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Volumn , Issue , 2010, Pages 1-458

Free energy computations: A mathematical perspective

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EID: 84967371786     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1142/P579     Document Type: Book
Times cited : (489)

References (226)
  • 1
    • 0004282301 scopus 로고
    • (Benjamin/Cummings Publishing Co. Inc. Advanced Book Program)
    • Abraham, R. and Marsden, J. E. (1978). Foundations of mechanics (Benjamin/Cummings Publishing Co. Inc. Advanced Book Program).
    • (1978) Foundations of mechanics
    • Abraham, R.1    Marsden, J.E.2
  • 3
    • 59149099805 scopus 로고    scopus 로고
    • A comparison of generalized Hybrid Monte-Carlo methods with and without momentum flip
    • Akhmatskaya, E., Bou-Rabee, N. and Reich, S. (2009). A comparison of generalized Hybrid Monte-Carlo methods with and without momentum flip, J. Comput. Phys. 228, 6, pp. 2256-2265.
    • (2009) J. Comput. Phys , vol.228 , Issue.6 , pp. 2256-2265
    • Akhmatskaya, E.1    Bou-Rabee, N.2    Reich, S.3
  • 7
    • 0006528348 scopus 로고    scopus 로고
    • Level set approach to mean curvature flow in arbitrary codimension
    • Ambrosio, L. and Soner, H. (1996b). Level set approach to mean curvature flow in arbitrary codimension, J. Differential Geom. 43, 4, pp. 693-737.
    • (1996) J. Differential Geom , vol.43 , Issue.4 , pp. 693-737
    • Ambrosio, L.1    Soner, H.2
  • 9
    • 0002042431 scopus 로고    scopus 로고
    • On convex Sobolev inequalities and the rate of convergence to equilibrium for Fokker-Planck type equations
    • Arnold, A., Markowich, P., Toscani, G. and Unterreiter, A. (2001). On convex Sobolev inequalities and the rate of convergence to equilibrium for Fokker-Planck type equations, Comm. Part. Diff. Eq. 26, pp. 43-100.
    • (2001) Comm. Part. Diff. Eq , vol.26 , pp. 43-100
    • Arnold, A.1    Markowich, P.2    Toscani, G.3    Unterreiter, A.4
  • 11
    • 0007806535 scopus 로고    scopus 로고
    • Diffusion Monte Carlo with a fixed number of walkers
    • Assaraf, R., Caffarel, M. and Khelif, A. (2000). Diffusion Monte Carlo with a fixed number of walkers, Phys. Rev. E 61, 4, pp. 4566-4575.
    • (2000) Phys. Rev. E , vol.61 , Issue.4 , pp. 4566-4575
    • Assaraf, R.1    Caffarel, M.2    Khelif, A.3
  • 12
    • 77949412635 scopus 로고    scopus 로고
    • The Wang-Landau algorithm for Monte-Carlo computation in general state spaces
    • Atchade, Y. F. and Liu, J. S. (2010). The Wang-Landau algorithm for Monte-Carlo computation in general state spaces, Stat. Sinica 20, 1, pp. 209-233.
    • (2010) Stat. Sinica , vol.20 , Issue.1 , pp. 209-233
    • Atchade, Y.F.1    Liu, J.S.2
  • 13
    • 3142550885 scopus 로고    scopus 로고
    • A path-sampling scheme for computing thermodynamic properties of a many-body system in a generalized ensemble
    • Athenes, M. (2004). A path-sampling scheme for computing thermodynamic properties of a many-body system in a generalized ensemble, Eur. Phys. J. B 38, pp. 651-663.
    • (2004) Eur. Phys. J. B , vol.38 , pp. 651-663
    • Athenes, M.1
  • 14
    • 10844282657 scopus 로고    scopus 로고
    • Equilibrium free energy estimates based on nonequilibrium work relations and extended dynamics
    • Atilgan, E. and Sun, S. X. (2004). Equilibrium free energy estimates based on nonequilibrium work relations and extended dynamics, J. Chem. Phys. 121, pp. 10392-10400.
    • (2004) J. Chem. Phys , vol.121 , pp. 10392-10400
    • Atilgan, E.1    Sun, S.X.2
  • 15
    • 41849093720 scopus 로고    scopus 로고
    • Adaptively biased molecular dynamics for free-energy calculations
    • Babin, V., Roland, C. and Sagui, C. (2008). Adaptively biased molecular dynamics for free-energy calculations, J. Chem. Phys. 128, p. 134101.
    • (2008) J. Chem. Phys , vol.128 , pp. 134101
    • Babin, V.1    Roland, C.2    Sagui, C.3
  • 16
    • 0002432396 scopus 로고    scopus 로고
    • On Sobolev and logarithmic Sobolev inequalities for Markov semigroups
    • (World Scientific)
    • Bakry, D. (1997). On Sobolev and logarithmic Sobolev inequalities for Markov semigroups, in New trends in stochastic analysis (World Scientific), pp. 43-75.
    • (1997) New trends in stochastic analysis , pp. 43-75
    • Bakry, D.1
  • 19
    • 0030560429 scopus 로고
    • The law of the Euler scheme for stochastic differential equations: I. Convergence rate of the distribution function
    • Bally, V. and Talay, D. (1995). The law of the Euler scheme for stochastic differential equations: I. Convergence rate of the distribution function, Probab. Theory Rel. 104, pp. 43-160.
    • (1995) Probab. Theory Rel , vol.104 , pp. 43-160
    • Bally, V.1    Talay, D.2
  • 20
    • 0002308425 scopus 로고    scopus 로고
    • The law of the Euler scheme for stochastic differential equations: II. Convergence rate of the density
    • Bally, V. and Talay, D. (1996). The law of the Euler scheme for stochastic differential equations: II. Convergence rate of the density, Monte-Carlo Methods and Applications 2, pp. 93-128.
    • (1996) Monte-Carlo Methods and Applications , vol.2 , pp. 93-128
    • Bally, V.1    Talay, D.2
  • 21
    • 38349091489 scopus 로고    scopus 로고
    • Well-tempered metadynamics: A smoothly converging and tunable free-energy method
    • Barducci, A., Bussi, G. and Parrinello, M. (2008). Well-tempered metadynamics: A smoothly converging and tunable free-energy method, Phys. Rev. Lett. 100, p. 020603.
    • (2008) Phys. Rev. Lett , vol.100 , pp. 020603
    • Barducci, A.1    Bussi, G.2    Parrinello, M.3
  • 22
    • 33749125733 scopus 로고
    • Modified embedded-atom potentials for cubic materials and impurities
    • Baskes, M. I. (1992). Modified embedded-atom potentials for cubic materials and impurities, Phys. Rev. B 46, 5, pp. 2727-2742.
    • (1992) Phys. Rev. B , vol.46 , Issue.5 , pp. 2727-2742
    • Baskes, M.I.1
  • 23
    • 5244304444 scopus 로고
    • Efficient estimation of free energy differences from Monte-Carlo data
    • Bennett, C. H. (1976). Efficient estimation of free energy differences from Monte-Carlo data, J. Comput. Phys. 22, pp. 245-268.
    • (1976) J. Comput. Phys , vol.22 , pp. 245-268
    • Bennett, C.H.1
  • 24
    • 2342648012 scopus 로고    scopus 로고
    • Ensemble variance in free energy calculations by thermodynamic integration: Theory, optimal “alchemical” path, and practical solutions
    • Blondel, A. (2004). Ensemble variance in free energy calculations by thermodynamic integration: theory, optimal “alchemical” path, and practical solutions, J. Comput. Chem. 25, pp. 985-993.
    • (2004) J. Comput. Chem , vol.25 , pp. 985-993
    • Blondel, A.1
  • 25
    • 0002829137 scopus 로고    scopus 로고
    • Exponential integrability and transportation cost related to logarithmic Sobolev inequalities
    • Bobkov, S. and Gotze, F. (1999). Exponential integrability and transportation cost related to logarithmic Sobolev inequalities, J. Funct. Anal. 163, 1, pp. 1-28.
    • (1999) J. Funct. Anal , vol.163 , Issue.1 , pp. 1-28
    • Bobkov, S.1    Gotze, F.2
  • 26
    • 0001471515 scopus 로고    scopus 로고
    • The Nose-Poincare method for constant temperature molecular dynamics
    • Bond, S. D., Leimkuhler, B. J. and Laird, B. B. (1999). The Nose-Poincare method for constant temperature molecular dynamics, J. Comput. Phys. 151, 1, pp. 114-134.
    • (1999) J. Comput. Phys , vol.151 , Issue.1 , pp. 114-134
    • Bond, S.D.1    Leimkuhler, B.J.2    Laird, B.B.3
  • 28
    • 0002658505 scopus 로고
    • Homogenization of Hamiltonian system with a strong constraining potential
    • Bornemann, F. and Schütte, C. (1992). Homogenization of Hamiltonian system with a strong constraining potential, Physica D 102, pp. 57-77.
