Rozprawy doktorskie na temat „Quantum Dot - Cellular Imaging”

Cancer, a generic group of diseases, can affect distant sites of the human body to cause sever health consequences. According to the World Health Organization, 9.8 million people died from cancer in 2015 worldwide, about 1600 people per day. More seriously, the number of new cases is expected to increase 70% by 2030 to cause 12 million deaths globally. Early detection, accurate diagnosis and effective treatment are crucial in increasing cancer survival rates and reducing patients’ suffering. In particular, precise cancer positioning that can guide surgery, chemotherapy and radiotherapy has important clinical significance in successful treatment. The nanotechnology-based diagnosis (e.g. QD/QR-bioconjugate probes) and/or treatment of different cancers have received great attention, which is growing to be a promising field in medical research. Over the past 20 years, not only have QD based probes been widely used in developing immunoassays, cellular labeling, cellular imaging, tissue imaging and in vivo imaging, but also being extended to researches such as the drug target and drug delivery system. And this thesis is composed of two parts: Part I An ultra-efficient ligand-exchange protocol (UCEP) to render commercial hydrophobic QDs completely water-soluble using >50-fold less of the air-stable lipoic acid (LA) based functional ligands with a rapid in situ reduction by tris(2-carboxylethyl phosphine, TECP) has been developed. The resulting water-soluble QDs are compact (Dh <10 nm), bright (retaining >90% of original fluorescence), resisting nonspecific adsorption and displaying good stabilities in biological buffers even with high salt contents (e.g. 2 M NaCl), making them well-suited for cell imaging and ratiometric biosensing. A DHLA-zwitterion capped QD prepared by the UCEP is readily biofunctionalized with hexa-histidine (His8)-tagged small antibody mimetic proteins (also known as Affimers), allowing for rapid, ratiometric detection of its target protein down to 5 pM via the QD-sensitized Förster resonance energy transfer (FRET) readout signal. Moreover, compact biotin functionalized QDs are prepared by a facile, one-step cap-exchange process for ratiometric quantitation detection of 5 pM protein such as NeutrAvidin as well as for fluorescence imaging of target model cancer cells. Part II A stable, water-soluble rod-shaped fluorescence semiconductor nanocrystal (CdSe/CdS core/shell quantum rod, QR) was made by an efficient cap exchange protocol as described in Part I. However, in most cases the fluorescence of the cap-exchanged QR was almost quenched, hindering their biomedical applications. Herein I have solved this problem by discovering a simple method that allows for efficient recovery of the QR quantum yield, making them suitable for biological applications. The resulting water-soluble QRs are compact (Dh < 20 nm), bright (recovering to > 67% of original fluorescence), resisting nonspecific adsorption and displaying good stabilities in biological buffers, making them well-suited for ratiometric biosensing. After tris(2-carboxylethyl phosphine, (TECP) reduction, a dihydrolipoic acid-zwitterion ligand (DHLA-ZW) capped QR was self-assembled with (His8)-tagged anti-yeast SUMO non-antibody binding proteins (nABPs), allowing for ratiometric detection of its target protein down to 5 pM by the QR-sensitized Förster resonance energy transfer (FRET) signal. Furthermore, compact biotin functionalized QRs are prepared by a facile, one-step cap-exchange process for ratiometric quantitation of labelled neutravidin down to 5 pM. Such sensitivity is among the very best for QR-FRET based biosensors.

Les conjugués QD-sdAbs sont des nano-sondes qui associent un quantum dot (QD) et des anticorps de domaine simple (sdAbs). Ces nano-sondes fluorescentes permettent des immunomarquages sur coupes tissulaires et sur cellules. L’objectif de ce travail est de montrer l’intérêt de l’excitation multi-photonique pour la détection et la localisation très spécifiques de biomarqueurs tumoraux.L’excitation multi-photonique des nano-sondes QD570-sdAb anti-CEA a été étudiée, sur coupes d’appendice et de carcinome du côlon humains pour optimiser le rapport signal/auto-fluorescence. L’utilisation du QD comme capteur d’énergie d’excitation dans un modéle de FRET QD-fluorophore organique a été démontré. Un modéle innovant pour une détéction ultra spécifique du CEA sur cellules MC38 CEA par double immunomarquage spécifique pour un transfert d’énergie résonnant entre QD et Alexa Fluor à été mis en oeuvre.Les résutats montrent l’intérêt de l’excitation multi-photonique par rapport à l’excitation à 458,9 nm pour la discrimination et l’optimisation du rapport signal/auto-fluorescence. Il est 40 fois supérieur en excitation à 800 nm qu’à 458,9 nm sur les coupes étudiées.L’utilisation des conjugués QD556-sdAb anti-CEA et d’un anticorps monoclonal permet un double immunomarquage du CEA membranaire sur cellules MC38 CEA. L’utilisation du QD comme nano-capteur d’énergie d’excitation multi-photonique permet une séléctivité d’excitation et un FRET entre QD et Alexa Fluor. Ce schéma permet une détéction spectrale aisée du FRET et une localisation très spécifique et sensible du CEA membranaire. Ceci est conforté par la diminution du temps de déclin du QD556 donneur d’énergie non radiative
The QD-sdAbs conjugates are nano-sensors that combine a quantum dot (QD) and single domain antibodies (sdAbs). These fluorescent nanoprobes allow immunostaining on tissue sections and cells. The objective of this work is to show the interest of the multi-photon excitation for the detection and highly specific location of tumor biomarkers.Multi-photon excitation of anti CEA QD570-sdAb nanoprobes was investigated on human appendix and colon carcinoma slides for specifical detection and an optimization of the signal/auto-fluorescence emission ratio. The use of QD as excitation energy sensor for a QD-organic fluorophore FRET model has been shown. An innovative model for ultra-specific detection of CEA on MC38 CEA membrane cells by double immunostaining for a resonant energy transfer between QD and Alexa Fluor has been implemented.Our results shows the great interest of the multi-photon excitation compared to 458.9 nm excitation for discrimination and optimization of the signal / autofluorescence. It is 40 times higher at 800 nm two photon excitation has 458.9 nm one photon excitation on the studied sections.The use of conjugated QD556-sdAb anti-CEA and a conventional monoclonal antibody allows a double immunostaining on CEA on MC38 CEA membrane cells. The QD is use as multi-photon excitation energy nano-sensor enables an excitation selectivity and FRET between QD and Alexa Fluor. This configuration enables easy spectral detection of FRET and a very specific and sensitive location of membrane CEA. This is reinforced by the decrease in decay time of QD556 as donor of non radiative energy

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2006.
Vita.
Includes bibliographical references.
Quantum dot-based fluorescent probes were synthesized and applied to biological imaging in two distinct size regimes: (1) 100-1000 nm and (2) < 10 nm in diameter. The larger diameter range was accessed by doping CdSe/ZnS or CdS/ZnS quantum dots (QDs) into shells grown on the surfaces of pre-formed sub-micron SiO2 microspheres. The smaller diameter range was accessed with two different materials: very small InAs/ZnSe QDs and CdSe/ZnS QDs, each water solubilized with small molecule ligands chosen for their ability not only to stabilize QDs in water but also to minimize the total hydrodynamic size of the QD-ligand conjugates. Indium arsenide QDs were synthesized because nanocrystals of this material can be tuned to fluoresce in the near infrared (NIR) portion of the electromagnetic spectrum, especially in the 700-900 nm window where many tissues in the body absorb and scatter minimally, while maintaining core sizes of 2 nm or less. The QD-containing microspheres were used to image tumor vasculature in living animals, and to generate maps of size-dependent extravasation. With subcutaneously delivered nAs/ZnSe QDs, multiple lymph node mapping was demonstrated in vivo for the first time with nanocrystals. When administered intravenously, < 10 nm QDs escaped from the vasculature, or were efficiently cleared from circulation by the kidney. Both of these behaviors, previously unreported, mark key milestones in the realization of an ideal fluorescent QD probe for imaging specific compartments in vivo. Also presented in this thesis is the growth of single-crystalline cobalt nanorods through the oriented attachment of spherical cobalt nanocrystal monomers.
(cont.) When administered intravenously, < 10 nm QDs escaped from the vasculature, or were efficiently cleared from circulation by the kidney. Both of these behaviors, previously unreported, mark key milestones in the realization of an ideal fluorescent QD probe for imaging specific compartments in vivo. Also presented in this thesis is the growth of single-crystalline cobalt nanorods through the oriented attachment of spherical cobalt nanocrystal monomers.
by John P. Zimmer.
Ph.D.

