The second law of thermodynamics states that entropy, as a measure of randomness in a system, increases over time. Although studies have investigated biological sequence randomness from different aspects, it remains unknown whether sequence randomness changes over time and whether this change consists with the second law of thermodynamics. To capture the dynamics of randomness in molecular sequ...

Living systems produce copies of information-carrying molecules such as DNA by assembling monomer units into finite-length oligomer (short polymer) copies. We explore the role initiation and termination copy process in thermodynamics copying. By splitting free-energy change formation informational chemical terms, we show that accuracy plays no direct overall thermodynamics. Instead, it is therm...

This chapter describes the major issues that are involved in the statistical thermodynamics of phospholipid membranes at the atomic level. The ingredients going into models of lipid bilayers are summarized: force fields, representation of long-range interactions, and boundary conditions. Next, the choice of thermodynamic ensembles, and the two main options for the generation of a representative...

Rigid body molecular dynamics simulations were carried out on pure liquid imidazole at four different temperatures and at 1 atm. Imidazole, which is important both in life science and materials science, is one of the simplest molecules to possess both a lone pair and a π system. These two features are known to benefit from multipolar electrostatics. Here the electrostatic interaction is governe...

We report the spontaneous dimerization process of the full-length Aβ42 proteins in water by using unguided, fully atomistic, explicit-water molecular dynamics simulations. Based on the thermodynamic analysis, we demonstrate that Aβ42 dimerization in water occurs via a two-step nucleation-accommodation mechanism driven by water-induced force and by protein internal force, respectively.

The gas dynamics of a stationary hot-gas jet supersonically expanding into a low pressure environment is studied through numerical simulations. A hybrid coupled continuum-molecular approach is used to model the flow field. Due to the low pressure and high thermodynamic gradients, continuum mechanics results are doubtful, while, because of its excessive time expenses, a full molecular method is ...

Identification of hub proteins from sequence is a challenge in molecular biology. Therefore, it is of interest to predict protein hubs in networks. We describe the prediction of protein "hub" using physiochemical, thermodynamic and conformational properties of amino acid residues in sequence. We have used twenty sequence based features to identify hub behaviour. Linear discriminant analysis and...

The origin of protein folding thermodynamics is examined in terms of the energy landscape, employing an off-lattice protein model with scaled non-native attractions, which is continuously tunable between a Go-like model and a highly frustrated system. Extensive statistical temperature molecular dynamics simulations, combined with inherent structure analysis, reveal the intimate connection betwe...