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

A Search for Jet Handedness in Hadronic Z0Z^0 Decays

We have searched for signatures of polarization in hadronic jets from $Z^0 \to q \bar{q}$ decays using the ``jet handedness'' method. The polar angle asymmetry induced by the high SLC electron-beam polarization was used to separate quark jets from antiquark jets, expected to be left- and right-polarized, respectively. We find no evidence for jet handedness in our global sample or in a sample of light quark jets and we set upper limits at the 95% C.L. of 0.063 and 0.099 respectively on the magnitude of the analyzing power of the method proposed by Efremov {\it et al.}Comment: Revtex, 8 pages, 2 figure

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

Autofix for backward-fit sidechains: using MolProbity and real-space refinement to put misfits in their place

Misfit sidechains in protein crystal structures are a stumbling block in using those structures to direct further scientific inference. Problems due to surface disorder and poor electron density are very difficult to address, but a large class of systematic errors are quite common even in well-ordered regions, resulting in sidechains fit backwards into local density in predictable ways. The MolProbity web site is effective at diagnosing such errors, and can perform reliable automated correction of a few special cases such as 180° flips of Asn or Gln sidechain amides, using all-atom contacts and H-bond networks. However, most at-risk residues involve tetrahedral geometry, and their valid correction requires rigorous evaluation of sidechain movement and sometimes backbone shift. The current work extends the benefits of robust automated correction to more sidechain types. The Autofix method identifies candidate systematic, flipped-over errors in Leu, Thr, Val, and Arg using MolProbity quality statistics, proposes a corrected position using real-space refinement with rotamer selection in Coot, and accepts or rejects the correction based on improvement in MolProbity criteria and on χ angle change. Criteria are chosen conservatively, after examining many individual results, to ensure valid correction. To test this method, Autofix was run and analyzed for 945 representative PDB files and on the 50S ribosomal subunit of file 1YHQ. Over 40% of Leu, Val, and Thr outliers and 15% of Arg outliers were successfully corrected, resulting in a total of 3,679 corrected sidechains, or 4 per structure on average. Summary Sentences: A common class of misfit sidechains in protein crystal structures is due to systematic errors that place the sidechain backwards into the local electron density. A fully automated method called “Autofix” identifies such errors for Leu, Val, Thr, and Arg and corrects over one third of them, using MolProbity validation criteria and Coot real-space refinement of rotamers

Ecological evaluation of proposed discharge of dredged material from Oakland Harbor into ocean waters (Phase 3 of 38-Foot Project). Volume 1, Background and appendixes A through H

At the request of the US Army Corps of Engineering (USACE), environmental studies were conducted by Battelle/Marine Sciences Laboratory (MSL) to evaluate the suitability of sediments from Oakland Inner Harbor for dredging and ocean disposal. During the Phase 3 38-Foot Project, sediment cores were collected from mudline to {minus}39 ft mean lower low water at various locations in Oakland Inner Harbor channel and allocated to six composite samples. These composites were evaluated through physical/chemical analyses, acute toxicity to sensitive marine organisms, and bioaccumulation potential. Sediment samples from individual locations were tested for physical/chemical parameters only. The results of toxicological and bioaccumulation testing may be used by USACE to determine the amount of potential dredged material from Oakland Inner Harbor channel acceptable for open-water disposal as defined by the Draft Implementation Manual (EPA/USACE 1990) and consistent with the Water Resources Development Act of 1986 (Public Law 99-662). This is Volume 1 of a two-volume data report that presents the data gathered during the Oakland Harbor Phase 3 38-Foot Project, conducted in the Fall of 1990. This data report does not include interpretation or statistical analysis of the 38-Foot data. Volume 1 includes the project background as well as a full presentation of data and results in Appendixes A through H. Volume 2 contains the remaining data in Appendixes I through L

Magnetic correlations and quantum criticality in the insulating antiferromagnetic, insulating spin liquid, renormalized Fermi liquid, and metallic antiferromagnetic phases of the Mott system V_2O_3

Magnetic correlations in all four phases of pure and doped vanadium sesquioxide V_2O_3 have been examined by magnetic thermal neutron scattering. While the antiferromagnetic insulator can be accounted for by a Heisenberg localized spin model, the long range order in the antiferromagnetic metal is an incommensurate spin-density-wave, resulting from a Fermi surface nesting instability. Spin dynamics in the strongly correlated metal are dominated by spin fluctuations in the Stoner electron-hole continuum. Furthermore, our results in metallic V_2O_3 represent an unprecedentedly complete characterization of the spin fluctuations near a metallic quantum critical point, and provide quantitative support for the SCR theory for itinerant antiferromagnets in the small moment limit. Dynamic magnetic correlations for energy smaller than k_BT in the paramagnetic insulator carry substantial magnetic spectral weight. However, the correlation length extends only to the nearest neighbor distance. The phase transition to the antiferromagnetic insulator introduces a sudden switching of magnetic correlations to a different spatial periodicity which indicates a sudden change in the underlying spin Hamiltonian. To describe this phase transition and also the unusual short range order in the paramagnetic state, it seems necessary to take into account the orbital degrees of freedom associated with the degenerate d-orbitals at the Fermi level in V_2O_3.Comment: Postscript file, 24 pages, 26 figures, 2 tables, accepted by Phys. Rev.