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Abbreviation : CG
Long Form : coarse-grained
No. Year Title Co-occurring Abbreviation
2003 The mechanism of vesicle fusion as revealed by molecular dynamics simulations. PC, PE
2004 Coarse-grained model for phospholipid/cholesterol bilayer. DPPC
2004 Molecular-dynamics simulation of amphiphilic bilayer membranes and wormlike micelles: a multi-scale modelling approach to the design of viscoelastic surfactant solutions. ---
2005 A multiscale coarse-graining method for biomolecular systems. DMPC, MD, MS-CG
2005 Allostery of actin filaments: molecular dynamics simulations and coarse-grained analysis. DB loop
2005 Finite-temperature quasicontinuum: molecular dynamics without all the atoms. MD
2005 Mechanical properties of surfactant bilayer membranes from atomistic and coarse-grained molecular dynamics simulations. ---
2005 Multi-scale modeling of phase separation in mixed lipid bilayers. MD
2005 Multiscale coarse graining of liquid-state systems. MS-CG
10  2005 Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model. DPPC
11  2006 A comparison of united atom, explicit atom, and coarse-grained simulation models for poly(ethylene oxide). EA, PEO, UA
12  2006 Coarse-grained modeling of the actin filament derived from atomistic-scale simulations. MD, NMA
13  2006 Comparison of atomic-level and coarse-grained models for liquid hydrocarbons from molecular dynamics configurational entropy estimates. AL, DOPC
14  2006 Configurational entropies of lipids in pure and mixed bilayers from atomic-level and coarse-grained molecular dynamics simulations. AL
15  2006 Equation of state for a coarse-grained DPPC monolayer at the air/water interface. RDS, SRT
16  2006 Loop motions of triosephosphate isomerase observed with elastic networks. ---
17  2006 Mapping all-atom models onto one-bead Coarse Grained Models: general properties and applications to a minimal polypeptide model. ---
18  2006 Molecular dynamics simulations of PAMAM dendrimer-induced pore formation in DPPC bilayers with a coarse-grained model. DPPC, MD, PAMAM
19  2006 Multiscale Coarse-Graining of Mixed Phospholipid/Cholesterol Bilayers. DMPC, MD, MS-CG
20  2007 Assembly of lipoprotein particles revealed by coarse-grained molecular dynamics simulations. HDL
21  2007 Atomistic and coarse-grained analysis of double spectrin repeat units: the molecular origins of flexibility. DSRUs, MD
22  2007 Coarse-grained model for phospholipid/cholesterol bilayer employing inverse Monte Carlo with thermodynamic constraints. IMC
23  2007 Coarse-grained molecular dynamics simulations of membrane proteins and peptides. MD
24  2007 Coarse-Grained Protein Model Coupled with a Coarse-Grained Water Model:  Molecular Dynamics Study of Polyalanine-Based Peptides. ---
25  2007 Comparison of thermodynamic properties of coarse-grained and atomic-level simulation models. AL, MD
26  2007 Dynamics of water in the hydration shells of C60: molecular dynamics simulation using a coarse-grained model. ---
27  2007 Multiscale coarse-graining and structural correlations: connections to liquid-state theory. MS-CG
28  2008 A Bayesian statistics approach to multiscale coarse graining. MS-CG
29  2008 A systematic methodology for defining coarse-grained sites in large biomolecules. ED-CG
30  2008 Bridging coarse-grained models by jump-in-sample simulations. WL
31  2008 Coarse-grained models reveal functional dynamics--II. Molecular dynamics simulation at the coarse-grained level--theories and biological applications. MD
32  2008 Comparing experimental and simulated pressure-area isotherms for DPPC. DPPC
33  2008 Fast dynamics in coarse-grained polymer models: the effect of the hydrogen bonds. HBs
34  2008 Gating motions in voltage-gated potassium channels revealed by coarse-grained molecular dynamics simulations. ---
35  2008 Improved sampling for simulations of interfacial membrane proteins: application of generalized shadow hybrid Monte Carlo to a peptide toxin/bilayer system. GSHMC, MD
36  2008 Packing of transmembrane helices in bacteriorhodopsin folding: structure and thermodynamics. AA, bR, HMPs, RMSD
37  2008 Peptide aggregation and pore formation in a lipid bilayer: a combined coarse-grained and all atom molecular dynamics study. AA
38  2008 REACH coarse-grained biomolecular simulation: transferability between different protein structural classes. MD
39  2008 Reconstructing atomistic detail for coarse-grained models with resolution exchange. AA
40  2008 Single-chain and aggregation properties of semiconducting polymer solutions investigated by coarse-grained langevin dynamics simulation. MD, MEH-PPV
41  2008 The interaction of phospholipase A2 with a phospholipid bilayer: coarse-grained molecular dynamics simulations. AT, MD, PLA2
42  2008 The MARTINI Coarse-Grained Force Field: Extension to Proteins. DOPC, DPPC
43  2008 The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models. MS-CG, PMF
44  2008 Toward a Coarse-Grained Protein Model Coupled with a Coarse-Grained Solvent Model: Solvation Free Energies of Amino Acid Side Chains. MD
45  2008 Transferability of coarse-grained force fields: the polymer case. ---
46  2008 Unique elastic properties of the spectrin tetramer as revealed by multiscale coarse-grained modeling. DSRU
47  2009 A coarse-grained model for polyethylene oxide and polyethylene glycol: conformation and hydrodynamics. FF, PEG, PEO
48  2009 A dual-scale approach toward structure prediction of retinal proteins. AA, bR, HR, RPs, SRI, SRII
49  2009 A rapid coarse residue-based computational method for x-ray solution scattering characterization of protein folds and multiple conformational states of large protein complexes. ---
50  2009 A Transferable Coarse Grain Non-bonded Interaction Model For Amino Acids. AA, LJ, SASA
51  2009 Bridging fluctuating hydrodynamics and molecular dynamics simulations of fluids. FH, MD
52  2009 Coarse-grained molecular dynamics study of cyclic peptide nanotube insertion into a lipid bilayer. AA, MD
53  2009 Defining coarse-grained representations of large biomolecules and biomolecular complexes from elastic network models. ED-CG, ENM, MD, PCA
54  2009 Dynamics of activation of lecithin:cholesterol acyltransferase by apolipoprotein A-I. apo, CE, HDL, LCAT, MD, UC
55  2009 Generic coarse-grained model for protein folding and aggregation. ---
56  2009 Hybrid coarse-graining approach for lipid bilayers at large length and time scales. HAS, MS-CG
57  2009 Inversion of radial distribution functions to pair forces by solving the Yvon-Born-Green equation iteratively. MD, RDFs, YBG
58  2009 Liquid crystalline and antinematic behavior of shape-persistent macrocycles from molecular-dynamics simulations. SPMs
59  2009 Multiscale modeling of dendrimers and their interactions with bilayers and polyelectrolytes. ---
60  2009 On using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models. ---
61  2009 Role of short-range directional interactions in coarse-graining of protic/aprotic liquids. ---
62  2009 Self-assembling dipeptides: conformational sampling in solvent-free coarse-grained simulation. MD
63  2009 Self-learning multiscale simulation for achieving high accuracy and high efficiency simultaneously. ---
64  2009 Simulations of the BM2 proton channel transmembrane domain from influenza virus B. ---
65  2009 Solvent-free lipid bilayer model using multiscale coarse-graining. MS-CG
66  2009 Structure, dynamics, and ion conductance of the phospholamban pentamer. AA, PLN
67  2009 Systematic coarse graining from structure using internal states: application to phospholipid/cholesterol bilayer. IMC, RDFs
68  2009 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. MD, MS-CG
69  2010 A Coarse Grained Model for Atomic-Detailed DNA Simulations with Explicit Electrostatics. ---
70  2010 A new coarse-grained model for water: the importance of electrostatic interactions. BMW
71  2010 A Nonradial Coarse-Grained Potential for Proteins Produces Naturally Stable Secondary Structure Elements. ---
72  2010 A systematically coarse-grained solvent-free model for quantitative phospholipid bilayer simulations. POPC
73  2010 Antimicrobial and cell-penetrating peptides: structure, assembly and mechanisms of membrane lysis via atomistic and coarse-grained molecular dynamics simulations. AMPs, MD
74  2010 Biological significance of nanograined/ultrafine-grained structures: Interaction with fibroblasts. NG/UFG
75  2010 Cellular activity of bioactive nanograined/ultrafine-grained materials. HA, NG/UFG, nHA
76  2010 Characterization of a clinical polymer-drug conjugate using multiscale modeling. AA, MD, PGG-PTX, PTX
77  2010 Characterizing protein energy landscape by self-learning multiscale simulations: application to a designed beta-hairpin. SLMS
78  2010 Chemically accurate coarse graining of double-stranded DNA. ---
79  2010 Coarse grained molecular dynamics simulations of transmembrane protein-lipid systems. ---
80  2010 Coarse-Grained Computer Simulations of Polymer/Fullerene Bulk Heterojunctions for Organic Photovoltaic Applications. P3HT
81  2010 Coarse-grained model for simulation of RNA three-dimensional structures. ---
82  2010 Coarse-grained molecular dynamics of tetrameric transmembrane peptide bundles within a lipid bilayer. AA, MD
83  2010 Coarse-Grained Representations of Large Biomolecular Complexes from Low-Resolution Structural Data. ED-CG
84  2010 How to predict diffusion of medium-sized molecules in polymer matrices. From atomistic to coarse grain simulations. ---
85  2010 Interactions between a voltage sensor and a toxin via multiscale simulations. AT, MD, VS
86  2010 Interpretation of 2H-NMR experiments on the orientation of the transmembrane helix WALP23 by computer simulations. MD, QS
