In January 2010, a magnitude 7.0 earthquake devastated Haiti, one of the poorest countries in the Western Hemisphere. Haiti’s weak sanitation infrastructure and limitations in the public health system made the country susceptible to the spread of waterborne diseases. Following the earthquake, cholera rapidly spread through Haiti, killing 4,672 people in 5 months and leaving thousands hospitalized (MSNBC, 2010). Cholera is an infectious diarrheal disease caused by the pathogen, Vibrio cholerae, which results in severe dehydration with a high mortality risk. The source of the epidemic was traced to the Artibonite River, the island’s longest and most essential drinking water source (Encyclopaedia Britannica. n.d.). The origin of the contamination was later discovered to be unsanitary conditions left from United Nations peacekeepers from Nepal. Eight years later, cholera cases are still prevalent, although numbers have declined recently due to aid from private organizations (Dowell, S.F. et al 2011, Katz, J.M. 2013). However, with climate-related increases in ocean water temperatures, scientists expect hurricanes to intensify and increase damage to developing countries (Center for Climate and Energy Solutions. n.d.). Natural disasters promote the spread of waterborne illness by isolating people from safe drinking water and destroying public health infrastructure such as happened with the cholera outbreak in Haiti (Funari, E. et al 2013). To prevent future waterborne disease epidemics in such areas with limited resources, it would be beneficial to improve environmental surveillance through development of rapid, reliable, and portable detection methods for waterborne pathogens. The advent of high-throughput sequencing technologies has enabled the detection and characterization of microbial communities in their natural environments, an approach known as metagenomics. Metagenomic sequencing, unlike more traditional PCR methodologies, is capable of sequencing thousands of organisms in a sample. This metagenomic shotgun sequencing approach detects the abundance of microbes and bacterial diversity in the environment (Illumina, n.d.). The Oxford Nanopore MinION is a shotgun sequencing device that is optimal for portable, rapid detection of the microbial diversity in an environmental sample (Oxford MinION, n.d.). This handheld device has enormous potential for field use in emergency preparedness and disease response, particularly in developing countries where more advanced analytical equipment may be inaccessible due to lack of facilities or damaged infrastructure. Having access to quick, infield assessment technology for rapidly emerging outbreaks would be beneficial to a disease-specific public health response. Current protocols recommend that DNA is extracted from environmental samples as rapidly as possible after collection. If cooling is available with an insulated ice chest, samples may be transported/stored for periods ranging from 6 to 24 hours. The shorter timeframes minimize unwanted shifts in microbial structure (U.S. Geological Survey, 1997, WHO, n.d.). Access to cold storage in remote areas is unlikely, and the use of liquid preservation methods could assist in maintaining quality of DNA, and hence produce more accurate data in metagenomic analyses. In the absence of cold storage facilities, infield filtration coupled with preservation techniques are necessary to maintain samples integrity for transport to laboratory facilities. This thesis aimed to develop an infield filtration and sequencing protocol, coupled with the Oxford Nanopore MinION sequencing platform, to identify the potential bacteria, viruses, protozoa, fungi, antimicrobial resistance (AMR), pathogenic strains, and virulence associated genes for use in remote locations. Five locations across Lake Warner, Massachusetts were used for method development, coupled with Millipore Sterivex filters for field filtration to determine the most effective method for sample preparation in remote locations. Additionally, a chemical preservation method was assessed using dimethyl sulfoxide, disodium EDTA, and saturated NaCl (DESS). A study by Gray et al, found that liquid preservation methods (DNAgard, RNAlater, and DESS) outperformed the card-based preservatives (FTA cards and FTA Elute cards) in terms of bacterial recovery (Gray, M.A., et al 2013). DESS was selected for investigation in this thesis because of the low cost compared to the other liquid-based preservatives. Lake Warner in Hadley, Massachusetts, which is heavily used for fishing and boating activities, flows into the Connecticut River via the Mill River. Historically, the lake experienced high Escherichia coli (E. coli) levels due to pollution from primary effluent released in the 1950s from the Amherst Wastewater Treatment Plant (Johnson, J., 2015). Similar to Vibrio cholerae, E.coli spp is a waterborne bacteria caused by fecal contamination. Although most E.coli are natural inhabitants of the gastrointestinal tract, pathogenic serotypes can result in severe complications in vulnerable populations such as kidney failure in children and the elderly adults. (Todar, K., 2012). Lake Warner was chosen for the method development because of its history of E. coli pollution and recreational traffic as well as its general accessibility for study. Designing a methodology for rapid detection of pathogenic bacteria using a metagenomic approach could help improve surveillance for environmental pathogens that pose future epidemic risk. These tools are becoming increasingly important for prediction and response to waterborne diseases as climate impacts increase the frequency, intensity, and duration of extreme weather events that damage critical infrastructure for vulnerable populations (van Aalst, M.K. 2006).

