The Langevin equation is a stochastic differential equation frequently used in molecular dynamics for simulating systems with a constant temperature. Recent developments have given rise to wide uses of Langevin dynamics at different levels of spatial resolution, which necessitate time step and friction parameter choices outside of the range for which many existing temporal discretization methods were originally developed. We first study the GJ--F, BAOAB and BBK numerical algorithms, originally developed for atomistic simulations, on a coarse-grained polymer melt, paying close attention to the large time step regime. The results of this study then inspire our search for new algorithms and lead to a general class of velocity Verlet-based time-stepping schemes designed to perform well for all parameter regions, by ensuring that they faithfully reproduce statistical quantities for the case of a free particle and harmonic oscillator. This family of methods depends on the choice of a single free parameter function and we explore some of the methods defined for certain choices of this parameter on realistic coarse-grained and atomistic molecular systems relevant in material and bio-molecular science. In addition, we provide an equivalent splitting formulation of this one-parameter family which allows for enhanced insight into the hidden time scaling induced by the choice of the free parameter in the Hamiltonian and stochastic time scales. / Mathematics

Measurements were made on three forward steps with step height to boundary layer ratio of approximately 3.8%, 15% and 60% and Reynolds number based on step height ranging from 6640 to 213,000. The measurements included mean wall pressure, single and 2 point wall pressure fluctuations, single and 2 point velocity fluctuations and, oil flow visualization. Pressure fluctuation measurements were made 5 boundary layer thicknesses upstream of step to 22 boundary layer thickness (or 600 step heights for smallest step size) downstream of the step. The results show that the steps remarkably enhance the wall pressure fluctuations that scale on the step height in the vicinity of the step and far downstream of the step. The decay of wall pressure fluctuations post reattachment is a slow process and elevated levels can be seen as far as 150 step heights downstream for the mid step size. The enhanced pressure fluctuations come from the unsteady reattachment region on top face of the step which was found to be a strong function of flow geometry and flow parameters such as Reynolds number. The 2 point pressure and velocity space-time correlations show a quasi-periodic structure which begins to develop close to the reattachment and grows in intensity and scale further downstream of reattachment and is responsible for the elevated pressure fluctuations downstream of the step. However, the velocity correlations lack in scale reflecting the fact that large scales reflected in pressure are masked by smaller scales that exist within them. / Master of Science

Ce manuscrit de thèse concerne le développement d'une stratégie de synthèse multi-étapes de nouveaux composés comportant plusieurs plateformes hétérocycliques (rhodanine, benzimidazole, pyrazole et imidazole) à visée thérapeutique multiple contre la malaria, la leishmaniose, le cancer et les maladies neurodégénératives. Les pharmacomodulations de ces composés ont été élaborées sur la base du modèle de la pentamidine 35 comportant 2 motifs benzamidines (parties « Ouest » et « Est »). En effet, la substitution de sa partie « Ouest » par une plateforme rhodanine ou benzimidazole et de sa partie « Est » par un système aromatique plan ou système azole (pyrazole, imidazole) a permis d’accéder respectivement aux 5-arylidènes rhodanines (50, 58), aux dérivés ''aza'' (99,100) et aux dérivés ''aza azoles'' 174 qui sont des analogues de la pentamidine. Les rendements de ces composés sont respectivement compris entre 26 et 98%, 10 et 93% et 10 et 97%. L’ensemble des composés synthétisés dans les chapitres II, III et IV de ces travaux ont été l'objet d'évaluations pour leur activité antiproliférative sur les lignées cellulaires et pour leur activité inhibitrice sur les protéines kinases. / This thesis manuscript is focused on the development of multi-steps synthesis strategy of new compounds bearing several heterocyclic platforms (rhodanine, benzimidazole, pyrazole and imidazole) for multiple therapeutic use to fight malaria, leishmaniasis, cancer et neurodegenarative diseases. The pharmacomodulations of these compounds were developped from the design of pentamidine 35 which containins 2 fragments benzamidine (parts ''West'' and ''East''). Indeed, the substitution of its part ''West'' by a platform rhodanine or benzimidazole and its part ''East'' by an "azole" aromatic ring system (pyrazole, imidazole) lead respectively to 5-arylidene rhodanines (50, 58), to derivatives ''aza'' (99,100) and to derivatives ''aza azoles'' 174 which are pentamidine analogs. The chemical yields of these compounds are ranging respectively from 26 to 98%, 10 to 93% and 10 to 97%. All the compounds synthesized in the chapters II, III and IV of this research work were evaluated for their antiproliferative activity on tumoral cell lines and for their inhibitory activity on protein kinases.

