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Volumn 372, Issue 2021, 2014, Pages

Recent applications of boxed molecular dynamics: A simple multiscale technique for atomistic simulations

Author keywords

Chemical dynamics; Dynamics of proteins; Kinetics; Molecular dynamics; Quantum mechanics

Indexed keywords

ATOMIC FORCE MICROSCOPY; CYCLIZATION; ENZYME KINETICS; PROTEINS; QUANTUM THEORY; REACTION KINETICS; SELF ASSEMBLED MONOLAYERS; THERMODYNAMICS;

EID: 84903977723     PISSN: 1364503X     EISSN: None     Source Type: Journal    
DOI: 10.1098/rsta.2013.0384     Document Type: Review
Times cited : (29)

References (40)
  • 1
    • 73349135352 scopus 로고    scopus 로고
    • Boxed molecular dynamics: A simple and general technique for accelerating rare event kinetics and mapping free energy in large molecular systems
    • doi:10.1021/jp9074898)
    • Glowacki DR, Paci E, Shalashilin DV. 2009 Boxed molecular dynamics: A simple and general technique for accelerating rare event kinetics and mapping free energy in large molecular systems. J. Phys. Chem. B 113, 16 603-16 611. (doi:10.1021/jp9074898)
    • (2009) J. Phys. Chem. B , vol.113 , pp. 16603-16611
    • Glowacki, D.R.1    Paci, E.2    Shalashilin, D.V.3
  • 2
    • 79955879778 scopus 로고    scopus 로고
    • Boxed molecular dynamics: Decorrelation time scales and the kinetic master equation
    • doi:10.1021/ct200011e)
    • Glowacki DR, Paci E, Shalashilin DV. 2011 Boxed molecular dynamics: decorrelation time scales and the kinetic master equation. J. Chem. Theory Comput. 7, 1244-1252. (doi:10.1021/ct200011e)
    • (2011) J. Chem. Theory Comput. , vol.7 , pp. 1244-1252
    • Glowacki, D.R.1    Paci, E.2    Shalashilin, D.V.3
  • 3
    • 84868338370 scopus 로고    scopus 로고
    • Peptide kinetics from picoseconds to microseconds using boxed molecular dynamics: Power law rate coefficients in cyclisation reactions
    • doi:10.1063/1.4759088)
    • Shalashilin DV, Beddard GS, Paci E, Glowacki DR. 2012 Peptide kinetics from picoseconds to microseconds using boxed molecular dynamics: power law rate coefficients in cyclisation reactions. J. Chem. Phys. 137, 165102. (doi:10.1063/1.4759088)
    • (2012) J. Chem. Phys. , vol.137 , pp. 165102
    • Shalashilin, D.V.1    Beddard, G.S.2    Paci, E.3    Glowacki, D.R.4
  • 4
    • 0043141427 scopus 로고    scopus 로고
    • Intramolecular dynamics diffusion theory approach to complex unimolecular reactions
    • Guo Y, Shalashilin DV, Krouse JA, Thompson DL. 1999 Intramolecular dynamics diffusion theory approach to complex unimolecular reactions. J. Chem. Phys. 110, 5521-5525. (doi:10.1063/1.478449) (Pubitemid 129645775)
    • (1999) Journal of Chemical Physics , vol.110 , Issue.12 , pp. 5521-5525
    • Guo, Y.1    Shalashilin, D.V.2    Krouse, J.A.3    Thompson, D.L.4
  • 5
    • 0009704365 scopus 로고    scopus 로고
    • Predicting nonstatistical unimolecular reaction rates using Kramers' theory
    • Guo Y, Shalashilin DV, Krouse JA, Thompson DL. 1999 Predicting nonstatistical unimolecular reaction rates using Kramers' theory. J. Chem. Phys. 110, 5514-5520. (doi:10.1063/1.478448) (Pubitemid 129645774)
