-
1
-
-
0035932735
-
Smart darting Monte Carlo
-
ANDRICIOAEI, J. STRAUB, AND A. VOTER, Smart darting Monte Carlo, J. Chem. Phys., 114 (2001), pp. 6994-7000.
-
(2001)
J. Chem. Phys
, vol.114
, pp. 6994-7000
-
-
ANDRICIOAEI1
STRAUB, J.2
VOTER, A.3
-
2
-
-
0036533049
-
A parallel solver for large scale Markov chains
-
M. BENZI AND M. TŮMA, A parallel solver for large scale Markov chains, Appl. Numer. Math., 41 (2002), pp. 135-153.
-
(2002)
Appl. Numer. Math
, vol.41
, pp. 135-153
-
-
BENZI, M.1
TŮMA, M.2
-
3
-
-
0030904524
-
Novel methods of sampling phase space in the simulation of biological systems
-
B. BERNE AND J. STRAUB, Novel methods of sampling phase space in the simulation of biological systems, Curr. Opin. Struct. Biol., 7 (1997), pp. 181-189.
-
(1997)
Curr. Opin. Struct. Biol
, vol.7
, pp. 181-189
-
-
BERNE, B.1
STRAUB, J.2
-
4
-
-
0022093129
-
-
W.-L. CAO AND W. J. STEWART, Iterative aggregation/ disaggregation techniques for nearly uncoupled Markov chains, J. Assoc. Comput. Mach., 32 (1985), pp. 702-719.
-
W.-L. CAO AND W. J. STEWART, Iterative aggregation/ disaggregation techniques for nearly uncoupled Markov chains, J. Assoc. Comput. Mach., 32 (1985), pp. 702-719.
-
-
-
-
6
-
-
0005616050
-
Permuting Markov Chains to Nearly Completely Decomposable Form
-
Technical report BU-CEIS-9808, Department of Computer Science and Engineering, Bilkent University, Ankara, Turkey
-
T. DAYAR, Permuting Markov Chains to Nearly Completely Decomposable Form, Technical report BU-CEIS-9808, Department of Computer Science and Engineering, Bilkent University, Ankara, Turkey, 1998, bttp://citeseer.ist.psu.edu/70412.html.
-
(1998)
-
-
DAYAR, T.1
-
7
-
-
0033709988
-
Comparison of partitioning techniques for two-level iterative solvers on large, sparse Markov chains
-
T. DAYAR AND W. J. STEWART, Comparison of partitioning techniques for two-level iterative solvers on large, sparse Markov chains, SIAM J. Sci. Comput., 21 (2000), pp. 1691-1705.
-
(2000)
SIAM J. Sci. Comput
, vol.21
, pp. 1691-1705
-
-
DAYAR, T.1
STEWART, W.J.2
-
8
-
-
3042829984
-
From molecular dynamics to conformational dynamics in drug design
-
M. Kirkilionis, S. Krömker, R. Rannacher, and F. Tomi, eds, Springer, Berlin
-
P. DEUFLHAAD, From molecular dynamics to conformational dynamics in drug design, in Trends in Nonlinear Analysis, M. Kirkilionis, S. Krömker, R. Rannacher, and F. Tomi, eds., Springer, Berlin, 2003, pp. 269-287.
-
(2003)
Trends in Nonlinear Analysis
, pp. 269-287
-
-
DEUFLHAAD, P.1
-
9
-
-
84862381097
-
Molecular conformation dynamics and computational drug design
-
J. M. Hill and R. Moore, eds, SIAM, Philadelphia
-
P. DEUFLHARD AND C. SCHÜTTE, Molecular conformation dynamics and computational drug design, in:, Applied Mathemetics Entering the 21st Century, J. M. Hill and R. Moore, eds., SIAM, Philadelphia, 2004, pp. 91-119.
-
(2004)
Applied Mathemetics Entering the 21st Century
, pp. 91-119
-
-
DEUFLHARD, P.1
SCHÜTTE, C.2
-
10
-
-
13544256263
-
Robust Perron cluster analysis in conformation dynamics
-
P. DEUFLHARD AND M. WEBER, Robust Perron cluster analysis in conformation dynamics, Linear Algebra Appl., 398 (2005), pp. 161-184.
