相关论文: Redox Entropy of Plastocyanin: Developing a Micros…

Molecular dynamics simulations have revealed a dramatic increase, with increasing temperature, of the amplitude of electrostatic fluctuations caused by water at the active site of metalloprotein plastocyanin. The increased breadth of…

Non-local electrostatic interactions associated with the finite solvent size and ion polarizability are investigated within the mean-field linear response theory. To this end, we introduce a field theoretic model of a polar liquid composed…

We report the results of Molecular Dynamics simulations of electron transfer activation parameters of plastocyanin metalloprotein involved as electron carrier in natural photosynthesis. We have discovered that slow, non-ergodic…

We study the dynamics of hydration water/protein association in folded proteins, using lysozyme and myoglobin as examples. Extensive molecular dynamics simulations are performed to identify underlying mechanisms of the dynamical transition…

For a first principles understanding of macromolecular processes, a quantitative understanding of the underlying free energy landscape and in particular its entropy contribution is crucial. The stability of biomolecules, such as proteins,…

We report microscopic calculations of free energies and entropies for intramolecular electron transfer reactions. The calculation algorithm combines the atomistic geometry and charge distribution of a molecular solute obtained from quantum…

Modelling micro- and meso-scopic scale thermodynamic and transport properties of soft condensed matter hinges upon its representation. This is especially relevant for polar solvents such as water, since these require effective…

The entropies of molecules in solution are routinely calculated using gas phase formulae. It is assumed that, because implicit solvation models are fitted to reproduce free energies, this is sufficient for modeling reactions in solution.…

Theoretical studies of protein folding on lattice models relie on the assumption that water close to amino-acids is always in thermal equilibrium all along the folding pathway. Within this framework, it has always been considered that…

Within the framework of a functional integral formalism incorporating ionic charge and hard-core (HC) interactions on an equal footing, we formulate a unified theory of equilibrium thermodynamics and ion association in charged solutions.…

A high level polarizable force field is used to study the temperature dependence of hydrophobic hydration of small-sized molecules from computer simulations. Molecular dynamics (MD) simulations of liquid water at various temperatures form…

A classical density functional theory is applied to study solvation of solutes in water. An approx- imate form of the excess functional is proposed for water. This functional requires the knowledge of pure solvent direct correlation…

The hydrophobic effect is the dominant force which drives a protein towards its native state, but its physics has not been thoroughly understood yet. We introduce an exactly solvable model of the solvation of non-polar molecules in water,…

Classical Molecular Dynamics (MD) simulations are employed as a tool to investigate structural properties of ice crystals under several temperature and pressure conditions. All ice crystal phases are analyzed by means of a computational…

This article serves as a summary outlining the mathematical entropy analysis of the ideal magnetohydrodynamic (MHD) equations. We select the ideal MHD equations as they are particularly useful for mathematically modeling a wide variety of…

Recent experiments have reported lower critical solution temperature (LCST) phase behavior of aqueous solutions of proteins induced by multivalent ions, where the solution phase separates upon heating. This phenomenon is linked to complex…

Globular proteins undergo thermal fluctuations in solution, while maintaining an overall well-defined folded structure. In particular, studies have shown that the core structure of globular proteins differs in small, but significant ways…

We introduce a computational method to discover polymorphs in molecular crystals at finite temperature. The method is based on reproducing the crystallization process starting from the liquid and letting the system discover the relevant…

Treating realistically the ambient water is one of the main difficulties in applying Monte Carlo methods to protein folding. The solvent-accessible area method, a popular method for treating water implicitly, is investigated by means of…

Molecular dynamics (MD) simulations are widely used to study biological systems, where water molecules often play a critical role in protein-ligand interactions. In conventional MD preparation protocols, water molecules are typically added…