    • (1999) Journal of Chemical Physics , vol.110 , Issue.12 , pp. 5514-5520
    • Guo, Y.1    Shalashilin, D.V.2    Krouse, J.A.3    Thompson, D.L.4
  • 6
    • 0030737277 scopus 로고    scopus 로고
    • Monte carlo variational transition-state theory study of the unimolecular dissociation of RDX
    • Shalashilin DV, Thompson DL. 1997 Monte Carlo variational transition-state theory study of the unimolecular dissociation of RDX. J. Phys. Chem. A 101, 961-966. (doi:10.1021/jp961755o) (Pubitemid 127578297)
    • (1997) Journal of Physical Chemistry A , vol.101 , Issue.5 , pp. 961-966
    • Shalashilin, D.V.1    Thompson, D.L.2
  • 7
    • 0000067119 scopus 로고    scopus 로고
    • Method for predicting IVR-limited unimolecular reaction rate coefficients
    • Shalashilin DV, Thompson DL. 1997 Method for predicting IVR-limited unimolecular reaction rate coefficients. J. Chem. Phys. 107, 6204-6212. (doi:10.1063/1.474285) (Pubitemid 127576443)
    • (1997) Journal of Chemical Physics , vol.107 , Issue.16 , pp. 6204-6212
    • Shalashilin, D.V.1    Thompson, D.L.2
  • 8
    • 0345878731 scopus 로고    scopus 로고
    • Intramolecular dynamics diffusion theory: Nonstatistical unimolecular reaction rates
    • Shalashilin DV, Thompson DL. 1997 Intramolecular dynamics diffusion theory: nonstatistical unimolecular reaction rates. ACS Symp. Ser. 678, 81-98. (doi:10.1021/bk-1997-0678.ch006) (Pubitemid 127439659)
    • (1997) ACS Symposium Series , vol.678 , pp. 81-98
    • Shalashilin, D.V.1    Thompson, D.L.2
  • 9
    • 33846188049 scopus 로고    scopus 로고
    • Acceleration of classical mechanics by phase space constraints
    • doi:10.1021/ct060042z)
    • Martinez-Nunez E, Shalashilin DV. 2006 Acceleration of classical mechanics by phase space constraints. J. Chem. Theory Comput. 2, 912-919. (doi:10.1021/ct060042z)
    • (2006) J. Chem. Theory Comput. , vol.2 , pp. 912-919
    • Martinez-Nunez, E.1    Shalashilin, D.V.2
  • 10
    • 34247897186 scopus 로고    scopus 로고
    • A milestoning study of the kinetics of an allosteric transition: Atomically detailed simulations of deoxy Scapharca hemoglobin
    • DOI 10.1529/biophysj.106.101899
    • Elber R. 2007 A milestoning study of the kinetics of an allosteric transition: Atomically detailed simulations of deoxy Scapharca hemoglobin. Biophys. J. 92, L85-L87. (doi:10.1529/ biophysj.106.101899) (Pubitemid 46691100)
    • (2007) Biophysical Journal , vol.92 , Issue.9
    • Elber, R.1
  • 11
    • 3042545299 scopus 로고    scopus 로고
    • Computing time scales from reaction coordinates by milestoning
    • doi:10.1063/1.1738640)
    • Faradjian AK, Elber R. 2004 Computing time scales from reaction coordinates by milestoning. J. Chem. Phys.120, 10 880-10 889. (doi:10.1063/1.1738640)
    • (2004) J. Chem. Phys. , vol.120 , pp. 10880-10889
    • Faradjian, A.K.1    Elber, R.2
  • 12
    • 67649601306 scopus 로고    scopus 로고
    • Kinetics of helix unfolding: Molecular dynamics simulations with milestoning
    • doi:10.1021/jp900407w)
