Tag brownian_dynamics [40 articles] Export

Recent papers classified by the tag brownian_dynamics.

	pH-Dependent Association of Proteins. The Test Case of Monoclonal Antibody HyHEL-5 and Its Antigen Hen Egg White Lysozyme [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 47. (26 November 2009), pp. 15662-15669. by Maciej Długosz, Jan M. Antosiewicz, Joanna Trylska posted to titration protein-protein kinetics electrostatics diffusion brownian_dynamics binding by jmccammon to the group McCammon on 2009-11-21 20:11:33 as
	A Langevin dynamics simulation study of the tribology of polymer loop brushes [My Copy] The Journal of Chemical Physics, Vol. 127, No. 8. (2007), 084910. by Fang Yin, Dmitry Bedrov, Grant D. Smith, S. Michael Kilbey, II posted to slip polymer interface brownian_dynamics by 6rheology on 2009-10-27 02:51:54 as
	Bridging from molecular simulation to biochemical networks [My Copy] Current Opinion in Structural Biology, Vol. 17, No. 2. (April 2007), pp. 166-172. by M. Stein, R. Gabdoulline, R. Wade posted to systemsbiology dynamics brownian_dynamics by anuragsethi on 2009-10-25 16:33:47 as along with 10 people and 1 group cjryan choonpeng oteri ocs aqeel Borelli cmmorel julius ras higueruelo Structural Biology Group TorVergata
	Interfacial Phenomena in Polymer Blends: A Self-Consistent Brownian Dynamics Study [My Copy] Macromolecules, Vol. 37, No. 26. (1 December 2004), pp. 10180-10194. by Bharadwaj Narayanan, Victor A. Pryamitsyn, Venkat Ganesan posted to polymer numerical_simulation interface brownian_dynamics blend by 6rheology on 2009-10-14 08:25:04 as
	Geometric frustration in small colloidal clusters [My Copy] Journal of Physics: Condensed Matter, Vol. 21, No. 42. (2009), 425103. by Alex Malins, Stephen R. Williams, Jens Eggers, Hajime Tanaka, C. Patrick Royall posted to simulation colloid cluster brownian_dynamics by ipwilliams on 2009-10-07 16:42:18 as
	Simulation of polymer chains in elongational flow. Steady-state properties and chain fracture [My Copy] The Journal of Chemical Physics, Vol. 95, No. 12. (1991), pp. 9384-9392. by J. J. Lopez Cascales, Garcia de la Torre posted to polymer molecular_dynamics elongation brownian_dynamics by 6rheology on 2009-09-26 18:31:02 as
	Modeling 2D and 3D Diffusion [My Copy] Methods in Membrane Lipids (2007), pp. 295-321. by Michael J. Saxton posted to spatial_simulation particle_based diffusion brownian_dynamics by m_j on 2009-09-16 14:50:58 as
	RedMD - Reduced molecular dynamics package [My Copy] Journal of Computational Chemistry, Vol. 30, No. 14. (2009), pp. 2364-2373. by Adam Górecki, Marcin Szypowski, Maciej D&lstrok;ugosz, Joanna Trylska posted to multiscale dynamics brownian_dynamics by anuragsethi on 2009-09-16 14:23:36 as along with 4 people and 1 group oteri flbarroso jmccammon shwu McCammon
	The multivariate Langevin and Fokker--Planck equations [My Copy] American Journal of Physics, Vol. 64, No. 10. (1996), pp. 1246-1257. by Daniel T. Gillespie posted to stochastic_simulation brownian_dynamics by m_j on 2009-09-16 09:18:58 as
	Coarse grained simulations of a small peptide: Effects of finite damping and hydrodynamic interactions [My Copy] The Journal of Chemical Physics, Vol. 131, No. 10. (2009), 104102. by Uwe Winter, Tihamér Geyer posted to molecular_dynamics hydrodynamics course_grained brownian_dynamics by whitead to the group Jiang Research Group on 2009-09-10 16:51:59 as along with 3 people dlimmer agrossfield paulschlesinger
	Insight or illusion? Seeing inside the cell with mesoscopic simulations. [My Copy] HFSP journal, Vol. 2, No. 1. (February 2008), pp. 1-6. by J. C. Shillcock posted to brownian_dynamics molecular_dynamics stochastic_simulation by m_j on 2009-07-27 01:30:12 as
