Characterizing the bending and flexibility induced by bulges in DNA duplexes

Advances in DNA nanotechnology have stimulated the search for simple motifs that can be used to control the properties of DNA nanostructures. One such motif, which has been used extensively in structures such as polyhedral cages, two-dimensional arrays, and ribbons, is a bulged duplex, that is, two helical segments that connect at a bulge loop. We use a coarse-grained model of DNA to characterize such bulged duplexes. We find that this motif can adopt structures belonging to two main classes: one where the stacking of the helices at the center of the system is preserved, the geometry is roughly straight, and the bulge is on one side of the duplex and the other where the stacking at the center is broken, thus allowing this junction to act as a hinge and increasing flexibility. Small loops favor states where stacking at the center of the duplex is preserved, with loop bases either flipped out or incorporated into the duplex. Duplexes with longer loops show more of a tendency to unstack at the bulge and adopt an open structure. The unstacking probability, however, is highest for loops of intermediate lengths, when the rigidity of single-stranded DNA is significant and the loop resists compression. The properties of this basic structural motif clearly correlate with the structural behavior of certain nano-scale objects, where the enhanced flexibility associated with larger bulges has been used to tune the self-assembly product as well as the detailed geometry of the resulting nanostructures. We further demonstrate the role of bulges in determining the structure of a "Z-tile," a basic building block for nanostructures

A criterion for the fragmentation of bubbly magma based on brittle failure theory

The fragmentation of bubbly magma is a defining point in a volcanic eruption-before fragmentation the magma flows relatively slowly, during fragmentation the bubbles break up to release compressed gas and, afterwards, the eruption becomes a violent gas flow carrying suspended magma particles. Seemingly benign lava flows or domes can suddenly fragment into deadly pyroclastic flows(1-3). Several criteria have been proposed to define the point of magma fragmentation or foam stability(4-7). The criterion of Papale(7) is based on melt relaxation theory and equates magma strain rate with the rate of increase of flow velocity with distance. It ignores, however, the role of bubble pressure in causing fragmentation. Two empirical approaches(4,5) consider the role of high bubble pressure in causing fragmentation but do not address the underlying physics of magma fragmentation. Here I develop a fragmentation criterion for bubbly magma based on brittle failure theory and apply it to the fragmentation of lava domes and flows. On the basis of this theory, a bubbly magma will fragment when the tensile stress at the inner walls of bubbles exceeds the tensile strength of the magma. The fragmentation conditions depend strongly on initial water content, with calculated vesicularity and final water levels coinciding reasonably well with those in observed pumices. This suggests that the proposed criterion captures the essence of the fragmentation process in bubbly magma.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/62724/1/402648a0.pd

Tissue and serum immune response in chronic hepatitis C with mild histological lesions

The immunopathogenesis of chronic hepatitis C virus (HCV) infection is a matter of great controversy and has been suggested to involve a complex balance between cytokines with pro and anti-inflammatory activity. We investigated the expression of inflammatory cells and cytokines in the liver and serum of 51 chronically HCV infected patients and compared them to data from two sets of normal controls: 51 healthy blood donors and 33 liver biopsies of healthy liver donors. We also assessed the relationship between selected cytokines and cell populations in hepatic compartments and the disease stage. Compared with controls, hepatitis C patients had a greater expression of portal TNF-α, TGF-β and CD4+ and acinar IFN-γ, TNF-α, IL-1β and IL-4, as well as a higher serum concentration of IL-2, IL-10 and TGF-β. Significant positive correlations were found between portal CD4+ and TNF-α, portal CD8+ and TGF-β, portal CD45+RO and TNF-α, acinar CD45+RO and IFN-γ and acinar CD57+ and TGF-β. In conclusion, we have shown that (i) in this sample of predominantly mild disease, the immune response was associated with a pro-inflammatory response pattern, (ii) CD4+ T-lymphocytes played a major role in orchestrating the immune response and (iii) these events primarily took place in the portal space.FAPES

IACT observations of gamma-ray bursts: prospects for the Cherenkov Telescope Array

Gamma rays at rest frame energies as high as 90 GeV have been reported from gamma-ray bursts (GRBs) by the Fermi Large Area Telescope (LAT). There is considerable hope that a confirmed GRB detection will be possible with the upcoming Cherenkov Telescope Array (CTA), which will have a larger effective area and better low-energy sensitivity than current-generation imaging atmospheric Cherenkov telescopes (IACTs). To estimate the likelihood of such a detection, we have developed a phenomenological model for GRB emission between 1 GeV and 1 TeV that is motivated by the high-energy GRB detections of Fermi-LAT, and allows us to extrapolate the statistics of GRBs seen by lower energy instruments such as the Swift-BAT and BATSE on the Compton Gamma-ray Observatory. We show a number of statistics for detected GRBs, and describe how the detectability of GRBs with CTA could vary based on a number of parameters, such as the typical observation delay between the burst onset and the start of ground observations. We also consider the possibility of using GBM on Fermi as a finder of GRBs for rapid ground follow-up. While the uncertainty of GBM localization is problematic, the small field-of-view for IACTs can potentially be overcome by scanning over the GBM error region. Overall, our results indicate that CTA should be able to detect one GRB every 20 to 30 months with our baseline instrument model, assuming consistently rapid pursuit of GRB alerts, and provided that spectral breaks below 100 GeV are not a common feature of the bright GRB population. With a more optimistic instrument model, the detection rate can be as high as 1 to 2 GRBs per year.Comment: 28 pages, 24 figures, 4 tables, submitted to Experimental Astronom

Carbon fragmentation measurements and validation of the GEANT4 nuclear reaction models for hadrontherapy

Nuclear fragmentation measurements are necessary when using heavy-ion beams in hadrontherapy to predict the effects of the ion nuclear interactions within the human body. Moreover, they are also fundamental to validate and improve the Monte Carlo codes for their use in planning tumor treatments. Nowadays, a very limited set of carbon fragmentation cross sections are being measured, and in particular, to our knowledge, no double-differential fragmentation cross sections at intermediate energies are available in the literature. In this work, we have measured the double-differential cross sections and the angular distributions of the secondary fragments produced in the C-12 fragmentation at 62 A MeV on a thin carbon target. The experimental data have been used to benchmark the prediction capability of the GEANT4 Monte Carlo code at intermediate energies, where it was never tested before. In particular, we have compared the experimental data with the predictions of two GEANT4 nuclear reaction models: the Binary Light Ions Cascade and the Quantum Molecular Dynamic. From the comparison, it has been observed that the Binary Light Ions Cascade approximates the angular distributions of the fragment production cross sections better than the Quantum Molecular Dynamic model. However, the discrepancies observed between the experimental data and the Monte Carlo simulations lead to the conclusion that the prediction capability of both models needs to be improved at intermediate energies