Computational prediction of structure for macromolecular fragments is a formidable challenge. Here we show that the differences in conformational thermodynamics, computed using the equilibrium distribution of dihedral angles from molecular dynamics simulation, can identify the better model for the missing residues in the metal ion free (apo) skeletal muscle Troponin C (TnC). We use the model to...

Mechanical energy from oxygen metabolism by mammalian tissues has been studied since 1837. The production of heat by mechanical work was studied by Fick in about 1860. Prior to Fick's work, energetics were revised by Joule's experiments which founded the First Law of Thermodynamics. Fenn in 1923/24 found that frog muscle contractions generated extra heat proportional to the amount of work done ...

Based on a recently developed formalism for mesoscopic stochastic dynamics of single macromolecules, such as motor proteins, in aqueous solution, we demonstrate mathematically the principle of the nonequilibrium thermodynamics originated by the Brussels group. The key concepts of excess entropy and excess entropy production, and their mathematical properties as well as physical interpretations,...

Single molecules perform a variety of tasks in cells, from replicating, controlling and translating the genetic material to sensing the outside environment. These operations all require that specific actions take place. In a sense, each molecule must make tiny decisions. To make a decision, each "molecular machine" must dissipate an energy Py in the presence of thermal noise Ny. The number of b...

A new split beta-lactamase assay promises experimental testing of the interplay of protein stability and function. Proteins are sufficiently stable to act effectively within cells. However, mutations generally destabilize structure, with effects on free energy that are comparable to the free energy of folding. Assays of protein functionality and stability in vivo enable a quick study of factors...

The melting of a 64 ion microcrystal of KCI was studied by means of a molecular dynamics computer simulation. We used a central pair interaction with an inverse power law repulsion. The thermodynamics, kinetic and structural properties such as melting temperature, latent heat, mean square displacement, diffusion constant, radial distribution function and bond angle distribution are calculated. ...

We describe the thermodynamic state of a single-phase fluid confined to porous medium with Hill’s thermodynamics small systems, also known as nanothermodynamics. This way defining system thermodynamics, separate set control variables, may be useful for study transport in non-deformable media, where presently no consensus exists on pressure computations. For fluid, we observe that there are two ...

The thermodynamics of gold cluster anions (AuN-, N=11,...,14) is investigated using quantum molecular dynamics. Our simulations suggest that AuN- may exhibit a novel, freestanding planar liquid phase which dynamically coexists with a normal three-dimensional liquid. Upon cooling with experimentally realizable cooling rates, the entropy-favored three-dimensional liquid clusters often supercool a...

Supercritical fluids play a significant role in elucidating fundamental aspects of liquid matter under extreme conditions. They have been extensively studied at pressures and temperatures relevant to various industrial applications. However, much less is known about the structural behaviour of supercritical fluids and no structural crossovers have been observed in static compression experiments...

We have examined a simple chemical reaction in a temperature gradient; 2F <==> F2. A mechanical model was used, based on Stillinger and Weber's 2- and 3-body potentials. Equilibrium and non-equilibrium molecular dynamics simulations showed that the chemical reaction is in local thermodynamic as well as in local chemical equilibrium (delta(r)G = 0) in the supercritical fluid, for temperature gra...