Related papers: Temperature and its control in molecular dynamics …
The dynamical behavior of a kind of models with hierarchically constrained dynamics is investigated. The models exhibit many properties resembling real structural glasses. In particular, we focus on the study of time-dependent temperature…
We use molecular dynamics simulations to study the dynamics of an ensemble of interacting self-propelled semi-flexible polymers in contact with a thermal bath. Our intention is to model complex systems of biological interest. We find that…
Almost all Molecular Dynamics (MD) simulations are discrete dynamics with Newton's algorithm first published in 1687, and much later by L. Verlet in 1967. Discrete Newtonian dynamics has the same qualities as Newton's classical analytic…
Thermal transport through nanosystems is central to numerous processes in chemistry, material sciences, electrical and mechanical engineering, with classical molecular dynamics as the key simulation tool. Here we focus on thermal junctions…
Simulation schemes that allow to change molecular representation in a subvolume of the simulation box while preserving the equilibrium with the surrounding introduce conceptual problems of thermodynamic consistency. In this work we present…
In this review the debated rapport between thermodynamics and quantum mechanics is addressed in the framework of the theory of periodically-driven/controlled quantum-thermodynamic machines. The basic model studied here is that of a…
An open problem in numerical analysis is to explain why molecular dynamics works. The difficulty is that numerical trajectories are only accurate for very short times, whereas the simulations are performed over long time intervals. It is…
In this work we present a calculation of the hamiltonian variables solving the molecular dynamics equations of motion for a system of nuclear matter relevant to the description of nuclear pasta. The temperature is kept fixed by using the…
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…
In mixed quantum-classical simulations of molecule-metal surface interactions, the discretization of the metallic electronic continuum typically results in a closed-system representation that fails to capture the open-system nature of the…
We investigate the motion of a colloidal particle driven out of equilibrium by an external torque. We use the molecular dynamics simulation that is alternative to the numerical integration approach based on the Langevin equation and is…
In the replica-exchange molecular dynamics method, where constant-temperature molecular dynamics simulations are performed in each replica, one usually rescales the momentum of each particle after replica exchange. This rescaling method had…
"Pedagogical derivations for Nos\'e's dynamics can be developed in two different ways, (i) by starting with a temperature-dependent Hamiltonian in which the variable $s$ scales the time or the mass, or (ii) by requiring that the equations…
Quantum many-body dynamics generically results in increasing entanglement that eventually leads to thermalization of local observables. This makes the exact description of the dynamics complex despite the apparent simplicity of…
Control of open quantum systems is an essential ingredient to the realization of contemporary quantum science and technology. We demonstrate such control by employing a thermodynamically consistent framework, taking into account the fact…
Originally formulated for macroscopic machines, the laws of thermodynamics were recently shown to hold for quantum systems coupled to ideal sources of work (external classical fields) and heat (systems at equilibrium). Ongoing efforts have…
Novel physical mechanism is proposed for explanation of temperature-independent transition reactions in molecular systems. The mechanism becomes effective in the case of conformation transitions between quasi-isoenergetic molecular states.…
We propose a variational formulation for the nonequilibrium thermodynamics of discrete open systems, i.e., discrete systems which can exchange mass and heat with the exterior. Our approach is based on a general variational formulation for…
Gene sequences of a deme evolve over time as new chromosome inversions appear in a population via mutations, some of which will replace an existing sequence. The underlying biochemical processes that generates these and other mutations are…
We study the finite-temperature dynamics of thin elastic sheets in a single-clamped cantilever configuration. This system is known to exhibit a tilt transition at which the preferred mean plane of the sheet shifts from horizontal to a plane…