sobolevnrm's molecular_dynamics [at least 200 articles] Export Sort

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	Understanding Nanoparticle Diffusion and Exploring Interfacial Nanorheology using Molecular Dynamics Simulations [My Copy] Langmuir, Vol. 26, No. 1. (5 January 2010), pp. 5-9. by Yanmei Song, Mingxiang Luo, Lenore L. Dai posted to nanotech molecular_dynamics interfaces by sobolevnrm on 2009-12-29 14:58:46 as along with 1 person qshao
	Bayesian Detection of Intensity Changes in Single Molecule and Molecular Dynamics Trajectories [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by Daniel L. Ensign, Vijay S. Pande posted to statistics molecular_dynamics by sobolevnrm on 2009-12-20 14:15:04 as along with 1 person and 1 group samjlord moernerlab
	Automated Event Detection and Activity Monitoring in Long Molecular Dynamics Simulations [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 10. (13 October 2009), pp. 2595-2605. by Willy Wriggers, Kate A. Stafford, Yibing Shan, et al.Stefano Piana, Paul Maragakis, Kresten Lindorff-Larsen, Patrick J. Miller, Justin Gullingsrud, Charles A. Rendleman, Michael P. Eastwood, Ron O. Dror, David E. Shaw posted to quasiharmonic_models molecular_simulation molecular_dynamics clustering by sobolevnrm on 2009-12-13 00:29:41 as along with 4 people and 1 group paulymer anuragsethi jmccammon pmung McCammon
	Boxed Molecular Dynamics: A Simple and General Technique for Accelerating Rare Event Kinetics and Mapping Free Energy in Large Molecular Systems [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 52. (31 December 2009), pp. 16603-16611. by David R. Glowacki, Emanuele Paci, Dmitrii V. Shalashilin posted to molecular_dynamics enhanced_sampling by sobolevnrm on 2009-12-12 21:52:14 as along with 4 people agrossfield mfajer yangsiyang anuragsethi
	The gates of ion channels and enzymes [My Copy] Trends in Biochemical Sciences (18 November 2009) by Huan-Xiang Zhou, J. Andrew McCammon posted to molecular_dynamics kinetics by sobolevnrm on 2009-12-12 20:32:16 as along with 1 person barry
	Algorithm for rigid-body Brownian dynamics [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 80, No. 6. (2009), 066703. by Dan Gordon, Matthew Hoyles, Shin H. Chung posted to molecular_dynamics hydrodynamics diffusion by sobolevnrm on 2009-12-12 00:24:21 as
	Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 9. (8 September 2009), pp. 2514-2530. by Eva Fadrná, Nad’a Špačková, Joanna Sarzyñska, et al.Jaroslav Koča, Modesto Orozco, Thomas E. Cheatham, Tadeusz Kulinski, Jiří Šponer posted to nucleic_acids molecular_simulation molecular_dynamics by sobolevnrm on 2009-10-27 11:39:52 as along with 1 person qshao
	Bayesian Single-Exponential Kinetics in Single-Molecule Experiments and Simulations [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 36. (10 September 2009), pp. 12410-12423. by Daniel L. Ensign, Vijay S. Pande posted to molecular_dynamics mathematics kinetics by sobolevnrm on 2009-10-16 13:42:25 as along with 2 people and 1 group paulymer samjlord moernerlab
	Enzymatic Activity versus Structural Dynamics: The Case of Acetylcholinesterase Tetramer [My Copy] Vol. 97, No. 3. (5 August 2009), pp. 897-905. by Alemayehu A. Gorfe, Benzhuo Lu, Zeyun Yu, J. Andrew McCammon posted to molecular_dynamics kinetics diffusion acetylcholinesterase by sobolevnrm on 2009-10-14 12:33:57 as along with 1 person anuragsethi
	Bayesian comparison of Markov models of molecular dynamics with detailed balance constraint [My Copy] The Journal of Chemical Physics, Vol. 131, No. 4. (2009), 045106. by Sergio Bacallado, John D. Chodera, Vijay Pande posted to molecular_dynamics mathematics kinetics by sobolevnrm on 2009-10-01 13:14:05 as along with 3 people and 1 group anuragsethi whitead dlimmer Jiang Research Group
