Jonathan A. Barker

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MOTIVATION Structural templates consisting of a few atoms in a specific geometric conformation provide a powerful tool for studying the relationship between protein structure and function. Current methods for template searching constrain template syntax and semantics by their design. Hence there is a need for a more flexible core algorithm upon which to(More)
This work describes a method for predicting DNA binding function from structure using 3-dimensional templates. Proteins that bind DNA using small contiguous helix-turn-helix (HTH) motifs comprise a significant number of all DNA-binding proteins. A structural template library of seven HTH motifs has been created from non-homologous DNA-binding proteins in(More)
Data from biological research is proliferating rapidlyand advanced data storage and analysis methods are requiredto manage it. We introduce the main sources of biologicaldata available and outline some of the domainspecific problems associated with automated analysis. We discuss two major areas in which we are likely experiencesoftware engineering(More)
New information on the electron-hole wave functions in InAs-GaAs self-assembled quantum dots is deduced from Stark effect spectroscopy. Most unexpectedly it is shown that the hole is localized towards the top of the dot, above the electron, an alignment that is inverted relative to the predictions of all recent calculations. We are able to obtain new(More)
We use a plane-wave technique to study the electron and hole wave functions in self-assembled InGaAs quantum rings, investigating the influence on the electron-hole overlap of variations in the ring shape and composition profiles, and including the effects of built-in strain and the piezoelectric potential. Lateral variation of the ground-state electron and(More)
We present a theoretical analysis of the mean electron and hole positions in self-assembled InAs-GaAs quantum-dot structures. Because of the asymmetric dot shape, the electron center of mass should be displaced with respect to the hole center of mass in such dots, giving rise to a built-in dipole moment. Theoretical calculations on ideal pyramidal dots(More)
We present far-/near-infrared double resonance measurements of self-assembled InAs/GaAs quantum dots. The far-infrared resonance is unambiguously associated with a bound-bound intraband transition in the neutral dots. The results show that the interband photoluminescence ͑PL͒ lines originate from conduction levels with successively increasing in-plane(More)
(2003) Using structural motifs to identify proteins with DNA binding function. This document is made available in accordance with publisher policies and may differ from the published version or from the version of record. If you wish to cite this item you are advised to consult the publisher's version. Please see the URL above for details on accessing the(More)
In this paper, the characteristics of organic bulk heterojunction solar cells have been designed and modeled using MATLAB R2010a version. Here, organic solar cell is considered as a diode and an equivalent circuit is developed with series and shunt resistances to obtain the I-V characteristics of the model. Non-linear equations are obtained in by solving(More)
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