-
1
-
-
0000619629
-
Generalized-ensemble approach for protein folding simulations
-
In, Edited by: Stauffer, D. Singapore: World Scientific.
-
Hansmann, U.H.E., and, Okamoto, Y. 1999. Generalized-ensemble approach for protein folding simulations. In Annual Reviews of Computational Physics VI, Edited by: Stauffer, D. 129-157. Singapore: World Scientific.
-
(1999)
Annual Reviews of Computational Physics VI
, pp. 129-157
-
-
Hansmann, U.H.E.1
Okamoto, Y.2
-
2
-
-
0034864528
-
Generalized-ensemble algorithms for molecular simulations of biopolymers
-
DOI 10.1002/1097-0282(2001)60:2<96::AID-BIP1007>3.0.CO;2-F
-
Mitsutake, A., Sugita, Y., and, Okamoto, Y. 2001. Generalized-ensemble algorithms for molecular simulations of biopolymers. Biopolymers, 60: 96-123. (Pubitemid 32743528)
-
(2001)
Biopolymers - Peptide Science Section
, vol.60
, Issue.2
, pp. 96-123
-
-
Mitsutake, A.1
Sugita, Y.2
Okamoto, Y.3
-
3
-
-
1942455272
-
Generalized-ensemble algorithms: Enhanced sampling techniques for Monte Carlo and molecular dynamics simulations
-
DOI 10.1016/j.jmgm.2003.12.009, PII S1093326303001980
-
Okamoto, Y. 2004. Generalized-ensemble algorithms: Enhanced sampling techniques for Monte Carlo and molecular dynamics simulations. J. Mol. Graphics Mod., 22: 425-439. e-print: cond-mat/0308360 (Pubitemid 38510308)
-
(2004)
Journal of Molecular Graphics and Modelling
, vol.22
, Issue.5
, pp. 425-439
-
-
Okamoto, Y.1
-
4
-
-
37549026242
-
Generalized-ensemble algorithms for protein folding simulations
-
In, Edited by: Janke, W. Berlin: Springer-Verlag. e-print: arXiv:0707.3382v1[cond-mat.stat-mech]
-
Sugita, Y., Mitsutake, A., and, Okamoto, Y. 2008. Generalized-ensemble algorithms for protein folding simulations. In Lecture Notes in Physics. Rugged Free Energy Landscapes: Common Computational Approaches in Spin Glasses, Structural Glasses and Biological Macromolecules, Edited by: Janke, W. 369-407. Berlin: Springer-Verlag. e-print: arXiv:0707.3382v1[cond-mat.stat-mech]
-
(2008)
Lecture Notes in Physics. Rugged Free Energy Landscapes: Common Computational Approaches in Spin Glasses, Structural Glasses and Biological Macromolecules
, pp. 369-407
-
-
Sugita, Y.1
Mitsutake, A.2
Okamoto, Y.3
-
5
-
-
4243819810
-
New Monte Carlo technique for studying phase transitions
-
Ferrenberg, A.M., and, Swendsen, R.H. 1988. New Monte Carlo technique for studying phase transitions. Phys. Rev. Lett., 61: 2635-2638.
-
(1988)
Phys. Rev. Lett.
, vol.61
, pp. 2635-2638
-
-
Ferrenberg, A.M.1
Swendsen, R.H.2
-
6
-
-
23544469152
-
New Monte Carlo technique for studying phase transitions
-
Ferrenberg, A.M., and, Swendsen, R.H. 1988. New Monte Carlo technique for studying phase transitions. Phys. Rev. Lett., 63: 1658
-
(1988)
Phys. Rev. Lett.
, vol.63
, pp. 1658
-
-
Ferrenberg, A.M.1
Swendsen, R.H.2
-
7
-
-
33646987405
-
Optimized Monte Carlo data analysis
-
Ferrenberg, A.M., and, Swendsen, R.H. 1989. Optimized Monte Carlo data analysis. Phys. Rev. Lett., 63: 1195-1198.
-
(1989)
Phys. Rev. Lett.
, vol.63
, pp. 1195-1198
-
-
Ferrenberg, A.M.1
Swendsen, R.H.2
-
8
-
-
84986519238
-
The weighted histogram analysis method for free-energy calculations on biomolecules. 1. 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. 1. The method. J. Comput. Chem., 13: 1011-1021.
