Enhancement of superconductive critical temperatures in almost empty or full bands in two dimensions: possible relevance to beta-HfNCl, C60 and MgB2

We examine possibility of enhancement of superconductive critical temperature in two-dimensions. The weak coupling BCS theory is applied, especially when the Fermi level is near the edges of the electronic bands. The attractive interaction depends on ${\bf k}$ due to screening. The density of states(DOS) does not have a peak near the bottom of the band, but $k$-dependent contribution to DOS (electron density on the Fermi surface) has a diverging peak at the bottom or top. These features lead to significant enhancement of the critical temperatures. The results are qualitatively consistent with the superconductive behaviors of HfNCl (\Tc \le 25K) and ZrNCl(\Tc \le 15K), C$_{60}$ with a field-effect transistor configuration (\Tc = 52K), and MgB$_2$ (\Tc \approx 40K) which have the unexpectedly high superconductive critical transition temperatures.Comment: 5 pages,4 figure

Effects of cluster diffusion on the island density and size distribution in submonolayer island growth

The effects of cluster diffusion on the submonolayer island density and island-size distribution are studied for the case of irreversible growth of compact islands on a 2D substrate. In our model, we assume instantaneous coalescence of circular islands, while the cluster mobility is assumed to exhibit power-law decay as a function of island-size with exponent mu. Results are presented for mu = 1/2, 1, and 3/2 corresponding to cluster diffusion via Brownian motion, correlated evaporation-condensation, and edge-diffusion respectively, as well as for higher values including mu = 2,3, and 6. We also compare our results with those obtained in the limit of no cluster mobility corresponding to mu = infinity. In agreement with theoretical predictions of power-law behavior of the island-size distribution (ISD) for mu < 1, for mu = 1/2 we find Ns({\theta}) ~ s^{-\tau} (where Ns({\theta}) is the number of islands of size s at coverage {\theta}) up to a cross-over island-size S_c. However, the value of {\tau} obtained in our simulations is higher than the mean-field (MF) prediction {\tau} = (3 - mu)/2. Similarly, the value of the exponent {\zeta} corresponding to the dependence of S_c on the average island-size S (e.g. S_c ~ S^{\zeta}) is also significantly higher than the MF prediction {\zeta} = 2/(mu+1). A generalized scaling form for the ISD is also proposed for mu < 1, and using this form excellent scaling is found for mu = 1/2. However, for finite mu >= 1 neither the generalized scaling form nor the standard scaling form Ns({\theta}) = {\theta} /S^2 f(s/S) lead to scaling of the entire ISD for finite values of the ratio R of the monomer diffusion rate to deposition flux. Instead, the scaled ISD becomes more sharply peaked with increasing R and coverage. This is in contrast to models of epitaxial growth with limited cluster mobility for which good scaling occurs over a wide range of coverages.Comment: 12 pages, submitted to Physical Review

The mRNA-bound proteome of the human malaria parasite Plasmodium falciparum.

BackgroundGene expression is controlled at multiple levels, including transcription, stability, translation, and degradation. Over the years, it has become apparent that Plasmodium falciparum exerts limited transcriptional control of gene expression, while at least part of Plasmodium's genome is controlled by post-transcriptional mechanisms. To generate insights into the mechanisms that regulate gene expression at the post-transcriptional level, we undertook complementary computational, comparative genomics, and experimental approaches to identify and characterize mRNA-binding proteins (mRBPs) in P. falciparum.ResultsClose to 1000 RNA-binding proteins are identified by hidden Markov model searches, of which mRBPs encompass a relatively large proportion of the parasite proteome as compared to other eukaryotes. Several abundant mRNA-binding domains are enriched in apicomplexan parasites, while strong depletion of mRNA-binding domains involved in RNA degradation is observed. Next, we experimentally capture 199 proteins that interact with mRNA during the blood stages, 64 of which with high confidence. These captured mRBPs show a significant overlap with the in silico identified candidate RBPs (p &lt; 0.0001). Among the experimentally validated mRBPs are many known translational regulators active in other stages of the parasite's life cycle, such as DOZI, CITH, PfCELF2, Musashi, and PfAlba1-4. Finally, we also detect several proteins with an RNA-binding domain abundant in Apicomplexans (RAP domain) that is almost exclusively found in apicomplexan parasites.ConclusionsCollectively, our results provide the most complete comparative genomics and experimental analysis of mRBPs in P. falciparum. A better understanding of these regulatory proteins will not only give insight into the intricate parasite life cycle but may also provide targets for novel therapeutic strategies

Nascent RNA sequencing reveals mechanisms of gene regulation in the human malaria parasite Plasmodium falciparum.

