A very high accuracy potential energy surface for H3

An exact quantum Monte Carlo (EQMC) method was used to calculate the potential energy surface (PES) for the ground electronic state of H3 over a grid of about 76000 nuclear geometries. The absolute abinitio statistical or sampling error of the calculation was ±0.01 kcal mol^-1 for energies (V) smaller than 3 eV. This PES was fitted by a three-dimensional cubic spline method and the fitting accuracy was determined from a set of 3684 randomly selected nuclear geometries not used in the fitting. For the range V3 eV the rms fitting error was ±0.010 kcal mol^-1, and the absolute value of the corresponding maximum error was 0.018 kcal mol^-1. This fitted EQMC PES is an order of magnitude more accurate than the best PES previously obtained for this system. Detailed comparisons are made with previous PESs, for the more dynamically important nuclear configurations

Cold Nuclear Matter In Holographic QCD

We study the Sakai-Sugimoto model of holographic QCD at zero temperature and finite chemical potential. We find that as the baryon chemical potential is increased above a critical value, there is a phase transition to a nuclear matter phase characterized by a condensate of instantons on the probe D-branes in the string theory dual. As a result of electrostatic interactions between the instantons, this condensate expands towards the UV when the chemical potential is increased, giving a holographic version of the expansion of the Fermi surface. We argue based on properties of instantons that the nuclear matter phase is necessarily inhomogeneous to arbitrarily high density. This suggests an explanation of the "chiral density wave" instability of the quark Fermi surface in large N_c QCD at asymptotically large chemical potential. We study properties of the nuclear matter phase as a function of chemical potential beyond the transition and argue in particular that the model can be used to make a semi-quantitative prediction of the binding energy per nucleon for nuclear matter in ordinary QCD.Comment: 31 pages, LaTeX, 1 figure, v2: some formulae corrected, qualitative results unchange

Electric Field-Tuned Topological Phase Transition in Ultra-Thin Na3Bi - Towards a Topological Transistor

The electric field induced quantum phase transition from topological to conventional insulator has been proposed as the basis of a topological field effect transistor [1-4]. In this scheme an electric field can switch 'on' the ballistic flow of charge and spin along dissipationless edges of the two-dimensional (2D) quantum spin Hall insulator [5-9], and when 'off' is a conventional insulator with no conductive channels. Such as topological transistor is promising for low-energy logic circuits [4], which would necessitate electric field-switched materials with conventional and topological bandgaps much greater than room temperature, significantly greater than proposed to date [6-8]. Topological Dirac semimetals(TDS) are promising systems in which to look for topological field-effect switching, as they lie at the boundary between conventional and topological phases [3,10-16]. Here we use scanning probe microscopy/spectroscopy (STM/STS) and angle-resolved photoelectron spectroscopy (ARPES) to show that mono- and bilayer films of TDS Na3Bi [3,17] are 2D topological insulators with bulk bandgaps >400 meV in the absence of electric field. Upon application of electric field by doping with potassium or by close approach of the STM tip, the bandgap can be completely closed then re-opened with conventional gap greater than 100 meV. The large bandgaps in both the conventional and quantum spin Hall phases, much greater than the thermal energy kT = 25 meV at room temperature, suggest that ultrathin Na3Bi is suitable for room temperature topological transistor operation

Magnetic Lattice Dynamics of the Oxygen-Free FeAs Pnictides: How Sensitive are Phonons to Magnetic Ordering?

To shed light on the role of magnetism on the superconducting mechanism of the oxygen-free FeAs pnictides, we investigate the effect of magnetic ordering on phonon dynamics in the low-temperature orthorhombic parent compounds, which present a spin-density wave. The study covers both the 122 (AFe2As2; A=Ca, Sr, Ba) and 1111 (AFeAsF; A=Ca, Sr) phases. We extend our recent work on the Ca (122 and 1111) and Ba (122) cases by treating computationally and experimentally the 122 and 1111 Sr compounds. The effect of magnetic ordering is investigated through detailed non-magnetic and magnetic lattice dynamical calculations. The comparison of the experimental and calculated phonon spectra shows that the magnetic interactions/ordering have to be included in order to reproduce well the measured density of states. This highlights a spin-correlated phonon behavior which is more pronounced than the apparently weak electron-phonon coupling estimated in these materials. Furthermore, there is no noticeable difference between phonon spectra of the 122 Ba and Sr, whereas there are substantial differences when comparing these to CaFe2As2 originating from different aspects of structure and bonding

Metabolomic biomarkers of pancreatic cancer: a meta-analysis study

Pancreatic cancer (PC) is an aggressive disease with high mortality rates, however, there is no blood test for early detection and diagnosis of this disease. Several research groups have reported on metabolomics based clinical investigations to identify biomarkers of PC, however there is a lack of a centralized metabolite biomarker repository that can be used for meta-analysis and biomarker validation. Furthermore, since the incidence of PC is associated with metabolic syndrome and Type 2 diabetes mellitus (T2DM), there is a need to uncouple these common metabolic dysregulations that may otherwise diminish the clinical utility of metabolomic biosignatures. Here, we attempted to externally replicate proposed metabolite biomarkers of PC reported by several other groups in an independent group of PC subjects. Our study design included a T2DM cohort that was used as a non-cancer control and a separate cohort diagnosed with colorectal cancer (CRC), as a cancer disease control to eliminate possible generic biomarkers of cancer. We used targeted mass spectrometry for quantitation of literature-curated metabolite markers and identified a biomarker panel that discriminates between normal controls (NC) and PC patients with high accuracy. Further evaluation of our model with CRC, however, showed a drop in specificity for the PC biomarker panel. Taken together, our study underscores the need for a more robust study design for cancer biomarker studies so as to maximize the translational value and clinical implementation.This work was supported by ACS IRG-92-152-17 pilot award number AWD4470404 to KU and AKC. The authors would like to acknowledge the Metabolomics Shared Resource in Georgetown University (Washington DC, USA) partially supported by NIH/NCI/CCSG grant P30-CA05100

Transcript-indexed ATAC-seq for precision immune profiling.

