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Viscosity in water from first-principles and deep-neural-network simulations
We report on an extensive study of the viscosity of liquid water at near-ambient conditions, performed within the Green-Kubo theory of linear response and equilibrium ab initio... -
Topological data analysis of superionic conductor silver iodide
Topological data analysis based on persistent homology has been applied to the molecular dynamics simulation for the fast ion-conducting phase (α-phase) of AgI, to show its... -
Free-Energy Surface Prediction by Flying Gaussian Method: Numerical Proof
Biomolecular simulations have a great potential in protein engineering, drug discovery and many other fields. Unfortunately, this method is computationally expensive, so many... -
On the effects of the degrees of freedom on calculating diffusion properties ...
If one carries out a molecular simulation of N particles using periodic boundary conditions, linear momentum is conserved and hence the number of degrees of freedom is set to... -
Investigating finite-size effects in computer simulations of superionic mater...
The effects of the finite size of the simulation box in equilibrium molecular dynamics simulations are investigated for prototypical superionic conductors of different types,... -
Atomistic simulation of carbohydrate-protein complex formation: Hevein-32 domain
Unbiased molecular dynamics simulation was used to simulate systems containing hevein (HEV32) domain and mono-, di- or trisaccharide of GlcNAc. Carbohydrate molecules were... -
The importance of reference frame for pressure at the liquid-vapour interface
This repository has the input files and a guide to recreate the data from "The importance of reference frame for pressure at the liquid-vapour interface"... -
Atomistic simulation of carbohydrate-protein complex formation: Hevein-32 domain
Unbiased molecular dynamics simulation was used to simulate systems containing hevein (HEV32) domain and mono-, di- or trisaccharide of GlcNAc. Carbohydrate molecules were... -
Regioselective 3-O-Substitution of Unprotected Thiodigalactosides: Direct Rou...
Regioselective derivatization of oligosaccharides is a challenging issue in carbohydrate chemistry. A commonly required series of (de)protection steps substantially lowers... -
A variational formulation of the Harris functional as correction to linear-sc...
Accurate descriptions of intermolecular interactions are of great importance in simulations of molecular liquids. We present a novel method that combines in a variational... -
Free-Energy Surface Prediction by Flying Gaussian Method
Molecular simulations are computationally expensive, especially in systems with multiple free energy minima. To address this problem many enhanced sampling techniques have been... -
Molecular dynamics based cohesive law for epoxy-graphene interfaces
Molecular dynamics (MD) simulations are performed to obtain mode I and II fracture energies and cohesive laws for bulk epoxy and interfaces formed between epoxy and single-layer... -
Finite-temperature materials modeling from the quantum nuclei to the hot elec...
Atomistic simulations provide insights into structure-property relations on an atomic size and length scale that are complementary to the macroscopic observables that can be... -
Viscosity in water from first-principles and deep-neural-network simulations
We report on an extensive study of the viscosity of liquid water at near-ambient conditions, performed within the Green-Kubo theory of linear response and equilibrium ab initio... -
Structure and energetics of dye-sensitized NiO interfaces in water from ab-in...
The energy level alignment across solvated molecule/semiconductor interfaces is a crucial property for the correct functioning of dye-sensitized photo-electrodes, where,... -
On the effects of the degrees of freedom on calculating diffusion properties ...
If one carries out a molecular simulation of N particles using periodic boundary conditions, linear momentum is conserved and hence the number of degrees of freedom is set to... -
Property map collective variable as a useful tool for force field correction
Molecular mechanics potentials for small molecules suffer inaccuracies. To apply corrections we used a concept called property map to calculate corrections. It was calculated as... -
Regioselective 3-O-Substitution of Unprotected Thiodigalactosides: Route to S...
Regioselective derivatization of oligosaccharides is a challenging issue in carbohydrate chemistry. A commonly required series of (de)protection steps substantially lowers... -
Data-driven simulation and characterisation of gold nanoparticles melting
We develop efficient, accurate, transferable, and interpretable machine learning force fields for Au nanoparticles, based on data gathered from Density Functional Theory... -
Regioselective 3-O-Substitution of Unprotected Thiodigalactosides: Direct Rou...
Regioselective derivatization of oligosaccharides is a challenging issue in carbohydrate chemistry. A commonly required series of (de)protection steps substantially lowers...
