0066-426X (in press).
    • A. Dickson and A. R. Dinner, " Enhanced sampling of nonequilibrium steady states.," Annu. Rev. Phys. Chem. 0066-426X (in press).
    • Annu. Rev. Phys. Chem.
    • Dickson, A.1    Dinner, A.R.2
  • 31
    • 44849101153 scopus 로고    scopus 로고
    • 0021-9606, 10.1063/1.2928844
    • R. P. Sear, J. Chem. Phys. 0021-9606 128, 214513 (2008). 10.1063/1.2928844
    • (2008) J. Chem. Phys. , vol.128 , pp. 214513
    • Sear, R.P.1
  • 32
    • 47249116937 scopus 로고    scopus 로고
    • 0021-9606, 10.1063/1.2953325
    • E. E. Borrero and F. A. Escobedo, J. Chem. Phys. 0021-9606 129, 024115 (2008). 10.1063/1.2953325
    • (2008) J. Chem. Phys. , vol.129 , pp. 024115
    • Borrero, E.E.1    Escobedo, F.A.2
  • 33
    • 0033593306 scopus 로고    scopus 로고
    • Molecular bases for circadian clocks
    • DOI 10.1016/S0092-8674(00)80566-8
    • J. C. Dunlap, Cell 0092-8674 96, 271 (1999). 10.1016/S0092-8674(00)80566- 8 (Pubitemid 29059356)
    • (1999) Cell , vol.96 , Issue.2 , pp. 271-290
    • Dunlap, J.C.1
  • 34
    • 33645429016 scopus 로고
    • 0022-3654, 10.1021/j100540a008
    • D. T. Gillespie, J. Phys. Chem. 0022-3654 81, 2340 (1977). 10.1021/j100540a008
    • (1977) J. Phys. Chem. , vol.81 , pp. 2340
    • Gillespie, D.T.1
  • 38
    • 2142746284 scopus 로고
    • 0021-9606, 10.1063/1.1749604
    • H. Eyring, J. Chem. Phys. 0021-9606 3, 107 (1935). 10.1063/1.1749604
    • (1935) J. Chem. Phys. , vol.3 , pp. 107
    • Eyring, H.1
  • 39
  • 40
    • 0037599010 scopus 로고
    • 0022-3654, 10.1021/j100238a002
    • K. J. Laidler and M. C. King, J. Phys. Chem. 0022-3654 87, 2657 (1983). 10.1021/j100238a002
    • (1983) J. Phys. Chem. , vol.87 , pp. 2657
    • Laidler, K.J.1    King, M.C.2


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