Stability of supercooled binary liquid mixtures

Recently the supercooled Wahnstrom binary Lennard-Jones mixture was partially crystallized into ${\rm MgZn_2}$ phase crystals in lengthy Molecular Dynamics simulations. We present Molecular Dynamics simulations of a modified Kob-Andersen binary Lennard-Jones mixture that also crystallizes in lengthy simulations, here however by forming pure fcc crystals of the majority component. The two findings motivate this paper that gives a general thermodynamic and kinetic treatment of the stability of supercooled binary mixtures, emphasizing the importance of negative mixing enthalpy whenever present. The theory is used to estimate the crystallization time in a Kob-Andersen mixture from the crystallization time in a series of relared systems. At T=0.40 we estimate this time to be 5$\times 10^{7}$ time units ($\approx 1. ms$). A new binary Lennard-Jones mixture is proposed that is not prone to crystallization and faster to simulate than the two standard binary Lennard-Jones mixtures; this is obtained by removing the like-particle attractions by switching to Weeks-Chandler-Andersen type potentials, while maintaining the unlike-particle attraction

Inflammation and changes in cytokine levels in neurological feline infectious peritonitis.

Feline infectious peritonitis (FIP) is a progressive, fatal, predominantly Arthus-type immune-mediated disease that is triggered when cats are infected with a mutant enteric coronavirus. The disease presents variably with multiple organ failure, seizures, generalized effusion, or shock. Neurological FIP is clinically and pathologically more homogeneous than systemic 'wet' or 'dry' FIP; thus, comparison of cytokine profiles from cats with neurological FIP, wet FIP, and non-FIP neurological disease may provide insight into some baseline characteristics relating to the immunopathogenesis of neurological FIP. This study characterizes inflammation and changes in cytokines in the brain tissue of FIP-affected cats. Cellular infiltrates in cats with FIP included lymphocytes, plasma cells, neutrophils, macrophages, and eosinophils. IL-1 beta, IL-6, IL-12, IL-18, TNF-alpha, macrophage inhibitory protein (MIP)-1 alpha, and RANTES showed no upregulation in the brains of control cats, moderate upregulation in neurological FIP cats, and very high upregulation in generalized FIP cats. Transcription of IFN-gamma appeared upregulated in cats with systemic FIP and slightly downregulated in neurological FIP. In most cytokines tested, variance was extremely high in generalized FIP and much less in neurological FIP. Principal components analysis was performed in order to find the least number of 'components' that would summarize the cytokine profiles in cats with neurological FIP. A large component of the variance (91.7%) was accounted for by levels of IL-6, MIP-1 alpha, and RANTES. These findings provide new insight into the immunopathogenesis of FIP and suggest targets for immune therapy of this disease

Crystallization of the Wahnstr\"om Binary Lennard-Jones Liquid

We report observation of crystallization of the glass-forming binary Lennard-Jones liquid first used by Wahnstr\"om [G. Wahnstr\"om, Phys. Rev. A 44, 3752 (1991)]. Molecular dynamics simulations of the metastable liquid on a timescale of microseconds were performed. The liquid crystallized spontaneously. The crystal structure was identified as MgZn_2. Formation of transient crystallites is observed in the liquid. The crystallization is investigate at different temperatures and compositions. At high temperature the rate of crystallite formation is the limiting factor, while at low temperature the limiting factor is growth rate. The melting temperature of the crystal is estimated to be T_m=0.93 at rho=0.82. The maximum crystallization rate of the A_2B composition is T=0.60+/-0.02.Comment: 4 pages, 4 figures; corrected typo

A mapping approach to synchronization in the "Zajfman trap": stability conditions and the synchronization mechanism

We present a two particle model to explain the mechanism that stabilizes a bunch of positively charged ions in an "ion trap resonator" [Pedersen etal, Phys. Rev. Lett. 87 (2001) 055001]. The model decomposes the motion of the two ions into two mappings for the free motion in different parts of the trap and one for a compressing momentum kick. The ions' interaction is modelled by a time delay, which then changes the balance between adjacent momentum kicks. Through these mappings we identify the microscopic process that is responsible for synchronization and give the conditions for that regime.Comment: 12 pages, 9 figures; submitted to Phys Rev

The Geometry of Slow Structural Fluctuations in a Supercooled Binary Alloy

The liquid structure of a glass-forming binary alloy is studied using molecular dynamics simulations. The analysis combines common neighbour analysis with the geometrical approach of Frank and Kasper to establish that the supercooled liquid contains extended clusters characterised by the same short range order as the crystal. Fluctuations in these clusters exhibit strong correlations with fluctuations in the inherent structure energy. The steep increase in the heat capacity on cooling is, thus, directly coupled to the growing fluctuations of the Frank-Kasper clusters. The relaxation of particles in the clusters dominates the slow tail of the self-intermediate scattering function

Strong pressure-energy correlations in liquids as a configuration space property: Simulations of temperature down jumps and crystallization

