Improved process for epitaxial deposition of silicon on prediffused substrates

Process for fabricating integrated circuits uniformly deposits silicon epitaxially on prediffused substrates without affecting the sublayer diffusion pattern. Two silicon deposits from different sources, and deposited at different temperatures, protect the sublayer pattern from the silicon tetrachloride reaction

Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation

Small-probe contact dot surface analysis, with all explicit hydrogen atoms added and their van der Waals contacts included, was used to choose between the two possible orientations for each of 1554 asparagine (Asn) and glutamine (Gln) side-chain amide groups in a dataset of 100 unrelated, high-quality protein crystal structures at 0.9 to 1.7 AÊ resolution. For the movable-H groups, each connected, closed set of local H-bonds was optimized for both H-bonds and van der Waals overlaps. In addition to the Asn/Gln ``¯ips'', this process included rotation of OH, SH, NH 3, and methionine methyl H atoms, ¯ip and protonation state of histidine rings, interaction with bound ligands, and a simple model of water interactions. However, except for switching N and O identity for amide ¯ips (or N and C identity for His ¯ips), no non-H atoms were shifted. Even in these very high-quality structures, about 20 % of the Asn/Gln side-chains required a 180 ¯ip to optimize H-bonding and/o

X-Ray Resonant Scattering as a Direct Probe of Orbital Ordering in Transition-Metal Oxides

X-ray resonant scattering at the K-edge of transition metal oxides is shown to measure the orbital order parameter, supposed to accompany magnetic ordering in some cases. Virtual transitions to the 3d-orbitals are quadrupolar in general. In cases with no inversion symmetry, such as V$_2$O$_3$, treated in detail here, a dipole component enhances the resonance. Hence, we argue that the detailed structure of orbital order in V$_2$O$_3$ is experimentally accessible.Comment: LaTex using RevTex, 4 pages and two included postscript figure

Theory for Phase Transitions in Insulating Vanadium Oxide

We show that the recently proposed S=2 bond model with orbital degrees of freedom for insulating V$_{2}$O$_{3}$ not only explains the anomalous magnetic ordering, but also other mysteries of the magnetic phase transition. The model contains an additional orbital degree of freedom that exhibits a zero temperature quantum phase transtion in the Ising universality class.Comment: 5 pages, 2 figure

Orbitally Degenerate Spin-1 Model for Insulating V2O3

Motivated by recent neutron, X-ray absorption and resonant scattering experiments, we revisit the electronic structure of V2O3. We propose a model in which S=1 V3+ ions are coupled in the vertical V-V pairs forming two-fold orbitally degenerate configurations with S=2. Ferro-orbital ordering of the V-V pairs gives a description which is consistent with all experiments in the antiferromagnetic insulating phase.Comment: 4 pages, including three figure

Fast automated placement of polar hydrogen atoms in protein-ligand complexes

<p>Abstract</p> <p>Background</p> <p>Hydrogen bonds play a major role in the stabilization of protein-ligand complexes. The ability of a functional group to form them depends on the position of its hydrogen atoms. An accurate knowledge of the positions of hydrogen atoms in proteins is therefore important to correctly identify hydrogen bonds and their properties. The high mobility of hydrogen atoms introduces several degrees of freedom: Tautomeric states, where a hydrogen atom alters its binding partner, torsional changes where the position of the hydrogen atom is rotated around the last heavy-atom bond in a residue, and protonation states, where the number of hydrogen atoms at a functional group may change. Also, side-chain flips in glutamine and asparagine and histidine residues, which are common crystallographic ambiguities must be identified before structure-based calculations can be conducted.</p> <p>Results</p> <p>We have implemented a method to determine the most probable hydrogen atom positions in a given protein-ligand complex. Optimality of hydrogen bond geometries is determined by an empirical scoring function which is used in molecular docking. This allows to evaluate protein-ligand interactions with an established model. Also, our method allows to resolve common crystallographic ambiguities such as as flipped amide groups and histidine residues. To ensure high speed, we make use of a dynamic programming approach.</p> <p>Conclusion</p> <p>Our results were checked against selected high-resolution structures from an external dataset, for which the positions of the hydrogen atoms have been validated manually. The quality of our results is comparable to that of other programs, with the advantage of being fast enough to be applied on-the-fly for interactive usage or during score evaluation.</p

Ground State and Excitations of Spin Chain with Orbital Degeneracy

The one dimensional Heisenberg model in the presence of orbital degeneracy is studied at the SU(4) symmetric viewpoint by means of Bethe ansatz. Following Sutherland's previous work on an equivalent model, we discuss the ground state and the low-lying excitations more extensively in connection to the spin systems with orbital degeneracy. We show explicitly that the ground state is a SU(4) singlet. We study the degeneracies of the elementary excitations and the spectra of the generalized magnons consisting of these excitations. We also discuss the complex 2-strings in the context of the Bethe ansatz solutions.Comment: Revtex, 9 pages, 3 figures; typos correcte

MolProbity: all-atom structure validation for macromolecular crystallography

MolProbity structure validation will diagnose most local errors in macromolecular crystal structures and help to guide their correction

Computation of protein geometry and its applications: Packing and function prediction

This chapter discusses geometric models of biomolecules and geometric constructs, including the union of ball model, the weigthed Voronoi diagram, the weighted Delaunay triangulation, and the alpha shapes. These geometric constructs enable fast and analytical computaton of shapes of biomoleculres (including features such as voids and pockets) and metric properties (such as area and volume). The algorithms of Delaunay triangulation, computation of voids and pockets, as well volume/area computation are also described. In addition, applications in packing analysis of protein structures and protein function prediction are also discussed.Comment: 32 pages, 9 figure