Tag molecular_simulation [at least 200 articles] Export

Recent papers classified by the tag molecular_simulation.

	Molecular Simulations of Adsorption Isotherms for Linear and Branched Alkanes and Their Mixtures in Silicalite [My Copy] The Journal of Physical Chemistry B, Vol. 103, No. 7. (1 February 1999), pp. 1102-1118. by T. J. H. Vlugt, R. Krishna, B. Smit posted to molecular_simulation adsorption by zhaidong on 2009-11-11 12:02:54 as
	Molecular Simulations of Zeolites: Adsorption, Diffusion, and Shape Selectivity [My Copy] Chemical Reviews, Vol. 108, No. 10. (8 October 2008), pp. 4125-4184. by Berend Smit, Theo L. M. Maesen posted to zeolite review molecular_simulation adsorption by zhaidong on 2009-11-10 11:59:55 as along with 1 person tovrstra
	Agreement between Analytical Theory and Molecular Dynamics Simulation for Adsorption and Diffusion in Crystalline Nanoporous Materials [My Copy] The Journal of Physical Chemistry B, Vol. 108, No. 1. (1 January 2004), pp. 376-386. by Mithun Kamat, Weijing Dang, David Keffer posted to zeolite review molecular_simulation adsorption by zhaidong on 2009-11-09 12:47:33 as
	Adsorption of Guest Molecules in Zeolitic Materials: Computational Aspects [My Copy] The Journal of Physical Chemistry B, Vol. 105, No. 31. (1 August 2001), pp. 7375-7383. by Alain H. Fuchs, Anthony K. Cheetham posted to zeolite review monte_carlo molecular_simulation adsorption by zhaidong on 2009-11-09 12:35:49 as along with 2 people apulido tovrstra
	Using molecular simulation to characterise metal-organic frameworks for adsorption applications [My Copy] Chem. Soc. Rev., Vol. 38, No. 5. (2009), pp. 1237-1247. by Tina Duren, Youn-Sang Bae, Randall Q. Snurr posted to molecular_simulation by matthiasvandichel on 2009-11-09 09:50:29 as
	Free Energy and Kinetics of Conformational Transitions from Voronoi Tessellated Milestoning with Restraining Potentials [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 10. (13 October 2009), pp. 2589-2594. by Luca Maragliano, Eric Vanden-Eijnden, Benoît Roux posted to molecular_simulation free_energy by sobolevnrm on 2009-10-31 00:16:11 as along with 1 person anuragsethi
	Computation of Absolute Hydration and Binding Free Energy with Free Energy Perturbation Distributed Replica-Exchange Molecular Dynamics [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 10. (13 October 2009), pp. 2583-2588. by Wei Jiang, Milan Hodoscek, Benoît Roux posted to solvation molecular_simulation electrostatics by sobolevnrm on 2009-10-31 00:09:30 as along with 1 person qshao
	Electrostatic Potential Derived Atomic Charges for Periodic Systems Using a Modified Error Functional [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 10. (13 October 2009), pp. 2866-2878. by Carlos Campañá, Bastien Mussard, Tom K. Woo posted to molecular_simulation electrostatics by sobolevnrm on 2009-10-31 00:09:02 as
	Molecular Simulation Study of Adsorption and Diffusion on Silicalite for a Benzene/CO2 Mixture [My Copy] Langmuir, Vol. 22, No. 7. (1 March 2006), pp. 3138-3147. by Xiaopeng Yue, Xiaoning Yang posted to zeolite molecular_simulation adsorption by zhaidong on 2009-10-30 17:34:22 as along with 1 person apulido
	Monte Carlo Investigations of the Water Adsorption Behavior in MFI Type Zeolites for different Si/Al Ratios with Regard to Heat Storage Applications [My Copy] Adsorption, Vol. 11, No. 0. (1 July 2005), pp. 361-366. by Stefan K. Henninger, Ferdinand P. Schmidt, Tomas Nunez, Hans-Martin Henning posted to zeolite molecular_simulation adsorption by zhaidong on 2009-10-30 17:19:14 as
