We have developed advanced numerical algorithms to model biological fluids in multiscale flow environments using the software framework developed under the SciDAC APDEC ISIC. The foundation of our computational effort is an approach for modeling DNA-laden fluids as ''bead-rod'' polymers whose dynamics are fully coupled to an incompressible viscous solvent. The method is capable of modeling short range forces and interactions between particles using soft potentials and rigid constraints. Our methods are based on higher-order finite difference methods in complex geometry with adaptivity, leveraging algorithms and solvers in the APDEC Framework. Our Cartesian grid embedded boundary approach to incompressible viscous flow in irregular geometries has also been interfaced to a fast and accurate level-sets method within the APDEC Framework for extracting surfaces from volume renderings of medical image data and used to simulate cardio-vascular and pulmonary flows in critical anatomies.

The grinding efficiency of semi autogenous milling or ball milling depends on the tumbling motion of the total charge within the mill. Utilization of this tumbling motion for efficient breakage of particles depends on the conditions inside the mill. However, any kind of monitoring device to measure the conditions inside the mill shell during operation is virtually impossible due to the severe environment presented by the tumbling charge. An instrumented grinding ball, which is capable of surviving a few hours and transmitting the impacts it experiences, is proposed here. The spectrum of impacts collected over 100 revolutions of the mills presents the signature of the grinding environment inside mill. This signature could be effectively used to optimize the milling performance by investigating this signature's relation to mill product size, mill throughput, make-up ball size, mill speed, liner profile and ball addition rates. At the same time, it can also be used to design balls and liner systems that can survive longer in the mill. The technological advances made in electronics and communication makes this leap in instrumentation certainly viable. Hence, the instrumented grinding ball offers the ability to qualitatively observe and optimize the milling environment.

Crenarchaea are ubiquitous and abundant microbial constituents of soils, sediments, lakes and ocean waters, yet relatively little is known about their fundamental evolutionary, ecological, and physiological properties. To better describe the ubiquitous nonthermophilic Crenarchaea, we analyzed the genome sequence of one representative, the uncultivated sponge symbiont, Cenarchaeum symbiosum. C. symbiosum genotypes coinhabiting the same host partitioned into two dominant populations, corresponding to previously described a- and b-type ribosomal RNA variants. Although synthetic, overlapping a- and b-type ribotypes harbored significant genetic variability. A single tiling path comprising the dominant a-type genotype was assembled, and used to explore the biological properties of C. symbiosum and its planktonic relatives. Out of a total of 2,066 predicted open reading frames, 36% were more highly conserved with other Archaea. The remainder partitioned between bacteria (18%), eukaryotes (1.5%) and viruses (0.1%). A total of 525 open reading frames were more highly conserved with sequences derived from marine environmental genomic surveys, most probably representing orthologous genes found in free-living planktonic Crenarchaea. The remaining genes partitioned between functional RNAs (2.4%), and hypotheticals (42%) with limited homology to known functional genes. The latter category likely contains genes specifically involved in mediated archaeal-sponge symbiosis. Phylogenetic analyses placed C. symbiosum as …