Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin.

Gene silencing by heterochromatin is proposed to occur in part as a result of the ability of heterochromatin protein 1 (HP1) proteins to spread across large regions of the genome, compact the underlying chromatin and recruit diverse ligands. Here we identify a new property of the human HP1α protein: the ability to form phase-separated droplets. While unmodified HP1α is soluble, either phosphorylation of its N-terminal extension or DNA binding promotes the formation of phase-separated droplets. Phosphorylation-driven phase separation can be promoted or reversed by specific HP1α ligands. Known components of heterochromatin such as nucleosomes and DNA preferentially partition into the HP1α droplets, but molecules such as the transcription factor TFIIB show no preference. Using a single-molecule DNA curtain assay, we find that both unmodified and phosphorylated HP1α induce rapid compaction of DNA strands into puncta, although with different characteristics. We show by direct protein delivery into mammalian cells that an HP1α mutant incapable of phase separation in vitro forms smaller and fewer nuclear puncta than phosphorylated HP1α. These findings suggest that heterochromatin-mediated gene silencing may occur in part through sequestration of compacted chromatin in phase-separated HP1 droplets, which are dissolved or formed by specific ligands on the basis of nuclear context

Viscoelastic Phase Separation in Shear Flow

We numerically investigate viscoelastic phase separation in polymer solutions under shear using a time-dependent Ginzburg-Landau model. The gross variables in our model are the polymer volume fraction and a conformation tensor. The latter represents chain deformations and relaxes slowly on the rheological time giving rise to a large viscoelastic stress. The polymer and the solvent obey two-fluid dynamics in which the viscoelastic stress acts asymmetrically on the polymer and, as a result, the stress and the diffusion are dynamically coupled. Below the coexistence curve, interfaces appear with increasing the quench depth and the solvent regions act as a lubricant. In these cases the composition heterogeneity causes more enhanced viscoelastic heterogeneity and the macroscopic stress is decreased at fixed applied shear rate. We find steady two-phase states composed of the polymer-rich and solvent-rich regions, where the characteristic domain size is inversely proportional to the average shear stress for various shear rates. The deviatoric stress components exhibit large temporal fluctuations. The normal stress difference can take negative values transiently at weak shear.Comment: 16pages, 16figures, to be published in Phys.Rev.

The Predicting Tree Growth App: an algorithmic approach to modelling individual tree growth

PredictingTreeGrowth is free and open-source application software written in Python 3.7 that allows easy and fast development of predictive models using the Recurrent Neural Network (RNN)/Long Short-Term Memory (LSTM) framework. RNNs have an upgraded architecture able to capture tree growth mechanisms related to time ordering and size dependence. The motivation for this App is to demystify the use of Machine Learning algorithms and allow accessibility of Machine Learning algorithms by the scientific community. Its simple graphical user interface (GUI) provides straightforward tools for building predictive models with the RNN algorithm.Fil: Magalhaes, Juliana G. de S.. University of British Columbia; CanadáFil: Polinko, Adam P.. Mississippi State University.; Estados UnidosFil: Amoroso, Mariano Martin. Universidad Nacional de Río Negro. Sede Andina. Instituto de Investigaciones en Recursos Naturales, Agroecología y Desarrollo Rural; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Kohli, Gursimran S.. University Fraser Simon; CanadáFil: Larson, Bruce C.. University of British Columbia; Canad

Isotropically Driven versus Outflow Driven Turbulence: Observational Consequences for Molecular Clouds

