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Group: baker-group - with tag kinetics [91 articles]

グループ baker-group のメンバーが最近追加した論文の一覧 with tag kinetics
  • Local spectral time splitting method for first- and second-order partial differential equations
    Journal of Computational Physics, Vol. 206, No. 2. (1 July 2005), pp. 727-780.
    by Sining Yu, Shan Zhao, GW Wei
    posted to kinetics mathematics molecular_dynamics by sobolevnrm to the group baker-group on 2008-07-01 03:10:54 as read
  • An Electrostatic Steering Mechanism of Cdc42 Recognition by Wiskott-Aldrich Syndrome Proteins
    Molecular Cell, Vol. 20, No. 2. (28 October 2005), pp. 313-324.
    by Lars Hemsath, Radovan Dvorsky, Dennis Fiegen, Marie-France Carlier, Mohammad R Ahmadian
    posted to diffusion electrostatics kinetics protein-protein_interactions by sobolevnrm to the group baker-group on 2008-07-01 02:55:17 as read along with 1 person mikaellund
  • Exact Solutions for Kinetic Models of Macromolecular Dynamics
    J. Phys. Chem. B, Vol. 112, No. 19. (15 May 2008), pp. 6025-6044.
    by YR Chemla, JR Moffitt, C Bustamante
    posted to kinetics mathematics by sobolevnrm to the group baker-group on 2008-06-26 12:01:41 as read
  • An interlacing theorem for reversible Markov chains
    Journal of Physics A: Mathematical and Theoretical, Vol. 41, No. 21. (2008), 212002.
    by Robert Grone, Karl H Hoffmann, Peter Salamon
    posted to kinetics mathematics by sobolevnrm to the group baker-group on 2008-06-20 11:36:58 as read
  • Unusual 1H NMR chemical shifts support (His) Cepsilon 1---Hmiddle dotmiddle dotmiddle dotO==C H-bond: Proposal for reaction-driven ring flip mechanism in serine protease catalysis
    Proceedings of the National Academy of Sciences, Vol. 97, No. 19. (12 September 2000), pp. 10371-10376.
    by Elissa L Ash, James L Sudmeier, Regina M Day, Matthew Vincent, Ekaterina V Torchilin, Kristin C Haddad, Elizabeth M Bradshaw, David G Sanford, William W Bachovchin
    posted to kinetics thrombin by sobolevnrm to the group baker-group on 2008-06-04 12:18:38 as read
  • Molecular dynamics simulations of the acyl-enzyme and the tetrahedral intermediate in the deacylation step of serine proteases
    Proteins, Vol. 47, No. 3. (2002), pp. 357-369.
    by M Topf, P Várnai, CJ Schofield, WG Richards
    posted to kinetics molecular_simulation thrombin by sobolevnrm to the group baker-group on 2008-06-04 11:58:07 as read
  • Coarse graining of master equations with fast and slow states
    The Journal of Chemical Physics, Vol. 128, No. 15. (2008)
    by Simone Pigolotti, Angelo Vulpiani
    posted to kinetics mathematics statistical_mechanics by sobolevnrm to the group baker-group on 2008-05-22 11:56:49 as read
  • Transition networks for modeling the kinetics of conformational change in macromolecules
    Current Opinion in Structural Biology, Vol. 18, No. 2. (April 2008), pp. 154-162.
    by Frank Noé, Stefan Fischer
    posted to allostery diffusion kinetics molecular_simulation by sobolevnrm to the group baker-group on 2008-04-18 11:47:00 as read along with 4 people and 2 groups aqeel barry paulschlesinger toerst structural_bioinformatics McCammon
  • Calculating enzyme kinetic parameters from protein structures
    Biochemical Society Transactions, Vol. 36 (2008), pp. 51-54.