	Absolute Hydration Entropies of Alkali Metal Ions from Molecular Dynamics Simulations [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 30. (30 July 2009), pp. 10255-10260. by Jens Carlsson, Johan Åqvist posted to molecular_dynamics solvation by sobolevnrm on 2009-08-03 21:17:12 as along with 2 people francescamocci carlosjavierna
	The impact of hydration water on the dynamics of side chains of hydrophobic peptides: From dry powder to highly concentrated solutions [My Copy] The Journal of Chemical Physics, Vol. 130, No. 23. (2009), 235101. by Daniela Russo, José Teixeira, Jacques Ollivier posted to kinetics molecular_dynamics solvation by sobolevnrm on 2009-08-03 21:16:50 as
	Conformational dynamics of the inner pore helix of voltage-gated potassium channels [My Copy] The Journal of Chemical Physics, Vol. 130, No. 21. (2009), 215103. by Seungho Choe, Michael Grabe posted to biomembranes ion_channels molecular_dynamics by sobolevnrm on 2009-06-24 12:21:32 as along with 1 person flbarroso
	Role of Cardiolipins in the Inner Mitochondrial Membrane: Insight Gained through Atom-Scale Simulations [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 11. (19 March 2009), pp. 3413-3422. by Tomasz Róg, Hector Martinez-Seara, Nana Munck, Matej Orešič, Mikko Karttunen, Ilpo Vattulainen posted to biomembranes molecular_dynamics by sobolevnrm on 2009-05-20 12:46:09 as along with 2 people and 1 group paulschlesinger carlosjavierna baker-group
	CHARMM: The biomolecular simulation program [My Copy] Journal of Computational Chemistry, Vol. 30, No. 10. (30 July 2009), pp. 1545-1614. by B. R. Brooks, C. L. Brooks, A. D. Mackerell, et al.L. Nilsson, R. J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R. W. Pastor, C. B. Post, J. Z. Pu, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu, W. Yang, D. M. York, M. Karplus posted to molecular_dynamics molecular_simulation by sobolevnrm on 2009-05-19 12:00:47 as along with 10 people and 1 group ckmyo dgront rodrigofaccioli mmuecke medic0747 flbarroso jrperillaj xavierprat saravan dimka baker-group
	Modeling dynamics from only output data [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 79, No. 5. (2009), 056208. by Evan Monroig, Kazuyuki Aihara, Yozo Fujino posted to clustering kinetics misc molecular_dynamics systems_biology by sobolevnrm on 2009-05-11 12:27:10 as along with 1 group baker-group
	Molecular dynamics simulations of strongly coupled plasmas [My Copy] Journal of Physics A: Mathematical and Theoretical, Vol. 42, No. 21. (2009), 214029. by Z. Donko posted to beyond_mean_field electrostatics molecular_dynamics statistical_mechanics by sobolevnrm on 2009-05-08 12:27:32 as along with 1 group baker-group
	Trapping Moving Targets with Small Molecules [My Copy] Science, Vol. 324, No. 5924. (10 April 2009), pp. 213-215. by Gregory M. Lee, Charles S. Craik posted to docking drug_design molecular_dynamics by sobolevnrm on 2009-05-08 12:26:48 as along with 6 people and 3 groups guhjy nanonan barry pablocarb Fortran friendpine baker-group structural_bioinformatics McCammon
	Lambda-dynamics free energy simulation methods. [My Copy] Journal of computational chemistry, Vol. 30, No. 11. (August 2009), pp. 1692-1700. by J. L. Knight, C. L. Brooks posted to free_energy molecular_dynamics review by sobolevnrm on 2009-05-07 13:00:25 as along with 3 people and 1 group ibuch klexa agrossfield baker-group
	Bad Seeds Sprout Perilous Dynamics: Stochastic Thermostat Induced Trajectory Synchronization in Biomolecules [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 6. (9 June 2009), pp. 1624-1631. by Daniel J. Sindhikara, Seonah Kim, Arthur F. Voter, Adrian E. Roitberg posted to molecular_dynamics by sobolevnrm on 2009-04-29 12:27:15 as along with 2 people and 2 groups jmccammon edws McCammon baker-group