Feedback from protostellar outflows can influence the nature of turbulence in star forming regions even if they are not the primary source of velocity dispersion for all scales of molecular clouds. For the rate and power expected in star forming regions, we previously (Carroll et al. 2009) demonstrated that outflows could drive supersonic turbulence at levels consistent with the scaling relations from Matzner 2007 although with a steeper velocity power spectrum than expected for an isotropically driven supersonic turbulent cascade. Here we perform higher resolution simulations and combine simulations of outflow driven turbulence with those of isotropically forced turbulence. We find that the presence of outflows within an ambient isotropically driven turbulent environment produces a knee in the velocity power spectrum at the outflow scale and a steeper slope at sub-outflow scales than for a purely isotropically forced case. We also find that the presence of outflows flattens the density spectrum at large scales effectively reducing the formation of large scale turbulent density structures. These effects are qualitatively independent of resolution. We have also carried out Principal Component Analysis (PCA) for synthetic data from our simulations. We find that PCA as a tool for identifying the driving scale of turbulence has a misleading bias toward low amplitude large scale velocity structures even when they are not necessarily the dominant energy containing scales. This bias is absent for isotropically forced turbulence but manifests strongly for collimated outflow driven turbulence.Comment: 30 pages, 10 figures, Submitted to Ap

A New Algorithm for Supernova Neutrino Transport and Some Applications

We have developed an implicit, multi-group, time-dependent, spherical neutrino transport code based on the Feautrier variables, the tangent-ray method, and accelerated ${\bf \Lambda}$ iteration. The code achieves high angular resolution, is good to O($v/c$), is equivalent to a Boltzmann solver (without gravitational redshifts), and solves the transport equation at all optical depths with precision. In this paper, we present our formulation of the relevant numerics and microphysics and explore protoneutron star atmospheres for snapshot post-bounce models. Our major focus is on spectra, neutrino-matter heating rates, Eddington factors, angular distributions, and phase-space occupancies. In addition, we investigate the influence on neutrino spectra and heating of final-state electron blocking, stimulated absorption, velocity terms in the transport equation, neutrino-nucleon scattering asymmetry, and weak magnetism and recoil effects. Furthermore, we compare the emergent spectra and heating rates obtained using full transport with those obtained using representative flux-limited transport formulations to gauge their accuracy and viability. Finally, we derive useful formulae for the neutrino source strength due to nucleon-nucleon bremsstrahlung and determine bremsstrahlung's influence on the emergent $\nu_{\mu}$ and $\nu_{\tau}$ neutrino spectra.Comment: 58 pages, single-spaced LaTeX, 23 figures, revised title, also available at http://jupiter.as.arizona.edu/~burrows/papers, accepted for publication in the Ap.

Protostellar Outflow Evolution in Turbulent Environments

The link between turbulence in star formatting environments and protostellar jets remains controversial. To explore issues of turbulence and fossil cavities driven by young stellar outflows we present a series of numerical simulations tracking the evolution of transient protostellar jets driven into a turbulent medium. Our simulations show both the effect of turbulence on outflow structures and, conversely, the effect of outflows on the ambient turbulence. We demonstrate how turbulence will lead to strong modifications in jet morphology. More importantly, we demonstrate that individual transient outflows have the capacity to re-energize decaying turbulence. Our simulations support a scenario in which the directed energy/momentum associated with cavities is randomized as the cavities are disrupted by dynamical instabilities seeded by the ambient turbulence. Consideration of the energy power spectra of the simulations reveals that the disruption of the cavities powers an energy cascade consistent with Burgers'-type turbulence and produces a driving scale-length associated with the cavity propagation length. We conclude that fossil cavities interacting either with a turbulent medium or with other cavities have the capacity to sustain or create turbulent flows in star forming environments. In the last section we contrast our work and its conclusions with previous studies which claim that jets can not be the source of turbulence.Comment: 24 pages, submitted to the Astrophysical Journa

Dynamics of gelling liquids: a short survey

The dynamics of randomly crosslinked liquids is addressed via a Rouse- and a Zimm-type model with crosslink statistics taken either from bond percolation or Erdoes-Renyi random graphs. While the Rouse-type model isolates the effects of the random connectivity on the dynamics of molecular clusters, the Zimm-type model also accounts for hydrodynamic interactions on a preaveraged level. The incoherent intermediate scattering function is computed in thermal equilibrium, its critical behaviour near the sol-gel transition is analysed and related to the scaling of cluster diffusion constants at the critical point. Second, non-equilibrium dynamics is studied by looking at stress relaxation in a simple shear flow. Anomalous stress relaxation and critical rheological properties are derived. Some of the results contradict long-standing scaling arguments, which are shown to be flawed by inconsistencies.Comment: 21 pages, 3 figures; Dedicated to Lothar Schaefer on the occasion of his 60th birthday; Changes: added comments on the gel phase and some reference