    by M Stein, RR Gabdoulline, RC Wade
    posted to diffusion electrostatics kinetics structure by sobolevnrm to the group baker-group on 2008-04-18 11:32:23 as read
  • Protein Sequence- and pH-Dependent Hydration Probed by Terahertz Spectroscopy
    J. Am. Chem. Soc., Vol. 130, No. 8. (27 February 2008), pp. 2374-2375.
    by S Ebbinghaus, SJ Kim, M Heyden, X Yu, M Gruebele, DM Leitner, M Havenith
    posted to kinetics protein_folding solvation by sobolevnrm to the group baker-group on 2008-03-03 11:46:31 as read
  • notes Coarse Master Equations for Peptide Folding Dynamics
    J. Phys. Chem. B (31 January 2008)
    by NV Buchete, G Hummer
    posted to kinetics multiscale protein_folding by sobolevnrm to the group baker-group on 2008-02-29 12:18:27 as read along with 2 people apaydin ruvido
  • Solvent Viscosity Dependence of the Protein Folding Dynamics
    J. Phys. Chem. B (30 January 2008)
    by YM Rhee, VS Pande
    posted to kinetics molecular_simulation protein_folding solvation by sobolevnrm to the group baker-group on 2008-02-27 12:33:44 as read
  • Theory and Simulation of Diffusion-Controlled Michaelis-Menten Kinetics for a Static Enzyme in Solution
    J. Phys. Chem. B (26 January 2008)
    by S Park, N Agmon
    posted to diffusion kinetics mathematics by sobolevnrm to the group baker-group on 2008-02-26 11:51:21 as read
  • Dynamics of the Acetylcholinesterase Tetramer
    Biophys. J., Vol. 94, No. 4. (15 February 2008), pp. 1144-1154.
    by Alemayehu A Gorfe, Chia-En A Chang, Ivaylo Ivanov, Andrew J Mccammon
    posted to acetylcholinesterase diffusion kinetics molecular_dynamics quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2008-02-22 12:09:51 as read
  • Usage of the Mori-Zwanzig method in time series analysis
    Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 77, No. 1. (2008)
    by Markus Niemann, Thomas Laubrich, Eckehard Olbrich, Holger Kantz
    posted to diffusion kinetics statistical_mechanics by sobolevnrm to the group baker-group on 2008-02-19 12:25:15 as read
  • Multiscale complex network of protein conformational fluctuations in single-molecule time series
    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 experimental_methodology kinetics quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2008-02-19 12:19:20 as read along with 3 people ruvido biehl hsekiguc
  • Kinetics of diffusion-influenced bimolecular reactions in solution. I. General formalism and relaxation kinetics of fast reversible reactions
    The Journal of Chemical Physics, Vol. 86, No. 4. (1987), pp. 1883-1903.
    by Sangyoub Lee, Martin Karplus
    posted to kinetics statistical_mechanics by sobolevnrm to the group baker-group on 2008-02-18 12:46:35 as read
  • Modeling diffusive dynamics in adaptive resolution simulation of liquid water
    The Journal of Chemical Physics, Vol. 128, No. 2. (2008)
    by Silvina Matysiak, Cecilia Clementi, Matej Praprotnik, Kurt Kremer, Luigi Delle Site
    posted to diffusion kinetics multiscale solvation by sobolevnrm to the group baker-group on 2008-02-18 12:34:37 as read
  • Automated Generation of Reduced Stochastic Weather Models I: Simultaneous Dimension and Model Reduction for Time Series Analysis
    Multiscale Modeling & Simulation, Vol. 6, No. 4. (2008), pp. 1125-1145.
    by Illia Horenko, Rupert Klein, Stamen Dolaptchiev, Christof Schütte
    posted to kinetics multiscale quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2008-02-15 12:41:46 as read along with 1 person nurban
  • notes A master equation model for bimolecular reaction via multi-well isomerizing intermediates
    Physical Chemistry Chemical Physics, Vol. 2 (2000), pp. 793-803.
    by TJ Frankcombe, SC Smith, KE Gates, SH Robertson
    posted to diffusion kinetics by sobolevnrm to the group baker-group on 2008-02-14 18:31:53 as **
  • Electrophoretic light scattering from macromolecular solutions and conformational dynamics
    The Journal of Chemical Physics, Vol. 87, No. 8. (1987), pp. 4339-4343.