	Long-timescale molecular dynamics simulations of protein structure and function. [My Copy] Current opinion in structural biology, Vol. 19, No. 2. (08 April 2009), pp. 120-127. by John L. Klepeis, Kresten Lindorff-Larsen, Ron O. Dror, David E. Shaw posted to enhanced_sampling molecular_dynamics review by sobolevnrm on 2009-04-21 12:30:19 as along with 12 people and 1 group loison xdeupi agrossfield allmensch bmduggan r2s2 apaydin kiekyon Borelli idoerg edws paulschlesinger baker-group
	Conservation of Side-Chain Dynamics Within a Protein Family [My Copy] Journal of the American Chemical Society, Vol. 0, No. 0. (0000) by Anthony B. Law, Ernesto J. Fuentes, Andrew L. Lee posted to bioinformatics molecular_dynamics nmr structure by sobolevnrm on 2009-04-20 12:33:39 as along with 4 people and 3 groups anuragsethi skywalkerus02 pablocarb barry structural_bioinformatics McCammon baker-group
	An [script O](N[sup 2]) approximation for hydrodynamic interactions in Brownian dynamics simulations [My Copy] The Journal of Chemical Physics, Vol. 130, No. 11. (2009), 114905. by Tihamér Geyer, Uwe Winter posted to diffusion hydrodynamics kinetics molecular_dynamics solvation by sobolevnrm on 2009-04-20 12:33:18 as along with 1 group baker-group
	Thermostat Artifacts in Replica Exchange Molecular Dynamics Simulations [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 5. (12 May 2009), pp. 1393-1399. by Edina Rosta, Nicolae-Viorel Buchete, Gerhard Hummer posted to free_energy molecular_dynamics molecular_simulation by sobolevnrm on 2009-04-16 12:35:09 as along with 1 group baker-group
	Bridging fluctuating hydrodynamics and molecular dynamics simulations of fluids [My Copy] The Journal of Chemical Physics, Vol. 130, No. 13. (2009), 134111. by Nikolaos K. Voulgarakis, Jhih W. Chu posted to molecular_dynamics solvation by sobolevnrm on 2009-04-15 12:12:32 as along with 1 person and 1 group vitroid baker-group
	Characterization of the Electrostatic Perturbation of a Catalytic Site (Cys)-S–/(His)-Im+H Ion-pair in One Type of Serine Proteinase Architecture by Kinetic and Computational Studies on Chemically Mutated Subtilisin Variants [My Copy] Journal of Molecular Biology, Vol. 257, No. 5. (19 April 1996), pp. 1088-1111. by F. Plou posted to molecular_dynamics by sobolevnrm on 2009-04-14 12:51:59 as along with 1 group baker-group
	Probing the Flexibility of Large Conformational Changes in Protein Structures through Local Perturbations [My Copy] PLoS Comput Biol, Vol. 5, No. 4. (3 April 2009), e1000343. by Bosco K. Ho, David A. Agard posted to enhanced_sampling molecular_dynamics by sobolevnrm on 2009-04-14 12:50:27 as along with 5 people and 3 groups skywalkerus02 dimka operon barry bourby baker-group structural_bioinformatics McCammon
	Assessing equilibration and convergence in biomolecular simulations. [My Copy] Proteins, Vol. 48, No. 3. (15 August 2002), pp. 487-496. by Lorna J. Smith, Xavier Daura, Wilfred F. van Gunsteren posted to molecular_dynamics molecular_simulation by sobolevnrm on 2009-03-25 11:37:45 as along with 3 people and 2 groups bmduggan oteri mleis baker-group Structural Biology Group TorVergata
	On using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models [My Copy] Phys. Chem. Chem. Phys., Vol. 11, No. 12. (28 March 2009), pp. 1934-1941. by Moritz Winger, Daniel Trzesniak, Riccardo Baron, Wilfred F. Gunsteren posted to molecular_dynamics multiscale by sobolevnrm on 2009-03-23 11:56:40 as along with 5 people and 1 group sunnytov arnaucordomi patvarilly mbeeby flbarroso baker-group
	Accelerating molecular dynamic simulation on graphics processing units [My Copy] Journal of Computational Chemistry, Vol. 30, No. 6. (2009), pp. 864-872. by Mark S. Friedrichs, Peter Eastman, Vishal Vaidyanathan, et al.Mike Houston, Scott Legrand, Adam L. Beberg, Daniel L. Ensign, Christopher M. Bruns, Vijay S. Pande posted to molecular_dynamics molecular_simulation programming software visualization by sobolevnrm on 2009-03-20 11:47:34 as along with 12 people and 4 groups paulymer oteri anuragsethi kevinchannon flbarroso r2s2 iantunbridge ihaque ruvido massivemayhem barry RamuAnandakrishnan GPGPU baker-group structural_bioinformatics McCammon
