Related papers: Comparison of free energy methods for molecular sy…
Finding optimal solutions to combinatorial optimization problems is pivotal in both scientific and technological domains, within academic research and industrial applications. A considerable amount of effort has been invested in the…
One reason that free energy difference calculations are notoriously difficult in molecular systems is due to insufficient conformational overlap, or similarity, between the two states or systems of interest. The degree of overlap is…
This article is concerned with the mathematical analysis of a family of adaptive importance sampling algorithms applied to diffusion processes. These methods, referred to as Adaptive Biasing Potential methods, are designed to efficiently…
Variational inference in probabilistic graphical models aims to approximate fundamental quantities such as marginal distributions and the partition function. Popular approaches are the Bethe approximation, tree-reweighted, and other types…
Sets of free energy differences are useful for finding the equilibria of chemical reactions, while absolute free energies have little physical meaning. However finding the relative free energy between two macrostates by subtraction of their…
Interacting defect systems are ubiquitous in materials under realistic scenarios, yet gaining an atomic-level understanding of these systems from a computational perspective is challenging - it often demands substantial resources due to the…
Sampling a target probability distribution with an unknown normalization constant is a fundamental challenge in computational science and engineering. Recent work shows that algorithms derived by considering gradient flows in the space of…
Excess contributions to the free energy due to interfaces occur for many problems encountered in the statistical physics of condensed matter when coexistence between different phases is possible (e.g. wetting phenomena, nucleation, crystal…
Flat histogram methods, such as Wang--Landau sampling, provide a means for high-throughput calculation of phase diagrams of atomistic/lattice model systems. Many parallelisation schemes with varying degrees of complexity have been proposed…
In recent years, the power system research community has seen an explosion of novel methods for formulating and solving power network optimization problems. These emerging methods range from new power flow approximations, which go beyond…
Sampling molecular conformations from the Boltzmann distribution is essential for computational chemistry, but iterative diffusion methods are prohibitively slow. Drifting Models offer one-step generation, yet their equilibrium matches the…
Due to the time scale problem, rare events are not accessible by straight forward molecular dynamics. The presence of multiple reaction channels complicates the problem even further. The feasibility of the standard free energy based methods…
Wang-Landau sampling (WLS) of large systems requires dividing the energy range into "windows" and joining the results of simulations in each window. The resulting density of states (and associated thermodynamic functions) are shown to…
The biological functions of proteins often depend on dynamic structural ensembles. In this work, we develop a flow-based generative modeling approach for learning and sampling the conformational landscapes of proteins. We repurpose highly…
Target-oriented discovery under limited evaluation budgets requires making reliable progress in high-dimensional, heterogeneous design spaces where each new measurement is costly, whether experimental or high-fidelity simulation. We present…
We propose using an adaptive sampling method to detect changes for a system with multiple lines. The adaptive sampling utilizes the information in responses to learn on which line is more likely to have a change thus allocating more units…
In this study, we carried out equilibrium molecular dynamics (EMD) simulations of the liquid-liquid interface between two different Lennard-Jones components with varying miscibility, where we examined the relation between the interfacial…
We consider within a finite element approach the usage of different adaptively refined meshes for different variables in systems of nonlinear, time-depended PDEs. To resolve different solution behaviours of these variables, the meshes can…
With more energy networks being interconnected to form integrated energy systems (IESs), the optimal energy flow (OEF) problem has drawn increasing attention. Extant studies on OEF models mostly utilize the finite difference method (FDM) to…
We propose a novel data-driven method to accelerate the convergence of Alternating Direction Method of Multipliers (ADMM) for solving distributed DC optimal power flow (DC-OPF) where lines are shared between independent network partitions.…