Tag molecular_dynamics [at least 200 articles] Export

Recent papers classified by the tag molecular_dynamics.

	Simulation of nanostructured lubricant films [My Copy] Magnetics, IEEE Transactions on, Vol. 39, No. 2. (07 May 2003), pp. 754-758. by M. S. Jhon, S. Izumisawa, Qian Guo, D. M. Phillips, Yiao-Tee Hsia posted to molecular_dynamics lubricant fluoropolymer by 6rheology on 2009-11-27 03:46:56 as
	Reorientations of Aromatic Amino Acids and Their Side Chain Models: Anisotropy Measurements and Molecular Dynamics Simulations [My Copy] The Journal of Physical Chemistry A, Vol. 0, No. 0. (0000) by Krzysztof Kuczera, Jay Unruh, Carey K. Johnson, Gouri S. Jas posted to molecular_dynamics fluorescence anisotropy aminoacid by A_Coletta_Thesis to the group Structural Biology Group TorVergata on 2009-11-25 17:42:59 as
	Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models [My Copy] Journal of Computational Chemistry, Vol. 13, No. 8. (1992), pp. 952-962. by Shuichi Miyamoto, Peter A. Kollman posted to molecular_dynamics by oteri on 2009-11-19 13:15:15 as along with 8 people Lombardo_7 choonpeng A_Coletta_Thesis jwagoner tji softsimu ashaytan robertvacha
	GPU-accelerated large-scale quantum molecular dynamics simulation of 3-dimensional C60 polymers [My Copy] (23 Oct 2009) by Toshiaki Iitaka posted to molecular_dynamics gpu by marinari on 2009-11-12 09:39:38 as
	An aPKC-Exocyst Complex Controls Paxillin Phosphorylation and Migration through Localised JNK1 Activation [My Copy] PLoS Biol, Vol. 7, No. 11. (3 November 2009), e1000235. by Carine Rosse, Etienne Formstecher, Katrina Boeckeler, et al.Yingming Zhao, Joachim Kremerskothen, Michael D. White, Jacques H. Camonis, Peter J. Parker posted to protein-structure programming molecular_dynamics maximum-likelifood by hryk on 2009-11-06 09:15:04 as along with 1 person renatomilani
	Full correlation analysis of conformational protein dynamics [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA. by Oliver F. Lange, Helmut Grubmüller posted to principal_component_analysis molecular_dynamics correlation_analysis allostery by jeargle on 2009-11-04 18:59:40 as along with 7 people and 1 group anuragsethi Diego_Prada softsimu barry choonpeng sobolevnrm LamBras baker-group
	MDLab: A molecular dynamics simulation prototyping environment [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Trevor Cickovski, Santanu Chatterjee, Jacob Wenger, Christopher R. Sweet, Jesús A. Izaguirre posted to simulation_methods nov09 molecular_dynamics mdlab jcc gpu by klexa on 2009-11-04 15:39:41 as
	Efficient nonbonded interactions for molecular dynamics on a graphics processing unit [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Peter Eastman, Vijay S. Pande posted to sampling nov09 nonbonded_interactions molecular_dynamics jcc gpu by klexa on 2009-11-04 15:38:14 as along with 1 person RamuAnandakrishnan
	Conformational populations of ligand-sized molecules by replica exchange molecular dynamics and temperature reweighting [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Hisashi Okumura, Emilio Gallicchio, Ronald M. Levy posted to replica_exchange populations nov09 molecular_dynamics ligand jcc conformation by klexa on 2009-11-04 15:36:26 as
	High-Performance Drug Discovery: Computational Screening by Combining Docking and Molecular Dynamics Simulations [My Copy] PLoS Comput Biol, Vol. 5, No. 10. (9 October 2009), e1000528. by Noriaki Okimoto, Noriyuki Futatsugi, Hideyoshi Fuji, et al.Atsushi Suenaga, Gentaro Morimoto, Ryoko Yanai, Yousuke Ohno, Tetsu Narumi, Makoto Taiji posted to screening sbdd plos nov09 molecular_dynamics docking by klexa on 2009-11-04 14:29:40 as along with 5 people and 1 group ibuch skywalkerus02 kentsis reyez barry McCammon
