메뉴 건너뛰기




Volumn 131, Issue 13, 2009, Pages

Exploration of effective potential landscapes using coarse reverse integration

Author keywords

[No Author keywords available]

Indexed keywords

ARC LENGTH; CLOSED FORM; DETERMINISTIC PROBLEMS; DIFFUSION COEFFICIENTS; EFFECTIVE POTENTIALS; ENERGY LANDSCAPE; EQUATION-FREE; ESTIMATION TECHNIQUES; INTEGRATION APPROACH; SADDLE POINT; SHORT BURSTS; STOCHASTIC SIMULATORS; TRANSITION PATHS;

EID: 70449096437     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3207882     Document Type: Article
Times cited : (16)

References (69)
  • 2
    • 0142236572 scopus 로고    scopus 로고
    • Low mode search. An efficient, automated computational method for conformational analysis: Application to cyclic and acyclic alkanes and cyclic peptides
    • DOI 10.1021/ja952478m
    • I. Kolossvary and W. C. Guida, J. Am. Chem. Soc. 0002-7863 118, 5011 (1996). 10.1021/ja952478m (Pubitemid 26200976)
    • (1996) Journal of the American Chemical Society , vol.118 , Issue.21 , pp. 5011-5019
    • Kolossvary, I.1    Guida, W.C.2
  • 4
    • 6644221271 scopus 로고    scopus 로고
    • Efficient, multiple-range random walk algorithm to calculate the density of states
    • DOI 10.1103/PhysRevLett.86.2050
    • F. Wang and D. Landau, Phys. Rev. Lett. 0031-9007 86, 2050 (2001). 10.1103/PhysRevLett.86.2050 (Pubitemid 32254758)
    • (2001) Physical Review Letters , vol.86 , Issue.10 , pp. 2050-2053
    • Wang, F.1    Landau, D.P.2
  • 6
    • 0036040917 scopus 로고    scopus 로고
    • Extending the time scale in atomistic simulation of materials
    • DOI 10.1146/annurev.matsci.32.112601.141541
    • A. F. Voter, F. Montalenti, and T. C. Germann, Annu. Rev. Mater. Res. 1531-7331 32, 321 (2002). 10.1146/annurev.matsci.32.112601.141541 (Pubitemid 34992574)
    • (2002) Annual Review of Materials Science , vol.32 , pp. 321-346
    • Voter, A.F.1    Montalenti, F.2    Germann, T.C.3
  • 7
    • 0037104864 scopus 로고    scopus 로고
    • 'Coarse' integration/bifurcation analysis via microscopic simulators: Micro-Galerkin methods
    • DOI 10.1016/S0098-1354(02)00020-0, PII S0098135402000200
    • C. W. Gear, I. G. Kevrekidis, and C. Theodoropoulos, Comput. Chem. Eng. 0098-1354 26, 941 (2002). 10.1016/S0098-1354(02)00020-0 (Pubitemid 36076773)
    • (2002) Computers and Chemical Engineering , vol.26 , Issue.7-8 , pp. 941-963
    • Gear, C.W.1    Kevrekidis, I.G.2    Theodoropoulos, C.3
  • 8
    • 0037865691 scopus 로고    scopus 로고
    • 0021-9606, 10.1063/1.1574777
    • G. Hummer and I. G. Kevrekidis, J. Chem. Phys. 0021-9606 118, 10762 (2003). 10.1063/1.1574777
    • (2003) J. Chem. Phys. , vol.118 , pp. 10762
    • Hummer, G.1    Kevrekidis, I.G.2
  • 11
    • 0035935802 scopus 로고    scopus 로고
    • Calculating free energies using average force
    • DOI 10.1063/1.1410978
    • E. Darve and A. Pohorille, J. Chem. Phys. 0021-9606 115, 9169 (2001). 10.1063/1.1410978 (Pubitemid 33128021)
    • (2001) Journal of Chemical Physics , vol.115 , Issue.20 , pp. 9169-9183
    • Darve, E.1    Pohorille, A.2
  • 12
    • 29744459271 scopus 로고    scopus 로고
    • Exploring the free-energy landscape of a short peptide using an average force