    by JB Hubbard, JA Mccammon
    posted to diffusion electrostatics experimental_methodology kinetics by sobolevnrm to the group baker-group on 2008-02-09 23:07:21 as read
  • Variable-free exploration of stochastic models: a gene regulatory network example
    (6 Nov 2006)
    by Radek Erban, Thomas A Frewen, Xiao Wang, Timothy C Elston, Ronald Coifman, Boaz Nadler, Ioannis G Kevrekidis
    posted to kinetics multiscale systems_biology by sobolevnrm to the group baker-group on 2008-02-01 21:23:37 as ***** along with 1 person j_vinals
  • An extended dynamical hydration shell around proteins.
    Proc Natl Acad Sci U S A, Vol. 104, No. 52. (26 December 2007), pp. 20749-20752.
    by S Ebbinghaus, SJ Kim, M Heyden, X Yu, U Heugen, M Gruebele, DM Leitner, M Havenith
    posted to diffusion experimental_methodology kinetics molecular_dynamics solvation by sobolevnrm to the group baker-group on 2008-01-31 12:59:41 as read along with 1 person choonpeng
  • Prediction of Salt and Mutational Effects on the Association Rate of U1A Protein and U1 Small Nuclear RNA Stem/Loop II
    J. Phys. Chem. B (22 December 2007)
    by S Qin, HX Zhou
    posted to diffusion kinetics protein-nucleic_acid_interactions by sobolevnrm to the group baker-group on 2008-01-30 12:33:48 as read
  • Dynamics of essential collective motions in proteins: Theory
    Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 76, No. 5. (2007)
    by Maria Stepanova
    posted to kinetics quasiharmonic-models_elastic-network_gnm_nma_pca_etc statistical_mechanics by sobolevnrm to the group baker-group on 2008-01-25 12:52:15 as read along with 2 people choonpeng Diego_Prada
  • Lateral Diffusion in Lipid Membranes through Collective Flows
    J. Am. Chem. Soc., Vol. 130, No. 1. (9 January 2008), pp. 44-45.
    by E Falck, T Rog, M Karttunen, I Vattulainen
    posted to biomembranes diffusion kinetics molecular_dynamics molecular_simulation by sobolevnrm to the group baker-group on 2008-01-24 12:49:16 as read along with 3 people ARobson paulschlesinger softsimu
  • How a Vicinal Layer of Solvent Modulates the Dynamics of Proteins
    Biophys. J., Vol. 94, No. 1. (1 January 2008), pp. 79-89.
    by Canan Atilgan, Ayse O Aykut, Ali R Atilgan
    posted to kinetics molecular_dynamics solvation by sobolevnrm to the group baker-group on 2008-01-22 12:27:09 as read along with 1 person pavanghatty
  • Continuum Simulations of Acetylcholine Consumption by Acetylcholinesterase: A Poisson-Nernst-Planck Approach
    J. Phys. Chem. B, Vol. 112, No. 2. (17 January 2008), pp. 270-275.
    by YC Zhou, B Lu, GA Huber, MJ Holst, JA Mccammon
    posted to acetylcholinesterase diffusion electrostatics kinetics by sobolevnrm to the group baker-group on 2008-01-10 12:51:17 as read
  • From the Cover: Mapping hydration dynamics around a protein surface.
    Proc Natl Acad Sci U S A, Vol. 104, No. 47. (20 November 2007), pp. 18461-18466.
    by L Zhang, L Wang, YT Kao, W Qiu, Y Yang, O Okobiah, D Zhong
    posted to kinetics solvation by sobolevnrm to the group baker-group on 2007-12-21 12:27:58 as read along with 2 people and 1 group skoch3 kjell Koch_Lab
  • Structure and dynamics of a molten globular enzyme.
