-
1
-
-
0346946971
-
Verlet-I/r-RESPA/Impulse is limited by non-linear instabilities
-
Q. Ma, J.A. Izaguirre, and R.D. Skeel Verlet-I/r-RESPA/Impulse is limited by non-linear instabilities SIAM J Comput 24 2003 1951 1973 An interesting negative paper suggesting that we are at a 'theoretical limit' with regard to solving initial value problems.
-
(2003)
SIAM J Comput
, vol.24
, pp. 1951-1973
-
-
Ma, Q.1
Izaguirre, J.A.2
Skeel, R.D.3
-
2
-
-
33646650705
-
Reversible multiple time scale molecular dynamics
-
M. Tuckerman, B.J. Berne, and G.J. Martyna Reversible multiple time scale molecular dynamics J Chem Phys 97 1992 1990 2001
-
(1992)
J Chem Phys
, vol.97
, pp. 1990-2001
-
-
Tuckerman, M.1
Berne, B.J.2
Martyna, G.J.3
-
3
-
-
0037439858
-
Inherent speedup limitations in multiple time step/particle mesh Ewald algorithms
-
D. Barash, L.J. Yang, X. Qian, and T. Schlick Inherent speedup limitations in multiple time step/particle mesh Ewald algorithms J Comput Chem 24 2003 77 88
-
(2003)
J Comput Chem
, vol.24
, pp. 77-88
-
-
Barash, D.1
Yang, L.J.2
Qian, X.3
Schlick, T.4
-
4
-
-
0141792364
-
Allosteric changes in protein structure computed by a simple mechanical model: Hemoglobin T<->R2 transition
-
C. Xu, D. Tobi, and I. Bahar Allosteric changes in protein structure computed by a simple mechanical model: hemoglobin T<->R2 transition J Mol Biol 333 2003 153 168 A new interesting direction for elastic networks. The authors attempt to interpolate between quadratic basins of elastic networks to estimate directions of transitional events. Although such interpolations were used in the past with harmonic analysis of atomic models, the extension and success of drastically simplified models is intriguing.
-
(2003)
J Mol Biol
, vol.333
, pp. 153-168
-
-
Xu, C.1
Tobi, D.2
Bahar, I.3
-
5
-
-
0000197372
-
Large amplitude elastic motions in proteins from a single parameter atomic analysis
-
M.M. Tirion Large amplitude elastic motions in proteins from a single parameter atomic analysis Phys Rev Lett 77 1996 1905 1908
-
(1996)
Phys Rev Lett
, vol.77
, pp. 1905-1908
-
-
Tirion, M.M.1
-
6
-
-
0030729453
-
Efficient characterization of collective motions and interresidue correlations in proteins by low resolution simulations
-
I. Bahar, B. Erman, T. Haliloglu, and R.L. Jernigan Efficient characterization of collective motions and interresidue correlations in proteins by low resolution simulations Biochemistry 36 1997 13512 13523
-
(1997)
Biochemistry
, vol.36
, pp. 13512-13523
-
-
Bahar, I.1
Erman, B.2
Haliloglu, T.3
Jernigan, R.L.4
-
7
-
-
2142716831
-
Theoretical analysis of twist/bond ratio and mechanical moduli of bacterial flagellar and filament
-
T.C. Flynn, and J.P. Ma Theoretical analysis of twist/bond ratio and mechanical moduli of bacterial flagellar and filament Biophys J 86 2004 3204 3210 An amusing application of a continuum/elastic description to a system that goes beyond typical molecular scales.