    • DOI 10.1063/1.2138694, 244906
    • C. Chipot and J. Henin, J. Chem. Phys. 0021-9606 123, 244906 (2005). 10.1063/1.2138694 (Pubitemid 43032198)
    • (2005) Journal of Chemical Physics , vol.123 , Issue.24 , pp. 1-6
    • Chipot, C.1    Henin, J.2
  • 14
    • 16844362197 scopus 로고    scopus 로고
    • 0021-9991, 10.1016/j.jc2004.11.003
    • T. S. van Erp and P. G. Bolhuis, J. Comput. Phys. 0021-9991 205, 157 (2005). 10.1016/j.jcp.2004.11.003
    • (2005) J. Comput. Phys. , vol.205 , pp. 157
    • Van Erp, T.S.1    Bolhuis, P.G.2
  • 15
    • 84988122931 scopus 로고
    • 0192-8651, 10.1002/jcc.540070402
    • J. Baker, J. Comput. Chem. 0192-8651 7, 385 (1986). 10.1002/jcc.540070402
    • (1986) J. Comput. Chem. , vol.7 , pp. 385
    • Baker, J.1
  • 16
    • 0000564001 scopus 로고
    • 0022-3654, 10.1021/j100250a026
    • H. Taylor and J. Simons, J. Phys. Chem. 0022-3654 89, 684 (1985). 10.1021/j100250a026
    • (1985) J. Phys. Chem. , vol.89 , pp. 684
    • Taylor, H.1    Simons, J.2
  • 17
    • 36749114393 scopus 로고
    • 0021-9606, 10.1063/1.442352
    • C. J. Cerjan and W. H. Miller, J. Chem. Phys. 0021-9606 75, 2800 (1981). 10.1063/1.442352
    • (1981) J. Chem. Phys. , vol.75 , pp. 2800
    • Cerjan, C.J.1    Miller, W.H.2
  • 18
    • 49549139879 scopus 로고
    • 0009-2614, 10.1016/0009-2614(75)85665-X
    • D. Poppinger, Chem. Phys. Lett. 0009-2614 34, 332 (1975). 10.1016/0009-2614(75)85665-X
    • (1975) Chem. Phys. Lett. , vol.34 , pp. 332
    • Poppinger, D.1
  • 19
    • 0009355757 scopus 로고    scopus 로고
    • 0009-2614, 10.1016/S0009-2614(98)00698-8
    • H. Goto, Chem. Phys. Lett. 0009-2614 292, 254 (1998). 10.1016/S0009-2614(98)00698-8
    • (1998) Chem. Phys. Lett. , vol.292 , pp. 254
    • Goto, H.1
  • 20
    • 36549103570 scopus 로고
    • 0021-9606, 10.1063/1.454172
    • M. Page and J. McIver, J. Chem. Phys. 0021-9606 88, 922 (1988). 10.1063/1.454172
    • (1988) J. Chem. Phys. , vol.88 , pp. 922
    • Page, M.1    McIver, J.2
  • 21
  • 22
    • 0000560755 scopus 로고
    • 0021-9606, 10.1063/1.465100
    • I. V. Ionova and E. A. Carter, J. Chem. Phys. 0021-9606 98, 6377 (1993). 10.1063/1.465100
    • (1993) J. Chem. Phys. , vol.98 , pp. 6377
    • Ionova, I.V.1    Carter, E.A.2
  • 23
    • 0035891086 scopus 로고    scopus 로고
    • The step and slide method for finding saddle points on multidimensional potential surfaces
    • DOI 10.1063/1.1412285
    • R. A. Miron and K. A. Fichthorn, J. Chem. Phys. 0021-9606 115, 8742 (2001). 10.1063/1.1412285 (Pubitemid 33099583)
    • (2001) Journal of Chemical Physics , vol.115 , Issue.19 , pp. 8742-8747
    • Miron, R.A.1    Fichthorn, K.A.2
  • 24
    • 0000327364 scopus 로고    scopus 로고
    • 0021-9606, 10.1063/1.480097
    • G. Henkelman and H. Jonsson, J. Chem. Phys. 0021-9606 111, 7010 (1999). 10.1063/1.480097
    • (1999) J. Chem. Phys. , vol.111 , pp. 7010
    • Henkelman, G.1    Jonsson, H.2
  • 26
    • 0000603016 scopus 로고
    • 0009-2614, 10.1016/0009-2614(87)80576-6
    • R. Elber and M. Karplus, Chem. Phys. Lett. 0009-2614 139, 375 (1987). 10.1016/0009-2614(87)80576-6
