Related papers: Efficient mixed-force first-principles molecular d…
We present a novel approach to investigate the long-time stochastic dynamics of multi-dimensional classical systems, in contact with a heat-bath. When the potential energy landscape is rugged, the kinetics displays a decoupling of short and…
Machine learning methods have nowadays become easy-to-use tools for constructing high-dimensional interatomic potentials with ab initio accuracy. Although machine learned interatomic potentials are generally orders of magnitude faster than…
In classical density (or density-functional) estimation, it is standard to assume that the underlying distribution has a density with respect to the Lebesgue measure. However, when the data distribution is a mixture of continuous and…
Many large MDPs can be represented compactly using a dynamic Bayesian network. Although the structure of the value function does not retain the structure of the process, recent work has shown that value functions in factored MDPs can often…
Convexity, though extremely important in mathematical programming, has not drawn enough attention in the field of dynamic programming. This paper gives conditions for verifying convexity of the cost-to-go functions, and introduces an…
The ability to predict accurate thermodynamic and kinetic properties in biomolecular systems is of both scientific and practical utility. While both remain very difficult, predictions of kinetics are particularly difficult because rates, in…
In this paper, we develop a highly efficient molecular dynamics code fully implemented on graphics processing units for thermal conductivity calculations using the Green-Kubo formula. We compare two different schemes for force evaluation, a…
We derive the expressions for configurational forces in Kohn-Sham density functional theory, which correspond to the generalized variational force computed as the derivative of the Kohn-Sham energy functional with respect to the position of…
We introduce a lightweight structure optimization approach for problems in which there is uncertainty in the force locations. Such uncertainty may arise due to force contact locations that change during use or are simply unknown a priori.…
In the framework of density functional theory (DFT) simulations of molecules and materials, anharmonic terms of the potential energy surface are commonly computed numerically, with an associated cost that rapidly increases with the size of…
Molecular Density Functional Theory (MDFT) offers an efficient implicit- solvent method to estimate molecule solvation free-energies whereas conserving a fully molecular representation of the solvent. Even within a second order ap-…
Computational complexity of the brute-force implementation of the bilateral filter (BF) depends on its filter kernel size. To achieve the constant-time BF whose complexity is irrelevant to the kernel size, many techniques have been…
Super-convergence of order 1.5 in pressure and velocity has been experimentally investigated for the two-dimensional Stokes problem discretised with the MINI mixed finite element. Even though the classic mixed finite element theory for the…
We study mixed finite element methods for the rotating shallow water equations with linearized momentum terms but nonlinear drag. By means of an equivalent second-order formulation, we prove long-time stability of the system without energy…
We present an efficient algorithm for learning mixed membership models when the number of variables $p$ is much larger than the number of hidden components $k$. This algorithm reduces the computational complexity of state-of-the-art tensor…
This article is devoted to one particular case of using universal accelerated proximal envelopes to obtain computationally efficient accelerated versions of methods used to solve various optimization problem setups. We propose a proximally…
Finding Minimum Energy Configurations (MECs) is essential in fields such as physics, chemistry, and materials science, as they represent the most stable states of the systems. In particular, identifying such MECs in multi-component alloys…
Many proteins in cells are capable of sensing and responding to piconewton scale forces, a regime in which conformational changes are small but significant for biological processes. In order to efficiently and effectively sample the…
We introduce a new discretization of a mixed formulation of the incompressible Stokes equations that includes symmetric viscous stresses. The method is built upon a mass conserving mixed formulation that we recently studied. The improvement…
We propose and analyze a mixed finite element method for the spatial approximation of a time-fractional Fokker--Planck equation in a convex polyhedral domain, where the given driving force is a function of space. Taking into account the…