Related papers: Coarse-Graining Simulation Approaches for Polymer …

Molecular conformer generation (MCG) is an important task in cheminformatics and drug discovery. The ability to efficiently generate low-energy 3D structures can avoid expensive quantum mechanical simulations, leading to accelerated virtual…

Molecular dynamics (MD) simulation is essential for various scientific domains but computationally expensive. Learning-based force fields have made significant progress in accelerating ab-initio MD simulation but are not fast enough for…

We present a new framework for coarse-graining molecular dynamics models for crystalline solids. The reduction method is based on a Galerkin projection to a subspace, whose dimension is much smaller than that of the full atomistic model.…

We introduce a particle-based simulation method for granular material in interactive frame rates. We divide the simulation into two decoupled steps. In the first step, a relatively small number of particles is accurately simulated with a…

The conjugate gradient (CG) method is an efficient iterative method for solving large-scale strongly convex quadratic programming (QP). In this paper we propose some generalized CG (GCG) methods for solving the $\ell_1$-regularized…

Algebraic multigrid (AMG) methods derive their optimal efficiency from the interplay between a relaxation process and a corresponding coarse grid correction. In many standard formulations, relaxation and coarse-graining are analyzed and…

Coarse-grained (CG) models parameterized using atomistic reference data, i.e., 'bottom up' CG models, have proven useful in the study of biomolecules and other soft matter. However, the construction of highly accurate, low resolution CG…

Coarse-grained molecular dynamics (CGMD) is a technique developed as a concurrent multiscale model that couples conventional molecular dynamics (MD) to a more coarse-grained description of the periphery. The coarse-grained regions are…

Geometric graph neural networks (GNNs) excel at capturing molecular geometry, yet their locality-biased message passing hampers the modeling of long-range interactions. Current solutions have fundamental limitations: extending cutoff radii…

In many numerical schemes, the computational complexity scales non-linearly with the problem size. Solving a linear system of equations using direct methods or most iterative methods is a typical example. Algebraic multi-grid (AMG) methods…

In this paper we investigate the approximation properties of the coarse-graining procedure applied to kinetic Monte Carlo simulations of lattice stochastic dynamics. We provide both analytical and numerical evidence that the hierarchy of…

Image reconstruction by Algebraic Methods (AM) outperforms the transform methods in situations where the data collection procedure is constrained by time, space, and radiation dose. AM algorithms can also be applied for the cases where…

We introduce a generalized machine learning framework to probabilistically parameterize upper-scale models in the form of nonlinear PDEs consistent with a continuum theory, based on coarse-grained atomistic simulation data of mechanical…

Sand production is an important issue for many hydrocarbon recovery applications in unconsolidated reservoirs. The model using the Computational Fluid Dynamics coupled with Discrete Element Method (CFD-DEM) can capture micro-scale features…

We present a coarse-grained model for linear polymers with a tunable number of effective atoms (blobs) per chain interacting by intra- and inter-molecular potentials obtained at zero density. We show how this model is able to accurately…

Coarse-grained (CG) force field models are extensively utilised in material simulations due to their scalability. Traditionally, these models are parameterized using hybrid strategies that integrate top-down and bottom-up approaches;…

We discuss a Bayesian formulation to coarse-graining (CG) of PDEs where the coefficients (e.g. material parameters) exhibit random, fine scale variability. The direct solution to such problems requires grids that are small enough to resolve…

Specialized function gradient computing hardware could greatly improve the performance of state-of-the-art optimization algorithms, e.g., based on gradient descent or conjugate gradient methods that are at the core of control, machine…

Controllable generative models have been widely used to improve the realism of synthetic visual content. However, such models must handle control conditions and content generation computational requirements, resulting in generally low…

-Molecular simulations allow the study of properties and interactions of molecular systems. This article presents an improved version of the Adaptive Resolution Scheme that links two systems having atomistic (also called fine-grained) and…