Simulated single molecule microscopy with SMeagol

SMeagol is a software tool to simulate highly realistic microscopy data based on spatial systems biology models, in order to facilitate development, validation, and optimization of advanced analysis methods for live cell single molecule microscopy data. Availability and Implementation: SMeagol runs on Matlab R2014 and later, and uses compiled binaries in C for reaction-diffusion simulations. Documentation, source code, and binaries for recent versions of Mac OS, Windows, and Ubuntu Linux can be downloaded from http://smeagol.sourceforge.net.Comment: v2: 14 pages including supplementary text. Pre-copyedited, author-produced version of an application note published in Bioinformatics following peer review. The version of record, and additional supplementary material is available online at: https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btw10

Turbulent Velocity Structure in Molecular Clouds

We compare velocity structure in the Polaris Flare molecular cloud at scales ranging from 0.015 pc to 20 pc to simulations of supersonic hydrodynamic and MHD turbulence computed with the ZEUS MHD code. We use several different statistical methods to compare models and observations. The Delta-variance wavelet transform is most sensitive to characteristic scales and scaling laws, but is limited by a lack of intensity weighting. The scanning-beam size-linewidth relation is more robust with respect to noisy data. Obtaining the global velocity scaling behaviour requires that large-scale trends in the maps not be removed but treated as part of the turbulent cascade. We compare the true velocity PDF in our models to velocity centroids and average line profiles in optically thin lines, and find that the line profiles reflect the true PDF better unless the map size is comparable to the total line-of-sight thickness of the cloud. Comparison of line profiles to velocity centroid PDFs can thus be used to measure the line-of-sight depth of a cloud. The observed density and velocity structure is consistent with supersonic turbulence with a driving scale at or above the size of the molecular cloud and dissipative processes below 0.05 pc. Ambipolar diffusion could explain the dissipation. The velocity PDFs exclude small-scale driving such as that from stellar outflows as a dominant process in the observed region. In the models, large-scale driving is the only process that produces deviations from a Gaussian PDF shape consistent with observations. Strong magnetic fields impose a clear anisotropy on the velocity field, reducing the velocity variance in directions perpendicular to the field. (abridged)Comment: 21 pages, 24 figures, accepted by A&A, with some modifications, including change of claimed direct detection of dissipation scale to an upper limi

Interactions among intermediate redshift galaxies. The case of SDSSJ134420.86+663717.8

We present the properties of the central supermassive black holes and the host galaxies of the interacting object SDSSJ134420.86+663717.8. We obtained optical long slit spectroscopy data from the Large Binocular Telescope (LBT) using the Multi Object Double Spectrograph (MODS). Analysing the spectra revealed several strong broad and narrow emission lines of ionised gas in the nuclear region of one galaxy, whereas only narrow emission lines were visible for the second galaxy. The optical spectra were used to plot diagnostic diagrams, deduce rotation curves of the two galaxies, and calculate the masses of the central supermassive black holes. We find that the galaxy with broad emission line features has Seyfert~1 properties, while the galaxy with only narrow emission line features seems to be star-forming in nature. Furthermore, we find that the masses of the central supermassive black holes are almost equal at a few times 10^7 solar mass. Additionally, we present a simple N-body simulation to shed some light on the initial conditions of the progenitor galaxies. We find that for an almost orthogonal approach of the two interacting galaxies, the model resembles the optical image of the system

AMI-LA Observations of the SuperCLASS Super-cluster

We present a deep survey of the SuperCLASS super-cluster - a region of sky known to contain five Abell clusters at redshift $z\sim0.2$ - performed using the Arcminute Microkelvin Imager (AMI) Large Array (LA) at 15.5$~$GHz. Our survey covers an area of approximately 0.9 square degrees. We achieve a nominal sensitivity of $32.0~\mu$Jy beam$^{-1}$ toward the field centre, finding 80 sources above a $5\sigma$ threshold. We derive the radio colour-colour distribution for sources common to three surveys that cover the field and identify three sources with strongly curved spectra - a high-frequency-peaked source and two GHz-peaked-spectrum sources. The differential source count (i) agrees well with previous deep radio source count, (ii) exhibits no evidence of an emerging population of star-forming galaxies, down to a limit of 0.24$~$mJy, and (iii) disagrees with some models of the 15$~$GHz source population. However, our source count is in agreement with recent work that provides an analytical correction to the source count from the SKADS Simulated Sky, supporting the suggestion that this discrepancy is caused by an abundance of flat-spectrum galaxy cores as-yet not included in source population models.Comment: 17 pages, 14 figures, 3 tables. Accepted for publication in MNRA

