Related papers: Coarse-graining the calcium dynamics on a stochast…
We study an element agglomeration coarsening strategy that requires data redistribution at coarse levels when the number of coarse elements becomes smaller than the used computational units (cores). The overall procedure generates coarse…
The dynamical cluster approximation (DCA) and its DCA$^+$ extension use coarse-graining of the momentum space to reduce the complexity of quantum many-body problems, thereby mapping the bulk lattice to a cluster embedded in a dynamical…
Monte Carlo simulations are performed to study structure and dynamics of a protein CoVE in random media generated by a random distribution of barriers at concentration c with a coarse-grained model in its native (low temperature) and…
The Dynamical Graph Grammar (DGG) formalism can describe complex system dynamics with graphs that are mapped into a master equation. An exact stochastic simulation algorithm may be used, but it is slow for large systems. To overcome this…
We have designed an improved algorithm that enables us to simulate the chemistry of cold dense interstellar clouds with a full gas-grain reaction network. The chemistry is treated by a unified microscopic-macroscopic Monte Carlo approach…
An efficient method for the simulation of strained heteroepitaxial growth with intermixing using kinetic Monte Carlo is presented. The model used is based on a solid-on-solid bond counting formulation in which elastic effects are…
The unfolding of molecular complexes or biomolecules under the influence of external mechanical forces can routinely be simulated with atomistic resolution. To obtain a match of the characteristic time scales with those of experimental…
In many far-from-equilibrium biological systems, energy injected by irreversible processes at microscopic scales propagates to larger scales to fulfill important biological functions. But given dissipative dynamics at the microscale, how…
Hybrid multiscale modelling has emerged as a useful framework for modelling complex biological phenomena. However, when accounting for stochasticity in the internal dynamics of agents, these models frequently become computationally…
The hard square lattice gas model on a square lattice is known to undergo a continuous phase transition from a low density fluid-like phase to high density phase with columnar or smectic order. We estimate the critical activity $z_c$ by…
We present a multiscale continuous Galerkin (MSCG) method for the fast and accurate stochastic simulation and optimization of time-harmonic wave propagation through photonic crystals. The MSCG method exploits repeated patterns in the…
This work presents a novel framework governing the development of an efficient, accurate, and transferable coarse-grained (CG) model of a polyether material. The proposed framework combines the two fundamentally different classical…
We consider a coarse-grained (CG) model with pairwise interactions, suitable to describe low-density solutions of star-branched polymers of functionality $f$. Each macromolecule is represented by a CG molecule with $(f+1)$ interaction…
A recent reformulation [1] of the problem of Coulomb gases in the presence of a dynamical dielectric medium showed that finite temperature simulations of such systems can be accomplished on the basis of completely local Hamiltonians on a…
In computational materials science, coarse-graining approaches often lack a priori uncertainty quantification (UQ) tools that estimate the accuracy of a reduced-order model before it is calibrated or deployed. This is especially the case in…
One of the most pressing issues for loop quantum gravity and spin foams is the construction of the continuum limit. In this paper, we propose a systematic coarse-graining scheme for three-dimensional lattice gauge models including spin…
We present a multi-lattice kinetic Monte Carlo (kMC) approach that efficiently describes the atomistic dynamics of morphological transitions between commensurate structures at crystal surfaces. As an example we study the reduction of a…
Results are presented from numerical experiments aiming at the computation of stochastic phase-field models for phase transformations by coarse-graining molecular dynamics. The studied phase transformations occur between a solid crystal and…
Molecular dynamics (MD) simulations provide detailed insight into atomic-scale mechanisms but are inherently restricted to small spatio-temporal scales. Coarse-grained molecular dynamics (CGMD) techniques allow simulations of much larger…
In random systems consisting of grains with size distributions the transport properties are difficult to explore by network models. However, the concentration dependence of effective conductivity and its critical properties can be…