    Nat Struct Mol Biol (11 November 2007)
    by Konstantin Pervushin, Katherina Vamvaca, Beat Vögeli, Donald Hilvert
    posted to kinetics structure by sobolevnrm to the group baker-group on 2007-12-20 12:26:00 as read along with 2 people cjeans cactus
  • First-passage times in complex scale-invariant media
    Nature, Vol. 450, No. 7166., pp. 77-80.
    by S Condamin, O Bénichou, V Tejedor, R Voituriez, J Klafter
    posted to kinetics mathematics statistical_mechanics by sobolevnrm to the group baker-group on 2007-12-20 12:22:08 as read along with 4 people mpotamias baronka JayDugger cactus
  • Lessons of Slicing Membranes: Interplay of Packing, Free Area, and Lateral Diffusion in Phospholipid/Cholesterol Bilayers
    Biophys. J., Vol. 87, No. 2. (1 August 2004), pp. 1076-1091.
    by Emma Falck, Michael Patra, Mikko Karttunen, Marja T Hyvonen, Ilpo Vattulainen
    posted to biomembranes diffusion kinetics by sobolevnrm to the group baker-group on 2007-12-19 20:48:36 as read along with 1 person softsimu
  • Estimating kinetic rates from accelerated molecular dynamics simulations: Alanine dipeptide in explicit solvent as a case study
    The Journal of Chemical Physics, Vol. 127, No. 17. (2007)
    by César, Donald Hamelberg, Andrew J Mccammon
    posted to enhanced_sampling kinetics molecular_dynamics by sobolevnrm to the group baker-group on 2007-12-17 12:55:05 as read
  • Low-Frequency Vibrational Spectrum of Water in the Hydration Layer of a Protein: A Molecular Dynamics Simulation Study
    J. Phys. Chem. B, Vol. 111, No. 48. (6 December 2007), pp. 13626-13631.
    by S Chakraborty, SK Sinha, S Bandyopadhyay
    posted to kinetics molecular_dynamics solvation by sobolevnrm to the group baker-group on 2007-12-14 12:26:09 as read
  • Exact solution for anisotropic diffusion-controlled reactions with partially reflecting conditions
    The Journal of Chemical Physics, Vol. 127, No. 18. (2007)
    by Sergey D Traytak, William S Price
    posted to diffusion kinetics mathematics by sobolevnrm to the group baker-group on 2007-12-12 12:32:15 as read
  • Random Walks on Lattices. III. Calculation of First-Passage Times with Application to Exciton Trapping on Photosynthetic Units
    Journal of Mathematical Physics, Vol. 10, No. 4. (1969), pp. 753-765.
    by Elliott W Montroll
    posted to diffusion kinetics mathematics by sobolevnrm to the group baker-group on 2007-11-26 12:45:23 as read
  • Mathematical physics: First encounters
    Nature, Vol. 450, No. 7166. (31 October 2007), pp. 40-41.
    by Michael F Shlesinger
    posted to diffusion kinetics mathematics by sobolevnrm to the group baker-group on 2007-11-26 12:44:18 as read
  • Corrections to the Saffman-Delbruck Mobility for Membrane Bound Proteins
    Biophys. J., Vol. 93, No. 11. (1 December 2007), pp. L49-51.
    by Ali Naji, Alex J Levine, PA Pincus
    posted to biomembranes diffusion kinetics by sobolevnrm to the group baker-group on 2007-11-16 00:16:44 as read
  • Dielectric Dispersion Interpretation of Single Enzyme Dynamic Disorder, Spectral Diffusion, and Radiative Fluorescence Lifetime
    J. Phys. Chem. B (23 October 2007)
    by MK Prakash, RA Marcus
    posted to kinetics solvation statistical_mechanics by sobolevnrm to the group baker-group on 2007-11-08 12:43:00 as read
  • Toward realistic modeling of dynamic processes in cell signaling: Quantification of macromolecular crowding effects
    The Journal of Chemical Physics, Vol. 127, No. 15. (2007)
    by Jian Sun, Harel Weinstein
    posted to diffusion kinetics systems_biology by sobolevnrm to the group baker-group on 2007-11-06 12:40:05 as read along with 1 person cactus
  • Kinetics of cholesterol extraction from lipid membranes by methyl-[beta]-cyclodextrin- a surface plasmon resonance approach
    Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. In Press, Accepted Manuscript
    by Mojca P Beseniear, Andrej Bavdek, Ales Kladnik, Peter Maeek, Gregor Anderluh
    posted to biomembranes cholesterol kinetics by sobolevnrm to the group baker-group on 2007-11-05 12:21:29 as read along with 1 person paulschlesinger
  • Electrostatic rate enhancement and transient complex of protein-protein association.
