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Recent papers classified by the tag coarse-grain.

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	Two-scale Brownian dynamics of suspensions of charged nanoparticles including electrostatic and hydrodynamic interactions [My Copy] The Journal of Chemical Physics, Vol. 131, No. 23. (2009), 234105. by V. Dahirel, M. Jardat, J. F. Dufrêche, P. Turq posted to coarse-grain by agrossfield on 2009-12-21 21:30:17 as along with 1 person paulschlesinger
	Free energies of stable and metastable pores in lipid membranes under tension [My Copy] The Journal of Chemical Physics, Vol. 131, No. 20. (2009), 205101. by Wouter K. den Otter posted to pores pore_size pore_formation coarse-grain by agrossfield on 2009-12-01 19:56:42 as along with 1 person paulschlesinger
	Membrane-Bending Mechanism of Amphiphysin N-BAR Domains [My Copy] Vol. 97, No. 10. (15 November 2009), pp. 2727-2735. by Anton Arkhipov, Ying Yin, Klaus Schulten posted to simulation membrane coarse-grain by okapi on 2009-11-26 10:16:46 as
	Location, Tilt, and Binding: A Molecular Dynamics Study of Voltage-Sensitive Dyes in Biomembranes [My Copy] The Journal of Physical Chemistry B (06 November 2009), 091106085645083. by Marlon J. Hinner, Siewert-J Marrink, Alex H. de Vries posted to dye coarse-grain by agrossfield on 2009-11-26 02:05:54 as
	Role of the Range in the Fluid−Crystal Coexistence for a Patchy Particle Model [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 46. (19 November 2009), pp. 15133-15136. by Flavio Romano, Eduardo Sanz, Francesco Sciortino posted to coarse-grain by agrossfield on 2009-11-17 02:36:07 as
	Solid-liquid phase equilibria of the Gaussian core model fluid [My Copy] The Journal of Chemical Physics, Vol. 131, No. 18. (2009), 184507. by Peter Mausbach, Alauddin Ahmed, Richard J. Sadus posted to coarse-grain by agrossfield on 2009-11-17 02:32:22 as
	A soft-core Gay--Berne model for the simulation of liquid crystals by Hamiltonian replica exchange [My Copy] The Journal of Chemical Physics, Vol. 131, No. 17. (2009), 174107. by Roberto Berardi, Claudio Zannoni, Juho S. Lintuvuori, Mark R. Wilson posted to replica-exchange coarse-grain by agrossfield on 2009-11-06 20:34:51 as
	Coarse-Grained Protein Model with Residue Orientation Energies Derived from Atomic Force Fields [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 44. (5 November 2009), pp. 14824-14830. by Marcos R. Betancourt posted to coarse-grain by agrossfield on 2009-10-30 03:02:32 as
	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 lipids coarse-grain cg bilayer by dimka on 2009-10-29 23:16:44 as along with 14 people and 3 groups loison arnaucordomi oteri sunrise flbarroso A_Coletta_Thesis krapnik Marine middledomain sobolevnrm Ema aqeel DanielParton softsimu Structural Biology Group TorVergata Molecular dynamics in MSU baker-group
	Surface morphology and molecular conformation for ultrathin lubricant films with functional end groups [My Copy] Journal of Applied Physics, Vol. 93, No. 10. (2003), pp. 8707-8709. by Qian Guo, Satoru Izumisawa, David M. Phillips, Myung S. Jhon posted to morphology lubricant_films coarse-grained-model coarse-grain bead_spring by 6rheology on 2009-10-21 08:20:17 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
	Coarse-Grained Molecular Dynamics Simulation of the Aggregation Properties of Multiheaded Cationic Surfactants in Water [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 41. (15 October 2009), pp. 13545-13550. by Suman K. Samanta, Santanu Bhattacharya, Prabal K. Maiti posted to coarse-grain antimicrobial-peptide by agrossfield on 2009-10-08 15:52:12 as
	Role of Short-Range Directional Interactions in Coarse-Graining of Protic/Aprotic Liquids [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 39. (1 October 2009), pp. 12988-12998. by Piotr Kowalczyk, Piotr A. Gauden, Alina Ciach posted to coarse-grain by agrossfield on 2009-09-25 17:51:06 as