    • (1992) Physica D , vol.102 , pp. 57-77
    • Bornemann, F.1    Schütte, C.2
  • 29
    • 77951824442 scopus 로고    scopus 로고
    • Pathwise accuracy and ergodicity of metropolized integrators for SDEs
    • Bou-Rabee, N. and Vanden-Eijnden, E. (2009). Pathwise accuracy and ergodicity of metropolized integrators for SDEs, Commun. Pure Appl. Math. 63, 5, pp. 655-696.
    • (2009) Commun. Pure Appl. Math , vol.63 , Issue.5 , pp. 655-696
    • Bou-Rabee, N.1    Vanden-Eijnden, E.2
  • 30
    • 48749137581 scopus 로고
    • Stochastic boundary conditions for molecular dynamics simulations of ST2 water
    • Brünger, A., Brooks, C. B. and Karplus, M. (1984). Stochastic boundary conditions for molecular dynamics simulations of ST2 water, Chem. Phys. Lett. 105, 5, pp. 495-500.
    • (1984) Chem. Phys. Lett , vol.105 , Issue.5 , pp. 495-500
    • Brünger, A.1    Brooks, C.B.2    Karplus, M.3
  • 31
    • 33644772083 scopus 로고    scopus 로고
    • Equilibrium free energies from nonequilibrium metadynamics
    • Bussi, G., Laio, A. and Parinello, M. (2006). Equilibrium free energies from nonequilibrium metadynamics, Phys. Rev. Lett. 96, p. 090601.
    • (2006) Phys. Rev. Lett , vol.96 , pp. 090601
    • Bussi, G.1    Laio, A.2    Parinello, M.3
  • 32
    • 10844287886 scopus 로고    scopus 로고
    • High-order averaging schemes with error bounds for thermodynamical properties calculations by molecular dynamics simulations
    • Cances, E., Castella, F., Chartier, P., Faou, E., Le Bris, C., Legoll, F. and Turinici, G. (2004). High-order averaging schemes with error bounds for thermodynamical properties calculations by molecular dynamics simulations, J. Chem. Phys. 121, 21, pp. 10346-10355.
    • (2004) J. Chem. Phys , vol.121 , Issue.21 , pp. 10346-10355
    • Cances, E.1    Castella, F.2    Chartier, P.3    Faou, E.4    Le Bris, C.5    Legoll, F.6    Turinici, G.7
  • 35
    • 34547539797 scopus 로고    scopus 로고
    • Theoretical and numerical comparison of sampling methods for molecular dynamics
    • Cances, E., Legoll, F. and Stoltz, G. (2007). Theoretical and numerical comparison of sampling methods for molecular dynamics, Math. Model. Numer. Anal. 41, 2, pp. 351-390.
    • (2007) Math. Model. Numer. Anal , vol.41 , Issue.2 , pp. 351-390
    • Cances, E.1    Legoll, F.2    Stoltz, G.3
  • 37
    • 4243606192 scopus 로고
    • Unified approach for molecular dynamics and density-functional theory
    • Car, R. and Parrinello, M. (1985). Unified approach for molecular dynamics and density-functional theory, Phys. Rev. Lett. 55, 22, pp. 2471-2474.
    • (1985) Phys. Rev. Lett , vol.55 , Issue.22 , pp. 2471-2474
    • Car, R.1    Parrinello, M.2
  • 38
    • 4243661501 scopus 로고
    • Constrained reaction coordinate dynamics for the simulation of rare events
    • Carter, E. A., Ciccotti, G., Hynes, J. T. and Kapral, R. (1989). Constrained reaction coordinate dynamics for the simulation of rare events, Chem. Phys. Lett. 156, 5, pp. 472-477.
    • (1989) Chem. Phys. Lett , vol.156 , Issue.5 , pp. 472-477
    • Carter, E.A.1    Ciccotti, G.2    Hynes, J.T.3    Kapral, R.4
  • 39
    • 0031527297 scopus 로고    scopus 로고
    • On Monte-Carlo methods for estimating ratios of normalizing constants
    • Chen, M.-H. and Shao, Q.-M. (1997). On Monte-Carlo methods for estimating ratios of normalizing constants, Ann. Stat. 25, 4, pp. 1563-1594.
    • (1997) Ann. Stat , vol.25 , Issue.4 , pp. 1563-1594
    • Chen, M.-H.1    Shao, Q.-M.2
  • 41
    • 47949084920 scopus 로고    scopus 로고
    • Calculating free energy differences using perturbation theory
    • C. Chipot and A. Pohorille (eds.), (Springer)
    • Chipot, C. and Pohorille, A. (2007a). Calculating free energy differences using perturbation theory, in C. Chipot and A. Pohorille (eds.), Free energy calculations (Springer), pp. 33-75.
    • (2007) Free energy calculations , pp. 33-75
    • Chipot, C.1    Pohorille, A.2
  • 43
    • 24944568819 scopus 로고    scopus 로고
    • Blue Moon sampling, vectorial reaction coordinates, and unbiased constrained dynamics
    • Ciccotti, G., Kapral, R. and Vanden-Eijnden, E. (2005). Blue Moon sampling, vectorial reaction coordinates, and unbiased constrained dynamics, Chem. Phys. Chem. 6, 9, pp. 1809-1814.
    • (2005) Chem. Phys. Chem , vol.6 , Issue.9 , pp. 1809-1814
    • Ciccotti, G.1    Kapral, R.2    Vanden-Eijnden, E.3
  • 44
    • 38949150015 scopus 로고    scopus 로고
    • Projection of diffusions on submanifolds: Application to mean force computation
    • Ciccotti, G., Lelievre, T. and Vanden-Eijnden, E. (2008). Projection of diffusions on submanifolds: Application to mean force computation, Commun. Pure Appl. Math. 61, 3, pp. 371-408.
    • (2008) Commun. Pure Appl. Math , vol.61 , Issue.3 , pp. 371-408
    • Ciccotti, G.1    Lelievre, T.2    Vanden-Eijnden, E.3
  • 46
    • 0032023968 scopus 로고    scopus 로고
    • Nonequilibrium measurements of free energy-differences for microscopically reversible markovian systems
    • Crooks, G. E. (1998). Nonequilibrium measurements of free energy-differences for microscopically reversible markovian systems, J. Stat. Phys. 90, 5, pp. 1481-1487.
    • (1998) J. Stat. Phys , vol.90 , Issue.5 , pp. 1481-1487
    • Crooks, G.E.1
  • 47
    • 0000765761 scopus 로고    scopus 로고
    • Entropy production fluctuation theorem and the nonequilibrium work relation for free-energy differences
    • Crooks, G. E. (1999). Entropy production fluctuation theorem and the nonequilibrium work relation for free-energy differences, Phys. Rev. E 60, 3, pp. 2721-2726.
    • (1999) Phys. Rev. E , vol.60 , Issue.3 , pp. 2721-2726
    • Crooks, G.E.1
  • 48
    • 34548665330 scopus 로고    scopus 로고
    • Thermodynamic integration using constrained and unconstrained dynamics
    • C. Chipot and A. Pohorille (eds.), (Springer)
    • Darve, E. (2007). Thermodynamic integration using constrained and unconstrained dynamics, in C. Chipot and A. Pohorille (eds.), Free Energy Calculations (Springer), pp. 119-170.
    • (2007) Free Energy Calculations , pp. 119-170
    • Darve, E.1
  • 49
    • 0035935802 scopus 로고    scopus 로고
    • Calculating free energy using average forces
    • Darve, E. and Porohille, A. (2001). Calculating free energy using average forces, J. Chem. Phys. 115, pp. 9169-9183.
    • (2001) J. Chem. Phys , vol.115 , pp. 9169-9183
    • Darve, E.1    Porohille, A.2
  • 50
    • 0038412705 scopus 로고    scopus 로고
    • Calculating free energies using a scaled-force molecular dynamics algorithm
    • Darve, E., Wilson, M. and Pohorille, A. (2002). Calculating free energies using a scaled-force molecular dynamics algorithm, Mol. Sim. 28, 1-2, pp. 113-144.
    • (2002) Mol. Sim , vol.28 , Issue.1-2 , pp. 113-144
    • Darve, E.1    Wilson, M.2    Pohorille, A.3
  • 51
    • 45149103368 scopus 로고
    • Dynamical stability of metastable states
    • Davies, E. (1982a). Dynamical stability of metastable states, J. Funct. Anal. 46, 3, pp. 373-386.
    • (1982) J. Funct. Anal , vol.46 , Issue.3 , pp. 373-386
    • Davies, E.1
  • 52
    • 0012986859 scopus 로고
    • Metastable states of symmetric Markov semigroups I
    • Davies, E. (1982b). Metastable states of symmetric Markov semigroups I, Proc. London Math. Soc. 45, 3, pp. 133-150.
    • (1982) Proc. London Math. Soc , vol.45 , Issue.3 , pp. 133-150
    • Davies, E.1
  • 53
    • 84959756705 scopus 로고
    • Metastable states of symmetric Markov semigroups II
    • Davies, E. (1982c). Metastable states of symmetric Markov semigroups II, J. London Math. Soc. 26, 3, pp. 541-556.