    • (1987) Chem. Phys. Lett. , vol.139 , pp. 375
    • Elber, R.1    Karplus, M.2
  • 27
    • 36449008311 scopus 로고
    • 0021-9606, 10.1063/1.463163
    • R. Gillilan and K. Wilson, J. Chem. Phys. 0021-9606 97, 1757 (1992). 10.1063/1.463163
    • (1992) J. Chem. Phys. , vol.97 , pp. 1757
    • Gillilan, R.1    Wilson, K.2
  • 28
    • 0034513054 scopus 로고    scopus 로고
    • Climbing image nudged elastic band method for finding saddle points and minimum energy paths
    • DOI 10.1063/1.1329672
    • G. Henkelman, B. Uberuaga, and H. Jonsson, J. Chem. Phys. 0021-9606 113, 9901 (2000). 10.1063/1.1329672 (Pubitemid 32076883)
    • (2000) Journal of Chemical Physics , vol.113 , Issue.22 , pp. 9901-9904
    • Henkelman, G.1    Uberuaga, B.P.2    Jonsson, H.3
  • 29
    • 1442282189 scopus 로고    scopus 로고
    • 0021-9606, 10.1063/1.1636455
    • S. Trygubenko and D. Wales, J. Chem. Phys. 0021-9606 120, 2082 (2004). 10.1063/1.1636455
    • (2004) J. Chem. Phys. , vol.120 , pp. 2082
    • Trygubenko, S.1    Wales, D.2
  • 30
    • 0036696910 scopus 로고    scopus 로고
    • 0163-1829, 10.1103/PhysRevB.66.052301
    • W. E, W. Ren, and E. Vanden-Eijnden, Phys. Rev. B 0163-1829 66, 052301 (2002). 10.1103/PhysRevB.66.052301
    • (2002) Phys. Rev. B , vol.66 , pp. 052301
    • Ren, W.1    Vanden-Eijnden, E.2
  • 33
    • 6944257068 scopus 로고    scopus 로고
    • 0925-5001, 10.1023/B:JOGO.0000044771.25100.2d
    • A. Lucia, P. A. DiMaggio, and P. Depa, J. Global Optim. 0925-5001 29, 297 (2004). 10.1023/B:JOGO.0000044771.25100.2d
    • (2004) J. Global Optim. , vol.29 , pp. 297
    • Lucia, A.1    Dimaggio, P.A.2    Depa, P.3
  • 34
    • 0037093312 scopus 로고    scopus 로고
    • Global terrain methods
    • DOI 10.1016/S0098-1354(01)00777-3, PII S0098135401007773
    • A. Lucia and F. Yang, Comput. Chem. Eng. 0098-1354 26, 529 (2002). 10.1016/S0098-1354(01)00777-3 (Pubitemid 34552707)
    • (2002) Computers and Chemical Engineering , vol.26 , Issue.4-5 , pp. 529-546
    • Lucia, A.1    Feng, Y.2
  • 35
    • 3042720018 scopus 로고    scopus 로고
    • Equation-free: The computer-aided analysis of complex multiscale systems
    • DOI 10.1002/aic.10106
    • I. G. Kevrekidis, C. W. Gear, and G. Hummer, AIChE J. 0001-1541 50, 1346 (2004). 10.1002/aic.10106 (Pubitemid 38856761)
    • (2004) AIChE Journal , vol.50 , Issue.7 , pp. 1346-1355
    • Kevrekidis, I.G.1    Gear, C.W.2    Hummer, G.3
  • 37
    • 1042300990 scopus 로고    scopus 로고
    • 0375-9601, 10.1016/j.physleta.2003.12.041
    • C. W. Gear and I. G. Kevrekidis, Phys. Lett. A 0375-9601 321, 335 (2004). 10.1016/j.physleta.2003.12.041
    • (2004) Phys. Lett. A , vol.321 , pp. 335
    • Gear, C.W.1    Kevrekidis, I.G.2
  • 39
    • 33644887761 scopus 로고    scopus 로고
    • Computing invariant manifolds by integrating fat trajectories
    • DOI 10.1137/040602894
    • M. Henderson, SIAM J. Appl. Dyn. Syst. 1536-0040 4, 832 (2005). 10.1137/040602894 (Pubitemid 43385152)
    • (2005) SIAM Journal on Applied Dynamical Systems , vol.4 , Issue.4 , pp. 832-882
    • Hendersont, M.E.1
  • 45
    • 0034704849 scopus 로고    scopus 로고
    • 1089-5639, 10.1021/jp992557a
