Tag coarse-grained [158 articles] Export

Recent papers classified by the tag coarse-grained.

	Coarse-Grained Simulations of Flow-Induced Nucleation in Semicrystalline Polymers [My Copy] Physical Review Letters, Vol. 103, No. 11. (2009), 115702. by Richard S. Graham, Peter D. Olmsted posted to simulations shear-flow polymer physics nucleation mds flow coarse-grained by chiufanlee on 2009-09-10 18:00:23 as
	A Bayesian statistics approach to multiscale coarse graining [My Copy] The Journal of Chemical Physics, Vol. 129, No. 21. (2008), 214114. by Pu Liu, Qiang Shi, Hal Daumé, Gregory A. Voth posted to time thermodynamics systems space physical multi-scale modelling large-scale force-field coarse-grained chemical bayesian atom by bertelsen on 2009-09-04 20:07:28 as along with 1 person tomweingarten
	Phase field crystals as a coarse-graining in time of molecular dynamics [My Copy] EPL (Europhysics Letters), Vol. 81, No. 4. (2008), 40007. by P. F. Tupper, M. Grant posted to theory physics phase-field-crystal mds ddft coarse-grained by chiufanlee on 2009-09-01 14:53:01 as along with 1 person lutsko
	Solvent-Free Lipid Bilayer Model Using Multiscale Coarse-Graining [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 13. (2 April 2009), pp. 4443-4455. by Sergei Izvekov, Gregory A. Voth posted to coarse-grained methodology transmembrane by choonpeng on 2009-07-27 11:43:15 as along with 3 people and 1 group flbarroso agrossfield sobolevnrm baker-group
	Protein folding on rugged energy landscapes: Conformational diffusion on fractal networks [My Copy] (24 Jun 2009) by Gregg Lois, J. Blawzdziewicz, Corey S. O'Hern posted to cmn coarse-grained complex_systems first_passage free-energy hp_model networks protein_dynamics protein_folding proteins reaction_paths transition_path by Diego_Prada on 2009-06-25 16:27:33 as
	Influence of macromolecular crowding on protein-protein association rates - a Brownian Dynamics study [My Copy] Biophys. J. (29 August 2008), biophysj.108.136291. by Grzegorz A. Wieczorek, Piotr Zielenkiewicz posted to coarse-grained crowding by choonpeng on 2009-05-25 09:32:02 as along with 3 people itmeson ocs paulschlesinger
	Predicting the order in which contacts are broken during single molecule protein stretching experiments [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 71, No. 1. (2008), pp. 45-60. by Joanna I. Su&lstrok;kowska, Andrzej Kloczkowski, Taner Z. Sen, Marek Cieplak, Robert L. Jernigan posted to coarse-grained mechanical-unfolding by choonpeng on 2009-05-19 04:17:01 as along with 1 person edws
	Probing the origin of tubulin rigidity with molecular simulations. [My Copy] Proceedings of the National Academy of Sciences of the United States of America (7 October 2008) by Ruxandra I I. Dima, Harshad Joshi posted to coarse-grained mechanical-unfolding by choonpeng on 2009-04-27 08:07:34 as along with 2 people and 1 group kshundyak barry McCammon
	Mechanical unfolding of RNA hairpins [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 19. (10 May 2005), pp. 6789-6794. by Changbong Hyeon, D. Thirumalai posted to coarse-grained rna simulation by cactus on 2009-04-06 11:01:45 as along with 1 person Elena_Zubova
	Extracting macroscopic stochastic dynamics: Model problems [My Copy] Communications on Pure and Applied Mathematics, Vol. 56, No. 2. (2003), pp. 234-269. by Wilhelm Huisinga, Christof Schütte, Andrew M. Stuart posted to stochastic_processes non_markovian markov coarse-grained chapt_cmn by Diego_Prada on 2009-03-09 17:53:37 as
	Free energy surfaces from an extended harmonic superposition approach and kinetics for alanine dipeptide [My Copy] Chemical Physics Letters, Vol. 466, No. 4-6. (04 December 2008), pp. 105-115. by Birgit Strodel, David J. Wales posted to amino articulo coarse-grained dialanine free-energy hexapeptide statistical_mechanics by Diego_Prada on 2009-03-07 12:18:52 as