Quantum-Dot Cellular Automata (QCA) is being investigated as a possible alternative for encoding and processing binary information in an attempt to realize dramatic improvements in device density and processing speed over conventional CMOS design. The binary information is encoded in the locations of two excess electrons in a system of four quantum dots. The dots are arranged with each on a corner of a square, and electrons are able to quantum-mechanically tunnel between dots. Each set of four dots and two excess electrons constitutes a QCA cell. Coulomb repulsion ensures that the electrons will tend to occupy antipodal sites, giving two possible polarizations, or lowest energy ground states for a QCA cell. The electrons would tend to align along one diagonal or the other. Arrangements of QCA cells can be used to pass along input binary information and perform necessary logic operations on the input signal.When electrons tunnel back and forth between dots, it is possible they will occupy excited states in the dots. Two undesirable effects result from this: 1) Energy will be dissipated to the environment and cause thermal heating, and 2) it is possible a cell could become locked in a metastable state, which may be a local energy minimum, but is not one of the ground state polarizations we desire. Through the modulation of the heights of the inter-dot potential barriers, it would be possible to allow electrons to more easily tunnel between dots. This would help prevent the system from reaching excited states. The time variance in the heights of the potential barriers must be greater than the time it takes for the electrons to tunnel between dots, thus, effectively clocking the QCA device.We present theoretical studies of controlling the inter-dot potential barriers in a QCA device using an electric field due to electrostatically charged rods. The amount of charge on the rods is varied in time to increase and decrease the electric field, which will raise and lower the inter-dot potential barriers as desired. Different arrangements of rods provide different time-dependent behavior in the electric field, which may be useful depending on the arrangements of QCA cells required to make a logic device.
Department of Physics and Astronomy

To have a useful QCA device it is first necessary to study how to control data flow in a device, then study how temperature and manufacturing defects will affect the proper output of the device. Theoretically a "quantum wire" of perfectly aligned QCA cells at zero Kelvin temperature has been examined. However, QCA processors will not be operating at a temperature of zero Kelvin and inherently the manufacturing process will introduce defects into the system. Many different types of defects could occur at the device level and the individual cell level, both kinds of defects should be examined. Device defects include but are not limited to linear and/or rotational translation, and missing or extra cell(s). The internal cell defects would include an odd sized cell, and one or more miss-sized or dislocated quantum dot(s). These defects may have little effect on the operation of the QCA device, or could cause a complete failure. In addition, the thermal effect on the QCA devices may also cause a failure of the device or system. The defect and thermal operating limit of a QCA device must be determined.In the present investigation, the thermal and defect tolerance of clocked QCA devices will be studied. In order to study tolerance of QCA devices theoretical models will be developed. In particular, some existing computer simulation programs will be studied and expanded.
Department of Physics and Astronomy

We present a theoretical study of quasi-adiabatic clocking and thermal effect in Quantum-dot Cellular Automata (QCA). Quasi-adiabatic clocking is the modulation of an inter-dot potential barrier in order to keep the QCA cells near the ground state throughout the switching process. A time-dependent electric field is calculated for arrays of charged rods. The electron tunneling between dots is controlled by raising and lowering a potential barrier in the cell.A quantum statistical model has been introduced to obtain the thermal average of polarization of a QCA cell. We have studied the thermal effect on QCA devices. The theoretical analysis has been approximated for a two-state model where the cells are in one of two possible eigenstates of the cell Hamiltonian. In general, the average polarization of each cell decreases with temperature and the distance from the driver cells. The results demonstrate the critical nature of temperature dependence for the operation of QCA.
Department of Physics and Astronomy

Photon detectors based on single-crystalline materials are of great interest for high performance imaging applications due to their low noise and fast response. The major detector materials for sensing in the long-wavelength infrared (LWIR) band (8-14 µm) are currently HgCdTe (MCT) and AlGaAs/GaAs quantum wells (QW) used in intraband-based quantum-well infrared photodetectors (QWIPs). These either suffer from compositional variations that are detrimental to the system performance as in the case of MCT, or, have an efficient dark current generation mechanism that limits the operating temperature as for QWIPs. The need for increased on-wafer uniformity and elevated operating temperatures has resulted in the development of various alternative approaches, such as type-II strained-layer superlattice detectors (SLSs) and intraband quantum-dot infrared photodetectors (QDIPs). In this work, we mainly explore two self-assembled quantum-dot (QD) materials for use as the absorber material in photon detectors for the LWIR, with the aim to develop low-dark current devices that can allow for high operating temperatures and high manufacturability. The detection mechanism is here based on type-II interband transitions from bound hole states in the QDs to continuum states in the matrix material. Metal-organic vapor-phase epitaxy (MOVPE) was used to fabricate (Al)GaAs(Sb)/InAs and In(Ga)Sb/InAs QD structures for the development of an LWIR active material. A successive analysis of (Al)GaAs(Sb) QDs using absorption spectroscopy shows strong absorption in the range 6-12 µm interpreted to originate in intra-valence band transitions. Moreover, record-long photoluminescence (PL) wavelength up to 12 µm is demonstrated in InSb- and InGaSb QDs. Mesa-etched single-pixel photodiodes were fabricated in which photoresponse is demonstrated up to 8 µm at 230 K with 10 In0.5Ga0.5Sb QD layers as the active region. The photoresponse is observed to be strongly temperature-dependent which is explained by hole trapping in the QDs. In the current design, the photoresponse is thermally limited at typical LWIR sensor operating temperatures (60-120 K), which is detrimental to the imaging performance. This can potentially be resolved by selecting a matrix material with a smaller barrier for thermionic emission of photo-excited holes. If such an arrangement can be achieved, type-II interband InGaSb QD structures can turn out to be interesting as a high-operating-temperature sensor material for thermal imaging applications.

QC 20130521

Quantum-dot Cellular Automata (QCA) is a new paradigm for computation that utilizes polarization states instead of using current switching. It is being studied because of the realization of the quickly approaching limitation of the current CMOS technology. The location of two excess electrons located within four or five quantum dots on a particular cell can transmit the binary information. These dots are located in the corner of a square cell, and if there is a fifth dot it is located in the center. The electrons are allowed to tunnel freely among the dots, but are restricted from tunneling between neighboring cells. Because of the interaction between the electrons, they will anti-align within the cell giving one of two particular configurations. This configuration can be transmitted to neighboring cells. In other words, data is flowing.We present a numerical study of the fabrication defect's influence on Quantum-dot Cellular Automata (QCA) operation. The statistical model that has been introduced simulates the random distribution of positional defects of the dots within cells and of cells within arrays. Missing dots within a QCA cell structure have also been studied.We have studied specific non-clocked QCA devices using the Inter-cellular Hartree Approximation, for different temperatures. Parameters such as success rate and breakdown displacement factor were defined and calculated numerically. Results show the thermal dependence of the breakdown displacement factor of the QCA devices. It has been shown, that the breakdown displacement factor decreases with increasing temperature. As expected, multiple defects within the same QCA array have shown a reduction in success rate greater than that of a single defect influencing the system.
Department of Physics and Astronomy

Quantum-dot Cellular Automata (QCA) are proposed models of quantum computation, which are articulated in analogy to Von Neumann's conventional models of cellular automata. These models are worthy for the architecture of ultra-dense low-power and high-performance digital circuits. Efficient solutions have recently been proposed for several arithmetic circuits, such as adders, multipliers, and comparators. Since the design of digital circuits in QCA still poses several challenges, novel implementation strategies and methodologies are highly desirable. This project demonstrates a new design approach oriented to the implementation of binary comparators using QCA. This strategy is implemented for designing various architectures of binary comparator. With respect to existing counterparts, the comparators proposed here exhibit significantly higher speed and reduced overall area.

