6,343 research outputs found
Pomelo, a tool for computing Generic Set Voronoi Diagrams of Aspherical Particles of Arbitrary Shape
We describe the development of a new software tool, called "Pomelo", for the
calculation of Set Voronoi diagrams. Voronoi diagrams are a spatial partition
of the space around the particles into separate Voronoi cells, e.g. applicable
to granular materials. A generalization of the conventional Voronoi diagram for
points or monodisperse spheres is the Set Voronoi diagram, also known as
navigational map or tessellation by zone of influence. In this construction, a
Set Voronoi cell contains the volume that is closer to the surface of one
particle than to the surface of any other particle. This is required for
aspherical or polydisperse systems.
Pomelo is designed to be easy to use and as generic as possible. It directly
supports common particle shapes and offers a generic mode, which allows to deal
with any type of particles that can be described mathematically. Pomelo can
create output in different standard formats, which allows direct visualization
and further processing. Finally, we describe three applications of the Set
Voronoi code in granular and soft matter physics, namely the problem of
packings of ellipsoidal particles with varying degrees of particle-particle
friction, mechanical stable packings of tetrahedra and a model for liquid
crystal systems of particles with shapes reminiscent of pearsComment: 4 pages, 9 figures, Submitted to Powders and Grains 201
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The self-relevance system?
We suggest that the Self Attention Network (SAN) maybe part of a larger self-regulatory system, which we term the Self-Relevance System (SRS) of which the “core” or default network is a major part. It is within the core network that memories are generated and the future imagined. Such memories and imaginings are the basis of preoccupations. Within the SRS then preoccupations drive the emergence of attentional biases (ABs). ABs in turn are modulated by the SAN activating and inhibiting circuits that shape behavior. We consider briefly how this might function in dysfunctional appetitive behaviors, e.g., substance abuse
In Situ Diazotroph Population Dynamics Under Different Resource Ratios in the North Pacific Subtropical Gyre.
Major advances in understanding the diversity, distribution, and activity of marine N2-fixing microorganisms (diazotrophs) have been made in the past decades, however, large gaps in knowledge remain about the environmental controls on growth and mortality rates. In order to measure diazotroph net growth rates and microzooplankton grazing rates on diazotrophs, nutrient perturbation experiments and dilution grazing experiments were conducted using free-floating in situ incubation arrays in the vicinity of Station ALOHA in March 2016. Net growth rates for targeted diazotroph taxa as well as Prochlorococcus, Synechococcus and photosynthetic picoeukaryotes were determined under high (H) and low (L) nitrate:phosphate (NP) ratio conditions at four depths in the photic zone (25, 45, 75, and 100 m) using quantitative PCR and flow cytometry. Changes in the prokaryote community composition in response to HNP and LNP treatments were characterized using 16S rRNA variable region tag sequencing. Microzooplankton grazing rates on diazotrophs were measured using a modified dilution technique at two depths in the photic zone (15 and 125 m). Net growth rates for most of the targeted diazotrophs after 48 h were not stimulated as expected by LNP conditions, rather enhanced growth rates were often measured in HNP treatments. Interestingly, net growth rates of the uncultivated prymnesiophyte symbiont UCYN-A1 were stimulated in HNP treatments at 75 and 100 m, suggesting that N used for growth was acquired through continuing to fix N2 in the presence of nitrate. Net growth rates for UCYN-A1, UCYN-C, Crocosphaera sp. (UCYN-B) and the diatom symbiont Richelia (associated with Rhizosolenia) were uniformly high at 45 m (up to 1.6 ± 0.5 d-1), implying that all were growing optimally at the onset of the experiment at that depth. Differences in microzooplankton grazing rates on UCYN-A1 and UCYN-C in 15 m waters indicate that the grazer assemblage preyed preferentially on UCYN-A1. Deeper in the water column (125 m), both diazotrophs were grazed at substantial rates, suggesting grazing pressure may increase with depth in the photic zone. Constraining in situ diazotroph growth and mortality rates are important steps for improving parameterization for diazotrophs in global ecosystem models
In vitro transfection of HeLa cells with temperature sensitive polycationic copolymers