	Adsorption and Separation of Ternary and Quaternary Mixtures of Short Linear Alkanes in Zeolites by Molecular Simulation [My Copy] Langmuir, Vol. 19, No. 25. (1 December 2003), pp. 10617-10623. by Linghong Lu, Qi Wang, Yingchun Liu posted to zeolite molecular_simulation adsorption by zhaidong on 2009-10-30 17:16:53 as
	Molecular modeling of binary liquid-phase adsorption of aromatics in silicalite [My Copy] AIChE Journal, Vol. 50, No. 2. (2004), pp. 463-469. by Shaji Chempath, Randall Q. Snurr, John J. Low posted to zeolite molecular_simulation adsorption by zhaidong on 2009-10-30 17:11:12 as
	Computer simulation of the adsorption of ethanethiol in silicalite of MFI and MOR [My Copy] The Journal of Chemical Physics, Vol. 121, No. 18. (2004), pp. 9098-9102. by Shen G. Ju, Yong P. Zeng, Hu Q. Yao posted to zeolite molecular_simulation adsorption by zhaidong on 2009-10-30 17:07:46 as
	Molecular siting in the liquid-phase adsorption of alkane and aromatic mixtures in MFI zeolites: An experimental and molecular modeling study [My Copy] In Recent Advances in the Science and Technology of Zeolites and Related Materials Part B, Proceedings of the 14 International Zeolite Conference, Vol. 154 (2004), pp. 1983-1990. by S. Chempath, R. Snurr, J. Denayer, G. Baron posted to zeolite molecular_simulation adsorption by zhaidong on 2009-10-30 17:04:22 as
	Experimental and molecular simulation studies of a ZSM-5-MCM-41 micro-mesoporous molecular sieve [My Copy] Microporous and Mesoporous Materials, Vol. 118, No. 1-3. (01 February 2009), pp. 396-402. by C. Huiyong, X. Hongxia, C. Xianying, Q. Yu posted to zeolite molecular_simulation materials_studio adsorption by zhaidong on 2009-10-30 12:29:19 as
	Adsorption of thiophene and benzene in sodium-exchanged MFI- and MOR-type zeolites: A molecular simulation study [My Copy] Separation and Purification Technology, Vol. 67, No. 1. (18 May 2009), pp. 71-78. by Yongping Zeng, Shengui Ju posted to zeolite monte_carlo molecular_simulation adsorption by zhaidong on 2009-10-30 12:23:04 as
	Interaction of nanoparticles with lipid layers [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 80, No. 2. (2009), 021607. by Jonghyun Park, Wei Lu posted to nanotech nanoparticles molecular_simulation biomembrane by sobolevnrm on 2009-10-29 13:54:24 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
	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
	Molecular Dynamics Simulation Study of Correlated Motions in Phospholipid Bilayer Membranes [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 40. (8 October 2009), pp. 13229-13234. by Matthew Roark, Scott E. Feller posted to molecular_simulation biomembranes by sobolevnrm on 2009-10-25 19:29:31 as along with 2 people agrossfield dimka
	Stability of Asymmetric Lipid Bilayers Assessed by Molecular Dynamics Simulations [My Copy] Journal of the American Chemical Society, Vol. 131, No. 42. (28 October 2009), pp. 15194-15202. by Santi Esteban-Martín, H. Jelger Risselada, Jesús Salgado, Siewert J. Marrink posted to molecular_simulation biomembranes by sobolevnrm on 2009-10-24 22:43:14 as
	Multiscale simulation of soft matter systems - from the atomistic to the coarse-grained level and back [My Copy] Soft Matter, Vol. 5, No. 22. (2009), pp. 4357-4366. by Christine Peter, Kurt Kremer posted to review multiscale molecular_simulation by sobolevnrm on 2009-10-17 01:33:54 as along with 2 people flbarroso anuragsethi
