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An invertible seven-dimensional Dirichlet cell characterization of lattices

Characterization of crystallographic lattices is an important tool in structure solution, crystallographic database searches and clustering of diffraction images in serial crystallography. Characterization of lattices by Niggli-reduced cells (based on the three shortest non-coplanar lattice vectors) or by Delaunay-reduced cells (based on four non-coplanar vectors summing to zero and all meeting at obtuse or right angles) is commonly performed. The Niggli cell derives from Minkowski reduction. The Delaunay cell derives from Selling reduction. All are related to the Wigner–Seitz (or Dirichlet, or Voronoi) cell of the lattice, which consists of the points at least as close to a chosen lattice point as they are to any other lattice point. The three non-coplanar lattice vectors chosen are here called the Niggli-reduced cell edges. Starting from a Niggli-reduced cell, the Dirichlet cell is characterized by the planes determined by 13 lattice half-edges: the midpoints of the three Niggli cell edges, the six Niggli cell face-diagonals and the four body-diagonals, but seven of the lengths are sufficient: three edge lengths, the three shorter of each pair of face-diagonal lengths, and the shortest body-diagonal length. These seven are sufficient to recover the Niggli-reduced cell.

Chemistry↗

Evaluating Mineral Lattices as Evolutionary Proxies for Metalloprotein Evolution

Protein coordinated iron-sulfur clusters drive electron flow within metabolic pathways for organisms throughout the tree of life. It is not known how iron-sulfur clusters were first incorporated into proteins. Structural analogies to iron-sulfde minerals present on early Earth, suggest a connection in the evolution of both proteins and minerals. The availability of large protein and mineral crystallographic structure data sets, provides an opportunity to explore co-evolution of proteins and minerals on a large-scale using informatics approaches. However, quantitative comparisons are confounded by the infnite, repeating nature of the mineral lattice, in contrast to metal clusters in proteins, which are fnite in size. We address this problem using the Niggli reduction to transform a mineral lattice to a fnite, unique structure that when translated reproduces the crystal lattice. Protein and reduced mineral structures were represented as quotient graphs with the edges and nodes corresponding to bonds and atoms, respectively. We developed a graph theory-based method to calculate the maximum common connected edge subgraph (MCCES) between mineral and protein quotient graphs. MCCES can accommodate differences in structural volumes and easily allows additional chemical criteria to be considered when calculating similarity. To account for graph size differences, we use the Tversky similarity index. Using consistent criteria, we found little similarity between putative ancient iron-sulfur protein clusters and iron-sulfur mineral lattices, suggesting these metal sites are not as evolutionarily connected as once thought. We discuss possible evolutionary implications of these findings in addition to suggesting an alternative proxy, mineral surfaces, for better understanding the coevolution of the geosphere and biosphere

Kenneth N. McGuinness↗

Approximating lattice similarity

A method is proposed for choosing unit cells for a group of crystals so that they all appear as nearly similar as possible to a selected cell. Related unit cells with varying cell parameters or indexed with different lattice centering can be accommodated.

36 MATERIALS SCIENCE↗

Simulation Environment For Radiotherapy Applications

SERA is a simulation environment for planning three-dimensional neutron capture therapy. SERA can allows creating models of the geometry of the tumor and surrounding tissue from CT or MRI data, and then planning and simulating the treatment of the tumor with Boron Neutron Capture Therapy. Boron Neutron Capture Therapy uses the combination of a boron containing drug and a neutron source to treat a tumor.

Cogliati, JoshuaJ. [Idaho National Laboratory (INL↗

Multipoint Geospace Science in 3D: The Paired Ionosphere-Thermosphere Orbiters(PITO) Mission

The science enabled by the Paired Ionosphere-Thermosphere Orbiters (PITO) mission is described and discussed. PITO has been designed to provide the concurrent, three-dimensional, multipoint measurements needed to advance geospace science while staying within a stringent resource envelope. The mission utilizes a pair of orbiting vehicles in eccentric, high-inclination, coplanar orbits. The orbits have arguments of perigee that differ by 180 degrees and are phased such that one vehicle is at perigee (~200 km) while the second is at apogee (~2000 km). Half an orbit later, the vehicles switch positions. Three complementary types of measurements exploit this scenario: local, in-situ measurements on both satellites, two-dimensional imaging from the higher satellite, and vertical sounders. The main idea is that two-dimensional context information for the low-altitude measurements is obtained by the high altitude imagers, while information on the third dimension is provided by vertical profiling. Such an observation system is capable of providing elements of global coverage, regional coverage, and concurrent coverage in three dimensions. Science goals are presented, as are the results of a detailed implementation plan, including several trade studies on key elements of the mission. The conclusion is that the mission would enable significant new understanding of the ionosphere-thermosphere system within a resource envelope that is consistent with that of NASA's Medium Explorer (MIDEX) line of science missions.

Clemmons, J.↗