We present a Monte Carlo technique for sampling from the canonical distribution in molecular dynamics. The method is built upon the Nosé-Hoover constant temperature formulation and the generalized hybrid Monte Carlo method. In contrast to standard hybrid Monte Carlo methods only the thermostat degree of freedom is stochastically resampled during a Monte Carlo step.
One of the main question arising in Extended Thermodynamics concerns the physical meaning of the temperature far from equilibrium. Some authors define thermodynamic temperature the inverse of the coefficient linking the entropy flux with the heat flux. Other authors, instead, define non-equilibrium temperature the inverse of the partial derivative of entropy with respect to energy, at density and heat flux constant. The aim of this paper is to determine the expression of entropy flux in some...
Molecular motors are nano- or colloidal machines that keep the living cell in a highly ordered, stationary state far from equilibrium. This self-organized order is sustained by the energy transduction of the motors, which couple exergonic or 'downhill' processes to endergonic or 'uphill' processes. A particularly interesting case is provided by the chemomechanical coupling of cytoskeletal motors which use the chemical energy released during ATP hydrolysis in order to generate mechanical forces and...