Semiconductor industry seems to approach a wall where physical geometry and power density issues could possibly render the device fabrication infeasible. Quantum-dot Cellular Automata (QCA) is a new nanotechnology that claims to offer the potential of manufacturing even denser integrated circuits, which can operate at high frequencies and low power consumption. In QCA technology, the signal propagation occurs as a result of electrostatic interaction among the electrons as opposed to flow to the electrons in a wire. The basic building block of QCA technology is a QCA cell which encodes binary information with the relative position of electrons in it. A QCA cell can be used either as a wire or as logic. In QCA, the directionality of the signal flow is controlled by phase-shifted electric field generated on a separate layer than QCA cell layer. This process is called clocking of QCA circuits. The logic realization using regular structures such as PLAs have played a significant role in the semiconductor field due to their manufacturability, behavioral predictability and the ease of logic mapping. Along with these benefits, regular structures in QCA's would allow for uniform QCA clocking structure. The clocking structure is important because the pioneers of QCA technology propose it to be fabricated in CMOS technology. This thesis presents a detailed design implementation and a comparative analysis of logic realization using regular structures, namely Shannon-Lattices and PLAs for QCAs. A software tool was developed as a part of this research, which automatically generates complete QCA-Shannon-Lattice and QCA-PLA layouts for single-output Boolean functions based on an input macro-cell library. The equations for latency and throughput for the new QCA-PLA and QCA-Shannon-Lattice design implementations were also formulated. The correctness of the equations was verified by performing simulations of the tool-generate layouts with QCADesigner. A brief design trade-off analysis between the tool-generated regular structure implementation and the unstructured custom layout in QCA is presented for the full-adder circuit.

Field-Coupled nanocomputing (FCN) paradigms offer fundamentally new approaches for digital computing without involving current transistors. Such paradigms perform computations using local field interactions between nanoscale building blocks which are organized with purposes. Among several FCN paradigms currently under active investigation, the Molecular Quantum-dot Cellular Automata (MQCA) is found to be the most promising and its unique features make it attractive as a candidate for post-CMOS nanocomputing. MQCA is based on electrostatic interactions among quantum cells with nanometer scale eliminating the need of charge transportation, hence its energy consumption is significantly decreased. Meanwhile it also possesses the potential of high throughput if efficient pipelining of information propagation is introduced. This could be realized adopting external clock signals which precisely control the adiabatic switching and direction of data flow in MQCA circuits. In this work, in order to model MQCA as electronic devices and analyze its information propagation with clock taken into account, an effective algorithm based on ab-initio simulations and modelling of molecular interactions has been applied in presence of a proposed clock mechanism for MQCA, including the binary wire, the wire bus and the majority voter. The quantitative results generated depict compelling clocked information propagation phenomena of MQCA devices and most importantly, provide crucial feedback for future MQCA experimental implementations

This work reports the development and spectroscopic studies of blinking-suppressed compact quantum dots. It is shown that a linearly graded alloy shell can be grown on a small CdSe core via a precisely controlled layer-by-layer process, and that this graded shell leads to a dramatic suppression of QD blinking both in organic solvents and in water. A substantial portion (over 25%) of the resulting QDs essentially does not blink (more than 99% of the time in the bright or “on” state). Theoretical modeling studies indicate that this type of linearly graded and relatively thin shells can not only minimize charge carrier access to surface traps, but also reduce accumulated lattice strains and defects at the core/shell interface, both of which are believed to be responsible for carrier trapping and QD blinking. Further, the biological utility of blinking-suppressed QDs by using both polyethylene glycol (PEG)-based and multidentate capping ligands is evaluated, and the results show that their optical properties are maintained regardless of surface coatings or solvating media, and that the blinking-suppressed QDs can provide continuous trajectories in live cell receptor tracking studies.

Quantum-dot Cellular Automata (QCA) provides a basis for classical computation without transistors. Many simulations of QCA rely upon the Intercellular Hartree Approximation (ICHA), which neglects the possibility of entanglement between cells. While simple and computationally efficient, the ICHA’s many shortcomings make it difficult to accurately model the dynamics of large systems of QCA cells. On the other hand, solving a full Hamiltonian for each circuit, while more accurate, becomes computationally intractable as the number of cells increases. This work explores an intermediate solution that exists somewhere in the solution space spanned by the ICHA and the full Hamiltonian. The solution presented in this thesis builds off of the work done by Toth et al., and studies the role that correlations play in the dynamics of QCA circuits. Using the coherence-vector formalism, we show that we can accurately capture the dynamical behaviour of QCA systems by including two-cell correlations. In order to capture the system’s interaction with the environment, we introduce a new method for computing the steady-state configurations of a QCA system using well-known stochastic methods, and use the relaxation-time approximation to drive the QCA system to these configurations. For relatively-low temperatures, we show that this approach is accurate to within a few percent, and can be computed in linear time. QCADesigner, the de facto simulation tool used in QCA research, has been used and cited in hundreds of papers since its creation in 2004. By implementing computationally accurate and efficient algorithms to the existing simulation engines present in QCADesigner, this research is expected to make a significant contribution to the future of QCA circuit design. In particular, researchers in the field will be able to identity a whole new set of design rules that will lead to more compact circuit design, realistic clocking schemes, and crosstalk-tolerant layouts. In addition, proper estimates on the power dissipation, pipelining, and limitations of room temperature operation will now be feasible for QCA circuits of any size; a huge step forward for QCA design.
Applied Science, Faculty of
Electrical and Computer Engineering, Department of
Graduate

I present a theoretical study of fault tolerant properties in Quantum-dot Cellular Automata (QCA) devices. The study consists of modeling and simulation of various possible manufacturing, fabrication and operational defects. My focus is to explore the effects of temperature and dot displacement defects at the cell level of various QCA devices. Results of simple devices such as binary wire, logical gates, inverter, cross-over and XOR will be presented. A Hubbard-type Hamiltonian and the inter-cellular Hartree approximation have been used for modeling the QCA devices. Random distribution has been used for defect simulations. In order to show the operational limit of a device, defect parameters have been defined and calculated. Results show fault tolerance of a device is strongly dependent on the temperature as well as on the manufacturing defects.
Cell design -- Basic logic gates -- The exclusive or gate.
Department of Physics and Astronomy

In recent years, semiconductor quantum dots (QDs) have arisen as a new class of fluorescent probes that possess unique optical and electronic properties well-suited for single-molecule imaging of dynamic live cell processes. Nonetheless, the large size of conventional QD-ligand constructs has precluded their widespread use in single-molecule studies, especially on cell interiors. A typical QD-ligand construct can range upwards of 35 nm in diameter, well exceeding the size threshold for cytosolic diffusion and posing steric hindrance to binding cell receptors. The objective of this research is to develop tagging strategies that allow QD-ligand conjugates to specifically bind their target proteins while maintaining a small overall construct size. To achieve this objective, we utilize the HaloTag protein (HTP) available from Promega Corporation, which reacts readily with a HaloTag ligand (HTL) to form a covalent bond. When HaloTag ligands are conjugated to size-minimized multidentate polymer coated QDs, compact QD-ligand constructs less than 15 nm in diameter can be produced. These quantum dot-HaloTag ligand (QD-HTL) conjugates can then be used to covalently bind and track cellular receptors genetically fused to the HaloTag protein. In this study, size-minimized quantum dot-HaloTag ligand conjugates are synthesized and evaluated for their ability to bind specifically to purified and cellular HTP. The effect of QD-HTL surface modifications on different types of specific and nonspecific cellular binding are systematically investigated. Finally, these QD-HTL conjugates are utilized for single-molecule imaging of dynamic live cell processes. Our results show that size-minimized QD-HTLs exhibit great promise as novel imaging probes for live cell imaging, allowing researchers to visualize cellular protein dynamics in remarkable detail.

Molecular quantum-dot cellular automaton (QCA) offers an alternative paradigm for computing at the nano-scale. Such Q C A circuits require an external clock, which can be generated using a network of submerged electrodes, to synchronize information flow, and provide the required power to drive the computation. In this thesis, the effect of electrode separation and applied potential on the likelihood of different Q C A cell states of molecular cells located above and in between two adjacent electrodes is analysed. Using this analysis, estimates of operational ranges are developed for the placement, applied potential, and relative phase between adjacent clocking electrodes to ensure that only those states that are used in the computation, are energetically favourable. Conclusions on the trade-off between cell size and applied clocking potential are drawn and the temperature dependency on the operation of fundamental Q C A building blocks is considered. Lastly, the impact of random phase shifts on the underlying clocking network is investigated and a set of universal Q C A building blocks is classified into distinct groups based on their sensitivity to these random phase shifts.
Applied Science, Faculty of
Electrical and Computer Engineering, Department of
Graduate

