An Eulerian simulation is developed to study an elastoplastic model of amorphous materials that is based upon the shear transformation zone theory developed by Langer and coworkers. In this theory, plastic deformation is controlled by an effective temperature that measures the amount of configurational disorder in the material. The simulation is used to model ductile fracture in a stretching bar that initially contains a small notch, and the effects of many of the model parameters are examined. The simulation tracks the shape of the bar using the level set method. Within the bar, a finite difference discretization is employed that makes use of the essentially non-oscillatory (ENO) scheme. The system of equations is moderately stiff due to the presence of large elastic constants, and one of the key numerical challenges is to accurately track the level set and construct extrapolated field values for use in boundary conditions. A new approach to field extrapolation is discussed that is second order accurate and requires a constant amount of work per gridpoint.

Bacterialmicrocompartments (BMCs) are organelles composed entirely of protein. They promote specific metabolic processes by encapsulatingand colocalizing enzymes with their substrates and cofactors, by protecting vulnerable enzymes in a defined microenvironment, and bysequestering toxic or volatile intermediates. Prototypes of the BMCsare the carboxysomes of autotrophic bacteria. However, structures of similarpolyhedral shape are being discovered in an ever-increasing number of heterotrophic bacteria, where they participate in the utilization ofspecialty carbon and energy sources.Comparative genomics reveals that the potential for this type of compartmentalization is widespread acrossbacterial phyla and suggests that genetic modules encoding BMCs are frequently laterally transferred among bacteria. The diverse functionsof these BMCs suggest that they contribute to metabolic innovation in bacteria in a broad range of environments.