87  2010 Membrane poration by antimicrobial peptides combining atomistic and coarse-grained descriptions. AMPs
88  2010 Membrane/Toxin Interaction Energetics via Serial Multiscale Molecular Dynamics Simulations. AT, MD, PMF, VS
89  2010 Minimalist models for proteins: a comparative analysis. FF
90  2010 Molecular dynamics simulation of protein adsorption at fluid interfaces: a comparison of all-atom and coarse-grained models. ---
91  2010 Molecular dynamics simulations of the dimerization of transmembrane alpha-helices. AT, GPA, MD, TM
92  2010 Multidomain assembled states of Hck tyrosine kinase in solution. BSS-SAXS, SAXS
93  2010 Multiscale coarse-graining of the protein energy landscape. ---
94  2010 Multiscale computer simulation of the immature HIV-1 virion. CTD, CTDs
95  2010 Multiscale simulations of protein landscapes: using coarse-grained models as reference potentials to full explicit models. ---
96  2010 Nanoparticle interaction potentials constructed by multiscale computation. vdW
97  2010 On the antibacterial action of cyclic peptides: insights from coarse-grained MD simulations. MD, POPE, POPG
98  2010 Parametrization and application of a coarse grained force field for benzene/fullerene interactions with lipids. AA, MD
99  2010 Parametrization of the Gay-Berne potential for conjugated oligomer with a high aspect ratio. AMD, GB, PMFs
100  2010 Polarizable water model for the coarse-grained MARTINI force field. ---
101  2010 Reconstruction of atomistic details from coarse-grained structures. MD
102  2010 Reference state for the generalized Yvon-Born-Green theory: application for coarse-grained model of hydrophobic hydration. g-YBG
103  2010 Relative entropy as a universal metric for multiscale errors. FP
104  2010 The multiscale coarse-graining method. V. Isothermal-isobaric ensemble. MS-CG
105  2010 Toward a Coarse Graining/All Atoms Force Field (CG/AA) from a Multiscale Optimization Method: An Application to the MCM-41 Mesoporous Silicates. CG/AA
106  2010 Use of the Ornstein-Zernike Percus-Yevick equation to extract interaction potentials from pair correlation functions. MD, OZPY, PCFs
107  2010 Zwitterionic lipid assemblies: molecular dynamics studies of monolayers, bilayers, and vesicles using a new coarse grain force field. DMPC, DPPC, MD, PEG
108  2011 A coarse-grained model for polyethylene glycol polymer. CGMD, DP, IBI, MD, PCF, PDFs, PEG
109  2011 A coarse-grained model of DNA with explicit solvation by water and ions. ---
110  2011 A New Coarse-Grained Force Field for Membrane-Peptide Simulations. BMW
111  2011 A simple, efficient polarizable coarse-grained water model for molecular dynamics simulations. ---
112  2011 A simulation study on nanoscale holes generated by gold nanoparticles on negative lipid bilayers. MD
113  2011 A Solvent-Free Coarse Grain Model for Crystalline and Amorphous Cellulose Fibrils. MD
114  2011 CafeMol: A Coarse-Grained Biomolecular Simulator for Simulating Proteins at Work. MD
115  2011 Coarse-Grain Model for Glucose, Cellobiose, and Cellotetraose in Water. ---
116  2011 Coarse-grained (multiscale) simulations in studies of biophysical and chemical systems. ---
117  2011 Coarse-grained model for PEGylated lipids: effect of PEGylation on the size and shape of self-assembled structures. DPPC, PEG, PEO
118  2011 Coarse-grained modeling study of nonpeptide RGD ligand density and PEG molecular weight on the conformation of poly(gamma-glutamyl-glutamate) paclitaxel conjugates. AA, MD, MW, PGG-PTX-PEG-npRGD
119  2011 Coarse-grained molecular dynamics simulations of the sphere to rod transition in surfactant micelles. CTAC, MD
120  2011 Coarse-grained Monte Carlo simulations of the phase transition of the Potts model on weighted networks. s-CG
121  2011 Coarse-graining entropy, forces, and structures. MS-CG
122  2011 Gay-Berne and electrostatic multipole based coarse-grain potential in implicit solvent. ---
123  2011 Heat conductivity of DNA double helix. MD
124  2011 Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites. SB
125  2011 Implementation of a protein reduced point charge model toward molecular dynamics applications. MD
126  2011 Improved pre-osteoblast response and mechanical compatibility of ultrafine-grained Ti-13Nb-13Zr alloy. ALP, UFG
127  2011 Key intermolecular interactions in the E. coli 70S ribosome revealed by coarse-grained analysis. MD
128  2011 Making structural sense of dimerization interfaces of delta opioid receptor homodimers. DOR, GPCR
129  2011 Micellization Studied by GPU-Accelerated Coarse-Grained Molecular Dynamics. CMCs, GPU, MD, PEG
130  2011 Modification of Martini force field for molecular dynamics simulation of hydrophobic charge induction chromatography of lysozyme. AA, HCIC, MD
131  2011 Molecular dynamics simulation of phase transitions in model lung surfactant monolayers. LC, Ld, LE
132  2011 Multiscale modelling of mesoscopic phenomena triggered by quantum events: light-driven azo-materials and beyond. MM
133  2011 Optimization of coarse-grained interaction potential: inside inherent limitations of coarse-graining methods. ---
134  2011 Particle-based multiscale coarse graining with density-dependent potentials: application to molecular crystals (hexahydro-1,3,5-trinitro-s-triazine). MS-CG
135  2011 Reconstructing protein remodeled membranes in molecular detail from mesoscopic models. EM
136  2011 Revealing extraordinary intrinsic tensile plasticity in gradient nano-grained copper. NG
137  2011 Semi-bottom-up coarse graining of water based on microscopic simulations. AAMD, DPD
138  2011 Study of the Alzheimer's Abeta40 peptide in SDS micelles using molecular dynamics simulations. SDS
139  2011 The CUMULUS coarse graining method: transferable potentials for water and solutes. MD
140  2011 The multiscale coarse-graining method. VII. Free energy decomposition of coarse-grained effective potentials. MD, MS-CG, PMF
141  2011 Transferability of Coarse Grained Potentials: Implicit Solvent Models for Hydrated Ions. ---
142  2012 A generic force field for protein coarse-grained molecular dynamics simulation. RMSDs, RMSFs
143  2012 A test of systematic coarse-graining of molecular dynamics simulations: thermodynamic properties. IBI, LJ, RDF
144  2012 Adaptive Resolution Simulation (AdResS): A Smooth Thermodynamic and Structural Transition from Atomistic to Coarse Grained Resolution and Vice Versa in a Grand Canonical Fashion. AdResS, AT, GC, MD, RDF
145  2012 Binary interactions and salt-induced coalescence of spherical micelles of cationic surfactants from molecular dynamics simulations. CTAC, DLVO, MD, PMF
146  2012 Chemically transferable coarse-grained potentials from conditional reversible work calculations. CRW
147  2012 Coarse grain lipid-protein molecular interactions and diffusion with MsbA flippase. ---
148  2012 Coarse grained model for exploring voltage dependent ion channels. ---
149  2012 Coarse-Grained and Atomistic Simulations of the Salt-Stable Cowpea Chlorotic Mottle Virus (SS-CCMV) Subunit 26-49: beta-Barrel Stability of the Hexamer and Pentamer Geometries. SS-CCMV
150  2012 Coarse-grained models for the solvents dimethyl sulfoxide, chloroform, and methanol. AL
151  2012 Coarse-grained molecular dynamics simulations of the phase behavior of the 4-cyano-4'-pentylbiphenyl liquid crystal system. ---
152  2012 Coarse-Grained Molecular Models of Water: A Review. ---
153  2012 Coarse-grained molecular simulations of large biomolecules. ---
154  2012 Coarse-grained simulations of protein aggregation. ---
155  2012 Coarse-Grained Structure-Based Model for RNA-Protein Complexes Developed by Fluctuation Matching. ---
156  2012 Coarse-graining provides insights on the essential nature of heterogeneity in actin filaments. ---
157  2012 Combining optimal control theory and molecular dynamics for protein folding. MD, TMD
158  2012 Computer simulation studies of self-assembling macromolecules. AA, MD
159  2012 Derivation of coarse grained models for multiscale simulation of liquid crystalline phase transitions. LC, MD, SmA
160  2012 Dynamical simulation of dipolar Janus colloids: equilibrium structure and thermodynamics. DJ, PW
161  2012 Early stages of the HIV-1 capsid protein lattice formation. CA
162  2012 Further optimization of a hybrid united-atom and coarse-grained force field for folding simulations: Improved backbone hydration and interactions between charged side chains. REMD
163  2012 Hydrophobic mismatch and lipid sorting near OmpA in mixed bilayers: atomistic and coarse-grained simulations. ---
164  2012 Large-scale motions in the adenylate kinase solution ensemble: coarse-grained simulations and comparison with solution X-ray scattering. AK, SAXS
165  2012 Membrane binding and self-association of the epsin N-terminal homology domain. ENTH, MD
166  2012 Mixing Atomistic and Coarse Grain Solvation Models for MD Simulations: Let WT4 Handle the Bulk. ---
167  2012 Mixing coarse-grained and fine-grained water in molecular dynamics simulations of a single system. FG
168  2012 Multi-layer coarse-graining polarization model for treating electrostatic interactions of solvated alpha-conotoxin peptides. ---
169  2012 Multiscale modeling of cellular actin filaments: from atomistic molecular to coarse-grained dynamics. ---
170  2012 Multiscale simulation of small peptides: consistent conformational sampling in atomistic and coarse-grained models. DOF
171  2012 On Atomistic and Coarse-Grained Models for C60 Fullerene. PMF
172  2012 On-the-fly coarse-graining methodology for the simulation of chain formation of superparamagnetic colloids in strong magnetic fields. ---
173  2012 Optimal number of coarse-grained sites in different components of large biomolecular complexes. ---
174  2012 Predicting the morphology of sickle red blood cells using coarse-grained models of intracellular aligned hemoglobin polymers. ---