    • (1982) J. London Math. Soc , vol.26 , Issue.3 , pp. 541-556
    • Davies, E.1
  • 54
    • 0013035186 scopus 로고
    • Spectral properties of metastable Markov semigroups
    • Davies, E. (1983). Spectral properties of metastable Markov semigroups, J. Funct. Anal. 52, pp. 315-329.
    • (1983) J. Funct. Anal , vol.52 , pp. 315-329
    • Davies, E.1
  • 56
    • 0002936641 scopus 로고    scopus 로고
    • Branching and interacting particle systems approximations of Feynman-Kac formulae with applications to nonlinear filtering
    • Del Moral, P. and Miclo, L. (2000). Branching and interacting particle systems approximations of Feynman-Kac formulae with applications to nonlinear filtering, Lect. Notes Math. 1729, pp. 1-145.
    • (2000) Lect. Notes Math , vol.1729 , pp. 1-145
    • Del Moral, P.1    Miclo, L.2
  • 57
    • 4444242987 scopus 로고    scopus 로고
    • On the calculation of reaction rate constants in the transition path ensemble
    • Dellago, C., Bolhuis, P. G. and Chandler, D. (1999). On the calculation of reaction rate constants in the transition path ensemble, J. Chem. Phys. 110, 14, pp. 6617-6625.
    • (1999) J. Chem. Phys , vol.110 , Issue.14 , pp. 6617-6625
    • Dellago, C.1    Bolhuis, P.G.2    Chandler, D.3
  • 61
    • 0032529893 scopus 로고    scopus 로고
    • The calculation of free-energy differences by constrained molecular-dynamics simulations
    • den Otter, W. and Briels, W. J. (1998). The calculation of free-energy differences by constrained molecular-dynamics simulations, J. Chem. Phys. 109, 11, pp. 4139-4146.
    • (1998) J. Chem. Phys , vol.109 , Issue.11 , pp. 4139-4146
    • Den Otter, W.1    Briels, W.J.2
  • 62
    • 0000280446 scopus 로고    scopus 로고
    • Thermodynamic integration of the free energy along a reaction coordinate in Cartesian coordinates
    • den Otter, W. K. (2000). Thermodynamic integration of the free energy along a reaction coordinate in Cartesian coordinates, J. Chem. Phys. 112, 17, pp. 7283-7292.
    • (2000) J. Chem. Phys , vol.112 , Issue.17 , pp. 7283-7292
    • Den Otter, W.K.1
  • 63
    • 77951779697 scopus 로고    scopus 로고
    • Free energy calculations: An efficient adaptive biasing potential method
    • Dickson, B., Legoll, F., Lelivre, T., Stoltz, G. and Fleura-Lessard, P. (2010). Free energy calculations: An efficient adaptive biasing potential method, J. Phys. Chem. B 114, 17, pp. 5823-5830.
    • (2010) J. Phys. Chem. B , vol.114 , Issue.17 , pp. 5823-5830
    • Dickson, B.1    Legoll, F.2    Lelivre, T.3    Stoltz, G.4    Fleura-Lessard, P.5
  • 64
  • 68
    • 17044437988 scopus 로고    scopus 로고
    • Metastability, conformation dynamics, and transition pathways in complex systems
    • S. Attinger and P. Koumoutsakos (eds.), (Springer, Berlin)
    • E, W. and Vanden-Eijnden, E. (2004). Metastability, conformation dynamics, and transition pathways in complex systems, in S. Attinger and P. Koumoutsakos (eds.), Multiscale Modelling and Simulation, Lect. Notes Comput. Sci. Eng., Vol. 39 (Springer, Berlin), pp. 35-68.
    • (2004) Multiscale Modelling and Simulation, Lect. Notes Comput. Sci. Eng , vol.39 , pp. 35-68
    • E, W.1    Vanden-Eijnden, E.2
  • 69
    • 0002344794 scopus 로고
    • Bootstrap methods: Another look at the jackknife
    • Efron, B. (1979). Bootstrap methods: Another look at the jackknife, Ann. Stat. 7, pp. 1-26.
    • (1979) Ann. Stat , vol.7 , pp. 1-26
    • Efron, B.1
  • 70
    • 34547523376 scopus 로고    scopus 로고
    • Diffusion Monte-Carlo method: Numerical analysis in a simple case
    • El Makrini, M., Jourdain, B. and Lelievre, T. (2007). Diffusion Monte-Carlo method: numerical analysis in a simple case, Math. Model. Numer. Anal. 41, 2, pp. 189-213.
    • (2007) Math. Model. Numer. Anal , vol.41 , Issue.2 , pp. 189-213
    • El Makrini, M.1    Jourdain, B.2    Lelievre, T.3
  • 75
    • 34547853476 scopus 로고    scopus 로고
    • Nose-Hoover dynamics in a shaker
    • Faou, E. (2006). Nose-Hoover dynamics in a shaker, J. Chem. Phys. 124, p. 184104.
    • (2006) J. Chem. Phys , vol.124 , pp. 184104
    • Faou, E.1
  • 76
    • 67650716388 scopus 로고    scopus 로고
    • Conservative stochastic differential equations: Mathematical and numerical analysis
    • Faou, E. and Lelievre, T. (2009). Conservative stochastic differential equations: Mathematical and numerical analysis, Math. Comput. 78, pp. 2047-2074.
    • (2009) Math. Comput , vol.78 , pp. 2047-2074
    • Faou, E.1    Lelievre, T.2
  • 77
    • 33646987405 scopus 로고
    • Optimized Monte-Carlo data analysis
    • Ferrenberg, A. M. and Swendsen, R. H. (1989). Optimized Monte-Carlo data analysis, Phys. Rev. Lett. 63, 12, pp. 1195-1198.
    • (1989) Phys. Rev. Lett , vol.63 , Issue.12 , pp. 1195-1198
    • Ferrenberg, A.M.1    Swendsen, R.H.2
  • 79
    • 0016273821 scopus 로고
    • Classical statistical mechanics of constraints: A theorem and application to polymers
    • Fixman, M. (1974). Classical statistical mechanics of constraints: A theorem and application to polymers, Proc. Nat. Acad. Sci. USA 71, 8, pp. 3050-3053.
    • (1974) Proc. Nat. Acad. Sci. USA , vol.71 , Issue.8 , pp. 3050-3053
    • Fixman, M.1
  • 80
    • 33845539992 scopus 로고
    • Simulation of polymer dynamics. I. General theory
    • Fixman, M. (1978). Simulation of polymer dynamics. I. General theory, J. Chem. Phys. 69, pp. 1527-1537.
    • (1978) J. Chem. Phys , vol.69 , pp. 1527-1537
    • Fixman, M.1
  • 81
    • 36549102647 scopus 로고
    • Error estimates on averages of correlated fata
    • Flyvbjerg, H. and Petersen, H. G. (1989). Error estimates on averages of correlated fata, J. Chem. Phys. 91, pp. 461-466.
    • (1989) J. Chem. Phys , vol.91 , pp. 461-466
    • Flyvbjerg, H.1    Petersen, H.G.2
  • 82
    • 33644848399 scopus 로고    scopus 로고
    • Molecular dynamics simulations of the complete satellite tobacco mosaic virus
    • Freddolino, P. L., Arkhipov, A. S., Larson, S. B., McPherson, A. and Schulten, K. (2006). Molecular dynamics simulations of the complete satellite tobacco mosaic virus, Structure 14, pp. 437-449.
    • (2006) Structure , vol.14 , pp. 437-449
    • Freddolino, P.L.1    Arkhipov, A.S.2    Larson, S.B.3    McPherson, A.4    Schulten, K.5
  • 83
    • 7244229982 scopus 로고    scopus 로고
    • Some remarks on the Smoluchowski-Kramers approximation
    • Freidlin, M. (2004). Some remarks on the Smoluchowski-Kramers approximation, J. Stat. Phys. 117, 3-4, pp. 617-634.
    • (2004) J. Stat. Phys , vol.117 , Issue.3-4 , pp. 617-634
    • Freidlin, M.1
  • 86
    • 0003580191 scopus 로고    scopus 로고
    • Texts and Monographs in Physics (Springer)
    • Gallavotti, G. (1999). Statistical Mechanics, Texts and Monographs in Physics (Springer).
    • (1999) Statistical Mechanics
    • Gallavotti, G.1
  • 87
    • 0000736067 scopus 로고    scopus 로고
    • Simulating normalizing constants: From importance sampling to bridge sampling to path sampling
    • Gelman, A. and Meng, X. L. (1998). Simulating normalizing constants: from importance sampling to bridge sampling to path sampling, Stat. Sci. 13, 2, pp. 163-185.
    • (1998) Stat. Sci , vol.13 , Issue.2 , pp. 163-185
    • Gelman, A.1    Meng, X.L.2
  • 89
    • 84972511893 scopus 로고
    • Practical Markov chain Monte Carlo (with discussion)
    • Geyer, C. J. (1992). Practical Markov chain Monte Carlo (with discussion), Stat. Sci. 7, 4, pp. 473-511.