    • Kuczera K, Jas GS, Elber R. 2009 Kinetics of helix unfolding: molecular dynamics simulations with milestoning. J. Phys. Chem. A 113, 7461-7473. (doi:10.1021/jp900407w)
    • (2009) J. Phys. Chem. A , vol.113 , pp. 7461-7473
    • Kuczera, K.1    Jas, G.S.2    Elber, R.3
  • 13
    • 73949127824 scopus 로고    scopus 로고
    • Free energy and kinetics of conformational transitions from voronoi tessellated milestoning with restraining potentials
    • doi:10.1021/ct900279z)
    • Maragliano L, Vanden-Eijnden E, Roux B. 2009 Free energy and kinetics of conformational transitions from voronoi tessellated milestoning with restraining potentials. J. Chem. Theory Comput. 5, 2589-2594. (doi:10.1021/ct900279z)
    • (2009) J. Chem. Theory Comput. , vol.5 , pp. 2589-2594
    • Maragliano, L.1    Vanden-Eijnden, E.2    Roux, B.3
  • 15
    • 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)
    • West AMA, Elber R, Shalloway D. 2007 Extending molecular dynamics time scales with milestoning: example of complex kinetics in a solvated peptide. J. Chem. Phys. 126, 145104. (doi:10.1063/1.2716389)
    • (2007) J. Chem. Phys. , vol.126 , pp. 145104
    • West, A.M.A.1    Elber, R.2    Shalloway, D.3
  • 16
    • 66049102550 scopus 로고    scopus 로고
    • Markovian milestoning with Voronoi tessellations
    • doi:10.1063/1.3129843)
    • Vanden-Eijnden E, Venturoli M. 2009 Markovian milestoning with Voronoi tessellations. J. Chem. Phys. 130, 194101. (doi:10.1063/1.3129843)
    • (2009) J. Chem. Phys. , vol.130 , pp. 194101
    • Vanden-Eijnden, E.1    Venturoli, M.2
  • 17
    • 80155195008 scopus 로고    scopus 로고
    • Ultrafast energy flow in the wake of solution-phase bimolecular reactions
    • doi:10.1038/ nchem.1154)
    • Glowacki DR, Rose RA, Greaves SJ, Orr-Ewing AJ, Harvey JN. 2011 Ultrafast energy flow in the wake of solution-phase bimolecular reactions. Nat. Chem. 3, 850-855. (doi:10.1038/ nchem.1154)
    • (2011) Nat. Chem. , vol.3 , pp. 850-855
    • Glowacki, D.R.1    Rose, R.A.2    Greaves, S.J.3    Orr-Ewing, A.J.4    Harvey, J.N.5
  • 18
    • 79952819082 scopus 로고    scopus 로고
    • Vibrationally quantum-state-specific reaction dynamics of H atom abstraction by CN radical in solution
    • doi:10.1126/science.1197796)
    • Greaves SJ et al. 2011 Vibrationally quantum-state-specific reaction dynamics of H atom abstraction by CN radical in solution. Science 331, 1423-1426. (doi:10.1126/science.1197796)
    • (2011) Science , vol.331 , pp. 1423-1426
    • Greaves, S.J.1
  • 19
    • 79958860023 scopus 로고    scopus 로고
    • Product energy deposition of CN+ alkane H abstraction reactions in gas and solution phases
    • doi:10.1063/1.3595259)
    • Glowacki DR, Orr-Ewing AJ, Harvey JN. 2011 Product energy deposition of CN+ alkane H abstraction reactions in gas and solution phases. J. Chem. Phys. 134, 214508. (doi:10.1063/1.3595259)
    • (2011) J. Chem. Phys. , vol.134 , pp. 214508
    • Glowacki, D.R.1    Orr-Ewing, A.J.2    Harvey, J.N.3
  • 20
    • 0031144465 scopus 로고    scopus 로고
    • Hyperdynamics: Accelerated molecular dynamics of infrequent events