	Molecular Dynamics Simulation of DNA-Functionalized Gold Nanoparticles [My Copy] The Journal of Physical Chemistry C, Vol. 113, No. 6. (12 February 2009), pp. 2316-2321. by One-Sun Lee, George C. Schatz posted to molecular_dynamics nanotech nucleic_acids by sobolevnrm on 2009-03-19 12:06:45 as along with 3 people and 1 group charlesvardeman georgwachter carlosjavierna baker-group
	Achieving energy conservation in Poisson–Boltzmann molecular dynamics: Accuracy and precision with finite-difference algorithms [My Copy] Chemical Physics Letters, Vol. 468, No. 4-6. (22 January 2009), pp. 112-118. by J. Wang, Q. Cai, Z. Li, H. Zhao, R. Luo posted to electrostatics molecular_dynamics solvation by sobolevnrm on 2009-03-18 11:27:48 as along with 1 person and 2 groups jmccammon baker-group McCammon
	What Makes Molecular Dynamics Work? [My Copy] SIAM Journal on Scientific Computing, Vol. 31, No. 2. (2009), pp. 1363-1378. by Robert D. Skeel posted to mathematics molecular_dynamics by sobolevnrm on 2009-03-18 11:23:54 as along with 1 person and 1 group onufriev baker-group
	Efficient evaluation of sampling quality of molecular dynamics simulations by clustering of dihedral torsion angles and Sammon mapping [My Copy] Journal of Computational Chemistry, Vol. 30, No. 3. (2009), pp. 479-492. by Stephan Frickenhaus, Srinivasaraghavan Kannan, Martin Zacharias posted to clustering molecular_dynamics quasiharmonic_models by sobolevnrm on 2009-03-12 12:31:38 as along with 3 people and 1 group Diego_Prada scampos agrossfield baker-group
	GridMAT-MD: A grid-based membrane analysis tool for use with molecular dynamics [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA. by William J. Allen, Justin A. Lemkul, David R. Bevan posted to biomembranes molecular_dynamics software by sobolevnrm on 2009-03-03 15:53:05 as along with 1 person and 1 group choonpeng baker-group
	Molecular Dynamics Simulations of Discoidal Bilayers Assembled from Truncated Human Lipoproteins [My Copy] Biophys. J., Vol. 88, No. 1. (1 January 2005), pp. 548-556. by Amy Y. Shih, Ilia G. Denisov, James C. Phillips, Stephen G. Sligar, Klaus Schulten posted to biomembranes molecular_dynamics nanotech by sobolevnrm on 2009-03-03 15:51:20 as along with 3 people and 1 group paulschlesinger gjuggler softsimu baker-group
	Dynamical transition, hydrophobic interface, and the temperature dependence of electrostatic fluctuations in proteins [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 78, No. 6. (2008) by David N. Lebard, Dmitry V. Matyushov posted to beyond_mean_field electrostatics kinetics molecular_dynamics nonpolar by sobolevnrm on 2009-02-28 21:49:12 as along with 1 group baker-group
	Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 2. (10 February 2009), pp. 350-358. by David L. Mobley, Christopher I. Bayly, Matthew D. Cooper, Michael R. Shirts, Ken A. Dill posted to molecular_dynamics molecular_simulation solvation by sobolevnrm on 2009-02-20 13:11:18 as along with 3 people and 1 group flbarroso carlosjavierna pmk baker-group
	Simulations of a Protein Crystal: Explicit Treatment of Crystallization Conditions Links Theory and Experiment in the Streptavidin−Biotin Complex† [My Copy] Biochemistry, Vol. 47, No. 46. (18 November 2008), pp. 12065-12077. by David S. Cerutti, Isolde Le Trong, Ronald E. Stenkamp, Terry P. Lybrand posted to molecular_dynamics protein-protein_interactions by sobolevnrm on 2009-02-20 13:09:26 as along with 1 group baker-group
