Inductive queries for a drug designing robot scientist

It is increasingly clear that machine learning algorithms need to be integrated in an iterative scientific discovery loop, in which data is queried repeatedly by means of inductive queries and where the computer provides guidance to the experiments that are being performed. In this chapter, we summarise several key challenges in achieving this integration of machine learning and data mining algorithms in methods for the discovery of Quantitative Structure Activity Relationships (QSARs). We introduce the concept of a robot scientist, in which all steps of the discovery process are automated; we discuss the representation of molecular data such that knowledge discovery tools can analyse it, and we discuss the adaptation of machine learning and data mining algorithms to guide QSAR experiments

First-principles study of (BiScO3){1-x}-(PbTiO3){x} piezoelectric alloys

We report a first-principles study of a class of (BiScO3)_{1-x}-(PbTiO3)_x (BS-PT) alloys recently proposed by Eitel et al. as promising materials for piezoelectric actuator applications. We show that (i) BS-PT displays very large structural distortions and polarizations at the morphotropic phase boundary (MPB) (we obtain a c/a of ~1.05-1.08 and P_tet of ~1.1 C/m^2); (ii) the ferroelectric and piezoelectric properties of BS-PT are dominated by the onset of hybridization between Bi/Pb-6p and O-2p orbitals, a mechanism that is enhanced upon substitution of Pb by Bi; and (iii) the piezoelectric responses of BS-PT and Pb(Zr_{1-x}Ti_x)O3 (PZT) at the MPB are comparable, at least as far as the computed values of the piezoelectric coefficient d_15 are concerned. While our results are generally consistent with experiment, they also suggest that certain intrinsic properties of BS-PT may be even better than has been indicated by experiments to date. We also discuss results for PZT that demonstrate the prominent role played by Pb displacements in its piezoelectric properties.Comment: 6 pages, with 3 postscript figures embedded. Uses REVTEX and epsf macros. Also available at http://www.physics.rutgers.edu/~dhv/preprints/ji_bi/index.htm

Phase transitions in BaTiO3_3 from first principles

We develop a first-principles scheme to study ferroelectric phase transitions for perovskite compounds. We obtain an effective Hamiltonian which is fully specified by first-principles ultra-soft pseudopotential calculations. This approach is applied to BaTiO$_3$, and the resulting Hamiltonian is studied using Monte Carlo simulations. The calculated phase sequence, transition temperatures, latent heats, and spontaneous polarizations are all in good agreement with experiment. The order-disorder vs.\ displacive character of the transitions and the roles played by different interactions are discussed.Comment: 13 page

Effects of seed-placed sulfur forms on wheat, canola and pea yields in Saskatchewan soils

Non-Peer Reviewe

First-principles study of stability and vibrational properties of tetragonal PbTiO_3

A first-principles study of the vibrational modes of PbTiO_3 in the ferroelectric tetragonal phase has been performed at all the main symmetry points of the Brillouin zone (BZ). The calculations use the local-density approximation and ultrasoft pseudopotentials with a plane-wave basis, and reproduce well the available experimental information on the modes at the Gamma point, including the LO-TO splittings. The work was motivated in part by a previously reported transition to an orthorhombic phase at low temperatures [(J. Kobayashi, Y. Uesu, and Y. Sakemi, Phys. Rev. B {\bf 28}, 3866 (1983)]. We show that a linear coupling of orthorhombic strain to one of the modes at Gamma plays a role in the discussion of the possibility of this phase transition. However, no mechanical instabilities (soft modes) are found, either at Gamma or at any of the other high-symmetry points of the BZ.Comment: 8 pages, two-column style with 3 postscript figures embedded. Uses REVTEX and epsf macros. Also available at http://www.physics.rutgers.edu/~dhv/preprints/index.html#ag_pbt

Broadening the Scope of Nanopublications

In this paper, we present an approach for extending the existing concept of nanopublications --- tiny entities of scientific results in RDF representation --- to broaden their application range. The proposed extension uses English sentences to represent informal and underspecified scientific claims. These sentences follow a syntactic and semantic scheme that we call AIDA (Atomic, Independent, Declarative, Absolute), which provides a uniform and succinct representation of scientific assertions. Such AIDA nanopublications are compatible with the existing nanopublication concept and enjoy most of its advantages such as information sharing, interlinking of scientific findings, and detailed attribution, while being more flexible and applicable to a much wider range of scientific results. We show that users are able to create AIDA sentences for given scientific results quickly and at high quality, and that it is feasible to automatically extract and interlink AIDA nanopublications from existing unstructured data sources. To demonstrate our approach, a web-based interface is introduced, which also exemplifies the use of nanopublications for non-scientific content, including meta-nanopublications that describe other nanopublications.Comment: To appear in the Proceedings of the 10th Extended Semantic Web Conference (ESWC 2013

Crop response to seed-row placed sulfur fertilizers

Non-Peer Reviewe

Nanotube Piezoelectricity

We combine ab initio, tight-binding methods and analytical theory to study piezoelectric effect of boron nitride nanotubes. We find that piezoelectricity of a heteropolar nanotube depends on its chirality and diameter and can be understood starting from the piezoelectric response of an isolated planar sheet, along with a structure specific mapping from the sheet onto the tube surface. We demonstrate that coupling between the uniaxial and shear deformation are only allowed in the nanotubes with lower chiral symmetry. Our study shows that piezoelectricity of nanotubes is fundamentally different from its counterpart in three dimensional (3D) bulk materials.Comment: 4 pages, with 3 postscript figures embedded. Uses REVTEX4 macros. Also available at http://www.physics.upenn.edu/~nsai/preprints/bn_piezo/index.htm

Semiconductor effective charges from tight-binding theory

We calculate the transverse effective charges of zincblende compound semiconductors using Harrison's tight-binding model to describe the electronic structure. Our results, which are essentially exact within the model, are found to be in much better agreement with experiment than previous perturbation-theory estimates. Efforts to improve the results by using more sophisticated variants of the tight-binding model were actually less successful. The results underline the importance of including quantities that are sensitive to the electronic wavefunctions, such as the effective charges, in the fitting of tight-binding models.Comment: 4 pages, two-column style with 2 postscript figures embedded. Uses REVTEX and epsf macros. Also available at http://www.physics.rutgers.edu/~dhv/preprints/index.html#jb_t

Pre-main-sequence Lithium Depletion

In this review I briefly discuss the theory of pre-main-sequence (PMS) Li depletion in low-mass (0.075<M<1.2 Msun) stars and highlight those uncertain parameters which lead to substantial differences in model predictions. I then summarise observations of PMS stars in very young open clusters, clusters that have just reached the ZAMS and briefly highlight recent developments in the observation of Li in very low-mass PMS stars.Comment: 8 pages, invited review at "Chemical abundances and mixing in stars in the Milky Way and its satellites", eds. L. Pasquini, S. Randich. ESO Astrophysics Symposium (Springer-Verlag