Name of diploma thesis: Physical activity and body composition in patients with ankylosing spondylitis Prepared by: Bc. Lucie Srovnalíková Supervisor: PhDr. Andrea Levitová, Ph.D. Target: The findings the size of physical activity and body composition in the groups of patients with ankylosing spondylitis with different duration of disease and subsequent comparison of the size of physical activity with selected health recommendations for a healthy population. Methods: The sample consists of participants (10 women and 36 men, n = 46, 42.8 ± 11.3 years old) with clinically diagnosed disease ankylosing spondylitis who have been outpatiently visiting Rheumatology institute in Prague. The sample was divided into three groups according to the duration of disease (1st group 0-6 years, 2nd group 7 -14 years, 3rd group 3-15 years). Accelerometer ActiGraph GT3X was used for determine the size of weekly physical activity. Bioelectrical impedance using a BIA 2000 was used to assess the body composition. Results: From the perspective of the physical activity health recommendations all three groups met health recommendation for minimum amount of moderate-intensity physical activity throughout the week (150 minutes). Neither group, however, did not meet health recommendation for minimum average daily number of...

Title of Bachelor thesis: Physical activity for health in sport youth Author: Bc. Jan Kokštejn Head of work: Mgr. Jakub Kokštejn, Ph.D. Aim: Findings the size of physical activity in youth soccer players during a week mode and comparison of selected indicators with recommendations of physical aktivity for health promotion. To identify possible differences in physical activity between younger (16-17 years old) and older (18-19 years old) players in adolescent category. Methods: The research samples consist of younger soccer players (n=25; 16,2±0,9 years old) and older soccer players (n=25; 18,6±0,3 years old). Accelerometers Actigraph GT3X were used for determining level of physical activity during the week. Results: The average daily amount of modern to high intensity physical activity exceeded in both groups of soccer players worldwide used recommendations, which is 60 minutes. For daily number of steps, the group of younger players exceeded recommended amount according to Sigmund et al. (2005). The group of older players remained just below this threshold, but within the recommended range. In terms of energy output both groups reached values between 8-9 kcal.kg-1 .day-1 , according to selected criteria met physical activity recommendations. Energy output value and the number of steps did not...

Title: The level of physical activity during the week in adolescent football players Author: Bc. Marek Vait Head of work: Mgr. Jakub Kokštejn, Ph.D. Aim: The aim of the research was to determine the level of physical activity (PA) in the weekly mode with teenage football players in the junior category (16 - 17 years old) and older adolescents (18 - 19 years old). At the same time to evaluate the level of the PA in relation to selected health recommendations for the size of the PA. Methods: In the research participated a total of n = 66 players (players younger junior players n = 36; 15.8 ± 0.8, older adolescents n = 30 players; 17.2 ± 0.75. For testing of selected player were used 25 accelerometers, 14 of them was a type ActiGraph GT3X and 11 type ActiGraph GTM1. The level of PA was observed during seven days. Results: The average daily value of energy expenditure reached in the younger category of 10.9 ± 2.7, with the older 9.1 ± 3.2. Both categories fulfilled health recommendations. In the case of the daily number of steps, both categories have reached the recommended values, the values of the younger reached 13,625 ± 3049 and the older 11061 ± 3873.The average daily value of medium to high intensity PA exceeded both categories used worldwide recommendations for the minimum daily amount of...

Shigella flexneri est une entérobactérie Gram négatif responsable de la forme endémique de la shigellose, l’une des quatre causes majeures d’infection diarrhéique chez les jeunes enfants. La cible majeure de la réponse immunitaire lors d’une infection naturelle est le polysaccharide de surface (PS). Chez S. flexneri 1b, l’un des sérotypes prévalents dans les pays en voie de développement, le PS est défini par le pentasaccharide ramifié α-L-rhamnopyranosyl-(1→2)-α-L-rhamnopyranosyl-(1→3)-α-L-rhamnopyranosyl-(1→3)-[α-D-glucopyranosyl-(1→4)]-2-acetamido-2-deoxy-β-D-glucopyranoside [I] di-O-acétylé. Ces travaux s’intègrent dans un projet visant le développement d’un vaccin basé sur des sucres synthétiques à couverture large contre les infections par Shigella. Afin de concevoir des glycoconjugués efficaces et induisant une bonne réponse immunitaire chez les enfants, des synthèses multi-grammes des précurseurs mono- à pentasaccharidiques ont été optimisées permettant une stratégie par blocs en vue de l’obtention d’oligosaccharides de grande taille. Au cours de ces synthèses, l’obtention du trisaccharide ramifié C(E)D clé a nécessité de nombreuses optimisations, permettant la conception de synthons tri- à pentasaccharides. Un choix des groupements protecteurs orthogonaux nous a permis d’investiguer les différentes conditions de couplages nous donnant accès à 28 oligosaccharides déprotégés courts diversement acétylés. La validation de ces condensations avec des partenaires plus complexes a permis d’accéder à un large panel d’une cinquantaine d’oligosaccharides de di- à pentadécasaccharides sous leur forme libre, ou encore protégés avec divers degrés d’acétylation. / 700,000 children die each year due to diarrheal diseases, making it the second cause of death among this population. Shigella flexneri is a Gram negative enterobacterium responsible of the endemic form of shigellosis in developing countries. The O-antigen part of the bacterial lipopolysaccharide is the major target of the immune system during natural infection. The O-antigen of S. flexeni 1b, one of the prevalent serotypes, is defined by a ramified pentasaccharide made of three L-rhamnose, one D-glucosamine and one D-glucose with two non-stoichiometric sites for acetylation (I). This work is part of the project aimed at the development of a synthetic carbohydrate-based vaccine against Shigella infections. In order to obtain suitable glyconjugates inducing a high level of protection especially in children, the synthesis of mono- to pentasaccharide precursors was optimized, allowing a convergent synthesis of oligosaccharides with different acetylation patterns. Optimization of the glycosylation conditions, acetylations and protecting group manipulations enable the access to fragments from di to pentadecasaccharides representing S. flexneri type I O-antigen.

