Diego_Prada's transition_path [26 articles] Export

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	Computing time scales from reaction coordinates by milestoning [My Copy] The Journal of Chemical Physics, Vol. 120, No. 23. (2004), pp. 10880-10889. by Anton K. Faradjian, Ron Elber posted to transition_path reaction_paths methods by Diego_Prada on 2009-11-25 19:23:28 as along with 1 person apaydin
	Transition Path Sampling Methods [My Copy] Computer Simulations in Condensed Matter Systems: From Materials to Chemical Biology Volume 1 (2006), pp. 349-391. by C. Dellago, P. G. Bolhuis, P. L. Geissler posted to transition_path sampling methods chapt_cmn by Diego_Prada on 2009-11-25 19:19:57 as
	TRANSITION PATH SAMPLING: Throwing Ropes Over Rough Mountain Passes, in the Dark [My Copy] Annual Review of Physical Chemistry, Vol. 53, No. 1. (2002), pp. 291-318. by Peter G. Bolhuis, David Chandler, Christoph Dellago, Phillip L. Geissler posted to transition_path reaction_paths methods chapt_cmn by Diego_Prada on 2009-11-25 18:42:21 as along with 5 people doktornoe cjryan apaydin allmensch jun
	String method for the study of rare events [My Copy] Physical Review B, Vol. 66, No. 5. (12 Aug 2002), 052301. by E. Weinan, Weiqing Ren, Eric V. Eijnden posted to transition_path methods chapt_cmn by Diego_Prada on 2009-11-25 18:14:52 as along with 1 person hugo_yas
	Nudged elastic band method for finding minimum energy paths of transition [My Copy] In Classical and quantum dynamics in condensed phase simulations (1998), pp. 385-404. by H. Jónsson, G. Mills, K. W. Jacobsen posted to transition_path methods chapt_cmn by Diego_Prada on 2009-11-25 17:59:57 as
	Methods for Finding Saddle Points and Minimum Energy Paths [My Copy] Theoretical Methods in Condensed Phase Chemistry (2001), pp. 269-302. by Graeme Henkelman, Gísli Jóhannesson, Hannes Jónsson posted to transition_path methods by Diego_Prada on 2009-11-25 17:40:14 as
	Structural mechanism of the recovery stroke in the Myosin molecular motor [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 19. (10 May 2005), pp. 6873-6878. by Stefan Fischer, BjÃ¶rn WindshÃ¼gel, Daniel Horak, Kenneth C. Holmes, Jeremy C. Smith posted to transition_path reaction_paths methods chapt_cmn by Diego_Prada on 2009-11-25 12:29:13 as along with 4 people and 2 groups ckmyo barry shuns yalexeev structural_bioinformatics Bioinformatics
	Steered molecular dynamics and mechanical functions of proteins [My Copy] Current Opinion in Structural Biology, Vol. 11, No. 2. (1 April 2001), pp. 224-230. by B. Isralewitz, M. Gao, K. Schulten posted to transition_path reaction_paths methods by Diego_Prada on 2009-11-24 18:31:21 as along with 4 people and 2 groups devinli barry ttjoseph LamBras structural_bioinformatics Bioinformatics
	Targeted molecular dynamics: A new approach for searching pathways of conformational transitions [My Copy] Journal of Molecular Graphics, Vol. 12, No. 2. (June 1994), pp. 84-89. by J. Schlitter, M. Engels, P. Krüger posted to transition_path reaction_paths problems_fel_dof methods chapt_cmn by Diego_Prada on 2009-11-24 17:52:14 as along with 2 people cactus LamBras
	Conjugate peak refinement: an algorithm for finding reaction paths and accurate transition states in systems with many degrees of freedom [My Copy] Chemical Physics Letters, Vol. 194, No. 3. (26 June 1992), pp. 252-261. by S. Fischer, M. Karplus posted to transition_path reaction_paths problems_fel_dof methods free-energy by Diego_Prada on 2009-11-23 17:38:17 as along with 1 person ckmyo
	Cis-Trans Imide Isomerization of the Proline Dipeptide [My Copy] Journal of the American Chemical Society, Vol. 116, No. 26. (1 December 1994), pp. 11931-11937. by Stefan Fischer, Roland L. Dunbrack, Martin Karplus posted to transition_path problems_fel_dof amino by Diego_Prada on 2009-11-23 17:09:55 as
	Simulation of activation free energies in molecular systems [My Copy] The Journal of Chemical Physics, Vol. 105, No. 5. (1996), pp. 1902-1921. by Eyal Neria, Stefan Fischer, Martin Karplus posted to transition_path problems_fel_dof force-fields dialanine alanine by Diego_Prada on 2009-11-23 16:30:50 as along with 1 person timg
	The Structural Coupling between ATPase Activation and Recovery Stroke in the Myosin II Motor [My Copy] Structure, Vol. 15, No. 7. (18 July 2007), pp. 825-837. by Sampath Koppole, Jeremy C. Smith, Stefan Fischer posted to transition_states transition_path problems_fel_dof by Diego_Prada on 2009-11-23 12:11:49 as along with 2 people ckmyo cactus
	Graph-based analysis of kinetics on multidimensional potential-energy surfaces [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 80, No. 3. (2009), 036112. by T. Okushima, T. Niiyama, K. S. Ikeda, Y. Shimizu posted to transition_path qha kinetic_models free-energy first_passage cmn by Diego_Prada on 2009-10-05 17:07:19 as
	Pathways for Conformational Change in Nitrogen Regulatory Protein C from Discrete Path Sampling [My Copy] The Journal of Physical Chemistry B, Vol. 112, No. 8. (1 February 2008), pp. 2456-2465. by Mey Khalili, David J. Wales posted to first_passage free-energy protein_dynamics qha reaction_paths transition_path transition_states by Diego_Prada on 2009-07-02 12:02:29 as
	Refined kinetic transition networks for the GB1 hairpin peptide [My Copy] Phys. Chem. Chem. Phys., Vol. 11, No. 18. (2009), pp. 3341-3354. by Joanne M. Carr, David J. Wales posted to beta-hairpin first_passage free-energy hexapeptide protein_dynamics protein_folding qha reaction_paths short-peptides transition_path transition_states by Diego_Prada on 2009-07-02 11:55:15 as
	Protein folding on rugged energy landscapes: Conformational diffusion on fractal networks [My Copy] (24 Jun 2009) by Gregg Lois, J. Blawzdziewicz, Corey S. O'Hern posted to cmn coarse-grained complex_systems first_passage free-energy hp_model networks protein_dynamics protein_folding proteins reaction_paths transition_path by Diego_Prada on 2009-06-25 16:27:33 as
	Calculating rate constants and committor probabilities for transition networks by graph transformation [My Copy] The Journal of Chemical Physics, Vol. 130, No. 20. (2009), 204111. by David J. Wales posted to reaction_paths transition_path transition_states by Diego_Prada on 2009-06-09 11:29:56 as
	A note on two problems in connexion with graphs [My Copy] Numerische Mathematik, Vol. 1, No. 1. (1 December 1959), pp. 269-271. by E. W. Dijkstra posted to transition_path transition_states by Diego_Prada on 2009-06-09 11:21:36 as along with 7 people jrperillaj Borelli ben500 hp2oo1 antonkratz mpotamias dylanwalker
	Temperature dependent reaction coordinates [My Copy] The Journal of Chemical Physics, Vol. 112, No. 13. (2000), pp. 5539-5545. by Ron Elber, David Shalloway posted to reaction_paths transition_path transition_states by Diego_Prada on 2009-06-08 21:13:47 as
	A statistical method for identifying transition states in high dimensional problems [My Copy] The Journal of Chemical Physics, Vol. 85, No. 9. (1986), pp. 5045-5048. by Lawrence R. Pratt posted to reaction_paths transition_path transition_states by Diego_Prada on 2009-06-08 21:04:01 as along with 1 person jrperillaj
	A method for determining reaction paths in large molecules: Application to myoglobin [My Copy] Chemical Physics Letters, Vol. 139 (1987), pp. 375-380. by R. Elber, M. Karplus posted to reaction_paths transition_path by Diego_Prada on 2009-06-08 20:43:50 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
	Transition pathways in a many-body system: Application to hydrogen-bond breaking in water [My Copy] The Journal of Chemical Physics, Vol. 109, No. 3. (1998), pp. 1125-1133. by Félix S. Csajka, David Chandler posted to transition_path water by Diego_Prada on 2009-05-29 19:01:24 as
	Theory of Kinetic Partitioning in Protein Folding (With Application to Prions) [My Copy] (25 Jun 1996) by V. I. Abkevich, A. M. Gutin, E. I. Shakhnovich posted to protein_dynamics transition_path by Diego_Prada on 2008-08-11 21:58:28 as along with 1 person and 1 group maurizio_prion prionbiology
	Thermodynamics and kinetics simulations of multi-time-scale processes for complex systems [My Copy] International Reviews in Physical Chemistry, Vol. 27, No. 2. (2008), pp. 201-227. by Yi Q. Gao, Lijiang Yang, Yubo Fan, Qiang Shao posted to complex_systems free-energy protein_dynamics transition_path cmn by Diego_Prada on 2008-08-10 20:26:43 as

