Group: baker-group - with tag multiscale [at least 200 articles] Export

Recent papers posted by members of the baker-group group with tag multiscale

	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 electrostatics multiscale solvation by sobolevnrm to the group baker-group on 2009-05-11 12:27:55 as along with 2 people tomweingarten agrossfield
	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
	Internal coarse-graining of molecular systems [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 16. (21 April 2009), pp. 6453-6458. by Jérôme Feret, Vincent Danos, Jean Krivine, Russ Harmer, Walter Fontana posted to graph_theory multiscale systems_biology by sobolevnrm to the group baker-group on 2009-04-23 12:31:17 as along with 9 people jvb leemond31 superpyrin Scis0000002 reyez trfield paulschlesinger jjray kshundyak
	Extracting the multiscale backbone of complex weighted networks [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 16. (21 April 2009), pp. 6483-6488. by M. Ãngeles Serrano, MariÃ¡n BoguÃ±Ã¡, Alessandro Vespignani posted to allostery graph_theory multiscale systems_biology by sobolevnrm to the group baker-group on 2009-04-23 12:30:54 as along with 9 people rdiaz tomt21 edws rsantana trfield pinney deanmalmgren kevinchannon kshundyak
	Systematic multiscale simulation of membrane protein systems [My Copy] Current Opinion in Structural Biology (09 April 2009) by Gary S. Ayton, Gregory A. Voth posted to biomembranes multiscale review by sobolevnrm to the group baker-group on 2009-04-21 12:29:42 as along with 2 people and 1 group barry paulschlesinger McCammon
	A multi-time-scale analysis of chemical reaction networks: I. Deterministic systems [My Copy] Journal of Mathematical Biology by Chang Lee, Hans Othmer posted to kinetics mathematics multiscale systems_biology by sobolevnrm to the group baker-group on 2009-04-15 12:11:57 as
	Hybrid Elastic and Discrete-Particle Approach to Biomembrane Dynamics with Application to the Mobility of Curved Integral Membrane Proteins [My Copy] Physical Review Letters, Vol. 102, No. 13. (2009), 138102. by Ali Naji, Paul J. Atzberger, Frank L. H. Brown posted to biomembranes multiscale by sobolevnrm to the group baker-group on 2009-04-14 12:50:18 as along with 2 people reister jeevanjyoti
	Equation-Free Multiscale Computation: Algorithms and Applications [My Copy] Annual Review of Physical Chemistry, Vol. 60, No. 1. (2009), pp. 321-344. by Ioannis G. Kevrekidis, Giovanni Samaey posted to diffusion mathematics multiscale review by sobolevnrm to the group baker-group on 2009-04-01 12:55:10 as along with 2 people Borelli nurban
	The middle way [My Copy] Proceedings of the National Academy of Sciences, Vol. 97, No. 1. (4 January 2000), pp. 32-37. by R. B. Laughlin, David Pines, Joerg Schmalian, Branko P. Stojkovic, Peter Wolynes posted to misc multiscale review by sobolevnrm to the group baker-group on 2009-03-26 11:33:49 as along with 4 people paulschlesinger Elena_Zubova madhadron samjlord
	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 biomembranes multiscale by sobolevnrm to the group baker-group on 2009-03-25 11:37:24 as along with 3 people choonpeng flbarroso agrossfield
	Numerical Multiscale Methods for Coupled Oscillators [My Copy] Multiscale Modeling & Simulation, Vol. 7, No. 3. (2009), pp. 1387-1404. by Gil Ariel, Bjorn Engquist, Richard Tsai posted to multiscale statistical_mechanics by sobolevnrm to the group baker-group on 2009-03-25 11:37:10 as along with 1 person madureira69
	On using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models. [My Copy] Physical chemistry chemical physics : PCCP, Vol. 11, No. 12. (28 March 2009), pp. 1934-1941. by M. Winger, D. Trzesniak, R. Baron, W. F. van Gunsteren posted to molecular_dynamics multiscale by sobolevnrm to the group baker-group on 2009-03-23 11:56:40 as along with 4 people arnaucordomi patvarilly mbeeby flbarroso
	Hybrid Coarse-Graining Approach for Lipid Bilayers at Large Length and Time Scales [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by Gary S. Ayton, Gregory A. Voth posted to biomembranes multiscale by sobolevnrm to the group baker-group on 2009-03-23 11:51:54 as along with 1 person agrossfield