	Structure and dynamics of topological defects in a glassy liquid on a negatively curved manifold [My Copy] (2 Nov 2009) by François Sausset, Gilles Tarjus, David R. Nelson posted to structural_glass molecular_dynamics liquid glass by marinari on 2009-11-04 11:10:57 as along with 1 person scratchmandoo
	On Finite-Size Corrections to the Free Energy of Ionic Hydration [My Copy] The Journal of Physical Chemistry B, Vol. 101, No. 29. (1 July 1997), pp. 5622-5623. by Francisco Figueirido, Gabriela S. Del Buono, Ronald M. Levy posted to molecular_dynamics implicit_solvation by onufriev on 2009-10-30 03:22:38 as
	Structural Relaxation of a Gel Modeled by Three Body Interactions [My Copy] (28 Oct 2009) by Shibu Saw, Niels L. Ellegaard, Walter Kob, Srikanth Sastry posted to weber stillinger molecular_dynamics gel by marinari on 2009-10-29 10:23:13 as
	Hard Spheres: Crystallization and Glass Formation [My Copy] (12 Aug 2009) by P. N. Pusey, E. Zaccarelli, C. Valeriani, E. Sanz, W. C. K. Poon, M. E. Cates posted to simulation molecular_dynamics hard_sphere glass_transition glass crystallization 3d by ghunter on 2009-10-28 20:09:39 as along with 4 people apatti marinari scratchmandoo danilov
	Crystallization of hard-sphere glasses [My Copy] Physical Review Letters, Vol. 103, No. 13. (20 Oct 2009), 135704. by E. Zaccarelli, C. Valeriani, E. Sanz, W. C. K. Poon, M. E. Cates, P. N. Pusey posted to simulation molecular_dynamics hard_sphere glass_transition glass crystallization 3d by ghunter on 2009-10-28 20:08:34 as along with 3 people marinari scratchmandoo joshBerryman
	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
	Adsorption and diffusion properties of hydrocarbons in zeolites [My Copy] Microporous and Mesoporous Materials, Vol. 104, No. 1-3. (23 August 2007), pp. 115-128. by Lijuan Song, Zhaolin Sun, Linhai Duan, Jianzhou Gui, Gordon S. McDougall posted to zeolite monte_carlo molecular_simulation molecular_dynamics materials_studio adsorption by zhaidong on 2009-10-27 09:21:02 as
	Analyzing adsorption and diffusion behaviors of ethanol/water through silicalite membranes by molecular simulation [My Copy] Journal of Membrane Science, Vol. 291, No. 1-2. (15 March 2007), pp. 1-9. by Jin Z. Yang, Qing L. Liu, Hai T. Wang posted to zeolite monte_carlo molecular_simulation molecular_dynamics materials_studio adsorption by zhaidong on 2009-10-27 07:57:39 as
	Adsorption and diffusion of benzene in the nanoporous catalysts FAU, ZSM-5 and MCM-22: A molecular dynamics study [My Copy] Journal of Molecular Graphics and Modelling, Vol. 24, No. 5. (March 2006), pp. 373-382. by Ratana Rungsirisakun, Tanin Nanok, Michael Probst, Jumras Limtrakul posted to zeolite molecular_simulation molecular_dynamics adsorption by zhaidong on 2009-10-27 07:53:30 as
	Slip, Immiscibility, and Boundary Conditions at the Liquid-Liquid Interface [My Copy] Physical Review Letters, Vol. 96, No. 4. (2006), 044505. by Joel Koplik, Jayanth R. Banavar posted to slip numerical_simulation multi-layer molecular_dynamics interface by 6rheology on 2009-10-27 02:43:22 as
	Clustering of Glycine Molecules in Aqueous Solution Studied by Molecular Dynamics Simulation [My Copy] The Journal of Physical Chemistry B, Vol. 112, No. 24. (1 June 2008), pp. 7280-7288. by Said Hamad, Colan E. Hughes, Catlow, Kenneth D. M. Harris posted to zwitterion molecular_dynamics md glyine glycine_dimer glycine by whitead to the group Jiang Research Group on 2009-10-26 06:13:40 as