    • K. Irikura and R. Johnson, J. Phys. Chem. A 1089-5639 104, 2191 (2000). 10.1021/jp992557a
    • (2000) J. Phys. Chem. A , vol.104 , pp. 2191
    • Irikura, K.1    Johnson, R.2
  • 49
    • 0004236801 scopus 로고
    • Monographs on Statistics and Applied Probability (Chapman and Hall, London).
    • M. P. Wand, Kernel Smoothing, Monographs on Statistics and Applied Probability (Chapman and Hall, London, 1995).
    • (1995) Kernel Smoothing
    • Wand, M.P.1
  • 50
    • 0001601301 scopus 로고
    • 0021-9002, 10.2307/3212214
    • D. A. McQuarrie, J. Appl. Probab. 0021-9002 4, 413 (1967). 10.2307/3212214
    • (1967) J. Appl. Probab. , vol.4 , pp. 413
    • McQuarrie, D.A.1
  • 51
    • 33645429016 scopus 로고
    • 0022-3654, 10.1021/j100540a008
    • D. Gillespie, J. Phys. Chem. 0022-3654 81, 2340 (1977). 10.1021/j100540a008
    • (1977) J. Phys. Chem. , vol.81 , pp. 2340
    • Gillespie, D.1
  • 52
    • 0035933994 scopus 로고    scopus 로고
    • 0021-9606, 10.1063/1.1378322
    • D. Gillespie, J. Chem. Phys. 0021-9606 115, 1716 (2001). 10.1063/1.1378322
    • (2001) J. Chem. Phys. , vol.115 , pp. 1716
    • Gillespie, D.1
  • 53
    • 22944477377 scopus 로고    scopus 로고
    • The numerical stability of leaping methods for stochastic simulation of chemically reacting systems
    • DOI 10.1063/1.1823412
    • Y. Cao, L. R. Petzold, M. Rathinam, and D. T. Gillespie, J. Chem. Phys. 0021-9606 121, 12169 (2004). 10.1063/1.1823412 (Pubitemid 41041575)
    • (2004) Journal of Chemical Physics , vol.121 , Issue.24 , pp. 12169-12178
    • Cao, Y.1    Petzold, L.R.2    Rathinam, M.3    Gillespie, D.T.4
  • 54
    • 0018456521 scopus 로고
    • 0002-7863, 10.1021/ja00502a001
    • P. J. Rossky and M. Karplus, J. Am. Chem. Soc. 0002-7863 101, 1913 (1979). 10.1021/ja00502a001
    • (1979) J. Am. Chem. Soc. , vol.101 , pp. 1913
    • Rossky, P.J.1    Karplus, M.2
  • 56
  • 58
    • 23244438863 scopus 로고    scopus 로고
    • Position-dependent diffusion coefficients and free energies from Bayesian analysis of equilibrium and replica molecular dynamics simulations
    • DOI 10.1088/1367-2630/7/1/034, PII S136726300587003X
    • G. Hummer, New J. Phys. 1367-2630 7, 34 (2005). 10.1088/1367-2630/7/1/034 (Pubitemid 41093480)
    • (2005) New Journal of Physics , vol.7
    • Hummer, G.1
  • 62
    • 0000577041 scopus 로고
    • 0031-9007, 10.1103/PhysRevLett.68.2696
    • A. E. García, Phys. Rev. Lett. 0031-9007 68, 2696 (1992). 10.1103/PhysRevLett.68.2696
    • (1992) Phys. Rev. Lett. , vol.68 , pp. 2696
    • García, A.E.1
  • 68
    • 85101445097 scopus 로고
    • Wiley Series in Probability and Mathematical Statistics (Wiley, New York).
    • N. R. Draper and H. Smith, Applied Regression Analysis, Wiley Series in Probability and Mathematical Statistics (Wiley, New York, 1981).
    • (1981) Applied Regression Analysis
    • Draper, N.R.1    Smith, H.2
  • 69
    • 0036216388 scopus 로고    scopus 로고
    • 0012-9682, 10.1111/1468-0262.00274
    • Y. Ait-Sahalia, Econometrica 0012-9682 70, 223 (2002). 10.1111/1468-0262.00274
    • (2002) Econometrica , vol.70 , pp. 223
    • Ait-Sahalia, Y.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.