Influence of the heterointerface sharpness on exciton recombination dynamics in an ensemble of (In,Al)As/AlAs quantum dots with indirect band-gap

The dynamics of exciton recombination in an ensemble of indirect band-gap (In,Al)As/AlAs quantum dots with type-I band alignment is studied. The lifetime of confined excitons which are indirect in momentum-space is mainly influenced by the sharpness of the heterointerface between the (In,Al)As quantum dot and the AlAs barrier matrix. Time-resolved photoluminescence experiments and theoretical model calculations reveal a strong dependence of the exciton lifetime on the thickness of the interface diffusion layer. The lifetime of excitons with a particular optical transition energy varies because this energy is obtained for quantum dots differing in size, shape and composition. The different exciton lifetimes, which result in photoluminescence with non-exponential decay obeying a power-law function, can be described by a phenomenological distribution function, which allows one to explain the photoluminescence decay with one fitting parameter only.Comment: 10 pages, 7 figure

Development of the mesospheric Na layer at 69° N during the Geminids meteor shower 2010

The ECOMA sounding rocket campaign in 2010 was performed to investigate the charge state and number density of meteoric smoke particles during the Geminids meteor shower in December 2010. The ALOMAR Na lidar contributed to the campaign with measurements of sodium number density, temperature and line-of-sight wind between 80 and 110 km altitude over Andøya in northern Norway. This paper investigates a possible connection between the Geminids meteor shower and the mesospheric sodium layer. We compare with data from a meteor radar and from a rocket-borne in situ particle instrument on three days. Our main result is that the sodium column density is smaller during the Geminids meteor shower than the winter average at the same latitude. Moreover, during two of the three years considered, the sodium column density decreased steadily during these three weeks of the year. Both the observed decrease of Na column density by 30% and of meteoric smoke particle column density correlate well with a corresponding decrease of sporadic meteor echoes. We found no correlation between Geminids meteor flux rates and sodium column density, nor between sporadic meteors and Na column density (<I>R</I> = 0.25). In general, we found the Na column density to be at very low values for winter, between 1.8 and 2.6 &times; 10¹³ m⁻². We detected two meteor trails containing sodium, on 13 December 2010 at 87.1 km and on 19 December 2010 at 84 km. From these meteor trails, we estimate a global meteoric Na flux of 121 kg d⁻¹ and a global total meteoric influx of 20.2 t d⁻¹

The Supremum Norm of the Discrepancy Function: Recent Results and Connections

A great challenge in the analysis of the discrepancy function D_N is to obtain universal lower bounds on the L-infty norm of D_N in dimensions d \geq 3. It follows from the average case bound of Klaus Roth that the L-infty norm of D_N is at least (log N) ^{(d-1)/2}. It is conjectured that the L-infty bound is significantly larger, but the only definitive result is that of Wolfgang Schmidt in dimension d=2. Partial improvements of the Roth exponent (d-1)/2 in higher dimensions have been established by the authors and Armen Vagharshakyan. We survey these results, the underlying methods, and some of their connections to other subjects in probability, approximation theory, and analysis.Comment: 15 pages, 3 Figures. Reports on talks presented by the authors at the 10th international conference on Monte Carlo and Quasi-Monte Carlo Methods in Scientific Computing, Sydney Australia, February 2011. v2: Comments of the referee are incorporate

Spin-flip Raman scattering of the Γ\Gamma-X mixed exciton in indirect band-gap (In,Al)As/AlAs quantum dots

The band structure of type-I (In,Al)As/AlAs quantum dots with band gap energy exceeding 1.63 eV is indirect in momentum space, leading to long-lived exciton states with potential applications in quantum information. Optical access to these excitons is provided by mixing of the $\Gamma$- and X-conduction band valleys, from which control of their spin states can be gained. This access is used here for studying the exciton spin-level structure by resonant spin-flip Raman scattering, allowing us to accurately measure the anisotropic hole and isotropic electron $g$ factors. The spin-flip mechanisms for the indirect exciton and its constituents as well as the underlying optical selection rules are determined. The spin-flip intensity is a reliable measure of the strength of $\Gamma$-X-valley mixing, as evidenced by both experiment and theory.Comment: 5 pages, 3 figure

Characterization of Two Soybean (Glycine max L.) LEA IV Proteins by Circular Dichroism and Fourier Transform Infrared Spectrometry

Late embryogenesis-abundant (LEA) proteins, accumulating to a high level during the late stages of seed development, may play a role as osmoprotectants. However, the functions and mechanisms of LEA proteins remained to be elucidated. Five major groups of LEA proteins have been described. In the present study, we report on the characterization of two members of soybean LEA IV proteins, basic GmPM1 and acidic GmPM28, by circular dichroism and Fourier transform infrared spectroscopy. The spectra of both proteins revealed limited defined secondary structures in the fully hydrated state. Thus, the soybean LEA IV proteins are members of ‘natively unfolded proteins’. GmPM1 or GmPM28 proteins showed a conformational change under hydrophobic or dry conditions. After fast or slow drying, the two proteins showed slightly increased proportions of defined secondary structures (α-helix and β-sheet), from 30 to 49% and from 34 to 42% for GmPM1 and GmPm28, respectively. In the dehydrated state, GmPM1 and GmPM28 interact with non-reducing sugars to improve the transition temperature of cellular glass, with poly-l-lysine to prevent dehydration-induced aggregation and with phospholipids to maintain the liquid crystal phase over a wide temperature range. Our work suggests that soybean LEA IV proteins are functional in the dry state. They are one of the important components in cellular glasses and may stabilize desiccation-sensitive proteins and plasma membranes during dehydration