There has been significant progress in the optical resolution of microscopes over the last two decades. However, the majority of currently used methods (e.g. STED, PALM, STORM) have a number of drawbacks, including high intensities of light that result in damage to living specimens in STED, and long data acquisition time leading to limitations on live-cell imaging. Therefore, there is a niche for faster image acquisition at lower intensities while maintaining resolution beyond the diffraction limit. Here, we have developed a new methodology - Quantum Dot-based Optical Spectral Separation (QDOSS) - which relies on using Quantum Dots (QDs) as fluorophores, and on their separation and localisation based on their spectral signatures. We utilise the key advantages of QDs over the usual organic fluorophores: broad excitation, narrow emission spectra and high resistance to photobleaching. Besides, since QDOSS is based on spectral differences for separation, QDs can be deterministically localised in a relatively short time - milliseconds and, potentially, microseconds. Last but not least, QDOSS is suitable for obtaining super-resolution images using a standard confocal fluorescence microscope equipped with a single laser excitation wavelength and capable of spectral signal separation (e.g. Leica TCS SP series or Zeiss LSM series). First, we demonstrated resolution down to 60 nm using triangular DNA origami as a reference. Furthermore, we labelled and imaged the alpha-tubulin structure in HEK293T cells. We showed that using a mixture of standard off-the-shelf QDs of different sizes, resolution down to 40 nm could be achieved via spectroscopic separation of QDs. Finally, we demonstrated that QDOSS could also be used for multicolour imaging of synaptic proteins distributed around synapsis in neurons within diffraction limit. All in all, we believe that these features of QDOSS make it a potential method for long-term live super-resolution imaging, which is going to have a high impact in biological sciences.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Materials Science and Engineering, 2018.
Cataloged from PDF version of thesis.
Includes bibliographical references.
The short-wave infrared region (SWIR; 1000-2000 nm) has excellent properties for in vivo imaging: low autofluorescence, reduced scattering, and little light absorption by blood and tissue. However, broad adoption of SWIR imaging in biomedical research is hampered by the availability of versatile and bright contrast materials. Quantum dots (QDs) are bright, compact SWIR emitters with narrow size distributions and emission spectra, qualities that make them ideal for labeling and multiplex SWIR imaging. Nevertheless, SWIR QDs have limited applications due to the shortcomings of established ligand systems. Established ligands result in QD probes with limited colloidal stability, large size and broad size distribution, or all three limitations. To address these limitations, we turned to polymeric ligands, beginning with the polymeric imidazole ligand (PIL) initially developed for visible-emitting CdSe/CdxZn₁₋xS QDs with L-type native ligands. We studied ligand exchange with PIL and InAs/CdSe/CdS SWIR QDs with native X-type ligands in a variety of conditions but only saw limited exchange. Our results combined with reports in the literature suggest that the mechanism of X-to-L ligand exchange is not amenable to polymeric ligands. These results led us to the concept of ligand-type matching: for straightforward exchange, QD native ligands should be the same type as the binding groups on the polymer. Thus, we synthesized InAs/CdSe/ZnS with L-type native ligands, which exchanged readily with PIL to produce probes with (<14 nm hydrodynamic diameter, Hd). We also synthesized a new ligand that is compatible with oleate-capped QDs: the polymeric acid ligand (PAL), which features carboxylic acids as the binding group and PEG₁₁ chains to solubilize the QD-ligand construct. We exchanged PAL with oleate-capped PbS and PbS/CdS QDs, resulting in compact probes ( <11 nm Hd) with narrow size distribution. The small size and narrow size distribution of these constructs are preserved for several months when stored in isotonic saline solution in air, addressing the size and stability limitations of existing ligand systems for SWIR QDs. Our constructs are bright in vivo and to demonstrate their suitability for imaging, we performed whole-body imaging as well as lymphatic imaging, including visualization of lymphatic flow.
by Daniel Mauricio Montana Fernandez.
Ph. D.

The defects and fault tolerance study is essential in the QCA devices in order to know its characteristics. Knowing the characteristics, one can understand the flow of information in a QCA system with and without manufacturing and operational defects. The manufacturing defects could be at device level or cell level. At the device level, the cell could be rotated, displaced vertically or horizontally, the cell could be missing or the size of the cell could be different. At the cell level, there could be a missing dot, dot could be displaced from its position or the size of the dots could be different. The operational defects are due to its surrounding, such as temperature or stray charge. Each of these defects and fault tolerances can be studies in detail in order to find the optimum working conditions where the information can be safely transmitted to the appropriate locations in the device.The theoretical studies have shown that at absolute temperature and without any defect, the QCA devices are operational. But it is almost impossible to manufacture a perfect or defect free device, and also it is impractical to think about operating a system at absolute zero temperature environment.Therefore, it is important to investigate the fault tolerant properties with defects and higher temperatures to see how far the QCA device can operate safely. Many studies have been done to investigate the fault tolerant properties in QCA devices. However, these studies have not completely exhausted the study of defects and temperature effects. In this study, the dot displacement and missing dots with temperature effects are investigated for the basic QCA devices and a Full Adder. In order to study fault tolerant properties, the existing theoretical model and computer simulation programs have been expanded and used. The defect characteristics have been simulated using normal distribution.
Department of Physics and Astronomy

Quantum-dot cellular automata is an emerging technology for digital computation that follows the More than Moore trends and aims to the simultaneous reduction of both device size and power consumption. In particular, the basic QCA device is a cell made of dots and in which a bunch of free charges are allowed to move without leaving the cell itself. Depending on which dots the free charges occupy inside the cell (called also charge localization inside the cell) the binary information could be encoded and the interaction between nearby cells is performed by the electrostatic interaction. This means that no current flows between QCA devices, thus strongly reducing the power dissipation. Regarding the physical implementation of the QCA technology, different solutions were proposed in literature (semiconductor, metallic, magnetic and molecular) and in some cases (metallic and magnetic) a prototype or more advanced circuits were developed. Among all the implementations proposed, molecular QCA is the most promising, since high operating frequencies (THz) and non cryogenic work temperature (room temperature) could be achieved due to the nanometer size of a molecular system. However, a molecular prototype still does not exist and in literature only preliminary attempts to demonstrate the molecular QCA feasibility were carried out. The main difficulties to achieve a molecular prototype arise from the lack of control in the fabrication processes at the molecular scale and the current resolution of the electronic instruments to read the state of a single molecular QCA cell. The work of this thesis focused on the characterization from an electronic point of view of a molecule synthesized ad hoc for QCA computing and called bis-ferrocene. The molecule was synthesized by a group of the chemical department of the University of Bologna, in collaboration with the ST Microelectronics company. This work aimed to evaluate the bis-ferrocene properties as QCA device both at the equilibrium and in presence of a bias system. In addition, the interaction between nearby molecules was evaluated and the simulation of the simplest QCA circuit, a molecular wire, was performed. The methodology adopted to carry on this analysis come from the needs to model the bis-ferrocene molecule by means of some figures of merit that could be measured by electronic instrumentations. This is because in literature all the candidate molecules proposed for QCA were characterized using chemical quantities derived from mathematical approximations (energy levels and molecular orbitals). Moreover, all the steps of this work were performed with the aim to set-up an experimental demonstration of the QCA functionalities focusing on a bis-ferrocene wire. For this reasons, the choice of the bias system, the QCA circuit and the definition of a new methodology come from the experimental scheme studied in this work. In particular, the scheme proposed here focused on the experimental evaluation of the three main mechanism involved during QCA computation: how to force the two logic states at the input (write-in system), the interaction between molecules (information propagation) and, finally, the study of system able to recognize the charge localization inside the cell (read-out stage). In addition, given the results obtained during parallel experimental activities, a fault tolerance evaluation of the bis-ferrocene wire in presence of real fabrication defects was performed.

Quantum dots are fluorescent semiconductor nanocrystals that have unique optical properties such as high quantum yield and photostability. These nanoparticles are superior to organic dyes and fluorescent proteins in many aspects and therefore show great potential for both in vivo and in vitro imaging and drug delivery applications. However, cytototoxicity is still one of the major problems associated with their biological applications. The aim of this study is in vitro characterization and assessment of biological application potential of a novel silver sulfide quantum dot coated with mercaptopropionic acid (2-MPA). In vitro studies reported in this work were conducted on a mouse fibroblast cell line (NIH/3T3) treated with Ag2S/2-MPA quantum dots in 10-600 &mu
g/mL concentration range for 24 h. Various fluorescence spectroscopy and microscopy methods were used to determine metabolic activity, proliferation rate and apoptotic fraction of QD-treated cells as well as QD internalization efficiency and intracellular localization. Metabolic activity and proliferation rate of the QD treated cells were measured with XTT and CyQUANT®
cell proliferation assays, respectively. Intracellular localization and qualitative uptake studies were conducted using confocal laser scanning microscopy. Apoptosis studies were performed with Annexin V assay. Finally, we also conducted a quantitative uptake assay to determine internalization efficiency of the silver sulfide particles. Correlated metabolic activity and proliferation assay results indicate that Ag2S/2-MPA quantum dots are highly cytocompatible with no significant toxicity up to 600 &mu
g/mL treatment. Optimal cell imaging concentration was determined as 200 &mu
g/mL. Particles displayed a punctuated cytoplasmic distribution indicating to endosomal entrapment. In vitro characterization studies reported in this study indicate that Ag2S/2-MPA quantum dots have great biological application potential due to their excellent spectral and cytocompatibility properties. Near-infrared emission of silver sulfide quantum dots provides a major advantage in imaging since signal interference from the cells (autofluorescence) which is a typical problem in microscopic studies is minimum in this part of the emission spectrum. The results of this study are presented in an article which was accepted by Journal of Materials Chemistry. DOI: 10.1039/C2JM31959D.

