Related papers: Comparison of free energy methods for molecular sy…
Finite element methods based on cut-cells are becoming increasingly popular because of their advantages over formulations based on body-fitted meshes for problems with moving interfaces. In such methods, the cells (or elements) which are…
Empirical force fields employed in molecular dynamics simulations of complex systems can be optimised to reproduce experimentally determined structural and thermodynamic properties. In contrast, experimental knowledge about the rates of…
The calculation of the interfacial free energy between two thermodynamic phases is crucial across various fields, including materials science, chemistry, and condensed matter physics. In this study, we apply an existing thermodynamic…
Jarzynski's identity for the free energy difference between two equilibrium states can be viewed as a special case of a more general procedure based on phase space mappings. Solving a system's equation of motion by approximate means…
A wide variety of numerical methods are evaluated and compared for solving the stochastic differential equations encountered in molecular dynamics. The methods are based on the application of deterministic impulses, drifts, and Brownian…
Nowadays, the use of soft computational techniques in power systems under the umbrella of machine learning is increasing with good reception. In this paper, we first present a deep learning approach to find the optimal configuration for…
Enhanced sampling techniques have become an essential tool in computational chemistry and physics, where they are applied to sample activated processes that occur on a time scale that is inaccessible to conventional simulations. Despite…
In the long-time pursuit of the solution to calculate the partition function (or free energy) of condensed matter, Monte-Carlo-based nested sampling should be the state-of-the-art method, and very recently, we established a direct integral…
This paper explores the integration of renewable energy sources into power systems, highlighting the resulting complexities such as variability and intermittency that challenge traditional power flow dynamics. We delve into innovative…
Identifying low-energy adsorption geometries on catalytic surfaces is a practical bottleneck for computational heterogeneous catalysis: the difficulty lies not only in the cost of density functional theory (DFT) but in proposing initial…
Despite the strength of Molecular Dynamics simulations in providing insights into the microscopic details of phenomenon in many fields in materials science, physics and biology, the biggest barrier is its limited timescale which is several…
Subsampling methods aim to select a subsample as a surrogate for the observed sample. Such methods have been used pervasively in large-scale data analytics, active learning, and privacy-preserving analysis in recent decades. Instead of…
This paper improves the performance of RRT$^*$-like sampling-based path planners by combining admissible informed sampling and local sampling (i.e., sampling the neighborhood of the current solution). An adaptive strategy regulates the…
To address the time-scale limitations in molecular dynamics (MD) simulations, numerous enhanced sampling methods have been developed to expedite the exploration of complex free energy landscapes. A commonly employed approach accelerates the…
We examine the performance of several molecular simulation techniques aimed at evaluation of the surface tension through its thermodynamic definition. For all methods explored, the surface tension is calculated by approximating the change…
Ensuring a satisfactory statistical convergence of anharmonic thermodynamic properties requires sampling of many atomic configurations, however the methods to obtain those necessarily produce correlated samples, thereby reducing the…
We revisit a unified methodology for the iterative solution of nonlinear equations in Hilbert spaces. Our key observation is that the general approach from [Heid & Wihler, Math. Comp. 89 (2020), Calcolo 57 (2020)] satisfies an energy…
Application of Jarzynski nonequilibrium work relation to free energy calculation is limited by the very slow convergence of the estimate when dissipation is high. We present a novel perturbation protocol able to improve the convergence of…
The performance of flow matching and diffusion models can be greatly improved at inference time using reward alignment algorithms, yet efficiency remains a major limitation. While several algorithms were proposed, we demonstrate that a…
We present a method to sample reactive pathways via biased molecular dynamics simulations in trajectory space. We show that the use of enhanced sampling techniques enables unconstrained exploration of multiple reaction routes. Time…