-
(2004)
Biophys J
, vol.86
, pp. 3204-3210
-
-
Flynn, T.C.1
Ma, J.P.2
-
8
-
-
0023140044
-
Multiple conformational states of proteins: A molecular dynamics analysis of myoglobin
-
R. Elber, and M. Karplus Multiple conformational states of proteins: a molecular dynamics analysis of myoglobin Science 235 1987 318 321
-
(1987)
Science
, vol.235
, pp. 318-321
-
-
Elber, R.1
Karplus, M.2
-
9
-
-
0001756405
-
An efficient deformation-based global optimization method for off-lattice polymer chains: Self-consistent basin-to-deformed-basin mapping (SCBDBM). Application to united-residue polypeptide chains
-
J. Pillardy, A. Liwo, M. Groth, and H.A. Scheraga An efficient deformation-based global optimization method for off-lattice polymer chains: self-consistent basin-to-deformed-basin mapping (SCBDBM). Application to united-residue polypeptide chains J Phys Chem B 103 1999 7353 7366
-
(1999)
J Phys Chem B
, vol.103
, pp. 7353-7366
-
-
Pillardy, J.1
Liwo, A.2
Groth, M.3
Scheraga, H.A.4
-
10
-
-
0000726792
-
Global optimization using bad derivatives: Derivative-free method for molecular energy minimization
-
I. Andricioaei, and J.E. Straub Global optimization using bad derivatives: derivative-free method for molecular energy minimization J Comput Chem 19 1998 1445 1455
-
(1998)
J Comput Chem
, vol.19
, pp. 1445-1455
-
-
Andricioaei, I.1
Straub, J.E.2
-
11
-
-
0036679628
-
Gravitational smoothing as a global optimization strategy
-
T.W. Whitfield, and J.E. Straub Gravitational smoothing as a global optimization strategy J Comput Chem 23 2002 1100 1103
-
(2002)
J Comput Chem
, vol.23
, pp. 1100-1103
-
-
Whitfield, T.W.1
Straub, J.E.2
-
12
-
-
0035933131
-
Top-down free-energy minimization on protein potential energy landscapes
-
B.W. Church, and D. Shalloway Top-down free-energy minimization on protein potential energy landscapes Proc Natl Acad Sci USA 98 2001 6098 6103
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 6098-6103
-
-
Church, B.W.1
Shalloway, D.2
-
13
-
-
0342929614
-
Non-physical sampling distributions in Monte-Carlo free energy estimation - Umbrella sampling
-
G.M. Torrie, and J.P. Valleau Non-physical sampling distributions in Monte-Carlo free energy estimation - umbrella sampling J Comput Phys 23 1977 187
-
(1977)
J Comput Phys
, vol.23
, pp. 187
-
-
Torrie, G.M.1
Valleau, J.P.2
-
14
-
-
0037326187
-
Solution effects and the order of the helix-coil transition in polyalanine
-
Y. Peng, U.H. Hansmann, and N.A. Alves Solution effects and the order of the helix-coil transition in polyalanine J Chem Phys 118 2003 2374 2380
-
(2003)
J Chem Phys
, vol.118
, pp. 2374-2380
-
-
Peng, Y.1
Hansmann, U.H.2
Alves, N.A.3
-
15
-
-
0037961507
-
Replica-exhange multicanonical and multicanonical replica exchange Monte Carlo simulations of peptides. I. Formulation and benchmarks
-
A. Mitsutake, Y. Sugita, and Y. Okamoto Replica-exhange multicanonical and multicanonical replica exchange Monte Carlo simulations of peptides. I. Formulation and benchmarks J Chem Phys 118 2003 6664 6675
-
(2003)
J Chem Phys
, vol.118
, pp. 6664-6675
-
-
Mitsutake, A.1
Sugita, Y.2
Okamoto, Y.3
-
16
-
-
0034337332
-
Protein folding simulations by simulated annealing and generalized-ensemble algorithms
-
Y. Okamoto Protein folding simulations by simulated annealing and generalized-ensemble algorithms Progress of Theoretical Physics Supplement 138 2000 301 310
-
(2000)
Progress of Theoretical Physics Supplement
, vol.138
, pp. 301-310
-
-
Okamoto, Y.1
-
17
-
-
0037080723
-
Predicting unimolecular chemical reactions: Chemical flooding
-
E.M. Muller, A. de Meijere, and H. Grubmüller Predicting unimolecular chemical reactions: chemical flooding J Chem Phys 116 2002 897 905
-
(2002)
J Chem Phys
, vol.116
, pp. 897-905
-
-
Muller, E.M.1
De Meijere, A.2
Grubmüller, H.3