175  2012 Realistic simulation of the activation of voltage-gated ion channels. ---
176  2012 Realistic simulations of the coupling between the protomotive force and the mechanical rotation of the F0-ATPase. PTR
177  2012 Replica exchange Monte-Carlo simulations of helix bundle membrane proteins: rotational parameters of helices. bR, HBMPs, HR, REMC, RMSD, TMHs
178  2012 Solvating atomic level fine-grained proteins in supra-molecular level coarse-grained water for molecular dynamics simulations. FG
179  2012 Specific binding structures of dendrimers on lipid bilayer membranes. DMPC, PAMAM
180  2012 Structure-based simulations of the translocation mechanism of the hepatitis C virus NS3 helicase along single-stranded nucleic acid. ss
181  2012 Structures of Abeta17-42 trimers in isolation and with five small-molecule drugs using a hierarchical computational procedure. AD
182  2012 The multiscale coarse-graining method. IX. A general method for construction of three body coarse-grained force fields. MS-CG
183  2012 The multiscale coarse-graining method. VIII. Multiresolution hierarchical basis functions and basis function selection in the construction of coarse-grained force fields. MS-CG
184  2012 The multiscale coarse-graining method. X. Improved algorithms for constructing coarse-grained potentials for molecular systems. MS-CG
185  2012 The role of many-body correlations in determining potentials for coarse-grained models of equilibrium structure. rdf's
186  2012 Thermodynamic transferability of coarse-grained potentials for polymer-additive systems. CRW
187  2012 Tunable, mixed-resolution modeling using library-based Monte Carlo and graphics processing units. AA, GBSA, GPU, LBMC
188  2012 Water-Driven Cavity-Ligand Binding: Comparison of Thermodynamic Signatures from Coarse-Grained and Atomic-Level Simulations. AL
189  2012 [Non-commutative geometrical drug discovery--the principle of geometrical regulation]. AA, QC
190  2013 A Hybrid Approach for Highly Coarse-grained Lipid Bilayer Models. DLPC, DOPC, DOPS, HCG, MD, MS-CG, RDF
191  2013 A test of systematic coarse-graining of molecular dynamics simulations: Transport properties. DPD
192  2013 A transferable coarse-grained model for diphenylalanine: how to represent an environment driven conformational transition. ---
193  2013 Acceleration of coarse grain molecular dynamics on GPU architectures. GPUs
194  2013 Aggregation of lipid-anchored full-length H-Ras in lipid bilayers: simulations with the MARTINI force field. ---
195  2013 Coarse grained molecular dynamics simulation of nanoconfined water. ---
196  2013 Coarse-grain modelling of protein-protein interactions. PPI
197  2013 Coarse-grained and all-atom modeling of structural states and transitions in hemoglobin. Hb, WAXS
198  2013 Coarse-grained model for colloidal protein interactions, B(22), and protein cluster formation. gD-Crys
199  2013 Coarse-Grained Potentials for Local Interactions in Unfolded Proteins. ---
200  2013 Combining coarse-grained nonbonded and atomistic bonded interactions for protein modeling. AT
201  2013 Corrosion and in vitro biocompatibility properties of cryomilled-spark plasma sintered commercially pure titanium. CP, EIS, SPS
202  2013 Cross-talk between the ligand- and DNA-binding domains of estrogen receptor. DBD, ERalpha, LBD
203  2013 Dynamical simulation of dipolar Janus colloids: dynamical properties. PW
204  2013 Effect of arginine-rich peptide length on the structure and binding strength of siRNA-peptide complexes. AA, Arg, MD
205  2013 Electrostatic-Consistent Coarse-Grained Potentials for Molecular Simulations of Proteins. ---
206  2013 Flexible docking and refinement with a coarse-grained protein model using ATTRACT. ---
207  2013 Gaussian curvature elasticity determined from global shape transformations and local stress distributions: a comparative study using the MARTINI model. DMPC
208  2013 Improved coarse-grained model for molecular-dynamics simulations of water nucleation. AA
209  2013 Influence of type of bur and acid etching on dentin hydraulic conductance. AE, FG, MG
210  2013 Insertion of the Ca⁺-independent phospholipase A₂ into a phospholipid bilayer via coarse-grained and atomistic molecular dynamics simulations. AA, DXMS, MD
211  2013 Interparticle dispersion, membrane curvature, and penetration induced by single-walled carbon nanotubes wrapped with lipids and PEGylated lipids. PEG, SWNTs
212  2013 Interplay between grain structure and protein adsorption on functional response of osteoblasts: ultrafine-grained versus coarse-grained substrates. NG/UFG
213  2013 Membrane penetration and curvature induced by single-walled carbon nanotubes: the effect of diameter, length, and concentration. MD, SWNTs
214  2013 Membrane sculpting by F-BAR domains studied by molecular dynamics simulations. BAR
215  2013 Membrane-mediated protein-protein interactions and connection to elastic models: a coarse-grained simulation analysis of gramicidin A association. gA, PMF
216  2013 Microcanonical thermostatistics of coarse-grained proteins with amyloidogenic propensity. hPrP
217  2013 Microscopic derivation of particle-based coarse-grained dynamics. GLE
218  2013 Mixing MARTINI: electrostatic coupling in hybrid atomistic-coarse-grained biomolecular simulations. AA-CG, PMFs
219  2013 Modeling Protein-Protein Recognition in Solution Using the Coarse-Grained Force Field SCORPION. ENM, MD, PCGS
220  2013 Modeling self-assembly of silica/surfactant mesostructures in the templated synthesis of nanoporous solids. ---
221  2013 Molecular basis for the dissociation dynamics of protein A-immunoglobulin G1 complex. hIgG1, IgG1, MD, SPA
222  2013 Multiscale enhanced path sampling based on the Onsager-Machlup action: application to a model polymer. OM
223  2013 Multiscale molecular dynamics simulations of membrane proteins. ---
224  2013 Nucleotide-dependent lateral and longitudinal interactions in microtubules. MT, nt
225  2013 Optimization of an elastic network augmented coarse grained model to study CCMV capsid deformation. ---
226  2013 Perspective: Coarse-grained models for biomolecular systems. ---
227  2013 Phase separation in a lipid/cholesterol system: comparison of coarse-grained and united-atom simulations. Chol, UA
228  2013 Prediction of fundamental properties of ionic liquid electrospray thrusters using molecular dynamics. IL, MD
229  2013 Representability and Transferability of Kirkwood-Buff Iterative Boltzmann Inversion Models for Multicomponent Aqueous Systems. KB-IBI
230  2013 SAFT-gamma force field for the simulation of molecular fluids: 2. Coarse-grained models of greenhouse gases, refrigerants, and long alkanes. AA, EOS, UA
231  2013 Simple Method for Simulating the Mixture of Atomistic and Coarse-Grained Molecular Systems. FG
232  2013 Structure-based coarse-graining for inhomogeneous liquid polymer systems. IBI, PFPE, RDF
233  2013 Systematic methods for structurally consistent coarse-grained models. ---
234  2013 The Theory of Ultra-Coarse-Graining. 1. General Principles. MS-CG, UCG
235  2013 Three-dimensional stress field around a membrane protein: atomistic and coarse-grained simulation analysis of gramicidin A. gA
236  2013 Toward optimized potential functions for protein-protein interactions in aqueous solutions: osmotic second virial coefficient calculations using the MARTINI coarse-grained force field. ---
237  2013 Understanding the impact of grain structure in austenitic stainless steel from a nanograined regime to a coarse-grained regime on osteoblast functions using a novel metal deformation-annealing sequence. NGs
238  2013 Unfolding thermodynamics of cysteine-rich proteins and molecular thermal-adaptation of marine ciliates. CD, MC
239  2013 Unraveling the role of the protein environment for [FeFe]-hydrogenase: a new application of coarse-graining. ESP
240  2013 Validating a Coarse-Grained Potential Energy Function through Protein Loop Modelling. ---
241  2013 Why do arginine and lysine organize lipids differently? Insights from coarse-grained and atomistic simulations. Arg, Lys, PE, PS
242  2014 A computer simulation of the networked structure of a hydrogel prepared from a tetra-armed star pre-polymer. ---
243  2014 A Newfound Cancer-Activating Mutation Reshapes the Energy Landscape of Estrogen-Binding Domain. LBD
244  2014 A Solvent-Mediated Coarse-Grained Model of DNA Derived with the Systematic Newton Inversion Method. FFs, IBI, IMC, NI
245  2014 Accurate coarse-grained models for mixtures of colloids and linear polymers under good-solvent conditions. FM
246  2014 An effective coarse-grained model for biological simulations: recent refinements and validations. ---
247  2014 Aqueous poly(amidoamine) dendrimer G3 and G4 generations with several interior cores at pHs 5 and 7: a molecular dynamics simulation study. BAPE, DAH, EDA, PAMAM
248  2014 Calibrated Langevin-dynamics simulations of intrinsically disordered proteins. IDPs
249  2014 CHARMM-GUI PACE CG Builder for solution, micelle, and bilayer coarse-grained simulations. UA
250  2014 Cholesterol solubility limit in lipid membranes probed by small angle neutron scattering and MD simulations. MD, SANS
251  2014 Coarse-grain model for natural cellulose fibrils in explicit water. MD
252  2014 Coarse-grained modeling of peptidic/PDMS triblock morphology. ---
253  2014 Coarse-grained molecular dynamics simulations of protein-ligand binding. CGMD
254  2014 Coarse-grained simulations of the gating current in the voltage-activated Kv1.2 channel. ---
255  2014 Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins. ---
256  2014 Coarse-graining poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) (PEO-PPO-PEO) block copolymers using the MARTINI force field. PEO, PPO
