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■ Abbreviation / Long Form : AA / all-atom

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Total Number of Papers: 71
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Abbreviation:   AA  (>> Co-occurring Abbreviation)
Long Form:   all-atom
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No. Year Title Co-occurring Abbreviation
2020 A coarse-grain force field based on quantum mechanics (CGq FF) for molecular dynamics simulation of poly(ethylene glycol)-block-poly(epsilon-caprolactone) (PEG-b-PCL) micelles. MD, NB, PCL, PEG, PEG-b-PCL, Rg
2020 Asymmetry and Rippling in Mixed Surfactant Bilayers from All-Atom and Coarse-Grained Simulations: Interdigitation and Per Chain Entropy†. BTMAC, CG, SA
2020 Computational simulations of TNF receptor oligomerization on plasma membrane. CG, MD, TNFR1, TNFs
2020 Extension of transferable coarse-grained models to dicationic ionic liquids. CG, DILs, HOPs, MILs
2020 Improved coarse-grain model to unravel the phase behavior of 1-alkyl-3-methylimidazolium-based ionic liquids through molecular dynamics simulations. CMC, FF, ILs, MD
2020 Integrating All-Atom and Coarse-Grained Simulations-Toward Understanding of IDPs at Surfaces. CG, IDP, MC
2020 Martini Force Field for Protonated Polyethyleneimine. CG, FF, PEI
2020 Molecular characterization of the outer membrane of Pseudomonas aeruginosa. CG, LPS, MD, OM
2020 Reactive Coarse-Grained Molecular Dynamics. CG, PMF, RCG
10  2019 Analysis of local density potentials. CG, LD, MS-CG
11  2019 Backmapping from Multiresolution Coarse-Grained Models to Atomic Structures of Large Biomolecules by Restrained Molecular Dynamics Simulations Using Bayesian Inference. CG, MD
12  2019 Curvature effect and stabilize ruptured membrane of BAX derived peptide studied by molecular dynamics simulations. CG, TMD
13  2019 Curvature induction and sensing of the F-BAR protein Pacsin1 on lipid membranes via molecular dynamics simulations. CG, F-BAR
14  2019 Effects of Ether Linkage on Membrane Dipole Potential and Cholesterol Flip-Flop Motion in Lipid Bilayer Membranes. CG
15  2019 Top-down Multiscale Approach To Simulate Peptide Self-Assembly from Monomers. CG
16  2018 Capturing Phase Behavior of Ternary Lipid Mixtures with a Refined Martini Coarse-Grained Force Field. CG, DOPC, DPPC, MD, Tm
17  2018 Disease-related metabolites affect protein-nanoparticle interactions. CG, MD, NPs
18  2018 Energy Renormalization Method for the Coarse-Graining of Polymer Viscoelasticity. CG, ER, GF, PB, PS
19  2018 Persistence Length, End-to-End Distance, and Structure of Coarse-Grained Polymers. CG, PE, PTFE
20  2018 Reconstruction of Atomistic Structures from Coarse-Grained Models for Protein-DNA Complexes. CG
21  2018 Theoretical approaches for dynamical ordering of biomolecular systems. CG, MD, QM, QM/MM
22  2018 Towards a coarse-grained model of the peptoid backbone: the case of N,N-dimethylacetamide. CG, DMA
23  2017 Effects of Coarse Graining and Saturation of Hydrocarbon Chains on Structure and Dynamics of Simulated Lipid Molecules. CG, UA
24  2017 Extending pressure-matching to inhomogeneous systems via local-density potentials. EOS
25  2017 Modeling of low temperature adsorption of hydrogen in carbon nanopores. UA
26  2017 Reduced Point Charge Models of Proteins: Effect of Protein-Water Interactions in Molecular Dynamics Simulations of Ubiquitin Systems. CG, FF, RPCM
27  2017 Role of Dynamic Heterogeneities in Ionic Liquids: Insights from All-Atom and Coarse-Grained Molecular Dynamics Simulation Studies. CG
28  2017 The orientation and stability of the GPCR-Arrestin complex in a lipid bilayer. CG, GPCRs
29  2017 The unfolding mechanism of monomeric mutant SOD1 by simulated force spectroscopy. HA-Go, SOD1
30  2017 Transferable coarse-grained model for perfluorosulfonic acid polymer membranes. CG, IBI, MD, PFSA, SDK
31  2016 As Simple As Possible, but Not Simpler: Exploring the Fidelity of Coarse-Grained Protein Models for Simulated Force Spectroscopy. AWSEM
32  2016 Bottom-up coarse-grained models with predictive accuracy and transferability for both structural and thermodynamic properties of heptane-toluene mixtures. CG
33  2016 Estimation of Liposome Penetration Barriers of Drug Molecules with All-Atom and Coarse-Grained Models. 5-ALA, CG
34  2016 Multiscale design of coarse-grained elastic network-based potentials for the mu opioid receptor. CG, ENM, FF, GPCR, MD, muOR, NMA