	Effective force coarse-graining [My Copy] Phys. Chem. Chem. Phys., Vol. 11, No. 12. (2009), pp. 2002-2015. by Yanting Wang, W. G. Noid, Pu Liu, Gregory A. Voth posted to molecular_simulation multiscale by sobolevnrm to the group baker-group on 2009-03-23 11:50:49 as along with 3 people and 1 group jmccammon mbeeby flbarroso McCammon
	Comparative atomistic and coarse-grained study of water: What do we lose by coarse-graining? [My Copy] The European Physical Journal E: Soft Matter and Biological Physics, Vol. 28, No. 2. (1 February 2009), pp. 221-229. by Han Wang, Christoph Junghans, Kurt Kremer posted to multiscale solvation by sobolevnrm to the group baker-group on 2009-03-20 11:51:57 as
	Curvature effects on lipid packing and dynamics in liposomes revealed by coarse grained molecular dynamics simulations [My Copy] Phys. Chem. Chem. Phys., Vol. 11, No. 12. (2009), pp. 2056-2067. by Jelger H. Risselada, Siewert J. Marrink posted to biomembranes multiscale by sobolevnrm to the group baker-group on 2009-03-19 12:12:34 as along with 1 person patvarilly
	The Interaction of Monotopic Membrane Enzymes with a Lipid Bilayer: A Coarse-Grained MD Simulation Study [My Copy] Biochemistry, Vol. 0, No. ja. (0000) by Kia Balali-Mood, Peter Bond, Mark Sansom posted to biomembranes multiscale protein-membrane_interactions by sobolevnrm to the group baker-group on 2009-03-19 12:07:08 as along with 2 people paulschlesinger carlosjavierna
	Evaluating the transferability of coarse-grained, density-dependent implicit solvent models to mixtures and chains [My Copy] The Journal of Chemical Physics, Vol. 130, No. 3. (2009) by Erik C. Allen, Gregory C. Rutledge posted to multiscale solvation by sobolevnrm to the group baker-group on 2009-03-19 12:06:55 as along with 1 person agrossfield
	Multidimensional Langevin modeling of biomolecular dynamics [My Copy] The Journal of Chemical Physics, Vol. 130, No. 3. (2009), 034106. by Rainer Hegger, Gerhard Stock posted to diffusion kinetics multiscale quasiharmonic_models by sobolevnrm to the group baker-group on 2009-03-18 11:28:11 as along with 1 person Diego_Prada
	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 biomembranes multiscale by sobolevnrm to the group baker-group on 2009-03-13 11:25:10 as along with 2 people agrossfield tomweingarten
	ABSINTH: a new continuum solvation model for simulations of polypeptides in aqueous solutions. [My Copy] Journal of computational chemistry, Vol. 30, No. 5. (15 April 2009), pp. 673-699. by A. Vitalis, R. V. Pappu posted to electrostatics molecular_simulation multiscale solvation by sobolevnrm to the group baker-group on 2009-03-05 12:34:48 as along with 2 people melo_mcr agrossfield
	Spontaneous Formation of a Barrel-Stave Pore in a Coarse-Grained Model of the Synthetic LS3 Peptide and a DPPC Lipid Bilayer [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by P. Gkeka, L. Sarkisov posted to biomembranes multiscale protein-membrane_interactions by sobolevnrm to the group baker-group on 2009-03-05 12:33:31 as along with 1 person agrossfield
	Dissipative particle dynamics of tension-induced membrane fusion [My Copy] Molecular Simulation, Vol. 99999, No. 1. (2009), pp. 1-1. by Andrea Grafmüller, Julian Shillcock, Reinhard Lipowsky posted to biomembranes multiscale by sobolevnrm to the group baker-group on 2009-03-04 13:11:51 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 biomembranes multiscale by sobolevnrm to the group baker-group on 2009-03-04 13:10:34 as along with 1 person agrossfield
	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 molecular_simulation multiscale by sobolevnrm to the group baker-group on 2009-03-03 15:57:34 as along with 7 people and 1 group barry A_Coletta_Thesis paulschlesinger choonpeng aqeel jmccammon rok McCammon
	Efficient solution of Poisson's equation using discrete variable representation basis sets for Car--Parrinello ab initio molecular dynamics simulations with cluster boundary conditions [My Copy] The Journal of Chemical Physics, Vol. 129, No. 22. (2008) by Hee S. Lee, Mark E. Tuckerman posted to electrostatics mathematics multiscale quantum_mechanics by sobolevnrm to the group baker-group on 2009-03-03 15:36:07 as
