Related papers: Integrated Tempering Enhanced Sampling Method as t…
We propose a new global optimization method ({\em Simulated Tempering}) for simulating effectively a system with a rough free energy landscape (i.e. many coexisting states) at finite non-zero temperature. This method is related to simulated…
We introduce dynamic nested sampling: a generalisation of the nested sampling algorithm in which the number of "live points" varies to allocate samples more efficiently. In empirical tests the new method significantly improves calculation…
The transition interface sampling (TIS) technique allows to overcome large free energy barriers within reasonable simulation time, which is impossible for straightforward molecular dynamics. Still, the method does not impose an artificial…
In this paper we present extensions to the original adaptive parallel tempering algorithm. Two different approaches are presented. In the first one we introduce state-dependent strategies using current information to perform a swap step. It…
Molecular Dynamics (MD) simulations are fundamental computational tools for the study of proteins and their free energy landscapes. However, sampling protein conformational changes through MD simulations is challenging due to the relatively…
Importance sampling (IS) is a technique that enables statistical estimation of output performance at multiple input distributions from a single nominal input distribution. IS is commonly used in Monte Carlo simulation for variance reduction…
Understanding the behaviour of the confined fast ions is important in both current and future fusion experiments. These ions play a key role in heating the plasma and will be crucial for achieving conditions for burning plasma in next-step…
We introduce a new update scheme to systematically improve the efficiency of parallel tempering simulations. We show that by adapting the number of sweeps between replica exchanges to the canonical autocorrelation time, the average…
Diffusion models achieve strong generation quality, diversity, and distribution coverage, but their performance often comes with expensive inference. In this work, we propose Stochastic Transition-Map Distillation (STMD), a teacher-free…
The widespread popularity of replica exchange and expanded ensemble algorithms for simulating complex molecular systems in chemistry and biophysics has generated much interest in enhancing phase space mixing of these protocols, thus…
Molecular simulations are playing an ever increasing role, finding applications in fields as varied as physics, chemistry, biology and material science. However, many phenomena of interest take place on time scales that are out of reach of…
This paper proposes an iterative method to solve Mixed-Integer Optimal Control Problems arising from systems with switched dynamics. The so-called relaxed problem plays a central role within this context. Through a numerical example, it is…
The Isochronous Mass Spectrometry (IMS) is a powerful technique developed in heavy-ion storage rings for measuring masses of very short-lived exotic nuclei. The IMS is based on the isochronous setting of the ring. One of the main parameters…
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,…
The light damping hypothesis is usually assumed in structural dynamics since dissipative forces are in general weak with respect to inertial and elastic forces. In this paper a novel numerical method of time integration based on the…
Recently, Large Language Models (LLMs) have demonstrated outstanding performance across a wide range of downstream language tasks. Temperature sampling is a commonly used decoding strategy for LLMs' generation process. However, a fixed…
Thermal Energy Storage (TES) devices, which leverage the constant-temperature thermal capacity of the latent heat of a Phase Change Material (PCM), provide benefits to a variety of thermal management systems by decoupling the absorption and…
We study the dynamics of parallel tempering simulations, also known as the replica exchange technique, which has become the method of choice for simulation of proteins and other complex systems. Recent results for the optimal choice of the…
Clinical randomized controlled trials (RCTs) collect hundreds of measurements spanning various metric types (e.g., laboratory tests, cognitive/motor assessments, etc.) across 100s-1000s of subjects to evaluate the effect of a treatment, but…
Markov Chain Monte Carlo methods are algorithms used to sample probability distributions, commonly used to sample the Boltzmann distribution of physical/chemical models (e.g., protein folding, Ising model, etc.). This allows us to study…