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It is a long-standing challenge to accurately and efficiently compute thermodynamic quantities of many-body systems at thermal equilibrium. The conventional methods, e.g., Markov chain Monte Carlo, require many steps to equilibrate. The…
We propose a method for efficient simulations in extended ensembles, useful, e.g., for the study of problems with complex energy landscapes and for free energy calculations. The main difficulty in such simulations is the estimation of the a…
Improvement of time series forecasting accuracy through combining multiple models is an important as well as a dynamic area of research. As a result, various forecasts combination methods have been developed in literature. However, most of…
The development of sophisticated experimental means to control nanoscale systems has motivated efforts to design driving protocols which minimize the energy dissipated to the environment. Computational models are a crucial tool in this…
The dissipative dynamics of a quantum bistable system coupled to a Ohmic heat bath is investigated beyond the spin-boson approximation. Within the path-integral approach to quantum dissipation, we propose an approximation scheme which…
We apply a recently developed adaptive algorithm that systematically improves the efficiency of parallel tempering or replica exchange methods in the numerical simulation of small proteins. Feedback iterations allow us to identify an…
While recent advances have established efficient quantum algorithms for preparing Gibbs states of finite-dimensional systems, comparable complexity results for bosonic and other infinite-dimensional models remain unexplored. We introduce…
We report here the experimental realization of multi-step cooling of a quantum system via heat-bath algorithmic cooling. The experiment was carried out using nuclear magnetic resonance (NMR) of a solid-state ensemble three-qubit system.
Massively-parallel molecular dynamics simulation is applied to systems containing electrolytes, vapour-liquid interfaces, and biomolecules in contact with water-oil interfaces. Novel molecular models of alkali halide salts are presented and…
This paper presents a generic framework for the numerical simulation of transformation-diffusion processes in complex volume geometric shapes. This work follows a previous one devoted to the simulation of microbial degradation of organic…
Numerical implementation of an explicit phonon bath requires a large number of oscillator modes in order to maintain oscillators at the initial temperature when modeling energy relaxation processes. An additional thermalization algorithm…
A new approach for integration of motion in many-body systems of interacting polyatomic molecules is proposed. It is based on splitting time propagation of pseudo-variables in a modified phase space, while the real translational and…
Recently, a so-called E-MS algorithm was developed for model selection in the presence of missing data. Specifically, it performs the Expectation step (E step) and Model Selection step (MS step) alternately to find the minimum point of the…
Experimental calibration of dynamic thermal models is required for model predictive control and characterization of building energy performance. In these applications, the uncertainty assessment of the parameter estimates is decisive; this…
We present a new molecular-dynamics algorithm for integrating the equations of motion for a system of particles interacting with mixed continuous/impulsive forces. This method, which we call Impulsive Verlet, is constructed using operator…
Many applications of computational fluid dynamics require multiple simulations of a flow under different input conditions. In this paper, a numerical algorithm is developed to efficiently determine a set of such simulations in which the…
Ordinary differential equations (ODEs) are widely used to describe dynamical systems in science, but identifying parameters that explain experimental measurements is challenging. In particular, although ODEs are differentiable and would…
We propose an ensemble algorithm, which provides a new approach for evaluating and summing up a set of function samples. The proposed algorithm is not a quantum algorithm, insofar it does not involve quantum entanglement. The query…
The computer simulation of many molecular processes is complicated by long time scales caused by rare transitions between long-lived states. Here, we propose a new approach to simulate such rare events, which combines transition path…
We investigate the theoretical foundations of the simulated tempering method and use our findings to design efficient algorithms. Employing a large deviation argument first used for replica exchange molecular dynamics [Plattner et al., J.…