-
(1992)
J. Comput. Chem.
, vol.13
, pp. 1011-1021
-
-
Kumar, S.1
Bouzida, D.2
Swendsen, R.H.3
Kollman, P.A.4
Rosenberg, J.M.5
-
9
-
-
0000106469
-
Multicanonical algorithms for 1st order phase transitions
-
Berg, B.A., and, Neuhaus, T. 1991. Multicanonical algorithms for 1st order phase transitions. Phys. Lett., B267: 249-253.
-
(1991)
Phys. Lett.
, vol.267 B
, pp. 249-253
-
-
Berg, B.A.1
Neuhaus, T.2
-
10
-
-
4243613377
-
Multicanonical ensemble: A new approach to simulate first-order phase transitions
-
Berg, B.A., and, Neuhaus, T. 1992. Multicanonical ensemble: A new approach to simulate first-order phase transitions. Phys. Rev. Lett., 68: 9-12.
-
(1992)
Phys. Rev. Lett.
, vol.68
, pp. 9-12
-
-
Berg, B.A.1
Neuhaus, T.2
-
11
-
-
84953648015
-
New approach to Monte Carlo calculation of the free energy - Method of expanded ensemble
-
Lyubartsev, A.P., Martinovski, A.A., Shevkunov, S.V., and, Vorontsov-Velyaminov, P.N. 1992. New approach to Monte Carlo calculation of the free energy-method of expanded ensemble. J. Chem. Phys., 96: 1776-1783.
-
(1992)
J. Chem. Phys.
, vol.96
, pp. 1776-1783
-
-
Lyubartsev, A.P.1
Martinovski, A.A.2
Shevkunov, S.V.3
Vorontsov-Velyaminov, P.N.4
-
12
-
-
33644899039
-
Simulated tempering - A new Monte Carlo scheme
-
Marinari, E., and, Parisi, G. 1992. Simulated tempering-a new Monte Carlo scheme. Europhys. Lett., 19: 451-458.
-
(1992)
Europhys. Lett.
, vol.19
, pp. 451-458
-
-
Marinari, E.1
Parisi, G.2
-
13
-
-
0030516672
-
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: 1604-1608. (Pubitemid 126456584)
-
(1996)
Journal of the Physical Society of Japan
, vol.65
, Issue.6
, pp. 1604-1608
-
-
Hukushima, K.1
Nemoto, K.2
-
14
-
-
0002795650
-
Markov chain Monte Carlo maximum likelihood
-
In, Edited by: Keramidas, E.M. Fairfax Station, VA: Interface Foundation.
-
Geyer, C.J. 1991. Markov chain Monte Carlo maximum likelihood. In Computing Science and Statistics: Proc. 23rd Symp. on the Interface, Edited by: Keramidas, E.M. 156-163. Fairfax Station, VA: Interface Foundation.
-
(1991)
Computing Science and Statistics: Proc. 23rd Symp. on the Interface
, pp. 156-163
-
-
Geyer, C.J.1
-
15
-
-
6644221271
-
Efficient, multiple-range random walk algorithm to calculate the density of states
-
DOI 10.1103/PhysRevLett.86.2050
-
Wang, F., and, Landau, D.P. 2001. Efficient, multiple-range random walk algorithm to calculate the density of states. Phys. Rev. Lett., 86: 2050-2053. (Pubitemid 32254758)
-
(2001)
Physical Review Letters
, vol.86
, Issue.10
, pp. 2050-2053
-
-
Wang, F.1
Landau, D.P.2
-
16
-
-
39749147672
-
Determining the density of states for classical statistical models: A random walk algorithm to produce a flat histogram
-
Wang, F., and, Landau, D.P. 2001. Determining the density of states for classical statistical models: A random walk algorithm to produce a flat histogram. Phys. Rev. E, 64: 056101
-
(2001)
Phys. Rev. e
, vol.64
, pp. 056101
-
-
Wang, F.1
Landau, D.P.2
-
18
-
-
5744249209
-
Equation of state calculations by fast computing machines
-
Metropolis, N., Rosenbluth, A.W., Rosenbluth, M.N., Teller, A.H., and, Teller, E. 1953. Equation of state calculations by fast computing machines. J. Chem. Phys., 21: 1087-1092.
-
(1953)
J. Chem. Phys.
, vol.21
, pp. 1087-1092
-
-
Metropolis, N.1
Rosenbluth, A.W.2
Rosenbluth, M.N.3
Teller, A.H.4
Teller, E.5
-
19
-
-
84943502952
-
A molecular dynamics method for simulations in the canonical ensemble
-
Nosé, S. 1984. A molecular dynamics method for simulations in the canonical ensemble. Mol. Phys., 52: 255-268.