	Assessing the performance of implicit solvation models at a nucleic acid surface [My Copy] Phys. Chem. Chem. Phys., Vol. 10, No. 32. (2008), pp. 4889-4902. by Feng Dong, Jason A. Wagoner, Nathan A. Baker posted to solvation nucleic_acids molecular_simulation electrostatics by sobolevnrm on 2009-10-16 13:35:01 as along with 3 people and 1 group onufriev simone jmccammon McCammon
	Mori-Zwanzig formalism as a practical computational tool [My Copy] Faraday Discuss. (2010) by Carmen Hijon, Pep Espanol, Eric Vanden-Eijnden, Rafael Delgado-Buscalioni posted to statistical_mechanics molecular_simulation by sobolevnrm on 2009-10-15 12:33:18 as
	Experimental verification of lipid bilayer structure through multi-scale modeling [My Copy] Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1788, No. 10. (17 October 2009), pp. 2284-2290. by Jason D. Perlmutter, Jonathan N. Sachs posted to multiscale molecular_simulation biomembranes by sobolevnrm on 2009-10-12 12:40:22 as
	Systematic coarse graining from structure using internal states: Application to phospholipid/cholesterol bilayer [My Copy] The Journal of Chemical Physics, Vol. 131, No. 5. (2009), 055101. by Teemu Murtola, Mikko Karttunen, Ilpo Vattulainen posted to sterols multiscale molecular_simulation biomembranes by sobolevnrm on 2009-10-07 12:45:28 as along with 3 people anuragsethi cjryan agrossfield
	Quantifying Correlations Between Allosteric Sites in Thermodynamic Ensembles [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 9. (8 September 2009), pp. 2486-2502. by Christopher L. McClendon, Gregory Friedland, David L. Mobley, Homeira Amirkhani, Matthew P. Jacobson posted to molecular_simulation correlations allostery by pmung on 2009-10-06 16:13:35 as along with 3 people and 1 group jmccammon anuragsethi acpan McCammon
	Docking Ligands on Protein Surfaces: The Case Study of Prion Protein‡ [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 9. (8 September 2009), pp. 2565-2573. by Agata Kranjc, Salvatore Bongarzone, Giulia Rossetti, et al.Xevi Biarnés, Andrea Cavalli, Maria L. Bolognesi, Marinella Roberti, Giuseppe Legname, Paolo Carloni posted to nmr_measurements molecular_simulation docking by pmung on 2009-10-05 19:47:13 as
	Staggered Mesh Ewald: An Extension of the Smooth Particle-Mesh Ewald Method Adding Great Versatility [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 9. (8 September 2009), pp. 2322-2338. by David S. Cerutti, Robert E. Duke, Thomas A. Darden, Terry P. Lybrand posted to molecular_simulation electrostatics by sobolevnrm on 2009-10-01 13:14:17 as
	Determining the Local Shear Viscosity of a Lipid Bilayer System by Reverse Non-Equilibrium Molecular Dynamics Simulations [My Copy] ChemPhysChem, Vol. 10, No. 13. (2009), pp. 2305-2315. by Thomas J. Müller, Florian Müller-Plathe posted to molecular_simulation diffusion biomembranes by sobolevnrm on 2009-09-24 12:36:20 as along with 1 person paulschlesinger
	Analysing the origin of long-range interactions in proteins using lattice models [My Copy] BMC Structural Biology, Vol. 9, No. 1. (29 January 2009), 4. by Orly N. Brik, Ron Unger, Amnon Horovitz posted to molecular_simulation allostery by sobolevnrm on 2009-09-24 12:35:34 as along with 2 people and 2 groups anuragsethi barry structural_bioinformatics McCammon
	CHARMM-GUI Membrane Builder for Mixed Bilayers and Its Application to Yeast Membranes [My Copy] Biophysical Journal, Vol. 97, No. 1. (08 July 2009), pp. 50-58. by Sunhwan Jo, Joseph B. Lim, Jeffery B. Klauda, Wonpil Im posted to software molecular_simulation biomembranes by sobolevnrm on 2009-09-01 12:44:11 as
