Thesis: B.S., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, 1978 / Includes bibliographical references. / B.S. / B.S. Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science

Call number: LD2668 .T4 1979 L64 / Master of Science

The Gram-positive pathogens Corynebacterium diphtheriae and Streptococcus pyogenes both require iron for survival. These bacteria have developed sophisticated heme uptake and transport protein machinery responsible for the import of iron into the cell, in the form of heme from the human host. The heme utilization pathway (hmu) of C. diphtheriae utilizes multiple proteins to bind and transport heme into the cell. One of these proteins, HmuT, delivers heme to the ABC transporter HmuUV. The axial ligation of the heme in HmuT was probed by examination of wild-type HmuT and a series of conserved heme pocket residue mutants, H136A, Y235A, R237A, Y272A, M292A, Y349A, and Y349F. Characterization by UV-visible absorption, resonance Raman, and magnetic circular dichroism spectroscopies indicated that H136 and Y235 are the axial ligands in HmuT. Electrospray ionization mass spectrometry was also utilized to assess the roles of conserved residues in contribution to heme binding. The S. pyogenes streptococcal iron acquisition (sia)/heme transport system (hts) utilizes multiple proteins to bring host heme to the intracellular space. Both the substrate binding protein SiaA and the hemoprotein surface receptor Shr were investigated. The kinetic effects on SiaA heme release were probed through chemical unfolding of axial ligand mutants M79A and H229A, as well mutants thought to contribute to heme binding, K61A and C58A, and a control mutant, C47A. The unfolding pathways showed two processes for protein denaturation. This is consistent with heme loss from protein forms differing by the orientation of the heme in the binding pocket. The ease of protein unfolding is related to the strength of interaction of the residues with the heme. Shr contains two NEAT (near-iron transporter) domains (Shr-N1 and Shr-N2) which can both bind heme. Biophysical studies of both Shr-N1 and Shr-N2 indicated a new class of NEAT domains which utilize methionine as an axial ligand, rather than a tyrosine. Thermal and chemical unfolding showed ferrous Shr-N1 and Shr-N2 to be most resistant to denaturation. Shr-N2 was prone to autoreduction. Together, sequence alignment, homology modeling, and spectral signatures are all consistent with two methionines as the heme ligands of this novel type of NEAT heme-binding domain.

In this thesis, the effect of the sample properties on the characteristics of the hot carrier luminescence in graphene is investigated. The present work focuses on the two main issues described below. The first issue is the modification effects of near-infrared pulsed laser excitation on graphene. For excitation fluences several orders of magnitude lower than the optical damage threshold, the interaction with ultrafast laser pulses is found to cause a stable change in the properties of graphene. This photomodification also results in a decrease of the hot photoluminescence intensity. The detailed analysis shows that ultrafast photoexcitation leads to an increase in the local level of hole doping, as well as a change in the mechanical strain. The variation of doping and strain are linked with the enhanced adsorption of atmospheric oxygen caused by the distortion of the graphene surface. These findings demonstrate that ultrashort pulsed excitation can be invasive even if a relatively low laser power is used. Secondly, the variation of the hot photoluminescence intensity with the increasing charge carrier density in graphene is investigated. The electro-optical measurements performed using graphene field-effect transistors show a strong dependence of the photoluminescence intensity on the intrinsic carrier concentration. The emission intensity has a maximum value in undoped graphene and decreases with the increasing doping level. The theoretical calculations performed using a refined two-temperature model suggest that the reduction of the photoluminescence intensity is caused by an increase in the hot carrier relaxation rate. The modification of the carrier relaxation dynamics caused by photoinduced doping is probed directly using the two-pulse correlation measurements. The discovered sensitivity of the hot photoluminescence to the intrinsic carrier concentration can be utilised for spatially-resolved measurements of the Fermi level position in graphene samples, offering an advantage in resolution and speed.