-
(1984)
Mol. Phys.
, vol.52
, pp. 255-268
-
-
Nosé, S.1
-
20
-
-
34547809547
-
A unified formulation of the constant temperature molecular dynamics methods
-
Nosé, S. 1984. A unified formulation of the constant temperature molecular dynamics methods. J. Chem. Phys., 81: 511-519.
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 511-519
-
-
Nosé, S.1
-
21
-
-
0030572603
-
Molecular dynamics, langevin and hybrid Monte Carlo simulations in a multicanonical ensemble
-
PII S0009261496007610
-
Hansmann, U.H.E., Okamoto, Y., and, Eisenmenger, F. 1996. Molecular dynamics, Langevin and hybrid Monte Carlo simulations in a multicanonical ensemble. Chem. Phys. Lett., 259: 321-330. (Pubitemid 126163255)
-
(1996)
Chemical Physics Letters
, vol.259
, Issue.3-4
, pp. 321-330
-
-
Hansmann, U.H.E.1
Okamoto, Y.2
Eisenmenger, F.3
-
22
-
-
0030819348
-
Multicanonical ensemble generated by molecular dynamics simulation for enhanced conformational sampling of peptides
-
Nakajima, N., Nakamura, H., and, Kidera, A. 1997. Multicanonical ensemble generated by molecular dynamics simulation for enhanced conformational sampling of peptides. J. Phys. Chem. B, 101: 817-824. (Pubitemid 127627951)
-
(1997)
Journal of Physical Chemistry B
, vol.101
, Issue.5
, pp. 817-824
-
-
Nakajima, N.1
Nakamura, H.2
Kidera, A.3
-
23
-
-
0001629677
-
New approach to spin-glass simulations
-
Berg, B.A., and, Celik, T. 1992. New approach to spin-glass simulations. Phys. Rev. Lett., 69: 2292-2295.
-
(1992)
Phys. Rev. Lett.
, vol.69
, pp. 2292-2295
-
-
Berg, B.A.1
Celik, T.2
-
24
-
-
0029342240
-
Thermodynamics of helix-coil transitions studied by multicanonical algorithms
-
Okamoto, Y., and, Hansmann, U.H.E. 1995. Thermodynamics of helix-coil transitions studied by multicanonical algorithms. J. Phys. Chem., 99: 11276-11287.
-
(1995)
J. Phys. Chem.
, vol.99
, pp. 11276-11287
-
-
Okamoto, Y.1
Hansmann, U.H.E.2
-
26
-
-
0001616080
-
Replica-exchange molecular dynamics method for protein folding
-
PII S0009261499011239
-
Sugita, Y., and, Okamoto, Y. 1999. Replica-exchange molecular dynamics method for protein folding. Chem. Phys. Lett., 314: 141-151. (Pubitemid 129556751)
-
(1999)
Chemical Physics Letters
, vol.314
, Issue.1-2
, pp. 141-151
-
-
Sugita, Y.1
Okamoto, Y.2
-
27
-
-
67249165701
-
Multidimensional generalized-ensemble algorithms for complex systems
-
Mitsutake, A., and, Okamoto, Y. 2009. Multidimensional generalized-ensemble algorithms for complex systems. J. Chem. Phys., 130: 214105-1-214105-14.
-
(2009)
J. Chem. Phys.
, vol.130
, pp. 2141051-21410514
-
-
Mitsutake, A.1
Okamoto, Y.2
-
28
-
-
77956248445
-
Generalized-ensemble algorithms for the isobaric-isothermal ensemble
-
Mori, Y., and, Okamoto, Y. 2010. Generalized-ensemble algorithms for the isobaric-isothermal ensemble. J. Phys. Soc. Jpn., 79: 074003-1-074003-5.
-
(2010)
J. Phys. Soc. Jpn.
, vol.79
, pp. 0740031-0740035
-
-
Mori, Y.1
Okamoto, Y.2
-
29
-
-
77956249820
-
Replica-exchange molecular dynamics simulations for various constant temperature algorithms
-
Mori, Y., and, Okamoto, Y. 2010. Replica-exchange molecular dynamics simulations for various constant temperature algorithms. J. Phys. Soc. Jpn., 79: 074001-1-074001-8.
