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Tag coarse-graining [88 articles]

Articoli recentemente classificati sotto il tag coarse-graining.
  • Coarse-Graining in Polymer Simulation: From the Atomistic to the Mesoscopic Scale and Back
    ChemPhysChem, Vol. 3, No. 9. (2002), pp. 754-769.
    by Florian Müller-Plathe
    posted to coarse-graining simulation by ttjoseph on 2007-02-28 22:55:38 as ** along with 1 person kaz229
  • Aggregation and vesiculation of membrane proteins by curvature-mediated interactions
    Nature, Vol. 447, No. 7143., pp. 461-464.
    by Benedict J Reynwar, Gregoria Illya, Vagelis A Harmandaris, Martin M Müller, Kurt Kremer, Markus Deserno
    posted to coarse-graining vesicles by softsimu on 2008-03-18 17:51:29 as ** along with 1 person choonpeng
  • Transmembrane Peptide-Induced Lipid Sorting and Mechanism of Lalpha-to-Inverted Phase Transition Using Coarse-Grain Molecular Dynamics
    Biophys. J., Vol. 87, No. 4. (1 October 2004), pp. 2107-2115.
    by Steve O Nielsen, Carlos F Lopez, Ivaylo Ivanov, Preston B Moore, John C Shelley, Michael L Klein
    posted to coarse-graining peptides by softsimu on 2008-03-18 18:53:51 as **
  • Polymorphic Phase Behavior of Cardiolipin Derivatives Studied by Coarse-Grained Molecular Dynamics
    J. Phys. Chem. B, Vol. 111, No. 25. (28 June 2007), pp. 7194-7200.
    by M Dahlberg
    posted to cardiolipin coarse-graining by softsimu on 2008-01-28 15:00:14 as **
  • Coarse Graining of Nonbonded Degrees of Freedom
    Physical Review Letters, Vol. 98, No. 26. (2007), 267801.
    by H Bock, KE Gubbins, SHL Klapp
    posted to coarse-graining by softsimu on 2007-12-12 03:50:41 as **
  • Implicit solvent simulation models for biomembranes
    European Biophysics Journal, Vol. 35, No. 2. (11 January 2006), pp. 104-124.
    by Grace Brannigan, Lawrence Lin, Frank Brown
    posted to coarse-graining implicit-solvent by softsimu on 2008-03-18 17:50:16 as **
  • Phase behavior of monomeric mixtures and polymer solutions with soft interaction potentials
    The Journal of Chemical Physics, Vol. 114, No. 17. (2001), pp. 7644-7654.
    by CM Wijmans, B Smit, RD Groot
    posted to coarse-graining dpd polymers by softsimu on 2008-02-22 19:35:34 as **
  • Coarse grain models and the computer simulation of soft materials
    Journal of Physics: Condensed Matter, Vol. 16, No. 15. (2004), pp. R481-R512.
    by Steve O Nielsen, Carlos F Lopez, Goundla Srinivas, Michael L Klein
    posted to coarse-graining by softsimu on 2008-02-08 17:44:08 as ** along with 2 people kaz229 RamuAnandakrishnan
  • Thermodynamically Admissible Form for Discrete Hydrodynamics
    Physical Review Letters, Vol. 83, No. 22. (29 November 1999), 4542.
    by Pep Español, Mar Serrano, Hans C Öttinger
    posted to generic coarse-graining by softsimu on 2008-06-27 21:44:04 as **
  • Coarse-grained transmembrane proteins: hydrophobic matching, aggregation, and their effect on fusion.
    J Phys Chem B, Vol. 110, No. 27. (13 July 2006), pp. 13614-13623.
    by AF Smeijers, K Pieterse, AJ Markvoort, PA Hilbers
    posted to coarse-graining proteins by softsimu on 2008-01-24 00:55:25 as **
  • Pores in bilayer membranes of amphiphilic molecules: Coarse-grained molecular dynamics simulations compared with simple mesoscopic models
    The Journal of Chemical Physics, Vol. 121, No. 4. (2004), pp. 1890-1900.
    by C Loison, M Mareschal, F Schmid
    posted to pores membranes coarse-graining by softsimu on 2008-01-23 06:35:02 as **
  • Coarse-grained computations for a micellar system.
