MTrack: Automated Detection, Tracking, and Analysis of Dynamic Microtubules

Microtubules are polar, dynamic filaments fundamental to many cellular processes. In vitro reconstitution approaches with purified tubulin are essential to elucidate different aspects of microtubule behavior. To date, deriving data from fluorescence microscopy images by manually creating and analyzing kymographs is still commonplace. Here, we present MTrack, implemented as a plug-in for the open-source platform Fiji, which automatically identifies and tracks dynamic microtubules with sub-pixel resolution using advanced objection recognition. MTrack provides automatic data interpretation yielding relevant parameters of microtubule dynamic instability together with population statistics. The application of our software produces unbiased and comparable quantitative datasets in a fully automated fashion. This helps the experimentalist to achieve higher reproducibility at higher throughput on a user-friendly platform. We use simulated data and real data to benchmark our algorithm and show that it reliably detects, tracks, and analyzes dynamic microtubules and achieves sub-pixel precision even at low signal-to-noise ratios.V.K. was supported by the IRI Life Sciences postdoc fellowship in the labs of S.R. and S.P. C.H. and S.R. acknowledge funding by the IRI Life Sciences (Humboldt-Universität zu Berlin, Excellence Initiative/DFG). W.H. was supported by the Alliance Berlin Canberra “Crossing Boundaries: Molecular Interactions in Malaria”, which is co-funded by a grant from the Deutsche Forschungsgemeinschaf (DFG) for the International Research Training Group (IRTG) 2290 and the Australian National University. S.P. was supported by the MDC Berlin

Science Requirements and Conceptual Design for a Polarized Medium Energy Electron-Ion Collider at Jefferson Lab

This report presents a brief summary of the science opportunities and program of a polarized medium energy electron-ion collider at Jefferson Lab and a comprehensive description of the conceptual design of such a collider based on the CEBAF electron accelerator facility.Comment: 160 pages, ~93 figures This work was supported by the U.S. Department of Energy, Office of Nuclear Physics, under Contract No. DE-AC05-06OR23177, DE-AC02-06CH11357, DE-AC05-060R23177, and DESC0005823. The U.S. Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce this manuscript for U.S. Government purpose

COUPLED LAGRANGE-EULER MODEL FOR SIMULATION OF BUBBLY FLOW IN VERTICAL PIPES CONSIDERING TURBULENT 3D RANDOM WALKS MODELS AND BUBBLES INTERACTION EFFECTS

Una nueva aproximación euleriana-lagarangiana, en su forma de acople en dos vías, para la simulación de flujo de burbujas, agua-aire es presentada en la tesis, en la que se incluyen los efectos de las colisiones entre burbujas, así como las posibles roturas o coalescencia de burbujas. Esta aproximación utiliza el modelo Continuous Random Walk, CRW, para tener en cuenta las fluctuaciones de la velocidad. Esta aproximación se enmarca dentro de un modelo de turbulencia k-epsilon para la fase continua del líquido. En esta tesis se estudiarán los métodos para realizar el acople entre ambas aproximaciones, el efecto de la fuerza lift y de la dispersión turbulenta sobre la distribución de la fracción de huecos, así como los modelos de coalescencia y rotura de burbujas que puedan ser empleados en este tipo de aproximación. Se ha partido de un código euleriano para simular la parte continua, y sobre él se ha acoplado la aproximación lagrangiana. Para que ese acople afecte a la fase continua sobre su solver ser han añadido fuentes de momento y turbulencia. Además se ha modificado el volumen computacional de cada celda para que tenga en consideración el volumen ocupado por la fase dispersa. El acople en doble vía hace que los perfiles de velocidad y turbulencia de la fase continua se modifiquen notablemente y que se aproximen a los reales, lo que resulta básico para la correcta simulación de las fuerzas interfaciales. La colisión entre burbujas, y burbujas y pared se ha incluido. Este efecto es necesario como paso previo a incluir los procesos de rotura o coalescencia de burbujas, aunque la colisión en sí tenga efectos limitados en la distribución de la fracción de huecos. El proceso de coalescencia se basa en el modelo de Chester ( 1991 ) , el modelo compara el tiempo de colisión con el tiempo de drenaje de la película entre burbujas para determinar si existe o no coalescencia. El modelo de rotura se basa en el modelo de Martínez-Bazán. Uno de los principales hitos deAli Abd El Aziz Essa ., M. (2012). COUPLED LAGRANGE-EULER MODEL FOR SIMULATION OF BUBBLY FLOW IN VERTICAL PIPES CONSIDERING TURBULENT 3D RANDOM WALKS MODELS AND BUBBLES INTERACTION EFFECTS [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/18068Palanci

Beam-beam simulation code BBSIM for particle accelerators

A highly efficient, fully parallelized, six-dimensional tracking model for simulating interactions of colliding hadron beams in high energy ring colliders and simulating schemes for mitigating their effects is described. The model uses the weak-strong approximation for calculating the head-on interactions when the test beam has lower intensity than the other beam, a look-up table for the efficient calculation of long-range beam-beam forces, and a self-consistent Poisson solver when both beams have comparable intensities. A performance test of the model in a parallel environment is presented. The code is used to calculate beam emittance and beam loss in the Tevatron at Fermilab and compared with measurements. We also present results from the studies of two schemes proposed to compensate the beam-beam interactions: a) the compensation of long-range interactions in the Relativistic Heavy Ion Collider (RHIC) at Brookhaven and the Large Hadron Collider (LHC) at CERN with a current-carrying wire, b) the use of a low energy electron beam to compensate the head-on interactions in RHIC

