Laser-induced currents along molecular wire junctions

The treatment of the previous paper is extended to molecular wires. Specifically, the effect of electron-vibrational interactions on the electronic transport induced by femtosecond $\omega+2\omega$ laser fields along unbiased molecular nanojunctions is investigated. For this, the photoinduced vibronic dynamics of trans-polyacetylene oligomers coupled to macroscopic metallic leads is followed in a mean-field mixed quantum-classical approximation. A reduced description of the dynamics is obtained by introducing projective lead-molecule couplings and deriving an effective Schr\"odinger equation satisfied by the orbitals in the molecular region. Two possible rectification mechanisms are identified and investigated. The first one relies on near-resonance photon-absorption and is shown to be fragile to the ultrafast electronic decoherence processes introduced by the wire's vibrations. The second one employs the dynamic Stark effect and is demonstrated to be highly efficient and robust to electron-vibrational interactions.Comment: 14 pages, 10 figures. Accepted in J. Chem. Phy

In silico evaluation of WHO-endorsed molecular methods to detect drug resistant tuberculosis

Universal drug susceptibility testing (DST) for tuberculosis is a major goal of the END TB strategy. PCR-based molecular diagnostic tests have been instrumental in increasing DST globally and several assays have now been endorsed by the World Health Organization (WHO) for use in the diagnosis of drug resistance. These endorsed assays, however, each interrogate a limited number of mutations associated with resistance, potentially limiting their sensitivity compared to sequencing-based methods. We applied an in silico method to compare the sensitivity and specificity of WHO-endorsed molecular based diagnostics to the mutation set identified by the WHO mutations catalogue using phenotypic DST as the reference. We found that, in silico, the mutation sets used by probe-based molecular diagnostic tests to identify rifampicin, isoniazid, pyrazinamide, levofloxacin, moxifloxacin, amikacin, capreomycin and kanamycin resistance produced similar sensitivities and specificities to the WHO mutation catalogue. PCR-based diagnostic tests were most sensitive for drugs where mechanisms of resistance are well established and localised to small genetic regions or a few prevalent mutations. Approaches using sequencing technologies can provide advantages for drugs where our knowledge of resistance is limited, or where complex resistance signatures exist

The Asymmetric Merger of Black Holes

We study event horizons of non-axisymmetric black holes and show how features found in axisymmetric studies of colliding black holes and of toroidal black holes are non-generic and how new features emerge. Most of the details of black hole formation and black hole merger are known only in the axisymmetric case, in which numerical evolution has successfully produced dynamical space-times. The work that is presented here uses a new approach to construct the geometry of the event horizon, not by locating it in a given spacetime, but by direct construction. In the axisymmetric case, our method produces the familiar pair-of-pants structure found in previous numerical simulations of black hole mergers, as well as event horizons that go through a toroidal epoch as discovered in the collapse of rotating matter. The main purpose of this paper is to show how new - substantially different - features emerge in the non-axisymmetric case. In particular, we show how black holes generically go through a toroidal phase before they become spherical, and how this fits together with the merger of black holes.Comment: 28 pages, 10 figures, uses REVTEX. Improved quality figures and additional color images are provided at http://www.phyast.pitt.edu/~shusa/EH

Application of pharmacogenomics and bioinformatics to exemplify the utility of human <i>ex vivo</i> organoculture models in the field of precision medicine

Here we describe a collaboration between industry, the National Health Service (NHS) and academia that sought to demonstrate how early understanding of both pharmacology and genomics can improve strategies for the development of precision medicines. Diseased tissue ethically acquired from patients suffering from chronic obstructive pulmonary disease (COPD), was used to investigate inter-patient variability in drug efficacy using ex vivo organocultures of fresh lung tissue as the test system. The reduction in inflammatory cytokines in the presence of various test drugs was used as the measure of drug efficacy and the individual patient responses were then matched against genotype and microRNA profiles in an attempt to identify unique predictors of drug responsiveness. Our findings suggest that genetic variation in CYP2E1 and SMAD3 genes may partly explain the observed variation in drug response

BINGO: A code for the efficient computation of the scalar bi-spectrum

We present a new and accurate Fortran code, the BI-spectra and Non-Gaussianity Operator (BINGO), for the efficient numerical computation of the scalar bi-spectrum and the non-Gaussianity parameter f_{NL} in single field inflationary models involving the canonical scalar field. The code can calculate all the different contributions to the bi-spectrum and the parameter f_{NL} for an arbitrary triangular configuration of the wavevectors. Focusing firstly on the equilateral limit, we illustrate the accuracy of BINGO by comparing the results from the code with the spectral dependence of the bi-spectrum expected in power law inflation. Then, considering an arbitrary triangular configuration, we contrast the numerical results with the analytical expression available in the slow roll limit, for, say, the case of the conventional quadratic potential. Considering a non-trivial scenario involving deviations from slow roll, we compare the results from the code with the analytical results that have recently been obtained in the case of the Starobinsky model in the equilateral limit. As an immediate application, we utilize BINGO to examine of the power of the non-Gaussianity parameter f_{NL} to discriminate between various inflationary models that admit departures from slow roll and lead to similar features in the scalar power spectrum. We close with a summary and discussion on the implications of the results we obtain.Comment: v1: 5 pages, 5 figures; v2: 35 pages, 11 figures, title changed, extensively revised; v3: 36 pages, 11 figures, to appear in JCAP. The BINGO code is available online at http://www.physics.iitm.ac.in/~sriram/bingo/bingo.htm

Distasteful nectar deters floral robbery

Toxic nectar is an ecological paradox[1,2]. Plants divert substantial resources to produce nectar that attracts pollinators [3], but toxins in this reward could disrupt the mutualism and reduce plant fitness [4]. Alternatively, such compounds could protect nectar from robbers [2], provided they do not significantly alter pollinator visitation to the detriment of plant fitness [1,5–8]. Indeed, very few studies have investigated the role of plant toxins in nectar for defence against nectar robbers [4,9,10]. Here, we compared two Aconitum species (A. napellus and A. lycoctonum) that have flowers specialized for long-tongued bumblebee pollinators (Bombus hortorum) but are occasionally robbed by short-tongued bumblebees (B. terrestris) [6,11–13]. Pollinator visits to flowers were much more frequent than by robbers but visits correlated negatively with nectar alkaloid concentration and declined sharply between 200-380ppm. However, alkaloid concentrations of > 20ppm were deterrent to B. terrestris suggesting robbers were less tolerant of nectar alkaloids. Nectar of both plant species contained similar concentrations of carbohydrates and toxic alkaloids, but A. lycoctonum was more likely to secrete nectar in each flower and was also visited more frequently by pollinators and robbers.  We conclude that alkaloids in Aconitum sp. nectar affect rates of both pollinator visitation and robbery but may have co-evolved with nectar availability to maintain the fitness benefits of specialized plant-pollinator relationships. Chemical defence of nectar is, however, ultimately constrained by pollinator gustatory sensitivity