• Macroscopic Properties of Hollow Cone Spray Using an Outwardly Opening Piezoelectric Injector in GCI Engine

      Cheng, Penghui (2016-07)
      Fuel mixture formation and spray characteristics are crucial for the advancement of Gasoline Compression Ignition (GCI) engine. For investigations of spray characteristics, a high-pressure high-temperature spray chamber with constant volume has been designed, tested and commissioned at CCRC, KAUST. Back light illumination technique has been applied to investigate the macroscopic spray properties of an outwardly opening piezoelec- tric injector. Three parameters including injection pressure, ambient pressure, and ambient temperature have been involved. A total of 18 combinations of experimental conditions were tested under non-reactive conditions. Through qualitative analysis of spray morphology under different operating conditions, an apparent distinction of spray morphology has been noticed. Spray morphology and propagation have shown strong dependencies on ambient pressure and ambient tempera- ture while injection pressure has a negligible effect on spray shape. Increasingly compact and bushier spray patterns were observed in the cases of high ambient pressure due to in- creasing aerodynamic drag force on spray boundary. It should also be noted that ambient temperature plays a fairly important role in fuel evaporation rate. At 200 °C, oscillating and considerably short spray shape was produced. Also, circumferential ring-like vortices and distinctive string-like structures have been identified for the fuel spray exiting this hollow cone injector. It has been observed that high ambient pressure conditions (Pamb = 4 bar and 10.5 bar) are favorable to the vortices generation, which has also been reported in previous literature. The quantitative description of macroscopic spray properties reveals that ambient pres- sure and ambient temperature are found to be the most influential parameters on liquid penetration length. The rise of ambient pressure results in considerably shorter liquid pen- etration length. Ambient temperature also appears to be a very effective factor of reducing penetration length. Injection pressure contributes to a notable increase of liquid penetra- tion length under ambient pressure of 1 atm. However, the influence of injection pressure is substantially reduced under ambient pressures of 4 bar and 10.5 bar, which indicates that ambient pressure exerts much stronger influence than injection pressure on liquid penetra- tion length. Furthermore, it has been revealed that the increase of injection pressure and ambient pressure are the predominant sources contributing to the enlargement of spray cone angle. The effect of injection pressure on spray cone angle has been amplified by the increase of ambient pressure. With increasing ambient pressure, the penetration of injected fuel tends to propagate axially in a much slower manner that leads to wider fuel distribution in the radial direction. Ambient temperature exerts a similar influence on spray cone angle as on liquid penetration length. The spray cone angle experiences a noticeable decline when ambient gas is increased to 200 °C.
    • Magnetic Carbon Nanotubes as a Theranostic Platform for Drug Delivery and Magnetic Resonance Imaging

      Alkattan, Nedah (2014-06)
      Carbon nanotubes (CNTs) have special characteristics that made them good agents especially for biomedical applications. In this study, Fe3O4 nanoparticles were incorporated onto the surface of CNTs followed by polyethylene glycol (PEG) grafting forming CNTs-Fe3O4-PEG hybrids. The PEGylation improves their biocompatibility, water solubility, and increases blood circulation. CNTs-Fe3O4-PEG was used as T2-contrat agent for magnetic resonance imaging (MRI). In addition, doxorubicin (DOX) was loaded onto CNTs-Fe3O4-PEG. The release of DOX from DOX-loaded CNTs-Fe3O4-PEG was tested under different pH conditions (7.4, 6.3 and 5.2). The release increased at acidic pH compared to neutral pH, which shows the sensitivity of the system to pH change. Triggering the release by Near Infra-Red (NIR) irradiation was furthermore investigated. The release increased after irradiation with NIR compared to control sample. These result prove that the designed system can be triggered by an internal stimuli (pH) and external stimuli (NIR irradiation) making it a promising candidate to be used for biomedical applications.
    • Magnetization Dynamics in Two Novel Current-Driven Spintronic Memory Cell Structures

