Comment on `Formation of a Dodecagonal Quasicrystalline Phase in a Simple Monatomic Liquid'

In a recent paper M. Dzugutov, Phys. Rev. Lett. 70 2924 (1993), describes a molecular dynamics cooling simulation where he obtained a large monatomic dodecagonal quasicrystal from a melt. The structure was stabilized by a special potential [Phys. Rev. A46 R2984 (1992)] designed to prevent the nucleation of simple dense crystal structures. In this comment we will give evidence that the ground state structure for Dzugutov's potential is an ordinary bcc crystal

Excitation of stellar oscillations by gravitational waves: hydrodynamic model and numerical results for the Sun

Starting from a general relativistic framework a hydrodynamic formalism is derived that yields the mean-square amplitudes and rms surface velocities of normal modes of non-relativistic stars excited by arbitrary gravitational wave (GW) radiation. In particular, stationary GW fields are considered and the resulting formulae are evaluated for two general types of GW radiation: radiation from a particular astrophysical source (e.g., a binary system) and a stochastic background of gravitational waves (SBGW). Expected sources and signal strengths for both types of GW radiation are reviewed and discussed. Numerical results for the Sun show that low-order quadrupolar g modes are excited more strongly than p modes by orders of magnitude. Maximal rms surface velocities in the case of excitation by astrophysical sources are found to be v {\le} 10^(-8) mm/s, assuming GW strain amplitudes of h {\le} 10^(-20). It is shown that current models for an SBGW produced by cosmic strings, with Omega_GW ~ 10^(-8)-10^(-5) in the frequency range of solar g modes, are able to produce maximal solar g-mode rms surface velocities of 10^(-5)-10^(-3) mm/s. This result lies close to or within the amplitude range of 10^(-3)-1 mm/s expected from excitation by turbulent convection, which is currently considered to be responsible for stellar g-mode excitation. It is concluded that studying g-mode observations of stars other than the Sun, in which excitation by GWs could be even more effective due to different stellar structures, might provide a new method to either detect GWs or to deduce a significant direct upper limit on an SBGW at intermediate frequencies between the pulsar bound and the bounds from interferometric detectors on Earth.Comment: 20 pages, 5 figure

On the Behavior of Hexane on Graphite at Near-Monolayer Densities

We present the results of molecular dynamics (MD) studies of hexane physisorbed onto graphite for eight coverages in the range $0.875 \le \rho \le 1.05$ (in units of monolayers). At low temperatures the adsorbate molecules form a uniaxially incommensurate herringbone (UI-HB) solid. At high coverages the solid consists of adsorbate molecules that are primarily rolled on their side perpen-dicular to the surface of the substrate. As the coverage is decreased, the amount of molecular rolling diminishes until $\rho$ = 0.933 where it disappears (molecules become primarily parallel to the surface). If the density is decreased enough, vacancies appear. As the temperature is increased we observe a three-phase regime for $\rho > 0.933$ (with an orientationally ordered nematic mesophase), for lower coverages the system melts directly to the disordered (and isotropic) liquid phase. The solid-nematic transition temperature is very sensitive to coverage whereas the melting temperature is quite insensitive to it, except for at low coverages where increased in-plane space and ultimately vacancies soften the solid phase and lower the melting temperature. Our results signal the importance of molecular rolling and tilting (which result from an the competition between molecule-molecule and molecule-substrate interactions) for the formation of the intermediate phase, while the insensitivity of the system's melting temperature to changing density is understood in terms of in-plane space occupation through rolling. Comparisons and contrasts with experimental results are discussed

