TY - JOUR AB - Recent studies aimed at investigating artificial analogs of bacterial colonies have shown that low-density suspensions of self-propelled particles confined in two dimensions can assemble into finite aggregates that merge and split, but have a typical size that remains constant (living clusters). In this Letter, we address the problem of the formation of living clusters and crystals of active particles in three dimensions. We study two systems: self-propelled particles interacting via a generic attractive potential and colloids that can move toward each other as a result of active agents (e.g., by molecular motors). In both cases, fluidlike “living” clusters form. We explain this general feature in terms of the balance between active forces and regression to thermodynamic equilibrium. This balance can be quantified in terms of a dimensionless number that allows us to collapse the observed clustering behavior onto a universal curve. We also discuss how active motion affects the kinetics of crystal formation. AU - Mognetti, B. M. AU - Šarić, Anđela AU - Angioletti-Uberti, S. AU - Cacciuto, A. AU - Valeriani, C. AU - Frenkel, D. ID - 10384 IS - 24 JF - Physical Review Letters KW - general physics and astronomy SN - 0031-9007 TI - Living clusters and crystals from low-density suspensions of active colloids VL - 111 ER - TY - JOUR AB - In this paper we review recent numerical and theoretical developments of particle self-assembly on fluid and elastic membranes and compare them to available experimental realizations. We discuss the problem and its applications in biology and materials science, and give an overview of numerical models and strategies to study these systems across all length-scales. As this is a very broad field, this review focuses exclusively on surface-driven aggregation of nanoparticles that are at least one order of magnitude larger than the surface thickness and are adsorbed onto it. In this regime, all chemical details of the surface can be ignored in favor of a coarse-grained representation, and the collective behavior of many particles can be monitored and analyzed. We review the existing literature on how the mechanical properties and the geometry of the surface affect the structure of the particle aggregates and how these can drive shape deformation on the surface. AU - Šarić, Anđela AU - Cacciuto, Angelo ID - 10386 IS - 29 JF - Soft Matter KW - condensed matter physics KW - general chemistry SN - 1744-683X TI - Self-assembly of nanoparticles adsorbed on fluid and elastic membranes VL - 9 ER - TY - JOUR AB - We show how self-assembly of sticky nanoparticles can drive radial collapse of thin-walled nanotubes. Using numerical simulations, we study the transition as a function of the geometric and elastic parameters of the nanotube and the binding strength of the nanoparticles. We find that it is possible to derive a simple scaling law relating all these parameters, and estimate bounds for the onset conditions leading to the collapse of the nanotube. We also study the reverse process – the nanoparticle release from the folded state – and find that the stability of the collapsed state can be greatly improved by increasing the bending rigidity of the nanotubes. Our results suggest ways to strengthen the mechanical properties of nanotubes, but also indicate that the control of nanoparticle self-assembly on these nanotubes can lead to nanoparticle-laden responsive materials. AU - Napoli, Joseph A. AU - Šarić, Anđela AU - Cacciuto, Angelo ID - 10385 IS - 37 JF - Soft Matter KW - condensed matter physics KW - general chemistry SN - 1744-683X TI - Collapsing nanoparticle-laden nanotubes VL - 9 ER - TY - JOUR AB - Stimfit is a free cross-platform software package for viewing and analyzing electrophysiological data. It supports most standard file types for cellular neurophysiology and other biomedical formats. Its analysis algorithms have been used and validated in several experimental laboratories. Its embedded Python scripting interface makes Stimfit highly extensible and customizable. AU - Schlögl, Alois AU - Jonas, Peter M AU - Schmidt-Hieber, C. AU - Guzman, S. J. ID - 10396 IS - SI-1-Track-G JF - Biomedical Engineering / Biomedizinische Technik KW - biomedical engineering KW - data analysis KW - free software SN - 0013-5585 TI - Stimfit: A fast visualization and analysis environment for cellular neurophysiology VL - 58 ER - TY - CONF AB - Fluxoid quantization provides a direct means to study phase coherence. In cuprate superconductors, there have been observations which suggest that phase coherent superconducting fluctuations may persist at temperatures significantly above Tc. The focus of this work is to study the vortex states in mesoscopic cuprate superconducting samples to directly probe phase coherence over a wide range of temperatures. We present cantilever torque susceptometry measurements of micron and sub-micron size Bi2212 rings and disks. The high sensitivity of this technique allowed observation of transitions between different fluxoid states of a single ring, and the discrete vortex states of micron size disks. The dependence of magnetic susceptibility on diameter and wall thickness of the ring was investigated. Measurements were made at different values of the in-plane magnetic field, and over a wide range of temperatures. AU - Polshyn, Hryhoriy AU - Budakian, Raffi AU - Gu, Genda ID - 10749 IS - 1 SN - 0003-0503 T2 - APS March Meeting 2013 TI - Cantilever micro-susceptometry of mesoscopic Bi2212 samples VL - 58 ER - TY - JOUR AB - Due to their sessile lifestyles, plants need to deal with the limitations and stresses imposed by the changing environment. Plants cope with these by a remarkable