	High Resolution Approach to the Native State Ensemble Kinetics and Thermodynamics [My Copy] Biophys. J. (19 September 2008), biophysj.108.136697. by Sangwook Wu, Pavel I. Zhuravlev, Garegin A. Papoian posted to multiscale protein_folding solvation by sobolevnrm to the group baker-group on 2009-02-28 21:54:20 as along with 1 person paulschlesinger
	Separation of variables in molecular-dynamics simulations: A criterion to estimate the quality of the approximation [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 78, No. 5. (2008) by Adolfo B. Poma, Luigi Delle Site posted to molecular_simulation multiscale by sobolevnrm to the group baker-group on 2009-02-28 21:49:41 as
	Multibody Interactions in Coarse-Graining Schemes for Extended Systems [My Copy] SIAM Journal on Scientific Computing, Vol. 31, No. 2. (2008), pp. 987-1015. by Sasanka Are, Markos A. Katsoulakis, Petr Plechác, Luc R. Bellet posted to molecular_simulation multiscale by sobolevnrm to the group baker-group on 2009-02-28 21:48:50 as
	Extracting macroscopic dynamics: model problems and algorithms [My Copy] Nonlinearity, Vol. 17, No. 6. (2004), pp. R55-R127. by Raz, Andrew Stuart posted to mathematics multiscale by sobolevnrm to the group baker-group on 2009-02-28 21:45:42 as along with 2 people Diego_Prada Borelli
	A semi-implicit solvent model for the simulation of peptides and proteins [My Copy] Journal of Computational Chemistry, Vol. 25, No. 8. (2004), pp. 1015-1029. by Nathalie Basdevant, Daniel Borgis, Tap Ha-Duong posted to multiscale solvation by sobolevnrm to the group baker-group on 2009-02-05 12:47:03 as along with 1 person jwagoner
	Particle-Based Implicit Solvent Model for Biosimulations: Application to Proteins and Nucleic Acids Hydration [My Copy] Journal of Chemical Theory and Computation, Vol. 2, No. 6. (1 November 2006), pp. 1646-1656. by Nathalie Basdevant, Tap Ha-Duong, Daniel Borgis posted to multiscale solvation by sobolevnrm to the group baker-group on 2009-02-05 12:46:51 as along with 2 people Elena_Zubova jwagoner
	Peptide Aggregation and Pore Formation in a Lipid Bilayer - A Combined Coarse Grained and All Atom Molecular Dynamics Study [My Copy] Biophys. J. (1 August 2008), biophysj.108.133330. by Lea Thogersen, Birgit Schiott, Thomas Vosegaard, Niels C. Nielsen, Emad Tajkhorshid posted to biomembranes multiscale protein-membrane_interactions by sobolevnrm to the group baker-group on 2009-01-27 12:33:44 as along with 1 person paulschlesinger
	Systematic Multiscale Parameterization of Heterogeneous Elastic Network Models of Proteins [My Copy] Biophys. J., Vol. 95, No. 9. (1 November 2008), pp. 4183-4192. by Edward Lyman, Jim Pfaendtner, Gregory A. Voth posted to multiscale quasiharmonic_models by sobolevnrm to the group baker-group on 2009-01-27 12:33:16 as along with 1 person aqeel
	Coarse-graining protein structures with local multivariate features from molecular dynamics. [My Copy] The journal of physical chemistry. B, Vol. 112, No. 44. (6 November 2008), pp. 14026-14035. by Zhiyong Zhang, Willy Wriggers posted to clustering multiscale quasiharmonic_models by sobolevnrm to the group baker-group on 2009-01-26 12:48:57 as along with 1 person choonpeng
	Coarse-Grained Molecular Dynamics Simulations of the Energetics of Helix Insertion into a Lipid Bilayer [My Copy] Biochemistry (2 October 2008) by Peter J. Bond, Chze L. Wee, Mark S. Sansom posted to biomembranes multiscale protein-membraneinteractions solvation by sobolevnrm to the group baker-group on 2008-12-27 14:39:09 as along with 3 people agrossfield paulschlesinger sunhwan
	On the application of the Arlequin method to the coupling of particle and continuum models [My Copy] Computational Mechanics, Vol. 42, No. 4. (2008), pp. 511-530. by Paul Bauman, Hachmi Dhia, Nadia Elkhodja, J. Oden, Serge Prudhomme posted to mathematics mechanics multiscale by sobolevnrm to the group baker-group on 2008-07-25 12:06:05 as
	Connecting Atomistic-to-Continuum Coupling and Domain Decomposition [My Copy] Multiscale Modeling & Simulation, Vol. 7, No. 1. (2008), pp. 362-380. by Michael L. Parks, Pavel B. Bochev, Richard B. Lehoucq posted to mathematics mechanics multiscale by sobolevnrm to the group baker-group on 2008-06-16 12:19:46 as
