Related papers: Hessian Matching for Machine-Learned Coarse-Graine…

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…

-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…

We present the construction of molecular force fields for small molecules (less than 25 atoms) using the recently developed symmetrized gradient-domain machine learning (sGDML) approach [Chmiela et al., Nat. Commun. 9, 3887 (2018); Sci.…

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.…

Conformational sampling of biomolecules using molecular dynamics simulations often produces large amount of high dimensional data that makes it difficult to interpret using conventional analysis techniques. Dimensionality reduction methods…

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…

Multiscale molecular modeling is widely applied in scientific research of molecular properties over large time and length scales. Two specific challenges are commonly present in multiscale modeling, provided that information between the…

Coarse grain (CG) molecular dynamics (MD) can simulate systems inaccessible to fine grain (FG) MD simulations. A CG simulation decreases the degrees of freedom by mapping atoms from an FG representation into agglomerate CG particles. The FG…

Optimizing with group sparsity is significant in enhancing model interpretability in machining learning applications, e.g., feature selection, compressed sensing and model compression. However, for large-scale stochastic training problems,…

Gaussian processes (GPs) have gained popularity as flexible machine learning models for regression and function approximation with an in-built method for uncertainty quantification. However, GPs suffer when the amount of training data is…

We introduce an unsupervised clustering algorithm to improve training efficiency and accuracy in predicting energies using molecular-orbital-based machine learning (MOB-ML). This work determines clusters via the Gaussian mixture model (GMM)…

This paper proposes a new approach for the calibration of material parameters in local elastoplastic constitutive models. The calibration is posed as a constrained optimization problem, where the constitutive model evolution equations for a…

Coarse-grained (CG) molecular models of proteins can substantially increase the time and length scales accessible to molecular dynamics simulations of proteins, but recovery of accurate all-atom (AA) ensembles from CG simulation…

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…

The paper studies the solution of stochastic optimization problems in which approximations to the gradient and Hessian are obtained through subsampling. We first consider Newton-like methods that employ these approximations and discuss how…

Integrating machine learning into reactive chemistry, materials discovery, and drug design is revolutionizing the development of novel molecules and materials. Machine Learning Interatomic Potentials (MLIPs) accurately predict energies and…

Coarse-grained models are a core computational tool in theoretical chemistry and biophysics. A judicious choice of a coarse-grained model can yield physical insight by isolating the essential degrees of freedom that dictate the…

Molecular dynamics (MD) simulations provide atomistic insight into biomolecular systems but are often limited by high computational costs required to access long timescales. Coarse-grained machine learning models offer a promising avenue…

Particle identification in large high-energy physics experiments typically relies on classifiers obtained by combining many experimental observables. Predicting the probability density function (pdf) of such classifiers in the multivariate…

We introduce a novel stochastic variational inference method for Gaussian process ($\mathcal{GP}$) regression, by deriving a posterior over a learnable set of coresets: i.e., over pseudo-input/output, weighted pairs. Unlike former free-form…