Related papers: Coarse-graining Algorithms for the Eulerian-Lagran…
We present a real-space formulation for coarse-graining Kohn-Sham Density Functional Theory that significantly speeds up the analysis of material defects without appreciable loss of accuracy. The approximation scheme consists of two steps.…
Numerous molecular systems, including solutions, proteins, and composite materials, can be modeled using mixed-resolution representations, of which the quantum mechanics/molecular mechanics (QM/MM) approach has become the most widely used.…
In this article, a stochastic gradient based online learning algorithm for Extreme Learning Machines (ELM) is developed (SG-ELM). A stability criterion based on Lyapunov approach is used to prove both asymptotic stability of estimation…
Coarse-graining or model reduction is a term describing a range of approaches used to extend the time-scale of molecular simulations by reducing the number of degrees of freedom. In the context of molecular simulation, standard…
The Dynamical Graph Grammar (DGG) formalism can describe complex system dynamics with graphs that are mapped into a master equation. An exact stochastic simulation algorithm may be used, but it is slow for large systems. To overcome this…
The simulation of thermochemical nonequilibrium for the atomic and molecular energy level populations in plasma flows requires a comprehensive modeling of all the elementary collisional and radiative processes involved. Coupling detailed…
This paper proposes a semi-implicit arbitrary Lagrangian-Eulerian (ALE) method for the solution of the unified Godunov-Peshkov-Romenski (GPR) model of continuum mechanics. To handle the curl free involutions arising in the solid limit of…
Coarse-grained (CG) molecular dynamics enables simulations of atomic systems such as biomolecules at timescales inaccessible to all-atom (AA) methods, but existing CG neural potentials trained via force matching capture only the gradient of…
Particle-based variational inference (VI) minimizes the KL divergence between model samples and the target posterior with gradient flow estimates. With the popularity of Stein variational gradient descent (SVGD), the focus of particle-based…
We introduce a general framework for constructing coarse-grained potential models without ad hoc approximations such as limiting the potential to two- and/or three-body contributions. The scheme, called Deep Coarse-Grained Potential…
Coarse-grained (CG) modeling has gained significant attention in recent years due to its wide applicability in enhancing the spatiotemporal scales of molecular simulations. While CG simulations, often performed with Hamiltonian mechanics,…
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…
Our work is motivated by the analysis of ash plume dynamics, arising in the study of volcanic eruptions. Such phenomena are characterized by large Reynolds number (exceeding $10^7$) and a large number of polydispersed particles~[1]. Thus,…
In nonparametric regression, it is common for the inputs to fall in a restricted subset of Euclidean space. Typical kernel-based methods that do not take into account the intrinsic geometry of the domain across which observations are…
Molecular dynamics (MD) is a crucial technique for simulating biological systems, enabling the exploration of their dynamic nature and fostering an understanding of their functions and properties. To address exploration inefficiency,…
In this report, we propose a collection of methods to make such an approach possible for Euler equations in one and two dimensions. We propose an explicit single-step ALE DG scheme for hyperbolic conservation laws. The scheme considerably…
The numerical simulation of multiphase flows involving dispersed components with large scale disparities, such as the collisions between millimeter-sized bubbles and micron-sized mineral particles in flotation, poses a significant…
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…
This study addresses the challenge of simulating realistic particle systems by proposing a novel particle decomposition scheme that improves the parallel performance of surface resolved particle simulations. Realistic particle systems often…
For a wide range of phenomena, current computational ability does not always allow for fully atomistic simulations of high-dimensional molecular systems to reach time scales of interest. Coarse-graining (CG) is an established approach to…