Ice Ih-Water Interfacial Free Energy of Simple Water Models with Full Electrostatic Interactions.

We employ the cleaving approach to calculate directly the ice Ih-water interfacial free energy for the simple models of water, TIP4P, TIP4P-Ew, and TIP5P-E, with full electrostatic interactions evaluated via the Ewald sums. The results are in good agreement with experimental values, but lower than previously obtained for TIP4P-Ew and TIP5P-E by indirect methods. We calculate the interfacial free energies for basal, prism, and {112̅0} interfaces and find that the anisotropy of the TIP5P-E model is different from that of the TIP4P models.

Tracking polypeptide folds on the free energy surface: effects of the chain length and sequence.

Characterization of the folding transition in polypeptides and assessing the thermodynamic stability of their structured folds are of primary importance for approaching the problem of protein folding. We use molecular dynamics simulations for a coarse grained polypeptide model in order to (1) obtain the equilibrium conformation diagram of homopolypeptides in a broad range of the chain lengths, N = 10, ..

Protein aggregation: kinetics versus thermodynamics.

In this study, we address the questions of how important is the kinetics in protein aggregation, and what are the intrinsic properties of proteins that cause this behavior. On the basis of our recent quantitative calculation of the equilibrium phase diagram of natively folded α-helical and β-sheet forming peptides, we perform molecular dynamics simulations to demonstrate how the aggregation mechanism and end product depend on the temperature, concentration, and starting point in the phase diagram. The results obtained show that there are severe differences between the thermodynamically predicted and the kinetically obtained aggregate structures.

Structure of ice crystallized from supercooled water.

The freezing of water to ice is fundamentally important to fields as diverse as cloud formation to cryopreservation. At ambient conditions, ice is considered to exist in two crystalline forms: stable hexagonal ice and metastable cubic ice. Using X-ray diffraction data and Monte Carlo simulations, we show that ice that crystallizes homogeneously from supercooled water is neither of these phases.

Communication: Conformation state diagram of polypeptides: a chain length induced α-β transition.

By using a generic coarse grained polypeptide model, we perform multicanonical molecular dynamics simulations for determining the equilibrium conformation state diagram of a single homopolypeptide chain as a function of the chain length and temperature. The state diagram highlights the thermal regimes of stability for various conformational patterns in polypeptides, including swollen, random and collapsed coils, globular structures, extended and bended α helices, and compact β bundles. Remarkably, at low temperatures we observe a sharp transition from extended α helix to compact β bundles as the chain length increases.

Phase behavior in suspensions of highly charged colloids.

Attractive interactions between like-charged aggregates (macromolecules, colloidal particles, or micelles) in solution due to electrostatic correlation effects are revisited. The associated phenomenon of phase separation in a colloidal solution of highly charged particles is directly observed in Monte Carlo simulations. We start with a simple, yet instructive, description of polarization effects in a "cloud" of counterions around a single charged aggregate and show how the ion-ion correlations can be mapped onto a classical analogue of the quantum-mechanical dispersion force.