    • (1992) Stat. Sci , vol.7 , Issue.4 , pp. 473-511
    • Geyer, C.J.1
  • 94
    • 0242268467 scopus 로고    scopus 로고
    • Bias and error in estimates of equilibrium free-energy differences from nonequilibrium measurements
    • Gore, J., Ritort, F. and Bustamante, C. (2003). Bias and error in estimates of equilibrium free-energy differences from nonequilibrium measurements, Proc. Nat. Acad. Sci. USA 100, 22, pp. 12564-12569.
    • (2003) Proc. Nat. Acad. Sci. USA , vol.100 , Issue.22 , pp. 12564-12569
    • Gore, J.1    Ritort, F.2    Bustamante, C.3
  • 95
    • 0001429116 scopus 로고
    • Logarithmic Sobolev inequalities
    • Gross, L. (1975). Logarithmic Sobolev inequalities, Amer. J. Math. 97, 4, pp. 1061-1083.
    • (1975) Amer. J. Math , vol.97 , Issue.4 , pp. 1061-1083
    • Gross, L.1
  • 97
    • 70349774467 scopus 로고    scopus 로고
    • Characteristic of Bennett’s acceptance ratio method
    • Hahn, A. M. and Then, H. (2009). Characteristic of Bennett’s acceptance ratio method, Phys. Rev. E 80, 3, p. 031111.
    • (2009) Phys. Rev. E , vol.80 , Issue.3 , pp. 031111
    • Hahn, A.M.1    Then, H.2
  • 98
    • 0346830423 scopus 로고    scopus 로고
    • Geometric numerical integration illustrated by the Stormer-Verlet method
    • Hairer, E., Lubich, C. and Wanner, G. (2003). Geometric numerical integration illustrated by the Stormer-Verlet method, Acta Numerica 12, pp. 399-450.
    • (2003) Acta Numerica , vol.12 , pp. 399-450
    • Hairer, E.1    Lubich, C.2    Wanner, G.3
  • 100
    • 38349019840 scopus 로고    scopus 로고
    • An ergodic sampling scheme for constrained Hamiltonian systems with applications to molecular dynamics
    • Hartmann, C. (2008). An ergodic sampling scheme for constrained Hamiltonian systems with applications to molecular dynamics, J. Stat. Phys. 130, 4, pp. 687-711.
    • (2008) J. Stat. Phys , vol.130 , Issue.4 , pp. 687-711
    • Hartmann, C.1
  • 101
    • 26844557034 scopus 로고    scopus 로고
    • A constrained Hybrid Monte-Carlo algorithm and the problem of calculating the free energy in several variables
    • Hartmann, C. and Schutte, C. (2005a). A constrained Hybrid Monte-Carlo algorithm and the problem of calculating the free energy in several variables, Z. Angew. Math. Mech. 85, 10, pp. 700-710.
    • (2005) Z. Angew. Math. Mech , vol.85 , Issue.10 , pp. 700-710
    • Hartmann, C.1    Schutte, C.2
  • 102
    • 85129686405 scopus 로고    scopus 로고
    • A geometric approach to constrained molecular dynamics and free-energy
    • Hartmann, C. and Schutte, C. (2005b). A geometric approach to constrained molecular dynamics and free-energy, Commun. Math. Sci. 3, 1, pp. 1-20.
    • (2005) Commun. Math. Sci , vol.3 , Issue.1 , pp. 1-20
    • Hartmann, C.1    Schutte, C.2
  • 104
    • 77956890234 scopus 로고
    • Monte Carlo sampling methods using Markov chains and their applications
    • Hastings, W. K. (1970). Monte Carlo sampling methods using Markov chains and their applications, Biometrika 57, pp. 97-109.
    • (1970) Biometrika , vol.57 , pp. 97-109
    • Hastings, W.K.1
  • 105
    • 0035826435 scopus 로고    scopus 로고
    • A “fast growth” method of computing free-energy differences
    • Hendrix, D. A. and Jarzynski, C. (2001). A “fast growth” method of computing free-energy differences, J. Chem. Phys. 114, pp. 5974-5981.
    • (2001) J. Chem. Phys , vol.114 , pp. 5974-5981
    • Hendrix, D.A.1    Jarzynski, C.2
  • 106
    • 4344660645 scopus 로고    scopus 로고
    • Overcoming free-energy barriers using unconstrained molecular dynamics simulations
    • Henin, J. and Chipot, C. (2004). Overcoming free-energy barriers using unconstrained molecular dynamics simulations, J. Chem. Phys. 121, pp. 29042914.
    • (2004) J. Chem. Phys , vol.121 , pp. 2904-2914
    • Henin, J.1    Chipot, C.2
  • 107
    • 0028461178 scopus 로고
    • Brownian motion with stiff bonds and rigid constraints
    • Hinch, E. J. (1994). Brownian motion with stiff bonds and rigid constraints, J. Non-Newtonian Fluid Mech. 271, pp. 219-234.
    • (1994) J. Non-Newtonian Fluid Mech , vol.271 , pp. 219-234
    • Hinch, E.J.1
  • 108
    • 0001359676 scopus 로고
    • Logarithmic Sobolev inequalities and stochastic Ising models
    • Holley, R. and Stroock, D. (1987). Logarithmic Sobolev inequalities and stochastic Ising models, J. Stat. Phys. 46, pp. 1159-1194.
    • (1987) J. Stat. Phys , vol.46 , pp. 1159-1194
    • Holley, R.1    Stroock, D.2
  • 109
    • 0001538909 scopus 로고
    • Canonical dynamics - Equilibrium phase-space distributions
    • Hoover, W. G. (1985). Canonical dynamics - Equilibrium phase-space distributions, Phys. Rev. A 31, 3, pp. 1695-1697.
    • (1985) Phys. Rev. A , vol.31 , Issue.3 , pp. 1695-1697
    • Hoover, W.G.1
  • 110
    • 15244346736 scopus 로고
    • Hypoelliptic second order differential equations
    • Hormander, L. (1967). Hypoelliptic second order differential equations, Acta Math. 119, pp. 147-171.
    • (1967) Acta Math , vol.119 , pp. 147-171
    • Hormander, L.1
  • 111
    • 0009349032 scopus 로고
    • A generalized guided Monte Carlo algorithm
    • Horowitz, A. M. (1991). A generalized guided Monte Carlo algorithm, Phys. Lett. B 268, pp. 247-252.
    • (1991) Phys. Lett. B , vol.268 , pp. 247-252
    • Horowitz, A.M.1
  • 113
    • 83255166989 scopus 로고    scopus 로고
    • Metastability and dominant eigenvalues of transfer operators
    • B. Leimkuhler, C. Chipot, R. Elber, A. Laaksonen, A. Mark, T. Schlick, C. Schutte and R. Skeel (eds.), (Springer)
    • Huisinga, W. and Schmidt, B. (2006). Metastability and dominant eigenvalues of transfer operators, in B. Leimkuhler, C. Chipot, R. Elber, A. Laaksonen, A. Mark, T. Schlick, C. Schutte and R. Skeel (eds.), New Algorithms for Macromolecular Simulation (Springer), pp. 167-182.
    • (2006) New Algorithms for Macromolecular Simulation , pp. 167-182
    • Huisinga, W.1    Schmidt, B.2
  • 114
    • 0030516672 scopus 로고    scopus 로고
    • Exchange Monte-Carlo method and application to spin glass simulations
    • Hukushima, K. and Nemoto, K. (1996). Exchange Monte-Carlo method and application to spin glass simulations, J. Phys. Soc. Jpn. 65, 6, pp. 1604-1608.
    • (1996) J. Phys. Soc. Jpn , vol.65 , Issue.6 , pp. 1604-1608
    • Hukushima, K.1    Nemoto, K.2
  • 115
    • 62849098480 scopus 로고    scopus 로고
    • Nonequilibrium methods for equilibrium free-energy calculations
    • C. Chipot and A. Pohorille (eds.), (Springer)
    • Hummer, G. (2007). Nonequilibrium methods for equilibrium free-energy calculations, in C. Chipot and A. Pohorille (eds.), Free Energy Calculations (Springer), pp. 171-198.
    • (2007) Free Energy Calculations , pp. 171-198
    • Hummer, G.1
  • 116
    • 0035957434 scopus 로고    scopus 로고
    • Free-energy reconstruction from nonequilibrium single-molecule pulling experiments
    • Hummer, G. and Szabo, A. (2001). Free-energy reconstruction from nonequilibrium single-molecule pulling experiments, Proc. Nat. Acad. Sci. USA 98, 7, pp. 3658-3661.