      Velazquez-Rizo, Martin (2017-07)
      In this work, two new spintronic memory cell structures are proposed. The first cell uses the diffusion of polarized spins into ferromagnets with perpendicular anisotropy to tilt their magnetization followed by their dipolar coupling to a fixed magnet (Bhowmik et al., 2014). The possibility of setting the magnetization to both stable magnetization states in a controlled manner using a similar concept remains unknown, but the proposed structure poses to be a solution to this difficulty. The second cell proposed takes advantage of the multiple stable magnetic states that exist in ferromagnets with configurational anisotropy and also uses spin torques to manipulate its magnetization. It utilizes a square-shaped ferromagnet whose stable magnetization has preferred directions along the diagonals of the square, giving four stable magnetic states allowing to use the structure as a multi-bit memory cell. Both devices use spin currents generated in heavy metals by the Spin Hall effect present in these materials. Among the advantages of the structures proposed are their inherent non-volatility and the fact that there is no need for applying external magnetic fields during their operation, which drastically improves the energy efficiency of the devices. Computational simulations using the Object Oriented Micromagnetic Framework (OOMMF) software package were performed to study the dynamics of the magnetization process in both structures and predict their behavior. Besides, we fabricated a 4-terminal memory cell with configurational anisotropy similar to the device proposed, and found four stable resistive states on the structure, proving the feasibility of this technology for implementation of high-density, non-volatile memory cells.
    • Mapping the Conformational Dynamics of E-selectin upon Interaction with its Ligands

      Aleisa, Fajr A (2013-05-15)
      Selectins are key adhesion molecules responsible for initiating a multistep process that leads a cell out of the blood circulation and into a tissue or organ. The adhesion of cells (expressing ligands) to the endothelium (expressing the selectin i.e.,E-selectin) occurs through spatio-temporally regulated interactions that are mediated by multiple intra- and inter-cellular components. The mechanism of cell adhesion is investigated primarily using ensemble-based experiments, which provides indirect information about how individual molecules work in such a complex system. Recent developments in single-molecule (SM) fluorescence detection allow for the visualization of individual molecules with a good spatio-temporal resolution nanometer spatial resolution and millisecond time resolution). Furthermore, advanced SM fluorescence techniques such as Förster Resonance Energy Transfer (FRET) and super-resolution microscopy provide unique opportunities to obtain information about nanometer-scale conformational dynamics of proteins as well as nano-scale architectures of biological samples. Therefore, the state-of-the-art SM techniques are powerful tools for investigating complex biological system such as the mechanism of cell adhesion. In this project, several constructs of fluorescently labeled E-selectin will be used to study the conformational dynamics of E-selectin binding to its ligand(s) using SM-FRET and combination of SM-FRET and force microscopy. These studies will be beneficial to fully understand the mechanistic details of cell adhesion and migration of cells using the established model system of hematopoietic stem cells (HSCs) adhesion to the selectin expressing endothelial cells (such as the E-selectin expressing endothelial cells in the bone marrow).
    • Marker Detection in Aerial Images

      Alharbi, Yazeed (2017-04-09)
      The problem that the thesis is trying to solve is the detection of small markers in high-resolution aerial images. Given a high-resolution image, the goal is to return the pixel coordinates corresponding to the center of the marker in the image. The marker has the shape of two triangles sharing a vertex in the middle, and it occupies no more than 0.01% of the image size. An improvement on the Histogram of Oriented Gradients (HOG) is proposed, eliminating the majority of baseline HOG false positives for marker detection. The improvement is guided by the observation that standard HOG description struggles to separate markers from negatives patches containing an X shape. The proposed method alters intensities with the aim of altering gradients. The intensity-dependent gradient alteration leads to more separation between filled and unfilled shapes. The improvement is used in a two-stage algorithm to achieve high recall and high precision in detection of markers in aerial images. In the first stage, two classifiers are used: one to quickly eliminate most of the uninteresting parts of the image, and one to carefully select the marker among the remaining interesting regions. Interesting regions are selected by scanning the image with a fast classifier trained on the HOG features of markers in all rotations and scales. The next classifier is more precise and uses our method to eliminate the majority of the false positives of standard HOG. In the second stage, detected markers are tracked forward and backward in time. Tracking is needed to detect extremely blurred or distorted markers that are missed by the previous stage. The algorithm achieves 94% recall with minimal user guidance. An average of 30 guesses are given per image; the user verifies for each whether it is a marker or not. The brute force approach would return 100,000 guesses per image.
    • Massively Parallel Dimension Independent Adaptive Metropolis