L'utilisation de matériaux organiques pour l'électronique de spin suscite actuellement un fort intérêt. En effet, le long temps de diffusion de spin, la possibilité de manipuler l'état de spin d'une molécule ainsi que son interaction avec une surface magnétique offrent a priori de nouvelles possibilités pour la réalisation de nouveaux dispositifs d'électronique de spin. L'incorporation dans des dispositifs de molécules possédant deux états de spin nécessite la compréhension du phénomène de transition de spin une fois que les molécules sont en contact direct avec des surfaces métalliques.L'objectif de ce travail de thèse est l'étude des interfaces molécule-métal. Dans une première partie, nous avons étudié le magnétisme d'interfaces ferromagnétique-organique en utilisant différentes molécules et différents métaux ferromagnétiques. Nous nous sommes particulièrement intéresses a l'anisotropie magnétique dans ces systèmes. Dans une deuxième partie, nous avons étudié le phénomène de transition de spin moléculaire en contact avec une surface métallique. La spectroscopie d'absorption et le dichroïsme magnétique des rayons x ont d'abord permis de mettre en évidence cette transition à l'échelle globale ensuite, nous avons utilise la microscopie a effet tunnel pour étudier ce phénomène à l'échelle moléculaire dans un cristal 2d de molécule. Nous avons notamment observe la dynamique de la transition sous irradiation laser pour la première fois à l'échelle moléculaire. / The use of organic materials in spintronic devices has recently raised a lot of interest. Large spin diffusion time in organic materials along with the flexibility of manipulating the spin state of the molecule and their interaction with the ferromagnetic metal electrode offers new functionalities in molecular spintronics. Understanding the spin crossover (sco) phenomenon for spin active molecules attached to metallic substrate is also necessary for a primary step towards device application.The main goal of the thesis work was to study these molecule—metal interfaces. In one part, we have studied the magnetism of the organic—ferromagnetic interface with different molecules and different ferromagnetic metals. The study was mainly focused on the magnetic anisotropy at the molecule-metal interfaces. In other part, we focused on the spin crossover phenomena of sco molecules attached to metallic substrates. X—ray absorption spectroscopy and magnetic circular dichroism techniques enabled us to study globally the spin crossover phenomenon. Using scanning tunneling microscopy we were able to study the sco phenomena at the single molecular level in a 2d crystal of molecules on a metal substrate. We have then studied locally the dynamics of the spin transition phenomenon upon laser exposure on a single 2d layer molecular crystal.

Molecular-based quantum cellular automata (m-QCA), as an extension of quantum-dot QCAs, offer a novel alternative in which binary information can be encoded in the molecular charge configuration of a cell and propagated via nearest-neighbor Coulombic cell–cell interactions. Appropriate functionality of m-QCAs involves a complex relationship between quantum mechanical effects, such as electron transfer processes within the molecular building blocks, and electrostatic interactions between cells. The influence of structural distortions of single m-QCA are addressed in this paper within a minimal model using an diabatic-to-adiabatic transformation. We show that even small changes of the classical square geometry between driver and target cells, such as those induced by distance variations or shape distortions, can make cells respond to interactions in a far less symmetric fashion, modifying and potentially impairing the expected computational behavior of the m-QCA.