PDZ domains are typical examples of binding motifs mediating the formation of protein-protein assemblies in many different cells. A quantitative characterization of the mechanisms intertwining structure, chemistry, and dynamics with the PDZ function represent a challenge in molecular biology. Here, we investigated the influence of native state topology on the thermodynamics and dissociation kin...

Interfacial thermodynamics has deep ramifications in understanding the boundary conditions of transport theories. We present a formulation of local equilibrium for interfaces that extends the thermodynamics of the "dividing surface," as introduced by Gibbs, to nonequilibrium settings such as evaporation or condensation. By identifying the precise position of the dividing surface in the interfac...

Molecular Dynamics Simulation in Nanoscale Heat Transfer: A review D. Poulikakos, S. Arcidiacono Laboratory of Thermodynamics in Emerging Technologies, Institute of Energy Technology, Department of Mechanical and Process Engineering, Swiss Federal Institute of Technology, ETH Center, CH-8092, Zurich Switzerland, [email protected], www.ltnt.ethz.ch and Shigeo Maruyama Department of Mechan...

A hybrid approach is described, which combines stochastic classical molecular dynamics and rst principles Density Functional theory to model the atomic and electronic structure of large molecular and solid-state systems. The stochastic molecular dynamics using Generalized Simulated Annealing (GSA) is based on the nonextensive statistical mechanics and thermodynamics. Examples are given of appli...

The thermodynamics of ligand-protein molecular recognition is investigated by the energy landscape approach for two systems: methotrexate(MTX)--dihydrofolate reductase(DHFR) and biotin-streptavidin. The temperature-dependent binding free energy profile is determined using the weighted histogram analysis method. Two different force fields are employed in this study: a simplified model of ligand-...

The thermodynamics of computation applies ideas from thermal and statistical physics to physical devices implementing computations. Its major focus has been to characterize the principled limits to thermal dissipation in these devices. The best case of no dissipation arises when we use processes that create no thermodynamic entropy. They are thermodynamically reversible processes in which all d...

In this work, thermodynamic phenomena in crystalline silicon irradiated by an ultrafast laser pulse were studied using the method of molecular dynamics simulations. The Stillinger–Weber potential was used to model the crystalline silicon. The temperature development in silicon when heated by an ultrafast laser pulse was tracked. Melting and resolidification processes and the resulting structura...

The exceptionally high temperature sensitivity of certain transient receptor potential (TRP) family ion channels is the molecular basis of hot and cold sensation in sensory neurons. The laws of thermodynamics dictate that opening of these specialized TRP channels must involve an unusually large conformational standard-state enthalpy, ΔH(o): positive ΔH(o) for heat-activated and negative ΔH(o) f...