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In this study, we investigate interactions of extended conformations of homodimeric peptides made of small (glycine or alanine) and large hydrophobic (valine or leucine) sidechains using all-atom molecular dynamics simulations to decipher driving forces for \beta-sheet formation. We make use of a periodic boundary condition setup in which individual peptides are infinitely long and stretched. Dimers adopt \beta-sheet conformations at short interpeptide distances (\xi ~ 0.5 nm) and at intermediate distances (~ 0.8 nm), valine and leucine homodimers assume cross-\beta-like conformations with side chains interpenetrating each other. These two states are identified as minima in the Potential of Mean Force (PMF). While the number of interpeptide hydrogen bonds increases with decreasing interpeptide distance, the total hydrogen bond number in the system does not change significantly, suggesting that formation of \beta-sheet structures from extended conformations is not driven by hydrogen bonds. This is supported by an increase in electrostatic energy at short interpeptide distances. A remarkable correlation between the volume of the system and the total electrostatic energy is observed, further reinforcing the idea that excluding water in proteins comes with an enthalpic penalty. We also discuss microscopic mechanisms accounting for \beta-sheet formation based on computed enthalpy and entropy and we show that they are different for peptides with small and large side chains.

We use molecular dynamics to study the nucleation of cracks in a two dimensional material without pre-existing cracks. We study models with zero and non-zero shear modulus. In both situations the time required for crack formation obeys an Arrhenius law, from which the energy barrier and pre-factor are extracted for different system sizes. For large systems, the characteristic time of rupture is found to decrease with system size, in agreement with classical Weibull theory. In the case of zero shear modulus, the energy opposing rupture is identified with the breakage of a single atomic layer. In the case of non-zero shear modulus, thermally activated fracture can only be studied within a reasonable time at very high strains. In this case the energy barrier involves the stretching of bonds within several layers, accounting for a much higher barrier compared to the zero shear modulus case. This barrier is understood within adiabatic simulations.

In this paper we introduce a three-dimensional version of the Mercedes-Benz model to describe water molecules. In this model van der Waals interactions and hydrogen bonds are given explicitly through a Lennard-Jones potential and a Gaussian orientation-dependent terms, respectively. At low temperature the model freezes forming Ice-I and it reproduces the main peaks of the experimental radial distribution function of water. In addition to these structural properties, the model also captures the thermodynamical anomalies of water: the anomalous density profile, the negative thermal expansivity, the large heat capacity and the minimum in the isothermal compressibility.

We elucidate the mechanism of cold denaturation through constant-pressure simulations for a model of hydrophobic molecules in an explicit solvent. We find that the temperature dependence of the hydrophobic effect is the driving force/induces/facilitates cold denaturation. The physical mechanism underlying this phenomenon is identified as the destabilization of hydrophobic contact in favor of solvent separated configurations, the same mechanism seen in pressure induced denaturation. A phenomenological explanation proposed for the mechanism is suggested as being responsible for cold denaturation in real proteins.

Among an infinite number of possible folds, nature has chosen only about 1000 distinct folds to form protein structures. Theoretical studies suggest that selected folds are intrinsically more designable than others; these selected folds are unusually stable, a property called the designability principle. In this paper we use the 2D hydrophobic-polar lattice model to classify structures according to their designability, and Langevin dynamics to account for their time evolution. We demonstrate that, among all possible folds, the more designable ones are easier to unfold due to their large number of surface-core bonds., Comment: 10 pages, 4 figures, Proceeding of the 3rd International Conference NEXT-SigmaPhi

We have used tight-binding molecular-dynamics simulations to investigate the role of point defects (vacancies and interstitials) on structural relaxation in amorphous silicon. Our calculations give unambiguous evidence that point defects can be defined in the amorphous solid, showing up as anomalies in the valence-charge/Voronoi-volume relation. The changes in the radial distribution functions that take place during annealing are shown to be in close agreement with recent, highly-accurate x-ray diffraction measurements. Our calculations provide strong evidence that structural relaxation in a-Si proceeds by the mutual annihilation of vacancies and interstitials, i.e., local structural changes rather than an overall relaxation of the network., Comment: 6 pages including 2 .eps figures; submitted to Physical Review Letters; additional publications on this and related topics can be found on web site http://www.esi.umontreal.ca/~grofnum