	Molecular Dynamics Simulation of a Polymer Melt/Solid Interface: Local Dynamics and Chain Mobility in a Thin Film of Polyethylene Melt Adsorbed on Graphite [My Copy] Macromolecules, Vol. 38, No. 13. (1 June 2005), pp. 5796-5809. by Vagelis A. Harmandaris, Kostas C. Daoulas, Vlasis G. Mavrantzas posted to molecular_dynamics interface film by 6rheology on 2009-10-21 08:30:27 as
	Molecular simulation of thin polymer films with functional endgroups [My Copy] The Journal of Chemical Physics, Vol. 117, No. 8. (2002), pp. 3972-3977. by Satoru Izumisawa, Myung S. Jhon posted to molecular_dynamics film coarse-grained-model bead_spring by 6rheology on 2009-10-21 08:29:21 as
	A general-purpose coarse-grained molecular dynamics program [My Copy] Computer Physics Communications, Vol. 145, No. 2. (15 May 2002), pp. 267-279. by T. Aoyagi posted to molecular_dynamics coarse-grained-model by 6rheology on 2009-10-21 08:24:05 as
	Shear rate threshold for the boundary slip in dense polymer films [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 80, No. 3. (2009), 031608. by Nikolai V. Priezjev posted to wall shear_rate molecular_dynamics film bead_spring by 6rheology on 2009-10-21 08:13:57 as
	Rheological study of polymer flow past rough surfaces with slip boundary conditions [My Copy] The Journal of Chemical Physics, Vol. 129, No. 14. (2008), 144902. by Anoosheh Niavarani, Nikolai V. Priezjev posted to wall slip rough rheological_study polmer_flow molecular_dynamics by 6rheology on 2009-10-21 08:11:02 as
	Nonequilibrium molecular dynamics of the rheological and structural properties of linear and branched molecules. Simple shear and poiseuille flows; instabilities and slip [My Copy] The Journal of Chemical Physics, Vol. 123, No. 5. (2005), 054907. by Jorge C. Tejas, Juan F. J. Alvarado, Guillermo G. Alatorre, et al.Gabriel L. Bárcenas, Isaac C. Sanchez, Ricardo M. Salinas, Octavio Manero posted to slip shear rheological_properties nonequilibrium molecular_dynamics by 6rheology on 2009-10-21 08:08:27 as
	Molecular dynamics simulation of the rheological and dynamical properties of a model alkane fluid under confinement [My Copy] The Journal of Chemical Physics, Vol. 111, No. 3. (1999), pp. 1273-1280. by S. T. Cui, P. T. Cummings, H. D. Cochran posted to rheological_properties molecular_dynamics alkane by 6rheology on 2009-10-21 08:06:16 as
	Molecular dynamics characterization of thin film viscosity for EHL simulation [My Copy] Tribology Letters, Vol. 21, No. 3. (1 March 2006), pp. 217-225. by A. Martini, Y. Liu, R. Q. Snurr, Q. J. Wang posted to viscosity molecular_dynamics film ehl_simulation by 6rheology on 2009-10-21 07:24:32 as
	Ageing and memory in the relaxation dynamics of collections of two-level subsystems [My Copy] Journal of Physics: Condensed Matter, Vol. 17, No. 21. (1 June 2005), pp. 3343-3354. by C. A. Viddal, R. M. Roshko posted to relaxation_dynamics molecular_dynamics by 6rheology on 2009-10-21 07:18:46 as
	A space–time multilevel method for molecular dynamics simulations [My Copy] Computer Methods in Applied Mechanics and Engineering, Vol. 195, No. 44-47. (15 September 2006), pp. 6542-6559. by H. Waisman, J. Fish posted to space_time molecular_dynamics by 6rheology on 2009-10-21 07:11:46 as
	A coarse grain model for n-alkanes parameterized from surface tension data [My Copy] The Journal of Chemical Physics, Vol. 119, No. 14. (2003), pp. 7043-7049. by Steve O. Nielsen, Carlos F. Lopez, Goundla Srinivas, Michael L. Klein posted to surface molecular_dynamics coarse-grain by 6rheology on 2009-10-21 07:09:43 as
	Shear thinning and shear dilatancy of liquid n-hexadecane via equilibrium and nonequilibrium molecular dynamics simulations: Temperature, pressure, and density effects [My Copy] The Journal of Chemical Physics, Vol. 129, No. 1. (2008), 014502. by Huan C. Tseng, Jiann S. Wu, Rong Y. Chang posted to shear_thinning shear molecular_dynamics by 6rheology on 2009-10-21 07:02:29 as