	Self-assembly of actin monomers into long filaments: Brownian dynamics simulations [My Copy] The Journal of Chemical Physics, Vol. 131, No. 1. (2009), 015102. by Kunkun Guo, Julian Shillcock, Reinhard Lipowsky posted to binding brownian_dynamics coarse_grain diffusion protein-protein by jmccammon to the group McCammon on 2009-07-10 22:23:32 as
	On the Contributions of Diffusion and Thermal Activation to Electron Transfer between Phormidium laminosum Plastocyanin and Cytochrome f: Brownian Dynamics Simulations with Explicit Modeling of Nonpolar Desolvation Interactions and Electron Transfer Events [My Copy] Journal of the American Chemical Society, Vol. 131, No. 26. (8 July 2009), pp. 9230-9238. by Razif R. Gabdoulline, Rebecca C. Wade posted to binding brownian_dynamics diffusion electrostatics protein-protein solvation by jmccammon to the group McCammon on 2009-07-10 22:08:28 as along with 2 people and 1 group choonpeng whitead Jiang Research Group
	Fruitful and Futile Encounters along the Association Reaction between Proteins [My Copy] Biophysical Journal, Vol. 96, No. 10. (20 May 2009), pp. 4237-4248. by Michal Harel, Alexander Spaar, Gideon Schreiber posted to brownian_dynamics diffusion electrostatics protein_protein by barry to the group structural_bioinformatics on 2009-06-23 23:55:06 as along with 1 person and 1 group jmccammon McCammon
	Aminoglycoside Association Pathways with the 30S Ribosomal Subunit [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by Maciej Długosz, Joanna Trylska posted to binding brownian_dynamics diffusion drug-discovery electrostatics by jmccammon to the group McCammon on 2009-06-11 01:54:17 as along with 1 person and 1 group sobolevnrm baker-group
	Brownian dynamics simulation of gelation and aging in interacting colloidal systems [My Copy] Physical Review E, Vol. 53, No. 5. (May 1996), pp. 5044-5050. by Martin T. A. Bos, Joost H. J. van Opheusden posted to 3d aging brownian_dynamics colloid hydrodynamics simulation by ghunter on 2009-06-01 21:59:03 as along with 1 person kdesmond2
	Theory and algorithms for mixed Monte Carlo-stochastic dynamics simulations [My Copy] Journal of Mathematical Chemistry, Vol. 18, No. 1. (21 March 1995), pp. 25-35. by Frank Guarnieri posted to brownian_dynamics monte_carlo simulation by ghunter on 2009-04-02 14:50:35 as
	Self-diffusion in sheared suspensions by dynamic simulation [My Copy] Journal of Fluid Mechanics, Vol. 401, No. -1. (1999), pp. 243-274. by David R. Foss, John F. Brady posted to 3d brownian_dynamics fluid_dynamics hard_sphere hydrodynamics shear simulation by ghunter on 2009-04-02 00:32:52 as along with 2 people elorenz dchen
	Collective diffusion in sheared colloidal suspensions [My Copy] Journal of Fluid Mechanics, Vol. 597, No. -1. (2008), pp. 305-341. by Alexander M. Leshansky, Jeffrey F. Morris, John F. Brady posted to 3d brownian_dynamics hard_sphere simulation by ghunter on 2009-04-01 20:13:49 as along with 1 person elorenz
	Brownian dynamics simulations of colloidal hard spheres. Effects of sample dimensionality on self-diffusion [My Copy] Journal of Statistical Physics, Vol. 74, No. 3. (28 February 1994), pp. 687-703. by W. Schaertl, H. Sillescu posted to 2d 3d brownian_dynamics hard_sphere simulation by ghunter on 2009-04-01 12:05:59 as along with 1 person gabe_rosser
	Brownian dynamics simulation of a hard-sphere suspension [My Copy] Physical Review E, Vol. 59, No. 2. (February 1999), 2175. by P. Strating posted to 3d brownian_dynamics hard_sphere simulation by ghunter on 2009-04-01 11:59:29 as along with 1 person sp80_smile
	Fundamental Aspects of Protein−Protein Association Kinetics [My Copy] Chemical Reviews, Vol. 109, No. 3. (11 March 2009), pp. 839-860. by G. Schreiber, G. Haran, H. X. Zhou posted to binding brownian_dynamics diffusion electrostatics protein-protein by jmccammon to the group McCammon on 2009-03-24 23:26:51 as along with 10 people and 1 group anuragsethi barry sunhwan sobolevnrm willard kafuitay carlosjavierna sschurer hadesnumb paulschlesinger baker-group
