Interband and intraband optical transitions in InAs nanocrystal quantum dots: A pseudopotential approach

An atomistic pseudopotential method is used to investigate the electronic and optical properties of spherical InAs nanocrystals. Our calculated interband (valence-to-conduction) absorption spectra reproduce the features observed experimentally both qualitatively and quantitatively. The results relative to intraband (valence-to-valence and conduction-to-conduction) absorption successfully reproduce the recently measured photoinduced absorption spectra, which had so far been addressed only qualitatively. They exclude the hypothesis of a thermal activation process between dot-interior-delocalized hole states to explain the temperature dependence observed experimentally. Furthermore, based on the agreement of our data with the experimental valence intersublevel transitions and the almost complete overlap of the latter with scanning tunneling microscopic (STM) measurements, we question the simplistic attribution of the observed STM peaks obtained for negative bias

Flucytosine and cryptococcosis: time to urgently address the worldwide accessibility of a 50-year-old antifungal.

Current, widely accepted guidelines for the management of HIV-associated cryptococcal meningoencephalitis (CM) recommend amphotericin B combined with flucytosine (5-FC) for ≥2 weeks as the initial induction treatment of choice. However, access to flucytosine in Africa and Asia, where disease burden is greatest, is inadequate at present. While research into identifying effective and well-tolerated antifungal combinations that do not contain flucytosine continues, an ever-increasing body of evidence from in vitro, in vivo and clinical studies points to the benefits of flucytosine in the treatment of CM in both intravenous combinations with amphotericin B and oral combinations with high-dose fluconazole. This article provides an up-to-date review of this evidence, and the current issues and challenges regarding increasing access to this key component of combination antifungal therapy for cryptococcosis

Heisenberg exchange in magnetic monoxides

The superexchange intertacion in transition-metal oxides, proposed initially by Anderson in 1950, is treated using contemporary tight-binding theory and existing parameters. We find also a direct exchange for nearest-neighbor metal ions, larger by a factor of order five than the superexchange. This direct exchange arises from Vddm coupling, rather than overlap of atomic charge densities, a small overlap exchange contribution which we also estimate. For FeO and CoO there is also an important negative contribution, related to Stoner ferromagnetism, from the partially filled minority-spin band which broadens when ionic spins are aligned. The corresponding J1 and J2 parameters are calculated for MnO, FeO, CoO, and NiO. They give good accounts of the Neel and the Curie-Weiss temperatures, show appropriate trends, and give a reasonable account of their volume dependences. For MnO the predicted value for the magnetic susceptibility at the Neel temperature and the crystal distortion arising from the antiferromagnetic transition were reasonably well given. Application to CuO2 planes in the cuprates gives J=1220oK, compared to an experimental 1500oK, and for LiCrO2 gives J1=4 50oK compared to an experimental 230oK.Comment: 21 pages, 1 figure, submitted to Phys. Rev. B 1/19/07. Realized J=4V^2/U applies generally, as opposed to J=2V^2/U from one-electron theory (1/28 revision

Using surveys of Affymetrix GeneChips to study antisense expression.

We have used large surveys of Affymetrix GeneChip data in the public domain to conduct a study of antisense expression across diverse conditions. We derive correlations between groups of probes which map uniquely to the same exon in the antisense direction. When there are no probes assigned to an exon in the sense direction we find that many of the antisense groups fail to detect a coherent block of transcription. We find that only a minority of these groups contain coherent blocks of antisense expression suggesting transcription. We also derive correlations between groups of probes which map uniquely to the same exon in both sense and antisense direction. In some of these cases the locations of sense probes overlap with the antisense probes, and the sense and antisense probe intensities are correlated with each other. This configuration suggests the existence of a Natural Antisense Transcript (NAT) pair. We find the majority of such NAT pairs detected by GeneChips are formed by a transcript of an established gene and either an EST or an mRNA. In order to determine the exact antisense regulatory mechanism indicated by the correlation of sense probes with antisense probes, a further investigation is necessary for every particular case of interest. However, the analysis of microarray data has proved to be a good method to reconfirm known NATs, discover new ones, as well as to notice possible problems in the annotation of antisense transcripts

Identifying the impact of G-quadruplexes on Affymetrix 3' arrays using cloud computing.

A tetramer quadruplex structure is formed by four parallel strands of DNA/ RNA containing runs of guanine. These quadruplexes are able to form because guanine can Hoogsteen hydrogen bond to other guanines, and a tetrad of guanines can form a stable arrangement. Recently we have discovered that probes on Affymetrix GeneChips that contain runs of guanine do not measure gene expression reliably. We associate this finding with the likelihood that quadruplexes are forming on the surface of GeneChips. In order to cope with the rapidly expanding size of GeneChip array datasets in the public domain, we are exploring the use of cloud computing to replicate our experiments on 3' arrays to look at the effect of the location of G-spots (runs of guanines). Cloud computing is a recently introduced high-performance solution that takes advantage of the computational infrastructure of large organisations such as Amazon and Google. We expect that cloud computing will become widely adopted because it enables bioinformaticians to avoid capital expenditure on expensive computing resources and to only pay a cloud computing provider for what is used. Moreover, as well as financial efficiency, cloud computing is an ecologically-friendly technology, it enables efficient data-sharing and we expect it to be faster for development purposes. Here we propose the advantageous use of cloud computing to perform a large data-mining analysis of public domain 3' arrays

Photonic band mixing in linear chains of optically coupled micro-spheres

The paper deals with optical excitations arising in a one-dimensional chain of identical spheres due optical coupling of whispering gallery modes (WGM). The band structure of these excitations depends significantly on the inter-mixing between WGMs characterized by different values of angular quantum number, $l$. We develop a general theory of the photonic band structure of these excitations taking these effects into account and applied it to several cases of recent experimental interest. In the case of bands originating from WQMs with the angular quantum number of the same parity, the calculated dispersion laws are in good qualitative agreement with recent experiment results. Bands resulting from hybridization of excitations resulting from whispering gallery modes with different parity of $l$ exhibits anomalous dispersion properties characterized by a gap in the allowed values of \emph{wave numbers} and divergence of group velocity.Comment: RevTex, 28 pages, 7 Figure