35  2016 Simulation of High Density Lipoprotein Behavior on a Few Layer Graphene Undergoing Non-Uniform Mechanical Load. CG, CNT, DPPC, HDL, SWNT
36  2016 Systematic Generation of Anisotropic Coarse-Grained Lennard-Jones Potentials and Their Application to Ordered Soft Matter. CG, LoD, vdW
37  2016 Van der Waals Perspective on Coarse-Graining: Progress toward Solving Representability and Transferability Problems. CG, PMF
38  2015 Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids. CG, PMF
39  2015 Coarse-grained model of glycosaminoglycans. CG, GAGs, MD
40  2015 Exploring LacI-DNA dynamics by multiscale simulations using the SIRAH force field. CG, LacI
41  2015 Molecular dynamics methods to predict peptide locations in membranes: LAH4 as a stringent test case. CG, PMF
42  2015 On the application of the MARTINI coarse-grained model to immersion of a protein in a phospholipid bilayer. CG, MD, POPC
43  2014 Investigation of coarse-grained mappings via an iterative generalized Yvon-Born-Green method. CG, g-YBG, MS-CG, RDFs
44  2014 Multi-scale ensemble modeling of modular proteins with intrinsically disordered linker regions: application to p53. CG, IDRs, MD, SAXS
45  2014 Multiscale molecular dynamics simulations of sodium dodecyl sulfate micelles: from coarse-grained to all-atom resolution. CG, MD, QM, SDS, UA
46  2014 Nanomechanics of beta-rich proteins related to neuronal disorders studied by AFM, all-atom and coarse-grained MD methods. AFM, CG MD, MD
47  2014 RESPAC: Method to Determine Partial Charges in Coarse-Grained Protein Model and Its Application to DNA-Binding Proteins. CG, RESP
48  2013 Comparison of two simulation methods to compute solvation free energies and partition coefficients. AAD, EE, OPLS, SPC/E, TI
49  2013 Effect of arginine-rich peptide length on the structure and binding strength of siRNA-peptide complexes. Arg, CG, MD
50  2013 Improved coarse-grained model for molecular-dynamics simulations of water nucleation. CG
51  2013 Insertion of the Ca⁺-independent phospholipase A₂ into a phospholipid bilayer via coarse-grained and atomistic molecular dynamics simulations. CG, DXMS, MD
52  2013 Molecular energetics in the capsomere of virus-like particle revealed by molecular dynamics simulations. MD, MM-PBSA, MPV, VLPs
53  2013 SAFT-gamma force field for the simulation of molecular fluids: 2. Coarse-grained models of greenhouse gases, refrigerants, and long alkanes. CG, EOS, UA
54  2012 Comparing normal modes across different models and scales: Hessian reduction versus coarse-graining. ---
55  2012 Computer simulation studies of self-assembling macromolecules. CG, MD
56  2012 Tunable, mixed-resolution modeling using library-based Monte Carlo and graphics processing units. CG, GBSA, GPU, LBMC
57  2012 [Non-commutative geometrical drug discovery--the principle of geometrical regulation]. CG, QC
58  2011 A hybrid all-atom/coarse grain model for multiscale simulations of DNA. ---
59  2011 Coarse-grained modeling study of nonpeptide RGD ligand density and PEG molecular weight on the conformation of poly(gamma-glutamyl-glutamate) paclitaxel conjugates. CG, MD, MW, PGG-PTX-PEG-npRGD
60  2011 Modification of Martini force field for molecular dynamics simulation of hydrophobic charge induction chromatography of lysozyme. CG, HCIC, MD
61  2010 Characterization of a clinical polymer-drug conjugate using multiscale modeling. CG, MD, PGG-PTX, PTX
62  2010 Coarse-grained molecular dynamics of tetrameric transmembrane peptide bundles within a lipid bilayer. CG, MD
63  2010 Parametrization and application of a coarse grained force field for benzene/fullerene interactions with lipids. CG, MD
64  2009 A dual-scale approach toward structure prediction of retinal proteins. bR, CG, HR, RPs, SRI, SRII
65  2009 A Transferable Coarse Grain Non-bonded Interaction Model For Amino Acids. CG, LJ, SASA
66  2009 Coarse-grained molecular dynamics study of cyclic peptide nanotube insertion into a lipid bilayer. CG, MD
67  2009 Structure, dynamics, and ion conductance of the phospholamban pentamer. CG, PLN
68  2008 Packing of transmembrane helices in bacteriorhodopsin folding: structure and thermodynamics. bR, CG, HMPs, RMSD
69  2008 Peptide aggregation and pore formation in a lipid bilayer: a combined coarse-grained and all atom molecular dynamics study. CG
70  2008 Reconstructing atomistic detail for coarse-grained models with resolution exchange. CG
71  2006 A novel united-atom force field for imidazolium-based ionic liquids. UA