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The textbook picture of nerve activity is that of a propagating voltage pulse driven by electrical currents through ion channel proteins, which are gated by changes in voltage, temperature, pressure or by drugs. All function is directly…
Reaction equations of homogeneously mixed pollutants in the atmosphere can lead to non-stationary periodic solutions. It is important to know in which respect these solutions are modified under the influence of the atmospheric currents. We…
Depletion forces play a role in the compaction and de-compation of chromosomal material in simple cells but it remains debatable whether they are sufficient to account for chromosomal collapse. We present coarse-grained molecular dynamics…
A scattering model is developed for ultracold molecular collisions, which allows inelastic processes, chemical reactions, and complex formation to be treated in a unified way. All these scattering processes and various combinations of them…
This study deals with the understanding of hydrogen atom scattering from graphene, a process critical for exploring C-H bond formation and energy transfer during the atom surface collision. In our previous work (J.Chem.Phys \textbf{159},…
The molecular dynamics (MD) simulation study of solvation structure and free energetics in 1-ethyl-3-methylimidazolium chloride and 1-ethyl-3-methylimidazolium hexafluorophosphate using a probe solute in the preceding article [Y. Shim, M.…
Realistic description of patient-specific mechanical properties of clotting dynamics presents a major challenge. Available patient-specific data falls short of robustly characterizing myriads of complex dynamic interactions that happen…
Structure and reaction studies with a method of antisymmetrized molecular dynamics (AMD) were reviewed. Applications of time-independent and time-dependent versions of the AMD were described. In applications of time-independent AMD to…
Most computer simulations of molecular dynamics take place under equilibrium conditions--in a closed, isolated system, or perhaps one held at constant temperature or pressure. Sometimes, extra tensions, shears, or temperature gradients are…
Biomolecular condensates play a crucial role in the spatial organization of living matter. These membrane-less organelles, resulting from liquid-liquid phase separation, operate far from thermodynamic equilibrium, with their size and…
We investigate the coupling of different quantum-embedding approaches with a third molecular-mechanics layer, which can be either polarizable or non-polarizable. In particular, such a coupling is discussed for the multilevel families of…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
The phoretic Brownian dynamics method is shown here to be an effective approach to simulate the properties of colloidal chemophoretic based systems. The method is then optimized to allow for the comparison with results from multiparticle…
We explored the composition dependence of a rather comprehensive set of properties of liquid water-ethanol mixtures by using the isobaric-isothermal molecular dynamics computer simulations. The united atom non-polarizable model from the…
We use machine learning to enable large-scale molecular dynamics (MD) of a correlated electron model under the Gutzwiller approximation scheme. This model exhibits a Mott transition as a function of on-site Coulomb repulsion $U$. The…
We constructed two new models for deuterium and spin-state chemistry for the purpose of modeling the low-temperature environment prevailing in starless and pre-stellar cores. The fundamental difference between the two models is in the…
Conformational dynamics is crucial for ribonucleic acid (RNA) function. Techniques such as nuclear magnetic resonance, cryo-electron microscopy, small- and wide-angle X-ray scattering, chemical probing, single-molecule F\"orster resonance…
Brownian Dynamics algorithms are widely used for simulating soft-matter and biochemical systems. In recent times, their application has been extended to the simulation of coarse-grained models of cellular networks in simple organisms. In…
We report on an investigation of the structural and dynamical properties of n-nonyltrimethylammonium chloride (C9TAC) and erucyl bis [2-hydroxyethyl] methylammonium chloride (EMAC) micelles in aqueous solution. A fully atomistic description…
A quantitative understanding of the evaporative drying kinetics and nucleation rates of aqueous based aerosol droplets is important for a wide range of applications, from atmospheric aerosols to industrial processes such as spray drying.…