Determination of reaction coordinates via locally scaled diffusion map.
about
Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and DynamicsMarkov state models of biomolecular conformational dynamicsRNA folding pathways in stop motion.A comparative analysis of clustering algorithms: O2 migration in truncated hemoglobin I from transition networks.Towards the prediction of order parameters from molecular dynamics simulations in proteins.Topological obstructions in the way of data-driven collective variables.Machine learning assembly landscapes from particle tracking data.Recent developments in methods for identifying reaction coordinates.Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitionsOn the Application of Molecular-Dynamics Based Markov State Models to Functional Proteins.Capturing transition paths and transition states for conformational rearrangements in the ribosome.Modeling and enhanced sampling of molecular systems with smooth and nonlinear data-driven collective variables.Kinetics of protein-ligand unbinding: Predicting pathways, rates, and rate-limiting steps.The social network (of protein conformations)From the Cover: Simplifying the representation of complex free-energy landscapes using sketch-map.Visualizing energy landscapes with metric disconnectivity graphsLocating landmarks on high-dimensional free energy surfaces.Multiscale approach to the determination of the photoactive yellow protein signaling state ensemble.Variational cross-validation of slow dynamical modes in molecular kinetics.Using sketch-map coordinates to analyze and bias molecular dynamics simulationsSpectral gap optimization of order parameters for sampling complex molecular systemsEvaluation of Dimensionality-reduction Methods from Peptide Folding-unfolding Simulations.New insights into the folding of a β-sheet miniprotein in a reduced space of collective hydrogen bond variables: application to a hydrodynamic analysis of the folding flow.Variational Koopman models: Slow collective variables and molecular kinetics from short off-equilibrium simulations.Charting molecular free-energy landscapes with an atlas of collective variables.Nonlinear machine learning and design of reconfigurable digital colloids.High-Resolution Free-Energy Landscape Analysis of α-Helical Protein Folding: HP35 and Its Double Mutant.Rapid exploration of configuration space with diffusion-map-directed molecular dynamicsHow wet should be the reaction coordinate for ligand unbinding?A benchmark for reaction coordinates in the transition path ensembleMolecular recognition of DNA by ligands: roughness and complexity of the free energy profile.PathOpt--a global transition state search approach: outline of algorithm.Identification of slow molecular order parameters for Markov model construction.Reaction coordinates, one-dimensional Smoluchowski equations, and a test for dynamical self-consistency.Nonlinear intrinsic variables and state reconstruction in multiscale simulations.Intrinsic map dynamics exploration for uncharted effective free-energy landscapes.Machine learning of single molecule free energy surfaces and the impact of chemistry and environment upon structure and dynamics.Interplay of non-Markov and internal friction effects in the barrier crossing kinetics of biopolymers: insights from an analytically solvable model.Cluster analysis of accelerated molecular dynamics simulations: A case study of the decahedron to icosahedron transition in Pt nanoparticles.Memory-induced acceleration and slowdown of barrier crossing.
P2860
Q26749162-457CABF0-282C-418A-9380-E697251510DAQ26827934-2B0488DF-05C6-4132-AD80-78FB91A956B7Q27323936-88819BEA-823E-4279-BDF4-D87143E2F427Q30370806-443A2B9E-A5B6-452C-B461-9F95C3174DDAQ30416380-4873E908-0F7B-4B65-800E-BF0AE508CD24Q30886821-E09AD7FF-E036-4216-B869-6DF3FA20ACFFQ30991481-78909D68-5701-43C3-A217-3EA8D8BAEFBBQ34125552-C90A139F-DC59-4115-A5D4-4083BEFE79DBQ34214770-C8727CB0-3D76-4169-AA03-E52DB408F518Q34593178-5C8C95D3-ED7B-453B-9667-F8A138BDAEB4Q34727629-7C45E257-BDCC-49E7-B30E-07EB1E0352AFQ35062703-04F9F50A-026E-4D85-A024-5568B73B1C3CQ35062738-ACAA16E7-34C4-46F9-B831-17BF720CFA0EQ35164737-B147D09D-D7CC-44A3-86A5-3A226017C22AQ35164774-7C237CCB-866D-4664-959B-45C93FC7AFD1Q35174897-0E28D1C7-5546-45B0-A64C-825ABB9AD291Q35212589-693D1ADE-A865-4AD8-9611-1A8E9256A1BEQ35377697-8C88028B-8B8B-49D0-BA91-04F76D2E13C7Q35430118-DABBBFA0-55ED-4F39-ABFA-2668AF9F3605Q35887074-2A881566-359E-4712-853E-71B1072140CCQ36710407-DEB97055-EDE4-4A47-B55A-B38C4955D1F9Q36919267-65E426F2-07E1-4ACE-AD12-169566403631Q37087946-3DE80753-9FBA-4B41-8CF2-606BA5AA7042Q38825262-D0BB49FA-8612-4ED7-82F9-27D631CFB2DCQ39204260-7AC25835-9508-4E58-90AB-7121D95798ACQ40395861-41CB70C9-E68A-4B15-9F54-E68B4FFA49ECQ41856685-56D36B8B-9CFA-41E0-894D-AA6FB381ACBDQ41896859-6926BE17-8F46-4815-BF09-DDDDBA9269BEQ42377074-60A510BE-8D4E-4E65-BCB6-B6B7E4C851D0Q42415254-67634245-7A84-4C7F-8CFE-8B43D617C73BQ42934331-9F1D2C40-0064-4EF9-B53C-B36477634A2AQ44737746-5F87A9EE-F4AE-4CB8-8824-9FD2C5381990Q44985905-4E7BC08D-5CE5-4722-8665-CE4A6E87F29BQ45156666-4F95463E-9CB7-4C72-8C2B-961B5B4AB224Q45412100-03F816EE-C693-447C-A41A-8C73576C41C4Q45947016-436E2631-8023-424A-A23D-E748FE5C92B4Q45954839-D4FA1B1F-326E-408B-8C8E-C19C75A621D1Q46133170-6D08AB4F-9E82-44D3-BA3E-FCE71F54D3E2Q47637624-0D07784E-F72E-4894-B53D-6AD1220FA5EBQ48044573-78B36C14-97D4-4170-A971-36B1A7324B57
P2860
Determination of reaction coordinates via locally scaled diffusion map.
description
2011 nî lūn-bûn
@nan
2011年の論文
@ja
2011年学术文章
@wuu
2011年学术文章
@zh
2011年学术文章
@zh-cn
2011年学术文章
@zh-hans
2011年学术文章
@zh-my
2011年学术文章
@zh-sg
2011年學術文章
@yue
2011年學術文章
@zh-hant
name
Determination of reaction coordinates via locally scaled diffusion map.
@en
Determination of reaction coordinates via locally scaled diffusion map.
@nl
type
label
Determination of reaction coordinates via locally scaled diffusion map.
@en
Determination of reaction coordinates via locally scaled diffusion map.
@nl
prefLabel
Determination of reaction coordinates via locally scaled diffusion map.
@en
Determination of reaction coordinates via locally scaled diffusion map.
@nl
P2093
P2860
P356
P1476
Determination of reaction coordinates via locally scaled diffusion map
@en
P2093
Cecilia Clementi
Mary A Rohrdanz
Wenwei Zheng
P2860
P304
P356
10.1063/1.3569857
P407
P577
2011-03-01T00:00:00Z