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Volumn 123, Issue 6, 2006, Pages 1251-1272

Equilibrium sampling from nonequilibrium dynamics

Author keywords

Free energy estimation; Genetic algorithms; Interacting particle system; Non equilibrium molecular dynamics

Indexed keywords


EID: 33748298996     PISSN: 00224715     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10955-006-9090-2     Document Type: Article
Times cited : (25)

References (32)
  • 1
    • 0007806535 scopus 로고    scopus 로고
    • Diffusion Monte Carlo with a fixed number of walkers
    • R. Assaraf, M. Caffarel and A. Khelif, Diffusion Monte Carlo with a fixed number of walkers. Phys. Rev. E 61(4):4566-4575 (2000).
    • (2000) Phys. Rev. E , vol.61 , Issue.4 , pp. 4566-4575
    • Assaraf, R.1    Caffarel, M.2    Khelif, A.3
  • 2
    • 48749137581 scopus 로고
    • Stochastic boundary conditions for molecular dynamics simulations of ST2 water
    • A. Brünger, C. B. Brooks and M. Karplus, Stochastic boundary conditions for molecular dynamics simulations of ST2 water. Chem. Phys. Lett. 105:495-500 (1983).
    • (1983) Chem. Phys. Lett. , vol.105 , pp. 495-500
    • Brünger, A.1    Brooks, C.B.2    Karplus, M.3
  • 3
    • 33748326944 scopus 로고    scopus 로고
    • Theoretical and numerical comparison of sampling methods for molecular dynamics
    • E. Cancès, F. Legoll and G. Stoltz, Theoretical and numerical comparison of sampling methods for molecular dynamics. IMA Preprint 2040 (2005).
    • (2005) IMA Preprint , vol.2040
    • Cancès, E.1    Legoll, F.2    Stoltz, G.3
  • 4
    • 4243661501 scopus 로고
    • Constrained reaction coordinate dynamics for the simulation of rare events
    • E. A. Carter, G. Ciccotti, J. T. Hynes and R. Kapral, Constrained reaction coordinate dynamics for the simulation of rare events. Chem. Phys. Lett. 156:472-477 (1989).
    • (1989) Chem. Phys. Lett. , vol.156 , pp. 472-477
    • Carter, E.A.1    Ciccotti, G.2    Hynes, J.T.3    Kapral, R.4
  • 7
    • 0002936641 scopus 로고    scopus 로고
    • Branching and interacting particle systems approximations of Feynman -Kac formulae with applications to nonlinear filtering
    • Séminaire de Probabilités XXXI
    • P. Del Moral and L. Miclo, Branching and Interacting Particle Systems approximations of Feynman -Kac formulae with applications to nonlinear filtering, Séminaire de Probabilités XXXI. Lecture notes in Mathematics 1729:1-145 (2000).
    • (2000) Lecture Notes in Mathematics , vol.1729 , pp. 1-145
    • Del Moral, P.1    Miclo, L.2
  • 12
    • 0035826435 scopus 로고    scopus 로고
    • A "fast growth" method of computing free energy differences
    • D. A. Hendrix and C. Jarzynski, A "fast growth" method of computing free energy differences. J. Chem. Phys. 114(14):5974-5981 (2001).
    • (2001) J. Chem. Phys. , vol.114 , Issue.14 , pp. 5974-5981
    • Hendrix, D.A.1    Jarzynski, C.2
  • 13
    • 33748331033 scopus 로고    scopus 로고
    • Population annealing and its application to a spin glass
    • K. Hukushima and Y. Iba, Population annealing and its application to a spin glass. AIP Conference Proceedings 690(1):200-206 (2003).
    • (2003) AIP Conference Proceedings , vol.690 , Issue.1 , pp. 200-206
    • Hukushima, K.1    Iba, Y.2
  • 14
    • 0035957434 scopus 로고    scopus 로고
    • Free energy reconstruction from nonequilibrium single-molecule pulling experiments
    • G. Hummer, and A. Szabo, Free energy reconstruction from nonequilibrium single-molecule pulling experiments. PNAS 98(7):3658-3661 (2001).
    • (2001) PNAS , vol.98 , Issue.7 , pp. 3658-3661
    • Hummer, G.1    Szabo, A.2
  • 15
    • 0035600220 scopus 로고    scopus 로고
    • Extended ensemble Monte Carlo
    • Y. Iba, Extended ensemble Monte Carlo. Int. J. Mod. Phys. C12:623-656 (2001).
    • (2001) Int. J. Mod. Phys. C , vol.12 , pp. 623-656
    • Iba, Y.1
  • 16
    • 4244116139 scopus 로고    scopus 로고
    • Equilibrium free energy differences from nonequilibrium measurements: A master equation approach
    • C. Jarzynski, Equilibrium free energy differences from nonequilibrium measurements: A master equation approach. Phys. Rev. E 56(5):5018-5035 (1997).
    • (1997) Phys. Rev. E , vol.56 , Issue.5 , pp. 5018-5035
    • Jarzynski, C.1
  • 17
    • 4243754128 scopus 로고    scopus 로고
    • Nonequilibrium equality for free energy differences