    J Chem Phys, Vol. 122, No. 4. (22 January 2005)
    by DI Kopelevich, AZ Panagiotopoulos, IG Kevrekidis
    posted to coarse-graining micelles by softsimu on 2008-01-19 16:06:47 as ** along with 1 person baaden
  • Configurational Entropies of Lipids in Pure and Mixed Bilayers from Atomic-Level and Coarse-Grained Molecular Dynamics Simulations
    J. Phys. Chem. B, Vol. 110, No. 31. (10 August 2006), pp. 15602-15614.
    by R Baron, AH Devries, PH Hunenberger, WF Vangunsteren
    posted to coarse-graining by softsimu on 2008-02-18 00:16:58 as **
  • Conformational analysis of lipid molecules by self-organizing maps
    The Journal of Chemical Physics, Vol. 126, No. 5. (2007)
    by Teemu Murtola, Mikko Kupiainen, Emma Falck, Ilpo Vattulainen
    posted to coarse-graining by softsimu on 2008-03-08 20:22:22 as **
  • Coarse Grained Model for Semiquantitative Lipid Simulations
    J. Phys. Chem. B, Vol. 108, No. 2. (15 January 2004), pp. 750-760.
    by SJ Marrink, AH Devries, AE Mark
    posted to coarse-graining by softsimu on 2008-02-18 00:16:34 as ** along with 1 person choonpeng
  • Multiscale Monte Carlo Algorithm for Simple Fluids
    Physical Review Letters, Vol. 97, No. 19. (2006)
    by AC Maggs
    posted to coarse-graining electrostatics by softsimu on 2008-01-21 22:18:37 as **
  • Automatic coarse graining of polymers
    Polymer, Vol. 45, No. 11. (May 2004), pp. 3869-3876.
    by Roland Faller
    posted to coarse-graining by softsimu on 2008-03-18 17:23:53 as **
  • A systematic method to derive force fields for coarse-grained simulations of phospholipids
    Computer Physics Communications, Vol. 175, No. 4. (15 August 2006), pp. 264-268.
    by J Elezgaray, M Laguerre
    posted to coarse-graining by softsimu on 2008-03-18 18:59:12 as **
  • The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations.
    Journal of Physical Chemistry B (15 June 2007)
    by Siewert J Marrink, HJ Risselada, Serge Yefimov, DP Tieleman, Alex H Vries
    posted to coarse-graining force force-field martini by softsimu on 2008-01-10 14:23:39 as ** along with 2 people dimka choonpeng
  • Coarse-grained model for phospholipid/cholesterol bilayer
    The Journal of Chemical Physics, Vol. 121, No. 18. (2004), pp. 9156-9165.
    by Teemu Murtola, Emma Falck, Michael Patra, Mikko Karttunen, Ilpo Vattulainen
    posted to cholesterol coarse-graining phospholipid by softsimu on 2008-01-21 18:05:17 as **
  • Structure of Spheroidal HDL Particles Revealed by Combined Atomistic and Coarse-Grained Simulations
    Biophys. J., Vol. 94, No. 6. (15 March 2008), pp. 2306-2319.
    by Andrea Catte, James C Patterson, Denys Bashtovyy, Martin K Jones, Feifei Gu, Ling Li, Aldo Rampioni, Durba Sengupta, Timo Vuorela, Perttu Niemela, Mikko Karttunen, Siewert J Marrink, Ilpo Vattulainen, Jere P Segrest
    posted to coarse-graining hdl by softsimu on 2008-03-05 20:55:23 as **
  • Simulations of biomembranes and water: Important technical aspects
    Fluid Phase Equilib., Vol. 261, No. 1-2. (2007), pp. 18-25.
    by SV Bennun, AN Dickey, C Xing, R Faller
    posted to coarse-graining by softsimu on 2008-04-11 19:21:52 as **
  • Coarse-Grained Molecular Dynamics Simulations of a Rotating Bacterial Flagellum.
    Biophys J (22 September 2006)
    by Anton Arkhipov, Peter L L Freddolino, Katsumi Imada, Keiichi Namba, Klaus Schulten
    posted to coarse-graining by softsimu on 2008-03-18 17:37:44 as ** along with 1 person choonpeng
  • Multiscale modeling of lipids and lipid bilayers
    European Biophysics Journal, Vol. 35, No. 1. (19 December 2005), pp. 53-61.
    by Alexander Lyubartsev
    posted to coarse-graining by softsimu on 2008-01-29 01:06:44 as **
  • Calculation of effective interaction potentials from radial distribution functions: A reverse Monte Carlo approach
    Physical Review E, Vol. 52, No. 4. (October 1995), 3730.
