Bayesian Model Selection for the Solution of Spatial Inverse Problems with Geophysical, Geotechnical and Thermodynamical Applications

Bayesian inference is based on three evidence components: experimental observations, model predictions and expert’s beliefs. Integrating experimental evidence into the calibration or selection of a model, either empirically of physically based, is of great significance in almost every area of science and engineering because it maps the response of the process of interest into a set of parameters, which aim at explaining the process’ governing characteristics. This work introduces the use of the Bayesian paradigm to construct full probabilistic description of parameters of spatial processes. The influence of uncertainty is first discussed on the calibration of an empirical relationship between remolded undrained shear strength Su−r and liquidity index IL, as a potential predictor of the soil strength. Two site-specific datasets are considered in the analysis. The key emphasis of the study is to construct a unified regression model reflecting the characteristics of the both contributing data sets, while the site dependency of the data is properly accounted for. We question the regular Bayesian updating process, since a test of statistics proves that the two data sets belong to different populations. Application of “Disjunction” probability operator is proposed as an alternative to arrive at a more conclusive Su−r−IL model. Next, the study is extended to a functional inverse problem where the object of inference constructs a spatial random field. We introduce a methodology to infer the spatial variation of the elastic characteristics of a heterogeneous earth model via Bayesian approach, given the probed medium’s response to interrogating waves measured at the surface. A reduced dimension, self regularized treatment of the inverse problem using partition modeling is introduced, where the velocity field is discretized by a variable number of disjoint regions defined by Voronoi tessellations. The number of partitions, their geometry and weights dynamically vary during the inversion, in order to recover the subsurface image. The idea of treating the number of tessellation (number of parameters) as a parameter itself is closely associated with probabilistic model selection. A reversible jump Markov chain Monte Carlo (RJMCMC) scheme is applied to sample the posterior distribution of varying dimension. Lastly, direct treatment of a Bayesian model selection through the definition of the Bayes factor (BF) is developed for linear models, where it is employed to define the most likely order of the virial Equation of State (EOS). Virial equation of state is a constitutive model describing the thermodynamic behavior of low-density fluids in terms of the molar density, pressure and temperature. Bayesian model selection has successfully determined the best EOS that describes four sets of isotherms, where approximate (BIC) method either failed to select a model or fevered an overly-flexible model, which specifically perform poorly in terms of prediction

Molecular Dynamics Insights into the Structural and Water Transport Properties of a Forward Osmosis Polyamide Thin-Film Nanocomposite Membrane Modified with Graphene Quantum Dots

An approach combining molecular dynamics (MD) simulations and laboratory experiments was applied to provide new theoretical insights into the chemical structure of polyamide (PA) thin-film composite (TFC) membranes modified with graphene quantum dots (GQDs). Interaction energies, fractional free volumes, mean-square displacements, densities, and water diffusion coefficients were computed for PA and four likely chemical structures of the GQD-embedded PA membranes. These theoretical results aided with experimentally measured water fluxes allowed for determining the most likely structure of the GQD-PA membrane. The compatibility of the GQDs and PA chains was found to be due to the formation of hydrogen and covalent bonds to m-phenylenediamine units. The modified membrane has a higher water diffusivity but a lower overall free volume, compared to the pristine PA membrane. MD simulations in concert with laboratory experiments were found to provide a good understanding of the relationship between the microscopic characteristics and macroscopic transport properties of TFC membranes

Optimization of the Groundwater Remediation Process Using a Coupled Genetic Algorithm-Finite Difference Method

In situ chemical oxidation using permanganate as an oxidant is a remediation technique often used to treat contaminated groundwater. In this paper, groundwater flow with a full hydraulic conductivity tensor and remediation process through in situ chemical oxidation are simulated. The numerical approach was verified with a physical sandbox experiment and analytical solution for 2D advection-diffusion with a first-order decay rate constant. The numerical results were in good agreement with the results of physical sandbox model and the analytical solution. The developed model was applied to two different studies, using multi-objective genetic algorithm to optimise remediation design. In order to reach the optimised design, three objectives considering three constraints were defined. The time to reach the desired concentration and remediation cost regarding the number of required oxidant sources in the optimised design was less than any arbitrary design

Toward Sustainable Tackling of Biofouling Implications and Improved Performance of TFC FO Membranes Modified by Ag-MOF Nanorods

