Related papers: Comparison of free energy methods for molecular sy…
We construct and analyze a projection-free linearly implicit method for the approximation of flows of harmonic maps into spheres. The proposed method is unconditionally energy stable and, under a sharp discrete regularity condition,…
A variety of methods are developed for characterising the free energy landscapes of continuum, Landau-type free energy models. Using morphologies of lipid vesicles and a multistable liquid crystal device as examples, I show that the methods…
The double distribution function approach is an efficient route towards extension of kinetic solvers to compressible flows. With a number of realizations available, an overview and comparative study in the context of high speed compressible…
We use a simulation study to compare three methods for adaptive experimentation: Thompson sampling, Tempered Thompson sampling, and Exploration sampling. We gauge the performance of each in terms of social welfare and estimation accuracy,…
Algorithms which compute locally optimal continuous designs often rely on a finite design space or on repeatedly solving a complex non-linear program. Both methods require extensive evaluations of the Jacobian Df of the underlying model.…
Several enhanced sampling techniques rely on the definition of collective variables to effectively explore free energy landscapes. Existing variables that describe the progression along a reactive pathway offer an elegant solution but face…
The DC Optimal Power Flow (DC-OPF) problem is fundamental to power system operations, requiring rapid solutions for real-time grid management. While traditional optimization solvers provide optimal solutions, their computational cost…
The Phase-Field Method (PFM) is employed to simulate two-phase flows with the fully-coupled Cahn-Hilliard-Navier-Stokes (CHNS) equations governing the temporal evolution. The methodology minimizes the total energy functional, accounting for…
We study the conformational equilibria of two peptides using a novel statistical mechanics approach designed for calculating free energy differences between highly dis-similar conformational states. Our results elucidate the contrasting…
Flux sampling is an analysis that, based on a distribution, picks randomly an efficient number of points from the solution space of a metabolic model. Unlike most constraint-based analyses, flux sampling does not require an objective…
The problem of energy harvesting from flutter instabilities in flexible slender structures in axial flows is considered. In a recent study, we used a reduced order theoretical model of such a system to demonstrate the feasibility for…
In this paper, we propose offline and online adaptive enrichment algorithms for the generalized multiscale approximation of a mixed finite element method with velocity elimination to solve the subsurface flow problem in high-contrast and…
In this paper, we consider Langevin processes with mechanical constraints. The latter are a fundamental tool in molecular dynamics simulation for sampling purposes and for the computation of free energy differences. The results of this…
The evaluation of produced items at the time of delivery is, in practice, usually amended by at least one inspection at later time points. We extend the methodology of acceptance sampling for variables for arbitrary unknown distributions…
Large deviation functions contain information on the stability and response of systems driven into nonequilibrium steady states, and in such a way are similar to free energies for systems at equilibrium. As with equilibrium free energies,…
We present a combination of the recently developed double incremental expansion of potential energy surfaces with the well-established adaptive density-guided approach to grid construction. This unique methodology is based on the use of an…
The calculation of potential energy surfaces for quantum dynamics can be a time consuming task -- especially when a high level of theory for the electronic structure calculation is required. We propose an adaptive interpolation algorithm…
Systematic inaccuracy is inherent in any computational estimate of a non-linear average, such as the free energy difference (Delta-F) between two states or systems, because of the availability of only a finite number of data values, N. In…
Though the convex optimization has been widely used in power systems, it still cannot guarantee to yield a tight (accurate) solution to some problems. To mitigate this issue, this paper proposes an ensemble learning based convex…
A fluctuation relation, which is an extended form of the Jarzynski equality, is introduced and discussed. We show how to apply this relation in order to evaluate the free energy landscape of simple systems. These systems are manipulated by…