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Hybrid quantum mechanical-molecular mechanical (QM/MM) simulations are widely used in enzyme simulation. Over ten convergence studies of QM/MM methods have revealed over the past several years that key energetic and structural properties…
The past twenty years have seen a resurgence of interest in nonequilibrium thermodynamics, thanks to advances in the theory of stochastic processes and in their thermodynamic interpretation. Fluctuation theorems provide fundamental…
We discuss a method to calculate with quantum molecular dynamics simulations the rate of energy exchanges between electrons and ions in two-temperature plasmas, liquid metals and hot solids. Promising results from this method were recently…
Fluctuation theorems impose constraints on possible work extraction probabilities in thermodynamical processes. These constraints are stronger than the usual second law, which is concerned only with average values. Here, we show that such…
The postulational basis of classical thermodynamics has been expanded to incorporate equilibrium fluctuations. The main additional elements of the proposed thermodynamic theory are the concept of quasi-equilibrium states, a definition of…
Many-body correlations developed in the constrained molecular dynamics approach in the frame-work of the CoMD model are analyzed in the case of a finite range effective interaction. The study is performed in the case of infinite nuclear…
In a generalized framework for the Landauer erasure protocol, we study bounds on the heat dissipated in typical nonequilibrium quantum processes. In contrast to thermodynamic processes, quantum fluctuations are not suppressed in the…
We present a new method for introducing stable non-equilibrium concentration gradients in molecular dynamics simulations of mixtures. This method extends earlier Reverse Non-Equilibrium Molecular Dynamics (RNEMD) methods which use kinetic…
To study the dynamics of chemical processes, we often adopt rate equations to observe the change in chemical concentrations. However, when the number of the molecules is small, the fluctuations cannot be neglected. We often study the…
We present mesoscale numerical simulations based on the coupling of the fluctuating lattice Boltzmann method (FLBM) for multicomponent systems with a wetted finite-size particle model. This newly coupled methodologies are used to study the…
The work approaches the study of the fluctuations for the thermodynamic systems in the presence of the fields. The approach is of phenomenological nature and developed in a Gaussian approximation. The study is exemplified on the cases of a…
A new method is proposed for a treatment of ideal quantum gases in the microcanonical ensemble near the thermodynamic limit. The method allows rigorous asymptotic calculations of the average number of particles and particle number…
Globular proteins undergo thermal fluctuations in solution, while maintaining an overall well-defined folded structure. In particular, studies have shown that the core structure of globular proteins differs in small, but significant ways…
Small nonequilibrium systems in contact with a heat bath can be analyzed with the framework of stochastic thermodynamics. In such systems, fluctuations, which are not negligible, follow universal relations such as the fluctuation theorem.…
Fluctuation theorems impose constraints on the probability of observing negative entropy production in small systems driven out of equilibrium. The range of validity of fluctuation theorems has been extensively tested for transitions…
The response of thermodynamic systems perturbed out of an equilibrium steady-state is described by the reciprocal and the fluctuation-dissipation relations. The so-called fluctuation theorems extended the study of fluctuations far beyond…
An important result in classical stochastic thermodynamics is the work fluctuation--dissipation relation (FDR), which states that the dissipated work done along a slow process is proportional to the resulting work fluctuations. Here we show…
A Hamiltonian model living in a bounded phase space and with long-range interactions is studied. It is shown, by analytical computations, that there exists an energy interval in which the microcanonical entropy is a decreasing convex…
Molecular dynamics (MD) simulations allow investigating the structural dynamics of biomolecular systems with unrivaled time and space resolution. However, in order to compensate for the inaccuracies of the utilized empirical force fields,…
In this letter we show that for isolated systems for which the energy current density is not equal to the momentum density, that means for systems with non-symmetric energy-momentum, the usual statements of the center of mass motion theorem…