A Rheometry Method to Assess The Evaporation-Induced Mechanical Strength Development of Polymer Solutions Used For Membrane Applications

Rotational and oscillatory shear rheometry were used to quantify the flow behavior under minimal and significant solvent evaporation conditions for polymer solutions used to fabricate isoporous asymmetric membranes by the self-assembly and non-solvent induced phase separation (SNIPS) method. Three different A-B-C triblock terpolymer chemistries of similar molar mass were evaluated: polyisoprene-^-polystyrene-6-poly(4-vinylpyridine) (ISV); polyisoprene-6- polystyrene-6-poly(V,A-dimethylacrylamide) (ISD); and polyisoprene-Z\u3e-polystyrene-h-poly(fer/- butyl methacrylate) (ISB). Solvent evaporation resulted in the formation of a viscoelastic film typical of asymmetric membranes. Solution viscosity and film viscoelasticity were strongly dependent on the chemical structure of the triblock terpolymer molecules. A hierarchical magnitude (ISV\u3eISB\u3eISD) was observed for both properties, with ISV solutions displaying the greatest solution viscosity, fastest film strength development, and greatest strength magnitude

Imaging of poly(α-hydroxy-ester) scaffolds with X-ray phase-contrast microcomputed tomography

Porous scaffolds based on poly(α-hydroxy-esters) are under investigation in many tissue engineering applications. A biological response to these materials is driven, in part, by their three-dimensional (3D) structure. The ability to evaluate quantitatively the material structure in tissue-engineering applications is important for the continued development of these polymer-based approaches. X-ray imaging techniques based on phase contrast (PC) have shown a tremendous promise for a number of biomedical applications owing to their ability to provide a contrast based on alternative X-ray properties (refraction and scatter) in addition to X-ray absorption. In this research, poly(α-hydroxy-ester) scaffolds were synthesized and imaged by X-ray PC microcomputed tomography. The 3D images depicting the X-ray attenuation and phase-shifting properties were reconstructed from the measurement data. The scaffold structure could be imaged by X-ray PC in both cell culture conditions and within the tissue. The 3D images allowed for quantification of scaffold properties and automatic segmentation of scaffolds from the surrounding hard and soft tissues. These results provide evidence of the significant potential of techniques based on X-ray PC for imaging polymer scaffolds

The Resolved Properties of Extragalactic Giant Molecular Clouds

We use high spatial resolution observations of CO to systematically measure the resolved size-line width, luminosity-line width, luminosity-size, and the mass-luminosity relations of Giant Molecular Clouds (GMCs) in a variety of extragalactic systems. Although the data are heterogeneous we analyze them in a consistent manner to remove the biases introduced by limited sensitivity and resolution, thus obtaining reliable sizes, velocity dispersions, and luminosities. We compare the results obtained in dwarf galaxies with those from the Local Group spiral galaxies. We find that extragalactic GMC properties measured across a wide range of environments are very much compatible with those in the Galaxy. We use these results to investigate metallicity trends in the cloud average column density and virial CO-to-H2 factor. We find that these measurements do not accord with simple predictions from photoionization-regulated star formation theory, although this could be due to the fact that we do not sample small enough spatial scales or the full gravitational potential of the molecular cloud. We also find that the virial CO-to-H2 conversion factor in CO-bright GMCs is very similar to Galactic, and that the excursions do not show a measurable metallicity trend. We contrast these results with estimates of molecular mass based on far-infrared measurements obtained for the Small Magellanic Cloud, which systematically yield larger masses, and interpret this discrepancy as arising from large H2 envelopes that surround the CO-bright cores. We conclude that GMCs identified on the basis of their CO emission are a unique class of object that exhibit a remarkably uniform set of properties from galaxy to galaxy (abridged).Comment: 21 pages, 7 figures, 4 tables (one of them electronic). The Astrophysical Journal, accepted. Revised to reflect changes made to proof