-
(2005)
Linear Algebra Appl
, vol.398
, pp. 161-184
-
-
DEUFLHARD, P.1
WEBER, M.2
-
11
-
-
4243137056
-
Hybrid Monte Carlo
-
S. DUANE, A. D. KENNEDY, B. J. PENDLETON, AND D. ROWETH, Hybrid Monte Carlo, Phys. Lett. B, 195 (1987), pp. 216-222.
-
(1987)
Phys. Lett. B
, vol.195
, pp. 216-222
-
-
DUANE, S.1
KENNEDY, A.D.2
PENDLETON, B.J.3
ROWETH, D.4
-
12
-
-
3042834593
-
-
Doctoral thesis, Freie Universität Berlin, Berlin, Germany
-
A. FISCHER, An Uncoupling-Coupling Method for Markov Chain Monte Carlo Simulations with an Application to Biomolecules, Doctoral thesis, Freie Universität Berlin, Berlin, Germany, 2003, http:// www.diss.fu-berlin.de/2003/234/indexe.html.
-
(2003)
An Uncoupling-Coupling Method for Markov Chain Monte Carlo Simulations with an Application to Biomolecules
-
-
FISCHER, A.1
-
13
-
-
0011984684
-
Hierarchical uncoupling-coupling of metastable conformations
-
T. Schlick and H. H. Gan, eds, Springer, Berlin, Heidelberg, New York
-
A. FISCHER, CH. SCHÜTTE, P. DEUFLHARD, AND F. CORDES, Hierarchical uncoupling-coupling of metastable conformations, in Computational Methods for Macromolecules: Challenges and Applications, T. Schlick and H. H. Gan, eds., Springer, Berlin, Heidelberg, New York, 2002, pp. 235-259.
-
(2002)
Computational Methods for Macromolecules: Challenges and Applications
, pp. 235-259
-
-
FISCHER, A.1
SCHÜTTE, C.H.2
DEUFLHARD, P.3
CORDES, F.4
-
14
-
-
47949121217
-
Understanding Molecular Simulation: From Algorithms to Applications
-
Academic Press, San Diego, London
-
D. FRENKEL AND B. SMIT, Understanding Molecular Simulation: From Algorithms to Applications, Comput. Sci. Ser. 1, Academic Press, San Diego, London, 2002.
-
(2002)
Comput. Sci. Ser
, pp. 1
-
-
FRENKEL, D.1
SMIT, B.2
-
15
-
-
0000736067
-
Simulating normalizing constants: From importance sampling to bridge sampling to path sampling
-
A. GELMAN AND X. MENG, Simulating normalizing constants: From importance sampling to bridge sampling to path sampling, Statist. Sci., 13 (1998), pp. 163-185.
-
(1998)
Statist. Sci
, vol.13
, pp. 163-185
-
-
GELMAN, A.1
MENG, X.2
-
16
-
-
0004236492
-
-
3rd ed, The Johns Hopkins University Press, Baltimore, MD
-
G. H. GOLUB AND C. F. VAN LOAN, Matrix Computations, 3rd ed., The Johns Hopkins University Press, Baltimore, MD, 1996.
-
(1996)
Matrix Computations
-
-
GOLUB, G.H.1
VAN LOAN, C.F.2
-
17
-
-
84893482610
-
A solution for the best rotation to relate two sets of vectors
-
W. KABSCH, A solution for the best rotation to relate two sets of vectors, Acta Cryst. Sect. A, 32 (1976), pp. 922-923.
-
(1976)
Acta Cryst. Sect. A
, vol.32
, pp. 922-923
-
-
KABSCH, W.1
-
18
-
-
12944249776
-
A discussion of the solution for the best rotation to relate two sets of vectors
-
W. KABSCH, A discussion of the solution for the best rotation to relate two sets of vectors, Acta Cryst. Sect. A, 34 (1978), pp. 827 828.
-
(1978)
Acta Cryst. Sect. A
, vol.34
, pp. 827-828
-
-
KABSCH, W.1
-
20
-
-
0000556573
-
Iterative methods for computing stationary distributions of nearly completely decomposable Markov chains
-
J. R. KOURY, D. F. MCALLISTER, AND W. J. STEWART, Iterative methods for computing stationary distributions of nearly completely decomposable Markov chains, SIAM J. Algebraic Discrete Methods, 5 (1984), pp. 164-186.
-
(1984)
SIAM J. Algebraic Discrete Methods
, vol.5
, pp. 164-186
-
-
KOURY, J.R.1
MCALLISTER, D.F.2
STEWART, W.J.3
-
21
-
-
45849120304
-
-
THEMATHWORKS INC. GERMANY, MATLAB 6.5.0, 1994-2005.
-
THEMATHWORKS INC. GERMANY, MATLAB 6.5.0, 1994-2005.
-
-
-
-
22
-
-
21444451325
-
-
X.-L. MENG AND W. H. WONG, Simulating ratios of normalizing constants via a simple identity: A theoretical exploration, Statist. Sinica, 6 (1996), pp. 831-860.