	Robust Variance Reduction for Random Walk Methods [My Copy] SIAM Journal on Scientific Computing, Vol. 25, No. 6. (2004), pp. 1964-1981. by Gang Zou, Robert D. Skeel posted to brownian_dynamics feynman-kac by stephenbond on 2009-03-24 18:42:27 as
	Brownian dynamics with hydrodynamic interactions [My Copy] The Journal of Chemical Physics, Vol. 69, No. 4. (1978), pp. 1352-1360. by Donald L. Ermak, J. A. Mccammon posted to brownian_dynamics hydrodynamics by stephenbond on 2009-03-24 15:47:27 as along with 2 people matthewhflamm Martin8223
	Brownian dynamics simulation of diffusion-influenced bimolecular reactions [My Copy] The Journal of Chemical Physics, Vol. 80, No. 4. (1984), pp. 1517-1524. by Scott H. Northrup, Stuart A. Allison, Andrew J. Mccammon posted to brownian_dynamics electrodiffusion electrostatics poisson poisson-boltzmann by stephenbond on 2009-03-23 23:56:44 as along with 3 people choonpeng barry Martin8223
	Striking Effects of Hydrodynamic Interactions on the Simulated Diffusion and Folding of Proteins [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 2. (10 February 2009), pp. 242-256. by Tamara Frembgen-Kesner, Adrian H. Elcock posted to brownian_dynamics diffusion by jmccammon to the group McCammon on 2009-03-07 22:18:17 as along with 2 people and 1 group sobolevnrm barry baker-group
	Noise-induced transport in a rough ratchet potential [My Copy] The Journal of Chemical Physics, Vol. 130, No. 7. (2009) by Debasish Mondal, Pulak K. Ghosh, Deb S. Ray posted to brownian_dynamics noise physics ratchet by jjray on 2009-02-20 20:57:32 as
	Triacylglycerol Is Synthesized in a Specific Subclass of Caveolae in Primary Adipocytes [My Copy] J. Biol. Chem., Vol. 280, No. 1. (7 January 2005), pp. 5-8. by Anita Ost, Unn Ortegren, Johanna Gustavsson, Fredrik H. Nystrom, Peter Stralfors posted to brownian_dynamics caveolae lipid_droplets by m_j on 2008-12-03 09:32:11 as
	Large scale dynamic simulation of plate-like particle suspensions. Part II: Brownian simulation [My Copy] Journal of Rheology, Vol. 52, No. 1. (2008), pp. 37-65. by Qingjun Meng, Jonathan J. L. Higdon posted to 2008a brownian_dynamics jspp_cae plate suspension by 6rheology on 2008-11-12 22:51:09 as
	Particle pressure in sheared Brownian suspensions [My Copy] Journal of Rheology, Vol. 52, No. 1. (2008), pp. 141-164. by Yevgeny Yurkovetsky, Jeffrey F. Morris posted to 2008a brownian_dynamics jspp_cae suspension by 6rheology on 2008-11-12 22:49:00 as
	Adsorption and order formation of colloidal nanoparticles on a substrate: A Brownian dynamics study [My Copy] The Journal of Chemical Physics, Vol. 120, No. 3. (2004), pp. 1524-1534. by Minoru Miyahara, Satoshi Watanabe, Yoshiaki Gotoh, Ko Higashitani posted to absorption brownian_dynamics suspension by 6rheology on 2008-11-08 14:11:53 as
	Dynamics of order formation by colloidal adsorption onto a substrate studied with Brownian dynamics [My Copy] The Journal of Chemical Physics, Vol. 122, No. 10. (2005) by Satoshi Watanabe, Minoru Miyahara, Ko Higashitani posted to adsorption brownian_dynamics suspension by 6rheology on 2008-11-08 14:10:46 as
	Dynamics of protein-protein encounter: A Langevin equation approach with reaction patches [My Copy] The Journal of Chemical Physics, Vol. 129, No. 15. (2008) by Jakob Schluttig, Denitsa Alamanova, Volkhard Helms, Ulrich S. Schwarz posted to brownian_dynamics kinetics langevin_dynamics protein-protein by jmccammon to the group McCammon on 2008-10-23 20:42:42 as along with 3 people and 1 group anuragsethi barry sobolevnrm baker-group