In this work, nanorods with high antibacterial properties were synthesized with silver acetate as the metal source and 2-aminoterephthalic acid as the organic linker and were then embedded into thin-film composite (TFC) membranes to amend their performance as well as to alleviate biofouling. Silver metal-organic framework (Ag-MOF) nanorods with a length smaller than 40 nm were incorporated within the polyamide thin selective layer of the membranes during interfacial polymerization. The interaction of the synthesized nanorods with the polyamide was favored because of the presence of amine-containing functional groups on the nanorod's surface. The results of X-ray photoelectron spectroscopy, scanning electron microscopy, energy-dispersive X-ray spectroscopy, and atomic force microscopy characterizations proved the presence of Ag-MOF nanorods in the selective layer of thin-film nanocomposite (TFN) membranes. TFN membranes demonstrated improved water permeance, salt selectivity, and superior antibacterial properties. Specifically, the increased hydrophilicity and antibacterial potential of the TFN membranes led to a synergetic effect toward biofouling mitigation. The number of live bacteria attached to the surface of the neat TFC membrane decreased by more than 92% when a low amount of Ag-MOF nanorods (0.2 wt %) was applied. Following contact of the TFN membrane surface with Escherichia coli and Staphylococcus aureus, full inactivation, and degradation of bacteria cells were observed with microscopy, colony-forming unit tests, and disc inhibition zone analyses. This result translated to a negligible amount of the biofilm formed on the active layer. Indeed, the incorporation of Ag-MOF nanorods decreased the metal-ion release rate and therefore provided prolonged antibacterial performance

Forward osmosis research trends in desalination and wastewater treatment: A review of research trends over the past decade

Issues of water scarcity and water security have driven the rapid development of various technologies to ensure water sustainability. The forward osmosis (FO) membrane process has been widely recognized as one of the more promising technologies to play an important role in alleviating the issues of water sustainability. Extensive research has been carried out worldwide to explore the potential of FO in desalination, water and wastewater treatment and reclamation. It is of the utmost importance to understand the topics of interest and research trends to further advance the development of FO process technology. In this study, a bibliometric analysis based on the Scopus database was carried out to identify and understand the global research trends of FO process based on 6 main analyses: basic growth trends, journals, countries, institutions, authors, and keywords. A total of 1462 article published between 1967-2018 were extracted from Scopus and used as the raw data for bibliometric analysis using VOSviewer software. The total number of FO articles has sharply increased since 2009 and stabilized at around 250 publications in the past three years. FO research started to diversify after the appearance of commercial FO membranes with improved characteristics, enabling the researchers to employ them for various application studies. Keywords analysis showed that the main directions of FO research could be categorized into three clusters: application of FO, membrane fouling study, and FO membrane synthesis. These bibliometric results provide a valuable reference and information on current research directions of FO for researchers and industry practitioners

Human MCTS1-dependent translation of JAK2 is essential for IFN-γ immunity to mycobacteria.

Human inherited disorders of interferon-gamma (IFN-γ) immunity underlie severe mycobacterial diseases. We report X-linked recessive MCTS1 deficiency in men with mycobacterial disease from kindreds of different ancestries (from China, Finland, Iran, and Saudi Arabia). Complete deficiency of this translation re-initiation factor impairs the translation of a subset of proteins, including the kinase JAK2 in all cell types tested, including T lymphocytes and phagocytes. JAK2 expression is sufficiently low to impair cellular responses to interleukin-23 (IL-23) and partially IL-12, but not other JAK2-dependent cytokines. Defective responses to IL-23 preferentially impair the production of IFN-γ by innate-like adaptive mucosal-associated invariant T cells (MAIT) and γδ T lymphocytes upon mycobacterial challenge. Surprisingly, the lack of MCTS1-dependent translation re-initiation and ribosome recycling seems to be otherwise physiologically redundant in these patients. These findings suggest that X-linked recessive human MCTS1 deficiency underlies isolated mycobacterial disease by impairing JAK2 translation in innate-like adaptive T lymphocytes, thereby impairing the IL-23-dependent induction of IFN-γ

Loss of C2orf69 defines a fatal autoinflammatory syndrome in humans and zebrafish that evokes a glycogen-storage-associated mitochondriopathy

Summary Human C2orf69 is an evolutionarily conserved gene whose function is unknown. Here, we report eight unrelated families from which 20 children presented with a fatal syndrome consisting of severe autoinflammation and progredient leukoencephalopathy with recurrent seizures; 12 of these subjects, whose DNA was available, segregated homozygous loss-of-function C2orf69 variants. C2ORF69 bears homology to esterase enzymes, and orthologs can be found in most eukaryotic genomes, including that of unicellular phytoplankton. We found that endogenous C2ORF69 (1) is loosely bound to mitochondria, (2) affects mitochondrial membrane potential and oxidative respiration in cultured neurons, and (3) controls the levels of the glycogen branching enzyme 1 (GBE1) consistent with a glycogen-storage-associated mitochondriopathy. We show that CRISPR-Cas9-mediated inactivation of zebrafish C2orf69 results in lethality by 8 months of age due to spontaneous epileptic seizures, which is preceded by persistent brain inflammation. Collectively, our results delineate an autoinflammatory Mendelian disorder of C2orf69 deficiency that disrupts the development/homeostasis of the immune and central nervous systems

