Article on the first-principles theory of correlated transport through nanojunctions.

With the completion of the human genome and the growing number of diverse genomes being sequenced, a new age of evolutionary research is currently taking shape. The myriad of technological breakthroughs in biology that are leading to the unification of broad scientific fields such as molecular biology, biochemistry, physics, mathematics and computer science are now known as systems biology. Here I present an overview, with an emphasis on eukaryotes, of how the postgenomics era is adopting comparative approaches that go beyond comparisons among model organisms to shape the nascent field of evolutionary systems biology.

AMTRAN, a one, two and three dimensional Sn neutron transport code with adaptive mesh refinement (AMR) has been parallelized with MPI over spatial domains and energy groups and with threads over angles. Block refined AMR is used with linear finite element representations for the fluxes, which are node centered. AMR requirements are determined by minimum mean free path calculations throughout the problem and can provide an order of magnitude or more reduction in zoning requirements for the same level of accuracy, compared to a uniformly zoned problem.

First-principles generalized pseudopotential theory (GPT) provides a fundamental basis for transferable multi-ion interatomic potentials in transition metals and alloys within density-functional quantum mechanics. In central bcc transition metals, where multi-ion angular forces are important to structural properties, simplified model GPT or MGPT potentials have been developed based on canonical d bands to allow analytic forms and large-scale atomistic simulations. Robust, advanced-generation MGPT potentials have now been obtained for Ta and Mo and successfully applied to a wide range of structural, thermodynamic, defect and mechanical properties at both ambient and extreme conditions. Selected applications to multiscale modeling discussed here include dislocation core structure and mobility, atomistically informed dislocation dynamics simulations of plasticity, and thermoelasticity and high-pressure strength modeling. Recent algorithm improvements have provided a more general matrix representation of MGPT beyond canonical bands, allowing improved accuracy and extension to f-electron actinide metals, an order of magnitude increase in computational speed for dynamic simulations, and the still-in-progress development of temperature-dependent potentials.

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