Multiple Track Performance of a Digital Magnetic Tape System : Experimental Study and Simulation using Parallel Processing Techniques

The primary aim of the magnetic recording industry is to increase storage capacities and transfer rates whilst maintaining or reducing costs. In multiple-track tape systems, as recorded track dimensions decrease, higher precision tape transport mechanisms and dedicated coding circuitry are required. This leads to increased manufacturing costs and a loss of flexibility. This thesis reports on the performance of a low precision low-cost multiple-track tape transport system. Software based techniques to study system performance, and to compensate for the mechanical deficiencies of this system were developed using occam and the transputer. The inherent parallelism of the multiple-track format was exploited by integrating a transputer into the recording channel to perform the signal processing tasks. An innovative model of the recording channel, written exclusively in occam, was developed. The effect of parameters, such as data rate, track dimensions and head misregistration on system performance was determined from the detailed error profile produced. This model may be run on a network of transputers, allowing its speed of execution to be scaled to suit the investigation. These features, combined with its modular flexibility makes it a powerful tool that may be applied to other multiple-track systems, such as digital HDTV. A greater understanding of the effects of mechanical deficiencies on the performance of multiple-track systems was gained from this study. This led to the development of a software based compensation scheme to reduce the effects of Lateral Head Displacement and allow low-cost tape transport mechanisms to be used with narrow, closely spaced tracks, facilitating higher packing densities. The experimental and simulated investigation of system performance, the development of the model and compensation scheme using parallel processing techniques has led to the publication of a paper and two further publications are expected.Thorn EMI, Central Research Laboratories, Hayes, Middlese

Quantum dynamics in condensed phases : charge carrier mobility, decoherence, and excitation energy transfer

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2006.Vita.Includes bibliographical references.In this thesis, we develop analytical models for quantum systems and perform theoretical investigations on several dynamical processes in condensed phases. First, we study charge-carrier mobilities in organic molecular crystals, and develop a microscopic theory that describes both the coherent band-like and incoherent hopping transport observed in organic crystals. We investigate the structures of polaron states using a variational scheme, and calculate both band-like and hopping mobilities at a broad range of parameters. Our mobility calculations in 1-D nearest-neighbor systems predict universal band-like to hopping transitions, in agreement with experiments. Second, motivated by recent developments in quantum computing with solid-state systems, we propose an effective Hamiltonian approach to describe quantum dissipation and decoherence. We then applied this method to study the effect of noise in a number of quantum algorithms and calculate noise threshold for fault-tolerant quantum error corrections (QEC). In addition, we perform a systematic investigation on several variables that can affect the efficiency of the fault-tolerant QEC scheme, aiming to generate a generic picture on how to search for optimal circuit design for real physical implementations.(cont.) Third, we investigate the quantum coherence in the B800 ring of' of the purple bacterium Rps. acidophila and how it affects the dynamics of excitation energy transfer in a single LH2 complex. Our calculations suggest that the coherence in the B800 ring plays a significant role in both spectral and dynamical properties. Finally, we discussed the validity of Markovian master equations, and propose a concatenation scheme for applying Markovian master equations that absorbs the non-Markovian effects at short times in a natural manner. Applications of the concatenation scheme on the spin-boson problem show excellent agreements with the results obtained from the non-Markovian master equation at all parameter range studied.by Yuan-Chung Cheng.Ph.D

Next-generation single-photon sources using two-dimensional hexagonal boron nitride