    • Voter AF. 1997 Hyperdynamics: Accelerated molecular dynamics of infrequent events. Phys. Rev. Lett. 78, 3908-3911. (doi:10.1103/PhysRevLett.78. 3908) (Pubitemid 127655393)
    • (1997) Physical Review Letters , vol.78 , Issue.20 , pp. 3908-3911
    • Voter, A.F.1
  • 21
    • 1442281293 scopus 로고    scopus 로고
    • A method for accelerating the molecular dynamics simulation of infrequent events
    • doi:10.1063/1.473503)
    • Voter AF. 1997 A method for accelerating the molecular dynamics simulation of infrequent events. J. Chem. Phys. 106, 4665-4677. (doi:10.1063/1.473503)
    • (1997) J. Chem. Phys. , vol.106 , pp. 4665-4677
    • Voter, A.F.1
  • 22
    • 36749113356 scopus 로고
    • Monte Carlo study of a phase-separating liquid mixture by umbrella sampling
    • doi:10.1063/1.434125)
    • Torrie GM, Valleau JP. 1977 Monte Carlo study of a phase-separating liquid mixture by umbrella sampling. J. Chem. Phys. 66, 1402-1408. (doi:10.1063/1.434125)
    • (1977) J. Chem. Phys. , vol.66 , pp. 1402-1408
    • Torrie, G.M.1    Valleau, J.P.2
  • 23
    • 0342929614 scopus 로고
    • Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
    • doi:10.1016/0021-9991(77) 90121-8)
    • Torrie GM, Valleau JP. 1977 Nonphysical sampling distributions in Monte Carlo free-energy estimation: umbrella sampling. J. Comput. Phys. 23, 187-199. (doi:10.1016/0021-9991(77) 90121-8)
    • (1977) J. Comput. Phys. , vol.23 , pp. 187-199
    • Torrie, G.M.1    Valleau, J.P.2
  • 24
    • 84855228281 scopus 로고    scopus 로고
    • Umbrella sampling. Wiley Interdiscip
    • doi:10.1002/wcms.66)
    • Kaestner J. 2011 Umbrella sampling. Wiley Interdiscip. Rev. Comput. Mol. Sci. 1, 932-942. (doi:10.1002/wcms.66)
    • (2011) Rev. Comput. Mol. Sci. , vol.1 , pp. 932-942
    • Kaestner, J.1
  • 26
    • 0000778098 scopus 로고    scopus 로고
    • Multiple time scales for dispersive kinetics in early events of peptide folding
    • PII S0009261498007581
    • Metzler R, Klafter J, Jortner J, Volk M. 1998 Multiple time scales for dispersive kinetics in early events of peptide folding. Chem. Phys. Lett. 293, 477-484. (doi:10.1016/S0009-2614(98)00758-1) (Pubitemid 128344646)
    • (1998) Chemical Physics Letters , vol.293 , Issue.5-6 , pp. 477-484
    • Metzler, R.1    Klafter, J.2    Jortner, J.3    Volk, M.4
  • 27
    • 0031251663 scopus 로고    scopus 로고
    • Peptide conformational dynamics and vibrational stark effects following photoinitiated disulfide cleavage
    • doi:10.1021/jp971951a)
    • Volk M, Kholodenko Y, Lu HSM, Gooding EA, DeGrado WF, Hochstrasser RM. 1997 Peptide conformational dynamics and vibrational stark effects following photoinitiated disulfide cleavage. J. Phys. Chem. B 101, 8607-8616. (doi:10.1021/jp971951a)
    • (1997) J. Phys. Chem. B , vol.101 , pp. 8607-8616
    • Volk, M.1    Kholodenko, Y.2    Lu, H.S.M.3    Gooding, E.A.4    Degrado, W.F.5    Hochstrasser, R.M.6
  • 29
    • 0001540417 scopus 로고    scopus 로고
    • Soft landing of polyatomic ions for selective modification of fluorinated self-assembled monolayer surfaces
    • PII S0168117697003029