-
X.-L. MENG AND W. H. WONG, Simulating ratios of normalizing constants via a simple identity: A theoretical exploration, Statist. Sinica, 6 (1996), pp. 831-860.
-
-
-
-
23
-
-
0024680811
-
Stochastic complementation, uncoupling Markov chains, and the theory of nearly reducible systems
-
C. D. MEYER, Stochastic complementation, uncoupling Markov chains, and the theory of nearly reducible systems, SIAM Rev., 31 (1989), pp. 240-272.
-
(1989)
SIAM Rev
, vol.31
, pp. 240-272
-
-
MEYER, C.D.1
-
24
-
-
0043256056
-
Sensitivity of the stationary distribution of a Markov chain
-
C. D. MEYER, Sensitivity of the stationary distribution of a Markov chain, SIAM J. Matrix Anal. Appl., 15 (1994), pp. 715-728.
-
(1994)
SIAM J. Matrix Anal. Appl
, vol.15
, pp. 715-728
-
-
MEYER, C.D.1
-
25
-
-
21144460955
-
Entrywise perturbation theory and error analysis for Markov chains
-
C. A. O'CINNEIDE, Entrywise perturbation theory and error analysis for Markov chains, Numer. Math., 65 (1993), pp. 109-120.
-
(1993)
Numer. Math
, vol.65
, pp. 109-120
-
-
O'CINNEIDE, C.A.1
-
26
-
-
0001473437
-
On estimation of a probability density function and mode
-
E. PARZEN, On estimation of a probability density function and mode, Ann. Math. Statist., 33 (1962), pp. 1065-1076.
-
(1962)
Ann. Math. Statist
, vol.33
, pp. 1065-1076
-
-
PARZEN, E.1
-
27
-
-
0008441139
-
Numerical methods in Markov chain modeling
-
B. PHILIPPE, Y. SAAD, AND W. J. STEWART, Numerical methods in Markov chain modeling, Oper. Res., 40 (1992), pp. 1156-1179.
-
(1992)
Oper. Res
, vol.40
, pp. 1156-1179
-
-
PHILIPPE, B.1
SAAD, Y.2
STEWART, W.J.3
-
28
-
-
45849126984
-
-
Master's thesis, Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
-
A. RIEMER, Accuracy, Stability, Convergence of Rigorous Thermodynamic Sampling Methods, Master's thesis, Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany, 2006, http://www.zib.de/bib/dipl/RiemerDiplom.pdf.
-
(2006)
Accuracy, Stability, Convergence of Rigorous Thermodynamic Sampling Methods
-
-
RIEMER, A.1
-
29
-
-
0001509947
-
Using randomization to break the curse of dimensionality
-
J. RUST, Using randomization to break the curse of dimensionality, Econometrica, 65 (1997), pp. 487-516.
-
(1997)
Econometrica
, vol.65
, pp. 487-516
-
-
RUST, J.1
-
30
-
-
45849151823
-
-
CH. SCHÜTTE, Conformational Dynamics: Modelling, Theory, Algorithm, and Application to Biomolecules, Habilitation thesis, Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany, 1999, http://www.zib.de/bib/habil/index.de.html.
-
CH. SCHÜTTE, Conformational Dynamics: Modelling, Theory, Algorithm, and Application to Biomolecules, Habilitation thesis, Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany, 1999, http://www.zib.de/bib/habil/index.de.html.
-
-
-
-
31
-
-
13544266845
-
Biomolecular conformations can be identified as metastable sets of molecular dynamics
-
X, P. G. Ciarlet and C. Le Bris, eds, North-Holland, Amsterdam
-
CH. SCHÜTTE AND W. HUISINGA, Biomolecular conformations can be identified as metastable sets of molecular dynamics, in Handbook of Numerical Analysis, Vol. X, P. G. Ciarlet and C. Le Bris, eds., North-Holland, Amsterdam, 2003, pp. 699-744.
-
(2003)
Handbook of Numerical Analysis
, pp. 699-744
-
-
SCHÜTTE, C.H.1
HUISINGA, W.2
-
32
-
-
0000167458
-
A smart Monte Carlo technique for free energy simulations of multiconformational molecules. Direct calculations of the conformational populations of organic molecules
-
H. SENDEROWITZ, F. GUARNIERI, AND W. C. STILL, A smart Monte Carlo technique for free energy simulations of multiconformational molecules. Direct calculations of the conformational populations of organic molecules, J. Am. Chem. Soc., 117 (1995), pp. 8211-8219.
