메뉴 건너뛰기




Volumn 83, Issue 2, 2011, Pages

Drift-oscillatory steering with the forward-reverse method for calculating the potential of mean force

Author keywords

[No Author keywords available]

Indexed keywords

AQUEOUS SOLUTIONS; BROWNIAN OSCILLATORS; CONSTANT VELOCITIES; IMPLICIT SOLVENTS; ION PAIRS; LENNARD JONES; LENNARD-JONES LIQUIDS; NON EQUILIBRIUM; PIECE-WISE; POTENTIAL OF MEAN FORCE; REVERSE PATH; SOFT-MATTER PHYSICS;

EID: 79952543578     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.83.021114     Document Type: Article
Times cited : (8)

References (35)
  • 1
    • 4243754128 scopus 로고    scopus 로고
    • PRLTAO 0031-9007 10.1103/PhysRevLett.78.2690
    • C. Jarzynski, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.78. 2690 78, 2690 (1997).
    • (1997) Phys. Rev. Lett. , vol.78 , pp. 2690
    • Jarzynski, C.1
  • 2
    • 4244116139 scopus 로고    scopus 로고
    • PLEEE8 1539-3755 10.1103/PhysRevE.56.5018
    • C. Jarzynski, Phys. Rev. E PLEEE8 1539-3755 10.1103/PhysRevE.56.5018 56, 5018 (1997).
    • (1997) Phys. Rev. e , vol.56 , pp. 5018
    • Jarzynski, C.1
  • 3
    • 0000186593 scopus 로고    scopus 로고
    • PLEEE8 1539-3755 10.1103/PhysRevE.61.2361
    • G. E. Crooks, Phys. Rev. E PLEEE8 1539-3755 10.1103/PhysRevE.61.2361 61, 2361 (2000).
    • (2000) Phys. Rev. e , vol.61 , pp. 2361
    • Crooks, G.E.1
  • 4
    • 4143087050 scopus 로고    scopus 로고
    • JCPSA6 0021-9606 10.1063/1.1651473
    • S. Park and K. Schulten, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1651473 120, 5946 (2004).
    • (2004) J. Chem. Phys. , vol.120 , pp. 5946
    • Park, S.1    Schulten, K.2
  • 5
    • 0035826435 scopus 로고    scopus 로고
    • A "fast growth" method of computing free energy differences
    • DOI 10.1063/1.1353552
    • D. A. Hendrix and C. Jarzynski, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1353552 114, 5974 (2001). (Pubitemid 32419574)
    • (2001) Journal of Chemical Physics , vol.114 , Issue.14 , pp. 5974-5981
    • Hendrix, D.A.1    Jarzynski, C.2
  • 6
    • 84901046065 scopus 로고    scopus 로고
    • JCPSA6 1742-5468 10.1088/1742-5468/2004/07/P07006
    • E. G. D. Cohen and D. Mauzerall, J. Stat. Mech. JCPSA6 1742-5468 10.1088/1742-5468/2004/07/P07006 (2004) P07006.
    • J. Stat. Mech. , vol.2004 , pp. 07006
    • Cohen, E.G.D.1    Mauzerall, D.2
  • 7
    • 24644450199 scopus 로고    scopus 로고
    • Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies
    • DOI 10.1038/nature04061
    • D. Collin, F. Ritort, C. Jarzynski, S. B. Smith, I. Tinoco Jr., and C. Bustamante, Nature (London) NATUAS 0028-0836 10.1038/nature04061 437, 231 (2005). (Pubitemid 41294482)
    • (2005) Nature , vol.437 , Issue.7056 , pp. 231-234
    • Collin, D.1    Ritort, F.2    Jarzynski, C.3    Smith, S.B.4    Tinoco Jr., I.5    Bustamante, C.6
  • 8
    • 19644401497 scopus 로고    scopus 로고
    • PRLTAO 0031-9007 10.1103/PhysRevLett.93.158105
    • O. Braun, A. Hanke, and U. Seifert, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.93.158105 93, 158105 (2004).
    • (2004) Phys. Rev. Lett. , vol.93 , pp. 158105