    • Luo H, Miller SA, Cooks RG, Pachuta SJ. 1998 Soft landing of polyatomic ions for selective modification of fluorinated self-assembled monolayer surfaces. Int. J. Mass Spectrom. 174, 193-217. (doi:10.1016/S0168-1176(97)00302- 9) (Pubitemid 128656431)
    • (1998) International Journal of Mass Spectrometry and Ion Processes , vol.174 , Issue.1-3 , pp. 193-217
    • Luo, H.1    Miller, S.A.2    Cooks, R.G.3    Pachuta, S.J.4
  • 31
    • 0031039897 scopus 로고    scopus 로고
    • Soft-landing of polyatomic ions at fluorinated self-assembled monolayer surfaces
    • DOI 10.1126/science.275.5305.1447
    • Miller SA, Luo H, Pachuta SJ, Cooks RG. 1997 Soft-landing of polyatomic ions at fluorinated self-assembled monolayer surfaces. Science 275, 1447-1450. (doi:10.1126/ science.275.5305.1447) (Pubitemid 27111285)
    • (1997) Science , vol.275 , Issue.5305 , pp. 1447-1450
    • Miller, S.A.1    Luo, H.2    Pachuta, S.J.3    Cooks, R.G.4
  • 32
    • 37749030526 scopus 로고    scopus 로고
    • Probing the mechanical stability of proteins using the atomic force microscope
    • doi:10.1042/BST0351564)
    • Brockwell DJ. 2007 Probing the mechanical stability of proteins using the atomic force microscope. Biochem. Soc. Trans. 35, 1564-1568. (doi:10.1042/BST0351564)
    • (2007) Biochem. Soc. Trans. , vol.35 , pp. 1564-1568
    • Brockwell, D.J.1
  • 35
    • 67650500988 scopus 로고    scopus 로고
    • Identification of a mechanical rheostat in the hydrophobic core of protein L
    • doi:10.1002/jcc.21287)
    • Brooks BR et al. 2009 Identification of a mechanical rheostat in the hydrophobic core of protein L. J. Comput. Chem. 30, 1545-1614. (doi:10.1002/jcc.21287)
    • (2009) J. Comput. Chem. , vol.30 , pp. 1545-1614
    • Brooks, B.R.1
  • 36
    • 84900825975 scopus 로고    scopus 로고
    • Unraveling the factors that control soft landing of small silyl ions on fluorinated self-assembled monolayers
    • doi:10.1021/jp501841a)
    • Nogueira JJ et al. 2014 Unraveling the factors that control soft landing of small silyl ions on fluorinated self-assembled monolayers. J. Phys. Chem. C. 118, 10 159-10 169. (doi:10.1021/jp501841a)
    • (2014) J. Phys. Chem. C. , vol.118 , pp. 10159-10169
    • Nogueira, J.J.1
  • 39
    • 84876722711 scopus 로고    scopus 로고
    • Non-equilibrium phenomena and molecular reaction dynamics: Mode space, energy space and conformer space
    • doi:10.1080/00268976.2013.780100)
    • Glowacki DR, Lightfoot R, Harvey JN. 2013 Non-equilibrium phenomena and molecular reaction dynamics: mode space, energy space and conformer space. Mol. Phys. 111, 631-640. (doi:10.1080/00268976.2013.780100)
    • (2013) Mol. Phys. , vol.111 , pp. 631-640
    • Glowacki, D.R.1    Lightfoot, R.2    Harvey, J.N.3
  • 40
    • 84863904186 scopus 로고    scopus 로고
    • Reaction dynamics of CN radicals with tetrahydrofuran in liquid solutions
    • doi:10.1039/c2cp40158d)
    • Rose RA et al. 2012 Reaction dynamics of CN radicals with tetrahydrofuran in liquid solutions. Phys. Chem. Chem. Phys. 14, 10 424-10 437. (doi:10.1039/c2cp40158d)
    • (2012) Phys. Chem. Chem. Phys. , vol.14 , pp. 10424-10437
    • Rose, R.A.1


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