-
18
-
-
0036040917
-
Extending the time scale in atomistic simulation of materials
-
A.F. Voter, F. Montalenti, and T.C. Germann Extending the time scale in atomistic simulation of materials Annu Rev Mater Res 32 2002 321 346
-
(2002)
Annu Rev Mater Res
, vol.32
, pp. 321-346
-
-
Voter, A.F.1
Montalenti, F.2
Germann, T.C.3
-
19
-
-
3142716857
-
Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules
-
D. Hamelberg, J. Mongan, and J.A. McCammon Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules J Chem Phys 120 2004 11919 11929
-
(2004)
J Chem Phys
, vol.120
, pp. 11919-11929
-
-
Hamelberg, D.1
Mongan, J.2
McCammon, J.A.3
-
20
-
-
0000220710
-
Nudge elastic band method for finding minimum energy paths of transitions
-
B.J. Berne G. Ciccotti D.F. Coker World Scientific
-
H. Jonsson, G. Mills, and K.W. Jacobsen Nudge elastic band method for finding minimum energy paths of transitions B.J. Berne G. Ciccotti D.F. Coker Classical and Quantum Dynamics in Condensed Phase Simulations 1998 World Scientific 385
-
(1998)
Classical and Quantum Dynamics in Condensed Phase Simulations
, pp. 385
-
-
Jonsson, H.1
Mills, G.2
Jacobsen, K.W.3
-
21
-
-
0942268404
-
A super-linear minimization scheme for the nudged elastic band method
-
J.W. Chu, B.L. Trout, and B.R. Brooks A super-linear minimization scheme for the nudged elastic band method J Chem Phys 119 2003 12708 12717
-
(2003)
J Chem Phys
, vol.119
, pp. 12708-12717
-
-
Chu, J.W.1
Trout, B.L.2
Brooks, B.R.3
-
23
-
-
3042660129
-
A statistical-method for identifying transition-states in high dimensional problems
-
L.R. Pratt A statistical-method for identifying transition-states in high dimensional problems J Chem Phys 85 1986 5045 5048
-
(1986)
J Chem Phys
, vol.85
, pp. 5045-5048
-
-
Pratt, L.R.1
-
24
-
-
0000603016
-
A method for determining reaction paths in large molecules: Application to myoglobin
-
R. Elber, and M. Karplus A method for determining reaction paths in large molecules: application to myoglobin Chem Phys Lett 139 1987 375 380
-
(1987)
Chem Phys Lett
, vol.139
, pp. 375-380
-
-
Elber, R.1
Karplus, M.2
-
25
-
-
35248857016
-
A new technique to calculate steepest descent paths in flexible polyatomic systems
-
A. Ulitsky, and R. Elber A new technique to calculate steepest descent paths in flexible polyatomic systems J Chem Phys 92 1990 1510 1511
-
(1990)
J Chem Phys
, vol.92
, pp. 1510-1511
-
-
Ulitsky, A.1
Elber, R.2
-
26
-
-
84987058840
-
Self-avoiding walk between 2 fixed-points as a tool to calculate reaction paths in large molecular-systems
-
R. Czerminski, and R. Elber Self-avoiding walk between 2 fixed-points as a tool to calculate reaction paths in large molecular-systems Int J Quantum Chem 24 1990 167 186
-
(1990)
Int J Quantum Chem
, vol.24
, pp. 167-186
-
-
Czerminski, R.1
Elber, R.2
-
27
-
-
4243691221
-
Yet another look at the steepest descent path
-
R. Olender, and R. Elber Yet another look at the steepest descent path J Mol Struct THEOCHEM 398 1997 63 71
-
(1997)
J Mol Struct THEOCHEM
, vol.398
, pp. 63-71
-
-
Olender, R.1
Elber, R.2
-
28
-
-
17044437988
-
Metastability, conformational dynamics, and transition pathways in complex systems
-
S. Attinger P. Koumoutsakos Springer
-
E. Weinan, and E. Vanden Eijnden Metastability, conformational dynamics, and transition pathways in complex systems S. Attinger P. Koumoutsakos Multiscale Modelling and Simulation vol 39 2004 Springer 35 68 [Series: Lecture Notes in Computational Science and Engineering]
-
(2004)
Multiscale Modelling and Simulation
, vol.39
, pp. 35-68
-
-
Weinan, E.1
Vanden Eijnden, E.2
-
29
-
-
0000055722
-
Diffusion-controlled reactions: A variational formula for the optimum reaction coordinate
-
M. Berkowitz, J.D. Morgan, J.A. McCammon, and J.H. Northrup Diffusion-controlled reactions: a variational formula for the optimum reaction coordinate J Chem Phys 79 1983 5563 5565