	DNA Attraction in Monovalent and Divalent Electrolytes [My Copy] Journal of the American Chemical Society, Vol. 130, No. 47. (26 November 2008), pp. 15754-15755. by Binquan Luan, Aleksei Aksimentiev posted to beyond_mean_field electrostatics molecular_dynamics nucleic_acids by sobolevnrm on 2009-02-06 11:51:49 as along with 1 group baker-group
	Prediction of pK<SUB><FONT SIZE='-1'>a</FONT></SUB> shifts in proteins using a combination of molecular mechanical and continuum solvent calculations [My Copy] Journal of Computational Chemistry, Vol. 25, No. 15. (2004), pp. 1865-1872. by Bernd Kuhn, Peter A. Kollman, Martin Stahl posted to electrostatics molecular_dynamics pka solvation by sobolevnrm on 2009-02-05 12:47:20 as along with 3 people and 1 group flbarroso dfgreen sim82 baker-group
	Open Science Grid Study of the Coupling between Conformation and Water Content in the Interior of a Protein [My Copy] Journal of Chemical Information and Modeling, Vol. 48, No. 10. (27 October 2008), pp. 2021-2029. by Ana Damjanović, Benjamin T. Miller, Torre J. Wenaus, Petar Maksimović, García-Moreno, Bernard R. Brooks posted to molecular_dynamics pka programming software solvation by sobolevnrm on 2008-12-28 15:34:46 as along with 1 group baker-group
	Hydration Water Dynamics Near Biological Interfaces† [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 13. (2 April 2009), pp. 4082-4092. by Margaret E. Johnson, Cecile Malardier-Jugroot, Rajesh K. Murarka, Teresa Head-Gordon posted to molecular_dynamics solvation by sobolevnrm on 2008-12-28 15:33:10 as along with 5 people and 2 groups whitead willard flbarroso Lombardo_7 kvilonen Jiang Research Group baker-group
	Spontaneous Formation of KCl Aggregates in Biomolecular Simulations: A Force Field Issue? [My Copy] Journal of Chemical Theory and Computation, Vol. 3, No. 5. (2007), 1851-9. by Auffinger posted to electrostatics solvation molecular_dynamics molecular_simulation by sobolevnrm on 2008-12-27 14:44:57 as
	Examining the Contributions of Lipid Shape and Headgroup Charge on Bilayer Behavior [My Copy] Biophysical Journal, Vol. 95, No. 6. (2008), 2636-2646. by Allison Dickey, Roland Faller posted to biomembranes molecular_dynamics by sobolevnrm on 2008-12-15 12:52:11 as
	Bilayer Edge and Curvature Effects on Partitioning of Lipids by Tail Length: Atomistic Simulations [My Copy] Biophysical Journal, Vol. 95, No. 6. (2008), 2647-2657. by Hao Wang, Jason de Joannis, Yong Jiang, et al.Jeffrey C. Gaulding, Birgit Albrecht, Fuchang Yin, Kunal Khanna, James T. Kindt posted to biomembranes molecular_dynamics by sobolevnrm on 2008-12-15 12:52:11 as
	Water in hydrated orthorhombic lysozyme crystal: Insight from atomistic simulations [My Copy] The Journal of Chemical Physics, Vol. 129, No. 7. (2008), 075105. by Zhongqiao Hu, Jianwen Jiang, Stanley I. Sandler posted to solvation molecular_dynamics by sobolevnrm on 2008-12-15 12:52:10 as
	Electrostatic Properties of Aqueous Salt Solution Interfaces: A Comparison of Polarizable and Nonpolarizable Ion Models [My Copy] Journal of Physical Chemistry B, Vol. 112, No. 37. (2008), 11679-11693. by Lee G. Warren, Sandeep Patel posted to electrostatics solvation molecular_dynamics by sobolevnrm on 2008-12-15 12:52:10 as
	Enhanced Hydrophobicity of Fluorinated Lipid Bilayer: A Molecular Dynamics Study [My Copy] J. Phys. Chem. B, Vol. 112, No. 36. (2008), 11305-11309. by Hiroaki Saito, Wataru Shinoda, Masuhiro Mikami posted to biomembranes perfluorocarbons solvation molecular_dynamics by sobolevnrm on 2008-12-15 12:52:09 as
	Large-Scale Molecular Dynamics Simulations of Self-Assembling Systems [My Copy] Science, Vol. 321, No. 5890. (2008), 798-800. by Michael L. Klein, Wataru Shinoda posted to multiscale review molecular_dynamics by sobolevnrm on 2008-12-15 12:52:09 as

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sobolevnrm's molecular_dynamics [at least 200 articles] Export Sort

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