    • C. Jarzynski, Nonequilibrium equality for free energy differences. Phys. Rev. Lett. 78(14):2690-2693 (1997).
    • (1997) Phys. Rev. Lett. , vol.78 , Issue.14 , pp. 2690-2693
    • Jarzynski, C.1
  • 18
    • 26444479778 scopus 로고
    • Optimization by simulated annealing
    • S. Kirkpatrick, C. G. Gelatt and M. P. Vecchi, Optimization by simulated annealing. Science. 220:671-680 (1983).
    • (1983) Science , vol.220 , pp. 671-680
    • Kirkpatrick, S.1    Gelatt, C.G.2    Vecchi, M.P.3
  • 19
    • 33646471468 scopus 로고
    • Statistical mechanics of fluid mixtures
    • J. G. Kirkwood, Statistical mechanics of fluid mixtures. J. Chem. Phys. 3:300-313 (1935).
    • (1935) J. Chem. Phys. , vol.3 , pp. 300-313
    • Kirkwood, J.G.1
  • 21
    • 33644899039 scopus 로고
    • Simulated tempering: A new Monte Carlo scheme
    • E. Marinari and G. Parisi, Simulated tempering: A new Monte Carlo scheme. Europhys. Lett.19:451-458 (1992).
    • (1992) Europhys. Lett. , vol.19 , pp. 451-458
    • Marinari, E.1    Parisi, G.2
  • 22
    • 0000273048 scopus 로고    scopus 로고
    • Annealing importance sampling
    • R. Neal, Annealing importance sampling. Statistics and Computing 11(2):125-139 (2001).
    • (2001) Statistics and Computing , vol.11 , Issue.2 , pp. 125-139
    • Neal, R.1
  • 23
    • 17444372741 scopus 로고    scopus 로고
    • Biased sampling of non-equilibrium trajectories: Can fast switching simulations outperform conventional free energy calculation methods?
    • H. Oberhofer, C. Dellago and P. L. Geissler, Biased sampling of non-equilibrium trajectories: Can fast switching simulations outperform conventional free energy calculation methods? J. Chem. Phys. B 109:6902-6915 (2005).
    • (2005) J. Chem. Phys. B , vol.109 , pp. 6902-6915
    • Oberhofer, H.1    Dellago, C.2    Geissler, P.L.3
  • 24
    • 0036041179 scopus 로고    scopus 로고
    • Free-energy calculations in materials research
    • J. M. Rickman and R. LeSar, Free-energy calculations in materials research. Annu. Rev. Matter. Res. 32:195-217 (2002).
    • (2002) Annu. Rev. Matter. Res. , vol.32 , pp. 195-217
    • Rickman, J.M.1    LeSar, R.2
  • 26
    • 33748289874 scopus 로고    scopus 로고
    • An interacting particle system approach for molecular dynamics
    • M. Rousset and G. Stoltz, An interacting particle system approach for molecular dynamics. Rapport de recherche CERMICS 283 (2005).
    • (2005) Rapport de Recherche CERMICS , vol.283
    • Rousset, M.1    Stoltz, G.2
  • 27
    • 33748331034 scopus 로고    scopus 로고
    • Phd Thesis, in preparation
    • M. Rousset Phd Thesis, in preparation.
    • Rousset, M.1
  • 28
    • 33748298666 scopus 로고    scopus 로고
    • Phd Thesis, in preparation
    • G. Stoltz Phd Thesis, in preparation.
    • Stoltz, G.1
  • 29
    • 0037398346 scopus 로고    scopus 로고
    • Equilibrium free energies from path sampling of nonequilibrium trajectories
    • S. Sun, Equilibrium free energies from path sampling of nonequilibrium trajectories. J. Chem. Phys. 118(13):5769-5775 (2003).
    • (2003) J. Chem. Phys. , vol.118 , Issue.13 , pp. 5769-5775
    • Sun, S.1
  • 30
    • 0342929614 scopus 로고
    • Nonphysical sampling distributions in Monte-Carlo free energy estimation: Umbrella sampling
    • G. M. Torrie and J. P. Valleau, Nonphysical sampling distributions in Monte-Carlo free energy estimation: Umbrella sampling. J. Comp. Phys. 23:187-199 (1977).
    • (1977) J. Comp. Phys. , vol.23 , pp. 187-199
    • Torrie, G.M.1    Valleau, J.P.2
  • 31
    • 3042688939 scopus 로고    scopus 로고
    • Single-ensemble nonequilibrium path sampling estimates of free energy differences
    • F. M. Ytreberg and D. M. Zuckerman. Single-ensemble nonequilibrium path sampling estimates of free energy differences. J. Chem. Phys. 120(3): 10876-10879 (2004).
    • (2004) J. Chem. Phys. , vol.120 , Issue.3 , pp. 10876-10879
    • Ytreberg, F.M.1    Zuckerman, D.M.2
  • 32
    • 36849122972 scopus 로고
    • High-temperature equation of state by a perturbation method: I. Nonpolar gases
    • R. Zwanzig, High-temperature equation of state by a perturbation method: I. Nonpolar gases. J. Chem. Phys. 22:1420-1426 (1954).
    • (1954) J. Chem. Phys. , vol.22 , pp. 1420-1426
    • Zwanzig, R.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.