    • (2001) Proc. Nat. Acad. Sci. USA , vol.98 , Issue.7 , pp. 3658-3661
    • Hummer, G.1    Szabo, A.2
  • 117
    • 0041810451 scopus 로고    scopus 로고
    • Efficient exploration of reactive potential energy surfaces using Car-Parrinello molecular dynamics
    • Iannuzzi, M., Laio, A. and Parrinello, M. (2003). Efficient exploration of reactive potential energy surfaces using Car-Parrinello molecular dynamics, Phys. Rev. Lett. 90, 23, p. 238302.
    • (2003) Phys. Rev. Lett , vol.90 , Issue.23 , pp. 238302
    • Iannuzzi, M.1    Laio, A.2    Parrinello, M.3
  • 119
    • 4244116139 scopus 로고    scopus 로고
    • Equilibrium free-energy differences from nonequilibrium measurements: A master-equation approach
    • Jarzynski, C. (1997a). Equilibrium free-energy differences from nonequilibrium measurements: A master-equation approach, Phys. Rev. E 56, 5, pp. 5018-5035.
    • (1997) Phys. Rev. E , vol.56 , Issue.5 , pp. 5018-5035
    • Jarzynski, C.1
  • 120
    • 4243754128 scopus 로고    scopus 로고
    • Nonequilibrium equality for free energy differences
    • Jarzynski, C. (1997b). Nonequilibrium equality for free energy differences, Phys. Rev. Lett. 78, 14, pp. 2690-2693.
    • (1997) Phys. Rev. Lett , vol.78 , Issue.14 , pp. 2690-2693
    • Jarzynski, C.1
  • 121
    • 33645666178 scopus 로고    scopus 로고
    • Rare events and the convergence of exponentially averaged work values
    • Jarzynski, C. (2006). Rare events and the convergence of exponentially averaged work values, Phys. Rev. E 73, p. 046105.
    • (2006) Phys. Rev. E , vol.73 , pp. 046105
    • Jarzynski, C.1
  • 122
    • 34547863202 scopus 로고    scopus 로고
    • On population-based simulation for static inference
    • Jasra, A., Stephens, D. A. and Holmes, C. C. (2007). On population-based simulation for static inference, Stat. Comput. 17, 3, pp. 263-279.
    • (2007) Stat. Comput , vol.17 , Issue.3 , pp. 263-279
    • Jasra, A.1    Stephens, D.A.2    Holmes, C.C.3
  • 123
    • 84967370710 scopus 로고    scopus 로고
    • Existence, uniqueness and convergence of a particle approximation for the Adaptive Biasing Force process, Accepted for publication
    • Jourdain, B., Lelievre, T. and Roux, R. (2009). Existence, uniqueness and convergence of a particle approximation for the Adaptive Biasing Force process, Accepted for publication in Math. Model. Numer. Anal.
    • (2009) Math. Model. Numer. Anal
    • Jourdain, B.1    Lelievre, T.2    Roux, R.3
  • 125
    • 33646471468 scopus 로고
    • Statistical mechanics of fluid mixtures
    • Kirkwood, J. G. (1935). Statistical mechanics of fluid mixtures, J. Chem. Phys. 3, 5, pp. 300-313.
    • (1935) J. Chem. Phys , vol.3 , Issue.5 , pp. 300-313
    • Kirkwood, J.G.1
  • 126
    • 0001633088 scopus 로고
    • Recurrence and invariant measures for degenerate diffusions
    • Kliemann, W. (1987). Recurrence and invariant measures for degenerate diffusions, Ann. Probab. 15, 2, pp. 690-707.
    • (1987) Ann. Probab , vol.15 , Issue.2 , pp. 690-707
    • Kliemann, W.1
  • 127
    • 0043173938 scopus 로고    scopus 로고
    • A theory of statistical models for Monte-Carlo integration
    • Kong, A., McCullagh, P., Meng, X. L., Nicolae, D. and Tan, Z. (2003). A theory of statistical models for Monte-Carlo integration, J. Roy. Stat. Soc. B 65, 3, pp. 585-618.
    • (2003) J. Roy. Stat. Soc. B , vol.65 , Issue.3 , pp. 585-618
    • Kong, A.1    McCullagh, P.2    Meng, X.L.3    Nicolae, D.4    Tan, Z.5
  • 128
    • 84986519238 scopus 로고
    • The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method
    • Kumar, S., Bouzida, D., Swendsen, R. H., Kollman, P. A. and Rosenberg, J. M. (1992). The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method, J. Comput. Chem. 13, 8, pp. 1011-1021.
    • (1992) J. Comput. Chem , vol.13 , Issue.8 , pp. 1011-1021
    • Kumar, S.1    Bouzida, D.2    Swendsen, R.H.3    Kollman, P.A.4    Rosenberg, J.M.5
  • 129
    • 0347975177 scopus 로고    scopus 로고
    • Long-term behaviour of large mechanical systems with random initial data
    • Kupferman, R., Stuart, A. M., Terry, J. R. and Tupper, P. F. (2002). Long-term behaviour of large mechanical systems with random initial data, Stoch. Dynam. 2, 4, pp. 1-30.
    • (2002) Stoch. Dynam , vol.2 , Issue.4 , pp. 1-30
    • Kupferman, R.1    Stuart, A.M.2    Terry, J.R.3    Tupper, P.F.4
  • 134
    • 33846889576 scopus 로고    scopus 로고
    • Derivation of symplectic numerical schemes for highly oscillatory Hamiltonian systems
    • Le Bris, C. and Legoll, F. (2007). Derivation of symplectic numerical schemes for highly oscillatory Hamiltonian systems, C. R. Acad. Sci. Paris Série I 344, 4, pp. 277-282.
    • (2007) C. R. Acad. Sci. Paris Série I , vol.344 , Issue.4 , pp. 277-282
    • Le Bris, C.1    Legoll, F.2
  • 135
    • 42749101300 scopus 로고    scopus 로고
    • On the efficiency of path sampling methods for the calculation of free energies from non-equilibrium simulations
    • Lechner, W. and Dellago, C. (2007). On the efficiency of path sampling methods for the calculation of free energies from non-equilibrium simulations, J. Stat. Mech.-Theory E., p. P04001.
    • (2007) J. Stat. Mech.-Theory E
    • Lechner, W.1    Dellago, C.2
  • 136
    • 34247162359 scopus 로고    scopus 로고
    • Non-ergodicity of the Nose-Hoover thermostatted harmonic oscillator
    • Legoll, F., Luskin, M. and Moeckel, R. (2007). Non-ergodicity of the Nose-Hoover thermostatted harmonic oscillator, Arch. Ration. Mech. Anal. 184, pp. 449-463.
    • (2007) Arch. Ration. Mech. Anal , vol.184 , pp. 449-463
    • Legoll, F.1    Luskin, M.2    Moeckel, R.3
  • 137
    • 67650763419 scopus 로고    scopus 로고
    • Non-ergodicity of Nose-Hoover dynamics
    • Legoll, F., Luskin, M. and Moeckel, R. (2009). Non-ergodicity of Nose-Hoover dynamics, Nonlinearity 22, pp. 1673-1694.
    • (2009) Nonlinearity , vol.22 , pp. 1673-1694
    • Legoll, F.1    Luskin, M.2    Moeckel, R.3
  • 139
    • 0000408065 scopus 로고
    • Symplectic numerical integrators in constrained Hamiltonian systems
    • Leimkuhler, B. J. and Skeel, R. D. (1994). Symplectic numerical integrators in constrained Hamiltonian systems, J. Comput. Phys. 112, 1, pp. 117-125.
    • (1994) J. Comput. Phys , vol.112 , Issue.1 , pp. 117-125
    • Leimkuhler, B.J.1    Skeel, R.D.2
  • 140
    • 60949099340 scopus 로고    scopus 로고
    • A general two-scale criteria for logarithmic Sobolev inequalities
    • Lelievre, T. (2009). A general two-scale criteria for logarithmic Sobolev inequalities, J. Funct. Anal. 256, 7, pp. 2211-2221.
    • (2009) J. Funct. Anal , vol.256 , Issue.7 , pp. 2211-2221
    • Lelievre, T.1
  • 141
    • 84967514470 scopus 로고    scopus 로고
    • Longtime convergence of an adaptive biasing force method: The bi-channel case
    • 00477302
    • Lelievre, T. and Minoukadeh, K. (2010). Longtime convergence of an adaptive biasing force method: The bi-channel case, Hal preprint 00477302.
    • (2010) Hal preprint
    • Lelievre, T.1    Minoukadeh, K.2
  • 142
    • 33847239163 scopus 로고    scopus 로고
    • Computation of free energy differences through nonequilibrium stochastic dynamics: The reaction coordinate case
    • Lelievre, T., Rousset, M. and Stoltz, G. (2007a). Computation of free energy differences through nonequilibrium stochastic dynamics: The reaction coordinate case, J. Comput. Phys. 222, 2, pp. 624-643.
    • (2007) J. Comput. Phys , vol.222 , Issue.2 , pp. 624-643
    • Lelievre, T.1    Rousset, M.2    Stoltz, G.3
  • 143
    • 34147094596 scopus 로고    scopus 로고
    • Computation of free energy profiles with adaptive parallel dynamics
    • Lelievre, T., Rousset, M. and Stoltz, G. (2007b). Computation of free energy profiles with adaptive parallel dynamics, J. Chem,. Phys. 126, p. 134111.