	Extended ensemble approach for deriving transferable coarse-grained potentials [My Copy] The Journal of Chemical Physics, Vol. 131, No. 10. (2009), 104110. by J. W. Mullinax, W. G. Noid posted to coarse-grain by agrossfield on 2009-09-15 13:10:10 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 integrator coarse-grain by agrossfield on 2009-09-15 13:09:33 as along with 3 people and 1 group dlimmer whitead paulschlesinger Jiang Research Group
	Theoretically informed coarse grain simulations of polymeric systems [My Copy] The Journal of Chemical Physics, Vol. 131, No. 8. (2009), 084903. by Darin Q. Pike, François A. Detcheverry, Marcus Müller, Juan J. de Pablo posted to field-theory coarse-grain by agrossfield on 2009-08-31 21:42:44 as
	Permeability of Small Molecules through a Lipid Bilayer: A Multiscale Simulation Study [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 35. (3 September 2009), pp. 12019-12029. by Mario Orsi, Wendy E. Sanderson, Jonathan W. Essex posted to gay-berne coarse-grain by agrossfield on 2009-08-28 15:57:25 as along with 1 person sobolevnrm
	Coarse-grained modeling of allosteric regulation in protein receptors [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 34. (25 August 2009), pp. 14253-14258. by Ilya A. Balabin, Weitao Yang, David N. Beratan posted to rhodopsin gpcr coarse-grain b2ar by agrossfield on 2009-08-28 14:04:12 as along with 4 people and 1 group sobolevnrm pmung jmccammon okapi McCammon
	The multiscale coarse-graining method. III. A test of pairwise additivity of the coarse-grained potential and of new basis functions for the variational calculation [My Copy] The Journal of Chemical Physics, Vol. 131, No. 3. (2009), 034102. by Avisek Das, Hans C. Andersen posted to force-fields fmm coarse-grain by tomweingarten on 2009-08-26 18:33:57 as along with 3 people sobolevnrm dlimmer agrossfield
	Coarse-Grained Model of Proteins Incorporating Atomistic Detail of the Active Site [My Copy] Physical Review Letters, Vol. 95, No. 21. (Nov 2005), 218102. by Marilisa Neri, Claudio Anselmi, Michele Cascella, Amos Maritan, Paolo Carloni posted to theory coarse-grain cascella by rdf on 2009-08-22 10:15:25 as along with 1 person RamuAnandakrishnan
	Focused Functional Dynamics of Supramolecules by Use of a Mixed-Resolution Elastic Network Model [My Copy] Vol. 97, No. 4. (19 August 2009), pp. 1178-1187. by Ozge Kurkcuoglu, Osman T. Turgut, Sertan Cansu, Robert L. Jernigan, Pemra Doruker posted to network-model coarse-grain by agrossfield on 2009-08-18 20:49:20 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 coarse-grain by agrossfield on 2009-08-07 20:37:29 as along with 3 people anuragsethi sobolevnrm cjryan
	Comparison of Atomic-Level and Coarse-Grained Models for Liquid Hydrocarbons from Molecular Dynamics Configurational Entropy Estimates [My Copy] The Journal of Physical Chemistry B, Vol. 110, No. 16. (1 April 2006), pp. 8464-8473. by Riccardo Baron, Alex H. de Vries, Philippe H. Hunenberger, Wilfred F. van Gunsteren posted to coarse-grain entropy by rpetrenko on 2009-08-05 00:20:36 as
	Water Modeled As an Intermediate Element between Carbon and Silicon† [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 13. (2 April 2009), pp. 4008-4016. by Valeria Molinero, Emily B. Moore posted to coarse-grain ion-solvation by agrossfield on 2009-07-21 20:44:59 as
	Coarse-grained ions without charges: Reproducing the solvation structure of NaCl in water using short-ranged potentials [My Copy] The Journal of Chemical Physics, Vol. 131, No. 3. (2009), 034107. by Robert C. Demille, Valeria Molinero posted to coarse-grain ion-solvation by agrossfield on 2009-07-21 20:42:34 as along with 1 person dlimmer
	A coarse-grained potential for fold recognition and molecular dynamics simulations of proteins [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 76, No. 4. (2009), pp. 822-836. by Peter Májek, Ron Elber posted to coarse-grain by agrossfield on 2009-07-17 21:45:43 as along with 1 person paulschlesinger