The manufacturing process of a photovoltaic Si wafer comprises of first a high temperature heating process to produce a Si ingot from polycrystalline Silicon, which is then cut into bricks and subsequently sawn into wafers using a wire saw. These processes create residual stresses both from the thermal gradient induced by solidification and from either the rolling-indenting or scratching-indenting processes caused by the type of wire saw used. The objective of this research is to study silicon wafer residual stress as a result of the typical industry manufacturing processes and by doing so, better understand the mechanical properties that lead to increased fracture. This thesis aims to quantify the amount of residual stress generated by the solidification/thermal gradient produced during the casting of Si ingots separately from the residual stress generated by the wire sawing process. Samples from industry are used to compare the effects of the manufacturing processes on residual stress in multi-crystalline silicon (mc-Si) wafers including the effects of fixed abrasive diamond wire sawing (DWS) vs. loose abrasive (LAWS) slurry wire sawing used in the wafering process. Near-infrared birefringence polariscopy and polarized micro-Raman spectroscopy are used to study wafer residual stresses within grains and at grain boundaries in mc-Si as a function of etch-depth. While near-infrared birefringence polariscopy allows for the measurement of full-field maximum shear stress, micro-Raman spectroscopy provides decomposition of the stress tensor into both principal and shear in-plane stress components. Consequently, regions of high tensile stress, which are detrimental to the mechanical integrity of the wafer, can be easily identified. In addition to the mechanical characterization, the residual stress produced by the thermal gradient/solidification process for multi-crystalline Si wafers was also correlated to electrical performance of mc-Si wafers using photoluminescence.

Solid oxide fuel cells (SOFCs) represent a next generation energy source with high energy conversion efficiency, low pollutant emission, good flexibility with a wide variety of fuels, and excellent modularity suitable for distributed power generation. As an electrochemical energy conversion device, SOFC’s performance and reliability depend sensitively on the catalytic activity and stability of the electrode materials. To date, however, the development of electrode materials and microstructures is still based largely on trial-and-error methods because of inadequate understanding of the mechanisms of the electrode processes. Identifying key descriptors/properties of electrode materials or functional heterogeneous interfaces, especially under in situ conditions, may provide guidance to the design of electrode materials and microstructures. This thesis aims to gain insight into the electrochemical and catalytic processes occurring on the electrode surfaces using unique characterization tools with superior sensitivity, high spatial resolution, and excellent surface specificity applicable under in situ/operando conditions. Carbon deposition on nickel-based anodes is investigated with in situ Raman spectroscopy and SERS. Analysis shows a rapid nucleation of carbon deposition upon exposure to small amount of propane. Such nucleation process is sensitive to the presence of surface coating (e.g., GDC) and the concentration of steam. In particular, operando analysis of the Ni-YSZ boundary indicates special function of the interface for coking initiation and reformation. The coking-resistant catalysts (BaO, BZY, and BZCYYb) are systematically studied using in situ Raman spectroscopy, SERS, and EFM. In particular, time-resolved Raman analysis of the surface functional groups (-OH, -CO3, and adsorbed carbon) upon exposure to different gas atmospheres provides insight into the mechanisms related to carbon removal. The morphology and distribution of early stage carbon deposition are investigated with EFM, and the impact of BaO surface modification is evaluated. The surface species formed as a result of sulfur poisoning on nickel-based anode are examined with SERS. To identify the key factors responsible for sulfur tolerance, model cells with welldefined electrode-electrolyte interfaces are systematically studied. The Ni-BZCYYb interface exhibits superior sulfur tolerance. The oxygen reduction kinetics on LSCF, a typical cathode material of SOFC, is studied using model cells with patterned electrodes. The polarization behaviors of these micro- electrodes, as probed using a micro-probe impedance spectroscopy system, were correlated with the systematically varied geometries of the electrodes to identify the dominant paths for oxygen reduction under different electrode configurations. Effects of different catalyst modifications are also evaluated to gain insight into the mechanisms that enhance oxygen reduction activity. The causes of performance degradation of LSCF cathodes over long term operation are investigated using SERS. Spectral features are correlated with the formation of surface contamination upon the exposure to air containing Cr vapor, H2O, and CO2. Degradation in cathode performance occurs under normal operating conditions due to the poisoning effect of Cr from the interconnect between cells and the high operating temperature. The surface-modified LSCF cathode resists surface reactions with Cr vapor that impairs electrode performance, suggesting promising ways to mitigate performance degradation.

