Droplet and cluster formation in freely falling granular streams

Particle beams are important tools for probing atomic and molecular interactions. Here we demonstrate that particle beams also offer a unique opportunity to investigate interactions in macroscopic systems, such as granular media. Motivated by recent experiments on streams of grains that exhibit liquid-like breakup into droplets, we use molecular dynamics simulations to investigate the evolution of a dense stream of macroscopic spheres accelerating out of an opening at the bottom of a reservoir. We show how nanoscale details associated with energy dissipation during collisions modify the stream's macroscopic behavior. We find that inelastic collisions collimate the stream, while the presence of short-range attractive interactions drives structure formation. Parameterizing the collision dynamics by the coefficient of restitution (i.e., the ratio of relative velocities before and after impact) and the strength of the cohesive interaction, we map out a spectrum of behaviors that ranges from gas-like jets in which all grains drift apart to liquid-like streams that break into large droplets containing hundreds of grains. We also find a new, intermediate regime in which small aggregates form by capture from the gas phase, similar to what can be observed in molecular beams. Our results show that nearly all aspects of stream behavior are closely related to the velocity gradient associated with vertical free fall. Led by this observation, we propose a simple energy balance model to explain the droplet formation process. The qualitative as well as many quantitative features of the simulations and the model compare well with available experimental data and provide a first quantitative measure of the role of attractions in freely cooling granular streams

Statistical characterization of the forces on spheres in an upflow of air

The dynamics of a sphere fluidized in a nearly-levitating upflow of air were previously found to be identical to those of a Brownian particle in a two-dimensional harmonic trap, consistent with a Langevin equation [Ojha {\it et al.}, Nature {\bf 427}, 521 (2004)]. The random forcing, the drag, and the trapping potential represent different aspects of the interaction of the sphere with the air flow. In this paper we vary the experimental conditions for a single sphere, and report on how the force terms in the Langevin equation scale with air flow speed, sphere radius, sphere density, and system size. We also report on the effective interaction potential between two spheres in an upflow of air.Comment: 7 pages, experimen

Avalanche statistics and time-resolved grain dynamics for a driven heap

We probe the dynamics of intermittent avalanches caused by steady addition of grains to a quasi-two dimensional heap. To characterize the time-dependent average avalanche flow speed v(t), we image the top free surface. To characterize the grain fluctuation speed dv(t), we use Speckle-Visibility Spectroscopy. During an avalanche, we find that the fluctuation speed is approximately one-tenth the average flow speed, and that these speeds are largest near the beginning of an event. We also find that the distribution of event durations is peaked, and that event sizes are correlated with the time interval since the end of the previous event. At high rates of grain addition, where successive avalanches merge into smooth continuous flow, the relationship between average and fluctuation speeds changes to dv Sqrt[v]

Shear band dynamics from a mesoscopic modeling of plasticity

The ubiquitous appearance of regions of localized deformation (shear bands) in different kinds of disordered materials under shear is studied in the context of a mesoscopic model of plasticity. The model may or may not include relaxational (aging) effects. In the absence of relaxational effects the model displays a monotonously increasing dependence of stress on strain-rate, and stationary shear bands do not occur. However, in start up experiments transient (although long lived) shear bands occur, that widen without bound in time. I investigate this transient effect in detail, reproducing and explaining a t^1/2 law for the thickness increase of the shear band that has been obtained in atomistic numerical simulations. Relaxation produces a negative sloped region in the stress vs. strain-rate curve that stabilizes the formation of shear bands of a well defined width, which is a function of strain-rate. Simulations at very low strain-rates reveal a non-trivial stick-slip dynamics of very thin shear bands that has relevance in the study of seismic phenomena. In addition, other non-stationary processes, such as stop-and-go, or strain-rate inversion situations display a phenomenology that matches very well the results of recent experimental studies.Comment: 10 pages, 10 figure