      Chen, Yuxin (2015-05-14)
      This work considers black-box Bayesian inference over high-dimensional parameter spaces. The well-known and widely respected adaptive Metropolis (AM) algorithm is extended herein to asymptotically scale uniformly with respect to the underlying parameter dimension, by respecting the variance, for Gaussian targets. The result- ing algorithm, referred to as the dimension-independent adaptive Metropolis (DIAM) algorithm, also shows improved performance with respect to adaptive Metropolis on non-Gaussian targets. This algorithm is further improved, and the possibility of probing high-dimensional targets is enabled, via GPU-accelerated numerical libraries and periodically synchronized concurrent chains (justified a posteriori). Asymptoti- cally in dimension, this massively parallel dimension-independent adaptive Metropolis (MPDIAM) GPU implementation exhibits a factor of four improvement versus the CPU-based Intel MKL version alone, which is itself already a factor of three improve- ment versus the serial version. The scaling to multiple CPUs and GPUs exhibits a form of strong scaling in terms of the time necessary to reach a certain convergence criterion, through a combination of longer time per sample batch (weak scaling) and yet fewer necessary samples to convergence. This is illustrated by e ciently sampling from several Gaussian and non-Gaussian targets for dimension d 1000.
    • Measurements of Drag Coefficients and Rotation Rates of Free-Falling Helixes

      Al-Omari, Abdulrhaman A. (2016-05)
      The motion of bacteria in the environment is relevant to several fields. At very small scales and with simple helical shapes, we are able to describe experimentally and mathematically the motion of solid spirals falling freely within a liquid pool. Using these shapes we intend to mimic the motion of bacteria called Spirochetes. We seek to experimentally investigate the linear and the rotational motion of such shapes. A better understanding of the dynamics of this process will be practical not only on engineering and physics, but the bioscience and environmental as well. In the following pages, we explore the role of the shape on the motion of passive solid helixes in different liquids. We fabricate three solid helical shapes and drop them under gravity in water, glycerol and a mixture of 30% glycerol in water. That generated rotation due to helical angle in water. However, we observe the rotation disappear in glycerol. The movement of the solid helical shapes is imaged using a high-speed video camera. Then, the images are analyzed using the supplied software and a computer. Using these simultaneous measurements, we examine the terminal velocity of solid helical shapes. Using this information we computed the drag coefficient and the drag force. We obtain the helical angular velocity and the torque applied to the solid. The results of this study will allow us to more accurately predict the motion of solid helical shape. This analysis will also shed light onto biological questions of bacteria movement.
    • Measuring Visual Closeness of 3-D Models

      Gollaz Morales, Jose Alejandro (2012-09)
      Measuring visual closeness of 3-D models is an important issue for different problems and there is still no standardized metric or algorithm to do it. The normal of a surface plays a vital role in the shading of a 3-D object. Motivated by this, we developed two applications to measure visualcloseness, introducing normal difference as a parameter in a weighted metric in Metro’s sampling approach to obtain the maximum and mean distance between 3-D models using 3-D and 6-D correspondence search structures. A visual closeness metric should provide accurate information on what the human observers would perceive as visually close objects. We performed a validation study with a group of people to evaluate the correlation of our metrics with subjective perception. The results were positive since the metrics predicted the subjective rankings more accurately than the Hausdorff distance.
    • Mechanism Design for Virtual Power Plant with Independent Distributed Generators

      Kulmukhanova, Alfiya (2018-07)
      We discuss a model of a virtual power plant (VPP) that provides market access to privately-owned distributed generations (DGs). The VPP serves passive loads, processes bids from generators, and trades in the wholesale market. The generators can be renewable or thermal, and they act strategically to maximize their own profit. The VPP establishes the rules of the internal market to minimize the cost of energy and the cost of balancing while ensuring generator participation and load balancing. We derive a heuristic mechanism for internal market and propose a dynamic programming approach for minimizing the VPP cost. We present illustrative simulations for both single and multistage market bidding and then compare the resulting performance to the centralized VPP model, where the DGs are assumed to be owned by the VPP. We show that the proposed design incentivizes the DG agents to behave the same as in the centralized case, but the optimal cost paid by VPP is higher due to the payments to the DG owners.
    • The Mechanism of the Silencing of a Transgene, NCED3‐LUC, in Arabidopsis Thaliana

