VMD

swMATH18651MaRDI QIDQ30483FDOQ30483

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Cited In (76)

• Revisiting chameleon sequences in the protein data bank
• Window Proper Orthogonal Decomposition: Application to Continuum and Atomistic Data
• Dynamic pull-in instability of multilayer graphene NEMSs: non-classical continuum model and molecular dynamics simulations
• Efficient perturbation analysis of elastic network models -- application to acetylcholinesterase of T. Californica
• Multiscale Hybrid Modeling of Proteins in Solvent: SARS-CoV2 Spike Protein as Test Case for Lattice Boltzmann – All Atom Molecular Dynamics Coupling
• Petri nets formalism facilitates analysis of complex biomolecular structural data
• Structural and energetic comparison of the complexes of aminoglycosides with the model of the ribosomal A-site
• Self-Propelled Jump Regime in Nanoscale Droplet Collisions: A Molecular Dynamics Study
• Ribosome Builder: a software project to simulate the ribosome
• Visualizing the dual space of biological molecules
• Molecular Geometry and Molecular Graphics: Natta’s Polypropylene and Beyond
• Vibration of carbon nanotubes with defects: order reduction methods
• Using computational approaches to study dengue virus capsid assembly
• Mechanics of water pore formation in lipid membrane under electric field
• Viral capsid nanoindentation simulations using octree-type data structures
• The fuzzy oil drop model, based on hydrophobicity density distribution, generalizes the influence of water environment on protein structure and function
• Quantum Dynamics with the Parallel Transport Gauge
• The solution of the boundary-value problems for the simulation of transition of protein confor\-mation
• Collective Mode Mining from Molecular Dynamics Simulations: A Comparative Approach
• Title not available (Why is that?)
• Statistical Mechanical Theory of Protein Folding in Water Environment
• Co-evolution and information signals in biological sequences
• Armchair or Zigzag? A tool for characterizing graphene edge
• Combined MPM-DEM for Simulating the Interaction Between Solid Elements and Fluid Particles
• A study of mechanical properties of pure and nitrogen-doped ultrananocrystalline diamond films under various loading conditions
• Insights into the molecular mechanisms of protein-ligand interactions by molecular docking and molecular dynamics simulation: a case of oligopeptide binding protein
• Metadynamics study of mutant human interferon-gamma forms
• Fast analysis of molecular dynamics trajectories with graphics processing units -- radial distribution function histogramming
• Browndye: A software package for Brownian dynamics
• The loading history and crystal orientation effects on the size-dependency of single crystal diamond properties
• Large-scale molecular dynamics simulation of flow under complex structure of endothelial glycocalyx
• Geometry-guided computation of 3D electrostatics for large biomolecules
• Myoglobin ligand gate mechanism analysis by a novel 3D visualization technique
• Using sacrificial cell spheroids for the bioprinting of perfusable 3D tissue and organ constructs: a computational study
• Large deformation and fracture mechanics of a beta-helical protein nanotube: Atomistic and continuum modeling
• Hydrophobic collapse in (in silico) protein folding
• Coupled applications on distributed resources
• Computing Localized Representations of the Kohn--Sham Subspace Via Randomization and Refinement
• Implication of crystal water molecules in inhibitor binding at ALR2 active site
• Analyses of tensile deformation of nanocrystalline \(\alpha-\text{Fe}_2\text{O}_3+fcc-\)Al composites using molecular dynamics simulations
• Numerical methods for the Poisson-Fermi equation in electrolytes
• Adaptive multiscale modeling of polymeric materials with Arlequin coupling and goals algorithms
• Accuracy limits of the blob model for a flexible polymer confined inside a cylindrical nano-channel
• PROSIGN: a method for protein secondary structure assignment based on three-dimensional coordinates of consecutive \(C_\alpha \) atoms
• Multiscale modeling using goal-oriented adaptivity and numerical homogenization. I: Mathematical formulation and numerical results
• NAMD2: Greater scalability for parallel molecular dynamics
• A boundary element formulation of protein electrostatics with explicit ions
• Folding of multi-layer graphene sheets induced by van der Waals interaction
• A treecode-accelerated boundary integral Poisson-Boltzmann solver for electrostatics of solvated biomolecules
• Evolutionary de Rham-Hodge method
• Combined grain size, strain rate and loading condition effects on mechanical behavior of nanocrystalline Cu under high strain rates
• DelEnsembleElec: Computing Ensemble-Averaged Electrostatics Using DelPhi
• Molecular dynamics simulation of peeling a DNA molecule on substrate
• Periodic boundary conditions for arbitrary deformations in molecular dynamics simulations
• ESPResSo 3.1: Molecular Dynamics Software for Coarse-Grained Models
• A novel canonical dual computational approach for prion AGAAAAGA amyloid fibril molecular modeling
• SDPhound, a mutual information-based method to investigate specificity-determining positions
• Algorithmic challenges in computational molecular biophysics
• Computational study of thermal dependence of accommodation coefficients in a nano-channel and the prediction of velocity profiles
• SDPBS web server for calculation of electrostatics of ionic solvated biomolecules
• Modelling excess surface energy in dry and wetted calcite systems
• Analyzing the sequence-structure relationship of a library of local structural prototypes
• Topological data analysis for the energy and stability of endohedral metallofullerenes
• Minimal formulation of joint motion for biomechanisms
• Visualization in Medicine and Life Sciences II. Progress and New Challenges. Selected papers based on the presentations at the second international workshop, VMLS, Bremerhaven, Germany, June 22--24, 2009
• Disentanglement via Entanglement: A Unified Method for Wannier Localization
• A stochastic thermostat algorithm for coarse-grained thermomechanical modeling of large-scale soft matters: theory and application to microfilaments
• Multiscale universal interface: a concurrent framework for coupling heterogeneous solvers
• A fast mollified impulse method for biomolecular atomistic simulations
• Atomistic insights into dislocation-based mechanisms of void growth and coalescence
• Molecular advection-diffusion through graphene nanopores
• Biomolecular electrostatics using a fast multipole BEM on up to 512 GPUs and a billion unknowns
• Molecular dynamics simulation study on the structural stabilities of polyglutamine peptides
• Minimizing the object dimensions in circle and sphere packing problems
• A comparative molecular dynamics-phase-field modeling approach to brittle fracture
• Understanding the intracellular-to-extracellular localization switch of polyhydroxybutyrate polymerase in \textit{Pseudomonas} backgrounds as a microevolutionary process

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