	General continuum boundary conditions for miscible binary fluids from molecular dynamics simulations [My Copy] The Journal of Chemical Physics, Vol. 125, No. 21. (2006), 214102. by Colin Denniston, Mark O. Robbins posted to molecular_dynamics miscible by 6rheology on 2009-10-21 06:55:30 as
	Slip boundary conditions for shear flow of polymer melts past atomically flat surfaces [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 77, No. 4. (2008), 041606. by Anoosheh Niavarani, Nikolai V. Priezjev posted to slip shear_flow polymer_melt molecular_dynamics by 6rheology on 2009-10-21 06:50:05 as along with 1 person dchen
	Shear viscosity of a supercooled polymer melt via nonequilibrium molecular dynamics simulations [My Copy] The Journal of Chemical Physics, Vol. 117, No. 13. (2002), pp. 6336-6349. by F. Varnik, K. Binder posted to viscosity shear polymer nonequilibrium molecular_dynamics by 6rheology on 2009-10-21 06:34:06 as
	Comparison of molecular dynamics with hybrid continuum--molecular dynamics for a single tethered polymer in a solvent [My Copy] The Journal of Chemical Physics, Vol. 121, No. 5. (2004), pp. 2403-2411. by Sandra Barsky, Rafael D. Buscalioni, Peter V. Coveney posted to solvent molecular_dynamics comparison by 6rheology on 2009-10-21 06:32:42 as
	Shear effects on phase separating polymer solutions: A molecular dynamics study [My Copy] The Journal of Chemical Physics, Vol. 112, No. 23. (2000), pp. 10582-10587. by Hong Liu, Amitabha Chakrabarti posted to shear polymer phase molecular_dynamics 2009_rinko_kouho by 6rheology on 2009-10-20 05:57:18 as
	Molecular dynamics study of polymer melt confined between walls [My Copy] The Journal of Chemical Physics, Vol. 115, No. 1. (2001), pp. 552-559. by Takeshi Aoyagi, Jun I. Takimoto, Masao Doi posted to wall polymer_melt molecular_dynamics 2009_rinko_kouho by 6rheology on 2009-10-20 05:49:03 as
	Molecular dynamics simulation of entangled polymers in shear flow [My Copy] Computational and Theoretical Polymer Science, Vol. 10, No. 3-4. (June 2000), pp. 317-321. by T. Aoyagi posted to shear molecular_dynamics entangled_polymer 2009_rinko_kouho by 6rheology on 2009-10-20 05:43:21 as
	Coarse-grained molecular dynamics simulations of polymer melts in transient and steady shear flow [My Copy] The Journal of Chemical Physics, Vol. 118, No. 22. (2003), pp. 10276-10286. by J. T. Padding, W. J. Briels posted to steady shear polymer molecular_dynamics 2009_rinko_kouho by 6rheology on 2009-10-20 05:37:09 as
	A Molecular Dynamics Study of Lubrication Rheology of Polymer Fluids [My Copy] Tribology Letters, Vol. 15, No. 3. (1 October 2003), pp. 293-299. by Yeau-Ren Jeng, Chia-Chen Chen, Shiuh-Hwa Shyu posted to wall slip rheology polymer molecular_dynamics lubricant 2009_rinko_kouho by 6rheology on 2009-10-20 05:34:47 as
	P<FONT SIZE='-2'>ACKMOL</FONT>: A package for building initial configurations for molecular dynamics simulations [My Copy] Journal of Computational Chemistry, Vol. 30, No. 13. (2009), pp. 2157-2164. by L. Martínez, R. Andrade, E. G. Birgin, J. M. Martínez posted to paper1 packmol molecular_dynamics by whitead to the group Jiang Research Group on 2009-10-18 19:01:35 as along with 2 people klexa middledomain
	Fast Parallel Algorithms for Short-Range Molecular Dynamics [My Copy] Journal of Computational Physics, Vol. 117, No. 1. (1 March 1995), pp. 1-19. by S. Plimpton posted to molecular_dynamics lammps by whitead to the group Jiang Research Group on 2009-10-18 19:00:03 as along with 4 people cjryan ashaytan3 gferencz jheco