257  2014 COFFDROP: A Coarse-Grained Nonbonded Force Field for Proteins Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of Amino Acids. BD, IBI, MD
258  2014 Construction of dissipative particle dynamics models for complex fluids via the Mori-Zwanzig formulation. DPD, MD, MZ
259  2014 De novo inference of protein function from coarse-grained dynamics. FF
260  2014 Density functional theory for the description of spherical non-associating monomers in confined media using the SAFT-VR equation of state and weighted density approximations. FMT, GCMC, NLDFT, SAFT-VR, WDA
261  2014 Dependence of cellular activity at protein adsorbed biointerfaces with nano- to microscale dimensionality. NG
262  2014 Dimerization of the EphA1 receptor tyrosine kinase transmembrane domain: Insights into the mechanism of receptor activation. MD, PMF, RTK, TM
263  2014 Dynamical simulation of electrostatic striped colloidal particles. PW
264  2014 Dynamics and stability of lipid bilayers modulated by thermosensitive polypeptides, cholesterols, and PEGylated lipids. DPPCs
265  2014 Electrochemical and cellular behavior of ultrafine-grained titanium in vitro. cpTi, SBF, UFG
266  2014 Electrochemical and surface analyses of nanostructured Ti-24Nb-4Zr-8Sn alloys in simulated body solution. NS
267  2014 Electrode materials, thermal annealing sequences, and lateral/vertical phase separation of polymer solar cells from multiscale molecular simulations. BHJ
268  2014 Exploring the dynamics and interaction of a full ErbB2 receptor and Trastuzumab-Fab antibody in a lipid bilayer model using Martini coarse-grained force field. ---
269  2014 Highly Scalable and Memory Efficient Ultra-Coarse-Grained Molecular Dynamics Simulations. MD, SFC
270  2014 Homo-oligomerization of transmembrane alpha-domain of integrin. POPC
271  2014 In situ study of defect migration kinetics in nanoporous Ag with enhanced radiation tolerance. NP
272  2014 Investigation of coarse-grained mappings via an iterative generalized Yvon-Born-Green method. AA, g-YBG, MS-CG, RDFs
273  2014 Mechanism of the exchange reaction in HRAS from multiscale modeling. CMD, GEFs, PCA, SMD
274  2014 Molecular Dynamics Studies of Liposomes as Carriers for Photosensitizing Drugs: Development, Validation, and Simulations with a Coarse-Grained Model. ---
275  2014 Molecular dynamics studies of PEGylated alpha-helical coiled coils and their self-assembled micelles. PEG
276  2014 More than the sum of its parts: coarse-grained peptide-lipid interactions from a simple cross-parametrization. ---
277  2014 Multi-scale ensemble modeling of modular proteins with intrinsically disordered linker regions: application to p53. AA, IDRs, MD, SAXS
278  2014 Multi-scale mechanical and transport properties of a hydrogel. PEGDGE
279  2014 Multi-scale modeling of mycosubtilin lipopeptides at the air/water interface: structure and optical second harmonic generation. SHG
280  2014 Multiscale modeling of biological functions: from enzymes to molecular machines (Nobel Lecture). Nobel Lecture, QM/MM
281  2014 Multiscale molecular dynamics simulations of sodium dodecyl sulfate micelles: from coarse-grained to all-atom resolution. AA, MD, QM, SDS, UA
282  2014 Nanoindentation hardness and elastic modulus of nano-grained titanium produced by asymmetric and symmetric rolling. NG, UFG
283  2014 Parameterizing the Morse Potential for Coarse-Grained Modeling of Blood Plasma. ---
284  2014 PITOMBA: Parameter Interface for Oligosaccharide Molecules Based on Atoms. ---
285  2014 Potential of mean force analysis of the self-association of leucine-rich transmembrane alpha-helices: difference between atomistic and coarse-grained simulations. AT, DLPC, PMFs, TM
286  2014 Protocols for efficient simulations of long-time protein dynamics using coarse-grained CABS model. ---
287  2014 Quantitative Predictions of the Interfacial Tensions of Liquid-Liquid Interfaces through Atomistic and Coarse Grained Models. EC
288  2014 Rapid Sampling of Folding Equilibria of beta-Peptides in Methanol Using a Supramolecular Solvent Model. FG
289  2014 Recent advances in transferable coarse-grained modeling of proteins. ---
290  2014 RESPAC: Method to Determine Partial Charges in Coarse-Grained Protein Model and Its Application to DNA-Binding Proteins. AA, RESP
291  2014 SecStAnT: secondary structure analysis tool for data selection, statistics and models building. ---
292  2014 Structural order in ultrathin films of the monolayer protected clusters based upon 4 nm gold nanocrystals: an experimental and theoretical study. GB, MD, MPCs, STEM
293  2014 The power of coarse graining in biomolecular simulations. ---
294  2014 The Theory of Ultra-Coarse-Graining. 2. Numerical Implementation. UCG
295  2014 Transferability of coarse-grained force field for nCB liquid crystal systems. LC
296  2014 Unusual, photo-induced self-assembly of azobenzene-containing amphiphiles. azo-containing, MD, UV
297  2014 Vibrational characteristics of graphene sheets elucidated using an elastic network model. BLGSs, ENM, NMA
298  2014 Web-based computational chemistry education with CHARMMing II: Coarse-grained protein folding. CHARMM, CHARMMing
299  2015 A Coarse Grained Model for a Lipid Membrane with Physiological Composition and Leaflet Asymmetry. MD
300  2015 A coarse-grain force-field for xylan and its interaction with cellulose. ---
301  2015 A coarse-grained simulation study of the structures, energetics, and dynamics of linear and circular DNA with its ions. MD
302  2015 A temperature-dependent coarse-grained model for the thermoresponsive polymer poly(N-isopropylacrylamide). PNIPAM, SDK
303  2015 Amphiphilic Peptides A6K and V6K Display Distinct Oligomeric Structures and Self-Assembly Dynamics: A Combined All-Atom and Coarse-Grained Simulation Study. REMD
304  2015 Atomistic and Coarse Grain Topologies for the Cofactors Associated with the Photosystem II Core Complex. ---
305  2015 Automated parametrization of the coarse-grained Martini force field for small organic molecules. ---
306  2015 Benchmark of Schemes for Multiscale Molecular Dynamics Simulations. FG
307  2015 Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids. AA, PMF
308  2015 Bottom-Up Coarse-Graining of Peptide Ensembles and Helix-Coil Transitions. g-YBG, MS-CG
309  2015 Coarse-grained model of glycosaminoglycans. AA, GAGs, MD
310  2015 Coarse-grained molecular dynamics simulation of water diffusion in the presence of carbon nanotubes. CNTs, DTI
311  2015 Coarse-Graining the Liquid-Liquid Interfaces with the MARTINI Force Field: How Is the Interfacial Tension Reproduced? ---
312  2015 Conformational Properties of Sodium Polystyrenesulfonate in Water: Insights from a Coarse-Grained Model with Explicit Solvent. BMW, POL
313  2015 Derivation of coarse-grained simulation models of chlorophyll molecules in lipid bilayers for applications in light harvesting systems. AA, DPPC, LHCII
314  2015 Domain Motion Enhanced (DoME) Model for Efficient Conformational Sampling of Multidomain Proteins. ADK, DoME, MD
315  2015 Dry Martini, a coarse-grained force field for lipid membrane simulations with implicit solvent. ---
316  2015 Dynamic force matching: A method for constructing dynamical coarse-grained models with realistic time dependence. MS-CG
317  2015 Enhanced Sampling of an Atomic Model with Hybrid Nonequilibrium Molecular Dynamics-Monte Carlo Simulations Guided by a Coarse-Grained Model. FG, MC, MD, neMD, NEMD
318  2015 Equilibrium fluctuation relations for voltage coupling in membrane proteins. ---
319  2015 Exploring LacI-DNA dynamics by multiscale simulations using the SIRAH force field. AA, LacI
320  2015 Flexible Boundaries for Multiresolution Solvation: An Algorithm for Spatial Multiscaling in Molecular Dynamics Simulations. FBMS, FG, MD
321  2015 Highly viscous antibody solutions are a consequence of network formation caused by domain-domain electrostatic complementarities: insights from coarse-grained simulations. mAb
322  2015 Incorporation of memory effects in coarse-grained modeling via the Mori-Zwanzig formalism. MD, NM-DPD
323  2015 Lipid insertion domain unfolding regulates protein orientational transition behavior in a lipid bilayer. LID, PC/CHO, UA
324  2015 Martini Coarse-Grained Force Field: Extension to DNA. dsDNA, ssDNA
325  2015 Microstructural Evolution at Micro/Meso-Scale in an Ultrafine-Grained Pure Aluminum Processed by Equal-Channel Angular Pressing with Subsequent Annealing Treatment. EBSD, ECAP, LAGBs, MEMS, TEM, UFG
326  2015 Modeling Structural Dynamics of Biomolecular Complexes by Coarse-Grained Molecular Simulations. ---
327  2015 Molecular dynamics methods to predict peptide locations in membranes: LAH4 as a stringent test case. AA, PMF
328  2015 Molecular dynamics simulations of cholesterol-rich membranes using a coarse-grained force field for cyclic alkanes. ---
329  2015 Molecular simulations of metal-coupled protein folding. QM
330  2015 Multiple stiffening effects of nanoscale knobs on human red blood cells infected with Plasmodium falciparum malaria parasite. Pf, RBC
331  2015 Multiscale modelling of nucleosome core particle aggregation. NCP
332  2015 Multiscale simulations of human telomeric G-quadruplex DNA. IBI, IMC, MD
333  2015 On the application of the MARTINI coarse-grained model to immersion of a protein in a phospholipid bilayer. AA, MD, POPC
334  2015 On the importance of shear dissipative forces in coarse-grained dynamics of molecular liquids. DPD, MS-CG, PMF
335  2015 Parametrization of Backbone Flexibility in a Coarse-Grained Force Field for Proteins (COFFDROP) Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of All Possible Two-Residue Peptides. BD, COFFDROP, IBI, MD
336  2015 Polarizable coarse-grained models for molecular dynamics simulation of liquid cyclohexane. FG