-
(1983)
J Chem Phys
, vol.79
, pp. 5563-5565
-
-
Berkowitz, M.1
Morgan, J.D.2
McCammon, J.A.3
Northrup, J.H.4
-
30
-
-
0242336065
-
Temperature dependent reaction coordinates
-
R. Elber, and D. Shalloway Temperature dependent reaction coordinates J Chem Phys 128 2000 118 127
-
(2000)
J Chem Phys
, vol.128
, pp. 118-127
-
-
Elber, R.1
Shalloway, D.2
-
31
-
-
0031256658
-
The MaxFlux algorithm for calculating variationally optimized reaction paths for conformational transitions in many body systems at finite temperature
-
S.H. Huo, and J.E. Straub The MaxFlux algorithm for calculating variationally optimized reaction paths for conformational transitions in many body systems at finite temperature J Chem Phys 107 1997 5000 5006
-
(1997)
J Chem Phys
, vol.107
, pp. 5000-5006
-
-
Huo, S.H.1
Straub, J.E.2
-
32
-
-
0012021417
-
Calculation of classical trajectories with a very large time step: Formalism and numerical examples
-
R. Olender, and R. Elber Calculation of classical trajectories with a very large time step: formalism and numerical examples J Chem Phys 105 1996 9299 9315
-
(1996)
J Chem Phys
, vol.105
, pp. 9299-9315
-
-
Olender, R.1
Elber, R.2
-
33
-
-
78751663166
-
Bridging the gap between reaction pathways, long time dynamics and calculation of rates
-
R. Elber, A. Ghosh, A. Cardenas, and H. Stern Bridging the gap between reaction pathways, long time dynamics and calculation of rates Adv Chem Phys 126 2003 93 129
-
(2003)
Adv Chem Phys
, vol.126
, pp. 93-129
-
-
Elber, R.1
Ghosh, A.2
Cardenas, A.3
Stern, H.4
-
34
-
-
0037326677
-
A concerted variational strategy for investigating rare events
-
D. Passerone, M. Ceccarelli, and M. Parrinello A concerted variational strategy for investigating rare events J Chem Phys 118 2003 2025 2032
-
(2003)
J Chem Phys
, vol.118
, pp. 2025-2032
-
-
Passerone, D.1
Ceccarelli, M.2
Parrinello, M.3
-
35
-
-
0344407048
-
Kinetics of cytochrome c folding: Atomically detailed simulations
-
A.E. Cardenas, and R. Elber Kinetics of cytochrome c folding: atomically detailed simulations Proteins 51 2003 245 257 This study presents approximate atomically detailed molecular dynamics trajectories for a highly complex folding process, with significant success in reproducing the order of events in protein folding.
-
(2003)
Proteins
, vol.51
, pp. 245-257
-
-
Cardenas, A.E.1
Elber, R.2
-
36
-
-
0242353856
-
Atomically detailed simulations of helix formation with the stochastic difference equation
-
A. Cardenas, and R. Elber Atomically detailed simulations of helix formation with the stochastic difference equation Biophys J 85 2003 2919 2939
-
(2003)
Biophys J
, vol.85
, pp. 2919-2939
-
-
Cardenas, A.1
Elber, R.2
-
37
-
-
0036424048
-
Transition path sampling: Throwing ropes over rough mountain passes, in the dark
-
P.G. Bolhuis, D. Chandler, C. Dellago, and P.L. Geissler Transition path sampling: throwing ropes over rough mountain passes, in the dark Annu Rev Phys Chem 53 2002 291 318
-
(2002)
Annu Rev Phys Chem
, vol.53
, pp. 291-318
-
-
Bolhuis, P.G.1
Chandler, D.2
Dellago, C.3
Geissler, P.L.4
-
38
-
-
0000729781
-
Transition path sampling and the calculation of rate constants
-
C. Dellago, P.G. Bolhuis, F.S. Csajka, and D. Chandler Transition path sampling and the calculation of rate constants J Chem Phys 108 1998 1964 1977
-
(1998)
J Chem Phys
, vol.108
, pp. 1964-1977
-
-
Dellago, C.1
Bolhuis, P.G.2
Csajka, F.S.3
Chandler, D.4
-
39
-
-
0142027789
-
Transition-path sampling of beta-hairpin folding
-
P.G. Bolhuis Transition-path sampling of beta-hairpin folding Proc Natl Acad Sci USA 100 2003 12129 12134 A most impressive application of the transition path sampling approach to the folding of a model peptide (β hairpin).