Experimental Verification of the Elastic Formula for the Aspirated Length of a Single Cell Considering the Size and Compressibility of Cell During Micropipette Aspiration

In this study, an aspiration system for elastic spheres was developed to verify the approximate elastic formula for the aspirated length of a single solid-like cell undergoing micropipette aspiration (MPA), which was obtained in our previous study by theoretical analysis and numerical simulation. Using this system, foam silicone rubber spheres with different diameters and mechanical properties were aspirated in a manner similar to the MPA of single cells. Comparisons between the approximate elastic formula and aspiration experiments of spheres indicated that the predictions of the formula agreed with the experimental results. Additionally, combined with the MPA data of rabbit chondrocytes, differences in terms of the elastic parameters derived from the half-space model, incompressible sphere model, and compressible sphere model were explored. The results demonstrated that the parameter ξ (ξ = R/a, where R is the radius of the cell and a is the inner radius of the micropipette) and Poisson’s ratio significantly influenced the determination of the elastic modulus and bulk modulus of the cell. This work developed for the first time an aspiration system of elastic spheres to study the elastic responses of the MPA of a single cell and provided new evidence supporting the use of the approximate elastic formula to determine cellular elastic parameters from the MPA data

IŞIK YÖNETİMİNDE DİZİLMİŞ KOLLOİDAL-MASKE UYGULAMALARI

Dielectric colloidal micro-/nanospheres (CMNS) are promising candidates for different applications. In this thesis, colloidal spheres are either used for light management in photonic devices such as solar cells or surface enhanced Raman scattering (SERS) substrates. CMNS arrays can direct the broad incident radiation into a set of tighter foci, at which light intensity becomes considerably concentrated, enabling higher conversion efficiency. Furthermore, the CMNS arrays acting as an effective medium on the device surface can reduce reflection and facilitate improved forward scattering and hence the utilization of light within the device. Therefore, uniform arrays of CMNS located on top of the photonic devices can behave as antireflection coatings or as micro-lenses which can be regarded as a surface distributed concentrator within the framework of concentrated photovoltaics (CPV). Fabrication of such a lighttrapping structure is low-cost and less complicated than common alternatives such as vacuum evaporated multilayer antireflection coatings. In this thesis, experimental demonstration and computational support of the optimal size and shape of such CMNS arrays are illustrated. Besides, thin metallic film coated dielectric nanospheres are demonstrated to have a high potential for fabrication of cost-effective SERS substrates. In addition to the morphological advantages that nanospheres offer for attaining a high density of hotspots, possessing shape adjustability by uncomplicated thermal treatment make them an attractive platform for tuneable SERS substrates. Furthermore, when combined with oblique angle metal deposition technique, adjustable gaps at a high density and adjustable shape of metal films, such as silver (Ag) films, can be achieved on nanospheres. Applying small changes in deposition angle can provide means for fine adjustment of the SERS enhancement factor (EF), resulting in EF up to 108 measured using crystal violet dye molecule as a Raman analyte. This practice paves the way for the fabrication of high EF SERS substrates at a reasonable cost using a monolayer of self-organized nanosphere pattern. An ultra-thin Ag film coated at 5o tilt is shown to be an excellent substitute for a film deposited at 0o with double the thickness. There is a strong agreement between the experimental results and finite element method based simulations exhibiting expected field enhancements up to 109 at a tilt angle of 5o. In summary, the demonstration of several ordered colloidal mask applications in light management for photonic devices is aimed at this thesis.Dielektrik kolloidal mikro-/nanoküreler (CMNS), farklı uygulamalar için umut vadeden adaylardır. Bu tezde, kolloidal küreler, güneş pilleri gibi fotonik cihazlarda veya yüzey artırımlı Raman saçılması (SERS) alttaşlarında ışık yönetimi için kullanılmıştır. CMNS