    • (2007) J. Chem,. Phys , vol.126 , pp. 134111
    • Lelievre, T.1    Rousset, M.2    Stoltz, G.3
  • 144
    • 45149117115 scopus 로고    scopus 로고
    • Long-time convergence of an Adaptive Biasing Force method
    • Lelievre, T., Rousset, M. and Stoltz, G. (2008). Long-time convergence of an Adaptive Biasing Force method, Nonlinearity 21, pp. 1155-1181.
    • (2008) Nonlinearity , vol.21 , pp. 1155-1181
    • Lelievre, T.1    Rousset, M.2    Stoltz, G.3
  • 147
    • 0035334524 scopus 로고    scopus 로고
    • Accuracy of free-energy perturbation calculations in molecular simulation. I. Modeling
    • Lu, N. and Kofke, D. A. (2001). Accuracy of free-energy perturbation calculations in molecular simulation. I. Modeling, J. Chem. Phys. 114, 17, pp. 7303-7311.
    • (2001) J. Chem. Phys , vol.114 , Issue.17 , pp. 7303-7311
    • Lu, N.1    Kofke, D.A.2
  • 148
    • 0006660845 scopus 로고
    • An improved hybrid Monte Carlo method
    • Mackenzie, P. B. (1989). An improved hybrid Monte Carlo method, Phys. Lett. B 226, 3-4, pp. 369-371.
    • (1989) Phys. Lett. B , vol.226 , Issue.3-4 , pp. 369-371
    • Mackenzie, P.B.1
  • 149
    • 33745762636 scopus 로고    scopus 로고
    • A temperature accelerated method for sampling free energy and determining reaction pathways in rare events simulations
    • Maragliano, L. and Vanden-Eijnden, E. (2006). A temperature accelerated method for sampling free energy and determining reaction pathways in rare events simulations, Chem. Phys. Lett. 426, 1-3, pp. 168-175.
    • (2006) Chem. Phys. Lett , vol.426 , Issue.1-3 , pp. 168-175
    • Maragliano, L.1    Vanden-Eijnden, E.2
  • 150
    • 33644899039 scopus 로고
    • Simulated tempering - a new Monte-Carlo scheme
    • Marinari, E. and Parisi, G. (1992). Simulated tempering - a new Monte-Carlo scheme, Europhys. Lett. 19, 6, pp. 451-458.
    • (1992) Europhys. Lett , vol.19 , Issue.6 , pp. 451-458
    • Marinari, E.1    Parisi, G.2
  • 151
    • 0038243436 scopus 로고    scopus 로고
    • On the trend to equilibrium for the Fokker-Planck equation: An interplay between physics and functional analysis
    • Markowich, P. A. and Villani, C. (2000). On the trend to equilibrium for the Fokker-Planck equation: An interplay between physics and functional analysis, Mat. Contemp. 19, pp. 1-29.
    • (2000) Mat. Contemp , vol.19 , pp. 1-29
    • Markowich, P.A.1    Villani, C.2
  • 152
    • 33746900781 scopus 로고    scopus 로고
    • Selfhealing Umbrella Sampling: A non-equilibrium approach for quantitative free energy calculations
    • Marsili, S., Barducci, A., Chelli, R., Procacci, P. and Schettino, V. (2006). Selfhealing Umbrella Sampling: A non-equilibrium approach for quantitative free energy calculations, J. Phys. Chem. B 110, 29, pp. 14011-14013.
    • (2006) J. Phys. Chem. B , vol.110 , Issue.29 , pp. 14011-14013
    • Marsili, S.1    Barducci, A.2    Chelli, R.3    Procacci, P.4    Schettino, V.5
  • 153
    • 0036789329 scopus 로고    scopus 로고
    • Ergodicity for SDEs and approximations: Locally Lipschitz vector fields and degenerate noise
    • Mattingly, J. C., Stuart, A. M. and Higham, D. J. (2002). Ergodicity for SDEs and approximations: locally Lipschitz vector fields and degenerate noise, Stoch. Process. Appl. 101, 2, pp. 185-232.
    • (2002) Stoch. Process. Appl , vol.101 , Issue.2 , pp. 185-232
    • Mattingly, J.C.1    Stuart, A.M.2    Higham, D.J.3
  • 155
    • 21444451325 scopus 로고    scopus 로고
    • Simulating ratios of normalizing constants via a simple identity: A theoretical exploration
    • Meng, X.-L. and Wong, W. H. (1996). Simulating ratios of normalizing constants via a simple identity: A theoretical exploration, Stat. Sinica 6, pp. 831-860.
    • (1996) Stat. Sinica , vol.6 , pp. 831-860
    • Meng, X.-L.1    Wong, W.H.2
  • 158
    • 43249106438 scopus 로고    scopus 로고
    • Optimized free energies from bidirectional single-molecule force spectroscopy
    • Minh, D. D. L. and Adib, A. B. (2008). Optimized free energies from bidirectional single-molecule force spectroscopy, Phys. Rev. Lett. 100, p. 180602.
    • (2008) Phys. Rev. Lett , vol.100 , pp. 180602
    • Minh, D.D.L.1    Adib, A.B.2
  • 160
    • 77951140202 scopus 로고    scopus 로고
    • Potential of mean force calculations: A multiple-walker adaptive biasing force approach
    • Minoukadeh, K., Chipot, C. and Lelievre, T. (2010). Potential of mean force calculations: A multiple-walker adaptive biasing force approach, J. Chem. Th. Comput. 6, 4, pp. 1008-1017.
    • (2010) J. Chem. Th. Comput , vol.6 , Issue.4 , pp. 1008-1017
    • Minoukadeh, K.1    Chipot, C.2    Lelievre, T.3
  • 161
    • 21144457044 scopus 로고    scopus 로고
    • Theory of constrained Brownian motion
    • Morse, D. (2004). Theory of constrained Brownian motion, Adv. Chem. Phys. 128, pp. 65-189.
    • (2004) Adv. Chem. Phys , vol.128 , pp. 65-189
    • Morse, D.1
  • 162
    • 33748775457 scopus 로고    scopus 로고
    • Time-reversible Born-Oppenheimer molecular dynamics
    • Niklasson, A. M. N., Tymczak, C. J. and Challacombe, M. (2006). Time-reversible Born-Oppenheimer molecular dynamics, Phys. Rev. Lett. 97, p. 123001.
    • (2006) Phys. Rev. Lett , vol.97 , pp. 123001
    • Niklasson, A.M.N.1    Tymczak, C.J.2    Challacombe, M.3
  • 163
    • 34547809547 scopus 로고
    • A unified formulation of the constant temperature molecular-dynamics methods
    • Nose, S. (1984). A unified formulation of the constant temperature molecular-dynamics methods, J. Chem. Phys. 81, 1, pp. 511-519.
    • (1984) J. Chem. Phys , vol.81 , Issue.1 , pp. 511-519
    • Nose, S.1
  • 164
    • 44649134762 scopus 로고    scopus 로고
    • Optimum bias for fast-switching free energy calculations
    • Oberhofer, H. and Dellago, C. (2008). Optimum bias for fast-switching free energy calculations, Comput. Phys. Commun. 179, pp. 41-45.
    • (2008) Comput. Phys. Commun , vol.179 , pp. 41-45
    • Oberhofer, H.1    Dellago, C.2
  • 165
    • 17444372741 scopus 로고    scopus 로고
    • Biased sampling of nonequilibrium trajectories: Can fast switching simulations outperform conventional free-energy calculation methods?
    • Oberhofer, H., Dellago, C. and Geissler, P. L. (2005). Biased sampling of nonequilibrium trajectories: Can fast switching simulations outperform conventional free-energy calculation methods? J. Phys. Chem. B 109, 14, pp. 6902-6915.
    • (2005) J. Phys. Chem. B , vol.109 , Issue.14 , pp. 6902-6915
    • Oberhofer, H.1    Dellago, C.2    Geissler, P.L.3
  • 168
    • 33846130924 scopus 로고    scopus 로고
    • A new criterion for the logarithmic Sobolev inequality and two applications
    • Otto, F. and Reznikoff, M. G. (2007). A new criterion for the logarithmic Sobolev inequality and two applications, J. Funct. Anal. 243, pp. 121-157.
    • (2007) J. Funct. Anal , vol.243 , pp. 121-157
    • Otto, F.1    Reznikoff, M.G.2
  • 169
    • 0001559554 scopus 로고    scopus 로고
    • Generalization of an inequality by Talagrand and links with the logarithmic Sobolev inequality
    • Otto, F. and Villani, C. (2000). Generalization of an inequality by Talagrand and links with the logarithmic Sobolev inequality, J. Funct. Anal. 173, 2, pp. 361-400.