-
(1995)
J. Am. Chem. Soc
, vol.117
, pp. 8211-8219
-
-
SENDEROWITZ, H.1
GUARNIERI, F.2
STILL, W.C.3
-
33
-
-
0012333020
-
Simple but smart Monte Carlo algorithm for free energy simulations of multiconformational molecules
-
H. SENDEROWITZ AND W. C. STILL, Simple but smart Monte Carlo algorithm for free energy simulations of multiconformational molecules, J. Comput. Chem., 19 (1998), pp. 1736-1745.
-
(1998)
J. Comput. Chem
, vol.19
, pp. 1736-1745
-
-
SENDEROWITZ, H.1
STILL, W.C.2
-
34
-
-
0001633546
-
Aggregation of variables in dynamical systems
-
H. A. SIMON AND A. ANDO, Aggregation of variables in dynamical systems, Econometrica, 29 (1961), pp. 111-138.
-
(1961)
Econometrica
, vol.29
, pp. 111-138
-
-
SIMON, H.A.1
ANDO, A.2
-
35
-
-
0346922977
-
Numerical methods for computing stationary distributions of finite irreducible Markov chains
-
W. Grassmann, ed, Kluwer Academic Publishers, Dordrecht, The Netherlands
-
W. J. STEWART, Numerical methods for computing stationary distributions of finite irreducible Markov chains, in Computational Probability, W. Grassmann, ed., Kluwer Academic Publishers, Dordrecht, The Netherlands, 1997, pp. 81-112.
-
(1997)
Computational Probability
, pp. 81-112
-
-
STEWART, W.J.1
-
36
-
-
0026880073
-
Numerical experiments with iteration and aggregation for Markov chains
-
W. J. STEWART AND W. WU, Numerical experiments with iteration and aggregation for Markov chains, ORSA J. Comput., 4 (1992), pp. 336-350.
-
(1992)
ORSA J. Comput
, vol.4
, pp. 336-350
-
-
STEWART, W.J.1
WU, W.2
-
37
-
-
36749113356
-
Monte Carlo study of a phase-separating liquid mixture by umbrella sampling
-
G. M. TORRIE AND J. P. VALLEAU, Monte Carlo study of a phase-separating liquid mixture by umbrella sampling, J. Chem. Phys., 66 (1977), pp. 1402-1408.
-
(1977)
J. Chem. Phys
, vol.66
, pp. 1402-1408
-
-
TORRIE, G.M.1
VALLEAU, J.P.2
-
38
-
-
45849097703
-
ConfJump: A Fast Biomolecular Sampling Method Which Drills Tunnels through High Mountains
-
06-26, Zuse Institute Berlin, Berlin, Germany
-
L. WALTER AND M. WEBER, ConfJump: A Fast Biomolecular Sampling Method Which Drills Tunnels through High Mountains, ZIB-Report 06-26, Zuse Institute Berlin, Berlin, Germany, 2006, http:/ /www.zib.de/bib/pub/pw/.
-
(2006)
ZIB-Report
-
-
WALTER, L.1
WEBER, M.2
-
39
-
-
45849139859
-
-
Verlag Dr. Hut, München, Germany, also available online from
-
M. WEBER, Meshless Methods in Conformation Dynamics, Verlag Dr. Hut, München, Germany, 2006; also available online from http://www.zib.de/bib/diss/index.de.html.
-
(2006)
Meshless Methods in Conformation Dynamics
-
-
WEBER, M.1
-
40
-
-
3042789465
-
Characterization of Transition States in Conformational Dynamics Using Fuzzy Sets
-
02-12, Zuse Institute Berlin, Berlin, Germany
-
M. WEBER AND T. GALLIAT, Characterization of Transition States in Conformational Dynamics Using Fuzzy Sets, ZIB-Report 02-12, Zuse Institute Berlin, Berlin, Germany, 2002, http://www.zib.de /bib/pub/pw/.
-
(2002)
ZIB-Report
-
-
WEBER, M.1
GALLIAT, T.2
-
41
-
-
45849115586
-
ZIBgridfree - Adaptive Conformation Analysis with Qualified Support of Transition States and Thermodynamic Weights
-
05-17, Zuse Institute Berlin, Berlin, Germany
-
M. WEBER AND H. MEYER, ZIBgridfree - Adaptive Conformation Analysis with Qualified Support of Transition States and Thermodynamic Weights, ZIB-Report 05-17, Zuse Institute Berlin, Berlin, Germany, 2005, http://www.zib.de/bib/pub/pw/.
-
(2005)
ZIB-Report
-
-
WEBER, M.1
MEYER, H.2
|