Using molecular dynamics simulations, we investigate the relation between the dynamic transitions of biomolecules (lysozyme and DNA) and the dynamic and thermodynamic properties of hydration water. We find that the dynamic transition of the macromolecules, sometimes called a "protein glass transition," occurs at the temperature of dynamic crossover in the diffusivity of hydration water and also...

We investigate by molecular dynamics simulations a continuous isotropic core-softened potential with attractive well in three dimensions, introduced by Franzese [J. Mol. Liq. 136, 267 (2007)], that displays liquid-liquid coexistence with a critical point and waterlike density anomaly. Besides the thermodynamic anomalies, here we find diffusion and structural anomalies. The anomalies, not observ...

We have computed the entropy of liquid water using a two-phase thermodynamic model and trajectories generated by ab initio molecular dynamics simulations. We present the results obtained with semilocal, hybrid, and van der Waals density functionals. We show that in all cases, at the experimental equilibrium density and at temperatures in the vicinity of 300 K, the computed entropies are underes...

Small DNA circles can occur in Nature, for example as protein-constrained loops, and can be synthesized by a number of methods. Such small circles provide tractable systems for the study of the structure, thermodynamics and molecular dynamics of closed-circular DNA. In the present article, we review the occurrence and synthesis of small DNA circles, and examine their utility in studying the pro...

Using molecular dynamic simulations we study a family of continuous core-softened potentials consisting of a hard core, a shoulder at closest distances, and an attractive well at further distance. The repulsive shoulder and the well distances represent two length scales. We show that if the first scale, the shoulder, is repulsive or has a small well, the potential has a region in the pressure-t...

A solvation term based on the solvent accessible surface area (SASA) is combined with the CHARMM polar hydrogen force field for the efficient simulation of peptides and small proteins in aqueous solution. Only two atomic solvation parameters are used: one is negative for favoring the direct solvation of polar groups and the other positive for taking into account the hydrophobic effect on apolar...

1. Introduction 2. Energy storage frees the organism from thermodynamic constraints Energy storage and mobilization in living systems Thermodynamics of the steady state vs thermodynamics of organized complexity The living system is free from immediate thermodynamic constraints 3. The exquisite sensitivity of organisms Energy self-sufficiency and sensitivity The polychromatic whole 4. The interc...

Catalysis as a scientific discipline originated in the early part of the last century. Earlier, the unique feature of a catalytic substance, namely that when added in small quantities to a reaction it affects its rate and selectivity but is not consumed, had become widely recognized, and many applications had been developed. Only after chemical thermodynamics had been defined did a rational app...

The thermodynamics and molecular structure of a supramolecular complex between a tubular molecule, (P)-(12,8)-[4]cyclo-2,8-anthanthrenylene, and fullerene were investigated. The enthalpy-driven characteristics of the association were enhanced upon lengthening of the curved sp-carbon networks in the tubular molecule as a result of an increase in the C–C contact areas in addition to the emergence...

The stochastic thermodynamics of a dilute, well-stirred mixture of chemically reacting species is built on the stochastic trajectories of reaction events obtained from the chemical master equation. However, when the molecular populations are large, the discrete chemical master equation can be approximated with a continuous diffusion process, like the chemical Langevin equation or low noise appr...