	Computational methods for diffusion-influenced biochemical reactions. [My Copy] Bioinformatics (Oxford, England), Vol. 23, No. 15. (1 August 2007), pp. 1969-1977. by Maciej Dobrzynski, Jordi Vidal V. Rodríguez, Jaap A. Kaandorp, Joke G. Blom posted to brownian_dynamics diffusion stochastic_simulation by m_j on 2008-10-20 13:52:38 as along with 6 people and 1 group gabe_rosser jjray ocs balabu dagmar jmccammon McCammon
	Robustness and dissipation of mitogen-activated protein kinases signal transduction network: Underlying funneled landscape against stochastic fluctuations [My Copy] The Journal of Chemical Physics, Vol. 129, No. 13. (2008) by Jin Wang, Kun Zhang, Erkwang Wang posted to brownian_dynamics mathematical_model robustness signaling stochastic by jjray on 2008-10-07 20:14:16 as
	Brownian Dynamics Simulation of Protein-Protein Diffusional Encounter [My Copy] Methods, Vol. 14, No. 3. (March 1998), pp. 329-341. by Razif R. Gabdoulline, Rebecca C. Wade posted to brownian_dynamics diffusion simulation by m_j on 2008-09-10 11:55:58 as along with 2 people and 2 groups barry Martin8223 structural_bioinformatics Bioinformatics
	Massively parallel non-equilibrium Brownian Dynamics simulations for complex fluids: the rheology of Brownian suspensions [My Copy] Computers & Chemical Engineering, Vol. 19, No. 6-7. ( 1995), pp. 693-718. by S. R. Rastogi, N. J. Wagner posted to brownian_dynamics electrolyte rheology suspension by 6rheology on 2008-07-26 18:12:34 as
	Association of Aminoglycosidic Antibiotics with the Ribosomal A-Site Studied with Brownian Dynamics [My Copy] J. Chem. Theory Comput., Vol. 4, No. 4. (8 April 2008), pp. 549-559. by Maciej Długosz, Jan M. Antosiewicz, Joanna Trylska posted to brownian_dynamics electrostatics by barry to the group McCammon on 2008-07-08 01:22:26 as along with 1 person and 1 group sobolevnrm baker-group
	Stochastic Binding of Ca2+ Ions in the Dyadic Cleft; Continuous versus Random Walk Description of Diffusion [My Copy] Biophys. J., Vol. 94, No. 11. (1 June 2008), pp. 4184-4201. by Johan Hake, Glenn T. Lines posted to binding brownian_dynamics ion_channel by barry to the group McCammon on 2008-07-08 00:47:05 as along with 1 person jmccammon
	Brownian dynamics simulations of protein folding: access to milliseconds time scale and beyond. [My Copy] Proc Natl Acad Sci U S A, Vol. 95, No. 8. (14 April 1998), pp. 4288-4292. by A. Rojnuckarin, S. Kim, S. Subramaniam posted to brownian_dynamics cgreview folding by baaden on 2006-01-09 13:54:09 as

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diffusion	33
binding	22
electrostatics	21
protein-protein	19
simulation	12
coarse_grain	9
kinetics	6
3d	5
hydrodynamics	5
suspension	5
hard_sphere	4
molecular_dynamics	4
dna	3
drug-discovery	3
ion_channel	3
langevin_dynamics	3
md_simulation	3
polymer	3
protein_dynamics	3
solvation	3
stochastic_simulation	3
text_book	3
titration	3
2008a	2
brownian	2
colloid	2
course_grained	2
dynamics	2
fluorescent-microscopy	2
interface	2
jspp_cae	2
protein_protein	2
stochastic_process	2
2009	1
2d	1
absorption	1
adsorption	1
aging	1
blend	1
brown_motion	1
caveolae	1
cgreview	1
chain_fracture	1
cluster	1
complex	1
crystallization	1
de_gennes	1
edwards	1
electrodiffusion	1
electrolyte	1
elongation	1
elongational_flow	1
feynman-kac	1
fluid_dynamics	1
folding	1
larson	1
lipid_droplets	1
mathematical_model	1
monte_carlo	1
multiscale	1
noise	1
numerical_simulation	1
particle_based	1
physics	1
plate	1
poisson	1
poisson-boltzmann	1
ratchet	1
reactions	1
rheology	1
robustness	1
schroeder	1
shear	1
signaling	1
slip	1
spatial_simulation	1
spinodal_mode	1
stochastic	1
stochastic_calculus	1
systemsbiology	1
yamamoto	1

Tag brownian_dynamics [40 articles] Export

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