      Zhao, Junsong (2011-06-20)
      The Arabidopsis thaliana NCED3‐LUC transgenic line was constructed by several groups to study the regulatory network of the NCED3 gene, the protein of which catalyzes the rate‐limiting step of ABA biosynthesis under drought. The transgenic luciferase gene is expressed when the plants encounter drought stress. Intriguingly, this transgenic luciferase gene is silenced after propagation for several generations. To determine the mechanism of this gene silencing, we used a forward genetics approach. The seeds of NCED3‐LUC (referred as the ‘wild type’) were mutagenized by ethane methyl sulfonate (EMS). One mutant line, denoted as #73, with recovered luciferase activity was selected for further study. Analysis of the methylation status by bisulfite sequencing revealed that the transgenic NCED3 promoter in the #73 mutant had less methylation than the wild type. Demethylation was also evident for the endogenous NCED3 promoter and retrotransposon AtSN1 in the #73 mutant. The phenotype of #73 mutant includes small size, rapid dehydration rate, altered morphology, and a thin epicuticular wax layer. By use of map‐based cloning, the region containing the mutated gene was delimited to a contig of two BAC clones, F11F19 and F9C22, on chromosome 2. Our results indicate that NCED3‐LUC gene silencing results from hypermethylation of its promoter region, but additional study is required to determine the exact position of the mutated gene and to fully understand the mechanism of NCED3‐LUC silencing. 4 ACKNOWLEDGEMENTS I would like to take this opportunity to thank my committee chair, Professor Jian‐Kang Zhu, who is also the supervisor of my master’s thesis, for his guidance throughout the course of this research. I also would like to thank my committee members, Professor Liming Xiong and Professor Samir Hamdan, for their patience and support in reviewing my thesis. My appreciation also goes to Dr. Zhenyu Wang for taking time to teach me basic experimental skills and for providing suggestions to my project. Meanwhile, my gratitude goes to my friends and lab mates and the department faculty. Thank you all for making my time at King Abdullah University of Science and Technology so wonderful. Finally, my heartfelt gratitude is extended to my parents for their everlasting support and encouragement.
    • Mechanisms of Contact Electrification at Aluminum-Polytetrafluoroethylene and Polypropylene-Water

      Nauruzbayeva, Jamilya (2017-04)
      Contact electrification refers to the transfer of electrical charges between two surfaces, similar and dissimilar, as they are brought into contact and separated; this phenomenon is also known as static electrification or triboelectrification. For example, everyone has experienced weak electrical shocks from metal doorknobs, wool and synthetic clothing on dry days. While contact electrification might appear insignificant, it plays a key role in numerous natural and industrial processes, including atmospheric lightning, accumulation of dust on solar panels, charging of liquids during pipetting and flow in the tubes, and fire hazards in granular media. Contact electrification at metal-metal interfaces is well understood in terms of transfer of electrons, but a comprehensive understanding of contact electrification at interfaces of electrical insulators, such as air, water, polytetrafluoroethylene (PTFE), polypropylene remains incomplete. In fact, a variety of mechanisms responsible for transfer of electrical charges during mechanical rubbing, slipping, sliding, or flow at interfaces have been proposed via: electrons, ions, protons, hydroxide ions from water, specific orientation of dipoles, mechanoradicals, cryptoelectrons, and transfer of material. We have noticed that the extent of contact electrification of solids in water is influenced by surface free energies, mobile ions, surface roughness, duration of contact, sliding speeds, and relative humidity. Herein, we present results of our experimental investigation of contact electrification at the following interfaces: (i) PTFE-aluminum in air and (ii) polypropylene-water interfaces. To identify the underlying mechanism, we started with various hypotheses and exploited a variety of experimental techniques to falsify most of them until we got an answer; our techniques included high-voltage power supply (0-10,000 V), Faraday cages, Kelvin probe force microscopy, electrodeposition, X-ray photoelectron spectroscopy, energy-dispersive spectroscopy, optical microscopy, a contact angle cell, and high-speed imaging. We concluded that contact electrification at the PTFE-aluminum interface was driven by electrons transferred from aluminum to PTFE. In contrast, contact electrification at the polypropylene-water interface was driven by the specific adsorption of OH- ions onto polypropylene. These insights should be helpful in designing applications of polymers where electrical charging could have influence, or applications that could be based on electrical charging at such interfaces, such as triboelectric generator.
    • Membrane Materials and Technology for Xylene Isomers Separation and Isomerization via Pervaporation