337  2015 Polymorphic Associations and Structures of the Cross-Seeding of Abeta1-42 and hIAPP1-37 Polypeptides. AD, hIAPP, MD, REMD
338  2015 Potentials of mean force and escape times of surfactants from micelles and hydrophobic surfaces using molecular dynamics simulations. MD, PMFs, SDS
339  2015 Predicting the Sensitivity of Multiscale Coarse-Grained Models to their Underlying Fine-Grained Model Parameters. FG, SCB, SCI
340  2015 Preferred supramolecular organization and dimer interfaces of opioid receptors from simulated self-association. MD, OR
341  2015 Protein Simulations in Fluids: Coupling the OPEP Coarse-Grained Force Field with Hydrodynamics. LB
342  2015 PSII-LHCII supercomplex organizations in photosynthetic membrane by coarse-grained simulation. EM, LHCII, PSII
343  2015 RedMDStream: Parameterization and Simulation Toolbox for Coarse-Grained Molecular Dynamics Models. MD
344  2015 Reversible and Irreversible Adsorption Energetics of Poly(ethylene glycol) and Sorbitan Poly(ethoxylate) at a Water/Alkane Interface. NMB, PEG, PMFs, WHAM
345  2015 Scaling Analysis of Ocean Surface Turbulent Heterogeneities from Satellite Remote Sensing: Use of 2D Structure Functions. Chl-a, SF, SST
346  2015 Self-assembly of triton X-100 in water solutions: a multiscale simulation study linking mesoscale to atomistic models. Nagg, TX-100
347  2015 Sequential data assimilation for single-molecule FRET photon-counting data. MD
348  2015 SIRAH: a structurally unbiased coarse-grained force field for proteins with aqueous solvation and long-range electrostatics. ---
349  2015 Solid-liquid work of adhesion of coarse-grained models of n-hexane on graphene layers derived from the conditional reversible work method. CRW
350  2015 Solubilization Behavior of Polyene Antibiotics in Nanomicellar System: Insights from Molecular Dynamics Simulation of the Amphotericin B and Nystatin Interactions with Polysorbate 80. AmB, MD, NYS, PAs, POE
351  2015 Spontaneous adsorption of coiled-coil model peptides K and E to a mixed lipid bilayer. ---
352  2015 Structure and Dynamics of Phospholipid Nanodiscs from All-Atom and Coarse-Grained Simulations. DMPC, MD
353  2015 Superior radiation-resistant nanoengineered austenitic 304L stainless steel for applications in extreme radiation environments. dpa, SS, UFG
354  2015 Supra-Atomic Coarse-Grained GROMOS Force Field for Aliphatic Hydrocarbons in the Liquid Phase. FG
355  2015 Supramolecular polymerization: a coarse grained molecular dynamics study. BTA, FE
356  2015 Systematic and simulation-free coarse graining of homopolymer melts: a relative-entropy-based study. RE-based
357  2015 Systematic and simulation-free coarse graining of homopolymer melts: a structure-based study. ---
358  2015 Systematic hierarchical coarse-graining with the inverse Monte Carlo method. IMC, MD
359  2015 Systematic methods for defining coarse-grained maps in large biomolecules. ED, ENM, MD, PCA
360  2015 The glass transition in cured epoxy thermosets: A comparative molecular dynamics study in coarse-grained and atomistic resolution. AA
361  2015 The impact of resolution upon entropy and information in coarse-grained models. GNM, PMF
362  2015 The multiscale coarse-graining method. XI. Accurate interactions based on the centers of charge of coarse-grained sites. ---
363  2015 Transferability of the coarse-grained potentials for trans-1,4-polybutadiene. FF
364  2015 Tuning Glass Transition in Polymer Nanocomposites with Functionalized Cellulose Nanocrystals through Nanoconfinement. CNCs, MD, PMMA, Tg
365  2015 Xenon NMR of liquid crystals confined to cylindrical nanocavities: a simulation study. LCs, MC, QC
366  2016 A Coarse-Grained Model of Stratum Corneum Lipids: Free Fatty Acids and Ceramide NS. Cer
367  2016 A comparative study of coarse-graining methods for polymeric fluids: Mori-Zwanzig vs. iterative Boltzmann inversion vs. stochastic parametric optimization. IBI, MD, MZ, SPO
368  2016 A Comparison of Multiscale Permutation Entropy Measures in On-Line Depth of Anesthesia Monitoring. DOA, MA, MSPE, ROC, RPE, SPE, TCNMM, TPE
369  2016 A kinetic chain growth algorithm in coarse-grained simulations. ---
370  2016 A Microscopic Capacitor Model of Voltage Coupling in Membrane Proteins: Gating Charge Fluctuations in Ci-VSD. Ci-VSP, VSDs
371  2016 A new algorithm for construction of coarse-grained sites of large biomolecules. SOBC
372  2016 Accurate optimization of amino acid form factors for computing small-angle X-ray scattering intensity of atomistic protein structures. EDM, SAXS
373  2016 Adaptive Resolution Simulation of Supramolecular Water: The Concurrent Making, Breaking, and Remaking of Water Bundles. AdResS, AT
374  2016 Bayesian calibration of coarse-grained forces: Efficiently addressing transferability. ---
375  2016 Bottom-up coarse-grained models with predictive accuracy and transferability for both structural and thermodynamic properties of heptane-toluene mixtures. AA
376  2016 Calculation of Enzyme Fluctuograms from All-Atom Molecular Dynamics Simulation. ---
377  2016 CG2AA: backmapping protein coarse-grained structures. ---
378  2016 Coarse-grained bond and angle distributions from atomistic simulations: On the systematic parameterisation of lipid models. AT
379  2016 Coarse-Grained Model for Water Involving a Virtual Site. MD, vdW
380  2016 Coarse-grained modeling of crystal growth and polymorphism of a model pharmaceutical molecule. ---
381  2016 Coarse-Grained Modeling of Nucleic Acids Using Anisotropic Gay-Berne and Electric Multipole Potentials. EMP
382  2016 Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation. ---
383  2016 Coarse-Grained Molecular Dynamics Simulations of Membrane-Trehalose Interactions. DLPC, DMPC, MD, PMFs, TRH
384  2016 Conformational states of HAMP domains interacting with sensory rhodopsin membrane systems: an integrated all-atom and coarse-grained molecular dynamics simulation approach. MD, Np
385  2016 Constructing Optimal Coarse-Grained Sites of Huge Biomolecules by Fluctuation Maximization. FM-CG, SLIO
386  2016 Development of a Coarse-Grained Model of Chitosan for Predicting Solution Behavior. DA, GlcNAc
387  2016 Development of DPD coarse-grained models: From bulk to interfacial properties. DPD
388  2016 Directly Modifying the Nonbonded Potential Based on the Standard Iterative Boltzmann Inversion Method for Coarse-Grained Force Fields. IBI
389  2016 Dissipative Particle Dynamics Simulations for Phospholipid Membranes Based on a Four-To-One Coarse-Grained Mapping Scheme. DPD
390  2016 Dynamic force matching: Construction of dynamic coarse-grained models with realistic short time dynamics and accurate long time dynamics. ---
391  2016 Dynamics of DNA Squeezed Inside a Nanochannel via a Sliding Gasket. BD, NPDE
392  2016 Effect of backbone chemistry on hybridization thermodynamics of oligonucleic acids: a coarse-grained molecular dynamics simulation study. LNAs, PNAs
393  2016 Effect of lipid head group interactions on membrane properties and membrane-induced cationic beta-hairpin folding. mIFs
394  2016 Effects of Polymer Conjugation on Hybridization Thermodynamics of Oligonucleic Acids. AA-MetaD, CG-NVT, ONAs, PEG, WC H-bonding
395  2016 Energy-conserving coarse-graining of complex molecules. DPDE
396  2016 Estimation of Liposome Penetration Barriers of Drug Molecules with All-Atom and Coarse-Grained Models. 5-ALA, AA
397  2016 Forced Unfolding Mechanism of Bacteriorhodopsin as Revealed by Coarse-Grained Molecular Dynamics. FD
398  2016 Improved prediction of bilayer and monolayer properties using a refined BMW-MARTINI force field. FF, Mma
399  2016 Irradiation Induced Microstructure Evolution in Nanostructured Materials: A Review. GBs, NS, VDZs
400  2016 Mechanism of Nucleation and Growth of Abeta40 Fibrils from All-Atom and Coarse-Grained Simulations. Abeta40
401  2016 Melt-phase behavior of collapsed PMMA/PVC chains revealed by multiscale simulations. ---
402  2016 Membrane Mediated Antimicrobial and Antitumor Activity of Cathelicidin 6: Structural Insights from Molecular Dynamics Simulation on Multi-Microsecond Scale. LLM, MD, TLM
403  2016 Molecular view of the interaction of S-methyl methanethiosulfonate with DPPC bilayer. DMSO, DPPC, MD, MMTS, PMF
404  2016 Multiscale approach for the construction of equilibrated all-atom models of a poly(ethylene glycol)-based hydrogel. PCFF, PEG
405  2016 Multiscale coarse-grained modelling of chromatin components: DNA and the nucleosome. NCP
406  2016 Multiscale Coarse-Graining of Polarizable Models through Force-Matched Dipole Fluctuations. MS-CG
407  2016 Multiscale design of coarse-grained elastic network-based potentials for the mu opioid receptor. AA, ENM, FF, GPCR, MD, muOR, NMA
408  2016 Multiscale enhanced sampling of intrinsically disordered protein conformations. IDPs, MSES, SA
409  2016 Multiscale Molecular Simulation of Solution Processing of SMDPPEH: PCBM Small-Molecule Organic Solar Cells. ---
410  2016 Multiscale simulations of protein-facilitated membrane remodeling. ---
411  2016 Necessity of high-resolution for coarse-grained modeling of flexible proteins. ---
412  2016 On interfacial properties of tetrahydrofuran: Atomistic and coarse-grained models from molecular dynamics simulation. THF
413  2016 On the representability problem and the physical meaning of coarse-grained models. ---
414  2016 Optimization of Analytical Potentials for Coarse-Grained Biopolymer Models. ---
415  2016 Predicting unfolding thermodynamics and stable intermediates for alanine-rich helical peptides with the aid of coarse-grained molecular simulation. CD
416  2016 Promiscuous Histone Mis-Assembly Is Actively Prevented by Chaperones. CENP-A, HJURP, MD
417  2016 Protein-Backbone Thermodynamics across the Membrane Interface. PMF
