Related papers: Molecular Dynamics in a Grand Ensemble: Bergmann-L…
A shadow molecular dynamics scheme for flexible charge models is presented, where the shadow Born-Oppenheimer potential is derived from a coarse-grained approximation of range-separated density functional theory. The interatomic potential,…
A lattice-Boltzmann model for the study of the dynamics of oil-water-surfactant mixtures is constructed. The model, which is based on a Ginzburg-Landau theory of amphiphilic systems with a single, scalar order parameter, is then used to…
Liquid chromatography mass spectrometry (LC-MS)-based metabolomics and exposomics aim to measure detectable small molecules in biological samples. The results facilitate hypothesis-generating discovery of metabolic changes and disease…
The general theory of a complex system of nonlinear chemical reactions is a primary language of chemistry that includes chemical engineering and cellular biochemistry. Its significance as an analytical framework, however, has not been fully…
Molecules in equilibrium follow a Boltzmann distribution, making the underlying energy landscape a physically grounded modeling objective. However, such landscapes are difficult to learn from data and, once learned, hard to sample from.…
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…
We are interested in dynamics of a system in an environment, or an open system. Such phenomena like {\it crossover} from Markovian to non-Markovian relaxation and {\it thermal equilibration} are of our interest. Open systems have…
The dynamics of unimolecular photo-triggered reactions can be strongly affected by the surrounding medium. An accurate description of these reactions requires knowing the free energy surface (FES) and the friction felt by the reactants.…
Efforts toward a comprehensive description of behavior have indeed facilitated the development of representation-based approaches that utilize deep learning to capture behavioral information. As behavior complexity increases, the expressive…
The lattice Boltzmann method (LBM) is known to suffer from stability issues when the collision model relies on the BGK approximation, especially in the zero viscosity limit and for non-vanishing Mach numbers. To tackle this problem, two…
Molecular dynamics (MD) simulations are used to investigate $^1$H nuclear magnetic resonance (NMR) relaxation and diffusion of bulk $n$-C$_5$H$_{12}$ to $n$-C$_{17}$H$_{36}$ hydrocarbons and bulk water. The MD simulations of the $^1$H NMR…
Because most chemical or biological experiments are performed under conditions of controlled pressure and temperature, it is important to simulate the isobaric-isothermal ensemble at the atomic level to reveal the microscopic mechanism. By…
Modeling and direct numerical simulation of particle-laden flows have a tremendous variety of applications in science and engineering across a vast spectrum of scales from pollution dispersion in the atmosphere, to fluidization in the…
openCOSMO-RS is an open-source predictive thermodynamic model that can be applied to a broad range of systems in various chemical and biochemical engineering domains. This study focuses on improving openCOSMO-RS by introducing a new…
Agent-based modeling (ABM) is a well-established paradigm for simulating complex systems via interactions between constituent entities. Machine learning (ML) refers to approaches whereby statistical algorithms 'learn' from data on their…
This article concerns numerical simulations of the dynamics of particles immersed in a continuum solvent. As prototypical systems, we consider colloidal dispersions of spherical particles and solutions of uncharged polymers. After a brief…
A collision model (CM) is a framework to describe open quantum dynamics. In its {\it memoryless} version, it models the reservoir $\mathcal R$ as consisting of a large collection of elementary ancillas: the dynamics of the open system…
Mathematical models of transport and reactions in biological systems have been traditionally written in terms of partial differential equations (PDEs) that describe the time evolution of population-level variables. In recent years, the use…
Molecular dynamics (MD) simulations can model the interactions between macromolecules with high spatiotemporal resolution but at a high computational cost. By combining high-throughput MD with Markov state models (MSMs), it is now possible…
Event-driven molecular dynamics simulations are carried out on two rigid body systems which differ in the symmetry of their molecular mass distributions. First, simulations of methane in which the molecules interact via discontinuous…