Nonlinear Elasticity of Amorphous Silicon and Silica from Density Functional Theory.

Density functional theory calculations and a finite deformation method are used to calculate second- and, most notably, third-order elastic constants of amorphous silicon and amorphous silicon dioxide, as represented by model structures generated via melt-quench force-field molecular dynamics simulations. Linear and nonlinear elastic constants are used to deduce macroscopic elastic moduli, such as the bulk and shear moduli, their pressure derivatives, and the elastic Grüneisen parameter. Our calculations show that the elastic properties of amorphous silicon reach the isotropic elastic limit within the nanometer length scale, attaining characteristics, both linear and nonlinear, comparable to those of crystalline silicon.

Correlation between protein conformations and water structure and thermodynamics at high pressure: A molecular dynamics study of the Bovine Pancreatic Trypsin Inhibitor (BPTI) protein.

Pressure-induced perturbation of a protein structure leading to its folding-unfolding mechanism is an important yet not fully understood phenomenon. The key point here is the role of water and its coupling with protein conformations as a function of pressure. In the current work, using extensive molecular dynamics simulation at 298 K, we systematically examine the coupling between protein conformations and water structures of pressures of 0.