	Strong Repulsive Forces between Protein and Oligo (Ethylene Glycol) Self-Assembled Monolayers: A Molecular Simulation Study [My Copy] Biophysical Journal, Vol. 89, No. 1. (July 2005), pp. 158-166. by J. Zheng posted to nonfouling molecular_dynamics by whitead to the group Jiang Research Group on 2009-10-18 18:16:29 as
	Hydration of “Nonfouling” Functional Groups [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 1. (8 January 2009), pp. 197-201. by Jason C. Hower, Matthew T. Bernards, Shengfu Chen, Heng-Kwong Tsao, Yu-Jane Sheng, Shaoyi Jiang posted to molecular_dynamics hydration by whitead to the group Jiang Research Group on 2009-10-18 17:45:10 as
	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 1 person and 1 group samjlord moernerlab
	Importance of the CMAP correction to the CHARMM22 protein force field: dynamics of hen lysozyme. [My Copy] Biophys J, Vol. 90, No. 4. (15 February 2006) by M. Buck, S. Bouguet-Bonnet, R. W. Pastor, A. D. MacKerell posted to molecular_dynamics charmm by jmparks on 2009-10-15 16:43:58 as along with 1 person allmensch
	All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins† [My Copy] The Journal of Physical Chemistry B, Vol. 102, No. 18. (1 April 1998), pp. 3586-3616. by A. D. MacKerell, D. Bashford, Bellott, et al.R. L. Dunbrack, J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, M. Karplus posted to molecular_dynamics force_field charmm by jmparks on 2009-10-15 16:39:07 as along with 12 people dsmueller rpetrenko jrperillaj Diego_Prada oceanwind dfgreen mkrishna timg dimka ttjoseph papatonyhill ssomani
	A smooth particle mesh Ewald method [My Copy] The Journal of Chemical Physics, Vol. 103, No. 19. (1995), pp. 8577-8593. by Ulrich Essmann, Lalith Perera, Max L. Berkowitz, Tom Darden, Hsing Lee, Lee G. Pedersen posted to pme molecular_dynamics by jmparks on 2009-10-15 16:37:36 as along with 15 people and 2 groups rpetrenko A_Coletta_Thesis r2s2 charris5 pavanghatty sobolevnrm choonpeng lillekatt and_ped10 easybakemuffin RamuAnandakrishnan ashaytan mikaellund 6rheology jteyra Structural Biology Group TorVergata baker-group

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molecular_simulation	111
electrostatics	68
solvation	60
biomembranes	47
parametrization	37
implicit_solvation	35
protein_structure	30
protein	29
dna	26
kinetics	26
fpga	24
simulation	24
folding	22
week9	22
ab-initio	21
free_energy	21
metadynamics	21
multiscale	19
structure	19
allostery	18
coarse_grained	18
enhanced_sampling	18
bioinformatics	17
force_field	17
gb	17
protein_folding	17
biophysics	15
monte_carlo	15
nucleic_acids	15
protein_dynamics	15
review	15
charmm	14
gabe	14
jspp_cae	14
nmr	14
pka	14
polymer	14
software	14
2008a	13
diffusion	13
free-energy	13
gpu	13
alexpogi	12
experimental_methodology	12
mathematics	12
oxygen_channel	12
2009	11
alternatives	11
docking	11
topoisomerase	11
data	10
dielectric	10
high-performance_computing	10
pca	10
pmf	10
computational_biology	9
dynamics	9
modeling	9
modelling	9
paper1	9
resp	9
simulation_methods	9
database	8
explicit_solvation	8
glass	8
jcc	8
nov09	8
protein-membrane_interactions	8
quasiharmonic_models	8
statistical_mechanics	8
clustering	7
conformation	7
gas_flow	7
nucleosome	7
shear	7
2009_rinko_kouho	6
beyond_mean_field	6
entropy	6
hydration	6
lab3	6
nanotech	6
nonpolar	6
pb	6
polymer_physics	6
quasiharmonic-models_elastic-network_gnm_nma_pca_etc	6
rna	6
slip	6
umbrella-sampling	6
dft	5
film	5
flexibility	5
fpgasupercomputing	5
hard-spheres	5
hard_sphere	5
hydrodynamics	5
interface	5
membrane	5
muriel	5
programming	5
solvent	5

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