Tractable Combinations of Global Constraints

We study the complexity of constraint satisfaction problems involving global constraints, i.e., special-purpose constraints provided by a solver and represented implicitly by a parametrised algorithm. Such constraints are widely used; indeed, they are one of the key reasons for the success of constraint programming in solving real-world problems. Previous work has focused on the development of efficient propagators for individual constraints. In this paper, we identify a new tractable class of constraint problems involving global constraints of unbounded arity. To do so, we combine structural restrictions with the observation that some important types of global constraint do not distinguish between large classes of equivalent solutions.Comment: To appear in proceedings of CP'13, LNCS 8124. arXiv admin note: text overlap with arXiv:1307.179

Development and application of a data-driven reaction classification model : comparison of an electronic lab notebook and the medicinal chemistry literature

Reaction classification has often been considered an important task for many different applications, and has traditionally been accomplished using hand-coded rule-based approaches. However, the availability of large collections of reactions enables data-driven approaches to be developed. We present the development and validation of a 336-class machine learning-based classification model integrated within a Conformal Prediction (CP) framework in order to associate reaction class predictions with confidence estimations. We also propose a data-driven approach for 'dynamic' reaction fingerprinting to maximise the effectiveness of reaction encoding, as well as developing a novel reaction classification system that organises labels in four hierarchical levels (SHREC: Sheffield Hierarchical REaction Classification). We show that the performance of the CP augmented model can be improved by defining confidence thresholds to detect predictions that are less likely to be false. For example, the external validation of the model reports 95% of predictions as correct by filtering out less than 15% of the uncertain classifications. The application of the model is demonstrated by classifying two reaction datasets: one extracted from an industrial ELN and the other from the medicinal chemistry literature. We show how confidence estimations and class compositions across different levels of information can be used to gain immediate insights on the nature of reaction collections and hidden relationship between reaction classes

Enhancing reaction-based de novo design using a multi-label reaction class recommender

Reaction-based de novo design refers to the in-silico generation of novel chemical structures by combining reagents using structural transformations derived from known reactions. The driver for using reaction-based transformations is to increase the likelihood of the designed molecules being synthetically accessible. We have previously described a reaction-based de novo design method based on reaction vectors which are transformation rules that are encoded automatically from reaction databases. A limitation of reaction vectors is that they account for structural changes that occur at the core of a reaction only, and they do not consider the presence of competing functionalities that can compromise the reaction outcome. Here, we present the development of a Reaction Class Recommender to enhance the reaction vector framework. The recommender is intended to be used as a filter on the reaction vectors that are applied during de novo design to reduce the combinatorial explosion of in-silico molecules produced while limiting the generated structures to those which are most likely to be synthesisable. The recommender has been validated using an external data set extracted from the recent medicinal chemistry literature and in two simulated de novo design experiments. Results suggest that the use of the recommender drastically reduces the number of solutions explored by the algorithm while preserving the chance of finding relevant solutions and increasing the global synthetic accessibility of the designed molecules

Relativistic effects and quasipotential equations

We compare the scattering amplitude resulting from the several quasipotential equations for scalar particles. We consider the Blankenbecler-Sugar, Spectator, Thompson, Erkelenz-Holinde and Equal-Time equations, which were solved numerically without decomposition into partial waves. We analyze both negative-energy state components of the propagators and retardation effects. We found that the scattering solutions of the Spectator and the Equal-Time equations are very close to the nonrelativistic solution even at high energies. The overall relativistic effect increases with the energy. The width of the band for the relative uncertainty in the real part of the scattering $T$ matrix, due to different dynamical equations, is largest for backward-scattering angles where it can be as large as 40%.Comment: Accepted for publication in Phys. Rev.

An evolutionarily-unique heterodimeric voltage-gated cation channel found in aphids

We describe the identification in aphids of a unique heterodimeric voltage-gated sodium channel which has an atypical ion selectivity filter and, unusually for insect channels, is highly insensitive to tetrodotoxin. We demonstrate that this channel has most likely arisen by adaptation (gene fission or duplication) of an invertebrate ancestral mono(hetero)meric channel. This is the only identifiable voltage-gated sodium channel homologue in the aphid genome(s), and the channel’s novel selectivity filter motif (DENS instead of the usual DEKA found in other eukaryotes) may result in a loss of sodium selectivity, as indicated experimentally in mutagenised Drosophila channels

Lattice Dynamics and the High Pressure Equation of State of Au

Elastic constants and zone-boundary phonon frequencies of gold are calculated by total energy electronic structure methods to twofold compression. A generalized force constant model is used to interpolate throughout the Brillouin zone and evaluate moments of the phonon distribution. The moments are used to calculate the volume dependence of the Gruneisen parameter in the fcc solid. Using these results with ultrasonic and shock data, we formulate the complete free energy for solid Au. This free energy is given as a set of closed form expressions, which are valid to compressions of at least V/V_0 = 0.65 and temperatures up to melting. Beyond this density, the Hugoniot enters the solid-liquid mixed phase region. Effects of shock melting on the Hugoniot are discussed within an approximate model. We compare with proposed standards for the equation of state to pressures of ~200 GPa. Our result for the room temperature isotherm is in very good agreement with an earlier standard of Heinz and Jeanloz.Comment: 13 pages, 8 figures. Accepted by Phys. Rev.

