Related papers: Adaptive Resolution Force Probe Simulations: Coars…
For optimal processing and design of entangled polymeric materials it is important to establish a rigorous link between the detailed molecular composition of the polymer and the viscoelastic properties of the macroscopic melt. We review…
When numerically solving partial differential equations, for a given problem and operating condition, adaptive mesh refinement (AMR) has proven its efficiency to automatically build a discretization achieving a prescribed accuracy at low…
Eyring theory provides a convenient approximation to the rate of a chemical reaction, as it uses only local information evaluated near extremal points of a given potential energy surface. However, in cases of pronounced anharmonicity and…
Understanding grain-surface processes is crucial to interpreting the chemistry of the ISM. However, accurate surface chemistry models are computationally expensive and are difficult to integrate with gas-phase simulations. A new…
Atrophic gastritis is a significant risk factor for developing gastric cancer. The incorporation of machine learning algorithms can efficiently elevate the possibility of accurately detecting atrophic gastritis. Nevertheless, when the…
In this work, we bridge standard adaptive mesh refinement and coarsening on scalable octree background meshes and robust unfitted finite element formulations for the automatic and efficient solution of large-scale nonlinear solid mechanics…
In this work, a coarse-graining method previously proposed by the authors in a companion paper based on solving diffusion equations is applied to CFD-DEM simulations, where coarse graining is used to obtain solid volume fraction, particle…
The solid acids CsH$_2$PO$_4$ and Cs$_7$(H$_4$PO$_4$)(H$_2$PO$_4$)$_8$ pose significant challenges for the simulation of proton transport phenomena. In this work, we use the recently developed machine-learned force field (MLFF) MACE to…
With the help of force spectroscopy, several analytical theories aim at estimating the rate coefficient of folding for various proteins. Nevertheless, a chief bottleneck lies in the fact that there is still no perfect consensus on how does…
In order to understand the physical processes of nanopore experiments at the molecular level, microscopic information from molecular dynamics is greatly needed. Coarse-grained models are a good alternative to classical all-atom models since…
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…
An Adaptive Mesh in Phase Space (AMPS) methodology has been developed for solving multi-dimensional kinetic equations by the discrete velocity method. A Cartesian mesh for both configuration (r) and velocity (v) spaces is produced using a…
Adaptive Molecular Resolution approaches in Molecular Dynamics are becoming relevant tools for the analysis of molecular liquids characterized by the interplay of different physical scales. The essential difference among these methods is in…
Multiscale non-equilibrium physics at large variations of local Knudsen number are encountered in applications of aerospace engineering and micro-electro-mechanical systems, such as high-speed flying vehicles and low pressure of the…
Simulations of condensed matter systems often focus on the dynamics of a few distinguished components but require integrating the dynamics of the full system. A prime example is a molecular dynamics simulation of a (macro)molecule in…
High-dimensional recordings of dynamical processes are often characterized by a much smaller set of effective variables, evolving on low-dimensional manifolds. Identifying these latent dynamics requires solving two intertwined problems:…
Despite the significant increase in computational power, molecular modeling of protein structure using classical all-atom approaches remains inefficient, at least for most of the protein targets in the focus of biomedical research. Perhaps…
We propose a new multi-scale molecular dynamics simulation method which can achieve high accuracy and high sampling efficiency simultaneously without aforehand knowledge of the coarse grained (CG) potential and test it for a biomolecular…
Coarse-grained modeling and efficient computer simulations are critical to the study of complex molecular processes with many degrees of freedom and multiple spatiotemporal scales. Variational implicit-solvent model (VISM) for biomolecular…
Coarse-grained (CG) molecular simulations have become a standard tool to study molecular processes on time- and length-scales inaccessible to all-atom simulations. Parameterizing CG force fields to match all-atom simulations has mainly…