418  2016 Self-Assembly and Critical Aggregation Concentration Measurements of ABA Triblock Copolymers with Varying B Block Types: Model Development, Prediction, and Validation. CAC, DPD
419  2016 Simulation of High Density Lipoprotein Behavior on a Few Layer Graphene Undergoing Non-Uniform Mechanical Load. AA, CNT, DPPC, HDL, SWNT
420  2016 SIRAH tools: mapping, backmapping and visualization of coarse-grained models. ---
421  2016 Systematic Generation of Anisotropic Coarse-Grained Lennard-Jones Potentials and Their Application to Ordered Soft Matter. AA, LoD, vdW
422  2016 The relative entropy is fundamental to adaptive resolution simulations. ---
423  2016 TMFF-A Two-Bead Multipole Force Field for Coarse-Grained Molecular Dynamics Simulation of Protein. RMSDs, RMSFs, TMFF
424  2016 Transferability of a coarse-grained atactic polystyrene model: the non-bonded potential effect. FF, LJ, PS, RDF
425  2016 Van der Waals Perspective on Coarse-Graining: Progress toward Solving Representability and Transferability Problems. AA, PMF
426  2017 A coarse-grained model for assisting the investigation of structure and dynamics of large nucleic acids by ion mobility spectrometry-mass spectrometry. CCS, IMS-MS, MD
427  2017 A dsDNA model optimized for electrokinetic applications. ---
428  2017 A framework for multi-scale simulation of crystal growth in the presence of polymers. Ac, API, Hp, SU
429  2017 A multi-state coarse grained modeling approach for an intrinsically disordered peptide. ---
430  2017 Aggregation and insertion of melittin and its analogue MelP5 into lipid bilayers at different concentrations: effects on pore size, bilayer thickness and dynamics. ---
431  2017 Biomembrane solubilization mechanism by Triton X-100: a computational study of the three stage model. MD, TX-100
432  2017 Bulk Heterojunction Morphologies with Atomistic Resolution from Coarse-Grain Solvent Evaporation Simulations. BHJ, P3HT
433  2017 Coarse-Grained Directed Simulation. QM/MM
434  2017 Coarse-Grained Modeling of Polyethylene Melts: Effect on Dynamics. IBI, MSDs, PE
435  2017 Coarse-Grained Simulation of Rodlike Higher-Order Quadruplex Structures at Different Salt Concentrations. ---
436  2017 Combined effect of grain refinement and surface modification of pure titanium on the attachment of mesenchymal stem cells and osteoblast-like SaOS-2 cells. ADMSC, SLA, SPD, UFG
437  2017 Combining the MARTINI and Structure-Based Coarse-Grained Approaches for the Molecular Dynamics Studies of Conformational Transitions in Proteins. ---
438  2017 Computational Modeling of Hydroxypropyl-Methylcellulose Acetate Succinate (HPMCAS) and Phenytoin Interactions: A Systematic Coarse-Graining Approach. HPMCAS
439  2017 Computing the non-Markovian coarse-grained interactions derived from the Mori-Zwanzig formalism in molecular systems: Application to polymer melts. DPD, GLE, MD, NM
440  2017 Construction of non-Markovian coarse-grained models employing the Mori-Zwanzig formalism and iterative Boltzmann inversion. IBI, MZ, NMDPD
441  2017 Data-driven coarse graining of large biomolecular structures. ---
442  2017 Differential Interaction of Antimicrobial Peptides with Lipid Structures Studied by Coarse-Grained Molecular Dynamics Simulations. POPC
443  2017 Dimerization and Structural Stability of Amyloid Precursor Proteins Affected by the Membrane Microenvironments. APP
444  2017 Effect of Concentration on the Supramolecular Polymerization Mechanism via Implicit-Solvent Coarse-Grained Simulations of Water-Soluble 1,3,5-Benzenetricarboxamide. BTA
445  2017 Effect of conjugation on phase transitions in thermoresponsive polymers: an atomistic and coarse-grained simulation study. ELPs, LCST, MD
446  2017 Effect of grain structure on Charpy impact behavior of copper. ECAP, NS, UFG
447  2017 Effects of Coarse Graining and Saturation of Hydrocarbon Chains on Structure and Dynamics of Simulated Lipid Molecules. AA, UA
448  2017 Efficient estimation of binding free energies between peptides and an MHC class II molecule using coarse-grained molecular dynamics simulations with a weighted histogram analysis method. MD, WHAM
449  2017 Energy-Renormalization for Achieving Temperature Transferable Coarse-Graining of Polymer Dynamics. AG
450  2017 Evaluation of mapping schemes for systematic coarse graining of higher alkanes. CRW
451  2017 Extended Ensemble Approach to Transferable Potentials for Low-Resolution Coarse-Grained Models of Ionomers. PEO, UA
452  2017 Extending the range and physical accuracy of coarse-grained models: Order parameter dependent interactions. FG, MS-CG
453  2017 Extension of CAVS coarse-grained model to phospholipid membranes: The importance of electrostatics. ---
454  2017 Free Energy-Based Coarse-Grained Force Field for Binary Mixtures of Hydrocarbons, Nitrogen, Oxygen, and Carbon Dioxide. FE-12-6, HOV, LB, VLE
455  2017 Ganglioside-Lipid and Ganglioside-Protein Interactions Revealed by Coarse-Grained and Atomistic Molecular Dynamics Simulations. ---
456  2017 Gentamicin-Eluting Titanium Dioxide Nanotubes Grown on the Ultrafine-Grained Titanium. ECAP, SEM, Ti, UFG
457  2017 High-Resolution Coarse-Grained Model of Hydrated Anion-Exchange Membranes that Accounts for Hydrophobic and Ionic Interactions through Short-Ranged Potentials. AEM, GAFF, RDFs, TMACl
458  2017 High-Resolution Insights into the Stepwise Self-Assembly of Nanofiber from Bioactive Peptides. AFM, ANS, CD, PUs
459  2017 HyRes: a coarse-grained model for multi-scale enhanced sampling of disordered protein conformations. HyRes, IDPs, MSES
460  2017 Immature HIV-1 lattice assembly dynamics are regulated by scaffolding from nucleic acid and the plasma membrane. CA, SP1
461  2017 Improved accuracy of hybrid atomistic/coarse-grained simulations using reparametrised interactions. AT
462  2017 Interplay between Conformational Heterogeneity and Hydration in the Folding Landscape of a Designed Three-Helix Bundle. ---
463  2017 Interplay of G Protein-Coupled Receptors with the Membrane: Insights from Supra-Atomic Coarse Grain Molecular Dynamics Simulations. GPCRs, MD
464  2017 Local and global dynamics of multi-resolved polymer chains: Effects of the interactions atoms-beads on the dynamic of the chains. ---
465  2017 Many-Body Coarse-Grained Interactions Using Gaussian Approximation Potentials. MD
466  2017 MD Simulations of Viruslike Particles with Supra CG Solvation Affordable to Desktop Computers. VLP
467  2017 Modification of the Surface Topography and Composition of Ultrafine and Coarse Grained Titanium by Chemical Etching. AFM, SEM, UFG, XPS, XRF
468  2017 Mori-Zwanzig theory for dissipative forces in coarse-grained dynamics in the Markov limit. DPD
469  2017 Multiscale Computational Modeling of the Nanostructure of Solid Dispersions of Hydroxypropyl Methylcellulose Acetate Succinate (HPMCAS) and Phenytoin. HPMCAS
470  2017 Multiscale mechanics of the lateral pressure effect on enhancing the load transfer between polymer coated CNTs. CNTs, MD
471  2017 Multiscale time-dependent density functional theory: Demonstration for plasmons. TDDFT
472  2017 Neural Network Based Prediction of Conformational Free Energies - A New Route toward Coarse-Grained Simulation Models. FES, MD, NN
473  2017 New Coarse-Grained Model and Its Implementation in Simulations of Graphene Assemblies. ---
474  2017 Onset of static and dynamic universality among molecular models of polymers. AMD, KG
475  2017 Overcoming the Limitations of the MARTINI Force Field in Simulations of Polysaccharides. LJ, MD
476  2017 Performance Comparison of Systematic Methods for Rigorous Definition of Coarse-Grained Sites of Large Biomolecules. ED-CG, FM-CG, SASD, SLIO
477  2017 Pipeline for inferring protein function from dynamics using coarse-grained molecular mechanics forcefield. CGMM, MD
478  2017 Plastic deformation mechanisms in a severely deformed Fe-Ni-Al-C alloy with superior tensile properties. CR
479  2017 Procedure for Transferable Coarse-Grained Models of Aqueous Polysaccharides. BI, FFs, MD, MS-CG
480  2017 Protein simulation using coarse-grained two-bead multipole force field with polarizable water models. MD, RMSDs, RMSFs, TMFF
481  2017 PyCGTOOL: Automated Generation of Coarse-Grained Molecular Dynamics Models from Atomistic Trajectories. ---
482  2017 Reduced Point Charge Models of Proteins: Effect of Protein-Water Interactions in Molecular Dynamics Simulations of Ubiquitin Systems. AA, FF, RPCM
483  2017 Role of Dynamic Heterogeneities in Ionic Liquids: Insights from All-Atom and Coarse-Grained Molecular Dynamics Simulation Studies. AA
484  2017 Self-assembling study of sarcolipin and its mutants in multiple molecular dynamic simulations. AT, Ile, MD, PMF, SLN, wSLN
485  2017 Sequence transferable coarse-grained model of amphiphilic copolymers. ---
486  2017 Significantly enhanced osteoblast response to nano-grained pure tantalum. NC, SFT, Ta
487  2017 Single molecule translocation in smectics illustrates the challenge for time-mapping in simulations on multiple scales. ---
488  2017 Solvation free energies and partition coefficients with the coarse-grained and hybrid all-atom/coarse-grained MARTINI models. AA/CG
489  2017 Temperature-Dependent Implicit-Solvent Model of Polyethylene Glycol in Aqueous Solution. ---
490  2017 The "sugar" coarse-grained DNA model. ---
491  2017 The dynamic binding of cholesterol to the multiple sites of C99: as revealed by coarse-grained and all-atom simulations. AD, AT, TMD
492  2017 The orientation and stability of the GPCR-Arrestin complex in a lipid bilayer. AA, GPCRs
493  2017 Thermodynamics of star polymer solutions: A coarse-grained study. ---
494  2017 Transferable coarse-grained model for perfluorosulfonic acid polymer membranes. AA, IBI, MD, PFSA, SDK
495  2017 Two-bead polarizable water models combined with a two-bead multipole force field (TMFF) for coarse-grained simulation of proteins. TMFF
