Multiple time scales in diffraction measurements of diffusive surface relaxation

We grew SrTiO3 on SrTiO3(001) by pulsed laser deposition, using x-ray scattering to monitor the growth in real time. The time-resolved small-angle scattering exhibits a well-defined length scale associated with the spacing between unit-cell high surface features. This length scale imposes a discrete spectrum of Fourier components and rate constants upon the diffusion equation solution, evident in multiple exponential relaxation of the "anti-Bragg" diffracted intensity. An Arrhenius analysis of measured rate constants confirms that they originate from a single activation energy.     

Toward prediction of class II mouse major histocompatibility complex peptide binding affinity: in silico bioinformatic evaluation using partial least squares, a robust multivariate statistical technique

The accurate identification of T-cell epitopes remains a principal goal of bioinformatics within immunology. As the immunogenicity of peptide epitopes is dependent on their binding to major histocompatibility complex (MHC) molecules, the prediction of binding affinity is a prerequisite to the reliable prediction of epitopes. The iterative self-consistent (ISC) partial-least-squares (PLS)-based additive method is a recently developed bioinformatic approach for predicting class II peptide-MHC binding affinity. The ISC-PLS method overcomes many of the conceptual difficulties inherent in the prediction of class II peptide-MHC affinity, such as the binding of a mixed population of peptide lengths due to the open-ended class II binding site. The method has applications in both the accurate prediction of class II epitopes and the manipulation of affinity for heteroclitic and competitor peptides. The method is applied here to six class II mouse alleles (I-Ab, I-Ad, I-Ak, I-As, I-Ed, and I-Ek) and included peptides up to 25 amino acids in length. A series of regression equations highlighting the quantitative contributions of individual amino acids at each peptide position was established. The initial model for each allele exhibited only moderate predictivity. Once the set of selected peptide subsequences had converged, the final models exhibited a satisfactory predictive power. Convergence was reached between the 4th and 17th iterations, and the leave-one-out cross-validation statistical terms--q2, SEP, and NC--ranged between 0.732 and 0.925, 0.418 and 0.816, and 1 and 6, respectively. The non-cross-validated statistical terms r2 and SEE ranged between 0.98 and 0.995 and 0.089 and 0.180, respectively. The peptides used in this study are available from the AntiJen database (http://www.jenner.ac.uk/AntiJen). The PLS method is available commercially in the SYBYL molecular modeling software package. The resulting models, which can be used for accurate T-cell epitope prediction, will be made freely available online (http://www.jenner.ac.uk/MHCPred).     

Effect of axially projected oligothiophene pendants and nitro-functionalized diimine ligands on the lowest excited state in cationic Ir(III) bis-cyclometalates

The novel terthiophene (3T) oligomer 6 and a series of cationic Ir(III) bis-cyclometalates [Ir(C^N)(2)(N^N)]PF(6) 9-12 were prepared. The synthesis, characterization, electrochemical, and photophysical properties are reported. The cyclometalating ligands (C^N) are 2-phenylpyridinato (ppy) or the 3T oligomer (3T-ppy), asymmetrically capped in the 5 and 5" positions with the ppy and mesityl groups. The diimine ligands (N^N) are 2,2'-bipyridine (bpy) or 4-NO(2)-bipyridine (4-NO(2)-bpy). Hybrid metal-organic complexes 11 and 12 bear 3T-pendants ligated through the ppy cap, 10 and 12 contain NO(2) functionalized diimines, whereas 9 contains neither. Structural characterization of 10 by single crystal X-ray diffraction confirms the presence of the NO(2) substituent and pseudo-octahedral coordination geometry about the Ir(III) ion. Cyclic voltammetry highlights the large electron withdrawing effect of the NO(2) substituent, providing an 850 mV shift toward lower potentials for the first diimine centered reduction of 10 and 12. Strong overlap of the intense π → π* absorptions of the 3T-pendants with Ir(III) charge transfer bands is evident in complexes of 11 and 12, precluding the possibility for selective excitation of either chromophore. Photoexcitation (λ(ex) = 400 nm) of the series affords strong luminescence from the 3T oligomer 6 and the unsubstituted 9, with φ(em) = 0.11. In stark contrast the NO(2) and 3T functionalized complexes 10-12 display near total quenching of luminescence. Computations of the ground and excited state electronic structure using density functional theory (DFT) and time-dependent DFT (TD-DFT) indicate that both the NO(2) and 3T substituents play an important role in excited state deactivation of complexes 10-12. A substantial electronic contribution of the NO(2) substituent results in stabilization of the diimine based molecular orbital (MO) and offers an efficient nonradiative decay pathway for the excited state. Spin-orbit coupling effects of the Ir(III) ion lead to efficient population of the low lying, nonluminescent, triplet states centered on the 3T-pendants.     

