Related papers: A non-equilibrium dynamic mechanism for the allost…
Ability of dynamical systems to relax to equilibrium has been investigated since the invention of statistical mechanics, which establishes the connection between dynamics of many-body Hamiltonian systems and phenomenological thermodynamics.…
We study the internal dynamics of an elementary quantum system placed close to a body held at a temperature different from that of the surrounding radiation. We derive general expressions for lifetime and density matrix valid for bodies of…
The model quantum system of fermions in a one dimensional harmonic oscillator potential is investigated by a molecular dynamics method at constant temperature. Although in quantum mechanics the equipartition theorem cannot be used like in…
Equilibrium and out-of-equilibrium transitions of an off-lattice protein model have been identified and studied. In particular, the out-of-equilibrium dynamics of the protein undergoing mechanical unfolding is investigated, and by using a…
Measuring and quantifying non-equilibrium dynamics in active biological systems is a major challenge, because of their intrinsic stochastic nature and the limited number of variables accessible in any real experiment. We investigate what…
Understanding the interplay among processes that occur over different timescales is a challenging issue in the physics of systems regulation. In gene regulation, the timescales for changes in chromatin states can differ from those for…
We present an application of the theory of stochastic processes to model and categorize non-equilibrium physical phenomena. The concepts of uniformly continuous probability measures and modular evolution lead to a systematic hierarchical…
Nonequilibrium molecular dynamics simulations often use mechanisms called thermostats to regulate the temperature. A Hamiltonian is presented for the case of the isoenergetic (constant internal energy) thermostat corresponding to a tunable…
Biological transport is supported by collective dynamics of enzymatic molecules that are called motor proteins or molecular motors. Experiments suggest that motor proteins interact locally via short-range potentials. We investigate the…
Nonlinear dynamics can impact the performance of a particle accelerator in a number of different ways, depending on the type of the accelerator and the parameter regime in which it operates. Effects can range from minor changes in beam…
A possible approach to description of the non equilibrium system has been proposed. Based on the Fokker-Plank equation in term of energy for non equilibrium distribution function of macroscopical system was obtained the stationary solution…
A novel energy landscape model, ELM, for proteins recently explained a collection of incoherent, elastic neutron scattering data from proteins. The ELM of proteins considers the elastic response of the proton and its environment to the…
Equilibrating proteins and other biomacromolecules is cardinal for molecular dynamics simulation of such biological systems in which they perform free dynamics without any externally-applied mechanical constraint, until thermodynamic…
Gene expression is controlled primarily by interactions between transcription factor proteins (TFs) and the regulatory DNA sequence, a process that can be captured well by thermodynamic models of regulation. These models, however, neglect…
A novel mechanism of reaction-induced active molecular motion, not involving any kind of self-propulsion, is proposed and analyzed. Because of the momentum exchange with the surrounding solvent, conformational transitions in…
An important process for antimatter experiments is the cooling of particles in a Penning-Malmberg trap to experimentally useful temperatures. A non-neutral plasma of one species (e.g. antiprotons) can be collisionally cooled on another…
We present an approach for carrying out non-adiabatic molecular dynamics simulations of systems in which non-adiabatic transitions arise from the coupling between the classical atomic motions and a quasi-continuum of electronic quantum…
Experience collected in mesoscopic dynamic modeling of externally driven systems indicates absence of potentials that could play role of equilibrium or nonequilibrium thermodynamic potentials yet their thermo-dynamics-like modeling is often…
For a single enzyme or molecular motor operating in an aqueous solution of non-equilibrated solute concentrations, a thermodynamic description is developed on the level of an individual trajectory of transitions between states. The concept…
Biology stores information and computes at the molecular scale, yet the ways in which it does so are often distinct from human-engineered computers. Mapping biological computation onto architectures familiar to computer science remains an…