	Absolute free energies estimated by combining pre-calculated molecular fragment libraries [My Copy] (30 Jan 2009) by Xin Zhang, Artem B. Mamonov, Daniel M. Zuckerman posted to coarse-grained dialanine free-energy short-peptides by Diego_Prada on 2009-03-04 12:12:11 as
	Flow boundary conditions from nano- to micro-scales [My Copy] (12 Dec 2006) by Lydéric Bocquet, J. L. Barrat posted to boundary_conditions coarse-grained nanotechnology shear_flow by j_vinals on 2009-01-06 16:24:58 as along with 1 person freddan
	Cluster formation of transmembrane proteins due to hydrophobic mismatching. [My Copy] Physical review letters, Vol. 101, No. 12. (19 September 2008) by U. Schmidt, G. Guigas, M. Weiss posted to coarse-grained transmembrane by choonpeng on 2008-12-29 08:44:28 as
	Molecular simulations of lipid mediated protein-protein interactions [My Copy] Biophys. J. (16 May 2008), biophysj.107.124164. by Frederick J. de Meyer, Maddalena Venturoli, Berend Smit posted to coarse-grained protein-interaction transmembrane by choonpeng on 2008-12-18 05:31:57 as along with 3 people and 1 group oteri paulschlesinger agrossfield Structural Biology Group TorVergata
	Unique elastic properties of the spectrin tetramer as revealed by multiscale coarse-grained modeling. [My Copy] Proc Natl Acad Sci U S A (17 January 2008) by Dina T T. Mirijanian, Gregory A A. Voth posted to coarse-grained model protein simulation by cactus on 2008-12-18 04:00:34 as along with 2 people and 1 group choonpeng sobolevnrm baker-group
	Toward a Coarse-Grained Protein Model Coupled with a Coarse-Grained Solvent Model: Solvation Free Energies of Amino Acid Side Chains [My Copy] Journal of Chemical Theory and Computation, Vol. 4, No. 11. (11 November 2008), pp. 1891-1901. by Wei Han, Cheuk-Kin Wan, Yun-Dong Wu posted to coarse-grained field force gromacs modeling parameter solvent thermodynamics water by rbaron on 2008-12-05 18:49:52 as along with 3 people sunrise agrossfield middledomain
	Lipids on the move: Simulations of membrane pores, domains, stalks and curves [My Copy] Biochimica et Biophysica Acta (BBA) - Biomembranes (25 October 2008) by S. Marrink, A. Devries, D. Tieleman posted to coarse-grained self-assembly by choonpeng on 2008-12-05 05:51:17 as along with 3 people and 1 group sobolevnrm priyaps paulschlesinger baker-group
	A Systematic Methodology for Defining Coarse-Grained Sites in Large Biomolecules [My Copy] Biophysical Journal, Vol. 95, No. 11. (01 December 2008), pp. 5073-5083. by Z. Zhang, L. Lu, W. Noid, V. Krishna, J. Pfaendtner, G. Voth posted to coarse-grained methodology pca by choonpeng on 2008-11-27 08:53:06 as along with 5 people and 2 groups okapi barry sobolevnrm agrossfield paulschlesinger structural_bioinformatics McCammon
	Helix-Helix Interactions in Membrane Proteins: Coarse-Grained Simulations of Glycophorin A Helix Dimerization [My Copy] Biochemistry, Vol. 47, No. 40. (7 October 2008), pp. 10503-10512. by Emi Psachoulia, Philip W. Fowler, Peter J. Bond, Mark S. Sansom posted to coarse-grained transmembrane by choonpeng on 2008-11-26 02:42:51 as along with 3 people jonathancooper agrossfield paulschlesinger
	Dynamics of Water in the Hydration Shells of C60: Molecular Dynamics Simulation Using a Coarse-Grained Model [My Copy] The Journal of Physical Chemistry B, Vol. 111, No. 35. (2007), pp. 10474-10480. by Niharendu Choudhury posted to c60-water coarse-grained simulation by Marine to the group Molecular dynamics in MSU on 2008-11-24 09:04:59 as
	Characterization of heteropolymer collapse [My Copy] The European Physical Journal E - Soft Matter, Vol. 2, No. 3. (19 July 2000), pp. 285-288. by Skjaeveland, K. Sneppen posted to coarse-grained langevin mds polymer protein simulations by chiufanlee on 2008-11-10 23:56:44 as