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free-energy	96
chapt_cmn	69
networks	66
short-peptides	63
hexapeptide	48
plos	47
md	41
communities	38
markov	35
stochastic_processes	34
protein_folding	33
gnm	32
cmn	31
protein_dynamics	31
pca	30
amino	28
amyloids	27
dialanine	27
md_history	27
methods	27
transition_path	26
articulo	21
complex_systems	21
coarse-grained	18
beta-hairpin	16
hp_model	16
dpca	15
proteins	15
force-fields	13
reaction_paths	13
water	13
chapt_amino	12
statistical_mechanics	12
transition_states	10
clustering	8
experimental	8
first_passage	8
markov_state_models	7
problems_fel_dof	7
active_site	6
glass_transition	6
mutual-information	6
rmsd	6
sampling	6
secondary_structure	6
struct_decorr	6
collective_motions	5
glycine	5
hot	5
kramers	5
langevin	5
mios	5
out_of_equilibrium	5
review	5
allostery	4
entropy	4
kinetic_models	4
mc	4
percolation	4
qha	4
alanine	3
dihedral	3
energy_landscape	3
rol_nodes	3
work_theorem	3
ala5	2
bayesian_analysis	2
conformational_entropy	2
fca	2
funnels	2
go	2
information	2
irreversibility	2
lanvegin	2
leas_action	2
non_markovian	2
probability_distributions	2
statistics	2
wavelets	2
aggregation	1
chain_interactions	1
discrete_breathers	1
enkaphalin	1
fibril_formation	1
flagellum	1
fre	1
hurst_exponent	1
information_theory	1
latex	1
mpi	1
nmr	1
nonequilibrium	1
opls	1
pendiente	1
protein_flexibility	1
relaxation_processes	1
statistical_models	1
t_dependence	1
temperature_dependence	1

Diego_Prada's transition_path [26 articles] Export

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