With the second quantum revolution unfolding, the realization of optical quantum technologies will transform future information processing, communication, and sensing. One of the crucial building blocks of quantum information architectures is a single-photon source. Promising candidates for such quantum light sources are quantum dots, trapped ions, color centers in solid-state crystals, and sources based on heralded spontaneous parametric down-conversion. The recent discovery of optically active defects hosted by 2D materials has added yet another class to the solid-state quantum emitters. Stable quantum emitters have been reported in semiconducting transition metal dichalcogenides (TMDs) and in hexagonal boron nitride (hBN). Owing to the large band gap, the energy levels of defects in hBN are well isolated from the band edges. In contrast to TMDs, this allows for operation at room temperature and prevents non-radiative decay, resulting in a high quantum yield. Unlike NV centers in diamond and other solid-state quantum emitters in 3D systems, the 2D crystal lattice of hBN allows for an intrinsically ideal extraction efficiency. In this thesis, advances in developing this new type of emitter are described. In the first experiment, quantum emitters hosted by hBN are attached by van der Waals force to the core of multimode fibers. The system features a free space and fiber-coupled single-photon generation mode. The results can be generalized to waveguides and other on-chip photonic quantum information processing devices, thus providing a path toward integration with photonic networks. Next, the fabrication process, based on a microwave plasma etching technique, is substantially improved, achieving a narrow emission linewidth, high single-photon purity, and a significant reduction of the excited state lifetime. The defect formation probability is influenced by the plasma conditions, while the emitter brightness correlates with the annealing temperature. Due to their low size, weight and power requirements, the quantum emitters in hBN are promising candidates as light sources for long-distance satellite-based quantum communication. The next part of this thesis focuses on the feasibility of using these emitters as a light source for quantum key distribution. The necessary improvement in the photon quality is achieved by coupling an emitter with a microcavity in the Purcell regime. The device is characterized by a strong increase in spectral and single-photon purity and can be used for realistic quantum key distribution, thereby outperforming efficient state-of-the-art decoy state protocols. Moreover, the complete source is integrated on a 1U CubeSat, a picoclass satellite platform encapsulated within a cube of length 10cm. This makes the source among the smallest, fully self-contained, ready-to-operate single-photon sources in the world. The emitters are also space-qualified by exposure to ionizing radiation. After irradiation with gamma-rays, protons and electrons, the quantum emitters show negligible change in photophysics. The space certification study is also extended to other 2D materials, suggesting robust suitability for use of these nanomaterials for space instrumentation. Finally, since the nature of the single-photon emission is still debated and highly controversial, efforts are made to locate the defects with atomic precision. The positions at which the defects form correlate with the fabrication method. This allows one to engineer the emitters to be close to the surface, where high-resolution electron microscopy can be utilized to identify the chemical defect. The results so far prove that quantum emitters in hBN are well suited for quantum information applications and can also be integrated on satellite platforms. A device based around this technology would thus provide an excellent building block for a worldwide quantum internet, where metropolitan fiber networks are connected through satellite relay stations

Simple, reliable protocol for high-yield solubilization of seedless amyloid-β monomer

Self-assembly of the amyloid-β (Aβ) peptide to form toxic oligomers and fibrils is a key causal event in the onset of Alzheimer’s disease, and Aβ is the focus of intense research in neuroscience, biophysics, and structural biology aimed at therapeutic development. Due to its rapid self-assembly and extreme sensitivity to aggregation conditions, preparation of seedless, reproducible Aβ solutions is highly challenging, and there are serious ongoing issues with consistency in the literature. In this paper, we use a liquid-phase separation technique, asymmetric flow field-flow fractionation with multiangle light scattering (AF4-MALS), to develop and validate a simple, effective, economical method for re-solubilization and quality control of purified, lyophilized Aβ samples. Our findings were obtained with recombinant peptide but are physicochemical in nature and thus highly relevant to synthetic peptide. We show that much of the variability in the literature stems from the inability of overly mild solvent treatments to produce consistently monomeric preparations and is rectified by a protocol involving high-pH (>12) dissolution, sonication, and rapid freezing to prevent modification. Aβ treated in this manner is chemically stable, can be stored over long timescales at −80 °C, and exhibits remarkably consistent self-assembly behavior when returned to near-neutral pH. These preparations are highly monomeric, seedless, and do not require additional rounds of size exclusion, eliminating the need for this costly procedure and increasing the flexibility of use. We propose that our improved protocol is the simplest, fastest, and most effective way to solubilize Aβ from diverse sources for sensitive self-assembly and toxicity assays