Continuous loading of a magnetic trap

We have realized a scheme for continuous loading of a magnetic trap (MT). ^{52}Cr atoms are continuously captured and cooled in a magneto-optical trap (MOT). Optical pumping to a metastable state decouples atoms from the cooling light. Due to their high magnetic moment (6 Bohr magnetons), low-field seeking metastable atoms are trapped in the magnetic quadrupole field provided by the MOT. Limited by inelastic collisions between atoms in the MOT and in the MT, we load 10^8 metastable atoms at a rate of 10^8 atoms/s below 100 microkelvin into the MT. After loading we can perform optical repumping to realize a MT of ground state chromium atoms.Comment: 4 pages, 4 figures, version 2, modified references, included additional detailed information, minor changes in figure 3 and in tex

Induced magnetic moment of Eu3+ ions in GaN

Magnetic semiconductors with coupled magnetic and electronic properties are of high technological and fundamental importance. Rare-earth elements can be used to introduce magnetic moments associated with the uncompensated spin of 4f-electrons into the semiconductor hosts. The luminescence produced by rare-earth doped semiconductors also attracts considerable interest due to the possibility of electrical excitation of characteristic sharp emission lines from intra 4f-shell transitions. Recently, electroluminescence of Eu-doped GaN in current-injection mode was demonstrated in p-n junction diode structures grown by organometallic vapour phase epitaxy. Unlike most other trivalent rare-earth ions, Eu3+ ions possess no magnetic moment in the ground state. Here we report the detection of an induced magnetic moment of Eu3+ ions in GaN which is associated with the 7F2 final state of 5D0→7F2 optical transitions emitting at 622 nm. The prospect of controlling magnetic moments electrically or optically will lead to the development of novel magneto-optic devices

Influence of micro-patterning of the growth template on defect reduction and optical properties of non-polar (11-20) GaN

We investigate the influence of different types of template micro-patterning on defect reduction and optical properties of non-polar GaN using detailed luminescence studies. Non-polar (11-20) (or a-plane) GaN exhibits a range of different extended defects compared with its more commonly used c-plane counterpart. In order to reduce the number of defects and investigate their impact on luminescence uniformity, non-polar GaN was overgrown on four different GaN microstructures. The micro-patterned structures consist of a regular microrod array; a microrod array where the -c-side of the microrods has been etched to suppress defect generation; etched periodic stripes and finally a subsequent combination of etched stripes and etched microrods (double overgrowth). Overall the presence of extended defects, namely threading dislocations and stacking faults (SFs) is greatly reduced for the two samples containing stripes compared with the two microrod samples. This is evidenced by more uniform emission and reduction in dark regions of non-radiative recombination in room temperature cathodoluminescence imaging as well as a reduction of the SF emission line in low temperature photoluminescence. The observed energy shifts of the GaN near band edge emission are related to anisotropic strain relaxation occurring during the overgrowth on these microstructures. A combination of stripes and microrods is a promising approach for defect reduction and emission uniformity in non-polar GaN for applications in light-emitting devices as well as power electronics

Regulation of WNT Signaling by VSX2 During Optic Vesicle Patterning in Human Induced Pluripotent Stem Cells

Few gene targets of Visual System Homeobox 2 (VSX2) have been identified despite its broad and critical role in the maintenance of neural retina (NR) fate during early retinogenesis. We performed VSX2 ChIP-seq and ChIP-PCR assays on early stage optic vesicle-like structures (OVs) derived from human iPS cells (hiPSCs), which highlighted WNT pathway genes as direct regulatory targets of VSX2. Examination of early NR patterning in hiPSC-OVs from a patient with a functional null mutation in VSX2 revealed mis-expression and upregulation of WNT pathway components and retinal pigmented epithelium (RPE) markers in comparison to control hiPSCOVs. Furthermore, pharmacological inhibition of WNT signaling rescued the early mutant phenotype, whereas augmentation of WNT signaling in control hiPSC-OVs phenocopied the mutant. These findings reveal an important role for VSX2 as a regulator of WNT signaling and suggest that VSX2 may act to maintain NR identity at the expense of RPE in part by direct repression of WNT pathway constituents