Premelting base pair opening probability and drug binding constant of a daunomycin-poly d(GCAT).poly d(ATGC) complex

We calculate room temperature thermal fluctuational base pair opening probability of a daunomycin-poly d(GCAT).poly d(ATGC) complex. This system is constructed at an atomic level of detail based on x-ray analysis of a crystal structure. The base pair opening probabilities are calculated from a modified self-consistent phonon approach of anharmonic lattice dynamics theory. We find that daunomycin binding substantially enhances the thermal stability of one of the base pairs adjacent the drug because of strong hydrogen bonding between the drug and the base. The possible effect of this enhanced stability on the drug inhibition of DNA transcription and replication is discussed. We also calculate the probability of drug dissociation from the helix based on the selfconsistent calculation of the probability of the disruption of drug-base H-bonds and the unstacking probability of the drug. The calculations can be used to determine the equilibrium drug binding constant which is found to be in good agreement with observations on similar daunomycin-DNA systems

Probing the stability of superheavy dark matter particles with high-energy neutrinos

Two of the most fundamental properties of the dark matter particle, the mass and the lifetime, are only weakly constrained by the astronomical and cosmological evidence of dark matter. We derive in this paper lower limits on the lifetime of dark matter particles with masses in the range 10 TeV-10^15 TeV from the non-observation of ultrahigh energy neutrinos in the AMANDA, IceCube, Auger and ANITA experiments. For dark matter particles which produce neutrinos in a two body or a three body decay, we find that the dark matter lifetime must be longer than O(10^26-10^28) s for masses between 10 TeV and the Grand Unification scale. Finally, we also calculate, for concrete particle physics scenarios, the limits on the strength of the interactions that induce the dark matter decay.Comment: 17 pages, 6 figures; v2: references added, discussion improved, matches the version published at JCA

The quadratic spinor Lagrangian is equivalent to the teleparallel theory

The quadratic spinor Lagrangian is shown to be equivalent to the teleparallel / tetrad representation of Einstein's theory. An important consequence is that the energy-momentum density obtained from this quadratic spinor Lagrangian is essentially the same as the ``tensor'' proposed by Moller in 1961.Comment: 10 pages, RevTe

InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation

peer-reviewedInnateDB (http://www.innatedb.com) is an integrated analysis platform that has been specifically designed to facilitate systems-level analyses of mammalian innate immunity networks, pathways and genes. In this article, we provide details of recent updates and improvements to the database. InnateDB now contains >196 000 human, mouse and bovine experimentally validated molecular interactions and 3000 pathway annotations of relevance to all mammalian cellular systems (i.e. not just immune relevant pathways and interactions). In addition, the InnateDB team has, to date, manually curated in excess of 18 000 molecular interactions of relevance to innate immunity, providing unprecedented insight into innate immunity networks, pathways and their component molecules. More recently, InnateDB has also initiated the curation of allergy- and asthma-related interactions. Furthermore, we report a range of improvements to our integrated bioinformatics solutions including web service access to InnateDB interaction data using Proteomics Standards Initiative Common Query Interface, enhanced Gene Ontology analysis for innate immunity, and the availability of new network visualizations tools. Finally, the recent integration of bovine data makes InnateDB the first integrated network analysis platform for this agriculturally important model organism.This work was supported by Genome BC through the Pathogenomics of Innate Immunity (PI2) project and by the Foundation for the National Institutes of Health and the Canadian Institutes of Health Research under the Grand Challenges in Global Health Research Initiative [Grand Challenges ID: 419]. Further funding was also provided by AllerGen grants 12ASI1 and 12B&B2. D.J.L. was funded in part during this project by a postdoctoral trainee award from the Michael Smith Foundation for Health Research (MSFHR). F.S.L.B. is a MSFHR Senior Scholar and R.E.W.H. holds a Canada Research Chair (CRC). Funding to enable bovine systems biology in InnateDB is provided by Teagasc [RMIS6018] and the Teagasc Walsh Fellowship scheme. IMEx is funded by the European Commission under the PSIMEx project [contract number FP7-HEALTH-2007-223411]. Funding for open access charge: Teagasc [RMIS6018]

Multiwalled Carbon Nanotubes for Heterogeneous Nanocatalytic Ozonation

Multiwalled carbon nanotubes functionalized by plasma oxygen (CNTs) have been used as heterogeneous catalysts for the ozonation of methyl orange (MO) dye (CI 13025) in aqueous solutions. It was found that the addition of CNTs significantly enhanced the dye decolorization as compared to ozone alone or when activated carbon was used at the same dose as CNTs. Both the initial ozone concentration and catalyst dosage enhanced the removal of MO. However, ozone gas concentrations higher than 6 g/m3 NTP did not further improve the decolorization rates. The removal efficiency of MO increased with pH in the range 2 to 3, while a reverse trend was observed when the pH increased from 3 to 9. The addition of a radical scavenger resulted in only a limited change in the decolorization rates suggesting that molecular ozone was the main pathway by which MO decolorization occurred in solution. However, under favorable conditions for MO attraction to CNT surface (pH = 3), the decolorization rate has significantly increased. At higher pH than the pKa value of MO (3.47) and the point of zero charge of CNT (3.87), a condition that favors the electrostatic repulsion of MO from CNT, the rates were reduced in the presence of CNT as compared to ozone alone possibly due to loss of part of the supplied ozone in un-useful parallel reactions