      Bilaus, Rakan (2014-11)
      P-xylene is one of the highly influential commodities in the petrochemical industry. It is used to make 90% of the world’s third largest plastic production, polyethylene terephthalate (PET). With a continuously increasing demand, the current technology’s high energy intensity has become a growing concern. Membrane separation technology is a potential low-energy alternative. Polymeric membranes were investigated in a pervaporation experiment to separate xylene isomers. Polymers of intrinsic microporosity (PIMs) as well as polyimides (PIM-PI), including thermally cross-linked PIM-1, PIM-6FDA-OH and thermally-rearranged PIM-6FDA-OH were investigated as potential candidates. Although they exhibited extremely high permeability to xylenes, selectivity towards p-xylene was poor. This was attributed to the polymers low chemical resistance which was apparent in their strong tendency to swell in xylenes. Consequently, a perfluoro-polymer, Teflon AF 2400, with a high chemical resistance was tested, which resulted in a slightly improved selectivity. A super acid sulfonated perfluoro-polymer (Nafion-H) was used as reactive membrane for xylenes isomerization. The membrane exhibited high catalytic activity, resulting in 19.5% p-xylene yield at 75ᵒC compared to 20% p-xylene yield at 450ᵒC in commercial fixed bed reactors. Nafion-H membrane outperforms the commercial technology with significant energy savings.
    • Membrane Separation of 2-Ethyl Hexyl Amine/1-Decene

      Bawareth, Bander (2012-12)
      1-Decene is a valuable product in linear alpha olefins plants that is contaminated with 2-EHA (2-ethyl hexyl amine). Using organic solvent nanofiltration membranes for this separation is quite challengeable. A membrane has to be a chemically stable in this environment with reasonable and stable separation factor. This paper shows that Teflon AF 2400 and cellulose acetate produced interesting results in 1-decene/2-EHA separation. The separation factor of Teflon AF 2400 is 3 with a stable permeance of 1.1x10-2 L/(m2·h·bar). Likewise, cellulose acetate gave 2-EHA/1-decene separation factor of 2 with a lower permeance of 3.67x10-3 L/(m2·h·bar). A series of hydrophilic membranes were tested but they did not give any separation due to high degree of swelling of 2-EHA with these polymers. The large swelling causes the membrane to lose its diffusivity selectivity because of an increase in the polymer's chain mobility.
    • Memristive Probabilistic Computing

      Alahmadi, Hamzah (2017-10)
      In the era of Internet of Things and Big Data, unconventional techniques are rising to accommodate the large size of data and the resource constraints. New computing structures are advancing based on non-volatile memory technologies and different processing paradigms. Additionally, the intrinsic resiliency of current applications leads to the development of creative techniques in computations. In those applications, approximate computing provides a perfect fit to optimize the energy efficiency while compromising on the accuracy. In this work, we build probabilistic adders based on stochastic memristor. Probabilistic adders are analyzed with respect of the stochastic behavior of the underlying memristors. Multiple adder implementations are investigated and compared. The memristive probabilistic adder provides a different approach from the typical approximate CMOS adders. Furthermore, it allows for a high area saving and design exibility between the performance and power saving. To reach a similar performance level as approximate CMOS adders, the memristive adder achieves 60% of power saving. An image-compression application is investigated using the memristive probabilistic adders with the performance and the energy trade-off.
    • Mesoporous Carbon Produced from Tri-constituent Mesoporous Carbon-silica Composite for Water Purification