    Proteins (11 October 2007)
    by Ramzi Alsallaq, Huan-Xiang X Zhou
    posted to diffusion electrostatics kinetics by sobolevnrm to the group baker-group on 2007-11-01 10:56:26 as read along with 1 person bicko
  • Convection, diffusion and reaction in a surface-based biosensor: Modeling of cooperativity and binding site competition on the surface and in the hydrogel
    Journal of Colloid and Interface Science, Vol. 296, No. 2. (15 April 2006), pp. 527-537.
    by Konstantin Lebedev, Salvador Mafe, Pieter Stroeve
    posted to diffusion experimental_methodology kinetics by sobolevnrm to the group baker-group on 2007-10-26 12:23:16 as read along with 1 person paulschlesinger
  • Steric hindrance effects on surface reactions: applications to BIAcore
    Journal of Mathematical Biology, Vol. 55, No. 4. (11 October 2007), pp. 517-539.
    by David Edwards
    posted to diffusion experimental_methodology kinetics by sobolevnrm to the group baker-group on 2007-10-26 12:09:00 as read along with 1 person paulschlesinger
  • Convection Effects in the BIAcore Dextran Layer: Surface Reaction Model
    Bulletin of Mathematical Biology, Vol. 68, No. 3. (23 April 2006), pp. 627-654.
    by David Edwards
    posted to diffusion experimental_methodology kinetics by sobolevnrm to the group baker-group on 2007-10-26 12:08:08 as read along with 1 person paulschlesinger
  • An interpretation of fluctuations in enzyme catalysis rate, spectral diffusion, and radiative component of lifetimes in terms of electric field fluctuations
    Proceedings of the National Academy of Sciences, Vol. 104, No. 41. (9 October 2007), pp. 15982-15987.
    by Meher K Prakash, RA Marcus
    posted to electrostatics kinetics by sobolevnrm to the group baker-group on 2007-10-25 15:32:50 as read along with 1 person and 1 group samjlord moernerlab
  • The narrow escape problem for diffusion in cellular microdomains
    Proceedings of the National Academy of Sciences, Vol. 104, No. 41. (9 October 2007), pp. 16098-16103.
    by Z Schuss, A Singer, D Holcman
    posted to diffusion kinetics mathematics statistical_mechanics by sobolevnrm to the group baker-group on 2007-10-25 15:01:43 as **
  • Molecular Recognition by Cholesterol Esterase of Active Site Ligands: Structure-Reactivity Effects for Inhibition by Aryl Carbamates and Subsequent Carbamylenzyme Turnover
    Biochemistry, Vol. 35, No. 51. (24 December 1996), pp. 16723-16734.
    by SR Feaster, K Lee, N Baker, DY Hui, DM Quinn
    posted to drug_design kinetics by sobolevnrm to the group baker-group on 2007-10-16 12:36:38 as read
  • The random walk's guide to anomalous diffusion: a fractional dynamics approach
    Physics Reports, Vol. 339, No. 1. (December 2000), pp. 1-77.
    by Ralf Metzler, Joseph Klafter
    posted to diffusion kinetics mathematics statistical_mechanics teaching by sobolevnrm to the group baker-group on 2007-10-11 12:52:13 as read along with 3 people ansobol Borelli ARobson
  • Random Walks on Lattices. II
    Journal of Mathematical Physics, Vol. 6, No. 2. (1965), pp. 167-181.
    by Elliott W Montroll, George H Weiss
    posted to diffusion kinetics mathematics statistical_mechanics by sobolevnrm to the group baker-group on 2007-10-11 12:50:02 as read along with 2 people ansobol yaroslavvb
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