Antifreeze proteins (AFPs) protect certain cold-adapted organisms from freezing to death by selectively adsorbing to internal ice crystals and inhibiting ice propagation. The molecular details of AFP adsorption-inhibition is uncertain but is proposed to involve the Gibbs-Thomson effect. Here we show by using unbiased molecular dynamics simulations a protein structure-function mechanism for the spruce budworm Choristoneura fumiferana AFP, including stereo-specific binding and consequential melting and freezing inhibition. The protein binds indirectly to the prism ice face through a linear array of ordered water molecules that are structurally distinct from the ice. Mutation of the ice binding surface disrupts water-ordering and abolishes activity. The adsorption is virtually irreversible, and we confirm the ice growth inhibition is consistent with the Gibbs-Thomson law.

Polydispersity is found to have a significant effect on the potential energy landscape; the average inherent structure energy decreases with polydispersity. Increasing polydispersity at a fixed volume fraction decreases the glass transition temperature and the fragility of glass formation analogous to the antiplasticization seen in some polymeric melts. An interesting temperature dependent crossover of heterogeneity with polydispersity is observed at low temperature due to the faster buildup of dynamic heterogeneity at lower polydispersity.

The persistence of shear stress fluctuations in viscous liquids is a direct consequence of the non-zero shear stress of the local potential minima which couples stress relaxation to transitions between inherent structures. In simulations of 2D and 3D glass forming mixtures, we calculate the distribution of this inherent shear stress and demonstrate that the variance is independent of temperature and obeys a power law in density. The inherent stress is shown to involve only long wavelength fluctuations, evidence of the central role of the static boundary conditions in determining the residual stress left after the minimization of the potential energy. A temperature T(η) is defined to characterise the crossover from stress relaxation governed by binary collisions at high temperatures to low temperature relaxation dominated by the relaxation of the inherent stress. T(η) is found to coincide with the breakdown of the Stokes-Einstein scaling of diffusion and viscosity.

Simulation studies of the atomic shear stress in the local potential energy minima (inherent structures) are reported for binary liquid mixtures in 2D and 3D. These inherent structure stresses are fundamental to slow stress relaxation and high viscosity in supercooled liquids.We find that the atomic shear stress in the inherent structures (IS) of both liquids at rest exhibits slowly decaying anisotropic correlations. We show that the stress correlations contributes significantly to the variance of the total shear stress of the IS configurations and consider the origins of the anisotropy and spatial extent of the stress correlations.

The relationship between the microscopic arrangement of molecules in a supercooled liquid and its slow dynamics at low temperature near glass transition is studied by molecular dynamics simulations. A Lennard-Jones liquid with polydispersity in size and mass of constituent particles is chosen as the model system. Our studies reveal that the local structure (that varies with polydispersity) plays a crucial role both in the slowing down of dynamics and in the growth of the dynamic heterogeneities, besides determining the glass forming ability of the system. Increasing polydispersity at fixed volume fraction is found to suppress the rate of growth of dynamic correlations, as detected by the growth in the peak of the nonlinear density response function, chi4(t). The growth in dynamical correlation is manifested in a stronger than usual breakdown of Stokes-Einstein relation at lower polydispersity at low temperatures and also leads to a decrease in the fragility of the system with polydispersity. We show that the suppression of the rate of growth of the dynamic heterogeneity can be attributed to the loss of structural correlations (as measured by the structure factor and the local bond orientational order) with polydispersity. While a critical polydispersity is required to avoid crystallization, we find that a further increase in polydispersity lowers the glass forming ability.