      Yu, Yanjie (2012-05)
      Highly ordered mesoporous carbon-silica nanocomposites with interpenetrating carbon and silica networks were synthesized by the evaporation-induced tri-constituent co- assembly approach. The removal of silica by concentrated NaOH solution produced mesoporous carbons, which contained not only the primary large pores, but also the secondary mesopores in the carbon walls. The thus synthesized mesoporous carbon was further activated by using ZnCl2. The activated mesoporous carbon showed an improved surface area and pore volume. The synthesized mesoporous carbon was tested for diuron removal from water and the results showed that the carbon gave a fast diuron adsorption kinetics and a high diuron removal capacity, which was attributable to the primary mesopore channels being the highway for mass transfer, which led to short diffusion path length and easy accessibility of the interpenetrated secondary mesopores. The optimal adsorption capacity of the porous carbon was determined to be 390 mg/g, the highest values ever reported for diuron adsorption on carbon-based materials.
    • Metabolite Profiling of Red Sea Corals

      Ortega, Jovhana Alejandra (2016-12)
      Looking at the metabolite profile of an organism provides insights into the metabolomic state of a cell and hence also into pathways employed. Little is known about the metabolites produced by corals and their algal symbionts. In particular, corals from the central Red Sea are understudied, but interesting study objects, as they live in one of the warmest and most saline environments and can provide clues as to the adjustment of corals to environmental change. In this study, we applied gas chromatography – mass spectrometry (GC–MS) metabolite profiling to analyze the metabolic profile of four coral species and their associated symbionts: Fungia granulosa, Acropora hemprichii, Porites lutea, and Pocillopora verrucosa. We identified and quantified 102 compounds among primary and secondary metabolites across all samples. F. granulosa and its symbiont showed a total of 59 metabolites which were similar to the 51 displayed by P. verrucosa. P. lutea and A. hemprichii both harbored 40 compounds in conjunction with their respective isolated algae. Comparing across species, 28 metabolites were exclusively present in algae, while 38 were exclusive to corals. A principal component and cluster analyses revealed that metabolite profiles clustered between corals and algae, but each species harbored a distinct catalog of metabolites. The major classes of compounds were carbohydrates and amino acids. Taken together, this study provides a first description of metabolites of Red Sea corals and their associated symbionts. As expected, the metabolites of coral hosts differ from their algal symbionts, but each host and algal species harbor a unique set of metabolites. This corroborates that host-symbiont species pairs display a fine-tuned complementary metabolism that provide insights into the specific nature of the symbiosis. Our analysis also revealed aquatic pollutants, which suggests that metabolite profiling might be used for monitoring pollution levels and assessing environmental impact.
    • Method Development for Efficient Incorporation of Unnatural Amino Acids

      Harris, Paul D. (2014-04)
      The synthesis of proteins bearing unnatural amino acids has the potential to enhance and elucidate many processes in biochemistry and molecular biology. There are two primary methods for site specific unnatural amino acid incorporation, both of which use the cell’s native protein translating machinery: in vitro chemical acylation of suppressor tRNAs and the use of orthogonal amino acyl tRNA synthetases. Total chemical synthesis is theoretically possible, but current methods severely limit the maximum size of the product protein. In vivo orthogonal synthetase methods suffer from the high cost of the unnatural amino acid. In this thesis I sought to address this limitation by increasing cell density, first in shake flasks and then in a bioreactor in order to increase the yield of protein per amount of unnatural amino acid used. In a parallel project, I used the in vitro chemical acylation system to incorporate several unnatural amino acids, key among them the fluorophore BODIPYFL, with the aim of producing site specifically fluorescently labeled protein for single molecule FRET studies. I demonstrated successful incorporation of these amino acids into the trial protein GFP, although incorporation was not demonstrated in the final target, FEN1. This also served to confirm the effectiveness of a new procedure developed for chemical acylation.
    • Micro-fabricated super-hydrophobic substrate for amyloid fibers characterization

