Three terminals optoelectronics devices integrated into a silicon on silicon waveguide

In this paper we describe two different kind of optoelectronic devices both based on a three terminals active device and exploit the plasma dispersion effect to achieve the desired working. The first device exploits this effect in order to obtain an optical modulation. The second device is an optoelectronic router based on the mode-mixing principle together with the injection-induced optical phase shift. Both devices are integrated into a Silicon on Silicon optical channel waveguide which can be realized using a standard bipolar process. The possibility of using standard, well-known technology presents several advantages with respect to III–V Optoelectronics. The active three terminal device used is a Bipolar Mode Field Effect Transistor (BMFET). Numerical simulation results are presented on both devices.     

The use of the consecutive adsorption of pyridine bases and carbon monoxide in the IR spectroscopic study of the accessibility of acid sites in microporous/mesoporous materials

A new approach to the evaluation of the accessibility of acid sites in microporous/mesoporous materials is developed and tested using a series of dealuminated mordenites. This approach is based on an IR-spectroscopic study of the consecutive adsorption of substituted alkylpyridines (pyridine, 2,4,6-trimethylpyridine, and 2,4,6-triethylpyridine) and carbon monoxide. This method allowed us to determine the strength and number of acid sites with various degrees of accessibility. The adsorption of 2,4,6-triethylpyridine on various types of materials is studied. The extinction coefficients of alkylpyridines are determined using a McBain balance placed in a cell for IR-spectroscopic measurements. Original Russian Text N.S. Nesterenko, F. Thibault-Starzyk, V. Montouilliout, V.V. Yushchenko, C. Fernandez, J.-P. Gilson, F. Fajula, I.I. Ivanova, 2006, published in Kinetika i Kataliz, 2006, Vol. 47, No. 1, pp. 45–53.     

Comparing ligand interactions with multiple receptors via serial docking

Standard uses of ligand-receptor docking typically focus on the association of candidate ligands with a single targeted receptor, but actual applications increasingly require comparisons across multiple receptors. This study demonstrates that comparative docking to multiple receptors can help to select homology models for virtual compound screening and to discover ligands that bind to one set of receptors but not to another, potentially similar, set. A serial docking algorithm is furthermore described that reduces the computational costs of such calculations by testing compounds against a series of receptor structures and discarding a compound as soon as it fails to satisfy specified bind/no bind criteria for each receptor. The algorithm also realizes substantial efficiencies by taking advantage of the fact that a ligand typically binds in similar conformations to similar receptors. Thus, once detailed docking has been used to fit a ligand into the first of a series of similar receptors, much less extensive calculations can be used for the remaining structures.     

Enhanced docking with the mining minima optimizer: acceleration and side-chain flexibility

The ligand-protein docking algorithm based on the Mining Minima method has been substantially enhanced. First, the basic algorithm is accelerated by: (1) adaptively determining the extent of each energy well to help avoid previously discovered energy minima; (2) biasing the search away from ligand positions at the surface of the receptor to prevent the ligand from staying at the surface when large sampling regions are used; (3) quickly testing multiple different ligand positions and orientations for each ligand conformation; and (4) tuning the source code to increase computational efficiency. These changes markedly shorten the time needed to discover an accurate result, especially when large sampling regions are used. The algorithm now also allows user-selected receptor sidechains to be treated as mobile during the docking procedure. The energies associated with the mobile side chains are computed as if they belonged to the ligand, except that atoms at the boundary between side chains and the rigid backbone are treated specially. This new capability is tested for several well-known ligand/protein systems, and preliminary application to an enzyme whose substrate is unknown--the recently solved hypothetical protein YecO (HI0319) from Haemophilus influenzae--indicates that side-chains relaxations allow candidate substrates of various sizes to be accommodated.     

First preparation of biotinylated gradient polyethylene surface to bind photoactive caged streptavidin

A gradient polyethylene (PE) surface was created through corona treatment, in which the corona power increased along the 5 cm length of the PE. The gradient surface was treated with polyethyleneimine and then biotin. Fluorescein-conjugated streptavidin (SAV) caged within 5-carboxymethoxy-2-nitrobenzyl (CMNB) adsorbed onto the biotinylated gradient PE surface following molecular recognition principles. Photoirradiation decomposed the CMNB cage and allowed the fluorescein-conjugated SAV to fluoresce, the intensity of which increased gradually along the PE surface.     

Chemical recovery of thallium-203 following production and separation of lead-201

Because of the cost and limited availability of isotopically enriched thallium (>92%²⁰³Tl), its use in the²⁰³Tl(p, 3n)²⁰¹Pb nuclear reaction necessitates chemical recovery. An adaptive method has been developed and evaluated. After the separation of²⁰¹Pb, the²⁰³Tl(I) is oxidized to²⁰³Tl(III) by Cl₂, Br₂ or [Fe(CN)₆]⁻², precipitated as Tl(OH)₃ with NaOH and subsequently converted to Tl₂O₃ by heating. Due to potential loss during recovery, the solubilities of Tl(OH)₃ and Tl₂O₃ in aqueous solution as a function of pH have been studied using the internal tracer²⁰²Tl (T=12.2d), produced during cyclotron irradiation. Effective solubility product constants have been determined to be 5.4·10⁻⁴⁸ and 2.5·10⁻⁴⁷ for Tl(OH)₃ and Tl₂O₃, respectively.     

The inclusion of electrostatic hydration energies in molecular mechanics calculations

Summary The problem of including solvent effects in molecular mechanics calculations is discussed. It is argued that the neglect of charge-solvent (solvation) interactions can introduce significant errors. The finite difference Poisson-Boltzmann (FDPB) method for calculating electrostatic interactions is summarized and is used as a basis for introducing a new pairwise energy term which accounts for charge-solvent interactions. This term acts between all pairs of atoms usually considered in molecular mechanics calculations and can be easily incorporated into existing force fields. As an example, a parameterization is developed for the CHARMm force field and the results compared to the predictions of the FDPB method. An approach to the realistic incorporation of solvent screening into force fields is also outlined.     

Stereoselective sp-sp bond formation via Negishi cross-coupling of vinylic tellurides and 2-heteroarylzinc chlorides

The Negishi cross-coupling reaction of vinylic- and aryltellurides with heteroarylzinc chlorides catalyzed by PdCl₂/CuI is described. This cross-coupling reaction is general and permits the formation of a new sp²-sp² carbon bond in good yields and high stereoselectivity.     

Orientation order and dynamics of CDCl3 in ethylcellulose/chloroform liquid crystal phases

Abstract

Deuterium quadrupole echo spectroscopy has been used to probe the orientational behaviour and dynamics of CDCl₃ molecules in ethylcellulose/chloroform chiral nematic phases. The ²H spectra of both left-handed and right-handed mesophases, formed by ethylcellulose with degrees of substitution of 2·3 and 3·0 respectively, were examined as functions of temperature and concentration. The observed quadrupolar splittings are relatively large and the magnitudes of the order parameters of the solvent molecules show little correlation with the handedness of the chiral phases. However, the ²H line shapes of these two types of chiral phase exhibit rather different temperature dependences. Spectral simulations show that the observed line shapes and their temperature variations are mainly determined by diffusion of CDCl₃ molecules along the pitch axis. The effects of centrifugation on the ²H spectra are also described.     

D3R grand challenge 4: blind prediction of protein–ligand poses,affinity rankings,and relative binding free energies

Journal of Computer-Aided Molecular Design - The Drug Design Data Resource (D3R) aims to identify best practice methods for computer aided drug design through blinded ligand pose prediction and...