Abstract: In this study, we predicted two new stable metallic Re-C based monolayer structures with a rectangular (r-ReC2) and a hexagonal (h-Re2C) crystal symmetry using first-principle calculations based on density functional theory. Our results obtained from mechanical and phonon calculations and high-temperature molecular dynamic simulations clearly proved the stability of these two-dimensional (2D) crystals. Interestingly, Re-C monolayers in common transition metal carbide structures (i.e. MXenes) were found to be unstable, contrary to expectations. We found that the stable structures, i.e. r-ReC2 and h-Re2C, display superior mechanical properties over the well-known 2D materials. The Young's modulus for r-ReC2 and h-Re2C are extremely high and were calculated as 351 (1310) and 617 (804) N/m (GPa), respectively. Both materials have larger Young's modulus values than the most of the well-known 2D materials. We showed that the combination of the short strong directional p-d bonds, the high coordination number of atoms in the unit-cell and high valence electron density result in strong mechanical properties. Due to its crystal structure, the r-ReC2 monolayer has anisotropic mechanical properties and the crystallographic direction parallel to the C-2 dimers is stiffer compared to perpendicular direction due to strong covalent bonding within C-2 dimers. h-Re2C was derived from the corresponding bulk structure for which we determined the critical thickness for the dynamically stable bulk-derived monolayer structures. In addition, we also investigated the electronic of these two stable structures. Both exhibit metallic behavior and Re-5d orbitals dominate the states around the Fermi level. Due to their ultra high mechanical stability and stiffness, these novel Re-C monolayers can be exploited in various engineering applications.

Abstract: For the first time, we demonstrate, using an atomistic description of a 30nm diameter spin-transfer-torque magnetic random access memories (STT-MRAM), that the difference in mechanical properties of its sub-nanometer layers induces a high compressive strain in the magnetic tunnel junction (MTJ) and leads to a detrimental magnetostrictive effect. Our model explains the issues met in engineering the electrical and magnetic performances in scaled STT-MRAM devices. The resulting high compressive strain built in the stack, particularly in the MgO tunnel barrier (t-MgO), and its associated non-uniform atomic displacements, impacts on the quality of the MTJ interface and leads to strain relieve mechanisms such as surface roughness and adhesion issues. We illustrate that the strain gradient induced by the different materials and their thicknesses in the stacks has a negative impact on the tunnel magneto-resistance (TMR), on the magnetic nucleation process and on the STT-MRAM performance.

Abstract: Superconductivity is one of the most important discoveries of the last century. With many applications in physics, engineering, and technology, superconductors are crucial to our way of living. Several material and engineering issues however prevent their widespread usage in everyday life. Comprehensive studies are being directed at these materials and their properties to come up with new technologies that will address these challenges and enhance their superconductive capabilities. In this context, numerical modeling plays an important role in the search of new solutions to existing material and engineering issues. The time-dependent Ginzburg-Landau (TDGL) theory is a powerful predictive tool for modeling the macroscopic behavior of superconductors. However most of the numerical algorithms developed so far are incapable of describing many basic properties of real superconducting devices, and are too slow on current hardware for large-scale numerical simulations necessary for their accurate description. Therefore, the purpose of this thesis is to develop high-performing numerical solutions that can correctly describe material features to be used as modeling tools of laboratory experiments. Some important innovations introduced in this work include the numerical modeling of nonrectangular geometrical shapes with complex electrical and insulating components, the inclusion of dynamic heating of the material, and the description of different types of material inhomogeneities. These encompass the principal features necessary for a complete description of the superconductive physics in real material samples. In this thesis a numerical solution is developed for modeling superconducting thin films and used to study the superconductive properties of three experimental configurations: the dynamics of vortex matter in a Corbino disk, the motion of ultrafast vortices in an hourglass-shaped microbridge, and the photon detection process in a meander-patterned nanowire. Moreover, a numerical solution is developed for modeling three-dimensional superconductors which are studied here for the first time in the type-I superconducting regime. These numerical algorithms are optimized to exploit the computational horsepower of graphics processing units (GPUs) and multicore central-processing unit (CPU) clusters such that they can achieve high-performance and be used to model large-scale problems previously impossible on conventional machines. Several computational tools are also designed to assist with the modeling of superconducting devices. These include a numerical library of the TDGL equations, a novel mechanism for the generation of complex geometries, a closed-form solver to conduct numerical simulations, and a graphics user interface (GUI) to visualize the dynamic behavior of superconductors. The contributions in this thesis ultimately push the boundaries on what is possible in state-of-the-art numerical modeling of superconductivity.

