Related papers: Coarse-graining molecular dynamics models using an…
Methods for electronic structure based on Gaussian and molecular orbital discretizations offer a well established, compact representation that forms much of the foundation of correlated quantum chemistry calculations on both classical and…
A novel scheme to simulate the evolution of a restricted set of observables of a quantum system is proposed. The set comprises the spectrum-generating algebra of the Hamiltonian. The idea is to consider a certain open-system evolution,…
Leveraging nonlinear parametrizations for model reduction can overcome the Kolmogorov barrier that affects transport-dominated problems. In this work, we build on the reduced dynamics given by Neural Galerkin schemes and propose to…
Although major advances have been achieved over the past decades for the reduction and identification of linear systems, deriving nonlinear low-order models still is a chal- lenging task. In this work, we develop a new data-driven framework…
The parametrization of coarse-grained (CG) simulation models for molecular systems often aims at reproducing static properties alone. The reduced molecular friction of the CG representation usually results in faster, albeit inconsistent,…
Electrostatic interactions between macroions largely govern the equilibrium thermodynamic and dynamical properties of charge-stabilized colloidal suspensions and polyelectrolyte solutions. Predicting the properties of such complex,…
Coarse-grained descriptions of dislocation motion in crystalline metals inherently represent a loss of information regarding dislocation-dislocation interactions. In the present work, we consider a coarse-graining framework capable of…
We present a novel learning framework that consistently embeds underlying physics while bypassing a significant drawback of most modern, data-driven coarse-grained approaches in the context of molecular dynamics (MD), i.e., the availability…
Neurocognitive disorders, such as Alzheimer's and Parkinson's, have a wide social impact. These proteinopathies involve misfolded proteins accumulating into neurotoxic aggregates. Mathematical and computational models describing the…
We develop a machine-learning method for coarse-graining condensed-phase molecular systems using anisotropic particles. The method extends currently available high-dimensional neural network potentials by addressing molecular anisotropy. We…
A general framework for the numerical approximation of evolution problems is presented that allows to preserve exactly an underlying Hamiltonian- or gradient structure. The approach relies on rewriting the evolution problem in a particular…
A computational tool for coarse-graining nonlinear systems of ordinary differential equations in time is discussed. Three illustrative model examples are worked out that demonstrate the range of capability of the method. This includes the…
We present an effective evolution equation for a coarse-grained distribution function of a long-range-interacting system preserving the symplectic structure of the non-collisional Boltzmann, or Vlasov, equation. We first derive a general…
Bottom-up coarse-grained (CG) modeling expands the spatial and temporal scales of molecular simulation by seeking a reduced, thermodynamically consistent representation of an atomistic model. Developments in CG theory have largely focused…
We present a hybrid continuous and discontinuous Galerkin spectral element approximation that leverages the advantages of each approach. The continuous Galerkin approximation is used on interior element faces where the equation properties…
We present and analyze a discontinuous Galerkin method for the numerical modeling of a Kelvin-Voigt thermo/poro-viscoelastic problem. We present the derivation of the model and we develop a stability analysis in the continuous setting that…
We propose a dynamic coarse-graining (CG) scheme for mapping heterogeneous polymer fluids onto extremely CG models in a dynamically consistent manner. The idea is to use as target function for the mapping a wave-vector dependent mobility…
The first paper of this series [J. Chem. Phys. 158, 034103 (2023)] demonstrated that excess entropy scaling holds for both fine-grained and corresponding coarse-grained (CG) systems. Despite its universality, a more exact determination of…
The Galerkin difference (GD) basis is a set of continuous, piecewise polynomials defined using a finite difference like grid of degrees of freedom. The one dimensional GD basis functions are naturally extended to multiple dimensions using…
Coarse-Graining (CG) models are low resolution approximation of high resolution models, such as all-atomic (AA) models. An effective CG model is expected to reproduce equilibrium values of sufficient physical quantities of its AA model,…