developmental flexibility, which is embedded in their strategy to survive. Plants can adjust their size, shape and number of organs, bend according to gravity and light, and regenerate tissues that were damaged, utilizing a coordinating, intercellular signal, the plant hormone, auxin. Another versatile signal is the cation, Ca2+, which is a crucial second messenger for many rapid cellular processes during responses to a wide range of endogenous and environmental signals, such as hormones, light, drought stress and others. Auxin is a good candidate for one of these Ca2+-activating signals. However, the role of auxin-induced Ca2+ signaling is poorly understood. Here, we will provide an overview of possible developmental and physiological roles, as well as mechanisms underlying the interconnection of Ca2+ and auxin signaling. AU - Vanneste, Steffen AU - Friml, Jiří ID - 10895 IS - 4 JF - Plants KW - Plant Science KW - Ecology KW - Ecology KW - Evolution KW - Behavior and Systematics SN - 2223-7747 TI - Calcium: The missing link in auxin action VL - 2 ER - TY - CONF AB - A prominent remedy to multicore scalability issues in concurrent data structure implementations is to relax the sequential specification of the data structure. We present distributed queues (DQ), a new family of relaxed concurrent queue implementations. DQs implement relaxed queues with linearizable emptiness check and either configurable or bounded out-of-order behavior or pool behavior. Our experiments show that DQs outperform and outscale in micro- and macrobenchmarks all strict and relaxed queue as well as pool implementations that we considered. AU - Haas, Andreas AU - Lippautz, Michael AU - Henzinger, Thomas A AU - Payer, Hannes AU - Sokolova, Ana AU - Kirsch, Christoph M. AU - Sezgin, Ali ID - 10898 IS - 5 SN - 978-145032053-5 T2 - Proceedings of the ACM International Conference on Computing Frontiers - CF '13 TI - Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation ER - TY - CHAP AU - Barton, Nicholas H ID - 10899 KW - Adaptive landscape KW - Cline KW - Coalescent process KW - Gene flow KW - Hybrid zone KW - Local adaptation KW - Natural selection KW - Neutral theory KW - Population structure KW - Speciation SN - 978-0-12-384720-1 T2 - Encyclopedia of Biodiversity TI - Differentiation ER - TY - JOUR AB - Faithful execution of developmental gene expression programs occurs at multiple levels and involves many different components such as transcription factors, histone-modification enzymes, and mRNA processing proteins. Recent evidence suggests that nucleoporins, well known components that control nucleo-cytoplasmic trafficking, have wide-ranging functions in developmental gene regulation that potentially extend beyond their role in nuclear transport. Whether the unexpected role of nuclear pore proteins in transcription regulation, which initially has been described in fungi and flies, also applies to human cells is unknown. Here we show at a genome-wide level that the nuclear pore protein NUP98 associates with developmentally regulated genes active during human embryonic stem cell differentiation. Overexpression of a dominant negative fragment of NUP98 levels decreases expression levels of NUP98-bound genes. In addition, we identify two modes of developmental gene regulation by NUP98 that are differentiated by the spatial localization of NUP98 target genes. Genes in the initial stage of developmental induction can associate with NUP98 that is embedded in the nuclear pores at the nuclear periphery. Alternatively, genes that are highly induced can interact with NUP98 in the nuclear interior, away from the nuclear pores. This work demonstrates for the first time that NUP98 dynamically associates with the human genome during differentiation, revealing a role of a nuclear pore protein in regulating developmental gene expression programs. AU - Liang, Yun AU - Franks, Tobias M. AU - Marchetto, Maria C. AU - Gage, Fred H. AU - HETZER, Martin W ID - 11086 IS - 2 JF - PLoS Genetics KW - Cancer Research KW - Genetics (clinical) KW - Genetics KW - Molecular Biology KW - Ecology KW - Evolution KW - Behavior and Systematics SN - 1553-7404 TI - Dynamic association of NUP98 with the human genome VL - 9 ER - TY - JOUR AB - Intracellular proteins with long lifespans have recently been linked to age-dependent defects, ranging from decreased fertility to the functional decline of neurons. Why long-lived proteins exist in metabolically active cellular environments and how they are maintained over time remains poorly understood. Here, we provide a system-wide identification of proteins with exceptional lifespans in the rat brain. These proteins are inefficiently replenished despite being translated robustly throughout adulthood. Using nucleoporins as a paradigm for long-term protein persistence, we found that nuclear pore complexes (NPCs) are maintained over a cell’s life through slow but finite exchange of even its most stable subcomplexes. This maintenance is limited, however, as some nucleoporin levels decrease during aging, providing a rationale for the previously observed age-dependent deterioration of NPC function. Our identification of a long-lived proteome reveals cellular components that are at increased risk for damage accumulation, linking long-term protein persistence to the cellular aging process. AU - Toyama, Brandon H. AU - Savas, Jeffrey N. AU - Park, Sung Kyu AU - Harris, Michael S. AU - Ingolia, Nicholas T. AU - Yates, John R. AU - HETZER, Martin W ID - 11087 IS - 5 JF - Cell KW - General Biochemistry KW - Genetics and Molecular Biology SN - 0092-8674 TI - Identification of long-lived proteins reveals exceptional stability of essential cellular structures VL - 154 ER -