Gene expression in Plasmodium falciparum is tightly regulated to ensure successful propagation of the parasite throughout its complex life cycle. The earliest transcriptomics studies in P. falciparum suggested a cascade of transcriptional activity over the course of the 48-hour intraerythrocytic developmental cycle (IDC); however, the just-in-time transcriptional model has recently been challenged by findings that show the importance of post-transcriptional regulation. To further explore the role of transcriptional regulation, we performed the first genome-wide nascent RNA profiling in P. falciparum. Our findings indicate that the majority of genes are transcribed simultaneously during the trophozoite stage of the IDC and that only a small subset of genes is subject to differential transcriptional timing. RNA polymerase II is engaged with promoter regions prior to this transcriptional burst, suggesting that Pol II pausing plays a dominant role in gene regulation. In addition, we found that the overall transcriptional program during gametocyte differentiation is surprisingly similar to the IDC, with the exception of relatively small subsets of genes. Results from this study suggest that further characterization of the molecular players that regulate stage-specific gene expression and Pol II pausing will contribute to our continuous search for novel antimalarial drug targets

QCD and total cross-sections: photons and hadrons

In this contribution, we discuss a total cross-section model which can be applied to both photon and purely hadronic processes. We find that the model can reproduce photo-production cross-sections, as well as extrapolations of gamma* p processes to gamma p using vector meson dominance models, with minimal modifications from the proton case.Comment: 5 pages, 1 figure, to be published in Proceedings of Diffraction 2008, September 9-14 2008, Marseille, Franc

DNA-encoded nucleosome occupancy is associated with transcription levels in the human malaria parasite Plasmodium falciparum.

BackgroundIn eukaryotic organisms, packaging of DNA into nucleosomes controls gene expression by regulating access of the promoter to transcription factors. The human malaria parasite Plasmodium falciparum encodes relatively few transcription factors, while extensive nucleosome remodeling occurs during its replicative cycle in red blood cells. These observations point towards an important role of the nucleosome landscape in regulating gene expression. However, the relation between nucleosome positioning and transcriptional activity has thus far not been explored in detail in the parasite.ResultsHere, we analyzed nucleosome positioning in the asexual and sexual stages of the parasite's erythrocytic cycle using chromatin immunoprecipitation of MNase-digested chromatin, followed by next-generation sequencing. We observed a relatively open chromatin structure at the trophozoite and gametocyte stages, consistent with high levels of transcriptional activity in these stages. Nucleosome occupancy of genes and promoter regions were subsequently compared to steady-state mRNA expression levels. Transcript abundance showed a strong inverse correlation with nucleosome occupancy levels in promoter regions. In addition, AT-repeat sequences were strongly unfavorable for nucleosome binding in P. falciparum, and were overrepresented in promoters of highly expressed genes.ConclusionsThe connection between chromatin structure and gene expression in P. falciparum shares similarities with other eukaryotes. However, the remarkable nucleosome dynamics during the erythrocytic stages and the absence of a large variety of transcription factors may indicate that nucleosome binding and remodeling are critical regulators of transcript levels. Moreover, the strong dependency between chromatin structure and DNA sequence suggests that the P. falciparum genome may have been shaped by nucleosome binding preferences. Nucleosome remodeling mechanisms in this deadly parasite could thus provide potent novel anti-malarial targets

Exchange interaction effects in the thermodynamic properties of quantum dots

We study electron-electron interaction effects in the thermodynamic properties of quantum-dot systems. We obtain the direct and exchange contributions to the specific heat C_v in the self-consistent Hartree-Fock approximation at finite temperatures. An exchange-induced phase transition is observed and the transition temperature is shown to be inversely proportional to the size of the system. The exchange contribution to C_v dominates over the direct and kinetic contributions in the intermediate regime of interaction strength (r_s ~ 1). Furthermore, the electron-electron interaction modifies both the amplitude and the period of magnetic field induced oscillations in C_v.Comment: 4 pages, 4 figures; To appear in Phys. Rev.