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Preparing thermal (Gibbs) states is a common task in physics and computer science. Recent algorithms mimic cooling via system-bath coupling, where the cost is determined by mixing time, akin to classical Metropolis-like algorithms. However,…
For an isolated generic quantum system out of equilibrium, the long time average of observables is given by the diagonal ensemble, i.e. the mixed state with the same probability for energy eigenstates as the initial state but without…
We propose a method to extend the fast on-the-fly weight determination scheme for simulated tempering to two-dimensional space including not only temperature but also pressure. During the simulated tempering simulation, weight parameters…
From the underlying Master equations we derive one-dimensional stochastic processes that describe generalized ensemble simulations as well as tempering (simulated and parallel) simulations. The representations obtained are either in the…
Acquiring genomes at single-cell resolution has many applications such as in the study of microbiota. However, deep sequencing and assembly of all of millions of cells in a sample is prohibitively costly. A property that can come to rescue…
We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a…
We describe a novel coarse-grained simulation method for modelling the dynamics of globular macromolecules, such as proteins. The macromolecule is treated as a continuum that is subject to thermal fluctuations. The model includes a…
Molecular or condensed matter systems are often well approximated by hybrid quantum-classical models: the electrons retain their quantum character, whereas the ions are considered to be classical particles. We discuss various alternative…
The concept of generalized Gibbs ensembles (GGEs) has been introduced to describe steady states of integrable models. Recent advances show that GGEs can also be stabilized in nearly integrable quantum systems when driven by external fields…
A simple model to fit experimental data of adsorption of gases and vapours on microporous adsorbents (type I isotherms) is proposed. The main assumption is that the adsorbate phase can be divided into identical and non-interacting effective…
We investigate a quasi-adiabatic thermal process for preparing finite-temperature ensembles in the thermodynamic limit. The process gradually transforms a thermal ensemble of a noninteracting system into that of an interacting system of…
In this paper, we develop an ensemble-based time-stepping algorithm to efficiently find numerical solutions to a group of linear, second-order parabolic partial differential equations (PDEs). Particularly, the PDE models in the group could…
In this work we extend the applicability of the microcanonical ensemble simulation method, originally proposed to study the Ising model (A. H\"uller and M. Pleimling, Int. Journal of Modern Physics C, 13, 947 (2002),…
We propose an ensemble method to improve the generalization performance of trading strategies trained by deep reinforcement learning algorithms in a highly stochastic environment of intraday cryptocurrency portfolio trading. We adopt a…
In this paper, three efficient ensemble algorithms are proposed for fast-solving the random fluid-fluid interaction model. Such a model can be simplified as coupling two heat equations with random diffusion coefficients and a friction…
Ensemble forecast post-processing is a necessary step in producing accurate probabilistic forecasts. Conventional post-processing methods operate by estimating the parameters of a parametric distribution, frequently on a per-location or…
In non-interacting isolated quantum systems out of equilibrium, local subsystems typically relax to non-thermal stationary states. In the standard framework, information on the rest of the system is discarded, and such states are described…
The Generalised Langevin Equation (GLE) method, as developed in Ref. [Phys. Rev. B 89, 134303 (2014)], is used to calculate the dissipative dynamics of systems described at the atomic level. The GLE scheme goes beyond the commonly used…
An expression is derived for calculating microcanonical-ensemble averages of the kinetic energies of atoms of different types in clusters isolated from the environment. This expression is a natural generalization of the solution to the…
Parallel tempering is a generic Markov chain Monte Carlo sampling method which allows good mixing with multimodal target distributions, where conventional Metropolis-Hastings algorithms often fail. The mixing properties of the sampler…