    by Alexander P Lyubartsev, Aatto Laaksonen
    posted to coarse-graining imc by softsimu on 2008-01-29 01:06:13 as **
  • A Quantitative Coarse-Grain Model for Lipid Bilayers
    J. Phys. Chem. B, Vol. 112, No. 3. (24 January 2008), pp. 802-815.
    by M Orsi, DY Haubertin, WE Sanderson, JW Essex
    posted to coarse-graining by softsimu on 2008-06-27 19:34:14 as ** along with 2 people and 1 group sobolevnrm paulschlesinger baker-group
  • Multiscale coarse graining of liquid-state systems
    The Journal of Chemical Physics, Vol. 123, No. 13. (2005)
    by Sergei Izvekov, Gregory A Voth
    posted to coarse-graining by softsimu on 2008-03-18 17:34:41 as **
  • The MARTINI Coarse-Grained Force Field: Extension to Proteins
    J. Chem. Theory Comput. (16 April 2008)
    by Luca Monticelli, Senthil K Kandasamy, Xavier Periole, Ronald G Larson, Peter D Tieleman, Siewert-Jan Marrink
    posted to martini coarse-graining by softsimu on 2008-06-27 19:29:01 as ** along with 5 people and 1 group Ema aqeel DanielParton sobolevnrm middledomain baker-group
  • Coarse-grained model for phospholipid/cholesterol bilayer employing inverse Monte Carlo with thermodynamic constraints
    J Chem Phys, Vol. 126, No. 7. (2007), 075101.
    by T Murtola, E Falck, M Karttunen, I Vattulainen
    posted to cholesterol coarse-graining imc membranes monte-carlo by softsimu on 2007-12-12 14:20:41 as **
  • A strategy for analysis of (molecular) equilibrium simulations: Configuration space density estimation, clustering, and visualization
    The Journal of Chemical Physics, Vol. 114, No. 5. (2001), pp. 2079-2089.
    by Fred A Hamprecht, Christine Peter, Xavier Daura, Walter Thiel, Wilfred F van Gunsteren
    posted to coarse-graining by softsimu on 2008-03-18 19:02:32 as **
  • Tunable generic model for fluid bilayer membranes
    Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 72, No. 1. (2005)
    by Ira R Cooke, Kurt Kremer, Markus Deserno
    posted to coarse-graining by softsimu on 2008-03-18 17:53:44 as **
  • Coarse-Graining and Self-Dissimilarity of Complex Networks
    (18 Oct 2004)
    by Shalev Itzkovitz, Reuven Levitt, Nadav Kashtan, Ron Milo, Michael Itzkovitz, Uri Alon
    posted to coarse-graining network resolution self-dissimilarity by scis0000001 on 2006-11-25 13:50:59 as **
  • Coarse-graining and self-dissimilarity of complex networks
    Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 71, No. 1. (2005)
    by Shalev Itzkovitz, Reuven Levitt, Nadav Kashtan, Ron Milo, Michael Itzkovitz, Uri Alon
    posted to coarse-graining network by rgb on 2006-08-03 17:24:33 as ** along with 1 group pileWorks
  • Exploring conformational space with a simple lattice model for protein structure.
    J Mol Biol, Vol. 243, No. 4. (4 November 1994), pp. 668-682.
    by DA Hinds, M Levitt
    posted to cgreview coarse-graining folding by baaden on 2006-01-09 14:18:56 as ** along with 1 person nigham
  • Dense orientationally ordered states of a single semiflexible macromolecule: an expanded ensemble Monte Carlo simulation.
    J Chem Phys, Vol. 122, No. 17. (1 May 2005)
    by JA Martemyanova, MR Stukan, VA Ivanov, M Müller, W Paul, K Binder
    posted to coarse-graining flexibility polymers by baaden on 2005-07-31 17:30:11 as **
  • Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model.
    Chem Phys Lipids, Vol. 135, No. 2. (June 2005), pp. 223-244.
    by SJ Marrink, J Risselada, AE Mark
    posted to cgreview coarse-graining lipid_bilayers simulations by baaden on 2005-07-31 17:29:07 as ** along with 1 person divadyrral
  • Reconstruction of the src-SH3 Protein Domain Transition State Ensemble using Multiscale Molecular Dynamics Simulations
    Journal of Molecular Biology, Vol. 350, No. 5. (29 July 2005), pp. 1035-1050.
    by Feng Ding, Weihua Guo, Nikolay V Dokholyan, Eugene I Shakhnovich, Joan-Emma Shea
    posted to coarse-graining folding by baaden on 2005-07-31 17:27:42 as ** along with 1 person nh
  • Protein flexibility prediction by an all-atom mean-field statistical theory.