A radio study of the superwind galaxy NGC1482

We present multifrequency radio continuum as well as HI observations of the superwind galaxy NGC1482, with both the GMRT and the VLA. This galaxy has a remarkable hourglass-shaped optical emission line outflow as well as bi-polar soft X-ray bubbles on opposite sides of the galactic disk. The low-frequency, lower-resolution radio observations show a smooth structure. From the non-thermal emission, we estimate the available energy in supernovae, and examine whether this would be adequate to drive the observed superwind outflow. The high-frequency, high-resolution radio images of the central starburst region located at the base of the superwind bi-cone shows one prominent peak and more extended emission with substructure. This image has been compared with the infrared, optical red-continuum, H_alpha, and, soft and hard X-ray images from Chandra. The peak of infrared emission is the only feature which is coincident with the prominent radio peak, and possibly defines the centre of the galaxy. The HI observations with the GMRT show two blobs of emission on opposite sides of the central region. These are rotating about the centre of the galaxy and are located at ~2.4 kpc from it. In addition, these observations also reveal a multicomponent HI-absorption profile against the central region of the radio source, with a total width of ~250 km/s. The extreme blue- and red-shifted absorption components are at 1688 and 1942 km/s respectively, while the peak absorption is at 1836 km/s. This is consistent with the heliocentric systemic velocity of 1850+/-20 km/s, estimated from a variety of observations. We discuss possible implications of these results.Comment: 11 pages, 10 figures, 4 tables, accepted for publication in MNRA

The Pierre Auger Observatory offline software

The Pierre Auger Observatory aims to discover the nature and origins of the highest energy cosmic rays. The large number of physicists involved in the project and the diversity of simulation and reconstruction tasks pose a challenge for the offline analysis software, not unlike the challenges confronting software for very large high energy physics experiments. Previously we have reported on the design and implementation of a general purpose but relatively lightweight framework which allows collaborators to contribute algorithms and sequencing instructions to build up the variety of applications they require. In this report, we update the status of this work and describe some of the successes and difficulties encountered over the last few years of use. We explain the machinery used to manage user contributions, to organize the abundance of configuration files, to facilitate multi-format file handling, and to provide access to event and time-dependent detector information residing in various data sources. We also describe the testing procedures used to help maintain stability of the code in the face of a large number of contributions. Foundation classes will also be discussed, including a novel geometry package which allows manipulation of abstract geometrical objects independent of coordinate system choice

Lack of Detectable HIV-1–Specific CD8+ T Cell Responses in Zambian HIV-1–Exposed Seronegative Partners of HIV-1–Positive Individuals

Human immunodeficiency virus type 1 (HIV-1)–specific T cell responses were characterized in a blinded study involving infected individuals and their seronegative exposed uninfected (EU) partners from Lusaka, Zambia. HIV-1–specific T cell responses were detected ex vivo in all infected individuals and amplified, on average, 27-fold following in vitro expansion. In contrast, no HIV-1–specific T cell responses were detected in any of the EU partners ex vivo or following in vitro expansion. These data demonstrate that the detection of HIV-1–specific T cell immunity in EU individuals is not universal and that alternative mechanisms may account for protection in these individuals

Variational and DMRG studies of the Frustrated Antiferromagnetic Heisenberg S=1 Quantum Spin Chain

We study a frustrated antiferromagnetic isotropic Heisenberg $S=1$ chain using a variational ansatz and the DMRG. At $\alpha_D=0.284(1)$, there is a disorder point of the second kind, marking the onset of incommensurate correlations in the chain. At $\alpha_L=0.3725(25)$ there is a Lifshitz point, at which the excitation spectrum develops a doubly degenerate structure. These points are the quantum remnants of the transition from antiferromagnetic to spiral order in the classical frustrated chain. At $\alpha_T=0.7444(6)$ there is a first order phase transition from an AKLT phase to a next-nearest neighbor generalization of the AKLT model. At the transition, the string order parameter shows a discontinuous jump of 0.085 to 0; the correlation length and the gap are both finite at the transition. The problem of edge states in open frustrated chains is discussed at length.Comment: 37 pages, 14 figures, submitted to Phys.Rev.