dizileri, geniş gelen radyasyonu, daha yüksek dönüşüm verimliliği sağlayarak ışık şiddetinin önemli ölçüde yoğunlaştığı bir dizi sıkı odak noktalarına yönlendirebilir.. Ayrıca, cihaz yüzeyinde etkili bir ortam görevi gören CMNS dizileri, yansımayı azaltabilir ve artırılmış ileri saçılımı ve dolayısıyla cihaz içinde ışığın kullanımını kolaylaştırabilir. Bu nedenle, fotonik cihazların üzerinde yer alan tek tip CMNS dizileri, yansıma önleyici kaplamalar veya konsantre fotovoltaikler (CPV) çerçevesinde yüzeyde dağıtılmış bir yoğunlaştırıcı olarak kabul edilebilen mikro lensler gibi davranabilir. Böyle bir ışık tutucu yapının üretimi, düşük maliyetli ve vakumla buharlaştırılan çok katmanlı yansıma önleyici kaplamalar gibi yaygın alternatiflerden daha az karmaşıktır. Bu tezde, bu tür CMNS dizilerinin en uygun boyut ve şeklinin deneysel gösterimi ve hesaplamalı desteği gösterilmiştir. Ayrıca, ince metalik film kaplıdielektrik nanokürelerin, uygun maliyetli SERS alttaşlarının üretimi için yüksek bir potansiyele sahip olduğu gösterilmiştir. Nanokürelerin yüksek yoğunluklu sıcak noktalar elde etmek için sunduğu morfolojik avantajlara ek olarak, karmaşık olmayan ısıl işlemle şekil ayarlanabilirliğine sahip olmaları, onları ayarlanabilir SERS alttaşları için çekici bir platform haline getirmektedir. Ayrıca, eğik açılı metal bırakım tekniği ile birleştirildiğinde, nanoküreler üzerinde ayarlanabilir şekildeki gümüş (Ag) filmler gibi metal filmler ve yüksek yoğunlukta ayarlanabilir boşluklar elde edilebilir. Kaplanma açısında küçük değişiklikler uygulamak, SERS artırım faktörünün (EF) ince ayarı için araçlar sağlayabilir ve bu, bir Raman analiti olarak kristal mor boya molekülü kullanılarak ölçülen EF'nin 108'e kadar çıkmasıyla sonuçlanır. Bu uygulama, yüksek EF değerine sahip SERS alttaşlarının, kendi kendini organize eden bir nanoküre deseninin tek tabakasını kullanarak makul bir maliyetle üretilmesinin yolunu açmaktadır. 5o eğimde kaplanmış ultra ince Ag filmin, 0o'de iki katı kalınlıkta kaplanmış olanlar için mükemmel bir alternatif olduğu gösterilmiştir. 5o eğim açısında 109'a kadar beklenen alan artırımlarını gösteren sonlu elemanlar metoduna dayalı simülasyonlar ile deneysel sonuçlar arasında güçlü bir uyum vardır. Özetle, bu tezde fotonik cihazlar için ışık yönetiminde çeşitli dizilmiş kolloidal maske uygulamalarının gösterilmesi amaçlanmaktadır.Ph.D. - Doctoral ProgramMicro and Nanotechnolog

Mikroakışkan tabanlı ayarlanabilir antenlerin geliştirilmesi.

The objective of this thesis is to develop fabrication methods to implement microfluidic-based reconfigurable antennas. As the initial structure, a microfluidic based reconfigurable antenna is developed for transmitarrays, which consists of a multi-layered structure incorporating a microfluidic channel to confine liquid metal. The microfluidic channels are fabricated using soft lithography techniques where the channel material is PDMS. PDMS-to-glass and PDMS-to-PDMS bonding processes are optimized to achieve a reservoir for the fluidic material. In particular, a split-ring resonator and a complementary split ring for transmitarray applications are manufactured using the optimized process. Instead of using direct metallization approach, which is inadequate because of the low surface strength of PDMS, a novel method is proposed for the bonding of two different surfaces. A thin layer of silicon dioxide (50 nm) is deposited on the metal layer before the oxygen plasma treatment. The oxygen plasma treatment is done for duration of 20 seconds at an RF power of 20 W. Bonding strength measurements are also performed in the frame of this thesis. It is noted that the bonding quality can be enhanced with the use of silicon dioxide intermediate layer. The other device that has been designed and manufactured is a frequency tunable patch antenna, which is formed by reconfiguring its dimension employing two rectangular patches that are joined to each other with a liquid metal channel. The microfluidic channel is created by applying the bonding method between PDMS and metallized glass layers. The antenna has two different operation modes: (i)The channel is empty and the antenna resonates at 10.68 GHz and (ii) the condition in which the channel is full of liquid metal and the antenna resonates at 9.62 GHz. In conclusion, microfluidic transmitarray and microfluidic reconfigurable antenna are fabricated using liquid metal channel embedded in the PDMS layer.M.S. - Master of Scienc