688 research outputs found
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 VO, treated in
detail here, a dipole component enhances the resonance. Hence, we argue that
the detailed structure of orbital order in VO 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 VO 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
Annual regulation of adrenocortical function in migrant and resident subspecies of white-crowned sparrow  
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
- …