Diego_Prada's markov [35 articles] Export

Recent papers added to Diego_Prada's library classified by the tag markov. You can also see everyone's markov.

	Efficient exploration of energy landscapes [My Copy] (14 Oct 2009) by Martin Mann, Konstantin Klemm posted to transition_states mutual-information mc markov free-energy by Diego_Prada on 2009-10-20 19:21:50 as along with 1 person apocapoc
	Rapid equilibrium sampling initiated from nonequilibrium data [My Copy] Proceedings of the National Academy of Sciences (29 September 2009) by Xuhui Huang, Gregory R. Bowman, Sergio Bacallado, Vijay S. Pande posted to nonequilibrium markov_state_models markov free-energy by Diego_Prada on 2009-10-05 16:42:54 as
	Multiscale complex network of protein conformational fluctuations in single-molecule time series [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 2. (15 January 2008), pp. 536-541. by Chun-Biu Li, Haw Yang, Tamiki Komatsuzaki posted to cmn markov out_of_equilibrium by Diego_Prada on 2009-07-21 15:16:32 as along with 4 people and 1 group ruvido sobolevnrm biehl hsekiguc baker-group
	Macroscopic Dynamics of Complex Metastable Systems: Theory, Algorithms, and Application to B-DNA [My Copy] SIAM Journal on Applied Dynamical Systems, Vol. 7, No. 2. (2008), pp. 532-560. by Illia Horenko, Evelyn Dittmer, Filip Lankas, John Maddocks, Philipp Metzner, Christof Schütte posted to cmn free-energy markov by Diego_Prada on 2009-05-30 20:53:56 as along with 1 person Elena_Zubova
	Identification of biomolecular conformations from incomplete torsion angle observations by hidden markov models [My Copy] Journal of Computational Chemistry, Vol. 28, No. 15. (2007), pp. 2453-2464. by Alexander Fischer, Sonja Waldhausen, Illia Horenko, Eike Meerbach, Christof Schütte posted to dpca markov by Diego_Prada on 2009-05-30 20:23:51 as
	Set-Oriented Dimension Reduction: Localizing Principal Component Analysis Via Hidden Markov Models [My Copy] Computational Life Sciences II (2006), pp. 74-85. by Illia Horenko, Johannes Schmidt-Ehrenberg, Christof Schütte posted to markov pca by Diego_Prada on 2009-05-30 20:14:05 as
	Extracting macroscopic dynamics: model problems and algorithms [My Copy] Nonlinearity, Vol. 17, No. 6. (2004), pp. R55-R127. by Raz, Andrew Stuart posted to markov methods stochastic_processes by Diego_Prada on 2009-05-30 18:54:10 as along with 2 people and 1 group sobolevnrm Borelli baker-group
	Reduced Stochastic Models for Complex Molecular Systems [My Copy] Computing and Visualization in Science, Vol. 9, No. 2. (1 July 2006), pp. 89-102. by Illia Horenko, Evelyn Dittmer, Christof Schütte posted to bayesian_analysis markov stochastic_processes by Diego_Prada on 2009-05-30 18:47:04 as
	Computing Best Transition Pathways in High-Dimensional Dynamical Systems: Application to the Alpha[sub L] ≤ftrightharpoons Beta ≤ftrightharpoons Alpha[sub R] Transitions in Octaalanine [My Copy] Multiscale Modeling & Simulation, Vol. 5, No. 2. (2006), pp. 393-419. by Frank Noé, Marcus Oswald, Gerhard Reinelt, Stefan Fischer, Jeremy C. Smith posted to hexapeptide markov statistical_mechanics stochastic_processes transition_path by Diego_Prada on 2009-05-29 19:05:53 as
	An Averaging Principle for Fast Degrees of Freedom Exhibiting Long-Term Correlations [My Copy] Multiscale Modeling & Simulation, Vol. 2, No. 3. (2004), pp. 501-526. by Christof Schütte, Jessika Walter, Carsten Hartmann, Wilhelm Huisinga posted to cmn free-energy markov stochastic_processes struct_decorr by Diego_Prada on 2009-05-29 18:19:26 as
	Transition Path Theory for Markov Jump Processes [My Copy] Multiscale Modeling & Simulation, Vol. 7, No. 3. (2009), pp. 1192-1219. by Philipp Metzner, Christof Schütte, Eric V. Eijnden posted to markov stochastic_processes by Diego_Prada on 2009-05-29 18:16:52 as
	Extracting macroscopic stochastic dynamics: Model problems [My Copy] Communications on Pure and Applied Mathematics, Vol. 56, No. 2. (2003), pp. 234-269. by Wilhelm Huisinga, Christof Schütte, Andrew M. Stuart posted to stochastic_processes non_markovian markov coarse-grained chapt_cmn by Diego_Prada on 2009-03-09 17:53:37 as
	Identification of almost invariant aggregates in reversible nearly uncoupled Markov chains [My Copy] Linear Algebra and its Applications, Vol. 315, No. 1-3. (15 August 2000), pp. 39-59. by P. Deuflhard, W. Huisinga, A. Fischer, Ch Schütte posted to chapt_cmn markov plos by Diego_Prada on 2009-03-05 10:53:56 as
	Foldamer dynamics expressed via Markov state models. II. State space decomposition [My Copy] The Journal of Chemical Physics, Vol. 123, No. 11. (2005) by Sidney P. Elmer, Sanghyun Park, Vijay S. Pande posted to free-energy markov short-peptides stochastic_processes by Diego_Prada on 2009-03-03 12:09:47 as
	Foldamer dynamics expressed via Markov state models. I. Explicit solvent molecular-dynamics simulations in acetonitrile, chloroform, methanol, and water [My Copy] The Journal of Chemical Physics, Vol. 123, No. 11. (2005) by Sidney P. Elmer, Sanghyun Park, Vijay S. Pande posted to free-energy markov short-peptides stochastic_processes by Diego_Prada on 2009-03-03 12:06:39 as along with 1 person toerst
	Testing lumpability in Markov chains [My Copy] Statistics & Probability Letters, Vol. 64, No. 1. (01 August 2003), pp. 17-23. by R. W. Jernigan, R. H. Baran posted to chapt_cmn markov plos statistical_mechanics stochastic_processes by Diego_Prada on 2009-02-19 19:03:03 as
	Validation of Markov state models using Shannon's entropy [My Copy] The Journal of Chemical Physics, Vol. 124, No. 5. (2006) by Sanghyun Park, Vijay S. Pande posted to chapt_cmn entropy markov plos stochastic_processes by Diego_Prada on 2009-02-19 18:23:05 as along with 1 person toerst