Quantum dots (QDs) are increasingly attracting attention in recent years due to their potential in biological imaging and drug delivery applications. Despite their significant advantages over organic dyes and fluorescent proteins, cytotoxicity is still a major problem in live-cell QD labeling. In this work, in-vitro characterization of a novel CdTe/2MPA quantum dot capped with CdS-DMSA was conducted on human cervical cancer (HeLa) and mouse fibroblast (NIH/3T3) cell lines. Biocompatibility of this novel particle was evaluated in comparison to a commercial quantum dot (Qdot 565) and various QDs with CdTe core. Cytotoxicity of quantum dots was investigated using XTT and proliferation assays. Cellular internalization and localization of particles were studied using confocal laser scanning microscopy. For quantitative determination of internalization and intracellular QD stability, we also performed uptake and cadmium release assays. Optimal cell imaging concentration with CdTe-CdS/2MPA-DMSA was determined as 10-50 ug/mL in HeLa cells. Localization of the internalized QD particles was observed in the perinuclear region of the cells. XTT and proliferation assays provided identical viability results for the tested QDs. CdS-DMSA capping increased cytocompatibility of CdTe/2MPA by 15% in NIH/3T3 cells. Biocompatibility of this capped particle was further increased by 3-folds with pegylation. For pegylated CdTe-CdS/2MPA-DMSA and commercial Qdot 565, we have not observed QD-related cytotoxicity on NIH/3T3 cells following 24-hr QD exposure at 50 ug/mL. Our in-vitro characterization studies indicate that CdTe-CdS/2MPA-DMSA is a promising live-cell imaging probe which can be effectively excited in the visible range of the electromagnetic spectrum.

Biomedicine has recently exploited many nanotechnology platforms for the detection and treatment of disease as well as for the fundamental study of cellular biology. A prime example of these successes is the implementation of semiconductor quantum dots in a wide range of biological and medical applications, from in vitro biosensing to in vivo cancer imaging. Quantum dots are nearly spherical nanocrystals composed of semiconductor materials that can emit fluorescent light with high intensity and a strong resistance to degradation. The aim of this thesis is to understand the fundamental physics of colloidal quantum dots, to engineer their optical and structural properties for applications in biology and medicine, and to examine the interaction of these particles with biomolecules and living cells. Toward these goals, new synthetic strategies for colloidal nanocrystals have been developed, implementing a cation exchange method for independent tuning of size and fluorescence, and a bandgap engineering technique that utilizes mechanical strain imposed by coherent shell growth. In addition, stable nanocrystals have been prepared with ultrathin coatings (< 2 nm), 'amphibious' solubility, and broadly tunable bioaffinity, induced by self-assembly with polyhistidine-sequences on recombinant proteins. Finally, colloidal quantum dots have been studied in biological fluids and living cells in order to elucidate their interactions with biological systems. It was found that these interactions are strongly dependent on the size of the nanocrystal, and cytotoxic effects of these particles are largely independent of their composition of heavy metal atoms, demonstrating that the rule book for toxicology must be rewritten for nanomaterials.

Cancer therapies are often limited by bulk and cellular barriers to transport. Nanoparticle or chemotherapeutic compound intracellular transport has implications in understanding therapeutic effect and toxicity. The scope of this thesis was to study the intracellular transport of carbon nanohorns and to improve the efficacy of various chemotherapeutic agents through increased intracellular transport. In the first study, fluorescent probes (quantum dots) were conjugated to carbon nanohorns to facilitate the optical visualization of the nanohorns. These hybrid particles were characterized with transmission electron microscopy, electron dispersive spectroscopy and UV-VIS/FL spectroscopy. Their cellular uptake kinetics, uptake efficiencies, and intracellular distribution were determined in three malignant cell lines (breast – MDA-MB-231, bladder – AY-27, and brain – U87-MG) using flow cytometry and confocal microscopy. Intracellular distribution did not vary greatly between cell lines; however, the uptake kinetics and efficiencies were highly dependent on cell morphology. In the second study, the efficacy of various chemotherapeutic agents (i.e., doxorubicin, cisplatin, and carboplatin) was evaluated in AY-27 rat bladder transitional cell carcinoma cells. In the future, severe hyperthermia and chemothermotherapy (chemotherapy + hyperthermia) will also be evaluated. Doxorubicin and cisplatin compounds were more toxic compared to carboplatin. Hyperthermia has previously shown to increase the cellular uptake of chemotherapeutic agents; therefore, chemothermotherapy is expected to have synergistic effects on cell death. This work can then be translated to carbon nanohorn-based laser heating to generate thermal energy in a local region for delivery of high concentrations of chemotherapeutic agents. Although these two concepts are small pieces of the overall scope of nanoparticle-based therapies, they are fundamental to the advancement of such therapies.
Master of Science

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2011.
Cataloged from PDF version of thesis.
Includes bibliographical references (p. 199-217).
In vivo multimodal, multiplexed microscopy allows real-time observation of hematopoietic cells, their stem and progenitor cells and metastatic cancer cells in their native bone marrow (BM) environment. Multiplexing has made possible detailed studies of the BM's microarchitecture, which helps define the niche of these cells; it has nonetheless been limited by the paucity of suitable probes fluorescent in the near-infrared spectrum that is favored by tissue optics. This project attempts to address this problem by developing cellular and vascular fluorescent imaging probes comprised of semiconductor nanocrystals, or quantum dots (QDs), with tunable fluorescence between 65o-8oonm and exhibiting photostability, robust quantum yield and narrow fluorescence profiles that are critical for such applications. The synthesis of alloyed CdTexSe1 x QDs will be detailed in the thesis. Reproducibility and workability in subsequent steps are emphasized in the methods. Special attention is also paid to the difference between working with alloyed versus single semiconductor QDs, especially the need to achieve physical and spectral uniformity when composition and its gradient are also variable. The steps for creating biological probes from these QD fluorophores are also described. They include overcoating, water solubilization and functionalization for cellular uptake and vascular retention. Finally, the thesis returns to its motivation and reports novel methods, developed using NIR QD vascular imaging probes, for visualizing in vivo 3-D imaging data of the murine BM and characterizing the tissue's architecture. Measuring the Euclidean distance between BM osteoblasts and blood vessels is presented to exemplify a potential platform for describing the geographic relationships between cells, molecules and structural components in any tissue.
by Juwell Wendy Wu.
Ph.D.

Since its inception, Moore's Law has been a reliable predictor of computational power. This steady increase in computational power has been due to the ability to fit increasing numbers of transistors in a single chip. A consequence of increasing the number of transistors is also increasing the power consumption. The physical properties of CMOS technologies will make this powerwall unavoidable and will result in severe restrictions to future progress and applications. A potential solution to the problem of rising power demands is to investigate alternative low power nanotechnologies for implementing logic circuits. The intrinsic properties of these emerging nanotechnologies result in them being low power in nature when compared to current CMOS technologies. This thesis specifically highlights quantum dot celluar automata (QCA) and nanomagnetic logic (NML) as just two possible technologies. Designs in NML and QCA are explored for simple arithmetic units such as full adders and subtractors. A new multilayer 5-input majority gate design is proposed for use in NML. Designs of reversible adders are proposed which are easily testable for unidirectional stuck at faults.