A matriz energética brasileira atualmente está concentrada na geração de energia hidrelétrica. Mas, devido aos últimos acontecimentos de escassez de recursos hídricos, faz-se necessário diversificar a matriz energética por meio do investimento em energias alternativas. O Brasil ainda possui muitas pessoas na área rural sem abastecimento de energia elétrica, fato que limita a implantação de técnicas agrícolas como a irrigação. Nesse contexto, a energia solar fotovoltaica (FV) é uma alternativa para diversificar a matriz energética brasileira e ampliar o uso de sistemas de irrigação. Foram instalados dois módulos FV, um estático e outro com um sistema de rastreamento solar manual de três passos, na área experimental do Departamento de Engenharia de Biossistemas - ESALQ/USP (22° 42\' 30\'\'S, 47° 38\' 00\'\'W, altitude de 546 metros). Para cada módulo FV, estático e móvel, foram acoplados sistemas de bombeamento de água para um sistema simulado de irrigação. O objetivo foi avaliar o incremento de energia FV gerada, tempo de bombeamento, volume bombeado e área irrigada; com o uso do sistema rastreador. A partir dos dados encontrados, verificou-se que o sistema rastreador solar manual de três passos apresentou maior eficiência na captação de energia (8 - 19% dia-1), quando comparado com geradores fixos; o que refletiu no incremento significativo do tempo de bombeamento (40 - 160 min dia-1), no volume bombeado (884 - 3479 litros dia-1) e na área irrigada (196 - 773 m² dia-1 para uma lâmina de irrigação de 4,5 mm). Com isso, o rastreador se mostrou uma alternativa técnica viável para melhorar a captação de energia solar e aumentar a área irrigada com um mesmo tamanho de área de gerador FV. Em relação ao investimento, o sistema rastreador custou apenas 0,2% do custo total da instalação FV, e proporcionou a redução do tempo de retorno do investimento em 2 anos e 5 meses comparado ao módulo FV estático. / The current Brazilian Energetic Matrix is concentrated in the generation of hydroelectric energy. But, due the latest water resources scarcity, it is necessary to diversify the energetic matrix by investing in alternatives energies. Brazil still have a plenty of people living in rural areas without supply of electric energy, this fact limits the implantation of agriculture techniques like irrigation. In this sense, the photovoltaic solar energy (PV) is an alternative to diversify the Brazilian Energetic Matrix and expand the use of irrigation systems. It were installed two PV modules, one static and another with solar three steps manual tracking system, Biosystems Engineering Department - ESALQ/USP (22° 42\' 30\'\'S, 47°38\' 00\'\'W, at 546 meters altitude). For each PV module, static and moving, it was coupled water pumping systems for simulated irrigation systems. The goal was evaluate the gain of the PV energy generated; pumping time; pumping volume and irrigated area; using the tracking system. From obtained data, it was observed that the solar three steps manual tracking system shows more efficiency in the energy harvesting (8 - 19% day-1), compared to static generator; which resulted in significant gain of pumping time (40 - 160 min day-1), pumping volume (884 - 3479 liters day-1) and irrigates area (196 - 773 m² day-1 for a irrigation depth equal 4.5 mm). Therewith, the tracking system shows a viable alternative technique to improve solar energy harvesting and increase the irrigated area with same area of PV generator. In relation to investment of the tracking system, it cost only 0.2 % of the total cost of PV installation and provided the reduction in the return on investment time of 2 years and 5 month compared to static PV module.