Optical trapping is a method which uses focused laser light to manipulate small objects. This optical manipulation can be scaled below the diffraction limit by using interactions between light and apertures in a metal film to localize electric fields. This method can trap objects as small as several nanometers. The ability to determine the properties of a trapped nanoparticle is among the most pressing issues to the utilization of this method to a broader range of research and industrial applications. Presented here are two methods which demonstrate the ability to determine the properties of a trapped nanoparticle. The first method incorporates Raman spectroscopy into a trapping setup to obtain single particle identification. Raman spectroscopy provides a way to uniquely identify an object based on the light it scatters. Because Raman scattering is an intrinsically weak process, it has been difficult to obtain single particle sensitivity. Using localized electric fields at the trapping aperture, the Raman integrated trapping setup greatly enhances the optical interaction with the trapped particle enabling the required sensitivity. In this work, the trapping and identification of 20 nm titania and polystyrene nanoparticles is demonstrated. The second method uses an aperture assisted optical trap to detect the response of a magnetite nanoparticle to a varying applied magnetic field. This information is then used to determine the magnetic susceptibility, remanence, refractive index, and size distribution of the trapped particle. / Graduate / 0544 / 0752 / stevenjones3.14@gmail.com

Alkali (A) and alkaline earth (AE) metals can form carbides and intercalated graphites with carbon. The carbides mostly represent acetylides which are salt-like compounds composed of C22− dumbbell anions and metal cations. Both the acetylide carbides and intercalated graphites are technologically important. Superconductivity has been observed in several intercalated graphites such as KC8 and CaC6. Li intercalated graphites are a major ingredient in Li ion batteries. CaC2 is an important commodity for producing acetylene and the fertilizer CaCN2. In spite of the extensive research on A–C and AE–C compounds, phase diagrams are largely unknown. The thermodynamic and kinetic properties of both carbides and intercalalated graphites are discussed controversially. Recent computational studies indicated that well-known carbides, like CaC2 and BaC2, are thermodynamically unstable. Additionally, computational studies predicted that acetylide carbides will generally form novel polymeric carbides (polycarbides) at high pressures. This thesis is intended to check the validity of theoretical predictions and to shed light on the complicated phase diagrams of the Li–C and the Ca–C systems. The Li–C and the Ca–C systems were investigated using well-controllable metal hydride–graphite reactions. Concerning the Li–C system, relative stabilities of the metastable lithium graphite intercalation compounds (Li-GICs) of stages I, IIa, IIb, III, IV and Id were studied close to the competing formation of the thermodynamically stable Li2C2. The stage IIa showed distinguished thermal stability. The phase Id showed thermodynamic stability and hence, was included in the Li–C phase diagram. In the Ca–C system, results from CaH2–graphite reactions indicate compositional variations between polymorphs I, II and III. The formation of CaC2  I was favored  only  at  1100  ◦C or  higher  temperature  and  with  excess calcium, which speculates phase I as carbon deficient CaC2−δ . To explore the potential existence of polycarbides, the acetylide carbides Li2C2 and CaC2 were investigated under various pressure and temperature conditions, employing diamond anvil cells for in situ studies and multi anvil techniques for large volume synthesis. The products were characterized by a combination of diffraction and spectroscopy techniques. For both Li2C2 and CaC2, a pressure induced structural transformation was observed at relatively low pressures (10–15 GPa), which was followed by an irreversible amorphization at higher pressures (25–30 GPa). For Li2C2 the structure of the high pressure phase prior to amorphization could be elucidated. The ground state with an antifluorite Immm structure (coordination number (CN) for C22− dumbbells = 8) transforms to a phase with an anticotunnite Pnma structure (CN for C22− dumbbells = 9). Polycarbides, as predicted from theory, could not be obtained. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 2: Manuscript.</p>