PredIG: a predictor of T-cell immunogenicity

The identification of immunogenic epitopes (such as fragments of proteins, in particular peptides, that can trigger an immune response) is a fundamental need for immune-based therapies. A computational tool that could predict such immunogenic epitopes would have vast potential applications in biomedicine ranging, from vaccine design against viruses or bacteria to therapeutic vaccination of cancer patients. While there are several methods that predict whether a peptide will be shown to the immune system via the Human Leukocyte Antigen (HLA) proteins of a patient, most of them cannot predict whether such presentation will indeed trigger an immune response. Additionally, T-cell immunogenicity is determined by multiple cellular processes, some of which are often overlooked by the current state-of-the-art immunogenicity predictors. The aim of this project is to build PredIG, an immunogenicity predictor that discriminates immunogenic from non-immunogenic T-cell epitopes given the peptide sequence and the HLA typing. After a careful study of the drivers of antigen processing and presentation on HLA class I molecules and an assessment of the physicochemical factors influencing epitope recognition by T-cell receptors (TCRs), we have used a selection of publicly available tools and in-house developed algorithms to identify the most relevant features that determine epitope immunogenicity. We then used these features to build an immunogenicity predictor (PredIG) modelled by XGBoost against immunogenically validated epitopes by the ImmunoEpitope DataBase (IEDB)(1), the PRIME dataset(2) and the TANTIGEN database(3). Pondering the feature importance in the model, the in-house developed softwares, NOAH for HLA Binding Affinity and NetCleave for Proteasomal Processing were identified as the major contributors to the performance of the model. Once PredIG was developed, we benchmarked the capacity to predict the immunogenicity of validated T-cell epitopes versus a set of state-of-the-art methods (Fig.1). Relevantly, PredIG showed a greater performance than the Immunogenicity predictors from Prime(2) and IEDB(4). Additionally, our results confirm that predicting T-cell immunogenicity based on data from T-cell assays is more accurate than using HLA Binding assays, the method mostly used in the field. An AUC value of 0.67 and an enrichment factor in the TOP10 epitopes of 90% outperforms the predictive performance of the available methods. In the context of the immune response against cancers, Tcell immunogenicity of tumoral mutations has been described as a response biomarker for immunotherapies such as immune checkpoint inhibitors. Similarly, the presence of immune infiltrate in a tumor has been related to a better prognosis for many cancer types. What is missing is the link between T-cell immunogenicity of tumoral mutations and the capacity of a tumor to attract immune cells. For this reason, we correlated the PredIG immunogenicity score obtained in a dataset of the The Cancer Genome Atlas (TCGA) against the tumor infiltrate in such tumors demonstrating that rather the total number of mutations a tumor accumulates, the tumor mutation burden (TMB), it is the number of immunogenic mutations what should be accounted for as biomarker of response

Vortex avalanches and magnetic flux fragmentation in superconductors

We report results of numerical simulations of non isothermal dendritic flux penetration in type-II superconductors. We propose a generic mechanism of dynamic branching of a propagating hotspot of a flux flow/normal state triggered by a local heat pulse. The branching occurs when the flux hotspot reflects from inhomogeneities or the boundary on which magnetization currents either vanish, or change direction. Then the hotspot undergoes a cascade of successive splittings, giving rise to a dissipative dendritic-type flux structure. This dynamic state eventually cools down, turning into a frozen multi-filamentary pattern of magnetization currents.Comment: 4 pages, 4 figures, accepted to Phys. Rev. Let

The break-up of Ekman theory in a flow subjected to background rotation and driven by a non-conservative body force