496  2017 Understanding the colloidal dispersion stability of 1D and 2D materials: Perspectives from molecular simulations and theoretical modeling. AA, h-BN, MD, TMDCs
497  2017 Validating a Coarse-Grained Voltage Activation Model by Comparing Its Performance to the Results of Monte Carlo Simulations. MC
498  2018 A coarse grained molecular dynamics simulation study on the structural properties of carbon nanotube-dendrimer composites. CNT, FTA, MD
499  2018 A multiscale scheme for simulating polymer Tg. AA, MD, Tg
500  2018 A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs. SPQR
501  2018 A structural coarse-grained model for clays using simple iterative Boltzmann inversion. ---
502  2018 A systematic analysis of nucleosome core particle and nucleosome-nucleosome stacking structure. NCPs
503  2018 Accuracy, Transferability, and Efficiency of Coarse-Grained Models of Molecular Liquids. IECG
504  2018 Addressing the temperature transferability of structure based coarse graining models. DA, DN, IMC
505  2018 Advances in coarse-grained modeling of macromolecular complexes. ---
506  2018 Application of a coupled smoothed particle hydrodynamics (SPH) and coarse-grained (CG) numerical modelling approach to study three-dimensional (3-D) deformations of single cells of different food-plant materials during drying. SPH
507  2018 Application of a Novel Coarse-Grained Soil Organic Matter Model in the Environment. DPD, HCB, HCBD, PFSAs, SOM
508  2018 Ballistic Performance of Nanostructured Metals Toughened by Elliptical Coarse-Grained Inclusions: A Finite Element Study with Failure Analysis. NS
509  2018 BOCS: Bottom-up Open-source Coarse-graining Software. g-YBG, MS-CG
510  2018 Bottom-up approach to represent dynamic properties in coarse-grained molecular simulations. DPD, MZ
511  2018 Capturing Phase Behavior of Ternary Lipid Mixtures with a Refined Martini Coarse-Grained Force Field. AA, DOPC, DPPC, MD, Tm
512  2018 Cholesteric ordering predicted using a coarse-grained polymeric model with helical interactions. FCh, MD
513  2018 Coarse-Grained Force Field for Imidazolium-Based Ionic Liquids. CGFFs, RE
514  2018 Coarse-Grained Molecular Dynamics Force-Field for Polyacrylamide in Infinite Dilution Derived from Iterative Boltzmann Inversion and MARTINI Force-Field. IBI
515  2018 Coarse-graining simulation approaches for polymer melts: the effect of potential range on computational efficiency. IECG
516  2018 Cues to Opening Mechanisms From in Silico Electric Field Excitation of Cx26 Hemichannel and in Vitro Mutagenesis Studies in HeLa Transfectans. hCx26
517  2018 Demonstrating aspects of multiscale modeling by studying the permeation pathway of the human ZnT2 zinc transporter. ---
518  2018 Development of a Coarse-Grained Model of Collagen-Like Peptide (CLP) for Studies of CLP Triple Helix Melting. CLP, CLPs, ELPs
519  2018 Development of New Transferable Coarse-Grained Models of Hydrocarbons. MD, PSO
520  2018 Disease-related metabolites affect protein-nanoparticle interactions. AA, MD, NPs
521  2018 Effect of Cholesterol on Membrane Dipole Potential: Atomistic and Coarse-Grained Molecular Dynamics Simulations. CAVS
522  2018 Electrochemical and biocompatibility examinations of high-pressure torsion processed titanium and Ti-13Nb-13Zr alloy. cpTi, EIS, TNZ, UFG
523  2018 Encoding and selecting coarse-grain mapping operators with hierarchical graphs. FG, MD
524  2018 Energy Renormalization Method for the Coarse-Graining of Polymer Viscoelasticity. AA, ER, GF, PB, PS
525  2018 Exploring DNA dynamics within oligonucleosomes with coarse-grained simulations: SIRAH force field extension for protein-DNA complexes. ---
526  2018 Exploring the free-energy landscape of GPCR activation. beta2AR, GPCRs
527  2018 How Does the Surface Tension Depend on the Surface Area with Coarse-Grained Models? DPD, L-L, LV, MDPD
528  2018 Impact of membrane partitioning on the spatial structure of an S-type cobra cytotoxin. CTs, DPC, FA, MD, POPC
529  2018 In vitro corrosion behavior and biocompatibility of nanostructured Ti6Al4V. FN, NG, SFT, VN
530  2018 Integral equation theory based direct and accelerated systematic coarse-graining approaches. HNC, IBI, MD, OZ
531  2018 Machine-Learned Coarse-Grained Models. ANN, FF, MD, PSO
532  2018 Machine-Learning Enabled New Insights into the Coil-to-Globule Transition of Thermosensitive Polymers Using a Coarse-Grained Model. LCST, MD, ML, NMDS, PNIPAM
533  2018 Mesoscopic coarse-grained representations of fluids rigorously derived from atomistic models. FG
534  2018 Microstructure and Corrosion Behavior of Composite Coating on Pure Mg Acquired by Sliding Friction Treatment and Micro-Arc Oxidation. FG, MAO, SFT
535  2018 Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models. ---
536  2018 Molecular Mechanism of Uptake of Cationic Photoantimicrobial Phthalocyanine across Bacterial Membranes Revealed by Molecular Dynamics Simulations. ---
537  2018 Multi-scale simulations of biological systems using the OPEP coarse-grained model. ---
538  2018 Multiscale Coarse-Graining with Effective Polarizabilities: A Fully Bottom-Up Approach. COM
539  2018 Multiscale Modeling of Structure, Transport and Reactivity in Alkaline Fuel Cell Membranes: Combined Coarse-Grained, Atomistic and Reactive Molecular Dynamics Simulations. AEMs, MD
540  2018 Multiscale molecular dynamics simulations of rotary motor proteins. FEL, MD
541  2018 On the Density Dependence of the Integral Equation Coarse-Graining Effective Potential. IECG
542  2018 Optimizing Protein-Polymer Interactions in a Poly(ethylene glycol) Coarse-Grained Model. PEG
543  2018 Parameterization of a coarse-grained model of cholesterol with point-dipole electrostatics. Chol
544  2018 Persistence Length, End-to-End Distance, and Structure of Coarse-Grained Polymers. AA, PE, PTFE
545  2018 Pore diameter dependence of catalytic activity: p-nitrobenzaldehyde conversion to an aldol product in amine-functionalized mesoporous silica. MSN, pNB
546  2018 Prediction of striped cylindrical micelles (SCMs) formed by dodecyl-beta-d-maltoside (DDM) surfactants. DDM, MD, SCM, SCMs
547  2018 PSO-Assisted Development of New Transferable Coarse-Grained Water Models. PSO
548  2018 Quantum mechanics/coarse-grained molecular mechanics (QM/CG-MM). QM/MM
549  2018 Quantum theory of multiscale coarse-graining. MS-CG, qCG, qMS-CG
550  2018 Reconstruction of Atomistic Structures from Coarse-Grained Models for Protein-DNA Complexes. AA
551  2018 Refining amino acid hydrophobicity for dynamics simulation of membrane proteins. ---
552  2018 Role of Charge and Hydrophobicity in Liprotide Formation: A Molecular Dynamics Study with Experimental Constraints. ALA, ITC, MD, MG, OA, SAXS
553  2018 Role of many-body interactions in the structure of coarse-grained polymers. ---
554  2018 SAFT-gamma Force Field for the Simulation of Molecular Fluids. 5. Hetero-Group Coarse-Grained Models of Linear Alkanes and the Importance of Intramolecular Interactions. UA
555  2018 Size of graphene sheets determines the structural and mechanical properties of 3D graphene foams. GFs, vdW
556  2018 Stretch and Breakage of Wormlike Micelles under Uniaxial Strain: A Simulation Study and Comparison with Experimental Results. ---
557  2018 Structural basis for the interaction of the beta-secretase with copper. MD
558  2018 The significance of deformation mechanisms on the fracture behavior of phase reversion-induced nanostructured austenitic stainless steel. NG/UFG, SFs
559  2018 Theoretical approaches for dynamical ordering of biomolecular systems. AA, MD, QM, QM/MM
560  2018 Towards a coarse-grained model of the peptoid backbone: the case of N,N-dimethylacetamide. AA, DMA
561  2018 Transferable Coarse-Grained Models of Liquid-Liquid Equilibrium Using Local Density Potentials Optimized with the Relative Entropy. ---
562  2018 Translational mobilities of proteins in nanochannels: A coarse-grained molecular dynamics study. NEMD
563  2018 Ultra-Coarse-Grained Liquid State Models with Implicit Hydrogen Bonding. UCG
564  2018 Ultra-Coarse-Grained Models Allow for an Accurate and Transferable Treatment of Interfacial Systems. MS-CG, UCG
565  2018 Ultrastrong nanocrystalline steel with exceptional thermal stability and radiation tolerance. 0.75 Tm, NC, NC-SS, Tm
566  2018 Unraveling the Molecular Mechanisms of Thermo-responsive Properties of Silk-Elastin-Like Proteins by Integrating Multiscale Modeling and Experiment. SELPs
567  2019 A coarse-grained red blood cell membrane model to study stomatocyte-discocyte-echinocyte morphologies. BCM, RBC, SDE
568  2019 A hybrid, bottom-up, structurally accurate, Go-like coarse-grained protein model. ---
569  2019 A multiscale analysis of DNA phase separation: from atomistic to mesoscale level. ---
570  2019 A new method for the construction of coarse-grained models of large biomolecules from low-resolution cryo-electron microscopy data. CK-CG, cryo-EM
571  2019 A Practical View of the Martini Force Field. MD
572  2019 Adversarial-residual-coarse-graining: Applying machine learning theory to systematic molecular coarse-graining. ---
573  2019 Aggregation Behavior of Model Asphaltenes Revealed from Large-Scale Coarse-Grained Molecular Simulations. EOS
574  2019 Analysis of local density potentials. AA, LD, MS-CG
575  2019 Back-mapping based sampling: Coarse grained free energy landscapes as a guideline for atomistic exploration. BMBS, FESs, NN
576  2019 Backmapping from Multiresolution Coarse-Grained Models to Atomic Structures of Large Biomolecules by Restrained Molecular Dynamics Simulations Using Bayesian Inference. AA, MD
577  2019 Bayesian selection for coarse-grained models of liquid water. ---
578  2019 Coarse-grained modeling of the nucleation of polycyclic aromatic hydrocarbons into soot precursors. PAH, PY
