Parallelization of the algorithm WHAM with NVIDIA CUDA.

The aim of my thesis is to parallelize the Weighting Histogram Analysis Method (WHAM), which is a popular algorithm used to calculate the Free Energy of a molucular system in Molecular Dynamics simulations. WHAM works in post processing in cooperation with another algorithm called Umbrella Sampling. Umbrella Sampling has the purpose to add a biasing in the potential energy of the system in order to force the system to sample a specific region in the configurational space. Several N independent simulations are performed in order to sample all the region of interest. Subsequently, the WHAM algorithm is used to estimate the original system energy starting from the N atomic trajectories. The parallelization of WHAM has been performed through CUDA, a language that allows to work in GPUs of NVIDIA graphic cards, which have a parallel achitecture. The parallel implementation may sensibly speed up the WHAM execution compared to previous serial CPU imlementations. However, the WHAM CPU code presents some temporal criticalities to very high numbers of interactions. The algorithm has been written in C++ and executed in UNIX systems provided with NVIDIA graphic cards. The results were satisfying obtaining an increase of performances when the model was executed on graphics cards with compute capability greater. Nonetheless, the GPUs used to test the algorithm is quite old and not designated for scientific calculations. It is likely that a further performance increase will be obtained if the algorithm would be executed in clusters of GPU at high level of computational efficiency. The thesis is organized in the following way: I will first describe the mathematical formulation of Umbrella Sampling and WHAM algorithm with their apllications in the study of ionic channels and in Molecular Docking (Chapter 1); then, I will present the CUDA architectures used to implement the model (Chapter 2); and finally, the results obtained on model systems will be presented (Chapter 3).

Graphic news: La nuova frontiera del fumetto, proposta di traduzione

Il presente elaborato si prefigge lo scopo di proporre una traduzione in francese di cinque fumetti di giornalismo a fumetti da pubblicare su un’ipotetica versione localizzata del sito http://graphic-news.com/. Si tratta di un sito di informazione a fumetti, che combina due grandi rivoluzione del fumetto: il fumetto digitale e il graphic journalism. Si cercherà di definire il fumetto in quanto linguaggio formato dall’interazione fra codice visivo e codice verbale, se ne traccerà la storia dalle sue origini fino agli sviluppi più recenti per individuare l’evoluzione che ha portato alla nascita del fumetto digitale, di cui saranno analizzate le principali caratteristiche insieme a una panoramica sul graphic journalism, un genere che ha permesso al fumetto di emanciparsi dalla sua nomea di letteratura per l’infanzia. In seguito, ci si concentrerà sull'ambiente digitale che accoglierà le traduzioni dei fumetti: si fornirà perciò una descrizione dell’organizzazione del sito e una sua analisi semiotica. Infine, si passeranno in rassegna le caratteristiche generali della traduzione dei fumetti con le sue specificità e si proporrà la traduzione dei cinque fumetti con relativo commento delle maggiori difficoltà incontrate nel processo di traduzione con un’attenzione particolare per i principali aspetti problematici legati all'interazione fra testo e immagini.

Laboratory-based ROTEM(®) analysis: implementing pneumatic tube transport and real-time graphic transmission

ROTEM(®) is considered a helpful point-of-care device to monitor blood coagulation. Centrally performed analysis is desirable but rapid transport of blood samples and real-time transmission of graphic results are an important prerequisite. The effect of sample transport through a pneumatic tube system on ROTEM(®) results is unknown. The aims of the present work were (i) to determine the influence of blood sample transport through a pneumatic tube system on ROTEM(®) parameters compared to manual transportation, and (ii) to verify whether graphic results can be transmitted on line via virtual network computing using local area network to the physician in charge of the patient.