    • Braun, O.1    Hanke, A.2    Seifert, U.3
  • 9
    • 26644469551 scopus 로고    scopus 로고
    • Force spectroscopy of single multidomain biopolymers: A master equation approach
    • DOI 10.1140/epje/i2005-10024-8
    • O. Braun and U. Seifert, Eur. Phys. J. E EPJSFH 1292-8941 10.1140/epje/i2005-10024-8 18, 1 (2005). (Pubitemid 41442646)
    • (2005) European Physical Journal E , vol.18 , Issue.1 , pp. 1-13
    • Braun, O.1    Seifert, U.2
  • 11
    • 33645666178 scopus 로고    scopus 로고
    • PNASA6 1539-3755 10.1103/PhysRevE.73.046105
    • C. Jarzynski, Phys. Rev. E PNASA6 1539-3755 10.1103/PhysRevE.73.046105 73, 046105 (2006).
    • (2006) Phys. Rev. e , vol.73 , pp. 046105
    • Jarzynski, C.1
  • 12
    • 33847255930 scopus 로고    scopus 로고
    • Dissipation: The phase-space perspective
    • DOI 10.1103/PhysRevLett.98.080602
    • R. Kawai, J. M. R. Parrondo, and C. Van den Broeck, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.98.080602 98, 080602 (2007). (Pubitemid 46326134)
    • (2007) Physical Review Letters , vol.98 , Issue.8 , pp. 080602
    • Kawai, R.1    Parrondo, J.M.R.2    Van Den Broeck, C.3
  • 13
    • 67651236152 scopus 로고    scopus 로고
    • NJOPFM 1367-2630 10.1088/1367-2630/11/7/073008
    • J. M. R. Parrondo, C. V. den Broeck, and R. Kawai, New J. Phys. NJOPFM 1367-2630 10.1088/1367-2630/11/7/073008 11, 073008 (2009).
    • (2009) New J. Phys. , vol.11 , pp. 073008
    • Parrondo, J.M.R.1    Den Broeck, C.V.2    Kawai, R.3
  • 14
    • 33749551180 scopus 로고    scopus 로고
    • Calculating potentials of mean force and diffusion coefficients from nonequilibrium processes without Jarzynski's equality
    • DOI 10.1063/1.2166379
    • I. Kosztin, B. Barz, and L. Janosi, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2166379 124, 064106 (2006). (Pubitemid 43248009)
    • (2006) Journal of Chemical Physics , vol.124 , Issue.6 , pp. 064106
    • Kosztin, I.1    Barz, B.2    Janosi, L.3
  • 15
    • 57149107204 scopus 로고    scopus 로고
    • JCPSA6 1539-3755 10.1103/PhysRevE.78.051913
    • M. W. Forney, L. Janosi, and I. Kosztin, Phys. Rev. E JCPSA6 1539-3755 10.1103/PhysRevE.78.051913 78, 051913 (2008).
    • (2008) Phys. Rev. e , vol.78 , pp. 051913
    • Forney, M.W.1    Janosi, L.2    Kosztin, I.3
  • 19
    • 50649124652 scopus 로고    scopus 로고
    • PRLTAO 0031-9007 10.1103/PhysRevLett.101.098901
    • J. Horowitz and C. Jarzynski, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.101.098901 101, 098901 (2008).
    • (2008) Phys. Rev. Lett. , vol.101 , pp. 098901
    • Horowitz, J.1    Jarzynski, C.2
  • 20
    • 0002121327 scopus 로고
    • RMPHAT 0034-6861 10.1103/RevModPhys.15.1
    • S. Chandrasekhar, Rev. Mod. Phys. RMPHAT 0034-6861 10.1103/RevModPhys.15. 1 15, 1 (1943).
    • (1943) Rev. Mod. Phys. , vol.15 , pp. 1
    • Chandrasekhar, S.1
  • 21
    • 84952104504 scopus 로고
    • MOPHAM 0026-8976 10.1080/00268978800101881
    • R. Pastor, B. Brooks, and A. Szabo, Mol. Phys. MOPHAM 0026-8976 10.1080/00268978800101881 65, 1409 (1988).
    • (1988) Mol. Phys. , vol.65 , pp. 1409