Influence of solvent granularity on the effective interaction between charged colloidal suspensions

We study the effect of solvent granularity on the effective force between two charged colloidal particles by computer simulations of the primitive model of strongly asymmetric electrolytes with an explicitly added hard sphere solvent. Apart from molecular oscillating forces for nearly touching colloids which arise from solvent and counterion layering, the counterions are attracted towards the colloidal surfaces by solvent depletion providing a simple statistical description of hydration. This, in turn, has an important influence on the effective forces for larger distances which are considerably reduced as compared to the prediction based on the primitive model. When these forces are repulsive, the long-distance behaviour can be described by an effective Yukawa pair potential with a solvent-renormalized charge. As a function of colloidal volume fraction and added salt concentration, this solvent-renormalized charge behaves qualitatively similar to that obtained via the Poisson-Boltzmann cell model but there are quantitative differences. For divalent counterions and nano-sized colloids, on the other hand, the hydration may lead to overscreened colloids with mutual attraction while the primitive model yields repulsive forces. All these new effects can be accounted for through a solvent-averaged primitive model (SPM) which is obtained from the full model by integrating out the solvent degrees of freedom. The SPM was used to access larger colloidal particles without simulating the solvent explicitly.Comment: 14 pages, 16 craphic

Controlling crystallization and its absence: Proteins, colloids and patchy models

The ability to control the crystallization behaviour (including its absence) of particles, be they biomolecules such as globular proteins, inorganic colloids, nanoparticles, or metal atoms in an alloy, is of both fundamental and technological importance. Much can be learnt from the exquisite control that biological systems exert over the behaviour of proteins, where protein crystallization and aggregation are generally suppressed, but where in particular instances complex crystalline assemblies can be formed that have a functional purpose. We also explore the insights that can be obtained from computational modelling, focussing on the subtle interplay between the interparticle interactions, the preferred local order and the resulting crystallization kinetics. In particular, we highlight the role played by ``frustration'', where there is an incompatibility between the preferred local order and the global crystalline order, using examples from atomic glass formers and model anisotropic particles.Comment: 11 pages, 7 figure

Machine-learning to Stratify Diabetic Patients Using Novel Cardiac Biomarkers and Integrative Genomics

Background: Diabetes mellitus is a chronic disease that impacts an increasing percentage of people each year. Among its comorbidities, diabetics are two to four times more likely to develop cardiovascular diseases. While HbA1c remains the primary diagnostic for diabetics, its ability to predict long-term, health outcomes across diverse demographics, ethnic groups, and at a personalized level are limited. The purpose of this study was to provide a model for precision medicine through the implementation of machine-learning algorithms using multiple cardiac biomarkers as a means for predicting diabetes mellitus development. Methods: Right atrial appendages from 50 patients, 30 non-diabetic and 20 type 2 diabetic, were procured from the WVU Ruby Memorial Hospital. Machine-learning was applied to physiological, biochemical, and sequencing data for each patient. Supervised learning implementing SHapley Additive exPlanations (SHAP) allowed binary (no diabetes or type 2 diabetes) and multiple classifcation (no diabetes, prediabetes, and type 2 diabetes) of the patient cohort with and without the inclusion of HbA1c levels. Findings were validated through Logistic Regression (LR), Linear Discriminant Analysis (LDA), Gaussian Naïve Bayes (NB), Support Vector Machine (SVM), and Classifcation and Regression Tree (CART) models with tenfold cross validation. Results: Total nuclear methylation and hydroxymethylation were highly correlated to diabetic status, with nuclear methylation and mitochondrial electron transport chain (ETC) activities achieving superior testing accuracies in the predictive model (~84% testing, binary). Mitochondrial DNA SNPs found in the D-Loop region (SNP-73G, -16126C, and -16362C) were highly associated with diabetes mellitus. The CpG island of transcription factor A, mitochondrial (TFAM) revealed CpG24 (chr10:58385262, P=0.003) and CpG29 (chr10:58385324, P=0.001) as markers correlating with diabetic progression. When combining the most predictive factors from each set, total nuclear methylation and CpG24 methylation were the best diagnostic measures in both binary and multiple classifcation sets. Conclusions: Using machine-learning, we were able to identify novel as well as the most relevant biomarkers associated with type 2 diabetes mellitus by integrating physiological, biochemical, and sequencing datasets. Ultimately, this approach may be used as a guideline for future investigations into disease pathogenesis and novel biomarker discover