Tuneable molecular doping of corrugated graphene

Density functional theory (DFT) modeling of the physisorption of four different types of molecules (toluene, bromine dimmer, water and nitrogen dioxide) over and above graphene ripples has been performed. For all types of molecules changes of charge transfer and binding energies in respect to flat graphene is found. The changes in electronic structure of corrugated graphene and turn of {\pi}-orbitals of carbon atoms in combination with chemical structure of adsorbed molecules are proposed as the causes of difference with the perfect graphene case and variety of adsorption properties of different types of the molecules. Results of calculation suggest that the tops of the ripples are more attractive for large molecules and valley between ripples for small molecules. Stability of molecules on the ripples and energy barriers for migration over flat and corrugated graphene is also discussed.Comment: 15 pages, 5 figures, accepted in Surface Scienc

Analytical and clinical evaluation of an electrochemiluminescence immunoassay for the determination of CA 125

The CA 125 II assay on the Elecsys(R) 2010 analyzer was evaluated in an international multicenter trial. Imprecision studies yielded within-run CVs of 0.8-3.3% and between-day CVs of 2.4-10.9%; CVs for total imprecision in the manufacturer's laboratory were 2.4-7.8%. The linear range of the assay extended to at least 4500 kilounits/L (three decades). Interference from triglycerides (10.3 mmol/L), bilirubin (850 micromol/L), hemoglobin (1.1 mmol/L), anticoagulants (plasma), and several widely used drugs was undetectable. Method comparisons with five other CA 125 II assays showed good correlation but differences in standardization. A 95th percentile cutoff value of 35 kilounits/L was calculated from values measured in 593 apparently healthy (pre- and postmenopausal) women. In 95% of patients with benign gynecological diseases CA 125 was </=190 kilounits/L; 63% of patients with newly diagnosed ovarian carcinoma had values >190 kilounits/L. A comparison of CA 125 values obtained with the Elecsys test and with other common CA 125 tests in monitored patients being treated for ovarian cancer showed identical patterns. In conclusion, the Elecsys CA 125 II assay is linear over a broad range, yields precise and accurate results, is free from interferences, and compares well with other assays

Structure Formation, Melting, and the Optical Properties of Gold/DNA Nanocomposites: Effects of Relaxation Time

We present a model for structure formation, melting, and optical properties of gold/DNA nanocomposites. These composites consist of a collection of gold nanoparticles (of radius 50 nm or less) which are bound together by links made up of DNA strands. In our structural model, the nanocomposite forms from a series of Monte Carlo steps, each involving reaction-limited cluster-cluster aggregation (RLCA) followed by dehybridization of the DNA links. These links form with a probability $p_{eff}$ which depends on temperature and particle radius $a$. The final structure depends on the number of monomers (i. e. gold nanoparticles) $N_m$, $T$, and the relaxation time. At low temperature, the model results in an RLCA cluster. But after a long enough relaxation time, the nanocomposite reduces to a compact, non-fractal cluster. We calculate the optical properties of the resulting aggregates using the Discrete Dipole Approximation. Despite the restructuring, the melting transition (as seen in the extinction coefficient at wavelength 520 nm) remains sharp, and the melting temperature $T_M$ increases with increasing $a$ as found in our previous percolation model. However, restructuring increases the corresponding link fraction at melting to a value well above the percolation threshold. Our calculated extinction cross section agrees qualitatively with experiments on gold/DNA composites. It also shows a characteristic ``rebound effect,'' resulting from incomplete relaxation, which has also been seen in some experiments. We discuss briefly how our results relate to a possible sol-gel transition in these aggregates.Comment: 12 pages, 10 figure

Anisotropic dark energy stars

A model of compact object coupled to inhomogeneous anisotropic dark energy is studied. It is assumed a variable dark energy that suffers a phase transition at a critical density. The anisotropic Lambda-Tolman-Oppenheimer-Volkoff equations are integrated to know the structure of these objects. The anisotropy is concentrated on a thin shell where the phase transition takes place, while the rest of the star remains isotropic. The family of solutions obtained depends on the coupling parameter between the dark energy and the fermion matter. The solutions share several features in common with the gravastar model. There is a critical coupling parameter that gives non-singular black hole solutions. The mass-radius relations are studied as well as the internal structure of the compact objects. The hydrodynamic stability of the models is analyzed using a standard test from the mass-radius relation. For each permissible value of the coupling parameter there is a maximum mass, so the existence of black holes is unavoidable within this model.Comment: 12 pages, 6 figures, final manuscript, Accepted for publication in Astrophysics & Space Scienc

Neutrino Mass from R-parity Violation in Split Supersymmetry

We investigate how the observed neutrino data can be accommodated by R-parity violation in Split Supersymmetry. The atmospheric neutrino mass and mixing are explained by the bilinear parameters $\xi_i$ inducing the neutrino-neutralino mixing as in the usual low-energy supersymmetry. Among various one-loop corrections, only the quark-squark exchanging diagrams involving the order-one trilinear couplings $\lambda'_{i23,i32}$ can generate the solar neutrino mass and mixing if the scalar mass $m_S$ is not larger than $10^9$ GeV. This scheme requires an unpleasant hierarchical structure of the couplings, e.g., $\lambda_{i23,i32}\sim 1$, $\lambda'_{i33} \lesssim 10^{-4}$ and $\xi_i \lesssim 10^{-6}$. On the other hand, the model has a distinct collider signature of the lightest neutralino which can decay only to the final states, $l_i W^{(*)}$ and $\nu Z^{(*)}$, arising from the bilinear mixing. Thus, the measurement of the ratio; $\Gamma(e W^{(*)}) : \Gamma(\mu W^{(*)}) : \Gamma(\tau W^{(*)})$ would provide a clean probe of the small reactor and large atmospheric neutrino mixing angles as far as the neutralino mass is larger than 62 GeV.Comment: 10 pages, 3 figures, version submitted to JHE