    • (2000) J. Funct. Anal , vol.173 , Issue.2 , pp. 361-400
    • Otto, F.1    Villani, C.2
  • 170
    • 0015730787 scopus 로고
    • Optimum Monte Carlo sampling using Markov chains
    • Peskun, P. (1973). Optimum Monte Carlo sampling using Markov chains, Biometrika 60, pp. 607-612.
    • (1973) Biometrika , vol.60 , pp. 607-612
    • Peskun, P.1
  • 172
    • 77956037053 scopus 로고    scopus 로고
    • Exact and non-stiff sampling of highly oscillatory systems: An implicit mass-matrix penalization approach
    • Plechac, P. and Rousset, M. (2010). Exact and non-stiff sampling of highly oscillatory systems: An implicit mass-matrix penalization approach, Multiscale Model. Simul. 8, pp. 498-539.
    • (2010) Multiscale Model. Simul , vol.8 , pp. 498-539
    • Plechac, P.1    Rousset, M.2
  • 175
    • 0001787214 scopus 로고
    • Smoothed dynamics of highly oscillatory Hamiltonian systems
    • Reich, S. (1995). Smoothed dynamics of highly oscillatory Hamiltonian systems, Physica D 89, pp. 28-42.
    • (1995) Physica D , vol.89 , pp. 28-42
    • Reich, S.1
  • 176
    • 0346057215 scopus 로고    scopus 로고
    • Smoothed Langevin dynamics of highly oscillatory systems
    • Reich, S. (2000). Smoothed Langevin dynamics of highly oscillatory systems, Physica D 138, pp. 210-224.
    • (2000) Physica D , vol.138 , pp. 210-224
    • Reich, S.1
  • 177
    • 33748951433 scopus 로고    scopus 로고
    • Open classical systems
    • Rey-Bellet, L. (2006). Open classical systems, Lect. Notes Math. 1881, pp. 41-78.
    • (2006) Lect. Notes Math , vol.1881 , pp. 41-78
    • Rey-Bellet, L.1
  • 178
    • 0036041179 scopus 로고    scopus 로고
    • Free-energy calculations in materials research
    • Rickman, J. M. and LeSar, R. (2002). Free-energy calculations in materials research, Ann. Rev. Mater. Res. 32, pp. 195-217.
    • (2002) Ann. Rev. Mater. Res , vol.32 , pp. 195-217
    • Rickman, J.M.1    LeSar, R.2
  • 179
    • 0031285157 scopus 로고    scopus 로고
    • Weak convergence and optimal scaling of random walk Metropolis algorithms
    • Roberts, G. O., Gelman, A. and Gilks, W. R. (1997). Weak convergence and optimal scaling of random walk Metropolis algorithms, Ann. Appl. Probab. 7, pp. 110-120.
    • (1997) Ann. Appl. Probab , vol.7 , pp. 110-120
    • Roberts, G.O.1    Gelman, A.2    Gilks, W.R.3
  • 180
    • 0000936678 scopus 로고    scopus 로고
    • Optimal scaling of discrete approximations to Langevin diffusions
    • Roberts, G. O. and Rosenthal, J. S. (1998). Optimal scaling of discrete approximations to Langevin diffusions, J. Roy. Stat. Soc. B 60, pp. 255-268.
    • (1998) J. Roy. Stat. Soc. B , vol.60 , pp. 255-268
    • Roberts, G.O.1    Rosenthal, J.S.2
  • 182
    • 34249076089 scopus 로고    scopus 로고
    • On the control of an interacting particle approximation of Schrodinger groundstates
    • Rousset, M. (2006b). On the control of an interacting particle approximation of Schrodinger groundstates, SIAM J. Math. Anal. 38, 3, pp. 824-844.
    • (2006) SIAM J. Math. Anal , vol.38 , Issue.3 , pp. 824-844
    • Rousset, M.1
  • 183
    • 33748298996 scopus 로고    scopus 로고
    • Equilibrium sampling from nonequilibrium dynamics
    • Rousset, M. and Stoltz, G. (2006). Equilibrium sampling from nonequilibrium dynamics, J. Stat. Phys. 123, 6, pp. 1251-1272.
    • (2006) J. Stat. Phys , vol.123 , Issue.6 , pp. 1251-1272
    • Rousset, M.1    Stoltz, G.2
  • 185
    • 0002339446 scopus 로고
    • Motion under a strong constraining force
    • Rubin, H. and Ungar, P. (1957). Motion under a strong constraining force, Commun. Pure Appl. Math. 10, pp. 65-87.
    • (1957) Commun. Pure Appl. Math , vol.10 , pp. 65-87
    • Rubin, H.1    Ungar, P.2
  • 187
    • 0008110398 scopus 로고
    • Molecular-dynamics of liquid alkanes
    • Ryckaert, J. P. and Bellemans, A. (1978). Molecular-dynamics of liquid alkanes, Faraday Discuss. 66, pp. 95-106.
    • (1978) Faraday Discuss , vol.66 , pp. 95-106
    • Ryckaert, J.P.1    Bellemans, A.2
  • 188
    • 33748989268 scopus 로고    scopus 로고
    • An efficient sampling algorithm for Variational Monte-Carlo
    • Scemama, A., Lelievre, T., Stoltz, G., Cances, E. and Caffarel, M. (2006). An efficient sampling algorithm for Variational Monte-Carlo, J. Chem. Phys. 125, p. 114105.
    • (2006) J. Chem. Phys , vol.125 , pp. 114105
    • Scemama, A.1    Lelievre, T.2    Stoltz, G.3    Cances, E.4    Caffarel, M.5
  • 190
    • 19944399334 scopus 로고
    • Methods for minimizing errors in linear thermodynamic integration
    • Schlitter, J. (1991). Methods for minimizing errors in linear thermodynamic integration, Molecular Simulation 7, 1, pp. 105-112.
    • (1991) Molecular Simulation , vol.7 , Issue.1 , pp. 105-112
    • Schlitter, J.1
  • 191
    • 33847786887 scopus 로고    scopus 로고
    • Optimal finite-time processes in stochastic thermodynamics
    • Schmiedl, T. and Seifert, U. (2007). Optimal finite-time processes in stochastic thermodynamics, Phys. Rev. Lett. 98, p. 108301.
    • (2007) Phys. Rev. Lett , vol.98 , pp. 108301
    • Schmiedl, T.1    Seifert, U.2
  • 193
    • 0242677537 scopus 로고    scopus 로고
    • Equilibrium free energies from nonequilibrium measurements using maximum-likelihood methods
    • Shirts, M. R., Bair, E., Hooker, G. and Pande, V. S. (2003). Equilibrium free energies from nonequilibrium measurements using maximum-likelihood methods, Phys. Rev. Lett. 91, p. 140601.
    • (2003) Phys. Rev. Lett , vol.91 , pp. 140601
    • Shirts, M.R.1    Bair, E.2    Hooker, G.3    Pande, V.S.4
  • 194
    • 52949088587 scopus 로고    scopus 로고
    • Statistically optimal analysis of samples from multiple equilibrium states
    • Shirts, M. R. and Chodera, J. D. (2008). Statistically optimal analysis of samples from multiple equilibrium states, J. Chem. Phys. 124, 12, p. 124105.
    • (2008) J. Chem. Phys , vol.124 , Issue.12 , pp. 124105
    • Shirts, M.R.1    Chodera, J.D.2
  • 195
    • 0001702831 scopus 로고    scopus 로고
    • Free energy from constrained molecular dynamics
    • Sprik, M. and Ciccoti, G. (1998). Free energy from constrained molecular dynamics, J. Chem. Phys. 109, 18, pp. 7737-7744.
    • (1998) J. Chem. Phys , vol.109 , Issue.18 , pp. 7737-7744
    • Sprik, M.1    Ciccoti, G.2
  • 196
    • 34447273343 scopus 로고    scopus 로고
    • Path sampling with stochastic dynamics: Some new algorithms
    • Stoltz, G. (2007). Path sampling with stochastic dynamics: Some new algorithms, J. Comput. Phys. 225, pp. 491-508.
    • (2007) J. Comput. Phys , vol.225 , pp. 491-508
    • Stoltz, G.1
  • 197
    • 0001167624 scopus 로고
    • Molecular-dynamics study of an isomerizing diatomic in a Lennard-Jones fluid
    • Straub, J. E., Borkovec, M. and Berne, B. J. (1988). Molecular-dynamics study of an isomerizing diatomic in a Lennard-Jones fluid, J. Chem. Phys. 89, 8, pp. 4833-4847.
    • (1988) J. Chem. Phys , vol.89 , Issue.8 , pp. 4833-4847
    • Straub, J.E.1    Borkovec, M.2    Berne, B.J.3
  • 199
    • 0037398346 scopus 로고    scopus 로고
    • Equilibrium free energies from path sampling of nonequilibrium trajectories
    • Sun, S. X. (2003). Equilibrium free energies from path sampling of nonequilibrium trajectories, J. Chem. Phys. 118, 13, pp. 5769-5775.
