Related papers: Grand-canonical-like molecular-dynamics simulation…
Radiative transfer is a notoriously difficult and computationally demanding problem. Yet, it is an indispensable ingredient in nearly all astrophysical and cosmological simulations. Choosing an appropriate discretization scheme is a crucial…
This paper deals also with a problem of gas absorption accompanied by an instantaneous, irreversible reaction in the liquid layer. The well-known methods for calculating such processes are based usually on the certain amendments to…
We develop analytic approximations to the density evolution of prestellar cores, based on the results of hydrodynamical simulations. We use these approximations as input for a time-dependent gas-grain chemical code to investigate the…
The reaction-diffusion master equation (RDME) is a model that allows for efficient on-lattice simulation of spatially resolved stochastic chemical kinetics. Compared to off-lattice hard-sphere simulations with Brownian Dynamics (BD) or…
We present an ab initio molecular dynamics (MD) investigation of the tautomeric equilibrium for aqueous solutions of glycine and acetone at realistic experimental conditions. Metadynamics is used to accelerate proton migration among…
We previously developed an algorithm, called resolution exchange, which improves canonical sampling of atomic resolution models by swapping conformations between high- and low-resolution simulations[1]. Here, we demonstrate a generally…
Quantum geometrical molecular dynamics provides a quantum geometric picture for understanding reactive dynamics, especially excited-state conical intersection dynamics, and also a numerically exact method for strongly correlated…
We present a method to estimate the transition rates of molecular systems under different environmental conditions which cause the formation or the breaking of bonds and require the sampling of the Grand Canonical Ensemble. For this…
We present new methods for radiative transfer on hierarchial grids. We develop a new method for calculating the scattered flux that employs the grid structure to speed up the computation. We describe a novel subiteration algorithm that can…
Gravitational instabilities naturally give rise to multi-scale structure, which is difficult for traditional Eulerian hydrodynamic methods to accurately evolve. This can be circumvented by adaptively adding resolution (in the form of…
We present an algorithm for solving the radiative transfer problem on massively parallel computers using adaptive mesh refinement and domain decomposition. The solver is based on the method of characteristics which requires an adaptive…
Compressed Sensing (CS) facilitates rapid image acquisition by selecting a small subset of measurements sufficient for high-fidelity reconstruction. Adaptive CS seeks to further enhance this process by dynamically choosing future…
We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a…
For a detailed understanding of chemical processes in nature and industry, we need accurate models of chemical reactions in complex environments. While Eyring transition state theory is commonly used for modeling chemical reactions, it is…
Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a…
Large-scale first principles molecular dynamics are crucial for simulating complex processes in chemical, biomedical, and materials sciences. However, the unfavorable time complexity with respect to system sizes leads to prohibitive…
We discuss the computational performance of the adaptive resolution technique in molecular simulation when it is compared with equivalent full coarse-grained and full atomistic simulations. We show that an estimate of its efficiency, within…
Implicit time integration is key to robustly simulating stiff materials and large deformations, but its performance is often dominated by repeatedly solving large linear systems. Adaptive coarsening can reduce this cost by concentrating…
We present an adaptive multiresolution method for the numerical simulation of ideal magnetohydrodynamics in two space dimensions. The discretization uses a finite volume scheme based on a Cartesian mesh and an explicit compact Rung-Kutta…
The Adaptive Multilevel Splitting (AMS) algorithm is a powerful and versatile method for the simulation of rare events. It is based on an interacting (via a mutation-selection procedure) system of replicas, and depends on two integer…