-
(2010)
J. Phys. Soc. Jpn.
, vol.79
, pp. 0740011-0740018
-
-
Mori, Y.1
Okamoto, Y.2
-
30
-
-
0000773431
-
Studies of an off-lattice model for protein folding - Sequence dependence and improved sampling at finite temperature
-
Irbck, A., and, Potthast, F. 1995. Studies of an off-lattice model for protein folding-sequence dependence and improved sampling at finite temperature. J. Chem. Phys., 103: 10298-10305.
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 10298-10305
-
-
Irbck, A.1
Potthast, F.2
-
31
-
-
0142013225
-
Numerical comparisons of three recently proposed algorithms in the protein folding problem
-
Hansmann, U.H.E., and, Okamoto, Y. 1997. Numerical comparisons of three recently proposed algorithms in the protein folding problem. J. Comput. Chem., 18: 920-933. (Pubitemid 127598578)
-
(1997)
Journal of Computational Chemistry
, vol.18
, Issue.7
, pp. 920-933
-
-
Hansmann, U.H.E.1
Okamoto, Y.2
-
32
-
-
0003160962
-
Numerical simulations of spin glass systems
-
In, Edited by: Young, A.P. Singapore: World Scientific.
-
Marinari, E., Parisi, G., and, Ruiz-Lorenzo, J.J. 1997. Numerical simulations of spin glass systems. In Spin Glasses and Random Fields, Edited by: Young, A.P. 59-98. Singapore: World Scientific.
-
(1997)
Spin Glasses and Random Fields
, pp. 59-98
-
-
Marinari, E.1
Parisi, G.2
Ruiz-Lorenzo, J.J.3
-
33
-
-
0037961507
-
Replica-exchange multicanonical and multicanonical replica-exchange Monte Carlo simulations of peptides. I. Formulation and benchmark test
-
Mitsutake, A., Sugita, Y., and, Okamoto, Y. 2003. Replica-exchange multicanonical and multicanonical replica-exchange Monte Carlo simulations of peptides. I. Formulation and benchmark test. J. Chem. Phys., 118: 6664-6675.
-
(2003)
J. Chem. Phys.
, vol.118
, pp. 6664-6675
-
-
Mitsutake, A.1
Sugita, Y.2
Okamoto, Y.3
-
34
-
-
0000888146
-
Replica-exchange multicanonical algorithm and multicanonical replica-exchange method for simulating systems with rough energy landscape
-
Sugita, Y., and, Okamoto, Y. 2000. Replica-exchange multicanonical algorithm and multicanonical replica-exchange method for simulating systems with rough energy landscape. Chem. Phys. Lett., 329: 261-270.
-
(2000)
Chem. Phys. Lett.
, vol.329
, pp. 261-270
-
-
Sugita, Y.1
Okamoto, Y.2
-
35
-
-
0037961506
-
Replica-exchange multicanonical and multicanonical replica-exchange Monte Carlo simulations of peptides. II. Application to a more complex system
-
Mitsutake, A., Sugita, Y., and, Okamoto, Y. 2003. Replica-exchange multicanonical and multicanonical replica-exchange Monte Carlo simulations of peptides. II. Application to a more complex system. J. Chem. Phys., 118: 6676-6688.
-
(2003)
J. Chem. Phys.
, vol.118
, pp. 6676-6688
-
-
Mitsutake, A.1
Sugita, Y.2
Okamoto, Y.3
-
36
-
-
0000855275
-
Replica-exchange simulated tempering method for simulations of frustrated systems
-
Mitsutake, A., and, Okamoto, Y. 2000. Replica-exchange simulated tempering method for simulations of frustrated systems. Chem. Phys. Lett., 332: 131-138.
-
(2000)
Chem. Phys. Lett.
, vol.332
, pp. 131-138
-
-
Mitsutake, A.1
Okamoto, Y.2
-
37
-
-
65549164421
-
From multidimensional replica-exchange method to multidimensional multicanonical algorithm and simulated tempering
-
Mitsutake, A., and, Okamoto, Y. 2009. From multidimensional replica-exchange method to multidimensional multicanonical algorithm and simulated tempering. Phys. Rev. E, 79: 047701-1-047701-4.
