Open Source Software: From Open Science to New Marketing Models

-Open source Software; Intellectual Property; Licensing; Business Model.

MonteCarlo simulation of the XENON1T experiment and first comparison with the Muon Veto data.

L’esperimento XENON1T, in acquisizione dati presso i Laboratori Nazionali del Gran Sasso, è una Time Projection Chamber (TPC) contenente 2 t di xeno liquido ed ha come obiettivo una sensibilità per sezioni d'urto WIMP-nucleone indipendenti dallo spin pari a 1.6 10^(-47) cm^(2), per WIMP di massa 50 GeV/c^(2), in 2 t y. A tale scopo è fondamentale la riduzione di tutte le sorgenti di fondo. Per abbattere il fondo esterno la TPC è inserita all'interno di un Muon Veto: una vasca cilindrica riempita di acqua, dotata di 84 fotomoltiplicatori (PMT) , che funge sia da schermo passivo contro la radiazione esterna (gamma e neutroni), sia da veto per i muoni grazie alla rivelazione della luce Cherenkov da essi prodotta in acqua. In questo lavoro presentiamo uno studio sulle configurazioni di trigger del Muon Veto e sulla sua efficienza. Lo studio è basato sul confronto di simulazioni Monte Carlo con i primi dati del rivelatore. Si ottiene un'efficienza del 99.5% per eventi di muone e del 43% per sciami generati da interazioni del muone nella roccia che circonda la sala sperimentale, e conseguente riduzione degli eventi di background attesi nell'attuale run scientifico a 1.3 10^(-3) eventi. È già previsto dalla collaborazione il futuro upgrade dell'esperimento: XENONnT. Uno studio sulle possibili geometrie della TPC di XENONnT è stato effettuato mediante simulazioni Monte Carlo. Tra le possibili migliorie apportabili a XENONnT vi è la sostituzione degli attuali sensori di luce con fotomoltiplicatori al silicio (SiPM). Le simulazioni mostrano che, mediante una copertura totale della TPC con i SiPM, si ha un aumento dell'efficienza nella collezione di luce (LCE) del 20%. La LCE è un parametro fondamentale per la rivelazione del segnale di luce (S1) nella TPC; in questa configurazione si raggiunge una soglia in energia per rinculi nucleari di circa 3 keV, aumentando in modo significativo la sensibilità dell'esperimento, in particolare per WIMP di piccola massa

Interactions between the plant Golgi apparatus and the cytoskeleton

In animal cells, the relationship between the Golgi apparatus and cytoskeleton has been well characterised but not much is known in plants. The functions of the Golgi apparatus are conserved amongst eukaryotes. It is one of the main stations in the secretory pathway and is involved in protein processing and sorting to different destinations. In plants, it is also involved in trafficking and positioning of cell wall components. In tobacco epidermal cells, fluorescent labelling with Golgi marker proteins has shown that the Golgi apparatus is made of hundreds of individual units scattered in the cortical cytoplasm and moving on the actin cytoskeleton. The contribution of actin filaments to Golgi body motility in plant has been extensively described, but this actin-centric view has recently been challenged. Emerging evidence suggests that microtubules may contribute to short distance movement and ‘fine tuning’ of Golgi body displacement. Moreover, proteomic studies linking the actin- cytoskeleton to microtubules have demonstrated that these two components of the cytoskeleton are closely related and a role of the microtubules in Golgi movement cannot be excluded. In this thesis, automated tracking of Golgi bodies was used to understand and quantify the contribution of actin filaments and microtubules to the organelle dynamics. The tracking technique is also used to assess how the labelling of the cytoskeleton, with a novel fluorescent nanoprobe, affects the dynamics and stability of the actin filaments and the movement of Golgi bodies; FRAP analysis (fluorescent recovery after photo-bleaching) was also used to investigate the binding properties of the fluorescent nanoprobe to the actin filaments. The nanoprobe was compared with another cytoskeletal marker, Lifeact-GFP, to evaluate their suitability for studying the organelle’s motility in relation to the actin-cytoskeleton. Micromanipulation of Golgi bodies with optical tweezers was used to test if there are physical links between the organelles and the cytoskeleton. The widely accepted model is that organelles move on actin filaments and movement is powered by myosins. The hypothesis that actin filaments slide one of top of the other, and drag the organelles along, was tested using the FRAP technique. Kinesin-13a is the only microtubule motor protein localized on Golgi bodies by immunochemical studies. Its localization was investigated in vivo to evaluate if it is involved in linking Golgi bodies to microtubules

Parallel multithreading algorithms forself-gravity computation inESyS-Particle

This thesis describes the design, implementation, and evaluation of efficient algorithms for self-gravity simulations in astronomical agglomerates. Due to the intrinsic complexity of modeling interactions between particles, agglomerate are studied using computational simulations. Self-gravity affects every particle in agglomerates, which can be composed of millions of particles. So, to perform a realistic simulation is computationally expensive. This thesis presents three parallel multithreading algorithms for self-gravity calculation, including a method that updates the occupied cells on an underlying grid and a variation of the Barnes & Hut method that partitions and arranges the simulation space in both an octal and a binary tree to speed up long range forces calculation. The goal of the algorithms is to make efficient use of the underlying grid that maps the simulated environment. The three methods were evaluated and compared over two scenarios: two agglomerates orbiting each other and a collapsing cube. The experimental evaluation comprises the performance analysis of the two scenarios using the two methods, including a comparison of the results obtained and the analysis of the numerical accuracy by the study of the conservation of the center of mass and angular momentum. Both scenarios were evaluated scaling the number of computational resources to simulate instances with different number of particles. Results show that the proposed octal tree Barnes & Hut method allows improving the performance of the self-gravity calculation up to 100 with respect to the occupied cell method. This way, efficient simulations are performed for the largest problem instance including 2,097,152 particles. The proposed algorithms are efficient and accurate methods for self-gravity simulations in astronomical agglomerates

Application of metabolomics to assess milk quality and traceability

Milk is a foodstuff widely consumed around the world originating from a variety of different species, animal management and production systems. In recent years, consumers have placed a much greater emphasis on the authenticity and origin of some food products often willing to pay a premium price for such products that is, for example 'Grass-Fed Dairy'. Therefore, it is important to establish methods to assess both quality and authentication of milk and dairy products for increased food security and consumer protection. Accordingly, NMR-based, GC–MS-based, and LC–MS-based metabolomics have been established as useful tools in the analysis of dairy products, such as raw and processed milk. This short-review provides an updated and critical overview on the most useful metabolomics-based platforms and the most useful multivariate statistical tools available for metabolomic data interpretation