Thermal Unparticles: A New Form of Energy Density in the Universe

Unparticle \U with scaling dimension d_\U has peculiar thermal properties due to its unique phase space structure. We find that the equation of state parameter \omega_\U, the ratio of pressure to energy density, is given by 1/(2d_\U +1) providing a new form of energy in our universe. In an expanding universe, the unparticle energy density \rho_\U(T) evolves dramatically differently from that for photons. For d_\U >1, even if \rho_\U(T_D) at a high decoupling temperature $T_D$ is very small, it is possible to have a large relic density \rho_\U(T^0_\gamma) at present photon temperature $T^0_\gamma$, large enough to play the role of dark matter. We calculate $T_D$ and \rho_\U(T^0_\gamma) using photon-unparticle interactions for illustration.Comment: 5 pages; v3, journal version

Biochar Extracts Can Modulate the Toxicity of Persistent Free Radicals in the Nematode Caenorhabditis elegans

As an effective soil amendment, biochars require a comprehensive ecological evaluation before they can be widely used in agriculture because endogenous contaminants, such as environmentally persistent free radicals (EPFRs), certainly pose an ecological risk to soil invertebrates. In this study, Caenorhabditis elegans (C. elegans) was used as a model organism to investigate the neurotoxicity of two rice straw biochars pyrolyzed at 500 and 700 °C. After 24 h exposure to unwashed biochar, washed biochar, and leaching fluids (supernatants), the neurobehavioral parameters of C. elegans were determined in a liquid toxicity test. The results showed that the washed 700 °C biochar particles significantly impaired locomotion and prolonged the defecation interval at a biochar concentration of 4 g·well−1, while the unwashed biochar and supernatants caused no apparent impairment. Supporting this, electron paramagnetic resonance (EPR) results showed that the intensity of EPFRs in unwashed 700 °C biochar was stronger than that of the corresponding washed particles. This indicates that, in the liquid test, the EPR signal alone is not indicative of particle toxicity. The accessibility and activity of the EPFRs should be considered. Dissolved organic matter (DOM) was observed in the leaching fluids. The neurotoxic activity of the washed biochar was alleviated after the re-addition of leaching fluids to the washed biochar, suggesting that the dissolved organic materials modulate the reactivity of the EPFRs in the liquid phase. This study suggests that the leaching process may increase the risk of biochar when used in the field environment.National Natural Scientific Foundation of ChinaYunnan Province Basic Research ProjectNSFC-NCNPeer Reviewe

Bianchi type I space and the stability of inflationary Friedmann-Robertson-Walker space

Stability analysis of the Bianchi type I universe in pure gravity theory is studied in details. We first derive the non-redundant field equation of the system by introducing the generalized Bianchi type I metric. This non-redundant equation reduces to the Friedmann equation in the isotropic limit. It is shown further that any unstable mode of the isotropic perturbation with respect to a de Sitter background is also unstable with respect to anisotropic perturbations. Implications to the choice of physical theories are discussed in details in this paper.Comment: 5 pages, some comment adde

The dependence of the EIT wave velocity on the magnetic field strength

"EIT waves" are a wavelike phenomenon propagating in the corona, which were initially observed in the extreme ultraviolet (EUV) wavelength by the EUV Imaging Telescope (EIT). Their nature is still elusive, with the debate between fast-mode wave model and non-wave model. In order to distinguish between these models, we investigate the relation between the EIT wave velocity and the local magnetic field in the corona. It is found that the two parameters show significant negative correlation in most of the EIT wave fronts, {\it i.e.}, EIT wave propagates more slowly in the regions of stronger magnetic field. Such a result poses a big challenge to the fast-mode wave model, which would predict a strong positive correlation between the two parameters. However, it is demonstrated that such a result can be explained by the fieldline stretching model, \emph{i.e.,} that "EIT waves" are apparently-propagating brightenings, which are generated by successive stretching of closed magnetic field lines pushed by the erupting flux rope during coronal mass ejections (CMEs).Comment: 11 pages, 8 figures, accepted for publication in Solar Phy

General dissipation coefficient in low-temperature warm inflation

In generic particle physics models, the inflaton field is coupled to other bosonic and fermionic fields that acquire large masses during inflation and may decay into light degrees of freedom. This leads to dissipative effects that modify the inflationary dynamics and may generate a nearly-thermal radiation bath, such that inflation occurs in a warm rather than supercooled environment. In this work, we perform a numerical computation and obtain expressions for the associated dissipation coefficient in supersymmetric models, focusing on the regime where the radiation temperature is below the heavy mass threshold. The dissipation coefficient receives contributions from the decay of both on-shell and off-shell degrees of freedom, which are dominant for small and large couplings, respectively, taking into account the light field multiplicities. In particular, we find that the contribution from on-shell decays, although Boltzmann-suppressed, can be much larger than that of virtual modes, which is bounded by the validity of a perturbative analysis. This result opens up new possibilities for realizations of warm inflation in supersymmetric field theories.Comment: 25 pages, 13 figures; revised version with new results added; published in JCA