T cells create vast amounts of diversity in the genes that encode their T cell receptors (TCRs), which enables individual clones to recognize specific peptide-major histocompatibility complex (MHC) ligands. Here we combined sequencing of the TCR-encoding genes with assay for transposase-accessible chromatin with sequencing (ATAC-seq) analysis at the single-cell level to provide information on the TCR specificity and epigenomic state of individual T cells. By using this approach, termed transcript-indexed ATAC-seq (T-ATAC-seq), we identified epigenomic signatures in immortalized leukemic T cells, primary human T cells from healthy volunteers and primary leukemic T cells from patient samples. In peripheral blood CD4+ T cells from healthy individuals, we identified cis and trans regulators of naive and memory T cell states and found substantial heterogeneity in surface-marker-defined T cell populations. In patients with a leukemic form of cutaneous T cell lymphoma, T-ATAC-seq enabled identification of leukemic and nonleukemic regulatory pathways in T cells from the same individual by allowing separation of the signals that arose from the malignant clone from the background T cell noise. Thus, T-ATAC-seq is a new tool that enables analysis of epigenomic landscapes in clonal T cells and should be valuable for studies of T cell malignancy, immunity and immunotherapy

Study of the nucleon-induced preequilibrium reactions in terms of the Quantum Molecular Dynamics

The preequilibrium (nucleon-in, nucleon-out) angular distributions of $^{27}$Al, $^{58}$Ni and $^{90}$Zr have been analyzed in the energy region from 90 to 200 MeV in terms of the Quantum Moleculear Dynamics (QMD) theory. First, we show that the present approach can reproduce the measured (p,xp') and (p,xn) angular distributions leading to continuous final states without adjusing any parameters. Second, we show the results of the detailed study of the preequilibrium reaction processes; the step-wise contribution to the angular distribution, comparison with the quantum-mechanical Feshbach-Kerman-Koonin theory, the effects of momentum distribution and surface refraction/reflection to the quasifree scattering. Finally, the present method was used to assess the importance of multiple preequilibrium particle emission as a function of projectile energy up to 1 GeV.Comment: 22pages, Revex is used, 10 Postscript figures are available by request from [email protected]

Silicon Mie Resonators for Highly Directional Light Emission from monolayer MoS2

Controlling light emission from quantum emitters has important applications ranging from solid-state lighting and displays to nanoscale single-photon sources. Optical antennas have emerged as promising tools to achieve such control right at the location of the emitter, without the need for bulky, external optics. Semiconductor nanoantennas are particularly practical for this purpose because simple geometries, such as wires and spheres, support multiple, degenerate optical resonances. Here, we start by modifying Mie scattering theory developed for plane wave illumination to describe scattering of dipole emission. We then use this theory and experiments to demonstrate several pathways to achieve control over the directionality, polarization state, and spectral emission that rely on a coherent coupling of an emitting dipole to optical resonances of a Si nanowire. A forward-to-backward ratio of 20 was demonstrated for the electric dipole emission at 680 nm from a monolayer MoS2 by optically coupling it to a Si nanowire

Mycobacterium tuberculosis Complex Lipid Virulence Factors Preserved in the 17,000-Year-Old Skeleton of an Extinct Bison, Bison antiquus

Tracing the evolution of ancient diseases depends on the availability and accessibility of suitable biomarkers in archaeological specimens. DNA is potentially information-rich but it depends on a favourable environment for preservation. In the case of the major mycobacterial pathogens, Mycobacterium tuberculosis and Mycobacterium leprae, robust lipid biomarkers are established as alternatives or complements to DNA analyses. A DNA report, a decade ago, suggested that a 17,000-year-old skeleton of extinct Bison antiquus, from Natural Trap Cave, Wyoming, was the oldest known case of tuberculosis. In the current study, key mycobacterial lipid virulence factor biomarkers were detected in the same two samples from this bison. Fluorescence high-performance liquid chromatography (HPLC) indicated the presence of mycolic acids of the mycobacterial type, but they were degraded and could not be precisely correlated with tuberculosis. However, pristine profiles of C29, C30 and C32 mycocerosates and C27 mycolipenates, typical of the Mycobacterium tuberculosis complex, were recorded by negative ion chemical ionization gas chromatography mass spectrometry of pentafluorobenzyl ester derivatives. These findings were supported by the detection of C34 and C36 phthiocerols, which are usually esterified to the mycocerosates. The existence of Pleistocene tuberculosis in the Americas is confirmed and there are many even older animal bones with well-characterised tuberculous lesions similar to those on the analysed sample. In the absence of any evidence of tuberculosis in human skeletons older than 9,000 years BP, the hypothesis that this disease evolved as a zoonosis, before transfer to humans, is given detailed consideration and discussion.The study was supported by Leverhulme Trust Project Grant F/00 094/BL (GSB, DEM, OY-CL) and Wellcome Trust Grant 080988/Z/06/Z (GSB, OY-CL). A grant from the UK Natural and Environmental Research Council (DEM, GSB) provided access to the Mass Spectrometry Unit at the University of Bristol, UK