Les boîtes quantiques (ou Quantum Dots en anglais - QD) sont une nouvelle génération de sondes polyvalentes pour la biologie, en particulier pour l’imagerie. Pour des applications de marquage des voies intra-cellulaires, les QDs peuvent être conjugués à des biomolécules telles que des acides nucléiques ou des protéines. En partant des travaux du LPEM portant sur le développement de ligands permettant la dispersion des QDs dans l’eau et leur fonctionnalisation, une nouvelle méthode de conjugaison de l'ADN sur les QDs a été développée dans cette thèse. Cette méthode utilise les motifs présents sur les polymères des QDs pour le greffage d'ADN. Les paramètres affectant cette réaction ont été étudiés et cette stratégie de couplage a été étendue à d'autres nanoparticules et biomolécules. En partant de ces QDs-ADN, des protéines modifiées ADN ont pu être attachées aux QDs en utilisant le principe d’hybridation de l’ADN. Les propriétés des conjugués ainsi générés ont été mises en évidence en utilisant la Transferrine (QD-ADN-Tf) et ces complexes ont été étudiés in vitro et in cellulo. Ces conjugués ont ensuite été utilisés pour le suivi de la dynamique des endosomes, exploitant ainsi pleinement le potentiel des QDs pour l’imagerie directe. Dans la dernière partie, des études supplémentaires sur les facteurs influençant la «performance biologique» des QDs ont été réalisées. Pour cela, une large gamme de ligands polymères développée par le groupe a été utilisée pour sonder l'interaction de la surface des QDs avec l'interface biologique. Des expériences biochimiques et cellulaires ont permis de démontrer que les QDs revêtus de divers polymères ont des comportements différents
Quantum dots (QD) are new generation of versatile probes for biology, particularly for bioimaging. For specific applications, QDs are conjugated to biomolecules such as nucleic acid or proteins and subsequently targeted to unique intra-cellular pathways. Building upon the state-of-the-art ligands for water-dispersible QDs developed by the lab, a novel and highly generalizable method to conjugate DNA to QD is developed in this thesis. This method employs thiols present on polymers on QDs for conjugation to maleimide-functionalized DNA. Extensive characterization of parameters affecting this reaction is carried out and the strategy is extended to other nanoparticles and biomolecules. Following this, a novel method to conjugate proteins to QD via DNA hybridization is discussed. Using a model protein Transferrin (Tf), the unique properties of thus generated QD-DNA-Tf conjugates are studied in-vitro and in-cellulo. These conjugates are subsequently used for tracking endosomal dynamics for up-to 20 minutes, exploiting the fullest potential of QDs for live imaging. In the last part, additional studies on factors affecting the ‘biological performance’ of QDs are carried out. Using a range of highly adaptable polymeric ligands developed by the group, interactions of surface-modified QDs with the biological interface are probed. Systematic biochemical and cellular experiments demonstrate that QDs coated with zwitterionic polymers have superior antifouling properties compared to poly(ethylene glycol)-based polymers and stability in diverse biological contexts

Ma thèse concerne le développent de systèmes ultra compactes auto-alignés et à faible coût intégréssur fibre optique monomode pour la collection fibrée de la luminescence locale. Dans un premiertemps, un axicon fibré auto-aligné (AXIGRIN) est proposé permettant de fournir la première imagerierésolue ultra-compacte fibrée de quantum dots PbS infrarouges. Ensuite, la première nano-imagerie(système entièrement fibrée) de quantum dots PbS uniques est réalisée à l’aide d’une nano-antenneà ouverture bowtie intégrée sur pointe fibrée. Enfin, le concept d’≪antenne cornet≫ nano-optiqueest proposé pour le couplage direct et efficace de la luminescence excitée par rayons X à une fibreoptique, dans le but de générer les premiers capteurs et dosimètres fibrés à rayons X
My thesis is devoted to develop ultra-compact, plug-and-play and low-cost single-mode optical fibersystems for in-fiber luminescence collection. First, a new fiber self-aligned axicon is proposed toprovide the first resolved infrared fluorescence imaging of PbS quantum dots in far field. Then,all-fiber near-field imaging of single PbS quantum dots is achieved by double resonance bowtienano-aperture antenna (BNA) with nanometer resolution. Finally, the concept of fiber nano-opticalhorn antenna is proposed for in-fiber X-ray excited luminescence out-coupling, with the purpose ofgenerating the first generation of fiber X-ray sensors and dosimeters

Reversible circuits are similar to conventional logic circuits except that they are built from reversible gates. In reversible gates, there is a unique, one-to-one mapping between the inputs and outputs, not the case with conventional logic. Also, reversible gates require constant ancilla inputs for reconfiguration of gate functions and garbage outputs that help in keeping reversibility. Reversible circuits hold promise in futuristic computing technologies like quantum computing, quantum dot cellular automata, DNA computing, optical computing, etc. Thus, it is important to minimize parameters such as ancilla and garbage bits, quantum cost and delay in the design of reversible circuits. The first contribution of this dissertation is the design of a new reversible gate namely the TR gate (Thapliyal-Ranganathan) which has the unique structure that makes it ideal for the realization of arithmetic circuits such as adders, subtractors and comparators, efficient in terms of the parameters such as ancilla and garbage bits, quantum cost and delay. The second contribution is the development of design methodologies and a synthesis framework to synthesize reversible data path functional units, such as binary and BCD adders, subtractors, adder-subtractors and binary comparators. The objective behind the proposed design methodologies is to synthesize arithmetic and logic functional units optimizing key metrics such as ancilla inputs, garbage outputs, quantum cost and delay. A library of reversible gates such as the Fredkin gate, the Toffoli gate, the TR gate, etc. was developed by coding in Verilog for use during synthesis. The third contribution of this dissertation is the set of methodologies for the design of reversible sequential circuits such as reversible latches, flip-flops and shift registers. The reversible designs of asynchronous set/reset D latch and the D flip-flop are attempted for the first time. It is shown that the designs are optimal in terms of number of garbage outputs while exploring the best possible values for quantum cost and delay. The other important contributions of this dissertation are the applications of reversible logic as well as a special class of reversible logic called conservative reversible logic towards concurrent (online) and offline testing of single as well as multiple faults in traditional and reversible nanoscale VLSI circuits, based on emerging nanotechnologies such as QCA, quantum computing, etc. Nanoelectronic devices tend to have high permanent and transient faults and thus are susceptible to high error rates. Specific contributions include (i) concurrently testable sequential circuits for molecular QCA based on reversible logic, (ii) concurrently testable QCA-based FPGA, (iii) design of self checking conservative logic gates for QCA, (iv) concurrent multiple error detection in emerging nanotechnologies using reversible logic, (v) two-vectors, all 0s and all 1s, testable reversible sequential circuits.