DEVELOPMENT OF A HIGH-THROUGHPUT ASSAY TO MEASURE DNA MISMATCH REPAIR EFFICIENCY IN VIVO

Whether due to mutagens or DNA replication errors, mismatches arise spontaneously in vivo. If left unrepaired, accumulation of mutations at a high rate can be detrimental to the survival of the organism. Cells recognize the mismatches and repair them via a dedicated mismatch repair system. Although its efficiency has been shown to depend on the type and the sequence context of the mismatch, only a small subset of possible mismatched sequences could be examined thus far. In this work, I describe a high-throughput sequencing based approach that can assess the repair efficiency of many different mismatches in parallel, enabling a systematic analysis of the sequence effect on mismatch repair. In this scheme, an in vitro synthesized plasmid containing a single mismatch is introduced to an E. coli cell. If the mismatch is repaired prior to replication, all of the descendants will share the same sequence. If, however, replication precedes mismatch repair, the descendants have a mixture of two different sequences, and therefore the event frequencies of these two types provide information on the repair efficiency. Use of DNA barcodes enables obtaining single-molecule level information regarding the fate of each mismatch carrying molecules, through which the repair of 4434 different mismatches and 1300 insertion loops were monitored in vivo under various conditions. The results showed that CC mismatches are always poorly repaired whereas local sequence context is a strong determinant of the highly heterogeneous repair efficiency of TT, AG and CT mismatches. In contrast, most of the insertion loops were repaired with a high efficiency without an appreciable sequence context dependence. The measurement of the repair efficiency in mutant cell strains of different mismatch repair pathway mutants also showed a residual repair capability, potentially an indication of side-processes that lead to an apparent repair of mismatch bearing plasmids

Plasmonic Nanostructures for Biosensing Applications

The aim of this work is the study, the design and the nanofabrication of innovative plasmonic nanostructured materials to develop label-free optical biosensors. Noble metalbased nanostructures have gained interest in the last years due to their extraordinary optical properties, which allow to develop optical biosensors able to detect very low concentrations of specific biomolecules, called analyte, down to the picomolar range. Such biosensors rely on the Surface Plasmon Resonance (SPR) excitation which occurs under specific conditions that depend both on the morphology of the nanostructure and on the adjacent dielectric medium. Therefore, the binding of the biomolecules to metal surfaces is revealed as a change in the SPR condition. Four kinds of nanostructures are investigated in this work: ordered and disordered nanohole array (o-NHA, d-NHA), nanoprism array (NPA) and nanodisk array (NDA). The o-NHA and d-NHA consist of a thin metallic film (50 - 100 nm) patterned with, respectively, a hexagonal and a disordered array of circular holes. The NPA consists of a honeycomb lattice of triangle shaped nanoprisms with edges of about 100 - 200 nm and height of 40 - 80 nm. Finally, the NDA consists of a disordered array of non-interacting disks with 100 - 300 nm diameter and 40 - 80 nm height. The first two support the Extended-SPR whereas the last two, due to their three-dimensional confinement, present Localized-SPR property. Two colloidal techniques are employed for the scalable and cost-effective synthesis of wide areas of nanostructures that allow a fine control of the morphology: NanoSphere Lithography (NSL) and Sparse Colloidal Lithography (SCL). Ordered arrays were nanofabricated by NSL (i.e., NPA and o-NHA) whereas disordered nanostructures were synthesized by the SCL (i.e., NDA and d-NHA). Firstly, the nanostructures are simulated by Finite Element Method (FEM) computations and their performances in revealing small variations of the dielectric medium at the interface is evaluated as a function of their geometrical parameters. Simulated local sensitivities range from 3.1 nm/RIU of the o-NHA up to 13.6 nm/RIU of the NPA. Afterwards, the sensing performances are evaluated experimentally with nanofabricated samples and comparable but slightly smaller sensitivities are obtained. Secondly, a proof-of-concept protocol for the detection assay, that relies on the binding of streptavidin protein to the biotinylated gold surfaces, is exploited to test the nanostructures as biosensors. A 4.4 nM limit of detection is reached with the best performing biosensor (NPA) and picomolar ones are expected for NPA and NDA with a suitable improvement of the functionalization protocol. Finally, complementary single stranded RNA molecules were used, respectively, as bioreceptor and analyte. Revealing short sequences of non-coding RNA, called microRNA, is fundamental for the medical research since these oligonucleotides act as biomarkers for specific diseases, like tumors. Signals of about 13 nm are obtained from the binding of bioreceptor to the nanostructure and from the hybridization of the analyte oligonucleotide at saturation concentrations (∼ 1 μM), indicating that for the moment the developed protocol is quite effective down to the 100 nM range. Of course, for reading the nm or even sub-nM range further optimizations are needed

