Analysis of commercial and public bioactivity databases

Activity data for small molecules are invaluable in chemoinformatics. Various bioactivity databases exist containing detailed information of target proteins and quantitative binding data for small molecules extracted from journals and patents. In the current work, we have merged several public and commercial bioactivity databases into one bioactivity metabase. The molecular presentation, target information, and activity data of the vendor databases were standardized. The main motivation of the work was to create a single relational database which allows fast and simple data retrieval by in-house scientists. Second, we wanted to know the amount of overlap between databases by commercial and public vendors to see whether the former contain data complementing the latter. Third, we quantified the degree of inconsistency between data sources by comparing data points derived from the same scientific article cited by more than one vendor. We found that each data source contains unique data which is due to different scientific articles cited by the vendors. When comparing data derived from the same article we found that inconsistencies between the vendors are common. In conclusion, using databases of different vendors is still useful since the data overlap is not complete. It should be noted that this can be partially explained by the inconsistencies and errors in the source data.     

Isoperimetric inequality from the poisson equation via curvature

In this paper, we establish an isoperimetric inequality in a metric measure space via the Poisson equation. Let (X,d,μ) be a complete, pathwise connected metric space with locally Ahlfors Q‐regular measure, where Q > 1, that supports a local L²‐Poincaré inequality. We show that, for the Poisson equation Δu = g, if the local L^∞‐norm of the gradient Du can be bounded by the Lorentz norm L^Q,1 of g, then we obtain an isoperimetric inequality and a Sobolev inequality in (X,d,μ) with optimal exponents. By assuming a suitable curvature lower bound, we establish such optimal bounds on $\||Du|\|_{L^\infty_{\rm loc}}$ . © 2011 Wiley Periodicals, Inc.     

Slow mappings of finite distortion

We examine mappings of finite distortion from Euclidean spaces into Riemannian manifolds. We use integral type isoperimetric inequalities to obtain Liouville type growth results under mild assumptions on the distortion of the mappings and the geometry of the manifolds.     

Weakened acute type condition for tetrahedral triangulations and the discrete maximum principle

We prove that a discrete maximum principle holds for continuous piecewise linear finite element approximations for the Poisson equation with the Dirichlet boundary condition also under a condition of the existence of some obtuse internal angles between faces of terahedra of triangulations of a given space domain. This result represents a weakened form of the acute type condition for the three-dimensional case.

     

Emission studies of InGaN layers and LEDs grown by plasma-assisted MBE

We prepared InGaN layers on GaN/sapphire substrates using rf-MBE. Photoluminescence (PL) from these layers, grown at different temperatures T_S, shows that there is a strong tendency of GaN to form a separate phase as T_S is increased from 600°C to 650°C. Concomitant with the phase separation, the PL from the InGaN phase broadens, which indicates that indium composition in this phase becomes increasingly non-uniform. Indium compositions measured by Rutherford backscattering (RBS) are consistent with these results. We also observed an increase in PL intensity for InGaN layers grown at higher temperatures. In this paper, we also report on preparing a top-contact InGaN/GaN light emitting diode. The device was operated at 447 nm and had the emission line width of 37 nm with no observable impurity related features. The turn-on voltage was 3.0 V. The output power was 20 μW at 60 mA drive current.     

Growth of strain-compensated GaInNAs/GaAsP quantum wells for 1.3 μm lasers

Strain-compensated GaInNAs/GaAsP quantum well structures and lasers were grown by gas source molecular beam epitaxy using a RF-plasma nitrogen radical beam source. The optimal growth condition for the quantum well structure was determined based on room-temperature photoluminescence measurements. Effects of rapid thermal annealing (RTA) on the optical properties of GaInNAs/GaAsP quantum well structures as well as laser diodes are examined. It was found to significantly increase the photoluminescence from the quantum wells and reduce the threshold current density of the lasers, due to a removal of N induced nonradiative centers from GaInNAs wells.     

Sharp inequalities via truncation

We show that Sobolev-Poincaré and Trudinger inequalities improve to inequalities on Lorentz-type scales provided they are stable under truncations.     

Covariant fuzzy observables and coarse-graining

A fuzzy observable is regarded as a smearing of a sharp observable, and the structure of covariant fuzzy observables is studied. It is shown that the covariant coarse-grainings of sharp observables are exactly the covariant fuzzy observables. A necessary and sufficient condition for a covariant fuzzy observable to be informationally equivalent to the corresponding sharp observable is given.