Abstract: This paper presents a previously unexplored biosensing strategy for detecting gliadin which exploits the crosslinking of gliadin with collagen, catalyzed by transglutaminase at the interfacial electron transfer rate, on a modified electrode. The process is monitored by electrochemical impedance spectroscopy using a glassy carbon electrode coated with a collagen layer. To validate the specificity of the response as well as to eliminate possible interferences from other proteins, such as soy protein or casein, the captured gliadin is further reacted with a specific anti-gliadin antibody. Changes in charge transfer resistance, measured from the Nyquist plots, scale linearly with the gliadin concentration in the range 5-20 mg/L, a range suitable for testing the gliadin concentration in gluten-free food commodities.

Abstract: The research of soil contamination by heavy metal is an important field due to its environmental and health implications. The goal was to study the elemental mobility as a function of depth. For this reason, the distribution of heavy metals (V, Cr, Co, Ni, Cu, Zn, As, Sn, and Pb) was investigated along soil profiles up to a depth of 15m at 9 sampling sites in the Nilufer industrial district (Bursa, Turkey). Elemental analyses were done with the Epsilon 5 energy dispersive X-ray fluorescence and inductively coupled plasma mass spectrometry equipment. Particle analysis was performed with a JEOL scanning electron microscope equipped with a Si(Li) X-ray detector. The crystallographic compositions of oxide compounds in soil samples were identified by a Rigaku X-ray diffraction instrument. Different parameters such as the soil's chemical (mineralogical structure, pH, and electrical conductivity) and physical properties (the number of blows, the stiffness index, the liquidity index, the plasticity index, and the water content) were analyzed. To assess the mobility of the heavy metals, diffusion (D) and convection coefficients (?) were calculated with the finite difference method. Convection was determined to dominate the studied region. In addition, the mobility coefficient was determined for each metal. High mobilities were determined for Zn and V, moderate mobilities for Cr, Ni, Cu, and As, and low mobilities were determined for Co and Pb. The results revealed that elements had reached depths of up to 15m, causing irreversible soil contamination that may lead to environmental health issues.

Abstract: Typically, nitrification is a two-stage microbial process and is key in wastewater treatment and nutrient recovery from waste streams. Changes in salinity represent a major stress factor that can trigger response mechanisms, impacting the activity and the physiology of bacteria. Despite its pivotal biotechnological role, little information is available on the specific response of nitrifying bacteria to varying levels of salinity. In this study, synthetic communities of ammonia-oxidizing bacteria (AOB Nitrosomonas europaea and/or Nitrosomonas ureae) and nitrite-oxidizing bacteria (NOB Nitrobacter winogradskyi and/or Nitrobacter vulgaris) were tested at 5, 10, and 30 mS cm-1 by adding sodium chloride to the mineral medium (0, 40, and 200 mM NaCl, respectively). Ammonia oxidation activity was less affected by salinity than nitrite oxidation. AOB, on their own or in combination with NOB, showed no significant difference in the ammonia oxidation rate among the three conditions. However, N. winogradskyi improved the absolute ammonia oxidation rate of both N. europaea and N. ureae. N. winogradskyis nitrite oxidation rate decreased to 42% residual activity upon exposure to 30 mS cm-1, also showing a similar behavior when tested with Nitrosomonas spp. The nitrite oxidation rate of N. vulgaris, as a single species, was not affected when adding sodium chloride up to 30 mS cm-1, however, its activity was completely inhibited when combined with Nitrosomonas spp. in the presence of ammonium/ammonia. The proteomic analysis of a co-culture of N. europaea and N. winogradskyi revealed the production of osmolytes, regulation of cell permeability and an oxidative stress response in N. europaea and an oxidative stress response in N. winogradskyi, as a result of increasing the salt concentration from 5 to 30 mS cm-1. A specific metabolic response observed in N. europaea suggests the role of carbon metabolism in the production of reducing power, possibly to meet the energy demands of the stress response mechanisms, induced by high salinity. For the first time, metabolic modifications and response mechanisms caused by the exposure to salinity were described, serving as a tool toward controllability and predictability of nitrifying systems exposed to salt fluctuations.

