Asymptotically Stable Numerical Method for Multispecies Momentum Transfer:Gas and Multifluid Dust Test Suite and Implementation in FARGO3D

We present an asymptotically and unconditionally stable numerical method to account for the momentum transfer between multiple species. Momentum is conserved to machine precision. This implies that the asymptotic equilibrium corresponds to the velocity of the center of mass. Aimed at studying dust dynamics, we implement this numerical method in the publicly available code FARGO3D. To validate our implementation, we develop a test suite for an arbitrary number of species, based on analytical or exact solutions of problems related to perfect damping, damped sound waves, shocks, local and global gas-dust radial drift in a disk and, linear streaming instability. In particular, we obtain first-order, steady-state solutions for the radial drift of multiple dust species in protoplanetary disks, in which the pressure gradient is not necessarily small. We additionally present non-linear shearing-box simulations of the streaming instability and compare them with previous results obtained with Lagrangian particles. We successfully validate our implementation by recovering the solutions from the test suite to second- and first-order accuracy in space and time, respectively. From this, we conclude that our scheme is suitable, and very robust, to study the self-consistent dynamics of several fluids. In particular, it can be used for solving the collisions between gas and dust in protoplanetary disks, with any degree of coupling.Comment: 27 pages, 12 figures; accepted for publication in ApJ

Early visual experience and the receptive-field organization of optic flow processing interneurons in the fly motion pathway

Karmeier K, Tabor R, Egelhaaf M, Krapp HG. Early visual experience and the receptive-field organization of optic flow processing interneurons in the fly motion pathway. Visual neuroscience. 2001;18(1):1-8.The distribution of local preferred directions and motion sensitivities within the receptive fields of so-called tangential neurons in the fly visual system was previously found to match optic flow fields as induced by certain self-motions. The complex receptive-field organization of the tangential neurons and the recent evidence showing that the orderly development of the fly's peripheral visual system depends on visual experience led us to investigate whether or not early visual input is required to establish the functional receptive field properties of such tangential neurons. In electrophysiological investigations of two identified tangential neurons, it turned out that dark-hatched flies which were kept in complete darkness for 2 days develop basically the same receptive-field organization as flies which were raised under seasonal light/dark conditions and were free to move in their cages. We did not find any evidence that the development of the sophisticated receptive-field organization of tangential neurons depends on sensory experience. Instead, the input to the tangential neurons seems to be "hardwired" and the specificity of these cells to optic flow induced during self-motions of the animal may have evolved on a phylogenetical time scale

Characterizing the variable dust permeability of planet-induced gaps

Aerodynamic theory predicts that dust grains in protoplanetary disks will drift radially inward on comparatively short timescales. In this context, it has long been known that the presence of a gap opened by a planet can alter the dust dynamics significantly. In this paper, we carry out a systematic study employing long-term numerical simulations aimed at characterizing the critical particle-size for retention outside a gap as a function of particle size and for various key parameters defining the protoplanetary disk model. To this end, we perform multifluid hydrodynamical simulations in two dimensions, including different dust species, which we treat as pressureless fluids. We initialize the dust outside of the planet's orbit and study under which conditions dust grains are able to cross the gap carved by the planet. In agreement with previous work, we find that the permeability of the gap depends both on dust dynamical properties and the gas disk structure: while small dust follows the viscously accreting gas through the gap, dust grains approaching a critical size are progressively filtered out. Moreover, we introduce and compute a depletion factor that enables us to quantify the way in which higher viscosity, smaller planet mass, or a more massive disk can shift this critical size to larger values. Our results indicate that gap-opening planets may act to deplete the inner reaches of protoplanetary disks of large dust grains -- potentially limiting the accretion of solids onto forming terrestrial planets.Comment: 18 pages, 14 figures, accepted for publication in Ap

Neural encoding of behaviourally relevant visual-motion information in the fly

Egelhaaf M, Kern R, Krapp HG, Kretzberg J, Kurtz R, Warzecha A-K. Neural encoding of behaviourally relevant visual-motion information in the fly. Trends in Neurosciences. 2002;25(2):96-102.Information processing in visual systems is constrained by the spatial and temporal characteristics of the sensory input and by the biophysical properties of the neuronal circuits. Hence, to understand how visual systems encode behaviourally relevant information, we need to know about both the computational capabilities of the nervous system and the natural conditions under which animals normally operate. By combining behavioural, neurophysiological and computational approaches, it is now possible in the fly to assess adaptations that process visual-motion information under the constraints of its natural input. It is concluded that neuronal operating ranges and coding strategies appear to be closely matched to the inputs the animal encounters under behaviourally relevant conditions

Localized direction selective responses in the dendrites of visual interneurons of the fly