579  2019 Coarse-grained molecular dynamics simulations of alpha-1,3-glucan. ---
580  2019 Coarse-graining involving virtual sites: Centers of symmetry coarse-graining. COM, COS
581  2019 Combination of coarse-grained molecular dynamics simulations and small-angle X-ray scattering experiments. MD, SAXS
582  2019 Compatible observable decompositions for coarse-grained representations of real molecular systems. MS-CODE, RE-CODE
583  2019 Computational simulations of TNF receptor oligomerization on plasma membrane. AA, MD, TNFR1, TNFs
584  2019 Conditional Reversible Work Coarse-Grained Models with Explicit Electrostatics-An Application to Butylmethylimidazolium Ionic Liquids. BMIM, CRW
585  2019 Curvature effect and stabilize ruptured membrane of BAX derived peptide studied by molecular dynamics simulations. AA, TMD
586  2019 Curvature induction and sensing of the F-BAR protein Pacsin1 on lipid membranes via molecular dynamics simulations. AA, F-BAR
587  2019 Developing a Transferable Coarse-Grained Model for the Prediction of Thermodynamic, Structural, and Mechanical Properties of Polyimides at Different Thermodynamic State Points. IBI, PI
588  2019 Development of Coarse-Grained Models for Polymers by Trajectory Matching. ---
589  2019 Development of Transferable Nonbonded Interactions between Coarse-Grained Hydrocarbon and Water Models. FF
590  2019 Direct route to reproducing pair distribution functions with coarse-grained models via transformed atomistic cross correlations. ---
591  2019 Dual approach for effective potentials that accurately model structure and energetics. ---
592  2019 Dual-potential approach for coarse-grained implicit solvent models with accurate, internally consistent energetics and predictive transferability. ---
593  2019 Effect of Chemical Permeation Enhancers on Skin Permeability: In silico screening using Molecular Dynamics simulations. APIs, CPEs, MD, SC
594  2019 Effect of Cholesterol and 6-Ketocholestanol on Membrane Dipole Potential and Sterol Flip-Flop Motion in Bilayer Membranes. 6-KC, Chol, DMPC
595  2019 Effect of Peptide Sequence on the LCST-Like Transition of Elastin-Like Peptides and Elastin-Like Peptide-Collagen-Like Peptide Conjugates: Simulations and Experiments. CLPs, ELPs, VPGXG
596  2019 Effects of Ether Linkage on Membrane Dipole Potential and Cholesterol Flip-Flop Motion in Lipid Bilayer Membranes. AA
597  2019 Electrochemical Corrosion Behavior and Mechanical Properties of Nanocrystalline Ti⁻6Al⁻4V Alloy Induced by Sliding Friction Treatment. NG, SFT
598  2019 Electronic structure at coarse-grained resolutions from supervised machine learning. ANN-ECG
599  2019 Electrostatically Mediated Protein-Protein Interactions for Monoclonal Antibodies: A Combined Experimental and Coarse-Grained Molecular Modeling Approach. PPI
600  2019 Energy renormalization for coarse-graining polymers having different segmental structures. ER, GET
601  2019 Equations of motion for position-dependent coarse-grain mappings obtained with Mori-Zwanzig theory. ---
602  2019 Establishing Computational Approaches Towards Identifying Malarial Allosteric Modulators: A Case Study of Plasmodium falciparum Hsp70s. BC, HSPs
603  2019 Evidence of information limitations in coarse-grained models. ---
604  2019 Fat SIRAH: Coarse-Grained Phospholipids To Explore Membrane-Protein Dynamics. ---
605  2019 Framework for Inverse Mapping Chemistry-Agnostic Coarse-Grained Simulation Models into Chemistry-Specific Models. CS
606  2019 Graph-Based Approach to Systematic Molecular Coarse-Graining. GBCG
607  2019 Hierarchical modelling of polystyrene melts: from soft blobs to atomistic resolution. PS
608  2019 Implicit-solvent coarse-grained modeling for polymer solutions via Mori-Zwanzig formalism. GLE, MD
609  2019 Importance of Interface in the Coarse-Grained Model of CNT /Epoxy Nanocomposites. AA, CNTs
610  2019 Invariance of experimental observables with respect to coarse-graining in standard and many-body dissipative particle dynamics. DPD
611  2019 Ionic transport through a protein nanopore: a Coarse-Grained Molecular Dynamics Study. ---
612  2019 Local and long range potentials for heparin-protein systems for coarse-grained simulations. GAGs
613  2019 Low-Resolution Models for the Interaction Dynamics of Coated Gold Nanoparticles with beta2-microglobulin. MS, NPs
614  2019 Machine learning coarse grained models for water. ---
615  2019 Martini Coarse-Grained Model for Clay-Polymer Nanocomposites. OMMT, TMA
616  2019 Martini coarse-grained model for polyethylenimine. PEI
617  2019 MARTINI-based simulation method for step-growth polymerization and its analysis by size exclusion characterization: a case study of cross-linked polyurethane. Tg
618  2019 Microscopic derivation of coarse-grained, energy-conserving generalized Langevin dynamics. GLE, NSO
619  2019 Model reduction of rigid-body molecular dynamics via generalized multipole potentials. ---
620  2019 Modeling Interactions between Liposomes and Hydrophobic Nanosheets. MD
621  2019 MOLC. A reversible coarse grained approach using anisotropic beads for the modelling of organic functional materials. ---
622  2019 Molecular dynamics simulation of thermo-mechanical behaviour of elastomer cross-linked via multifunctional zwitterions. Tg, VMD, ZCLs
623  2019 Multiconfigurational Coarse-Grained Molecular Dynamics. MCCG
624  2019 Parametrization of MARTINI for Modeling Hinging Motions in Membrane Proteins. TM
625  2019 pH-Dependent aggregation and pH-independent cell membrane adhesion of monolayer-protected mixed charged gold nanoparticles. ---
626  2019 Phase Equilibria Modeling with Systematically Coarse-Grained Models-A Comparative Study on State Point Transferability. ---
627  2019 Pitfalls of the Martini Model. ---
628  2019 Relative entropy indicates an ideal concentration for structure-based coarse graining of binary mixtures. IMC, LJ
629  2019 Revisiting the protomotive vectorial motion of F0-ATPase. ---
630  2019 Self-Assembly of Polymer-Encased Lipid Nanodiscs and Membrane Protein Reconstitution. MD, SMAEA
631  2019 Simple Simulation Model for Exploring the Effects of Solvent and Structure on Asphaltene Aggregation. ---
632  2019 Styrene/Maleic Acid Copolymers Form SMALPs by Pulling Lipid Patches out of the Lipid Bilayer. MD, SMA, SMALPs
633  2019 Systematic Coarse-Grained Lipid Force Fields with Semiexplicit Solvation via Virtual Sites. DOPC, DPPC, MS-CG, REM, VCG
634  2019 Systematic study of temperature and density variations in effective potentials for coarse-grained models of molecular liquids. PMF
635  2019 The multi-dimensional generalized Langevin equation for conformational motion of proteins. GLE
636  2019 The SIRAH 2.0 Force Field: Altius, Fortius, Citius. CaM
637  2019 Top-down Multiscale Approach To Simulate Peptide Self-Assembly from Monomers. AA
638  2019 Toward Multiscale Modeling of Proteins and Bioagglomerates: An Orientation-Sensitive Diffusion Model for the Integration of Molecular Dynamics and the Discrete Element Method. DEM, MD, MDEM
639  2019 Transferability of Local Density-Assisted Implicit Solvation Models for Homogeneous Fluid Mixtures. LD
640  2019 tSPICA: Temperature- and Pressure-Dependent Coarse-Grained Force Field for Organic Molecules. ---
641  2019 Understanding Missing Entropy in Coarse-Grained Systems: Addressing Issues of Representability and Transferability. FG, PMF
642  2020 A good combination of strength and ductility of ultra-coarse-grained Cu-Al alloy with coarse-grained surface layer via pre-torsional treatment. UCG
643  2020 Atomic-level reconstruction of biomolecules by a rigid-fragment- and local-frame-based (RF-LF) strategy. RF-LF
644  2020 Capturing choline-aromatics cation-pi interactions in the MARTINI force field. ---
645  2020 Determining Optimal Coarse-Grained Representation for Biomolecules Using Internal Cluster Validation Indexes. ---
646  2020 Development of Coarse-Grained Force Field by Combining Multilinear Interpolation Technique and Simplex Algorithm. FF
647  2020 Free Energies of the Disassembly of Viral Capsids from a Multiscale Molecular Simulation Approach. MD, TrV
648  2020 Integrating All-Atom and Coarse-Grained Simulations-Toward Understanding of IDPs at Surfaces. AA, IDP, MC
649  2020 Martini Force Field for Protonated Polyethyleneimine. AA, FF, PEI
650  2020 Modeling DNA Flexibility: Comparison of Force Fields from Atomistic to Multiscale Levels. FFs
651  2020 Molecular characterization of the outer membrane of Pseudomonas aeruginosa. AA, LPS, MD, OM
652  2020 Molecular Dynamics of the Recruitment of Immunoreceptor Signaling Module DAP12 Homodimer to Lipid Raft Boundary Regulated by PIP2. ITAMs, NK, TCR
653  2020 Molecular dynamics simulation of imidazolium CnMIM-BF4 ionic liquids using a coarse grained force-field. ILs
654  2020 Molecular dynamics trajectories for 630 coarse-grained drug-membrane permeations. MD
655  2020 On the mechanical behavior of austenitic stainless steel with nano/ultrafine grains and comparison with micrometer austenitic grains counterpart and their biological functions. ---
656  2020 Performance of Coarse Graining in Estimating Polymer Properties: Comparison with the Atomistic Model. ---
657  2020 Post-Translational Modifications at the Coarse-Grained Level with the SIRAH Force Field. PTMs
658  2020 Prediction of Mechanical Hemolysis in Medical Devices via a Lagrangian Strain-Based Multiscale Model. FDA, Hb, IH, MD, RBCs
659  2020 pSPICA: A Coarse-Grained Force Field for Lipid Membranes Based on a Polar Water Model. FF
660  2020 Reactive Coarse-grained Molecular Dynamics. AA, PMF, RCG
661  2020 Role of membrane curvature on the activation/deactivation of Carnitine Palmitoyltransferase 1A: A coarse grain molecular dynamic study. CPT 1A, NTD, OMM, TM