-
(2009)
Phys. Rev. e
, vol.79
, pp. 0477011-0477014
-
-
Mitsutake, A.1
Okamoto, Y.2
-
38
-
-
69949183901
-
Simulated-tempering replica-exchange method for the multidimensional version
-
Mitsutake, A. 2009. Simulated-tempering replica-exchange method for the multidimensional version. J. Chem. Phys., 131: 094105-1-094105-15.
-
(2009)
J. Chem. Phys.
, vol.131
, pp. 0941051-09410515
-
-
Mitsutake, A.1
-
39
-
-
0342929614
-
Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
-
Torrie, G.M., and, Valleau, J.P. 1977. Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling. J. Comput. Phys., 23: 187-199.
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 187-199
-
-
Torrie, G.M.1
Valleau, J.P.2
-
40
-
-
0034294024
-
Multidimensional replica-exchange method for free-energy calculations
-
Sugita, Y., Kitao, A., and, Okamoto, Y. 2000. Multidimensional replica-exchange method for free-energy calculations. J. Chem. Phys., 113: 6042-6051.
-
(2000)
J. Chem. Phys.
, vol.113
, pp. 6042-6051
-
-
Sugita, Y.1
Kitao, A.2
Okamoto, Y.3
-
41
-
-
0002307060
-
Simulation of an ensemble with varying magnetic field: A numerical determination of the order-order interface tension in the D=2 Ising model
-
Berg, B.A., Hansmann, U.H.E., and, Neuhaus, T. 1993. Simulation of an ensemble with varying magnetic field: A numerical determination of the order-order interface tension in the D=2 Ising model. Phys. Rev. B, 47: 497-500.
-
(1993)
Phys. Rev. B
, vol.47
, pp. 497-500
-
-
Berg, B.A.1
Hansmann, U.H.E.2
Neuhaus, T.3
-
42
-
-
0001597074
-
Multibondic cluster algorithm for Monte Carlo simulations of first-order phase transitions
-
Janke, W., and, Kappler, S. 1995. Multibondic cluster algorithm for Monte Carlo simulations of first-order phase transitions. Phys. Rev. Lett., 74: 212-215.
-
(1995)
Phys. Rev. Lett.
, vol.74
, pp. 212-215
-
-
Janke, W.1
Kappler, S.2
-
43
-
-
0032285722
-
Simulation of Lattice Polymers with Multi-Self-Overlap Ensemble
-
Iba, Y., Chikenji, G., and, Kikuchi, M. 1998. Simulation of lattice polymers with multi-self-overlap ensemble. J. Phys. Soc. Jpn., 67: 3327-3330. (Pubitemid 128477660)
-
(1998)
Journal of the Physical Society of Japan
, vol.67
, Issue.10
, pp. 3327-3330
-
-
Iba, Y.1
Chikenji, G.2
Kikuchi, M.3
-
44
-
-
0242579552
-
Multioverlap simulations for transitions between reference configurations
-
Berg, B.A., Noguchi, H., and, Okamoto, Y. 2003. Multioverlap simulations for transitions between reference configurations. Phys. Rev. E, 68: 036126-1-036126-11.
-
(2003)
Phys. Rev. e
, vol.68
, pp. 0361261-03612611
-
-
Berg, B.A.1
Noguchi, H.2
Okamoto, Y.3
-
45
-
-
10344247635
-
Multi-overlap molecular dynamics methods for biomolecular systems
-
Itoh, S.G., and, Okamoto, Y. 2004. Multi-overlap molecular dynamics methods for biomolecular systems. Chem. Phys. Lett., 400: 308-313.
-
(2004)
Chem. Phys. Lett.
, vol.400
, pp. 308-313
-
-
Itoh, S.G.1
Okamoto, Y.2
-
46
-
-
1642534558
-
Monte Carlo simulations in multibaric-multithermal ensemble
-
Okumura, H., and, Okamoto, Y. 2004. Monte Carlo simulations in multibaric-multithermal ensemble. Chem. Phys. Lett., 383: 391-396.
-
(2004)
Chem. Phys. Lett.
, vol.383
, pp. 391-396
-
-
Okumura, H.1
Okamoto, Y.2
-
47
-
-
2942550984
-
Molecular dynamics simulations in the multibaric-multithermal ensemble
-
Okumura, H., and, Okamoto, Y. 2004. Molecular dynamics simulations in the multibaric-multithermal ensemble. Chem. Phys. Lett., 391: 248-253.
-
(2004)
Chem. Phys. Lett.
, vol.391
, pp. 248-253
-
-
Okumura, H.1
Okamoto, Y.2
|