Proteome profiling outperforms transcriptome profiling for coexpression based gene function prediction

Coexpression of mRNAs under multiple conditions is commonly used to infer cofunctionality of their gene products despite well-known limitations of this "guilt-by-association" (GBA) approach. Recent advancements in mass spectrometry-based proteomic technologies have enabled global expression profiling at the protein level; however, whether proteome profiling data can outperform transcriptome profiling data for coexpression based gene function prediction has not been systematically investigated. Here, we address this question by constructing and analyzing mRNA and protein coexpression networks for three cancer types with matched mRNA and protein profiling data from The Cancer Genome Atlas (TCGA) and the Clinical Proteomic Tumor Analysis Consortium (CPTAC). Our analyses revealed a marked difference in wiring between the mRNA and protein coexpression networks. Whereas protein coexpression was driven primarily by functional similarity between coexpressed genes, mRNA coexpression was driven by both cofunction and chromosomal colocalization of the genes. Functionally coherent mRNA modules were more likely to have their edges preserved in corresponding protein networks than functionally incoherent mRNA modules. Proteomic data strengthened the link between gene expression and function for at least 75% of Gene Ontology (GO) biological processes and 90% of KEGG pathways. A web application Gene2Net (http://cptac.gene2net.org) developed based on the three protein coexpression networks revealed novel gene-function relationships, such as linking ERBB2 (HER2) to lipid biosynthetic process in breast cancer, identifying PLG as a new gene involved in complement activation, and identifying AEBP1 as a new epithelial-mesenchymal transition (EMT) marker. Our results demonstrate that proteome profiling outperforms transcriptome profiling for coexpression based gene function prediction. Proteomics should be integrated if not preferred in gene function and human disease studies

Reionization by active sources and its effects on the cosmic microwave background

We investigate the possible effects of reionization by active sources on the cosmic microwave background. We concentrate on the sources themselves as the origin of reionization, rather than early object formation, introducing an extra period of heating motivated by the active character of the perturbations. Using reasonable parameters, this leads to four possibilities depending on the time and duration of the energy input: delayed last scattering, double last scattering, shifted last scattering and total reionization. We show that these possibilities are only very weakly constrained by the limits on spectral distortions from the COBE FIRAS measurements. We illustrate the effects of these reionization possibilities on the angular power spectrum of temperature anisotropies and polarization for simple passive isocurvature models and simple coherent sources, observing the difference between passive and active models. Finally, we comment on the implications of this work for more realistic active sources, such as causal white noise and topological defect models. We show for these models that non-standard ionization histories can shift the peak in the CMB power to larger angular scales.Comment: 21 pages LaTeX with 11 eps figures; replaced with final version accepted for publication in Phys. Rev.

Effects of Large CP violating phases on g_{\m}-2 in MSSM

Effects of CP violation on the supersymmetric electro-weak correction to the anomalous magnetic moment of the muon are investigated with the most general allowed set of CP violating phases in MSSM. The analysis includes contributions from the chargino and the neutralino exchanges to the muon anomaly. The supersymmetric contributions depend only on specific combinations of CP phases. The independent set of such phases is classified. We analyse the effects of the phases under the EDM constraints and show that large CP violating phases can drastically affect the magnitude of the supersymmetric electro-weak contribution to $a_{\mu}$ and may even affect its overall sign.Comment: 26 pages Latex file including 4 figure

Possible origins of macroscopic left-right asymmetry in organisms

I consider the microscopic mechanisms by which a particular left-right (L/R) asymmetry is generated at the organism level from the microscopic handedness of cytoskeletal molecules. In light of a fundamental symmetry principle, the typical pattern-formation mechanisms of diffusion plus regulation cannot implement the "right-hand rule"; at the microscopic level, the cell's cytoskeleton of chiral filaments seems always to be involved, usually in collective states driven by polymerization forces or molecular motors. It seems particularly easy for handedness to emerge in a shear or rotation in the background of an effectively two-dimensional system, such as the cell membrane or a layer of cells, as this requires no pre-existing axis apart from the layer normal. I detail a scenario involving actin/myosin layers in snails and in C. elegans, and also one about the microtubule layer in plant cells. I also survey the other examples that I am aware of, such as the emergence of handedness such as the emergence of handedness in neurons, in eukaryote cell motility, and in non-flagellated bacteria.Comment: 42 pages, 6 figures, resubmitted to J. Stat. Phys. special issue. Major rewrite, rearranged sections/subsections, new Fig 3 + 6, new physics in Sec 2.4 and 3.4.1, added Sec 5 and subsections of Sec

Dimers, Effective Interactions, and Pauli Blocking Effects in a Bilayer of Cold Fermionic Polar Molecules

We consider a bilayer setup with two parallel planes of cold fermionic polar molecules when the dipole moments are oriented perpendicular to the planes. The binding energy of two-body states with one polar molecule in each layer is determined and compared to various analytic approximation schemes in both coordinate- and momentum-space. The effective interaction of two bound dimers is obtained by integrating out the internal dimer bound state wave function and its robustness under analytical approximations is studied. Furthermore, we consider the effect of the background of other fermions on the dimer state through Pauli blocking, and discuss implications for the zero-temperature many-body phase diagram of this experimentally realizable system.Comment: 18 pages, 10 figures, accepted versio