	How to obtain statistically converged MM/GBSA results [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Samuel Genheden, Ulf Ryde posted to solvation molecular_simulation free_energy electrostatics by sobolevnrm on 2009-08-19 12:54:22 as along with 3 people and 1 group pmung barry RamuAnandakrishnan McCammon
	Solving the equations of motion for mixed atomistic and coarse-grained systems [My Copy] Molecular Simulation, Vol. 35, No. 10. (2009), pp. 962-973. by Jong H. Park, Andreas Heyden posted to multiscale molecular_simulation by sobolevnrm on 2009-08-18 12:37:18 as along with 1 person flbarroso
	A Cartesian treecode for screened coulomb interactions [My Copy] Journal of Computational Physics, Vol. 228, No. 10. (01 June 2009), pp. 3858-3868. by Peijun Li, Hans Johnston, Robert Krasny posted to electrostatics mathematics molecular_simulation by sobolevnrm on 2009-07-17 12:52:57 as
	Hydration Free Energies of Amino Acids: Why Side Chain Analog Data Are Not Enough [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 26. (2 July 2009), pp. 8967-8974. by Gerhard König, Stefan Boresch posted to molecular_simulation solvation by sobolevnrm on 2009-06-26 12:55:07 as along with 2 people flbarroso carlosjavierna
	Self-learning multiscale simulation for achieving high accuracy and high efficiency simultaneously [My Copy] The Journal of Chemical Physics, Vol. 130, No. 21. (2009), 214108. by Wenfei Li, Shoji Takada posted to molecular_simulation multiscale by sobolevnrm on 2009-06-24 12:21:39 as
	Integrated Continuum Dielectric Approaches To Treat Molecular Polarizability and the Condensed Phase: Refractive Index and Implicit Solvation [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 7. (14 July 2009), pp. 1785-1802. by Jean-François Truchon, Anthony Nicholls, Benoît Roux, Radu I. Iftimie, Christopher I. Bayly posted to electrostatics molecular_simulation solvation by sobolevnrm on 2009-06-21 14:46:03 as along with 1 person carlosjavierna
	United Atom Lipid Parameters for Combination with the Optimized Potentials for Liquid Simulations All-Atom Force Field [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 7. (14 July 2009), pp. 1803-1813. by Jakob P. Ulmschneider, Martin B. Ulmschneider posted to biomembranes molecular_simulation by sobolevnrm on 2009-06-15 00:14:16 as along with 1 person arnaucordomi
	Force field dependence of phospholipid headgroup and acyl chain properties: Comparative molecular dynamics simulations of DMPC bilayers [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Priyanka Prakash, Ramasubbu Sankararamakrishnan posted to biomembranes molecular_simulation by sobolevnrm on 2009-06-12 12:57:33 as
	Salt induced asymmetry in membrane simulations by partial restriction of ionic motion. [My Copy] The Journal of chemical physics, Vol. 130, No. 19. (21 May 2009) by Fernando E E. Herrera, Sergio Pantano posted to biomembranes electrostatics molecular_simulation by sobolevnrm to the group baker-group on 2009-05-27 12:02:13 as
	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 to the group baker-group on 2009-05-19 12:00:47 as along with 8 people rodrigofaccioli mmuecke medic0747 flbarroso jrperillaj xavierprat saravan dimka
	Characterizing Structural Transitions Using Localized Free Energy Landscape Analysis [My Copy] PLoS ONE, Vol. 4, No. 5. (13 May 2009), e5525. by Nilesh K. Banavali, Alexander D. Mackerell posted to free_energy molecular_simulation nucleic_acids by sobolevnrm to the group baker-group on 2009-05-13 12:12:15 as along with 1 person and 1 group barry McCammon
