Related papers: A general, efficient and robust method to calculat…
In this paper we study computationally feasible bounds for relative free energies between two many-particle systems. Specifically, we consider systems out of equilibrium that do not necessarily satisfy a fluctuation-dissipation relation,…
An open question in the field of non-equilibrium statistical physics is whether there exists a unique way through which non-equilibrium systems equilibrate irrespective of how far they are away from equilibrium. To answer this question we…
Biomolecular machines transduce between different forms of energy. These machines make directed progress and increase their speed by consuming free energy, typically in the form of nonequilibrium chemical concentrations. Machine dynamics…
The recently proposed Einstein molecule approach is extended to compute the free energy of molecular solids. This method is a variant of the Einstein crystal method of Frenkel and Ladd[J. Chem. Phys. 81,3188 (1984)]. In order to show its…
Estimating free energy differences, an important problem in computational drug discovery and in a wide range of other application areas, commonly involves a computationally intensive process of sampling a family of high-dimensional…
In the context of complex systems and, particularly, of protein folding, a physically meaningful distance is defined which allows to make useful statistical statements about the way in which energy differences are modified when two…
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…
The Jarzynski Equality relates the free energy difference between two equilibrium states of a system to the average of the work over all irreversible paths to go from one state to the other. We claim that the derivation of this equality is…
We present a method for computing free-energy differences using thermodynamic integration with a neural network potential that interpolates between two target Hamiltonians. The interpolation is defined at the sample distribution level, and…
The present paper proposes an adaptive biasing potential for the computation of free energy landscapes. It is motivated by statistical learning arguments and unifies the tasks of biasing the molecular dynamics to escape free energy wells…
We introduce a straightforward, single-ensemble, path sampling approach to calculate free energy differences based on Jarzynski's relation. For a two-dimensional ``toy'' test system, the new (minimally optimized) method performs roughly one…
We offer an insight into our mathematical endeavors, which aim to advance the foundational understanding of energy systems in a broad context, encompassing facets such as charge transport, energy storage, markets, and collective behavior.…
The computational modelling of reactions is simple in theory but can be quite tricky in practice. This article aims at the purpose of providing an assistance to a proper way of describing reactions theoretically and provides rough…
In this paper, I investigate more closely the recently proposed Free Energy Monte Carlo algorithm that is devised in particular for calculations where conventional Monte Carlo simulations struggle with ergodicity problems. The simplest…
The stochastic differential equations for a model of dissipative particle dynamics, with both total energy and total momentum conservation at every time-step, are presented. The algorithm satisfies detailed balance as well as the…
Free energy calculation is critical in predictive tasks such as protein folding, docking and design. However, rigorous calculation of free energy change is prohibitively expensive in these practical applications. The minimum potential…
Thermodynamic phase transitions, a central concept in physics and chemistry, are typically controlled by an interplay of enthalpic and entropic contributions. In most cases, the estimation of the enthalpy in simulations is straightforward…
The proposed method of the free energy calculation is based on the approximation of the energy distribution in the microcanonical ensemble by the Gaussian distribution. We hope that our approach will be effective for the systems with…
In this short communication, I give a very simple derivation of the Jarzynski equality, which allows to compute the free energy difference of a body, which is driven between two equilibrium states $A$ and $B$ by an external (time-dependent)…
We consider a simple model to describe the widths of the mode locked intervals for the critical circle map. Using two different partitions of the rational numbers, based on Farey series and Farey tree levels respectively, we calculate the…