	Nonequilibrium Statistical Mechanics [My Copy] (26 March 2001) by Robert Zwanzig posted to chapt_cmn markov plos statistical_mechanics by Diego_Prada on 2009-02-19 11:00:14 as along with 3 people NitinCR chiufanlee kkims
	The free energy landscape and dynamics of met-enkephalin [My Copy] The Journal of Chemical Physics, Vol. 119, No. 18. (2003), pp. 9947-9955. by David A. Evans, David J. Wales posted to chapt_cmn free-energy hexapeptide markov plos by Diego_Prada on 2009-02-17 15:55:06 as
	Describing Protein Folding Kinetics by Molecular Dynamics Simulations. 2. Example Applications to Alanine Dipeptide and a β-Hairpin Peptide [My Copy] J. Phys. Chem. B, Vol. 108, No. 21. (27 May 2004), pp. 6582-6594. by W. C. Swope, J. W. Pitera, F. Suits, et al.M. Pitman, M. Eleftheriou, B. G. Fitch, R. S. Germain, A. Rayshubski, T. J. C. Ward, Y. Zhestkov, R. Zhou posted to beta-hairpin hexapeptide markov md stochastic_processes by Diego_Prada on 2009-02-16 11:17:38 as along with 1 person toerst
	Describing Protein Folding Kinetics by Molecular Dynamics Simulations. 1. Theory [My Copy] J. Phys. Chem. B, Vol. 108, No. 21. (27 May 2004), pp. 6571-6581. by W. C. Swope, J. W. Pitera, F. Suits posted to chapt_cmn free-energy markov md plos protein_dynamics stochastic_processes by Diego_Prada on 2009-02-16 11:14:57 as along with 2 people mtw apaydin
	Remarks on non-Markov processes [My Copy] BRAZILIAN JOURNAL OF PHYSICS, Vol. 28, No. 2. (1998) by N. G. van Kampen posted to chapt_cmn langevin markov plos stochastic_processes by Diego_Prada on 2009-02-13 11:52:05 as
	Stochastic Processes in Physics and Chemistry (North-Holland Personal Library) [My Copy] (01 July 2001) by N. G. van Kampen posted to chapt_cmn kramers langevin markov plos statistical_mechanics stochastic_processes by Diego_Prada on 2009-02-13 11:41:48 as along with 2 people ddcttrl madhadron
	Transition networks for modeling the kinetics of conformational change in macromolecules [My Copy] Current Opinion in Structural Biology In Theory and simulation / Macromolecular assemblages, Vol. 18, No. 2. (April 2008), pp. 154-162. by Frank Noé, Stefan Fischer posted to chapt_cmn cmn hexapeptide markov networks plos by Diego_Prada on 2009-02-11 18:08:45 as along with 5 people and 3 groups aqeel barry sobolevnrm paulschlesinger toerst structural_bioinformatics baker-group McCammon
	Coarse Master Equations for Peptide Folding Dynamics [My Copy] J. Phys. Chem. B (31 January 2008) by N. V. Buchete, G. Hummer posted to chapt_cmn hexapeptide markov plos stochastic_processes by Diego_Prada on 2008-12-16 16:27:49 as along with 3 people and 1 group apaydin ruvido sobolevnrm baker-group
	Eigenvalue spectrum of the master equation for hierarchical dynamics of complex systems [My Copy] Phys. Chem. Chem. Phys., Vol. 4, No. 20. (2002), pp. 5052-5058. by Yaakov Levy, Joshua Jortner, Stephen R. Berry posted to hexapeptide markov by Diego_Prada on 2008-12-16 11:45:00 as
	Simulating replica exchange simulations of protein folding with a kinetic network model [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 39. (25 September 2007), pp. 15340-15345. by Weihua Zheng, Michael Andrec, Emilio Gallicchio, Ronald M. Levy posted to cmn markov md methods by Diego_Prada on 2008-11-29 15:56:08 as along with 1 person zwang
	Long-Time Protein Folding Dynamics from Short-Time Molecular Dynamics Simulations [My Copy] Multiscale Modeling & Simulation, Vol. 5, No. 4. (2006), pp. 1214-1226. by John D. Chodera, William C. Swope, Jed W. Pitera, Ken A. Dill posted to chapt_cmn dialanine markov md plos by Diego_Prada on 2008-08-01 19:30:32 as along with 2 people allmensch ucbcjbm
	On mean residence and first passage times in finite one-dimensional systems [My Copy] The Journal of Chemical Physics, Vol. 109, No. 13. (1998), pp. 5187-5193. by Arie B. Haim, Joseph Klafter posted to markov stochastic_processes cmn by Diego_Prada on 2008-05-10 11:47:32 as
	Graph transformation method for calculating waiting times in Markov chains [My Copy] The Journal of Chemical Physics, Vol. 124, No. 23. (2006) by Semen A. Trygubenko, David J. Wales posted to chapt_cmn free-energy markov plos by Diego_Prada on 2008-04-11 19:40:07 as along with 1 person apaydin
	Hierarchical analysis of conformational dynamics in biomolecules: transition networks of metastable states. [My Copy] J Chem Phys, Vol. 126, No. 15. (21 April 2007) by F. Noé, I. Horenko, C. Schütte, J. C. Smith posted to chapt_cmn hexapeptide markov plos protein_dynamics by Diego_Prada on 2008-03-30 16:22:35 as along with 3 people barmak7282 choonpeng toerst
	Calculation of the distribution of eigenvalues and eigenvectors in Markovian state models for molecular dynamics [My Copy] The Journal of Chemical Physics, Vol. 126, No. 24. (2007) by Nina S. Hinrichs, Vijay S. Pande posted to markov protein_dynamics by Diego_Prada on 2008-03-30 16:17:53 as
	Statistically optimal analysis of samples from multiple equilibrium states [My Copy] (9 Jan 2008) by Michael R. Shirts, John D. Chodera posted to markov protein_dynamics stochastic_processes by Diego_Prada on 2008-03-30 16:14:48 as along with 1 person and 1 group sobolevnrm baker-group
	Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics [My Copy] The Journal of Chemical Physics, Vol. 126, No. 15. (21 April 2007), 155101. by John D. Chodera, Nina Singhal, Vijay S. Pande, Ken A. Dill, William C. Swope posted to chapt_cmn markov plos protein_dynamics by Diego_Prada on 2008-03-30 16:13:45 as along with 2 people ruvido allmensch
	Stochastic embedding of dynamical systems [My Copy] (30 Sep 2005) by Jacky Cresson, Sébastien Darses posted to markov stochastic_processes by Diego_Prada on 2008-03-05 17:23:06 as