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 12129-12134
-
-
Bolhuis, P.G.1
-
40
-
-
1942437505
-
Orchestration of cooperative events in DNA synthesis and repair mechanism unraveled by transition path sampling of DNA polymerase beta's closing
-
R. Radhakrishnan, and T. Schlick Orchestration of cooperative events in DNA synthesis and repair mechanism unraveled by transition path sampling of DNA polymerase beta's closing Proc Natl Acad Sci USA 101 2004 5970 5975
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 5970-5975
-
-
Radhakrishnan, R.1
Schlick, T.2
-
42
-
-
1842581318
-
Rate constants for diffusive processes by partial path sampling
-
• ] suggest a novel and interesting way to deal with corrugated surfaces with many, but relatively small, barriers that lead to long-timescale diffusion processes. An example of a study appropriate to this approach is the first step in protein folding, which includes chain collapse to the molten globule state.
-
(2004)
J Chem Phys
, vol.120
, pp. 4055-4065
-
-
Moroni, D.1
Bolhuis, P.G.2
Van Erp, T.S.3
-
43
-
-
2342448436
-
Simulations of the role of water in the protein folding mechanism
-
V.S. Pande Simulations of the role of water in the protein folding mechanism Proc Natl Acad Sci USA 101 2004 6456 6461 An impressive and computationally expensive study of the role of waters in protein folding, using tens of thousands of independent trajectories on the author's unique computational resource.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 6456-6461
-
-
Pande, V.S.1
-
44
-
-
0037388193
-
Meeting halfway on the bridge between protein folding theory and experiment
-
V.S. Pande Meeting halfway on the bridge between protein folding theory and experiment Proc Natl Acad Sci USA 100 2003 3555 3556
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 3555-3556
-
-
Pande, V.S.1
-
45
-
-
0037235952
-
Atomistic protein folding simulations on the sub millisecond time scale using worldwide distributed computing
-
V.S. Pande, I. Baker, J. Chapman, S.P. Elmer, S. Khaliq, S.M. Larson, Y.M. Rhee, M.R. Shirts, C.D. Snow, and E.J. Sorin Atomistic protein folding simulations on the sub millisecond time scale using worldwide distributed computing Biopolymers 68 2003 91 109
-
(2003)
Biopolymers
, vol.68
, pp. 91-109
-
-
Pande, V.S.1
Baker, I.2
Chapman, J.3
Elmer, S.P.4
Khaliq, S.5
Larson, S.M.6
Rhee, Y.M.7
Shirts, M.R.8
Snow, C.D.9
Sorin, E.J.10
-
46
-
-
0141990949
-
Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force field for proteins
-
M.R. Shirts, J.W. Pitera, W.C. Swope, and V.S. Pande Extremely precise free energy calculations of amino acid side chain analogs: comparison of common molecular mechanics force field for proteins J Chem Phys 119 2003 5740 5761
-
(2003)
J Chem Phys
, vol.119
, pp. 5740-5761
-
-
Shirts, M.R.1
Pitera, J.W.2
Swope, W.C.3
Pande, V.S.4
-
47
-
-
0036892389
-
Thoroughly sampling sequence space: Large-scale protein design of structural ensembles
-
S.M. Larson, J.L. England, J.R. Desjarlais, and V.S. Pande Thoroughly sampling sequence space: large-scale protein design of structural ensembles Protein Sci 11 2002 2804 2813
-
(2002)
Protein Sci
, vol.11
, pp. 2804-2813
-
-
Larson, S.M.1
England, J.L.2
Desjarlais, J.R.3
Pande, V.S.4
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