Abstract: Complete removal of estrogens such as estrone (E1), estradiol (E2), estriol (E3) and ethinylestradiol (EE2) in wastewater treatment is essential since their release and accumulation in natural water bodies are giving rise to environment and health issues. To improve our understanding towards the estrogen bioremediation process, a mathematical model was proposed for describing estrogen removal by nitrifying activated sludge. Four pathways were involved in the developed model: i) biosorption by activated sludge flocs; ii) cometabolic biodegradation linked to ammonia oxidizing bacteria (AOB) growth; iii) non growth biodegradation by AOB; and iv) biodegradation by heterotrophic bacteria (HB). The degradation kinetics was implemented into activated sludge model (ASM) framework with consideration of interactions between substrate update and microorganism growth as well as endogenous respiration. The model was calibrated and validated by fitting model predictions against two sets of batch experimental data under different conditions. The model could satisfactorily capture all the dynamics of nitrogen, organic matters (COD), and estrogens. Modeling results suggest that for El, E2 and EE2, AOB-linked biodegradation is dominant over biodegradation by HB at all investigated COD dosing levels. However, for E3, the increase of COD dosage triggers a shift of dominant pathway from AOB biodegradation to HB biodegradation. Adsorption becomes the main contributor to estrogen removal at high biomass concentrations. (C) 2018 Elsevier Ltd. All rights reserved.

Abstract: During the past decades, the poration of cell membrane induced by pulsed electric fields has been widely investigated. Since the basic mechanisms of this process have not yet been fully clarified, many research activities are focused on the development of suitable theoretical and numerical models. To this end, a nonlinear, nonlocal, dispersive, and space-time numerical algorithm has been developed and adopted to evaluate the transmembrane voltage and pore density along the perimeter of realistic irregularly shaped cells. The presented model is based on the Maxwell's equations and the asymptotic Smoluchowski's equation describing the pore dynamics. The dielectric dispersion of the media forming the cell has been modeled by using a general multirelaxation Debye-based formulation. The irregular shape of the cell is described by using the Gielis' superformula. Different test cases pertaining to red blood cells, muscular cells, cell in mitosis phase, and cancer-like cell have been investigated. For each type of cell, the influence of the relevant shape, the dielectric properties, and the external electric pulse characteristics on the electroporation process has been analyzed. The numerical results demonstrate that the proposed model is an efficient numerical tool to study the electroporation problem in arbitrary-shaped cells.

Abstract: Long-term human Space missions depend on regenerative life support systems (RLSS) to produce food, water and oxygen from waste and metabolic products. Microbial biotechnology is efficient for nitrogen conversion, with nitrate or nitrogen gas as desirable products. A prerequisite to bioreactor operation in Space is the feasibility to reactivate cells exposed to microgravity and radiation. In this study, microorganisms capable of essential nitrogen cycle conversions were sent on a 44-days FOTON-M4 flight to Low Earth Orbit (LEO) and exposed to 10(-3)-10(-4) g (gravitational constant) and 687 +/- 170 mu Gy (Gray) d(-1) (20 +/- 4 degrees C), about the double of the radiation prevailing in the International Space Station (ISS). After return to Earth, axenic cultures, defined and reactor communities of ureolytic bacteria, ammonia oxidizing archaea and bacteria, nitrite oxidizing bacteria, denitrifiers and anammox bacteria could all be reactivated. Space exposure generally yielded similar or even higher nitrogen conversion rates as terrestrial preservation at a similar temperature, while terrestrial storage at 4 degrees C mostly resulted in the highest rates. Refrigerated Space exposure is proposed as a strategy to maximize the reactivation potential. For the first time, the combined potential of ureolysis, nitritation, nitratation, denitrification (nitrate reducing activity) and anammox is demonstrated as key enabler for resource recovery in human Space exploration.

Abstract: Moore’s Law has driven the electronics industry for the past half century. However, the doubling of transistors about every two years is beginning to break down, owing to fundamental limits that arise as they approach the atomic length. As a result, the search for new pathways for electronics has become crucial. Among potential candidates, the discovery of magnetic textures known as skyrmions has attracted considerable interest and attention in spintronic technology, which relies on both the electron charge and its spin. The unusual topological and particle-like behavior launched skyrmions into the spotlight of scientific research. Topological protected stability, nanoscale size, and low driving currents needed to move them make skyrmions promising candidates for future consumer nanoelectronics. Recent advances in the field have provided all of the basic functions needed for carrying and processing information. In this thesis, we procure to advance the current understanding of skyrmion physics, and explore their potential to replace conventional electronics technology. First, the fundamental properties and lifetimes of racetrack skyrmions at room temperature are investigated. We discover that skyrmions can easily collapse at the boundary in laterally finite systems, and propose ways to improve their stability for constrained geometries. Then, pinning of single skyrmions on atomic defects of distinct origins are studied. We reveal that the preferred pinning positions depend on the skyrmion size and type of defect being considered, and discuss applications where control of skyrmions by defects is of particular interest. Next, we explore other magnetic configurations that can compete with skyrmions when considering new materials, and describe a previously unseen mechanism for collapse of skyrmions into cycloidal spin backgrounds. Finally, switching and interactions between skyrmions with distinct topologies are reported. We find that skyrmions transition to higher or lower topologies by absorbing a unit spin texture. The interactions between skyrmions of different topological charges can be attractive or repulsive, leading to the formation of arranged clusters. We conclude with a numerical library for simulating magnetic skyrmions in various scenarios.