    • (2003) J. Chem. Phys , vol.118 , Issue.13 , pp. 5769-5775
    • Sun, S.X.1
  • 201
    • 0026202362 scopus 로고
    • Approximation of upper Lyapunov exponents of bilinear stochastic differential systems
    • Talay, D. (1991). Approximation of upper Lyapunov exponents of bilinear stochastic differential systems, SIAM J. Numer. Anal. 28, 4, pp. 1141-1164.
    • (1991) SIAM J. Numer. Anal , vol.28 , Issue.4 , pp. 1141-1164
    • Talay, D.1
  • 202
    • 0000124397 scopus 로고
    • Expansion of the global error for numerical schemes solving stochastic differential equations
    • (1991)
    • Talay, D. and Tubaro, L. (1990). Expansion of the global error for numerical schemes solving stochastic differential equations, Stoch. Anal. Appl. 8, 4, pp. 483-509 (1991).
    • (1990) Stoch. Anal. Appl , vol.8 , Issue.4 , pp. 483-509
    • Talay, D.1    Tubaro, L.2
  • 203
    • 10844294119 scopus 로고    scopus 로고
    • On a likelihood approach for Monte-Carlo integration
    • Tan, Z. (2004). On a likelihood approach for Monte-Carlo integration, J. Am. Stat. Assoc. 99, 468, pp. 1027-1036.
    • (2004) J. Am. Stat. Assoc , vol.99 , Issue.468 , pp. 1027-1036
    • Tan, Z.1
  • 204
    • 27744577658 scopus 로고
    • Modeling solid-state chemistry: Interatomic potentials for multicomponent systems
    • Tersoff, J. (1989). Modeling solid-state chemistry: Interatomic potentials for multicomponent systems, Phys. Rev. B 39, pp. 5566-5568.
    • (1989) Phys. Rev. B , vol.39 , pp. 5566-5568
    • Tersoff, J.1
  • 205
    • 16444385400 scopus 로고
    • Monte-Carlo free energy estimates using non-Boltzmann sampling: Application to the sub-critical Lennard-Jones fluid
    • Torrie, G. M. and Valleau, J. P. (1974). Monte-Carlo free energy estimates using non-Boltzmann sampling: Application to the sub-critical Lennard-Jones fluid, Chem. Phys. Lett. 28, 4, pp. 578-581.
    • (1974) Chem. Phys. Lett , vol.28 , Issue.4 , pp. 578-581
    • Torrie, G.M.1    Valleau, J.P.2
  • 206
    • 0342929614 scopus 로고
    • Non-physical sampling distributions in Monte-Carlo free-energy estimation - Umbrella sampling
    • Torrie, G. M. and Valleau, J. P. (1977). Non-physical sampling distributions in Monte-Carlo free-energy estimation - Umbrella sampling, J. Comput. Phys. 23, 2, pp. 187-199.
    • (1977) J. Comput. Phys , vol.23 , Issue.2 , pp. 187-199
    • Torrie, G.M.1    Valleau, J.P.2
  • 208
    • 43949083060 scopus 로고    scopus 로고
    • Escorted free energy simulations: Improving convergence by reducing dissipation
    • Vaikuntanathan, S. and Jarzynski, C. (2008). Escorted free energy simulations: Improving convergence by reducing dissipation, Phys. Rev. Lett. 100, p. 190601.
    • (2008) Phys. Rev. Lett , vol.100 , pp. 190601
    • Vaikuntanathan, S.1    Jarzynski, C.2
  • 211
    • 0019690668 scopus 로고
    • Statistical mechanics for trimers
    • van Kampen, N. G. (1981). Statistical mechanics for trimers, App. Sci. Res. 37, pp. 67-75.
    • (1981) App. Sci. Res , vol.37 , pp. 67-75
    • Van Kampen, N.G.1
  • 212
    • 0002157780 scopus 로고
    • Elimination of fast variables
    • van Kampen, N. G. (1985). Elimination of fast variables, Phys. Rep. 124, 2, pp. 9-160.
    • (1985) Phys. Rep , vol.124 , Issue.2 , pp. 9-160
    • Van Kampen, N.G.1
  • 213
    • 22944467757 scopus 로고
    • Computer “experiments” on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules
    • Verlet, L. (1967). Computer “experiments” on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules, Phys. Rev. 159, pp. 98-103.
    • (1967) Phys. Rev , vol.159 , pp. 98-103
    • Verlet, L.1
  • 214
    • 67649344144 scopus 로고    scopus 로고
    • A review of mathematical topics in collisional kinetic theory
    • (North-Holland, Amsterdam)
    • Villani, C. (2002). A review of mathematical topics in collisional kinetic theory, in Handbook of Mathematical Fluid Dynamics, Vol. I (North-Holland, Amsterdam), pp. 71-305.
    • (2002) Handbook of Mathematical Fluid Dynamics, Vol. I , pp. 71-305
    • Villani, C.1
  • 216
  • 217
    • 39749147672 scopus 로고    scopus 로고
    • Determining the density of states for classical statistical models: A random walk algorithm to produce a flat histogram
    • Wang, F. and Landau, D. (2001a). Determining the density of states for classical statistical models: A random walk algorithm to produce a flat histogram, Phys. Rev. E 64, p. 056101.
    • (2001) Phys. Rev. E , vol.64 , pp. 056101
    • Wang, F.1    Landau, D.2
  • 218
    • 6644221271 scopus 로고    scopus 로고
    • Efficient, multiple-range random walk algorithm to calculate the density of states
    • Wang, F. G. and Landau, D. P. (2001b). Efficient, multiple-range random walk algorithm to calculate the density of states, Phys. Rev. Lett. 86, 10, pp. 2050-2053.
    • (2001) Phys. Rev. Lett , vol.86 , Issue.10 , pp. 2050-2053
    • Wang, F.G.1    Landau, D.P.2
  • 220
    • 33750970530 scopus 로고    scopus 로고
    • Comparison of free energy methods for molecular systems
    • Ytreberg, F. M., Swendsen, R. H. and Zuckerman, D. M. (2006). Comparison of free energy methods for molecular systems, J. Chem. Phys. 125, p. 184114.
    • (2006) J. Chem. Phys , vol.125 , pp. 184114
    • Ytreberg, F.M.1    Swendsen, R.H.2    Zuckerman, D.M.3
  • 221
    • 3042688939 scopus 로고    scopus 로고
    • Single-ensemble nonequilibrium path-sampling estimates of free energy differences
    • Ytreberg, F. M. and Zuckerman, D. M. (2004). Single-ensemble nonequilibrium path-sampling estimates of free energy differences, J. Chem. Phys. 120, 23, pp. 10876-10879.
    • (2004) J. Chem. Phys , vol.120 , Issue.23 , pp. 10876-10879
    • Ytreberg, F.M.1    Zuckerman, D.M.2
  • 222
    • 44649157295 scopus 로고    scopus 로고
    • Determination of free energy profiles by repository based adaptive Umbrella sampling: Bridging nonequilibrium and quasiequilibrium simulations
    • Zheng, H. and Zhang, Y. (2008). Determination of free energy profiles by repository based adaptive Umbrella sampling: Bridging nonequilibrium and quasiequilibrium simulations, J. Chem. Phys. 128, p. 204106.
    • (2008) J. Chem. Phys , vol.128 , pp. 204106
    • Zheng, H.1    Zhang, Y.2
  • 223
    • 18744379822 scopus 로고    scopus 로고
    • Theory of a systematic computational error in free energy differences
    • Zuckerman, D. M. and Woolf, T. B. (2002). Theory of a systematic computational error in free energy differences, Phys. Rev. Lett. 89, p. 180602.
    • (2002) Phys. Rev. Lett , vol.89 , pp. 180602
    • Zuckerman, D.M.1    Woolf, T.B.2
  • 224
    • 3142740709 scopus 로고    scopus 로고
    • Systematic finite-sampling inaccuracy in free energy differences and other nonlinear quantities
    • Zuckerman, D. M. and Woolf, T. B. (2004). Systematic finite-sampling inaccuracy in free energy differences and other nonlinear quantities, J. Stat. Phys. 114, 5-6, pp. 1303-1323.
    • (2004) J. Stat. Phys , vol.114 , Issue.5-6 , pp. 1303-1323
    • Zuckerman, D.M.1    Woolf, T.B.2
  • 225
    • 18844402460 scopus 로고
    • Nonlinear generalized Langevin equations
    • Zwanzig, R. (1973). Nonlinear generalized Langevin equations, J. Stat. Phys. 9, pp. 215-220.
    • (1973) J. Stat. Phys , vol.9 , pp. 215-220
    • Zwanzig, R.1
  • 226
    • 36849122972 scopus 로고
    • High-temperature equation of state by a perturbation method I. Nonpolar gases
    • Zwanzig, R. W. (1954). High-temperature equation of state by a perturbation method I. Nonpolar gases, J. Chem. Phys. 22, 8, pp. 1420-1426.
    • (1954) J. Chem. Phys , vol.22 , Issue.8 , pp. 1420-1426
    • Zwanzig, R.W.1


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