An objective comparison of cell-tracking algorithms

We present a combined report on the results of three editions of the Cell Tracking Challenge, an ongoing initiative aimed at promoting the development and objective evaluation of cell segmentation and tracking algorithms. With 21 participating algorithms and a data repository consisting of 13 data sets from various microscopy modalities, the challenge displays today's state-of-the-art methodology in the field. We analyzed the challenge results using performance measures for segmentation and tracking that rank all participating methods. We also analyzed the performance of all of the algorithms in terms of biological measures and practical usability. Although some methods scored high in all technical aspects, none obtained fully correct solutions. We found that methods that either take prior information into account using learning strategies or analyze cells in a global spatiotemporal video context performed better than other methods under the segmentation and tracking scenarios included in the challenge

ML-Space: hybrid spatial Gillespie and Brownian motion simulation at multiple levels, and a rule-based description language

Computer simulations of biological cells as well-stirred systems are well established but neglect the spatial distribution of key actors. In this thesis, a simulation algorithm "ML-Space" for spatial models with dynamic hierarchies is presented. It combines stochastic spatial algorithms in discretized space with individual particles moving in continuous space that have spatial extensions and can contain other particles. For formal descriptions of the systems to be simulated spatially, ML-Space provides a rule-based specification language.Computersimulationen mikrobiologischer Prozesse, bei denen eine homogene Verteilung der Akteure einer Zelle angenommen wird, sind gut etabliert. In dieser Arbeit wird ein räumlicher Simulationsalgorithmus "ML-Space" für Mehrebenenmodelle vorgestellt, der auch dynamische Hierarchien abdeckt. Er vereint stochastische räumliche Algorithmen in diskretisiertem Raum mit individuellen Partikeln mit kontinuierlichen Koordinaten, die andere Partikel enthalten können. Zur formalen Beschreibung der räumlich zu simulierenden Systeme bietet ML-Space eine regelbasierte Modellierungssprache

Influence of droplet collision modelling in Euler/Lagrange calculations of spray evolution

The numerical computation of spraying systems is favourably conducted by applying the Euler/Lagrange approach. Although sprays downstream of the breakup region are very often rather dilute, droplet collisions may still have a significant influence on the spray evolution and especially the produced droplet size spectrum. Consequently, they have to be reliably modelled in the Lagrangian tracking approach. For this purpose, the fully stochastic droplet collision model is applied, which is numerically very efficient. It is demonstrated that this model is largely independent of the considered flow mesh and hence grid size, as well as the number of tracked parcels and the Lagrangian time step size. Moreover, this model includes the impact efficiency which may remarkably reduce collision rates for a wide droplet size spectrum. An essential ingredient of any droplet collision model is the proper description of the collision outcome through the so-called collision maps (i.e. the non-dimensional impact parameter plotted versus collision Weber number; B = f(We)), where the outcome regions (i.e. bouncing, coalescence and stretching or reflexive separation) are demarked by appropriate, mostly theory-based boundary lines. There are a number of different correlations available which may be applied for this purpose. The structure of the collision maps strongly depends on the kind of liquid being atomised. Different types of boundary lines and collision map structures are analysed here in detail with regard to the conditional collision rates or numbers within a rather simple hollow cone spray. The comparison of the averaged Sauter mean diameters along the spray demonstrates the importance of droplet collisions and how strongly this result is affected by the presumed droplet collision maps. Crude approximations to such collision maps may result in large errors and wrong predictions of the produced droplet size spectrum. Moreover, it is demonstrated that the effective PDF (probability density function) of the colliding droplet size ratio has typically a maximum in the range 0.1 < Δ < 0.3, a condition where no experimental data are available so far and some of the commonly used boundary lines are not suitable. Naturally, the spray simulations are compared to experimental data for a water hollow-cone spray, showing excellent agreement if the droplet collision map is selected properly. This concerns profiles of both gas and droplet velocities as well as droplet concentration development and local droplet size distributions. Expectedly, the prediction of the velocities is less sensitive with respect to the presumed droplet collision ma

Particle Capture and Pattern Evolution on Big Drops in Three-phase Turbulence

The process of particle capture and trapping by large deformable drops in turbulent channel flow are investigated in this thesis using an Eulerian-Lagrangian approach specifically developed for this three-phase flow. The flow field in the carrier fluid and inside the droplets is obtained from Direct Numerical Simulation of the Navier-Stokes equations; the drop interface dynamics are provided by a Phase Field Model; and par- ticle trajectories are calculated via Lagrangian tracking. Drops have the same density and viscosity of the carrier fluid in order to mimic a liquid-liquid dispersion of water and low-viscosity oil. Particles are modelled as neutrally- buoyant, sub-Kolmogorov spheres that interact with each other through collisions (excluded-volume interaction). Simulation results allow a detailed characterization of the particle dynamics during the interface capture and trapping stages. Particle capture is driven by the capillary forces of the interface in combination with near-interface turbulent motions: Particles are transported towards the interface by jet-like turbulent motions and, once close enough, are captured by interfacial forces in regions of positive surface velocity diver- gence. These regions appear to be well correlated with high-enstrophy flow topologies that contribute to enstrophy production via vortex compression or stretching. Upon capture, particles sample preferentially regions of positive surface velocity divergence, which correlate with jet-like fluid motions directed towards the interface. At later times, however, particles are observed to move from these regions under the action of the tangential stresses to the areas where the surface divergence vanishes and form the two-dimensional cluster. long- term trapping regions correlate well with the surface area characterized by higher-than-mean curvature. This finding is important since the presence of tiny particles at the interface is known to affect locally the surface tension, particularly in the presence of concentration gradi- ents: present results suggest that particle-induced modifications of the surface tension should be stronger where the curvature of the interface is higher