Computer simulations recently revealed that several liquids exhibit strong correlations between virial and potential energy equilibrium fluctuations in the NVT ensemble [U. R. Pedersen {\it et al.}, Phys. Rev. Lett. {\bf 100}, 015701 (2008)]. In order to investigate whether these correlations are present also far from equilibrium constant-volume aging following a temperature down jump from equilibrium was simulated for two strongly correlating liquids, an asymmetric dumbbell model and Lewis-Wahnstr{\"o}m OTP, as well as for SPC water that is not strongly correlating. For the two strongly correlating liquids virial and potential energy follow each other closely during the aging towards equilibrium. For SPC water, on the other hand, virial and potential energy vary with little correlation as the system ages towards equilibrium. Further proof that strong pressure-energy correlations express a configuration space property comes from monitoring pressure and energy during the crystallization (reported here for the first time) of supercooled Lewis-Wahnstr{\"o}m OTP at constant temperature

bíogo/hts: high throughput sequence handling for the Go language

biogo/hts provides a Go native implementation of the SAM specification (Group 2016) for SAM and BAM alignment formats (H. et al. 2012) commonly used for representation of high throughput genomic data, the BAI, CSI and tabix indexing formats, and the BGZF blocked compression format. The biogo/hts packages perform parallelized read and write operations and are able to cache recent reads according to user-specified caching methods. The parallelisation approach used by the biogo/hts package is influenced by the approach of the D implementation, sambamba by Tarazov et al. (T. A. et al. 2015). The biogo/hts APIs have been constructed to provide a consistent interface to sequence alignment data and the underlying compression system in order to aid ease of use and tool development.R. Daniel Kortschak, Brent S. Pedersen, and David L. Adelso

The ac-Driven Motion of Dislocations in a Weakly Damped Frenkel-Kontorova Lattice

By means of numerical simulations, we demonstrate that ac field can support stably moving collective nonlinear excitations in the form of dislocations (topological solitons, or kinks) in the Frenkel-Kontorova (FK) lattice with weak friction, which was qualitatively predicted by Bonilla and Malomed [Phys. Rev. B{\bf 43}, 11539 (1991)]. Direct generation of the moving dislocations turns out to be virtually impossible; however, they can be generated initially in the lattice subject to an auxiliary spatial modulation of the on-site potential strength. Gradually relaxing the modulation, we are able to get the stable moving dislocations in the uniform FK lattice with the periodic boundary conditions, provided that the driving frequency is close to the gap frequency of the linear excitations in the uniform lattice. The excitations have a large and noninteger index of commensurability with the lattice (suggesting that its actual value is irrational). The simulations reveal two different types of the moving dislocations: broad ones, that extend, roughly, to half the full length of the periodic lattice (in that sense, they cannot be called solitons), and localized soliton-like dislocations, that can be found in an excited state, demonstrating strong persistent internal vibrations. The minimum (threshold) amplitude of the driving force necessary to support the traveling excitation is found as a function of the friction coefficient. Its extrapolation suggests that the threshold does not vanish at the zero friction, which may be explained by radiation losses. The moving dislocation can be observed experimentally in an array of coupled small Josephson junctions in the form of an {\it inverse Josephson effect}, i.e., a dc-voltage response to the uniformly applied ac bias current.Comment: Plain Latex, 13 pages + 9 PostScript figures. to appear on Journal of Physics: condensed matte

Ptychographic X-ray computed tomography of extended colloidal networks in food emulsions

As a main structural level in colloidal food materials, extended colloidal networks are important for texture and rheology. By obtaining the 3D microstructure of the network, macroscopic mechanical properties of the material can be inferred. However, this approach is hampered by the lack of suitable non-destructive 3D imaging techniques with submicron resolution. We present results of quantitative ptychographic X-ray computed tomography applied to a palm kernel oil based oil-in-water emulsion. The measurements were carried out at ambient pressure and temperature. The 3D structure of the extended colloidal network of fat globules was obtained with a resolution of around 300 nm. Through image analysis of the network structure, the fat globule size distribution was computed and compared to previous findings. In further support, the reconstructed electron density values were within 4% of reference values.Comment: 19 pages, 4 figures, to be published in Food Structur

Observations of electron gyroharmonic waves and the structure of the Io torus

Narrow-banded emissions were observed by the Planetary Radio Astronomy experiment on the Voyager 1 spacecraft as it traversed the Io plasma torus. These waves occur between harmonics of the electron gyrofrequency and are the Jovian analogue of electrostatic emissions observed and theoretically studied for the terrestrial magnetosphere. The observed frequencies always include the component near the upper hybrid resonant frequency, (fuhr) but the distribution of the other observed emissions varies in a systematic way with position in the torus. A refined model of the electron density variation, based on identification of the fuhr line, is included. Spectra of the observed waves are analyzed in terms of the linear instability of an electron distribution function consisting of isotropic cold electrons and hot losscone electrons. The positioning of the observed auxiliary harmonics with respect to fuhr is shown to be an indicator of the cold to hot temperature ratio. It is concluded that this ratio increases systematically by an overall factor of perhaps 4 or 5 between the inner and outer portions of the torus