Performance improvement of SS-WDM passive optical networks using semiconductor optical amplifiers: Modeling and experiment

Les sources incohérentes sont proposées comme alternatives aux lasers stabilisés en longueur d'onde pour réduire le coût des réseaux optiques passifs utilisant le multiplexage par longueur d'onde découpée dans le spectre (SS-WDM PONs). À cause de leur nature incohérente, ces sources génèrent au récepteur un large bruit d'intensité. Ce bruit limite l'efficacité spectrale et/ou le taux binaire pouvant être achevé. Cette thèse étudie l'utilisation des amplificateurs optique à semi-conducteur SOAs pour nettoyer le bruit d'intensité. De plus, lors de cette thèse, nous explorons les outils numériques et expérimentaux qui nous permettent d'analyser les performances des SOAs dans le cadre de systèmes de communication multi-canaux, incluant le SS-WDM. Nous présentons des modèles mathématiques pour le bruit d'intensité, ce bruit étant celui qui limite les performances des systèmes de communication utilisant des sources incohérentes. Nous discutons les dynamiques complexes des SOAs et présentons les équations qui gouvernent l'évolution des porteurs de charges dans ces amplificateurs. Nous identifions et soulignons l'effet des paramètres les plus importants, qui affectent le processus ainsi que la dynamique de nettoyage du bruit d'intensité. Nous passons en revue, les différentes techniques de nettoyage de bruit avec les SOAs, qui ont démontré les meilleurs résultats connus. De plus, nous effectuons une revue de littérature poussée pour ce qui a attrait au problème de post-filtrage lorsque le SOA est placé au transmetteur, avant la modulation. Notre première contribution pendant ce travail de recherche est de démontrer, en utilisant l'intermodulation de gain d'un SOA au récepteur pour convertir le signal incohérent en laser cohérent, une amélioration significative du taux d'erreur binaire BER. Cette méthode est spectralement efficace, d'autant plus qu'elle ne souffre point la limitation occasionnée par le post-filtrage au récepteur. En contre partie elle nécessite un ample budget de puissance qui doit assurer une saturation suffisante de l'amplificateur au récepteur. Une source laser est aussi nécessaire au récepteur. Ceci est un inconvénient, même si une telle source n'ait pas besoin d'une quelconque stabilisation. Pour contourner le problème causé par le post-filtrage quand le SOA est au transmetteur, nous proposons un nouveau récepteur pour les systèmes de communication WDM, qui permet de mieux garder le nettoyage de bruit, et ce malgré le filtrage optique au récepteur. La nouvelle méthode consiste en un détecteur balancé utilisé au récepteur: d'un bord, tous les canaux sont détectés sans distinction. De l'autre, le signal désiré est bloqué pendant que tous les autres canaux sont détectés. Avec cette méthode, il est facile de saturer l'amplificateur pour une meilleure suppression de bruit tout en évitant en grande partie la dégradation causé par le post-filtrage. Nous avons expérimentalement démontré un système WDM dense de 8 x 10 Gbps avec une source incohérente et un SOA en saturation. Une autre contribution originale de ce travail est le développement d'un outil de simulation pour les SOAs qui est numériquement plus efficace et léger que les modèles connus à ce jour. Nous avons donc développé un modèle théorique simple, pouvant être implémenté par diagramme block, dans le but de simuler les performances des hens de communications WDM. Notre modèle démontre une bonne concordance avec les résultats expérimentaux ainsi qu'une diminution de temps de calcul de l'ordre de 20 fois. Finalement, lors de la dernière partie de ces travaux, nous nous sommes occupés de mesurer, de façon précise, le temps de recouvrement du gain dans un SOA. Le temps de recouvrement des porteurs dans un SOA est un des paramètres les plus importants qui sont à l'origine du phénomène de nettoyage de bruit et qui régissent le comportement ainsi que les dynamiques de l'amplificateur. Nous avons étudié en particulier, la dépendance de ce temps de recouvrement r de la longueur d'onde. Pour le SOA utilisé lors de notre étude expérimentale, nous avons démontré que r dépendait de la longueur d'onde de façon similaire au spectre de gain. Ces mesures ont été possibles grâce au développement d'un nouveau dispositif de mesure pompe/sonde, qui permettait de mesurer le recouvrement du gain pour une pompe et une sonde à la même longueur d'onde et ayant le même état de polarisation