	Determining the Critical Nucleus and Mechanism of Fibril Elongation of the Alzheimer’s Aβ1–40 Peptide [My Copy] Journal of Molecular Biology, Vol. 365, No. 2. (12 January 2007), pp. 535-550. by N. Fawzi, Y. Okabe, E. Yap, T. Headgordon posted to abeta amyloid coarse-grained elongation kinetics mds simulations by chiufanlee on 2008-11-10 22:50:59 as
	Oligomerization of Amyloid Abeta16-22 Peptides Using Hydrogen Bonds and Hydrophobicity Forces [My Copy] Biophys. J., Vol. 87, No. 6. (1 December 2004), pp. 3657-3664. by Giorgio Favrin, Anders Irback, Sandipan Mohanty posted to abeta amyloid coarse-grained simulations thermodynamics by chiufanlee on 2008-11-10 22:49:42 as
	Allostery of actin filaments: molecular dynamics simulations and coarse-grained analysis. [My Copy] Proc Natl Acad Sci U S A, Vol. 102, No. 37. (13 September 2005), pp. 13111-13116. by J. W. Chu, G. A. Voth posted to actin coarse-grained filament fullatom md protein by cactus on 2008-11-07 07:48:40 as along with 2 people BragilMassoud choonpeng
	Coarse-grained molecular simulation of diffusion and reaction kinetics in a crowded virtual cytoplasm [My Copy] Biophys. J. (30 January 2008), biophysj.107.116053. by Douglas Ridgway, Gordon Broderick, Ana Lopez-Campistrous, et al.Melania Ru'aini, Philip Winter, Matthew Hamilton, Pierre Boulanger, Andriy Kovalenko, Michael J. Ellison posted to coarse-grained crowding kinetics simulation by ras on 2008-10-31 15:49:20 as along with 4 people and 1 group ocs paulschlesinger sobolevnrm arjunan baker-group
	Nanopore–Protein Interactions Dramatically Alter Stability and Yield of the Native State in Restricted Spaces [My Copy] Journal of Molecular Biology, Vol. 357, No. 2. (24 March 2006), pp. 632-643. by M. Cheung, D. Thirumalai posted to chaperonin coarse-grained confinement md simulation by cactus on 2008-10-07 08:39:21 as
	Assembly and Kinetic Folding Pathways of a Tetrameric beta-Sheet Complex: Molecular Dynamics Simulations on Simplified Off-Lattice Protein Models [My Copy] Biophys. J., Vol. 86, No. 1. (1 January 2004), pp. 31-49. by Hyunbum Jang, Carol K. Hall, Yaoqi Zhou posted to amyloid coarse-grained for_ref md oligomer simulation by cactus on 2008-10-07 07:28:49 as
	Molecular crowding enhances native state stability and refolding rates of globular proteins [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 13. (29 March 2005), pp. 4753-4758. by Margaret S. Cheung, Dmitri Klimov, D. Thirumalai posted to coarse-grained crowding for_ref md simulation by cactus on 2008-10-02 07:00:45 as along with 2 people ras sikorski
	The influence of macromolecular crowding on HIV-1 protease internal dynamics. [My Copy] Journal of the American Chemical Society, Vol. 128, No. 18. (10 May 2006), pp. 6006-6007. by D. D. Minh, C. E. Chang, J. Trylska, V. Tozzini, J. A. McCammon posted to coarse-grained crowding for_ref md simulation by cactus on 2008-10-01 07:56:42 as
	Structural transitions of confined model proteins: molecular dynamics simulation and experimental validation. [My Copy] Biophys J, Vol. 90, No. 9. (1 May 2006), pp. 3224-3238. by D. Lu, Z. Liu, J. Wu posted to coarse-grained confinement experiment md simulation by cactus on 2008-09-29 09:07:42 as along with 1 person allmensch
	The MARTINI Coarse-Grained Force Field: Extension to Proteins [My Copy] Journal of Chemical Theory and Computation, Vol. 4, No. 5. (1 May 2008), pp. 819-834. by Luca Monticelli, Senthil K. Kandasamy, Xavier Periole, Ronald G. Larson, D. Peter Tieleman, Siewert-Jan Marrink posted to coarse-grained force-field martini protein simulation by Marine to the group Molecular dynamics in MSU on 2008-09-22 10:01:59 as along with 13 people and 2 groups arnaucordomi dimka oteri sunrise flbarroso A_Coletta_Thesis krapnik middledomain sobolevnrm Ema aqeel DanielParton softsimu Structural Biology Group TorVergata baker-group