Los puntos cuánticos son nanopartículas semiconductoras que exhiben unas propiedades ópticas y electrónicas dependientes del tamaño. Debido a sus dimensiones en el rango de 1-100 nm, la relación superficie-volumen de estos materiales llega a ser enorme y sus estados electrónicos se vuelven discretos. Además, por el hecho de que el tamaño del nanocristal es más pequeño que el de un excitón, las cargas están espacialmente confinadas y esto eleva sus energías en lo que se conoce como confinamiento cuántico. Así, las propiedades optoelectrónicas están atribuidas a este efecto de confinamiento y esto permite calibrar la emisión. Los puntos cuánticos tienen una fluorescencia muy estable en comparación con los fluoróforos orgánicos que la pierden en cuestión de minutos. Además, y contrariamente a los fluoróforosogánicos, estos nanocristales tienen una amplia excitación y una emisión estrecha lo que los hace extremadamente aplicables para visualización multicolor. Calibrar la longitud de onda de emisión de los puntos cuánticos es simplemente una cuestión de calibrar su tamaño. Por todo estas razones, explicadas en el capítulo 1, los puntos cuánticos han desplazado a los fluoróforos convencionales como método para visualización en los últimos 5 años. Estos puntos cuánticos son tóxicos y necesitan ser encapsulados para prevenir envenenamiento por metales pesados cuando son usados en bioaplicaciones. Un trabajo previo en nuestro laboratorio, detallado en el capítulo 2, encontró un método de síntesis capa-a-capa para obtener nanocebollas, que consisten en varias capas de sílica rellenas con diferentes puntos cuánticos. Esta disposición es muy útil para tener diferentes colores, como si fuesen viales diferentes, confinados en unos pocos nanómetros. La matriz de sílica juega un papel importante para hacer a los puntos cuánticos solubles en agua y proteger su fotoluminiscencia del efecto de apagado, al menos en el rago de pH útil para las aplicaciones viológicas. Cuanto mayor es el grosor de la capa de sílica o mayor el número de capas, mayor es la protección ofrecida a los puntos cuánticos del interior. Basándonos en este principio, mostramos que estas nanocebollas, que nosotros llamamos nanocebollasmulticódigo (Quantum-onion-multicode, QOM), pueden ser usadas como sensor de pH, como se detalla en el capítulo 3. Se ha demostrado que la relación entre la intensidad de fotoluminiscencia entre dos poblaciones de puntos cuánticos se corresponde con el valor de pH del medio, haciendo que nuestro sistema confiera un carácter potencialmente aplicable como sensor ratiométrico de pH. Además, el desarrollo de puntos cuánticos dentro de espferas de sílica como sondas biomoleculares puede dar nuevas percepciones para paliar algunas limitaciones que tienen los puntos cuánticos por sí mismos de forma individual como marcadores biológicos, por ejemplo: mejor fotostabilidad si están dentro de la matriz, mayor superficie disponible para reacciones químicas, mejor capacidad de unión de las esferas, menor toxicidad, y mejor manipulación. Sin embargo, la mayoría de las nanopartículas orgánicas requieren de una funcionalización química con silano, tiol, amino, carboxilo u otros grupos con el fin de otorgarles propiedades aplicables para ser suministradas a células, como son: buena compatibilidad, gran afinidad entre el transportador y la carga, marcaje celular, estabilidad y mayor tiempo de circulación. En el pasado, los hidróxidos de doble capa, también conocidos como materiales tipo hidrotalcita o arcillas aniónicas, han sido la excepción a esta regla. Estos materiales consisten en capas de nanoláminas cargadas positivamente en estructura tipo brucita neutralizada por aniones en el espacio interlaminar. Desde un punto de vista médico, se han publicado muchos cambios interesantes con estos materiales para albergar fármacos y biomoléculas ya sea por intercambio aniónico o por proceso de delaminación-relapilamiento. Este tipo de material has sido usado para transportar puntos cuánticos solubles en agua hechos de teulro de cadmio (capítulo 4) o nanopalos (capítulo 5). Por una parte, las hidrotalcitas intercalan a los puntos cuánticos de teluro de cadmio muy rápido y no se necesitan delaminarse previamente. El material híbrido muestra una alta estabilidad en medio fisiológico a diferentes pH, convirtiéndolo en una herramienta de visualización aplicable para el diagnóstico en nanomedicina. Notoriamente, las propiedades ópticas de los puntos cuánticos sufrieron un salto hacia el azul, atribuido a diferentes factores, como se detalla en el capítulo 4. Sin embargo, este efecto es reversible tras la disolución de la transportador sólido, la hidrotalcita. Con lo que podemos decir que los puntos cuánticos de teluro de cadmio muestran un efecto de memoria óptica. Estas transiciones ópticas se detienen cuando rodeamos los puntos cuánticos de una capa de sílica, preparando puntos cuánticos@silica/hidrotalcita, siendo la capa de sílica una barrera entre las nanopartículas y las arcillas. Esta combinación conduce a una barrera eficiente para los procesos de liberación de puntos cuánticos al medio biológico, tratándose por tanto de un andamiaje inorgánico nanoestructurado que evita toxicidad a la vez que permite una visualización múltiple y un diagnóstico simultáneo en sistemas terapéuticos avanzados. Por otro lado, se prepararon hidrotalcitas cargadas con partículas elongadas luminiscentes de CdSe@CdS, siendo la delaminación el mejor proceso para la carga debido al mayor tamaño de las nanopartículas, como se detalla en el capítulo 5. Este material híbrido resultó tener más luminiscencia y mayor tiempo de vida que cuando estaba cargado con puntos cuánticos, lo que supone una ventaja y un requisito para observaciones in vitro de tiempos prolongados. En consecuencia, se requieren una menor cantidad de nanopartículas y una menor excitación, lo que implica una menor toxicidad o daño a las células. Con estos resultados remarcamos que la combinación de dos campos como son el óptico y el de los nanomateriales, puede crear herramientos potentes para bioaplicaciones. En el capítulo 6, se usan cultivos celulares incubados con los materiales híbridos detallados en los capítulos 4 y 5 para demostrar la utilidad de esta clase de materiales como agentes de visualización. Observamos una dependencia respecto al diámetro de las nanopartículas y la calidad de los resultados, pero se necesitan más pruebas para esclarecer si esta correlación es verdadera o otros factores como la estructura del material transportador están implicados. Finalmente, en el capítulo 7, detallo como, combinando la especificidad de interacciones biomoleculares y la capacidad de calibrado de las propiedades ópticas de puntos cuánticos y fluoróforos, hemos desarrollado por primera vez un sistema in vitro para detectar fibrosis quística tanto de forma cualitativa (1nanoSi) como cuantitativa (2nanoSi). La novedad de nuestro sistema es el uso de procesos de transferencia de energía (FRET), cuyo mecanismo describe como se produce transferencia de energía de un dador (inicialmente en su estado electrónico excitado) y un aceptor a través de un emparejamiento dipolo-dipolo no radiativo. Para que se dé este proceso debe de haber un buen solapamiento entre la emisión del dador y la absorción del aceptor. Además, es un proceso muy dependiente y limitado por la distancia. Hemos anclado un péptido corto previamente marcado con un derivado de rodamina llamado TAMRA a la superficie de las nanoesferas rellenas de un tipo (1nanoSi, rellenas con CdSe540) o dos tipos (2nanoSi, rellanas con CdSe540 y CdSe660, siendo los números las longitudes de emisión) puntos cuánticos. Estas esferas se funcionalizaron con grupos amino para unir los péptidos marcados con TAMRA. Las secuencias de los péptidos diferían en un solo aminoácido: uno tiene prolina y el otro arginina en su lugar. La gente con fibrosis quística tiene mala digestión de péptidos porque los enzimas proteolíticos tienen problemas para llegar al duodeno, que es donde estos enzimas son activos. Elegimos la tripsina como enzima proteolítico por su especificidad de corte, ya que solo corta tras lisina y arginina pero no si estos van seguidos por prolina. Por tanto, en condiciones sanas, la secuencia peptídica sufrirá corte y no se observará FRET en el péptido que no tiene prolina. Al observar los espectros de emisión de los sistemas 1nanoSi vimso que había FRET debido a un buen solapamiento entre la emisión de los puntos cuánticos verdes (CdSe540) y la absorción del fluoróforo TAMRA. Cuando se produce el corte del péptido por la acción de la tripsina, se rompe este proceso de transferencia de energía y la relación entre la fluorescencia entre el dador y el aceptor cambia: el pico del TAMRA decrece mientras que el de los puntos cuánticos verdes aumenta durante la digestión. Pero estos es solo cualitativo, el sistema necesita un tercer componente que no se vea afectado por el FRET para ser cuantitativo. Decidimos usar puntos cuánticos rojos (CdSe660). Ahora nuestro sistema tenia dos capas (2nanoSi), la más interna rellena con puntos cuánticos rojos y la más externa con puntos cuánticos verdes. Tras observar los espectros de emisión vimos que solo cambiaban los picos de los puntos cuánticos verdes y fluoróforo, en cambio el pico de los puntos cuánticos rojos no variaba, lo que significa que solo se producía FRET entre los CdSe540 y el TAMRA. A pesar del pequeño solapamiento entre la emisión del TAMRA y la absorción de los puntos cuánticos rojos, la distancia entre ellos es demasiado grande y no se produce el FRET. Observamos diferentes comportamientos dependiendo de la concentración de tripsina. Usamos la relación entre la intensidad de fluorescencia entre las dos poblaciones de puntos cuánticos como sensor ratiométrico. Dibujando los valores de esta relación de intensidades a través del tiempo obtuvimos las cinéticas de la digestión para diferentes concentraciones de tripsina. A mayor concentración, más rápida era la digestión. La recta patrón resultante de dibujar los valores experimentales de la relación de intensidades I540/I660 para un tiempo de digestión de 10 minutos demostró una buena linearidad que permite determinar la concetración de enzima a niveles clínicamente relevantes para poder diagnosticar la fibrosis quística. En global, estos resultados nos permiten proponer el sistema 2nanoSi como un sensor ratiométrico de fluorescencia y herramienta para calcular la concentración de tripsina, siendo además un método para detectar la fibrosis quítica y otras enfermedades relacionadas con el páncreas fácil de usar, rápido y no invasivo.