Cataloged from PDF version of article.In this study, we investigated different types of polyethyleneimine (PEI) and their block copolymers with N-isopropylacrylamide (NIPA) as temperature-sensitive polycationic non-viral vectors for transfection of HeLa cells in cell culture media. First carboxyl-terminated poly(NIPA) was synthesized and then copolymerized with PEIs branched or linear and with two different molecular weights (2 and 25 kDa). Addition of PEI units to the poly(NIPA) chains increased the LCST values up to body temperature. Zeta potentials of the copolymers were significantly lower than the corresponding PEI homopolymers. A green fluorescent protein expressing plasmid was used as a model. Complexes of this plasmid both with PEIs and their copolymers were formed. The zeta potentials of these complexes were between -3.1 and +21.3. Higher values were observed for the complexes prepared with branched and higher molecular weight PEIs. Copolymerization caused a profound decrease in the positive charges. Particle sizes of the complexes were in the range of 190-1235 nm. Using high polymer/plasmid ratios caused aggregation. The smallest complexes were obtained with the copolymer prepared with branched PEI with 25-kDa molecular weight. Copolymers were able to squeeze plasmid DNA more at the body temperature. Cytotoxicity was observed with PEIs especially with the branched higher molecular weights. Copolymerization reduced the cytotoxicity. The best in vitro DNA uptake efficiency (70%) was achieved with the complex prepared with poly(NIPA)/PEI25B. However, poly(NIPA)/PEI25L was the most successful vector for an effective gene expression without any significant toxicity. © 2004 Elsevier B.V. All rights reserved
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Symbiotic unicellular cyanobacteria fix nitrogen in the Arctic Ocean.
Biological dinitrogen (N2) fixation is an important source of nitrogen (N) in low-latitude open oceans. The unusual N2-fixing unicellular cyanobacteria (UCYN-A)/haptophyte symbiosis has been found in an increasing number of unexpected environments, including northern waters of the Danish Straight and Bering and Chukchi Seas. We used nanoscale secondary ion mass spectrometry (nanoSIMS) to measure 15N2 uptake into UCYN-A/haptophyte symbiosis and found that UCYN-A strains identical to low-latitude strains are fixing N2 in the Bering and Chukchi Seas, at rates comparable to subtropical waters. These results show definitively that cyanobacterial N2 fixation is not constrained to subtropical waters, challenging paradigms and models of global N2 fixation. The Arctic is particularly sensitive to climate change, and N2 fixation may increase in Arctic waters under future climate scenarios
Appearance of the Single Gyroid Network Phase in Nuclear Pasta Matter
Nuclear matter under the conditions of a supernova explosion unfolds into a
rich variety of spatially structured phases, called nuclear pasta. We
investigate the role of periodic network-like structures with negatively curved
interfaces in nuclear pasta structures, by static and dynamic Hartree-Fock
simulations in periodic lattices. As the most prominent result, we identify for
the first time the {\it single gyroid} network structure of cubic chiral
symmetry, a well known configuration in nanostructured soft-matter
systems, both as a dynamical state and as a cooled static solution. Single
gyroid structures form spontaneously in the course of the dynamical
simulations. Most of them are isomeric states. The very small energy
differences to the ground state indicate its relevance for structures in
nuclear pasta.Comment: 7 pages, 4 figure
Minkowski Tensors of Anisotropic Spatial Structure
This article describes the theoretical foundation of and explicit algorithms
for a novel approach to morphology and anisotropy analysis of complex spatial
structure using tensor-valued Minkowski functionals, the so-called Minkowski
tensors. Minkowski tensors are generalisations of the well-known scalar
Minkowski functionals and are explicitly sensitive to anisotropic aspects of
morphology, relevant for example for elastic moduli or permeability of
microstructured materials. Here we derive explicit linear-time algorithms to
compute these tensorial measures for three-dimensional shapes. These apply to
representations of any object that can be represented by a triangulation of its
bounding surface; their application is illustrated for the polyhedral Voronoi
cellular complexes of jammed sphere configurations, and for triangulations of a
biopolymer fibre network obtained by confocal microscopy. The article further
bridges the substantial notational and conceptual gap between the different but
equivalent approaches to scalar or tensorial Minkowski functionals in
mathematics and in physics, hence making the mathematical measure theoretic
method more readily accessible for future application in the physical sciences
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