Cited in
(only showing first 100 items - show all)- \(\Pi\)4U: a high performance computing framework for Bayesian uncertainty quantification of complex models
- Implementing molecular dynamics on hybrid high performance computers-short range forces
- Numerical modelling of ion transport in 5-HT3 serotonin receptor using molecular dynamics
- A novel method for calculating relative free energy of similar molecules in two environments
- Guided motion of short carbon nanotube driven by non-uniform electric field
- The Sigma MD programm and a generic interface applicable to multi-functional programs with complex, hierarchical command structure
- sGDML
- Computing committors in collective variables via Mahalanobis diffusion maps
- Dimensionality reduction of complex metastable systems via kernel embeddings of transition manifolds
- Connecting the Dots: Numerical Randomized Hamiltonian Monte Carlo with State-Dependent Event Rates
- Mechanics of water pore formation in lipid membrane under electric field
- A generalized Newton iteration for computing the solution of the inverse Henderson problem
- Generator estimation of Markov jump processes
- A comparison of generalized hybrid Monte Carlo methods with and without momentum flip
- Physical modeling of aqueous solvation
- Entropy-based wavelet de-noising method for time series analysis
- Molecular crowding effects on conformation and stability of G-quadruplex DNA structure: insights from molecular dynamics simulation
- Data-driven molecular modeling with the generalized Langevin equation
- Single channel quantum color image encryption algorithm based on HSI model and quantum Fourier transform
- The mechanism of pulsed electric field (PEF) targeting location on the spatial conformation of pine nut peptide
- Molecular dynamics of dewetting of ultra-thin water films on solid substrate
- Rational design, conformational analysis and membrane-penetrating dynamics study of Bac2A-derived antimicrobial peptides against gram-positive clinical strains isolated from pyemia
- Exploration of synthetic multifunctional amides as new therapeutic agents for Alzheimer's disease through enzyme inhibition, chemoinformatic properties, molecular docking and dynamic simulation insights
- TweTriS
- A comparative molecular dynamics-phase-field modeling approach to brittle fracture
- Automated parameterization of intermolecular pair potentials using global optimization techniques
- \textit{In silico} analysis of \textit{plasmodium falciparum} CDPK5 protein through molecular modeling, docking and dynamics
- Insights into the interaction of key biofilm proteins in \textit{Pseudomonas aeruginosa} PAO1 with TiO\(_2\) nanoparticle: an \textit{in silico} analysis
- Coupled Navier-Stokes - molecular dynamics simulations using a multi-physics flow simulation framework
- Fast analytical methods for macroscopic electrostatic models in biomolecular simulations
- A meshless discretization method for Markov state models applied to explicit water peptide folding simulations
- A data-driven framework for sparsity-enhanced surrogates with arbitrary mutually dependent randomness
- Molecular dynamics study of multicomponent droplet dissolution in a sparingly miscible liquid
- Investigating protein-protein and protein-ligand interactions by molecular dynamics simula\-tions
- Combining stochastic and deterministic approaches within high efficiency molecular simulations
- Classical investigation of long-range coherence in biological systems
- Convergence analysis of truncated incomplete Hessian Newton minimization method and application in biomolecular potential energy minimization
- Computer modeling of binding of diverse weak toxins to nicotinic acetylcholine receptors
- High-performance large-scale atomistic simulation of thin films deposition
- A Random Batch Ewald Method for Particle Systems with Coulomb Interactions
- AMINO
- Normal mode dynamics of voltage-gated \(\mathrm{K}^+\) channels: gating principle, opening mechanism, and inhibition
- Numerical aspect of large-scale electronic state calculation for flexible device material
- Metadynamics study of mutant human interferon-gamma forms
- Molecular dynamics simulations of the full-length prion protein
- Molecular dynamics study of the fibril elongation of the prion protein fragment PrP106-126
- GANM: A protein-ligand docking approach based on genetic algorithm and normal modes
- Molecular insights of the G2019S substitution in LRRK2 kinase domain associated with Parkinson's disease: A molecular dynamics simulation approach
- Generalized Fickian approach for phase separating fluid mixtures in smoothed particle hydrodynamics
- Orientations of special water dipoles that accelerate water molecules exiting from carbon nanotube
- A short note on the fast evaluation of dihedral angle potentials and their derivatives
- Reactive molecular dynamics: numerical methods and algorithmic techniques
- Virtual model validation of complex multiscale systems: applications to nonlinear elastostatics
- Nose-Hoover thermostat length effect on thermal conductivity of single wall carbon nanotubes
- Analyzing effects of naturally occurring missense mutations
- Molecular dynamics simulation of HIV fusion inhibitor T-1249: insights on peptide-lipid interac\-tion
- Spectral accuracy in fast Ewald-based methods for particle simulations
- A semi-analytical approach to molecular dynamics
- A novel approach for large-scale polypeptide folding based on elastic networks using continuous optimization
- Protein interaction network analysis -- approach for potential drug target identification in \textit{Mycobacterium tuberculosis}
- Progress in developing Poisson-Boltzmann equation solvers
- Why does \(\beta \)-secretase zymogen possess catalytic activity? Molecular modeling and molecular dynamics simulation studies
- Molecular Dynamics Performance Evaluation with Modern Computer Architecture
- The GROMACS and NAMD software packages comparison.
- Folding of SAM-II riboswitch explored by replica-exchange molecular dynamics simulation
- Length scale effect on the buckling behavior of a graphene sheets using modified couple stress theory and molecular dynamics method
- A hybrid lattice Boltzmann-molecular dynamics-immersed boundary method model for the simulation of composite foams
- Molecular modeling, simulation and virtual screening of ribosomal phosphoprotein P1 from \textit{Plasmodium falciparum}
- Molecular modeling and molecular dynamics simulations of GPI 14 in \textit{Leishmania major}: insight into the catalytic site for active site directed drug design
- Zonal methods for the parallel execution of range-limited \(N\)-body simulations
- Efficient implementation of the many-body reactive bond order (REBO) potential on GPU
- B-spline tight frame based force matching method
- Coarse-grained molecular dynamics modeling of DNA -- carbon nanotube complexes
- Molecular dynamics. With deterministic and stochastic numerical methods
- A boundary element formulation of protein electrostatics with explicit ions
- A theoretical framework for the biophysics of tubulins
- Multiscale Hybrid Modeling of Proteins in Solvent: SARS-CoV2 Spike Protein as Test Case for Lattice Boltzmann – All Atom Molecular Dynamics Coupling
- Massively parallel Monte Carlo for many-particle simulations on GPUs
- The interlayer shear effect on graphene multilayer resonators
- Task-based parallel computation of the density matrix in quantum-based molecular dynamics using graph partitioning
- Molecular dynamics simulation of heat transfer and stresses in thin films caused by a short laser pulse
- Molecular dynamics simulation of peeling a DNA molecule on substrate
- IMD
- AMBER
- MPICH-G2
- OOMPAA
- GSHMC
- GAMESS
- NAMD
- TINKER
- WebMO
- APBS
- CHARMM
- LAMMPS
- CPMD
- DESMOND
- PLUMED
- MCELL
- AdResS
- ESPResSo
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