相关论文: Coarse Grained Computations for a Micellar System
A new procedure for coarse-graining dynamical triangulations is presented. The procedure provides a meaning for the relevant value of observables when "probing at large scales", e.g. the average scalar curvature. The scheme may also be…
We study coarse-graining methods for stochastic differential equations. In particular we consider averaging and a type of projection operator method, sometimes referred to as effective dynamic via conditional expectations. The projection…
Equilibrium aspects of molecular recognition of rigid biomolecules are investigated using coarse-grained lattice models. The analysis is carried out in two stages. First an ensemble of probe molecules is designed with respect to the target…
Machine-learned coarse-grained (CG) models have the potential for simulating large molecular complexes beyond what is possible with atomistic molecular dynamics. However, training accurate CG models remains a challenge. A widely used…
Coarse-grained (CG) modeling simplifies molecular systems by mapping groups of atoms into representative units. However, traditional CG approaches rely on fixed mapping rules, which limit their ability to handle diverse chemical systems and…
The computer-assisted modeling of re-entrant production lines, and, in particular, simulation scalability, is attracting a lot of attention due to the importance of such lines in semiconductor manufacturing. Re-entrant flows lead to…
As a complementary tool to laboratory experiments, discrete numerical simulation, applied to granular materials, provides valuable information on the grain and contact scale microstructure, thereby enabling one to better understand the…
Computational physics is an important tool for analysing, verifying, and -- at times -- replacing physical experiments. Nevertheless, simulating quantum systems and analysing quantum data has so far resisted an efficient classical treatment…
We have developed and implemented a numerical evolution scheme for a class of stochastic problems in which the temporal evolution occurs on widely-separated time scales, and for which the slow evolution can be described in terms of a small…
Proposed here is a dynamic Monte-Carlo algorithm that is efficient in simulating dense systems of long flexible chain molecules. It expands on the configurational-bias Monte-Carlo method through the simultaneous generation of a large set of…
In soft matter systems the local displacement field can be accessed directly by video microscopy enabling one to compute local strain fields and hence the elastic moduli using a coarse-graining procedure. We study this process for a simple…
Two very basic constructions involving experimental procedures are the formation of coarse-grained versions of experiments, and the formation of branching sequential experiments. The latter allow for the conditioning of states on the…
Coarse-graining (CG) enables molecular dynamics (MD) simulations of larger systems and longer timescales that are otherwise infeasible with atomistic models. Machine learning potentials (MLPs), with their capacity to capture many-body…
Coarse-grained molecular dynamics often sacrifices accuracy and transferability for computational efficiency, but the use of machine learned potentials is helping coarse-grained models attain performance on par with atomistic molecular…
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…
Gomez proposes a formal and systematic approach for characterizing stochastic global optimization algorithms. Using it, Gomez formalizes algorithms with a fixed next-population stochastic method, i.e., algorithms defined as stationary…
We present a new adaptive resolution technique for efficient particle-based multiscale molecular dynamics (MD) simulations. The presented approach is tailor-made for molecular systems where atomistic resolution is required only in spatially…
This study presents a coarse-grained molecular dynamics simulation model to investigate the process of oxidative aging in polymers. The chemical aging effect is attributed to the auto-oxidation mechanism, which is initiated by radicals,…
All-atom and coarse-grained molecular dynamics are two widely used computational tools to study the conformational states of proteins. Yet, these two simulation methods suffer from the fact that without access to supercomputing resources,…
The issue of the parameterization of small-scale dynamics is addressed in the context of passive-scalar turbulence. The basic idea of our strategy is to identify dynamical equations for the coarse-grained scalar dynamics starting from…