	The multiscale coarse-graining method. IV. Transferring coarse-grained potentials between temperatures [My Copy] The Journal of Chemical Physics, Vol. 131, No. 2. (2009), 024103. by Vinod Krishna, Will G. Noid, Gregory A. Voth posted to coarse-grain by agrossfield on 2009-07-15 12:25:44 as along with 2 people tomweingarten sobolevnrm
	Computational Investigation of Interaction between Nanoparticles and Membranes: Hydrophobic/Hydrophilic Effect [My Copy] The Journal of Physical Chemistry B, Vol. 112, No. 51. (25 December 2008), pp. 16647-16653. by Yang Li, Xin Chen, Ning Gu posted to bilayers coarse-grain molecular-dynamics nanoparticle by dcheong on 2009-07-09 08:56:53 as along with 1 person qshao
	Systematic Coarse-Graining of Nanoparticle Interactions in Molecular Dynamics Simulation [My Copy] The Journal of Physical Chemistry B, Vol. 109, No. 36. (1 September 2005), pp. 17019-17024. by Sergei Izvekov, Angela Violi, Gregory A. Voth posted to coarse-grain molecular-dynamics nanoparticle by dcheong on 2009-07-09 08:51:58 as along with 2 people and 1 group A_Coletta_Thesis Marine Molecular dynamics in MSU
	Toy amphiphiles on the computer: What can we learn from generic models? [My Copy] Macromolecular Rapid Communications, Vol. 30, No. 9-10. (2009), pp. 741-751. by Friederike Schmid posted to coarse-grain membrane-forcefield by agrossfield on 2009-06-28 17:05:43 as along with 1 person edws
	Generic coarse-grained model for protein folding and aggregation [My Copy] The Journal of Chemical Physics, Vol. 130, No. 23. (2009), 235106. by Tristan Bereau, Markus Deserno posted to coarse-grain protein-folding by agrossfield on 2009-06-22 17:07:01 as
	Coarse-grained molecular dynamics of ligands binding into protein: The case of HIV-1 protease inhibitors [My Copy] The Journal of Chemical Physics, Vol. 130, No. 21. (2009), 215102. by Dechang Li, Ming S. Liu, Baohua Ji, Kehchih Hwang, Yonggang Huang posted to coarse-grain by agrossfield on 2009-06-08 20:37:09 as
	Coarse-grained, density dependent implicit solvent model reliably reproduces behavior of a model surfactant system [My Copy] The Journal of Chemical Physics, Vol. 130, No. 20. (2009), 204903. by Erik C. Allen, Gregory C. Rutledge posted to coarse-grain by agrossfield on 2009-06-02 19:55:48 as
	Coarse-Grain Simulations of the R-SNARE Fusion Protein in its Membrane Environment Detect Long-Lived Conformational Sub-States [My Copy] ChemPhysChem, Vol. 9999, No. 9999. (2009), NA. by Marie-Pierre Durrieu, Peter j, Mark s, Richard Lavery, Marc Baaden posted to coarse-grain durrie09pdf membrane simulation snare by paulschlesinger on 2009-06-01 22:54:34 as
	Molecular Renormalization Group Coarse-Graining of Electrolyte Solutions: Application to Aqueous NaCl and KCl [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 22. (4 June 2009), pp. 7785-7793. by Alexey Savelyev, Garegin A. Papoian posted to coarse-grain ion-solvation by agrossfield on 2009-05-29 19:25:59 as along with 2 people and 1 group tomweingarten sobolevnrm baker-group
	Pairwise energies for polypeptide coarse-grained models derived from atomic force fields [My Copy] The Journal of Chemical Physics, Vol. 130, No. 19. (2009), 195103. by Marcos R. Betancourt, Sheyore J. Omovie posted to coarse-grain forcefield by agrossfield on 2009-05-22 12:23:42 as
	Molecular Renormalization Group Coarse-Graining of Polymer Chains: Application to Double-Stranded DNA [My Copy] Vol. 96, No. 10. (20 May 2009), pp. 4044-4052. by Alexey Savelyev, Garegin A. Papoian posted to coarse-grain dna by onufriev on 2009-05-21 07:13:43 as along with 2 people tomweingarten Elena_Zubova
	Molecular dynamics study of the effect of cholesterol on the properties of lipid monolayers at low surface tensions [My Copy] Phys. Chem. Chem. Phys., Vol. 11, No. 12. (2009), pp. 1916-1922. by Cameron Laing, Svetlana Baoukina, Peter D. Tieleman posted to cholesterol coarse-grain dopg dppc free-energy lipid simulaiton by dimka on 2009-05-15 19:52:13 as along with 3 people and 1 group patvarilly sobolevnrm flbarroso baker-group