Measuring Ages and Elemental Abundances from Unresolved Stellar Populations: Fe, Mg, C, N, and Ca

We present a method for determining mean light-weighted ages and abundances of Fe, Mg, C, N, and Ca, from medium resolution spectroscopy of unresolved stellar populations. The method, pioneered by Schiavon (2007), is implemented in a publicly available code called EZ_Ages. The method and error estimation are described, and the results tested for accuracy and consistency, by application to integrated spectra of well-known Galactic globular and open clusters. Ages and abundances from integrated light analysis agree with studies of resolved stars to within +/-0.1 dex for most clusters, and to within +/-0.2 dex for nearly all cases. The results are robust to the choice of Lick indices used in the fitting to within +/-0.1 dex, except for a few systematic deviations which are clearly categorized. The realism of our error estimates is checked through comparison with detailed Monte Carlo simulations. Finally, we apply EZ_Ages to the sample of galaxies presented in Thomas et al. (2005) and compare our derived values of age, [Fe/H], and [alpha/Fe] to their analysis. We find that [alpha/Fe] is very consistent between the two analyses, that ages are consistent for old (Age > 10 Gyr) populations, but show modest systematic differences at younger ages, and that [Fe/H] is fairly consistent, with small systematic differences related to the age systematics. Overall, EZ_Ages provides accurate estimates of fundamental parameters from medium resolution spectra of unresolved stellar populations in the old and intermediate-age regime, for the first time allowing quantitative estimates of the abundances of C, N, and Ca in these unresolved systems. The EZ_Ages code can be downloaded at http://www.ucolick.org/~graves/EZ_Ages.htmlComment: Accepted to ApJ

Design of ultraprecision machine tools with application to manufacturing of miniature and micro components

Currently the underlying necessities for predictability, producibility and productivity remain big issues in ultraprecision machining of miniature/microproducts. The demand on rapid and economic fabrication of miniature/microproducts with complex shapes has also made new challenges for ultraprecision machine tool design. In this paper the design for an ultraprecision machine tool is introduced by describing its key machine elements and machine tool design procedures. The focus is on the review and assessment of the state-of-the-art ultraprecision machining tools. It also illustrates the application promise of miniature/microproducts. The trends on machine tool development, tooling, workpiece material and machining processes are pointed out

Expansion and Collapse in the Cosmic Web

We study the kinematics of the gaseous cosmic web at high redshift with Lyman alpha forest absorption in multiple QSO sightlines. Using a simple analytic model and a cosmological hydrodynamic simulation we constrain the underlying three-dimensional distribution of velocities from the observed line-of-sight distribution of velocity shear across the plane of the sky. The distribution is found to be in good agreement with the intergalactic medium (IGM) undergoing large scale motions dominated by the Hubble flow. Modeling the Lyman alpha clouds analytically and with a hydrodynamics simulation, the average expansion velocity of the gaseous structures causing the Lyman alpha forest in the lower redshift (z = 2) sample appears about 20 percent lower than the local Hubble expansion velocity. We interpret this as tentative evidence for some clouds undergoing gravitational collapse. However, the distribution of velocities is highly skewed, and the majority of clouds at redshifts from 2 to 3.8 expand typically about 5 - 20 percent faster than the Hubble flow. This behavior is explained if most absorbers in the column density range typically detectable are expanding filaments that stretch and drain into more massive nodes. We find no evidence for the observed distribution of velocity shear being significantly influenced by processes other than Hubble expansion and gravitational instability, like galactic winds. To avoid overly disturbing the IGM, winds may be old and/or limp by the time we observe them in the Lyman alpha forest, or they may occupy only an insignificant volume fraction of the IGM. (abridged)Comment: 63 pages, 26 figures, AAS Latex; ApJ, in pres

Atomic-scale confinement of optical fields

In the presence of matter there is no fundamental limit preventing confinement of visible light even down to atomic scales. Achieving such confinement and the corresponding intensity enhancement inevitably requires simultaneous control over atomic-scale details of material structures and over the optical modes that such structures support. By means of self-assembly we have obtained side-by-side aligned gold nanorod dimers with robust atomically-defined gaps reaching below 0.5 nm. The existence of atomically-confined light fields in these gaps is demonstrated by observing extreme Coulomb splitting of corresponding symmetric and anti-symmetric dimer eigenmodes of more than 800 meV in white-light scattering experiments. Our results open new perspectives for atomically-resolved spectroscopic imaging, deeply nonlinear optics, ultra-sensing, cavity optomechanics as well as for the realization of novel quantum-optical devices