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free-energy	87
networks	66
short-peptides	62
chapt_cmn	61
hexapeptide	48
plos	47
md	41
communities	38
markov	35
stochastic_processes	34
cmn	29
pca	29
protein_dynamics	29
protein_folding	27
amino	26
amyloids	26
md_history	26
dialanine	25
gnm	25
articulo	21
complex_systems	21
coarse-grained	18
hp_model	16
beta-hairpin	15
dpca	15
proteins	15
methods	14
transition_path	13
water	13
chapt_amino	12
force-fields	12
statistical_mechanics	12
clustering	8
experimental	8
first_passage	8
reaction_paths	7
transition_states	7
active_site	6
glass_transition	6
mutual-information	6
struct_decorr	6
glycine	5
hot	5
kramers	5
langevin	5
mios	5
out_of_equilibrium	5
rmsd	5
secondary_structure	5
allostery	4
entropy	4
kinetic_models	4
mc	4
percolation	4
qha	4
collective_motions	3
dihedral	3
energy_landscape	3
rol_nodes	3
work_theorem	3
ala5	2
alanine	2
bayesian_analysis	2
fca	2
funnels	2
go	2
information	2
irreversibility	2
lanvegin	2
leas_action	2
non_markovian	2
statistics	2
wavelets	2
chain_interactions	1
conformational_entropy	1
discrete_breathers	1
enkaphalin	1
flagellum	1
hurst_exponent	1
information_theory	1
latex	1
markov_state_models	1
mpi	1
nmr	1
nonequilibrium	1
opls	1
pendiente	1
protein_flexibility	1
relaxation_processes	1
review	1
statistical_models	1
t_dependence	1

Diego_Prada's markov [35 articles] Export

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