Related papers: A non-equilibrium dynamic mechanism for the allost…
Binding and unbinding of ligands to specific sites of a macromolecule are one of the most elementary molecular interactions inside the cell that embody the computational processes of biological regulations. The interaction between…
We investigate the thermodynamic implications of two control mechanisms of open chemical reaction networks. The first controls the concentrations of the species that are exchanged with the surroundings, while the other controls the exchange…
What is really measured in dynamic calorimetric experiments is still an open question. This paper is devoted to this question, which can be usefully envisaged by means of macroscopic non-equilibrium thermodynamics. From the pioneer work of…
In this article we consider the possibility of controlling the dynamics of nonlinear discrete systems. A new method of control is by mixing states of the system (or the functions of these states) calculated on previous steps. This approach…
Despite the importance of non-equilibrium statistical mechanics in modern physics and related fields, the topic is often omitted from undergraduate and core-graduate curricula. Key aspects of non-equilibrium physics, however, can be…
We perform molecular-dynamics simulations of a molecular system in supercooled states for different values of inertia parameters to provide evidence that the long-time dynamics depends only on the equilibrium structure. This observation is…
The physics of critical phenomena in a many-body system far from thermal equilibrium is an interesting and important issue to be addressed both experimentally and theoretically. The trapped cold atoms have been actively used as a clean and…
Fluctuations in the abundance of molecules in the living cell may affect its growth and well being. For regulatory molecules (e.g., signaling proteins or transcription factors), fluctuations in their expression can affect the levels of…
Protein dynamics has been investigated on a wide range of time scales. Nano- and picosecond dynamics have been assigned to local fluctuations, while slower dynamics have been attributed to larger conformational changes. However, it is…
Controlling the non adiabatic dynamics of isolated quantum systems driven through a critical point is of interest in a variety of fields ranging from quantum simulation to finite-time thermodynamics. We briefly review the different methods…
In these lectures we give an overview of nonequilibrium stochastic systems. In particular we discuss in detail two models, the asymmetric exclusion process and a ballistic reaction model, that illustrate many general features of…
We present a general and systematic theory of non-equilibrium dynamics of multi-component fluid membranes, in general, and membranes containing transmembrane proteins, in particular. Developed based on a minimal number of principles of…
We present two simplified models of protein dynamics based on Langevin's equation of motion in a viscous medium. We explore the effect of the potential energy function's symmetry on the kinetics and thermodynamics of simulated folding. We…
Stochastic thermodynamics provides a useful set of tools to analyze and constrain the behavior of far from equilibrium systems. In this paper, we report an application of ideas from stochastic thermodynamics to the problem of membrane…
Many-body systems relaxing to equilibrium can exhibit complex dynamics even if their steady state is trivial. At low temperatures or high densities their evolution is often dominated by steric hindrances affecting particle motion [1,2,3].…
A Hamiltonian-based model of many harmonically interacting massive particles that are subject to linear friction and coupled to heat baths at different temperatures is used to study the dynamic approach to equilibrium and non-equilibrium…
We show that, in nonequilibrium systems with small heat flows, there is a time-scale dependent effective temperature which plays the same role as the thermodynamical temperature, in that it controls the direction of heat flows and acts as a…
Work fluctuation and total entropy production play crucial roles in small thermodynamic systems subject to large thermal fluctuations. We investigate a trade-off relation between them in a nonequilibrium situation in which a system starts…
We describe a novel coarse-grained simulation method for modelling the dynamics of globular macromolecules, such as proteins. The macromolecule is treated as a continuum that is subject to thermal fluctuations. The model includes a…
Stochastic thermodynamics is formulated under the assumption of perfect knowledge of all thermodynamic parameters. However, in any real-world experiment, there is non-zero uncertainty about the precise value of temperatures, chemical…