We present an experimental/numerical study of a dipolar flow structure in a shallow layer of electrolyte driven by electromagnetic forcing and subjected to background rotation. The aim of this study is to determine the influence of a non-conservative body force on the range of applicability of the classical Ekman boundary layer theory in rapidly rotating systems. To address this question, we study the response of the flow to the three control parameters: the magnitude of the forcing, the rotation rate of the system, and the shallowness of the layer. This response is quantified taking into account the magnitude of the flow velocity (represented by the Reynolds number), the symmetry between both vortex cores, and the vertical profile of the horizontal velocity. As in the case without background rotation, the response of the flow exhibits two scaling regimes (a linear and a nonlinear regime) in which the flow exhibits different vertical profiles of velocity. The transition between the two regimes occurs when the convective acceleration becomes of the same order as the viscous damping. This suggests that the applicability of the Ekman theory depends on the existence of a balance between the forcing and the damping due to the Ekman layers and does not depend solely on the value of the Rossby number as for decaying flows. On the other hand, the cyclone/anticyclone asymmetry is governed exclusively by the Rossby number. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4766818

Velocity profile of granular flows inside silos and hoppers

We measure the flow of granular materials inside a quasi-two dimensional silo as it drains and compare the data with some existing models. The particles inside the silo are imaged and tracked with unprecedented resolution in both space and time to obtain their velocity and diffusion properties. The data obtained by varying the orifice width and the hopper angle allows us to thoroughly test models of gravity driven flows inside these geometries. All of our measured velocity profiles are smooth and free of the shock-like discontinuities ("rupture zones") predicted by critical state soil mechanics. On the other hand, we find that the simple Kinematic Model accurately captures the mean velocity profile near the orifice, although it fails to describe the rapid transition to plug flow far away from the orifice. The measured diffusion length $b$, the only free parameter in the model, is not constant as usually assumed, but increases with both the height above the orifice and the angle of the hopper. We discuss improvements to the model to account for the differences. From our data, we also directly measure the diffusion of the particles and find it to be significantly less than predicted by the Void Model, which provides the classical microscopic derivation of the Kinematic Model in terms of diffusing voids in the packing. However, the experimental data is consistent with the recently proposed Spot Model, based on a simple mechanism for cooperative diffusion. Finally, we discuss the flow rate as a function of the orifice width and hopper angles. We find that the flow rate scales with the orifice size to the power of 1.5, consistent with dimensional analysis. Interestingly, the flow rate increases when the funnel angle is increased.Comment: 17 pages, 8 figure

Enraizamento de estacas de Cordia verbenacea DC. tratadas com Cyperus rotundus L.

Cyperus rotundus L., conhecida como tiririca, possui folhas e tubérculos ricos em fitormônios e por isso tem sido usada para o enraizamento de estacas. O objetivo deste estudo foi avaliar o efeito da solução aquosa de tiririca no enraizamento da erva-baleeira (Cordia verbenacea DC.). Foram utilizados folhas e tubérculos de tiririca. Foram testadas três concentrações de extrato aquoso de tiririca (T1 = 0%, T2 = 7,5% e T3 = 2,5%), no delineamento em blocos casualizados, em três repetições de 20 estacas cada. O terço basal das estacas ficou imerso no extrato por 40 minutos. Aos 31 dias após o plantio avaliou-se o desenvolvimento de raízes (número, comprimento, massa fresca e massa seca) e da parte aérea (altura, massa fresca e massa seca). Obteve-se baixa taxa de mortalidade em todos os tratamentos. Assim, conclui-se que o extrato de tiririca, nas concentrações testadas, não influencia o enraizamento de estacas de erva-baleeira.Disponível também em: Cadernos de Agroecologia, V. 5, n.1, 2010

Report of the ICES\NAFO Joint Working Group on Deep-water Ecology (WGDEC), 11–15 March 2013, Floedevigen, Norway.

On 11 February 2013, the joint ICES/NAFO WGDEC, chaired by Francis Neat (UK) and attended by ten members met at the Institute for Marine Research in Floedevi-gen, Norway to consider the terms of reference (ToR) listed in Section 2. WGDEC was requested to update all records of deep-water vulnerable marine eco-systems (VMEs) in the North Atlantic. New data from a range of sources including multibeam echosounder surveys, fisheries surveys, habitat modelling and seabed imagery surveys was provided. For several areas across the North Atlantic, WGDEC makes recommendations for areas to be closed to bottom fisheries for the purposes of conservation of VMEs