Abstract: Even though nitrification/denitrification is a robust technology to remove nitrogen from sewage, economic incentives drive its future replacement by shortcut nitrogen removal processes. The latter necessitates high potential activity ratios of ammonia oxidizing to nitrite oxidizing bacteria (rAOB/rNOB). The goal of this study was to identify which wastewater and process parameters can govern this in reality. Two sewage treatment plants (STP) were chosen based on their inverse rAOB/rNOB values (at 20 °C): 0.6 for Blue Plains (BP, Washington DC, US) and 1.6 for Nieuwveer (NV, Breda, NL). Disproportional and dissimilar relationships between AOB or NOB relative abundances and respective activities pointed towards differences in community and growth/activity limiting parameters. The AOB communities showed to be particularly different. Temperature had no discriminatory effect on the nitrifiers' activities, with similar Arrhenius temperature dependences (ΘAOB = 1.10, ΘNOB = 1.061.07). To uncouple the temperature effect from potential limitations like inorganic carbon, phosphorus and nitrogen, an add-on mechanistic methodology based on kinetic modelling was developed. Results suggest that BP's AOB activity was limited by the concentration of inorganic carbon (not by residual N and P), while NOB experienced less limitation from this. For NV, the sludge-specific nitrogen loading rate seemed to be the most prevalent factor limiting AOB and NOB activities. Altogether, this study shows that bottom-up mechanistic modelling can identify parameters that influence the nitrification performance. Increasing inorganic carbon in BP could invert its rAOB/rNOB value, facilitating its transition to shortcut nitrogen removal.

Abstract: Synthetic micro‐ and nanomotors (MNMs) are tiny objects that can autonomously move under the influence of an appropriate source of energy, such as a chemical fuel, magnetic field, ultrasound, or light. Chemically driven MNMs are composed of or contain certain reactive material(s) that convert chemical energy of a fuel into kinetic energy (motion) of the particles. Several different materials have been explored over the last decade for the preparation of a wide variety of MNMs. Here, the discovery of materials and approaches to enhance the efficiency of chemically driven MNMs are reviewed. Several prominent applications of the MNMs, especially in the fields of biomedicine and environmental science, are also discussed, as well as the limitations of existing materials and future research directions.

Abstract: Metal-air batteries and fuel cells show a great deal of promise in advancing low-cost, high-energy-density charge storage solutions for sustainable energy applications. To improve the activities and stabilities of electrocatalysts for the critical oxygen reduction and evolution reactions (ORR and OER, respectively), a greater understanding is needed of the catalyst/carbon interactions and carbon stability. Herein, we report how LaNiO3 (LNO) supported on nitrogen-doped carbon nanotubes (N-CNT) made from a high-yield synthesis lowers the overpotential for both the OER and ORR markedly to enable a low bifunctional window of 0.81 V at only a 51 mu g cm(-2) mass loading. Furthermore, the addition of LNO to the N-CNTs improves the galvanostatic stability for the OER by almost 2 orders of magnitude. The nanoscale geometries of the perovskites and the CNTs enhance the number of metal-support and charge transfer interactions and thus the activity. We use rotating ring disk electrodes (RRDEs) combined with Tafel slope analysis and ICP-OES to quantitatively separate current contributions from the OER, carbon oxidation, and even anodic iron leaching from carbon nanotubes.

Abstract: The research presented here examined at which spatial and temporal resolution urban metabolism should be analysed to generate results that are useful for implementation of urban planning and design interventions aiming at optimization of resource flows. Moreover, it was researched whether a lack of data currently hampers analysing resource flows at this desired level of detail. To facilitate a stakeholder based research approach, the SIRUP tool Space-time Information analysis for Resource-conscious Urban Planning was developed. The tool was applied in a case study of Amsterdam, focused on the investigation of energy and water flows. Results show that most urban planning and design interventions envisioned in Amsterdam require information on a higher spatiotemporal resolution than the resolution of current urban metabolism analyses, i.e., more detailed than the city level and at time steps smaller than a year. Energy-related interventions generally require information on a higher resolution than water-related interventions. Moreover, for the majority of interventions information is needed on a higher resolution than currently available. For energy, the temporal resolution of existing data proved inadequate, for water, data with both a higher spatial and temporal resolution is required. Modelling and monitoring techniques are advancing for both water and energy and these advancements are likely to contribute to closing these data gaps in the future. These advancements can also prove useful in developing new sorts of urban metabolism analyses that can provide a systemic understanding of urban resource flows and that are tailored to urban planning and design.