" Hydrodechlorination is the reaction of a chlorinated organic compound (R-Cl) with hydrogen to form a carbon-hydrogen bond and HCl: R-Cl + H2 = R-H + HCl. This reaction is used in refrigerant manufacturing, industrial by-product reclamation and waste management. These practical applications require in-depth understanding of hydrodechlorination reaction. In this research work, we studied four families of chlorinated compounds; CF3CF3-xClx(x=1-3), CH4-xClx (x=1-4), CF4-xClx (x=1-4) and dichloropropanes (1,1-, 1,2-, 1,3-, 2,2-), on supported palladium catalysts to create a theory capable of predicting the hydrodechlorination rate on chlorinated compounds and to explore the reaction mechanism. A possible set of elementary reaction steps of hydrodechlorination reaction was proposed from our kinetics study of all these compounds. In this set of reaction steps, the irreversible scission of the first C-Cl bond in a chlorinated compound was proposed to be the rate-determining step; gas phase H2 and HCl were suggested to be in equilibrium with surface H and Cl species; adsorbed Cl was assumed to be the most abundant surface intermediate. The overall rate of hydrodechlorination reaction could be derived from these reaction steps as r=k'[R-Cl]/(1+K'[HCl]/[H2]0.5). In this rate equation, k'is the product of the adsorption equilibrium constant of the chlorinated compound on catalyst surface times the rate constant for the scission of the first C-Cl bond scission step, and K'is the square root of the equilibrium constant for the equilibrium between H2, HCl and their corresponding surface species: 2HCl + 2* = H2 + 2Cl*. The hydrodechlorination reaction of CF3CFCl2 was performed in the presence of H37Cl to study the reversibility of C-Cl bond scission, and the removal of the first Cl atom from CF3CFCl2 was found to be an irreversible step. Hydrodechlorination experiments of CF3CFCl2 with D2 and HCl mixture revealed that D2 and HCl were in equilibrium with surface adsorbed hydrogen and chlorine during reaction. The forward rate and reverse rate of this equilibrium were at least 400 times higher than the overall hydrodechlorination rate. This result supported the assumption of equilibrium for 2HCl + 2* = H2 + 2Cl*. Additionally, the activation energy for the rate determining step was extracted from hydrodechlorination reaction kinetics results of CH4-xClx (x=1-4), CF4-xClx (x=1-4) and dichloropropanes (1,1-, 1,2-, 1,3-, 2,2-) compounds. It was found that for each of the series compounds, a linear relationship existed between C-Cl bond scission activation energy and gas phase C-Cl bond strength. This observation corroborates our assumption that the removal of the first Cl atom from a chlorinated compound is the rate-determining step in the hydrodechlorination reaction. Thus, all kinetic and isotope experimental results obtained from this study are consistent with the proposed reaction steps for the chlorinated compounds tested. This set of reaction steps can also be used to predict the hydrodechlorination reaction rate of a chlorinated compound, once its gas phase C-Cl bond energy is calculated and the turnover rate of a reference chlorinated compound with similar structure is known. Some work has been done to study hydrodechlorination reaction steps and reaction intermediates beyond the rate-limiting step. Isotope tracing experiments with D2 indicated that CH3-, CH2- groups adjacent to a C-Cl bond could undergo deuterium exchange. The study of reactions steps using ab initio methods, including calculation of rate constants, is also under way. Calculations for the CH4-xClx (x=1-4) family showed that the heat of adsorption and C-Cl bond dissociation energy on a Pd surface were linearly related to their gas phase C-Cl bond strength."

Laurentide Ice Sheet outburst floods to the Gulf of Mexico have been mainly documented based on deep-sea cores, especially the megafloods, only during the last several interglacial episodes in the late Pleistocene. The paleoclimatic significance of giant sedimentary structures developed under unconfined Froude-supercritical turbidity currents in subaqueous settings is considerably under-examined. This research extensively documents >20-km-wide and 200-m-thick Plio-Pleistocene giant sediment waves for the first time on the northern Gulf of Mexico continental slope using 3D seismic data, which show waveform morphology in unprecedented detail. The results suggest that such large-scale bedforms were formed under sheet-like unconfined Froudesupercritical turbidity currents as cyclic steps, based on numerical and morphological analyses. Paleohydraulic reconstruction (e.g., flow velocity, discharge, and unit flux), in association with other evidence like geologic age, stable isotope records, and temporal rarity, points out that the responsible Froude-supercritical turbidity currents were most likely triggered by deglacial catastrophic outburst floods during the late Pliocene to early Pleistocene. These flooding events constitute, by far, the oldest record of the glacial outburst floods during the Quaternary Ice Age. The results propose that such pervasive occurrence of large-scale sediment waves are a proxy for catastrophic megaflood events