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We consider two phase accretion disk-corona models for active galactic nuclei and some X-ray binaries. We describe in detail how one can exactly solve the polarized radiative transfer and Comptonization using the iterative scattering…
A temperature (T)-dependent coarse-grained (CG) Hamiltonian of polyethylene glycol/oxide (PEG/PEO) in aqueous solution is reported to be used in implicit-solvent material models in a wide temperature (i.e., solvent quality) range. The…
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…
To acquire the ability to numerically study the rheology of particulate two-phase flows that lack scale separation, we present a general method to average or coarse-grain the equations of motion of a mixture of a continuous fluid of…
We propose a simple scheme to construct composition-dependent interatomic potentials for multicomponent systems that when superposed onto the potentials for the pure elements can reproduce not only the heat of mixing of the solid solution…
While there have been many developments in computational probes of both strongly-correlated molecular systems and machine-learning accelerated molecular dynamics, there remains a significant gap in capabilities in simulating accurate…
Molecular dynamics (MD) simulations employing classical force fields constitute the cornerstone of contemporary atomistic modeling in chemistry, biology, and materials science. However, the predictive power of these simulations is only as…
Large classes of materials systems in physics and engineering are governed by magnetic and electrostatic interactions. Continuum or mesoscale descriptions of such systems can be cast in terms of integral equations, whose direct…
Despite the modern level of development of computational chemistry methods and techno-logical progress, fast and accurate determination of solvation free energy remains a huge problem for physical chemists. In this paper, we describe two…
Coarse-graining has become an area of tremendous importance within many different research fields. For molecular simulation, coarse-graining bears the promise of finding simplified models such that long-time simulations of large-scale…
The zero-range potentials of the radial Schrodinger equation are investigated from a point of Darboux transformations scheme. The dressing procedure is realized as a sequence of Darboux transformations in a way similar to that used to…
We present a dynamic coarse-graining technique that allows to simulate the mechanical unfolding of biomolecules or molecular complexes on experimentally relevant time scales. It is based on Markov state models (MSM), which we construct from…
We formulate a simple solvation potential based on a coarsed-grain representation of amino acids with two spheres modeling the $C_\alpha$ atom and an effective side-chain centroid. The potential relies on a new method for estimating the…
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…
Simulations of colloidal suspensions consisting of mesoscopic particles and smaller species such as ions or depletants are computationally challenging as different length and time scales are involved. Here, we introduce a machine learning…
We report an approach to obtain effective pair potentials which describe the structure of two-dimensional systems of active Brownian particles. The pair potential is found by an inverse method, which matches the radial distribution function…
Although RNAs play many cellular functions little is known about the dynamics and thermodynamics of these molecules. In principle, all-atom molecular dynamics simulations can investigate these issues, but with current computer facilities,…
A hallmark of meso-scale interfacial fluids is the multi-faceted, scale-dependent interfacial energy, which often manifests different characteristics across the molecular and continuum scale. The multi-scale nature imposes a challenge to…
One key factor that limits the predictive power of molecular dynamics simulations is the accuracy and transferability of the input force field. Force fields are challenged by heterogeneous environments, where electronic responses give rise…
A numerical method is presented for first-principle simulations of charged colloidal dispersions in electrolyte solutions. Utilizing a smoothed profile for colloid-solvent boundaries, efficient mesoscopic simulations are enabled for…