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Multiscale simulation methods have been developed based on the local stress sampling strategy and applied to three flow problems with different difficulty levels: (a) general flow problems of simple fluids, (b) parallel (one-dimensional)…
We use a novel non-equilibrium algorithm to simulate steady-state fluid transport through a two-dimensional (2D) membrane due to a concentration gradient by molecular dynamics (MD) for the first time. We confirm that, as required by the…
First principles molecular dynamics simulation protocol is established using revised functional of Perdew-Burke-Ernzerhof (revPBE) in conjunction with Grimme's third generation of dispersion (D3) correction to describe properties of water…
In this paper, a three-dimensional numerical solver is developed for suspensions of rigid and soft particles and droplets in viscoelastic and elastoviscoplastic (EVP) fluids. The presented algorithm is designed to allow for the first time…
Oxide-water interfaces govern a wide range of physical and chemical processes fundamental to many fields like catalysis, geochemistry, corrosion, electrochemistry, and sensor technology. Near solid oxide surfaces, water behaves differently…
We present a novel up-resing technique for generating high-resolution liquids based on scene flow estimation using deep neural networks. Our approach infers and synthesizes small- and large-scale details solely from a low-resolution…
This paper outlines a numerical algorithm that could be used for simulating full 3D dynamics of magnetic fluid droplet shapes in external magnetic fields, by solving boundary integral equations. The algorithm works with arbitrary droplet…
The structure and function of biological molecules are strongly influenced by the water and dissolved ions that surround them. This aqueous solution (solvent) exerts significant electrostatic forces in response to the biomolecule's…
This paper investigates the problems large-scale distributed composite convex optimization, with motivations from a broad range of applications, including multi-agent systems, federated learning, smart grids, wireless sensor networks,…
Molecular dynamics simulations are a powerful tool to study diffusion processes in battery electrolyte and electrode materials. From a single molecular dynamics simulation many properties relevant to diffusion can be obtained, including the…
We extend the application of the adaptive resolution technique (AdResS) to liquid systems composed of alkane chains of different lengths. The aim of the study is to develop and test the modifications of AdResS required in order to handle…
Experiment Directed Simulations (EDS) is a method within a class of techniques seeking to improve molecular simulations by minimally biasing the system Hamiltonian to reproduce certain experimental observables. In a previous application of…
Solvation free energies are efficiently predicted by molecular density functionnal theory (MDFT) if one corrects the overpressure introduced by the usual homogeneous reference fluid approximation. Sergiievskyi et al. [Sergiievskyi et al.,…
Molecular simulations of the forced unfolding and refolding of biomolecules or molecular complexes allow to gain important kinetic, structural and thermodynamic information about the folding process and the underlying energy landscape. In…
Electrochemical interfaces are crucial in catalysis, energy storage, and corrosion, where their stability and reactivity depend on complex interactions between the electrode, adsorbates, and electrolyte. Predicting stable surface structures…
A reliable prediction of 3D protein structures from sequence data remains a big challenge due to both theoretical and computational difficulties. We have previously shown that our kinetostatic compliance method (KCM) implemented into the…
Continuum solvent models have become a standard technique in the context of electronic structure calculations, yet, no implementations have been reported capable to perform molecular dynamics at solid-liquid interfaces. We propose here such…
Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations…
The growing interest in the dynamical properties of colloidal suspensions, both in equilibrium and under an external drive such as shear or pressure flow, requires the development of accurate methods to correctly include hydrodynamic…
The molecular mechanism of the solvent motion that is required to instigate the protein structural relaxation above a critical hydration level or transition temperature has yet to be determined. In this work we use quasi-elastic neutron…