	Simulation approaches to soft matter: Generic statistical properties vs. chemical details [My Copy] Computer Physics Communications In Special issue based on the Conference on Computational Physics 2007 - CCP 2007, Vol. 179, No. 1-3. (July 2008), pp. 51-60. by Matej Praprotnik, Christoph Junghans, Luigi Delle Site, Kurt Kremer posted to molecular_simulation multiscale by sobolevnrm to the group baker-group on 2008-06-07 15:37:58 as
	Tension-induced vesicle fusion: pathways and pore dynamics [My Copy] Soft Matter, Vol. 4 (2008), pp. 1208-1214. by L. Gao, R. Lipowsky, J. Shillcock posted to biomembranes molecular_simulation multiscale by sobolevnrm to the group baker-group on 2008-06-04 11:43:25 as
	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 diffusion multiscale by sobolevnrm to the group baker-group on 2008-05-27 11:40:19 as along with 4 people ocs ras paulschlesinger arjunan
	Redox entropy of plastocyanin: Developing a microscopic view of mesoscopic polar solvation [My Copy] The Journal of Chemical Physics, Vol. 128, No. 15. (2008) by David N. Lebard, Dmitry V. Matyushov posted to molecular_simulation multiscale solvation by sobolevnrm to the group baker-group on 2008-05-22 12:03:41 as
	A novel algorithm for creating coarse-grained, density dependent implicit solvent models [My Copy] The Journal of Chemical Physics, Vol. 128, No. 15. (2008) by Erik C. Allen, Gregory C. Rutledge posted to electrostatics molecular_simulation multiscale solvation by sobolevnrm to the group baker-group on 2008-05-22 11:54:29 as along with 1 person agrossfield
	Concurrent triple-scale simulation of molecular liquids [My Copy] The Journal of Chemical Physics, Vol. 128, No. 11. (2008) by Rafael D. Buscalioni, Kurt Kremer, Matej Praprotnik posted to molecular_simulation multiscale solvation by sobolevnrm to the group baker-group on 2008-05-20 11:35:10 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 biomembranes molecular_dynamics multiscale by sobolevnrm to the group baker-group on 2008-05-19 11:39:49 as along with 13 people and 2 groups arnaucordomi dimka oteri sunrise flbarroso A_Coletta_Thesis krapnik Marine middledomain Ema aqeel DanielParton softsimu Structural Biology Group TorVergata Molecular dynamics in MSU
	Coarse-Grained MD Simulations of Membrane Protein-Bilayer Self-Assembly [My Copy] Structure, Vol. 16, No. 4. (8 April 2008), pp. 621-630. by Kathryn A. Scott, Peter J. Bond, Anthony Ivetac, Alan P. Chetwynd, Syma Khalid, Mark S. Sansom posted to biomembranes ion_channels multiscale by sobolevnrm to the group baker-group on 2008-05-14 12:02:45 as along with 2 people choonpeng sebk
	Normal mode partitioning of Langevin dynamics for biomolecules [My Copy] The Journal of Chemical Physics, Vol. 128, No. 14. (2008) by Christopher R. Sweet, Paula Petrone, Vijay S. Pande, Jesús A. Izaguirre posted to molecular_dynamics multiscale quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2008-05-12 11:53:54 as along with 2 people paulschlesinger aqeel
	Coarse-Graining in Interaction Space: A Systematic Approach for Replacing Long-Range Electrostatics with Short-Range Potentials [My Copy] J. Phys. Chem. B (27 March 2008) by S. Izvekov, J. M. J. Swanson, G. A. Voth posted to electrostatics multiscale by sobolevnrm to the group baker-group on 2008-05-05 11:18:11 as along with 2 people softsimu sunhwan
	Coupled composition-deformation phase-field method for multicomponent lipid membranes [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 76, No. 1. (2007) by Chloe M. Funkhouser, Francisco J. Solis, K. Thornton posted to biomembranes multiscale by sobolevnrm to the group baker-group on 2008-04-21 11:38:27 as along with 1 person softsimu
	A transferable coarse-grained model for hydrogen-bonding liquids [My Copy] Physical Chemistry Chemical Physics, Vol. 2008 by P. A. Golubkov, J. C. Wu, P. Ren posted to multiscale solvation by sobolevnrm to the group baker-group on 2008-03-28 11:01:11 as

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coarse-grain	7
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protein-membrane_interactions	7
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protein	6
protein_folding	6
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Group: baker-group - with tag multiscale [at least 200 articles] Export

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