Predicting mostly disordered proteins by using structure-unknown protein data

BACKGROUND: Predicting intrinsically disordered proteins is important in structural biology because they are thought to carry out various cellular functions even though they have no stable three-dimensional structure. We know the structures of far more ordered proteins than disordered proteins. The structural distribution of proteins in nature can therefore be inferred to differ from that of proteins whose structures have been determined experimentally. We know many more protein sequences than we do protein structures, and many of the known sequences can be expected to be those of disordered proteins. Thus it would be efficient to use the information of structure-unknown proteins in order to avoid training data sparseness. We propose a novel method for predicting which proteins are mostly disordered by using spectral graph transducer and training with a huge amount of structure-unknown sequences as well as structure-known sequences. RESULTS: When the proposed method was evaluated on data that included 82 disordered proteins and 526 ordered proteins, its sensitivity was 0.723 and its specificity was 0.977. It resulted in a Matthews correlation coefficient 0.202 points higher than that obtained using FoldIndex, 0.221 points higher than that obtained using the method based on plotting hydrophobicity against the number of contacts and 0.07 points higher than that obtained using support vector machines (SVMs). To examine robustness against training data sparseness, we investigated the correlation between two results obtained when the method was trained on different datasets and tested on the same dataset. The correlation coefficient for the proposed method is 0.14 higher than that for the method using SVMs. When the proposed SGT-based method was compared with four per-residue predictors (VL3, GlobPlot, DISOPRED2 and IUPred (long)), its sensitivity was 0.834 for disordered proteins, which is 0.052–0.523 higher than that of the per-residue predictors, and its specificity was 0.991 for ordered proteins, which is 0.036–0.153 higher than that of the per-residue predictors. The proposed method was also evaluated on data that included 417 partially disordered proteins. It predicted the frequency of disordered proteins to be 1.95% for the proteins with 5%–10% disordered sequences, 1.46% for the proteins with 10%–20% disordered sequences and 16.57% for proteins with 20%–40% disordered sequences. CONCLUSION: The proposed method, which utilizes the information of structure-unknown data, predicts disordered proteins more accurately than other methods and is less affected by training data sparseness

Differences in the Number of Intrinsically Disordered Regions between Yeast Duplicated Proteins, and Their Relationship with Functional Divergence

BACKGROUND: Intrinsically disordered regions are enriched in short interaction motifs that play a critical role in many protein-protein interactions. Since new short interaction motifs may easily evolve, they have the potential to rapidly change protein interactions and cellular signaling. In this work we examined the dynamics of gain and loss of intrinsically disordered regions in duplicated proteins to inspect if changes after genome duplication can create functional divergence. For this purpose we used Saccharomyces cerevisiae and the outgroup species Lachancea kluyveri. PRINCIPAL FINDINGS: We find that genes duplicated as part of a genome duplication (ohnologs) are significantly more intrinsically disordered than singletons (p<2.2(e)-16, Wilcoxon), reflecting a preference for retaining intrinsically disordered proteins in duplicate. In addition, there have been marked changes in the extent of intrinsic disorder following duplication. A large number of duplicated genes have more intrinsic disorder than their L. kluyveri ortholog (29% for duplicates versus 25% for singletons) and an even greater number have less intrinsic disorder than the L. kluyveri ortholog (37% for duplicates versus 25% for singletons). Finally, we show that the number of physical interactions is significantly greater in the more intrinsically disordered ohnolog of a pair (p = 0.003, Wilcoxon). CONCLUSION: This work shows that intrinsic disorder gain and loss in a protein is a mechanism by which a genome can also diverge and innovate. The higher number of interactors for proteins that have gained intrinsic disorder compared with their duplicates may reflect the acquisition of new interaction partners or new functional roles

The GTOP database in 2009: updated content and novel features to expand and deepen insights into protein structures and functions

The Genomes TO Protein Structures and Functions (GTOP) database (http://spock.genes.nig.ac.jp/~genome/gtop.html) freely provides an extensive collection of information on protein structures and functions obtained by application of various computational tools to the amino acid sequences of entirely sequenced genomes. GTOP contains annotations of 3D structures, protein families, functions, and other useful data of a protein of interest in user-friendly ways to give a deep insight into the protein structure. From the initial 1999 version, GTOP has been continually updated to reap the fruits of genome projects and augmented to supply novel information, in particular intrinsically disordered regions. As intrinsically disordered regions constitute a considerable fraction of proteins and often play crucial roles especially in eukaryotes, their assignments give important additional clues to the functionality of proteins. Additionally, we have incorporated the following features into GTOP: a platform independent structural viewer, results of HMM searches against SCOP and Pfam, secondary structure predictions, color display of exon boundaries in eukaryotic proteins, assignments of gene ontology terms, search tools, and master files