      Ricco, Andrea (2018-11-22)
      In recent years super-hydrophobic micro-patterned substrates (SHS) have been successfully used for the suspension of a few biological molecules, allowing the further characterization in a background-free environment by label-free techniques such as Raman spectroscopy, SEM and TEM in one device. This result is due to the combined action of laminar flow and shear stress exerted on the molecules contained in a drop that is spotted on top of the SHS and slowly evaporates. This new method is here proposed for the label-free formation and background-free characterization of amyloid fibers. Amyloids are insoluble aggregates formed by proteins that convert from a misfolded form into highly-organized β-sheet structures that could accumulate in different organs and compromise their normal physiological functions. Known amyloid-related diseases, named amyloidosis, are for instance Alzheimer, Parkinson, and type 2 diabetes. In classical crystallography, the study of the amyloid aggregates structure is often hampered by the laborious and time consuming sample preparation techniques. Therefore the need of a quick reproducible technique, has emerged. The amyloid fibers investigated in this work are derived from a lysozyme protein and a Tau-derived short peptide, both known to be related to two forms of amyloidosis. With this technique we demonstrate that threads of protein fibers are deposited on the substrate helped by the patterning of the SHS and its properties, and by characterizing them with Raman spectroscopy technique we revealed that they are anisotropic structures of amyloid nature. This type of sample preparation technique arises from the effect of the evaporation on the SHS, and opens up new possibilities for the formation of oriented fibers of amyloids and more in general, of proteins, ready for a substrate-free characterization, while classic crystallographic methods could have a limitation.
    • Micro-Raman Imaging for Biology with Multivariate Spectral Analysis

      Malvaso, Federica (2015-05-05)
      Raman spectroscopy is a noninvasive technique that can provide complex information on the vibrational state of the molecules. It defines the unique fingerprint that allow the identification of the various chemical components within a given sample. The aim of the following thesis work is to analyze Raman maps related to three pairs of different cells, highlighting differences and similarities through multivariate algorithms. The first pair of analyzed cells are human embryonic stem cells (hESCs), while the other two pairs are induced pluripotent stem cells (iPSCs) derived from T lymphocytes and keratinocytes, respectively. Although two different multivariate techniques were employed, ie Principal Component Analysis and Cluster Analysis, the same results were achieved: the iPSCs derived from T-lymphocytes show a higher content of genetic material both compared with the iPSCs derived from keratinocytes and the hESCs . On the other side, equally evident, was that iPS cells derived from keratinocytes assume a molecular distribution very similar to hESCs.
    • Micro-seismic Imaging Using a Source Independent Waveform Inversion Method

      Wang, Hanchen (2016-04-18)
      Micro-seismology is attracting more and more attention in the exploration seismology community. The main goal in micro-seismic imaging is to find the source location and the ignition time in order to track the fracture expansion, which will help engineers monitor the reservoirs. Conventional imaging methods work fine in this field but there are many limitations such as manual picking, incorrect migration velocity and low signal to noise ratio (S/N). In traditional surface survey imaging, full waveform inversion (FWI) is widely used. The FWI method updates the velocity model by minimizing the misfit between the observed data and the predicted data. Using FWI to locate and image microseismic events allows for an automatic process (free of picking) that utilizes the full wavefield. Use the FWI technique, and overcomes the difficulties of manual pickings and incorrect velocity model for migration. However, the technique of waveform inversion of micro-seismic events faces its own problems. There is significant nonlinearity due to the unknown source location (space) and function (time). We have developed a source independent FWI of micro-seismic events to simultaneously invert for the source image, source function and velocity model. It is based on convolving reference traces with the observed and modeled data to mitigate the effect of an unknown source ignition time. The adjoint-state method is used to derive the gradient for the source image, source function and velocity updates. To examine the accuracy of the inverted source image and velocity model the extended image for source wavelet in z-axis is extracted. Also the angle gather is calculated to check the applicability of the migration velocity. By inverting for the source image, source wavelet and the velocity model simultaneously, the proposed method produces good estimates of the source location, ignition time and the background velocity in the synthetic experiments with both parts of the Marmousi and the SEG Overthrust model. On the other hand, a new imaging condition of natural Green’s function has been implemented to mitigate the effect of the unknown velocity model. It is based on putting receivers in a horizontal well close to the micro-seismic events so that only a small part of the velocity model is required for the imaging. In order to focus the multi scattering energy to the source location, as well as to suppress the influence of the noise in the data, we introduced a new method to compensate the energy in the receiver wavefield. It is based on reflection waveform inversion (RWI) theory. We simply migrate for the scatters (reflectors) in the medium, and set the image as a secondary source to compensate for the multi scattering energy in the receiver wavefield. By applying the same imaging condition, the energy of those scattering events can be traced to the source location. Thus the source point has higher energy in the source image. A simple two-layer medium test demonstrates the features.