Στην παρούσα μεταπτυχιακή εργασία ειδίκευσης περιγράφεται η σύνθεση και ο χαρακτηρισμός νέων μεσοπορωδών βιοενεργών υλικών. Παρουσιάζονται οι συσχετιζόμενες με τα πορώδη/μεσοπορώδη υλικά έννοιες, οι ιδιότητες τους και διάφοροι τρόποι σύνθεσης τους. Εν συνεχεία, αναλύονται θέματα βιουλικών, δίνοντας έμφαση στις βιοϋάλους και τις ιδιότητες τους, και ειδικότερα στη βιονεργότητα, που αποτελεί την πιο χαρακτηριστική ιδιότητα αυτών, ενώ δίνεται έμφαση, επίσης στις διάφορες μεθόδους που χρησιμοποιούνται για την σύνθεση τους. Στην συνέχεια αναλύονται οι τεχνικές που χρησιμοποιήθηκαν για το χαρακτηρισμό των προαναφερθέντων υλικών καθώς και ο τρόπος λειτουργίας της κάθε τεχνικής. Επίσης, γίνεται αναφορά στα διαφορετικά χαρακτηριστικά των υλικών που μπορούν να μελετηθούν για κάθε τεχνική ξεχωριστά. Στο τελευταίο κεφάλαιο παρουσιάζεται αναλυτικά η διαδικασία διεξαγωγής των πειραμάτων, οι διάφοροι τρόποι σύνθεσης που χρησιμοποιήθηκαν, καθώς και σχολιασμός των αποτελεσμάτων. Τέλος, παρουσιάζονται τα συμπεράσματα που προέκυψαν από τα πειραματικά αποτελέσματα για την παρούσα μεταπτυχιακή εργασία. Επίσης γίνεται αναφορά και σε μελλοντικές κατευθύνσεις που περιλαμβάνουν την χρήση αυτών των υλικών σε σύνθετα υλικά για παλμική εναπόθεση με Laser και τεχνικές εναπόθεσης λεπτού υμενίου. / In this master thesis the synthesis and characterization of novel bioactive mesoporous materials is being reported. The notions related to porous/mesoporous materials, their properties and various synthetic methods are being discussed. Subsequently, the notion of “biomaterials” is further analyzed, focusing on bioglasses and their properties. The meaning of bioactivity is also analyzed as the most characteristic feature of bioglasses while various methods used for the synthesis of these are discussed. Following the techniques used to characterize these materials as well as the operating mode of each technique is discussed. In the last chapter, the experimental processes are reported as well as the results are being discussed. Finally, the conclusions of all the experiments and analysis are reported. Also, future directions include the usage of these materials in composite materials for laser ablation and thin film deposition techniques are mentioned.