	The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations [My Copy] The Journal of Physical Chemistry B, Vol. 111, No. 27. (1 July 2007), pp. 7812-7824. by Siewert J. Marrink, H. Jelger Risselada, Serge Yefimov, D. Peter Tieleman, Alex H. de Vries posted to coarse-grained martini simulation by Marine to the group Molecular dynamics in MSU on 2008-09-22 09:59:35 as along with 7 people and 1 group anuragsethi sunrise A_Coletta_Thesis choonpeng softsimu dimka sunnytov Structural Biology Group TorVergata
	Coarse Grained Model for Semiquantitative Lipid Simulations [My Copy] The Journal of Physical Chemistry B, Vol. 108, No. 2. (1 January 2004), pp. 750-760. by Siewert J. Marrink, Alex H. de Vries, Alan E. Mark posted to coarse-grained by Marine to the group Molecular dynamics in MSU on 2008-09-22 09:58:13 as along with 5 people dsmueller Elena_Zubova choonpeng softsimu sunnytov
	Computational approaches to nanobiotechnology: probing the interaction of synthetic molecules with phospholipid bilayers via a coarse grain model [My Copy] Nanotechnology, Vol. 15, No. 9. (2004), pp. 1289-1295. by Goundla Srinivas, Michael L. Klein posted to coarse-grained membrane simulation by Marine on 2008-09-21 19:56:59 as along with 1 group Molecular dynamics in MSU
	Intrinsic Bending and Structural Rearrangement of Tubulin Dimer: Molecular Dynamics Simulations and Coarse-grained Analysis [My Copy] Biophys. J. (30 May 2008), biophysj.108.129072. by Yeshitila Gebremichael, Jhih-Wei Chu, Gregory A. Voth posted to 2008 coarse-grained md microtubule simulation tubulin-dimer by tengli on 2008-09-16 15:30:59 as
	REACH Coarse-Grained Biomolecular Simulation: Transferability between Different Protein Structural Classes [My Copy] Biophys. J. (9 May 2008), biophysj.108.131714. by Kei Moritsugu, Jeremy C. Smith posted to coarse-grained force_field md simulation by rok on 2008-08-21 19:45:50 as along with 7 people and 2 groups barry sobolevnrm A_Coletta_Thesis paulschlesinger choonpeng aqeel jmccammon baker-group McCammon
	Energy landscape of a model protein [My Copy] The Journal of Chemical Physics, Vol. 111, No. 14. (1999), pp. 6610-6616. by Mark A. Miller, David J. Wales posted to coarse-grained hp_model by Diego_Prada on 2008-08-20 10:44:26 as
	Diffusion maps, spectral clustering and reaction coordinates of dynamical systems [My Copy] ArXiv Mathematics e-prints (March 2005) by B. Nadler, S. Lafon, R. R. Coifman, I. G. Kevrekidis posted to coarse-grained stochastic by j_vinals on 2008-08-06 02:46:16 as along with 2 people and 1 group sobolevnrm kb baker-group
	Variable-free exploration of stochastic models: a gene regulatory network example [My Copy] (6 Nov 2006) by Radek Erban, Thomas A. Frewen, Xiao Wang, et al.Timothy C. Elston, Ronald Coifman, Boaz Nadler, Ioannis G. Kevrekidis posted to coarse-grained regulatory_network stochastic by j_vinals on 2008-08-06 02:44:43 as along with 1 person and 1 group sobolevnrm baker-group
	Comparison of Thermodynamic Properties of Coarse-Grained and Atomic-Level Simulation Models. [My Copy] Chemphyschem, Vol. 8, No. 3. (8 February 2007), pp. 452-461. by Riccardo Baron, Daniel Trzesniak, Alex H H. de Vries, Andreas Elsener, Siewert J J. Marrink, Wilfred F F. van Gunsteren posted to coarse-grained dynamics entropy field fluid force gibbs gromos helmoltz hydrocarbons method modeling molecular multiscale reorganization solute solvent thermodynamics by rbaron on 2008-08-05 01:55:58 as along with 1 person choonpeng
	Gating Mechanisms of Mechanosensitive Channels of Large Conductance, I: A Continuum Mechanics-Based Hierarchical Framework [My Copy] Biophys. J., Vol. 95, No. 2. (15 July 2008), pp. 563-580. by Xi Chen, Qiang Cui, Yuye Tang, Jejoong Yoo, Arun Yethiraj posted to coarse-grained multi-scale by choonpeng on 2008-08-03 04:36:05 as along with 1 person agrossfield