Design Of Genetically-Encoded Ca2+ Probes With Rapid Kinetics For Subcellular Application

The spatio-temporal attributes of intracellular calcium (Ca2+) transients activate various biological functions. These Ca2+ signaling events are triggered extracellularly through different stimuli and controlled intracellularly by the major Ca2+ storage organelle and by numerous Ca2+ pumps, channels, and Ca2+ binding proteins. Ca2+ transients can be significantly altered as a result of defects with signal modulation, leading to different diseases. Because of the fragility and intricacy of the Ca2+ signaling system, with the endo- and sarcoplasmic reticulum at the center, genetically-encoded Ca2+ probes that have been optimized for mammalian expression and fast kinetics are needed to observe global and local Ca2+ changes in different cells. Here, we first report the crystal structure determination of our genetically-encoded Ca2+ sensor CatchER which utilizes EGFP as the scaffold protein. Crystal structures of CatchER were resolved in the Ca2+-free, Ca2+-loaded, and gadolinium-loaded forms at 1.66, 1.20, and 1.78 Å, respectively. Analysis of all three structures established conformational changes in T203 and E222 produce the varying ratios of the neutral and anionic chromophore reflected in the absorbance spectrum where Ca2+ stabilizes the anionic chromophore and enhances the optical output. Since CatchER has miniscule fluorescence when expressed at 37˚C in mammalian cells, we enhanced its brightness by improving the folding at 37˚C, facilitating better chromophore formation. The resulting mutants are the CatchER-T series of Ca2+ sensors with CatchER-T’ having the most improvement in brightness at 37˚C. We also introduced the N149E mutation in the binding site to alter the Kd along with the brightness mutations. The resulting mutants were characterized and found to have weaker Kds compared to wild-type CatchER, similar quantum yields, and altered ratios of the neutral and anionic chromophore in the apo form. Then, CatchER-T’ was applied in situ to monitor Ca2+ changes globally in the ER/SR of C2C12, HEK293, and Cos-7 cells. A new construct consisting of CatchER-T’ and JP-45 was created to monitor local Ca2+ dynamics in the SR lumen of skeletal muscle cells. The results showed a difference between global and local SR Ca2+ release. We also examined the potential and spectroscopic properties to utilize some of our sensors in T cells to monitor the magnesium (Mg2+) flux in immune cells with faulty MagT1 receptors to understand the role of Mg2+ in the immune response