	Coarse-grained Models for Simulations of Multiprotein Complexes: Application to Ubiquitin Binding [My Copy] Journal of Molecular Biology, Vol. 375, No. 5. (01 February 2008), pp. 1416-1433. by Young C. Kim, Gerhard Hummer posted to coarse-grain binding by okapi on 2009-05-06 14:12:56 as along with 4 people and 3 groups barry sobolevnrm iantunbridge mikaellund structural_bioinformatics Bioinformatics baker-group
	Replica exchange simulations of transient encounter complexes in protein–protein association [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 35. (2 September 2008), pp. 12855-12860. by Young C. Kim, Chun Tang, G. Marius Clore, Gerhard Hummer posted to coarse-grain binding by okapi on 2009-05-06 14:07:15 as along with 2 people and 2 groups barry cactus structural_bioinformatics McCammon
	Bottom-up derivation of an effective thermostat for united atoms simulations of water [My Copy] The Journal of Chemical Physics, Vol. 130, No. 16. (2009), 164509. by Anders Eriksson, Martin N. Jacobi, Johan Nyström, Kolbjo posted to coarse-grain thermostats by agrossfield on 2009-05-01 12:15:34 as along with 1 person dlimmer
	Hybrid Coarse-Graining Approach for Lipid Bilayers at Large Length and Time Scales [My Copy] The Journal of Physical Chemistry B In The Journal of Physical Chemistry B, Vol. 113, No. 13. (2 April 2009), pp. 4413-4424. by Gary S. Ayton, Gregory A. Voth posted to coarse-grain multiscale by agrossfield on 2009-03-28 15:11:40 as along with 2 people and 1 group choonpeng sobolevnrm baker-group
	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-grain multiscale by agrossfield on 2009-03-28 15:10:57 as along with 4 people and 1 group loison choonpeng flbarroso sobolevnrm baker-group
	Four-Scale Description of Membrane Sculpting by BAR Domains [My Copy] Vol. 95, No. 6. (15 September 2008), pp. 2806-2821. by Anton Arkhipov, Ying Yin, Klaus Schulten posted to coarse-grain lipid-protein-interactions by agrossfield on 2009-03-17 10:51:38 as
	Simulation Study of Protein-Mediated Vesicle Fusion [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 3. (22 January 2009), pp. 589-591. by Shaogui Wu, Hongxia Guo posted to coarse-grain membrane-fusion membrane-proteins by agrossfield on 2009-02-18 18:05:52 as along with 1 person and 1 group sobolevnrm baker-group
	Systematic Coarse-graining of a Multicomponent Lipid Bilayer [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by Lanyuan Lu, Gregory Voth posted to coarse-grain membrane membrane-forcefield by agrossfield on 2009-02-16 18:16:34 as along with 2 people and 1 group sobolevnrm tomweingarten baker-group
	Mesoscopic modeling for nucleic acid chain dynamics [My Copy] Physical Review E, Vol. 71, No. 5. (5 May 2005), 051902. by M. Sales-Pardo, R. Guimerà, A. A. Moreira, J. Widom, L. A. N. Amaral posted to coarse-grain by Elena_Zubova on 2009-02-06 14:30:54 as
	Computer Simulations of Vesicle Fission Induced by External Amphipathic Inclusions [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 4. (29 January 2009), pp. 1048-1057. by Kai Yang, Yu-Qiang Ma posted to coarse-grain dpd fission by agrossfield on 2009-01-26 13:23:21 as along with 1 person and 1 group sobolevnrm baker-group
	Multi-scale modelling of heterogeneous materials with fixed and evolving microstructures [My Copy] Modelling and Simulation in Materials Science and Engineering, Vol. 13, No. 1. (2005), pp. 95-121. by Jiun-Shyan Chen, Shafigh Mehraeen posted to coarse-grain by Elena_Zubova on 2009-01-15 16:40:30 as
	Coarse-grained peptide modeling using a systematic multiscale approach. [My Copy] Biophysical journal, Vol. 92, No. 12. (15 June 2007), pp. 4289-4303. by J. Zhou, I. F. Thorpe, S. Izvekov, G. A. Voth posted to coarse-grain by Elena_Zubova on 2009-01-15 15:45:17 as

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