Vertex and edge spread of zero forcing number,maximum nullity,and minimum rank of a graph

The minimum rank of a simple graph G is defined to be the smallest possible rank over all symmetric real matrices whose ijth entry (for $i\ne j$) is nonzero whenever $\{i\text{,}j\}$ is an edge in G and is zero otherwise; maximum nullity is taken over the same set of matrices. The zero forcing number is the minimum size of a zero forcing set of vertices and bounds the maximum nullity from above. The spread of a graph parameter at a vertex v or edge e of G is the difference between the value of the parameter on G and on $G-v$ or $G-e$. Rank spread (at a vertex) was introduced in [4]. This paper introduces vertex spread of the zero forcing number and edge spreads for minimum rank/maximum nullity and zero forcing number. Properties of the spreads are established and used to determine values of the minimum rank/maximum nullity and zero forcing number for various types of grids with a vertex or edge deleted.     

Variations in binding among several agonists at two stoichiometries of the neuronal, α4β2 nicotinic receptor

Drug-receptor binding interactions of four agonists, ACh, nicotine, and the smoking cessation compounds varenicline (Chantix) and cytisine (Tabex), have been evaluated at both the 2:3 and 3:2 stoichiometries of the α4β2 nicotinic acetylcholine receptor (nAChR). Previous studies have established that unnatural amino acid mutagenesis can probe three key binding interactions at the nAChR: a cation-π interaction, and two hydrogen-bonding interactions to the protein backbone of the receptor. We find that all drugs make a cation-π interaction to TrpB of the receptor. All drugs except ACh, which lacks an N(+)H group, make a hydrogen bond to a backbone carbonyl, and ACh and nicotine behave similarly in acting as a hydrogen-bond acceptor. However, varenicline is not a hydrogen-bond acceptor to the backbone NH that interacts strongly with the other three compounds considered. In addition, we see interesting variations in hydrogen bonding interactions with cytisine that provide a rationalization for the stoichiometry selectivity seen with this compound.     

Adaptive numerical algorithms in space weather modeling

Space weather describes the various processes in the Sun–Earth system that present danger to human health and technology. The goal of space weather forecasting is to provide an opportunity to mitigate these negative effects. Physics-based space weather modeling is characterized by disparate temporal and spatial scales as well as by different relevant physics in different domains. A multi-physics system can be modeled by a software framework comprising several components. Each component corresponds to a physics domain, and each component is represented by one or more numerical models. The publicly available Space Weather Modeling Framework (SWMF) can execute and couple together several components distributed over a parallel machine in a flexible and efficient manner. The framework also allows resolving disparate spatial and temporal scales with independent spatial and temporal discretizations in the various models.Several of the computationally most expensive domains of the framework are modeled by the Block-Adaptive Tree Solarwind Roe-type Upwind Scheme (BATS-R-US) code that can solve various forms of the magnetohydrodynamic (MHD) equations, including Hall, semi-relativistic, multi-species and multi-fluid MHD, anisotropic pressure, radiative transport and heat conduction. Modeling disparate scales within BATS-R-US is achieved by a block-adaptive mesh both in Cartesian and generalized coordinates. Most recently we have created a new core for BATS-R-US: the Block-Adaptive Tree Library (BATL) that provides a general toolkit for creating, load balancing and message passing in a 1, 2 or 3 dimensional block-adaptive grid. We describe the algorithms of BATL and demonstrate its efficiency and scaling properties for various problems.BATS-R-US uses several time-integration schemes to address multiple time-scales: explicit time stepping with fixed or local time steps, partially steady-state evolution, point-implicit, semi-implicit, explicit/implicit, and fully implicit numerical schemes. Depending on the application, we find that different time stepping methods are optimal. Several of the time integration schemes exploit the block-based granularity of the grid structure.The framework and the adaptive algorithms enable physics-based space weather modeling and even short-term forecasting.     

The preparation of ribose-free ‘artificial dinucleotides’: A new approach to molecular recognition?

The synthesis of the cytosine-guanine linked dimer1, and its symmetric guanine-guanine analogue2 are described. Compound1 is the first homogeneous ribose-free system to be prepared and characterized in which molecular recognition by complementary guanine-cytosine base-pairing might be possible. It is thus prototypical of a new and potentially large class of artificial oligonucleotides.