Η παρούσα διατριβή εξειδίκευσης αποτελεί το προοίμιο μιας μακρόπνοης εμπλοκής του εργαστηρίου υλοποίησής της στη μελέτη ενδεχόμενης μετανάστευσης ουσιών που χρησιμοποιούνται ως ενισχυτικά φραγής ή/και ως χημικοί αισθητήρες σε βιοπολυμερικές συσκευασίες τροφίμων και αποδέσμευσής τους σε προσομοιωτές τροφίμων. Στο πλαίσιο αυτό, η εργασία αυτή αποτελεί μια προσπάθεια ανάδειξης της μεθόδου επιφανειακής ενίσχυσης της σκέδασης Raman (Surafce Enhanced Raman Scattering) ως κατάλληλης για τον ποσοτικό προσδιορισμό μικρού μοριακού βάρους ενώσεων που ενδεχομένως αποδεσμεύονται σε υδατικά διαλύματα ή/και συγκεκριμένους προσομοιωτές τροφίμων. Η μελέτη εστιάστηκε στην ελεγχόμενη αποδέσμευση φαρμακευτικών ουσιών από μια βιοπολυμερική μήτρα κυρίως κατά το πρώιμο στάδιο της μελέτης και τις παραμέτρους που επηρεάζουν το φαινόμενο αυτό. Βασικός στόχος της μελέτης ήταν η κατά το δυνατό μείωση του ορίου ανίχνευσης με SERS της αποδεσμευόμενης ουσίας με την εμβάπτιση της βιοπολυμερικής μήτρας που την εμπεριέχει σε πρότυπα υδατικά διαλύματα. Πραγματοποιήθηκε μια διεξοδική μελέτη των υποστρωμάτων που χρησιμοποιούνται στο SERS και συγκεκριμένα του νανοκολλοειδούς αργύρου (Ag). Για τον σκοπό αυτό, πραγματοποιήθηκαν πειράματα τα οποία έδειξαν την εξάρτηση της έντασης SERS από τη συσσωμάτωση των υποστρωμάτων Ag συναρτήσει του χρόνου και του παράγοντα συσσωμάτωσης, NaCl. Η εφαρμογή του SERS σε μελέτες ουσιών εξαιρετικά χαμηλών συγκεντρώσεων αναδεικνύεται ως ένα πολύ ενδιαφέρον πεδίο έρευνας. Επίσης, ως πρότυπο πείραμα, παρουσιάζεται μεθοδολογία μελέτης με την τεχνική SERS της αποδέσμευσης του αντικαρκινικού φαρμάκου Μitoxantrone (ΜΤΧ) από εμπορικά ράμματα Maxon. Για το σκοπό αυτό, παρασκευάστηκαν πολυμερικά υμένια με εγκλωβισμένη τη δραστική ουσία και η μελέτη της αποδέσμευσης της σε νερό και PBS (phosphate buffered saline) πραγματοποιήθηκε με SERS και UV-Vis, αντίστοιχα. Η φασματοσκοπία UV-Vis χρησιμοποιήθηκε συμπληρωματικά. Στηριζόμενοι στη μεθοδολογία που αναπτύξαμε εξάγαμε ποσοτικά αποτελέσματα από τρία διαφορετικά εργαστηριακά δείγματα, τα οποία προήλθαν από ανάμιξη εμπορικών ραμμάτων Maxon με 1% κ.β. MTX: (α) στην άμορφη φάση έπειτα από ταχεία ψύξη του τήγματος, (β) στην ημικρυσταλλική φάση με σχετικά χαμηλό ποσοστό κρυσταλλικότητας, που λάβαμε έπειτα από ανόπτηση της άμορφης φάσης για περιορισμένο χρόνο στη θερμοκρασία κρυστάλλωσης και (γ) σε μια επίσης ημικρυσταλλική φάση με αρκετά μεγάλο ποσοστό κρυστάλλωσης (όσης και τα εμπορικά ράμματα). Τα αποτελέσματα δείχνουν πως υπάρχει συσχέτιση μεταξύ κρυσταλλικότητας και αποδέσμευσης του φαρμάκου, με τα μικρότερα ποσά αποδέσμευσης στην περίπτωση του άμορφου δείγματος. Αυτό που παρατηρήθηκε στα πρώιμα στάδια της αποδέσμευσης από τις μετρήσεις SERS φαίνεται να επαληθεύεται από αντίστοιχα αποτελέσματα σε μεταγενέστερα στάδια αποδέσμευσης που λάβαμε με εφαρμογή της συμβατικής τεχνικής απορρόφησης ορατού – υπεριώδους (UV-Vis). Ωστόσο, οι ποσοτικές μετρήσεις με τη χρήση του SERS σε πολύ μικρές συγκεντρώσεις έδειξαν μεγαλύτερη ανιχνευτική ευαισθησία σε σχέση με αυτές που πραγματοποιήθηκαν με την απορρόφηση UV-Vis. Συμπερασματικά, το SERS δείχνει ικανό στον ποσοτικό προσδιορισμό ενεργών ουσιών που αποδεσμεύονται από βιοσυμβατά πολυμερικά συστήματα μεταφοράς δραστικών ουσιών σε πολύ μικρές συγκεντρώσεις. / This thesis of specialization is the precursor of a long-term involvement of the laboratory of Applied Molecular Spectroscopy of FORTH/ICE-HT in the implementation of the study of the migration of substances used as barrier and/or as chemical sensors in biopolymer based food packaging and their release into food simulants. In this context, this work attempts to highlight the method of surface enhanced Raman scattering (SERS) as appropriate for quantifying low molecular weight compounds that may be released in aqueous solutions and/or specific food simulants. The study focused on the controlled release of pharmaceuticals from a biopolymeric matrix mainly during the early stage of the study and the parameters affecting this phenomenon. The main objective of the study was to reduce SERS detection limit of the released substance by emerging the substance-incorporated biopolymeric matrix in standard aqueous solutions. In this context, we developed methods to maximize SERS enhancement and consequently reduce the limit of detection of an active substance, Mitoxantrone (MTX). This was achieved by a thorough study of the substrates used in SERS, namely nanocolloidal silver (Ag) suspensions. For this purpose, we contacted experiments which show the dependence of the SERS intensity on the aggregation of Ag substrates as a function of both time and the aggregating agent, NaCl. Also, as a standard experiment, present SERS methodology was applied in the study of the release of the anticancer drug Mitoxantrone (MTX) from commercially available sutures, Maxon. For this purpose, polymeric films prepared with the encapsulated active substance were immersed either in water or/and in PBS (phosphate buffered saline) and the release of MTX was probed by both SERS and UV-Vis. Based on the developed methodology we obtained quantitative results from three different laboratory samples produced by mixing commercial Maxon sutures with 1 wt% MTX: (a) an almost completely amorphous mixture produced by quenching from the melt, (b) a semi-crystalline one possessing low crystallinity that was produced by annealing the amorphous sample at the temperature close to the crystallization one and (c) a semi-crystalline one possessing high crystallinity similar to the commercial product. The results indicate a correlation between crystallinity and drug release rate; the more amorphous the sample is the less quantity of the drug is released. SERS was able to probe the active agent at the early state of release; UV-Vis has supported these results at a later state of the release process. In conclusion, SERS may enable low concentration quantitative assessment of controlled release of drugs from biopolymer-based delivery systems.