    • Pastor, R.1    Brooks, B.2    Szabo, A.3
  • 22
    • 0012002071 scopus 로고
    • JCPSA6 0021-9606 10.1063/1.1731425
    • B. J. Alder and T. E. Wainwright, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1731425 33, 1439 (1960).
    • (1960) J. Chem. Phys. , vol.33 , pp. 1439
    • Alder, B.J.1    Wainwright, T.E.2
  • 23
    • 33847005283 scopus 로고
    • PHRVAO 0031-899X 10.1103/PhysRev.136.A405
    • A. Rahman, Phys. Rev. PHRVAO 0031-899X 10.1103/PhysRev.136.A405 136, A405 (1964).
    • (1964) Phys. Rev. , vol.136 , pp. 405
    • Rahman, A.1
  • 24
    • 22944467757 scopus 로고
    • PHRVAO 0031-899X 10.1103/PhysRev.159.98
    • L. Verlet, Phys. Rev. PHRVAO 0031-899X 10.1103/PhysRev.159.98 159, 98 (1967).
    • (1967) Phys. Rev. , vol.159 , pp. 98
    • Verlet, L.1
  • 25
    • 36049060961 scopus 로고
    • PHRVAO 0031-899X 10.1103/PhysRev.165.201
    • L. Verlet, Phys. Rev. PHRVAO 0031-899X 10.1103/PhysRev.165.201 165, 201 (1968).
    • (1968) Phys. Rev. , vol.165 , pp. 201
    • Verlet, L.1
  • 26
    • 0029878720 scopus 로고    scopus 로고
    • VMD: Visual molecular dynamics
    • DOI 10.1016/0263-7855(96)00018-5
    • W. Humphrey, A. Dalke, and K. Schulten, J. Mol. Graphics JMGRDV 0263-7855 10.1016/0263-7855(96)00018-5 14, 33 (1996). (Pubitemid 26152973)
    • (1996) Journal of Molecular Graphics , vol.14 , Issue.1 , pp. 33-38
    • Humphrey, W.1    Dalke, A.2    Schulten, K.3
  • 28
    • 77949709452 scopus 로고    scopus 로고
    • JCPSA6 0021-9606 10.1063/1.3360310
    • J. Timko, D. Bucher, and S. Kuyucak, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.3360310 132, 114510 (2010).
    • (2010) J. Chem. Phys. , vol.132 , pp. 114510
    • Timko, J.1    Bucher, D.2    Kuyucak, S.3
  • 29
    • 0030574785 scopus 로고    scopus 로고
    • CHPLBC 0009-2614 10.1016/0009-2614(96)00058-9
    • T. Simonson, Chem. Phys. Lett. CHPLBC 0009-2614 10.1016/0009-2614(96) 00058-9 250, 450 (1996).
    • (1996) Chem. Phys. Lett. , vol.250 , pp. 450
    • Simonson, T.1
  • 31
    • 44949157296 scopus 로고    scopus 로고
    • JPCBFK 1520-6106 10.1021/jp0733163
    • D. Minh and J. McCammon, J. Phys. Chem. B JPCBFK 1520-6106 10.1021/jp0733163 112, 5892 (2008).
    • (2008) J. Phys. Chem. B , vol.112 , pp. 5892
    • Minh, D.1    McCammon, J.2
  • 32
    • 33748269730 scopus 로고    scopus 로고
    • Free energy calculations with non-equilibrium methods: Applications of the Jarzynski relationship
    • DOI 10.1007/s00214-005-0072-2
    • H. Xiong, A. Crespo, M. Marti, D. Estrin, and A. Roitberg, Theor. Chem. Acc. TCACFW 1432-881X 10.1007/s00214-005-0072-2 116, 338 (2006). (Pubitemid 44318435)
    • (2006) Theoretical Chemistry Accounts , vol.116 , Issue.1-3 , pp. 338-346
    • Xiong, H.1    Crespo, A.2    Marti, M.3    Estrin, D.4    Roitberg, A.E.5
  • 35
    • 0026097503 scopus 로고
    • FEBLAL 0014-5793 10.1016/0014-5793(91)80069-F
    • G. von Heijne and K. Nishikawa, FEBS Lett. FEBLAL 0014-5793 10.1016/0014-5793(91)80069-F 278, 1 (1991).
    • (1991) FEBS Lett. , vol.278 , pp. 1
    • Von Heijne, G.1    Nishikawa, K.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.