    Protein Sci, Vol. 14, No. 7. (July 2005), pp. 1772-1777.
    by BP Pandey, C Zhang, X Yuan, J Zi, Y Zhou
    posted to cgreview coarse-graining flexibility by baaden on 2005-07-31 17:04:36 as ** along with 3 people and 2 groups aqeel yongzhao jessicaopacic TSRI_MGL LabCompMed
  • Balancing energy and entropy: A minimalist model for the characterization of protein folding landscapes.
    Proc Natl Acad Sci U S A, Vol. 102, No. 29. (19 July 2005), pp. 10141-10146.
    by P Das, S Matysiak, C Clementi
    posted to coarse-graining folding methods by baaden on 2005-07-31 17:03:26 as **
  • Interior segment regrowth configurational-bias algorithm for the efficient sampling and fast relaxation of coarse-grained polyethylene and polyoxyethylene melts on a high coordination lattice.
    J Chem Phys, Vol. 122, No. 23. (15 June 2005)
    by SS Rane, WL Mattice
    posted to coarse-graining methods polymers by baaden on 2005-07-31 17:01:31 as **
  • Coarse-grained strategy for modeling protein stability in concentrated solutions.
    Biophys J (22 July 2005)
    by Jason K K Cheung, Thomas M M Truskett
    posted to coarse-graining by baaden on 2005-07-31 16:59:31 as ** along with 1 person bentenin
  • Exploring Global Motions and Correlations in the Ribosome.
    Biophys J (10 June 2005)
    by Joanna Trylska, Valentina Tozzini, J Andrew A McCammon
    posted to cgreview coarse-graining simulations by baaden on 2005-07-31 16:52:21 as ** along with 4 people and 2 groups apaydin anita yongzhao eckart_bindewald structure-bii TSRI_MGL
  • The energy landscape as a unifying theme in molecular science.
    Philos Transact A Math Phys Eng Sci, Vol. 363, No. 1827. (15 February 2005)
    by DJ Wales
    posted to cgreview coarse-graining by baaden on 2005-07-31 16:49:22 as **
  • Structural dynamics of nucleosome core particle: comparison with nucleosomes containing histone variants.
    Proteins, Vol. 58, No. 3. (15 February 2005), pp. 683-696.
    by A Ramaswamy, I Bahar, I Ioshikhes
    posted to coarse-graining elastic_network gnm by baaden on 2005-07-31 16:48:04 as **
  • Maturation dynamics of bacteriophage HK97 capsid.
    Structure (Camb), Vol. 13, No. 3. (March 2005), pp. 413-421.
    by AJ Rader, DH Vlad, I Bahar
    posted to coarse-graining elastic_network gnm by baaden on 2005-07-31 16:47:34 as **
  • Coupling between catalytic site and collective dynamics: a requirement for mechanochemical activity of enzymes.
    Structure (Camb), Vol. 13, No. 6. (June 2005), pp. 893-904.
    by LW Yang, I Bahar
    posted to coarse-graining elastic_network enzymes flexibility gnm by baaden on 2005-07-31 16:46:43 as ** along with 4 people BragilMassoud lna aqeel chrn
  • Spatially adaptive grand canonical ensemble Monte Carlo simulations.
    Phys Rev E Stat Nonlin Soft Matter Phys, Vol. 71, No. 2 Pt 2. (February 2005)
    by A Chatterjee, MA Katsoulakis, DG Vlachos
    posted to coarse-graining by baaden on 2005-07-31 16:45:20 as *
  • Topological coarse graining of polymer chains using wavelet-accelerated Monte Carlo. I. Freely jointed chains.
    J Chem Phys, Vol. 122, No. 23. (15 June 2005)
    by AE Ismail, GC Rutledge, G Stephanopoulos
    posted to coarse-graining methods by baaden on 2005-07-31 16:43:00 as **
  • Topological coarse graining of polymer chains using wavelet-accelerated Monte Carlo. II. Self-avoiding chains.
    J Chem Phys, Vol. 122, No. 23. (15 June 2005)
    by AE Ismail, G Stephanopoulos, GC Rutledge
    posted to coarse-graining methods by baaden on 2005-07-31 16:41:38 as **
  • Statistically based reduced representation of amino acid side chains.
    J Chem Inf Comput Sci, Vol. 44, No. 3. (n 2004), pp. 817-830.
    by JK Rainey, MC Goh
    posted to cgreview coarse-graining protein_structure proteins by baaden on 2005-07-31 14:32:15 as ** along with 1 person blackbart
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