	Reproducing Basic pKa Values for Turkey Ovomucoid Third Domain Using a Polarizable Force Field [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by Timothy H. Click, George A. Kaminski posted to electrostatics molecular_simulation pka solvation by sobolevnrm to the group baker-group on 2009-05-13 12:10:31 as
	Explicitly Representing the Solvation Shell in Continuum Solvent Calculations [My Copy] The Journal of Physical Chemistry A, Vol. 0, No. 0. (0000) by Eirik F. da Silva, Hallvard F. Svendsen, Kenneth M. Merz posted to electrostatics molecular_simulation multiscale quantum_mechanics solvation by sobolevnrm to the group baker-group on 2009-05-11 12:27:40 as along with 2 people goncalojustino carlosjavierna
	Elucidating the Inhibition Mechanism of HIV-1 Non-Nucleoside Reverse Transcriptase Inhibitors through Multicopy Molecular Dynamics Simulations [My Copy] Journal of Molecular Biology, Vol. 388, No. 3. (08 May 2009), pp. 644-658. by Anthony Ivetac, J. Andrew Mccammon posted to enhanced_sampling molecular_simulation protein-ligand_interactions by sobolevnrm to the group baker-group on 2009-04-23 12:32:31 as along with 2 people bmduggan paulschlesinger
	Increasing the precision of comparative models with YASARA NOVA - a self-parameterizing force field [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 47, No. 3. (2002), pp. 393-402. by Elmar Krieger, Günther Koraimann, Gert Vriend posted to molecular_simulation optimization structure_prediction by sobolevnrm to the group baker-group on 2009-04-23 12:29:22 as
	Molecular dynamics simulations of membrane channels and transporters [My Copy] Current Opinion in Structural Biology (01 April 2009) by Fatemeh Khalili-Araghi, James Gumbart, Po-Chao Wen, Marcos Sotomayor, Emad Tajkhorshid, Klaus Schulten posted to biomembranes ion_channels molecular_simulation review by sobolevnrm to the group baker-group on 2009-04-21 12:30:01 as along with 2 people dimka paulschlesinger

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solvation	136
electrostatics	122
molecular_dynamics	111
biomembranes	88
multiscale	52
enhanced_sampling	38
allostery	32
free_energy	32
quasiharmonic_models	23
nucleic_acids	22
protein-ligand_interactions	16
statistical_mechanics	15
adsorption	14
zeolite	14
mathematics	13
protein_folding	12
quasiharmonic-models_elastic-network_gnm_nma_pca_etc	11
interfaces	10
nonpolar	10
review	10
diffusion	9
software	9
experimental_methodology	8
quantum_mechanics	8
structure	8
fluid_dynamics	7
microfluidics	7
clustering	6
ion_channels	6
kinetics	6
protein-membrane_interactions	6
protein-protein_interactions	6
bioinformatics	5
nanotech	5
beyond_mean_field	4
metalloregulation	4
monte_carlo	4
perfluorocarbons	4
pka	4
teaching	4
visualization	4
materials_studio	3
model_building	3
nucleic_acid_builder	3
oct09	3
ribosome	3
sterols	3
correlated_mutations	2
correlations	2
cytoskeleton	2
docking	2
drug_design	2
emulsions	2
generalized_born	2
ligand-membrane_interactions	2
mechanics	2
misc	2
networks	2
nitric_oxide	2
nmr	2
nmr_measurements	2
optimization	2
programming	2
protein-nucleic_acid_interactions	2
statistics	2
structure_prediction	2
thrombin	2
biomembrane	1
coarse-grained	1
elastic	1
intermolecular	1
nanoparticles	1
network	1
sabio	1
simulation	1

Tag molecular_simulation [at least 200 articles] Export

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