	Coarse molecular dynamics of a peptide fragment: Free energy, kinetics, and long-time dynamics computations [My Copy] J. Chem. Phys., Vol. 118 (June 2003), pp. 10762-10773. by G. Hummer, I. G. Kevrekidis posted to chapt_cmn coarse-grained dialanine md plos by Diego_Prada on 2008-08-01 19:40:41 as
	Coarse-Grained Biomolecular Simulation with REACH: Realistic Extension Algorithm via Covariance Hessian☆ [My Copy] Biophysical Journal, Vol. 93, No. 10. (15 November 2007), pp. 3460-3469. by K. Moritsugu, J. Smith posted to coarse-grained by choonpeng on 2008-07-30 13:49:05 as along with 5 people and 1 group edws Diego_Prada aqeel hmk sobolevnrm baker-group
	Tubulin: from atomistic structure to supramolecular mechanical properties [My Copy] Journal of Materials Science, Vol. 42, No. 21. (November 2007), pp. 8864-8872. by Marco Deriu, Søren Enemark, Monica Soncini, Franco Montevecchi, Alberto Redaelli posted to coarse-grained cytoskeletal-dynamics multi-scale by choonpeng on 2008-07-01 01:42:01 as
	On the Octagonal Structure of the Nuclear Pore Complex: Insights from Coarse-Grained Models. [My Copy] Biophysical journal (16 May 2008) by Christopher B B. Wolf, Mohammad R K R. Mofrad posted to coarse-grained by choonpeng on 2008-06-27 09:13:07 as
	Gating of the mechanosensitive channel protein MscL: The interplay of membrane and protein [My Copy] Biophys. J. (22 January 2008), biophysj.107.109850. by Jonggu Jeon, Gregory A. Voth posted to coarse-grained mechanotransduction by choonpeng on 2008-04-23 02:06:12 as along with 1 person paulschlesinger
	Annealed importance sampling of dileucine peptide [My Copy] (3 Apr 2007) by Edward Lyman, Daniel M. Zuckerman posted to coarse-grained protein_dynamics struct_decorr by Diego_Prada on 2008-04-21 10:15:40 as
	Demonstrated convergence of the equilibrium ensemble for a fast united-residue protein model [My Copy] (24 Mar 2007) by Marty F. Ytreberg, Svetlana, Daniel M. Zuckerman posted to coarse-grained protein_dynamics struct_decorr by Diego_Prada on 2008-04-21 10:13:08 as
	Free energy landscapes of model peptides and proteins [My Copy] The Journal of Chemical Physics, Vol. 118, No. 8. (2003), pp. 3891-3897. by David A. Evans, David J. Wales posted to coarse-grained free-energy proteins by Diego_Prada on 2008-04-11 20:05:03 as

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md	34
simulation	21
protein-folding	17
go-model	9
gnm	8
nma	8
polystyrene	7
protein	7
mechanical-unfolding	6
kremer	5
protein-domains	5
thermodynamics	5
crowding	4
force-field	4
free-energy	4
martini	4
mds	4
multi-scale	4
pca	4
review	4
simulations	4
theory	4
transmembrane	4
amyloid	3
charged	3
dialanine	3
for_ref	3
force-probe-md	3
mechanotransduction	3
methodology	3
polyelectrolyte	3
protein_dynamics	3
protein_protein	3
self_assembly	3
ubiqutin	3
abeta	2
allostery	2
atom	2
bayesian	2
bead-rod	2
block_copolymer	2
c60-water	2
chapt_cmn	2
chemical	2
cmn	2
confinement	2
cytoskeletal-dynamics	2
diffusion	2
doi	2
domain_motions	2
dpd	2
entanglement	2
field	2
flagellar	2
folding	2
force	2
hexagonal_phase	2
hp_model	2
hydrophobicity	2
kinetics	2
large-scale	2
martini_force_field	2
md_simulation	2
modeling	2
modelling	2
multiscale	2
multiscale_modeling	2
physical	2
physics	2
polyisoprene	2
polymer	2
pore	2
potential	2
protein-interaction	2
protein-mechanics	2
protein_folding	2
proteins	2
rheology	2
rouse_to_reptation	2
self-assembly	2
signaling	2
solvent	2
solvent-effects	2
space	2
stochastic	2
struct_decorr	2
systems	2
text_book	2
time	2
unentangled_polymer	2
chi_parameter	1
cognac	1
ddft	1
elastic-network	1
elongation	1
langevin	1
molecular_simulation	1
network	1
symmetry_breaking	1
tubulin-dimer	1

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