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We study experimentally and numerically the motion of a self-phoretic active particle in two-dimensional (2D) loosely-packed colloidal crystals at fluid interfaces. Two scenarios emerge depending on the interaction between the active…
Molecular dynamics simulations have been performed on pure liquid water, aqueous solutions of sodium chloride, and polymer solutions exposed to a strong external electric field with the goal to gain molecular insight into the structural…
We present a quantum algorithm based on the Tensor-Train Thermo-Field Dynamics (TT-TFD) method to simulate the open quantum system dynamics of intramolecular charge transfer modulated by an optical cavity on noisy intermediate-scale quantum…
We study the dynamical correlation functions and heat conduction for the simplest model of quasi one-dimensional (1d) dielectric crystal i.e. a chain of classical particles coupled by quadratic and cubic intersite potential. Even in the…
We investigate proteins within heterogeneous cell membranes where non-equilibrium phenomena arises from spatial variations in concentration and temperature. We develop simulation methods building on non-equilibrium statistical mechanics to…
A novel combination of discontinuous molecular dynamics and the Langevin equation, together with an intermediate-resolution model, are used to carry out long (several $\mu$s) simulation and study folding transition and transport of proteins…
The electrochemical permeation test is one of the most used methods for characterising hydrogen diffusion in metals. The flux of hydrogen atoms registered in the oxidation cell might be fitted to obtain apparent diffusivities. The magnitude…
Atomistic simulations of heat transport in complex materials are costly and hard to converge. This has led to the development of several noise-reduction techniques applicable to equilibrium molecular-dynamics (MD) simulations. We analyze…
We study reversible deterministic dynamics of classical charged particles on a lattice with hard-core interaction. It is rigorously shown that the system exhibits three types of transport phenomena, ranging from ballistic, through diffusive…
The dynamics of colloidal particles in potential energy landscapes have mainly been investigated theoretically. In contrast, here we discuss the experimental realization of potential energy landscapes with the help of light fields and the…
We present one-dimensional simulation results for the cold atom tunneling experiments by the Heidelberg group [G. Z\"urn {\em{et al.}}, Phys. Rev. Lett. {\bf{108}}, 075303 (2012) and G. Z\"urn {\em{et al.}}, Phys. Rev. Lett. {\bf{111}},…
We present a new model for the dynamics of the presynaptic intracellular calcium concentration in neurons evoked by various stimulation protocols. The aim of the model is twofold: We want to discuss the calcium transients during and after…
A double-stranded system, modeled by a Frenkel-Kontorova lattice, is studied through nonequilibrium molecular dynamics simulations. We have investigated the thermal conductance influenced by the intra-chain interaction as well as by the…
We employ two different atomistic methods to investigate solute-defect interactions in nanosized palladium-hydrogen (Pd-H) systems across multiple time scales. The first method, referred to as Diffusive Molecular Dynamics (DMD), focuses on…
In this article we address the study of ion charge transport in the biological channels separating the intra and extracellular regions of a cell. The focus of the investigation is devoted to including thermal driving forces in the…
Aims. We probe the effect of turbulent diffusion on the chemistry at the interface between a cold neutral medium (CNM) cloudlet and the warm neutral medium (WNM). Methods. We perform moving grid, multifluid, 1D, hydrodynamical simulations…
Computational modeling is usually applied to aid experimental exploration of advanced materials to better understand the fundamental plasticity mechanisms during mechanical testing. In this work, we perform Molecular dynamics (MD)…
Machine-learned interatomic potentials have transformed computational research in the physical sciences. Recent atomistic `foundation' models have changed the field yet again: trained on many different chemical elements and domains, these…
In the present study, the nuclear quantum effects (NQEs) on proton diffusivity in oxides were evaluated by molecular dynamics (MD) simulations with the quantum thermal bath (QTB) based on the Langevin dynamics. We employed the proton…
We explore excitation transport within a one-dimensional chain of atoms where the atomic transition dipoles are coupled to the free radiation field. When the atoms are separated by distances smaller or comparable to the wavelength of the…