Related papers: DeePCG: constructing coarse-grained models via dee…

The accuracy and efficiency of a coarse-grained (CG) force field are pivotal for high-precision molecular simulations of large systems with complex molecules. We present an automated mapping and optimization framework for molecular…

A versatile and transferable coarse-grained (CG) model was developed to investigate the self-assembly of two ubiquitous methacrylate-based copolymers: poly(ethylene oxide-b-methylmethacrylate) (PEO-b-PMMA) and poly(ethylene…

Modeling a high-dimensional Hamiltonian system in reduced dimensions with respect to coarse-grained (CG) variables can greatly reduce computational cost and enable efficient bottom-up prediction of main features of the system for many…

In this study, we propose a novel deep learning-based method to predict an optimized structure for a given boundary condition and optimization setting without using any iterative scheme. For this purpose, first, using open-source topology…

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…

Recently, the development of machine learning (ML) potentials has made it possible to perform large-scale and long-time molecular simulations with the accuracy of quantum mechanical (QM) models. However, for high-level QM methods, such as…

Using machine learning, we explore the utility of various deep neural networks (NN) when applied to high harmonic generation (HHG) scenarios. First, we train the NNs to predict the time-dependent dipole and spectra of HHG emission from…

We propose a data-driven framework for identifying coarse-grained (CG) Lennard-Jones (LJ) potential parameters in confined systems for simple liquids. Our approach involves the use of a Deep Neural Network (DNN) that is trained to…

The prediction of molecular properties is a crucial task in the field of material and drug discovery. The potential benefits of using deep learning techniques are reflected in the wealth of recent literature. Still, these techniques are…

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…

Recent research has used deep learning to develop partial differential equation (PDE) models in science and engineering. The functional form of the PDE is determined by a neural network, and the neural network parameters are calibrated to…

Deep Gaussian processes (DGPs) are multi-layer hierarchical generalisations of Gaussian processes (GPs) and are formally equivalent to neural networks with multiple, infinitely wide hidden layers. DGPs are probabilistic and non-parametric…

We introduce a machine-learning-based coarse-grained molecular dynamics (CGMD) model that faithfully retains the many-body nature of the inter-molecular dissipative interactions. Unlike common empirical CG models, the present model is…

Effective and powerful methods for denoising real electrocardiogram (ECG) signals are important for wearable sensors and devices. Deep Learning (DL) models have been used extensively in image processing and other domains with great success…

Deep generative models (DGMs) are data-eager because learning a complex model on limited data suffers from a large variance and easily overfits. Inspired by the classical perspective of the bias-variance tradeoff, we propose regularized…

In the present article, novel Coarse-Graining (CG) algorithms for the Eulerian-Lagrangian (EL) simulation of particle-laden flows are proposed. These include different variants of Reproducing Kernel Particle Methods (RKPM) and an extended…

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…

In recent years, simulation methods based on the scaling of atomic potential functions, such as quasi-coarse-grained dynamics and coarse-grained dynamics, have shown promising results for modeling crystalline systems at multiple scales.…

Machine-learning-based interatomic potential energy surface (PES) models are revolutionizing the field of molecular modeling. However, although much faster than electronic structure schemes, these models suffer from costly computations via…

Recent advances in equivariant graph neural networks (GNNs) have made deep learning amenable to developing fast surrogate models to expensive ab initio quantum mechanics (QM) approaches for molecular potential predictions. However, building…