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January 2018 |
GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations: GENESIS
- Jung, Jaewoon; Mori, Takaharu; Kobayashi, Chigusa
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Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 5, Issue 4
https://doi.org/10.1002/wcms.1220
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May 2015 |
Two-dimensional semiconductors in the regime of strong light-matter coupling
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July 2018 |
Simple application of fibronectin–mimetic coating enhances osseointegration of titanium implants
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August 2008 |
CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data
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July 2013 |
Development of an Empirical Force Field for Silica. Application to the Quartz−Water Interface
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February 2006 |
A force field for tricalcium aluminate to characterize surface properties, initial hydration, and organically modified interfaces in atomic resolution
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January 2014 |
Optimization of the CHARMM Additive Force Field for DNA: Improved Treatment of the BI/BII Conformational Equilibrium
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December 2011 |
Scalable molecular dynamics with NAMD
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January 2005 |
The Amber biomolecular simulation programs
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Formation of Solid-Supported Lipid Bilayers: An Integrated View
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April 2006 |
Building two-dimensional materials one row at a time: Avoiding the nucleation barrier
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December 2018 |
Simulations of inorganic–bioorganic interfaces to discover new materials: insights, comparisons to experiment, challenges, and opportunities
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January 2016 |
Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides †
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July 2001 |
Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
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Fast Parallel Algorithms for Short-Range Molecular Dynamics
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Understanding the Surface Reactivity of Ligand-Protected Metal Nanoparticles for Biomass Upgrading
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April 2020 |
Chemistry with ADF
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January 2001 |
Anisotropic mean-square displacements (MSD) in single-crystals of 2 H - and 3 R -MoS 2
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August 1983 |
Deciphering chemical order/disorder and material properties at the single-atom level
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February 2017 |
GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers
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September 2015 |
CHARMM-GUI Membrane Builder toward realistic biological membrane simulations
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August 2014 |
Matrix Macromolecules in Hard Tissues Control the Nucleation and Hierarchical Assembly of Hydroxyapatite
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January 2007 |
CHARMM: The biomolecular simulation program
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July 2009 |
Development and testing of a general amber force field
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January 2004 |
Structure and Phase Transitions of Alkyl Chains on Mica
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August 2003 |
Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types
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June 2010 |
Following the Formation of Supported Lipid Bilayers on Mica: A Study Combining AFM, QCM-D, and Ellipsometry
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May 2005 |
Thermodynamically Consistent Force Fields for the Assembly of Inorganic, Organic, and Biological Nanostructures: The INTERFACE Force Field
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January 2013 |
CHARMM36m: an improved force field for folded and intrinsically disordered proteins
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November 2016 |
A force-matching Stillinger-Weber potential for MoS 2 : Parameterization and Fisher information theory based sensitivity analysis
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December 2017 |
Force Field for Tricalcium Silicate and Insight into Nanoscale Properties: Cleavage, Initial Hydration, and Adsorption of Organic Molecules
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April 2013 |
Round Robin Study: Molecular Simulation of Thermodynamic Properties from Models with Internal Degrees of Freedom
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August 2017 |
CHARMM-GUI Membrane Builder for Mixed Bilayers and Its Application to Yeast Membranes
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July 2009 |
Construction of a web-based nanomaterial database by big data curation and modeling friendly nanostructure annotations
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May 2020 |
Accurate simulation of surfaces and interfaces of ten FCC metals and steel using Lennard–Jones potentials
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January 2021 |
Molecular Mechanism of Specific Recognition of Cubic Pt Nanocrystals by Peptides and of the Concentration-Dependent Formation from Seed Crystals
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January 2015 |
XXV. Zur Frage der Geschwindigkeit des Wachsthums und der Auflösung der Krystallflächen
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CHARMM-GUI: A web-based graphical user interface for CHARMM
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March 2008 |
Silica-Based Mesoporous Organic–Inorganic Hybrid Materials
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Overview — clay mineral applications
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pysimm: A python package for simulation of molecular systems
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January 2017 |
Force Field and a Surface Model Database for Silica to Simulate Interfacial Properties in Atomic Resolution
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April 2014 |
Carbon Nanotube Dispersion in Solvents and Polymer Solutions: Mechanisms, Assembly, and Preferences
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October 2016 |
LINCS: A linear constraint solver for molecular simulations
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Tinker 8: Software Tools for Molecular Design
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August 2018 |
Clay minerals for nanocomposites and biotechnology: surface modification, dynamics and responses to stimuli
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June 2012 |
CHARMM-GUI supports the Amber force fields
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July 2020 |
Controlled wettability of quartz surfaces
- Lamb, Robert N.; Furlong, D. Neil
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Journal of the Chemical Society, Faraday Transactions 1: Physical Chemistry in Condensed Phases, Vol. 78, Issue 1
https://doi.org/10.1039/f19827800061
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CHARMM-GUI Polymer Builder for Modeling and Simulation of Synthetic Polymers
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April 2021 |
Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ 1 and χ 2 Dihedral Angles
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August 2012 |
Mesoporous Silica Nanoparticles for Drug Delivery and Biosensing Applications
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April 2007 |
MoSDeF, a Python Framework Enabling Large-Scale Computational Screening of Soft Matter: Application to Chemistry-Property Relationships in Lubricating Monolayer Films
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January 2020 |
Molecular dynamics---Scalable algorithms for molecular dynamics simulations on commodity clusters
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New spherical-cutoff methods for long-range forces in macromolecular simulation
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Nanoparticle decoration with surfactants: Molecular interactions, assembly, and applications
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February 2017 |
CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field
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December 2015 |
Interpretable molecular models for molybdenum disulfide and insight into selective peptide recognition
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January 2020 |
Automated Builder and Database of Protein/Membrane Complexes for Molecular Dynamics Simulations
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September 2007 |
NanoMaterialsCAD: Flexible Software for the Design of Nanostructures
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November 2020 |
Computer simulations of fibronectin adsorption on hydroxyapatite surfaces
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January 2014 |
The Use of Some Clay Minerals as Natural Resources for Drug Carrier Applications
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October 2018 |
Molecular Dynamics Simulations of Structural and Mechanical Properties of Muscovite: Pressure and Temperature Effects
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July 2012 |
Carbon nanotube bundles with tensile strength over 80 GPa
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May 2018 |
Structure and stability of the (001) α-quartz surface
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January 2007 |
The Dissociated Amorphous Silica Surface: Model Development and Evaluation
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October 2010 |
NanoModeler: A Webserver for Molecular Simulations and Engineering of Nanoparticles
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February 2019 |
The potential of atomistic simulations and the knowledgebase of interatomic models
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July 2011 |
Surface energies of elemental crystals
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September 2016 |
A smooth particle mesh Ewald method
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November 1995 |
Definition and testing of the GROMOS force-field versions 54A7 and 54B7
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April 2011 |
Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset
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October 2016 |
Abiotic tooth enamel
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March 2017 |
Accurate Force Field Parameters and pH Resolved Surface Models for Hydroxyapatite to Understand Structure, Mechanics, Hydration, and Biological Interfaces
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February 2016 |
OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
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July 2017 |
Accurate Simulation of Surfaces and Interfaces of Face-Centered Cubic Metals Using 12−6 and 9−6 Lennard-Jones Potentials
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October 2008 |
The three-dimensional structure of the tenth type III module of fibronectin: An insight into RGD-mediated interactions
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November 1992 |
Force field for calcium sulfate minerals to predict structural, hydration, and interfacial properties
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January 2021 |
CHARMM-GUI PDB Manipulator for Advanced Modeling and Simulations of Proteins Containing Nonstandard Residues
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book
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August 2014 |