<p>Abstract</p> <p>Background</p> <p>The various tasks of visual systems, including course control, collision avoidance and the detection of small objects, require at the neuronal level the dendritic integration and subsequent processing of many spatially distributed visual motion inputs. While much is known about the pooled output in these systems, as in the medial superior temporal cortex of monkeys or in the lobula plate of the insect visual system, the motion tuning of the elements that provide the input has yet received little attention. In order to visualize the motion tuning of these inputs we examined the dendritic activation patterns of neurons that are selective for the characteristic patterns of wide-field motion, the lobula-plate tangential cells (LPTCs) of the blowfly. These neurons are known to sample direction-selective motion information from large parts of the visual field and combine these signals into axonal and dendro-dendritic outputs.</p> <p>Results</p> <p>Fluorescence imaging of intracellular calcium concentration allowed us to take a direct look at the local dendritic activity and the resulting local preferred directions in LPTC dendrites during activation by wide-field motion in different directions. These 'calcium response fields' resembled a retinotopic dendritic map of local preferred directions in the receptive field, the layout of which is a distinguishing feature of different LPTCs.</p> <p>Conclusions</p> <p>Our study reveals how neurons acquire selectivity for distinct visual motion patterns by dendritic integration of the local inputs with different preferred directions. With their spatial layout of directional responses, the dendrites of the LPTCs we investigated thus served as matched filters for wide-field motion patterns.</p

MoleculARweb: A Web Site for Chemistry and Structural Biology Education through Interactive Augmented Reality out of the Box in Commodity Devices

Augmented/virtual realities (ARs/VRs) promise to revolutionize STEM education. However, most easy-to-use tools are limited to static visualizations, which limits the approachable content, whereas more interactive and dynamic alternatives require costly hardware, preventing large-scale use and evaluation of pedagogical effects. Here, we introduce https://MoleculARweb.epfl.ch, a free, open-source web site with interactive AR webpage-based apps that work out-of-the-box in laptops, tablets, and smartphones, where students and teachers can naturally handle virtual objects to explore molecular structure, reactivity, dynamics, and interactions, covering topics from inorganic, organic, and biological chemistry. With these web apps, teachers and science communicators can develop interactive material for their lessons and hands-on activities for their students and target public, in person or online, as we exemplify. Thousands of accesses to moleculARweb attest to the ease of use; teacher feedback attests to the utility in online teaching and homework during a pandemic; and in-class plus online surveys show that users find AR engaging and useful for teaching and learning chemistry. These observations support the potential of AR in future education and show the large impact that modern web technologies have in democratizing access to digital learning tools, providing the possibility to mass-test the pedagogical effect of these technologies in STEM education.Fil: Rodríguez, Fabio Cortés. École Polytechnique Fédérale de Lausanne; Suiza. Swiss Institute of Bioinformatics; SuizaFil: Frattini, Gianfranco. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas; ArgentinaFil: Krapp, Lucien F.. Ecole Polytechnique Federale de Lausanne; Francia. Swiss Institute of Bioinformatics; SuizaFil: Martinez Hung, Hassan. Universidad de Oriente; VenezuelaFil: Moreno, Diego Martin. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Química Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Química Rosario; ArgentinaFil: Roldán, Mariana. Provincia de Córdoba. Instituto Colbert; ArgentinaFil: Salomón, Jorge Eduardo. Provincia de Buenos Aires. Escuela de Educación Técnica Nro. 4; ArgentinaFil: Stemkoski, Lee. Adelphi University; Estados UnidosFil: Traeger, Sylvain. École Polytechnique Fédérale de Lausanne; Suiza. Swiss Institute of Bioinformatics; SuizaFil: Dal Peraro, Matteo. École Polytechnique Fédérale de Lausanne; Suiza. Swiss Institute of Bioinformatics; SuizaFil: Abriata, Luciano Andres. École Polytechnique Fédérale de Lausanne; Suiza. Swiss Institute of Bioinformatics; Suiz

Cytokinesis and the contractile ring in fission yeast: towards a systems-level understanding

Cytokinesis, the final stage of the cell division cycle, requires the proper placement, assembly and contraction of an actomyosin-based contractile ring. Conserved sets of cytokinesis proteins and pathways have now been identified and characterized functionally. Additionally, fluorescent protein fusion technology enables quantitative high-resolution imaging of protein dynamics in living cells. For these reasons, the study of cytokinesis is now ripe for quantitative, systems-level approaches. Here, we review our current understanding of the molecular mechanisms of contractile ring dynamics in the model organism Schizosaccharomyces pombe (fission yeast), focusing on recent examples that illustrate a synergistic integration of quantitative experimental data with computational modeling. A picture of a highly dynamic and integrated system consisting of overlapping networks is beginning to emerge, the detailed nature of which remains to be elucidated.National Institutes of Health (U.S.) (NIH grant GM05683)Massachusetts Institute of Technology (Samuel A. Goldblith Career Development Professorship)Massachusetts Institute of Technology (Faculty startup funds

The mitosis-to-interphase transition is coordinated by cross talk between the SIN and MOR pathways in Schizosaccharomyces pombe

The SIN pathway blocks inappropriate actin rearrangements during cytokinesis by preventing activation of the MOR pathway component Orb6