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).

Hydraulic evaluation of the gyro electric wave energy converter

Motivation Thanks for a scholarship offered by ALma Mater Studiorum I could stay in Denmark for six months during which I could do physical tests on the device Gyro PTO at the Departmet of Civil Engineering of Aalborg University. Aim The goal of my thesis is an hydraulic evaluation of the device: Gyro PTO, a gyroscopic device for conversion of mechanical energy in ocean surface waves to electrical energy. The principle of the system is the application of the gyroscopic moment of flywheels equipped on a swing float excited by waves. The laboratory activities were carried out by: Morten Kramer, Jan Olsen, Irene Guaraldi, Morten Thøtt, Nikolaj Holk. The main purpose of the tests was to investigate the power absorption performance in irregular waves, but testing also included performance measures in regular waves and simple tests to get knowledge about characteristics of the device, which could facilitate the possibility of performing numerical simulations and optimizations. Methodology To generate the waves and measure the performance of the device a workstation was created in the laboratory. The workstation consist of four computers in each of wich there was a different program. Programs have been used : Awasys6, LabView, Wave lab, Motive optitrack, Matlab, Autocad Main Results Thanks to the obtained data with the tank testing was possible to make the process of wave analisys. We obtained significant wave height and period through a script Matlab and then the values of power produced, and energy efficiency of the device for two types of waves: regular and irregular. We also got results as: physical size, weight, inertia moments, hydrostatics, eigen periods, mooring stiffness, friction, hydrodynamic coefficients etc. We obtained significant parameters related to the prototype in the laboratory after which we scale up the results obtained for two future applications: one in Nissun Brending and in the North Sea. Conclusions The main conclusion on the testing is that more focus should be put into ensuring a stable and positive power output in a variety of wave conditions. In the irregular waves the power production was negative and therefore it does not make sense to scale up the results directly. The average measured capture width in the regular waves was 0.21 m. As the device width is 0.63 m this corresponds to a capture width ratio of: 0.21/0.63 * 100 = 33 %. Let’s assume that it is possible to get the device to produce as well in irregular waves under any wave conditions, and lets further assume that the yearly absorbed energy can be converted into electricity at a PTO-efficiency of 90 %. Under all those assumptions the results in table are found, i.e. a Nissum Bredning would produce 0.87 MWh/year and a North Sea device 85 MWh/year.

Estimation of the ephemerides and gravity fields of the Galilean moons through orbit determination of the JUICE mission

Jupiter and its moons are a complex dynamical system that include several phenomenon like tides interactions, moon's librations and resonances. One of the most interesting characteristics of the Jovian system is the presence of the Laplace resonance, where the orbital periods of Ganymede, Europa and Io maintain a 4:2:1 ratio respectively. It is interesting to study the role of the Laplace Resonance in the dynamic of the system, especially regarding the dissipative nature of the tidal interaction between Jupiter and its closest moon, Io. Numerous theories have been proposed regarding the orbital evolution of the Galilean satellites, but they disagree about the amount of dissipation of the system, therefore about the magnitude and the direction of the evolution of the system, mainly because of the lack of experimental data. The future JUICE space mission is a great opportunity to solve this dispute. JUICE is an ESA (European Space Agency) L-class mission (the largest category of missions in the ESA Cosmic Vision) that, at the beginning of 2030, will be inserted in the Jovian system and that will perform several flybys of the Galilean satellites, with the exception of Io. Subsequently, during the last part of the mission, it will orbit around Ganymede for nine months, with a possible extension of the mission. The data that JUICE will collect during the mission will have an exceptional accuracy, allowing to investigate several aspects of the dynamics the system, especially, the evolution of Laplace Resonance of the Galilean moons and its stability. This thesis will focus on the JUICE mission, in particular in the gravity estimation and orbit reconstruction of the Galilean satellites during the Jovian orbital phase using radiometric data. This is accomplished through an orbit determination technique called multi-arc approach, using the JPL's orbit determination software MONTE (Mission-analysis, Operations and Navigation Tool-kit Environment).

Study on health status and remediation potential of Phragmites australis employed in an Emilia Romagna (IT) Constructed Wetland to assess zonal variability of the facility.

Phragmites australis (Cav.) Trin. ex Steud. is a hydrophyte particularly resistant to harsh conditions, e.g. drought, high salinity, contaminants, such as heavy metals and toxic molecules, and high nutrients concentrations. These resistances render the plant suitable for water depuration, where its particular metabolism is exploited to remove pollutants and excessive nutrients from the environment. In constructed wetlands, this principle is applied to phyto-purify wastewater with various origins, such as industrial, agricultural and household, with the aim to improve its quality to an extent which would render its reuse possible. In the framework of a pre-existing project of Department of Agricultural and Food Sciences (DiSTAl), this work integrates the knowledge and data relative to an Emilia Romagna (IT) constructed wetland plant, in order to expand the knowledge about this particular facility and of the system in general. By assaying antioxidants, both non- enzymatic and enzymatic, chlorophylls content and net photosynthetic rates, and by measuring the elemental composition of the specimens, the health status and the elemental uptake of the wetland plants sampled in different areas were investigated. The results were compared amongst the examined specimens with the aim to detect areas where there may be a higher stress due to a different wastewater composition, potentially varying along the constructed route. In addition, different parameters regarding the extraction and assay protocols were investigated, in order to optimise the procedure and to select the best conditions to perform the analyses, as well as to integrate information missing in literature or found as contradictory.