The successful era of CMOS technology is coming to an end. The limit on minimum fabrication dimensions of transistors and the increasing leakage power hinder the technological scaling that has characterized the last decades. In several different ways, this problem has been addressed changing the architectures implemented in CMOS, adopting parallel processors and thus increasing the throughput at the same operating frequency. However, architectural alternatives cannot be the definitive answer to a continuous increase in performance dictated by Moore’s law. This problem must be addressed from a technological point of view. Several alternative technologies that could substitute CMOS in next years are currently under study. Among them, magnetic technologies such as NanoMagnet Logic (NML) are interesting because they do not dissipate any leakage power. More- over, magnets have memory capability, so it is possible to merge logic and memory in the same device. However, magnetic circuits, and NML in this specific research, have also some important drawbacks that need to be addressed: first, the circuit clock frequency is limited to 100 MHz, to avoid errors in data propagation; second, there is a connection between circuit layout and timing, and in particular, longer wires will have longer latency. These drawbacks are intrinsic to the technology and for this reason they cannot be avoided. The only chance is to limit their impact from an architectural point of view. The first step followed in the research path of this thesis is indeed the choice and optimization of architectures able to deal with the problems of NML. Systolic Ar- rays are identified as an ideal solution for this technology, because they are regular structures with local interconnections that limit the long latency of wires; more- over they are composed of several Processing Elements that work in parallel, thus exploit parallelization to increase throughput (limiting the impact of the low clock frequency). Through the analysis of Systolic Arrays for NML, several possible im- provements have been identified and addressed: 1) it has been defined a rigorous way to increase throughput with interleaving, providing equations that allow to esti- mate the number of operations to be interleaved and the rules to provide inputs; 2) a latency insensitive circuit has been designed, that exploits a data communication protocol between processing elements to avoid data synchronization problems. This feature has been exploited to design a latency insensitive Systolic Array that is able to execute the Floyd-Steinberg dithering algorithm. All the improvements presented in this framework apply to Systolic Arrays implemented in any technology. So, they can also be exploited to increase performance of today’s CMOS parallel circuits. This research path is presented in Chapter 3. While Systolic Arrays are an interesting solution for NML, their usage could be quite limited because they are normally application-specific. The second re- search path addresses this problem. A Reconfigurable Systolic Array is presented, that can be programmed to execute several algorithms. This architecture has been tested implementing many algorithms, including FIR and IIR filters, Discrete Cosine Transform and Matrix Multiplication. This research path is presented in Chapter 4. In common Von Neumann architectures, the logic part of the circuit and the memory one are separated. Today bus communication between logic and memory represents the bottleneck of the system. This problem is addressed presenting Logic- In-Memory (LIM), an architecture where memory elements are merged in logic ones. This research path aims at defining a real LIM architectures. This has been done in two steps. The first step is represented by an architecture composed of three layers: memory, routing and logic. In the second step instead the routing plane is no more present, and its features are inherited by the memory plane. In this solution, a pyramidal memory model is used, where memories near logic elements contain the most probably used data, and other memory layers contain the remaining data and instruction set. This circuit has been tested with odd-even sort algorithms and it has been benchmarked against GPUs and ASIC. This research path is presented in Chapter 5. MagnetoElastic NML (ME-NML) is a technological improvement of the NML principle, proposed by researchers of Politecnico di Torino, where the clock system is based on the induced stretch of a piezoelectric substrate when a voltage is ap- plied to its boundaries. The main advantage of this solution is that it consumes much less power than the classic clock implementation. This technology has not yet been investigated from an architectural point of view and considering complex circuits. In this research field, a standard methodology for the design of ME-NML circuits has been proposed. It is based on a Standard Cell Library and an enhanced VHDL model. The effectiveness of this methodology has been proved designing a Galois Field Multiplier. Moreover the serial-parallel trade-off in ME-NML has been investigated, designing three different solutions for the Multiply and Accumulate structure. This research path is presented in Chapter 6. While ME-NML is an extremely interesting technology, it needs to be combined with other faster technologies to have a real competitive system. Signal interfaces between NML and other technologies (mainly CMOS) have been rarely presented in literature. A mixed-technology multiplexer is designed and presented as the basis for a CMOS to NML interface. The reverse interface (from ME-NML to CMOS) is instead based on a sensing circuit for the Faraday effect: a change in the polarization of a magnet induces an electric field that can be used to generate an input signal for a CMOS circuit. This research path is presented in Chapter 7. The research work presented in this thesis represents a fundamental milestone in the path towards nanotechnologies. The most important achievement is the de- sign and simulation of complex circuits with NML, benchmarking this technology with real application examples. The characterization of a technology considering complex functions is a major step to be performed and that has not yet been ad- dressed in literature for NML. Indeed, only in this way it is possible to intercept in advance any weakness of NanoMagnet Logic that cannot be discovered consid- ering only small circuits. Moreover, the architectural improvements introduced in this thesis, although technology-driven, can be actually applied to any technology. We have demonstrated the advantages that can derive applying them to CMOS cir- cuits. This thesis represents therefore a major step in two directions: the first is the enhancement of NML technology; the second is a general improvement of parallel architectures and the development of the new Logic-In-Memory paradigm.

Les Quantum Dots (QDs) sont des particules cristallines de semi-conducteur ou du métal de forme sphérique et de dimension nanométrique. L'intérêt majeur des QDs réside dans leur grande adaptabilité à de nombreuses applications biologiques.Le but de mon travail était de développer une nouvelle classe de QDs de faible toxicité afin de les utiliser pour la bio-imagerie des cellules cancéreuses. Pour cela, il est nécessaire de préparer des sondes hydrosolubles, photostables, biocompatibles, de luminescence élevée et possédant une faible toxicité. La synthèse des cœurs de type ZnS and ZnSe dopés au manganèse ou au cuivre et stabilisés par l’acide 3-mercapropropionique ou par le 1-thioglycérol a été réalisée par la voie hydrothermale. Les techniques analytiques de caractérisation utilisées sont la spectroscopie UV-visible, la spectroscopie de fluorescence, la diffraction des rayons X (XRD), la spectroscopie photoélectronique de rayon X (XPS), la microscopie électronique à transmission (TEM), la diffusion dynamique de la lumière DLS, la spectroscopie infra-rouge (IR), et la résonance paraélectronique (RPE). La toxicité des QDs a été déterminée sur des cellules cancéreuses. Les différents test de cytotoxicité (MTT, XTT et ferrous oxidation-xylenol orange) ont été réalisés. Finalement, les QDs de type ZnS:Mn conjugués à l’acide folique ont été utilisés pour la bio-imagerie des cellules cancéreuses par le biais d’une excitation biphotonique
Semiconductor QDs are tiny light-emitting crystals, and are emerging as a new class of fluorescent labels for medicine and biology. The aim of this work was to develop a new class of non-toxic QDs probes with essential attributes such as water dispersibility, photostability, biocompatibility, high luminescence and possible excitation with low-energy visible light, using simple processing method. Such nanoprobes could be used for bio-imaging of cancer cells. In the performed studies, I focused on ZnS and ZnSe QDs as they are cadmium-free and might be excited biphotonically.The synthesis protocols of ZnS and ZnSe QDs doped with two ions such as Mn or Cu and stabilized by 3-mercaptopropionic acid or 1-thioglycerol were established, followed by NCs characterization (diameter, surface charge, photophysical properties, …) using analytical techniques such as spectrophotometry UV-vis, fluorimetry, X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), transmission electron microscopy (TEM), dynamic light scattering (DLS), infra-red analysis (FT-IR), thin layer chromatography (TLC) and electron paramagnetic resonance (EPR). The cytotoxicity of synthesized bare and conjugated NPs was evaluated on cancer cell lines using MTT, XTT and ferrous oxidation-xylenol orange assay.Finally, chosen well fluorescent and weakly toxic types of as-prepared and characterized QDs were used for bio-imaging of cancer cells. In these experiments, FA-functionalized NCs were excited biphotonically. The performed experiments showed the potential of QDs as cancer cells fluorescent markers and that they accumulate around the cell nuclei

Lab-on-chip systems have been developed for various applications like point of care diagnostics and compact imaging systems. Compact, on-chip imaging systems face a challenge in the integration of multicolor light sources on-chip. This is because of the unavailability of compact, individually addressable, multicolor light sources on a single planar substrate. Colloidal Quantum Dot based Light Emitting Diodes (QDLEDs), which have found wide appeal, due to their unique properties like their tunable and narrow emission bandwidth and easy fabrication, are ideal for lab-on-chip integration. Among different types of QDLED structures implemented, inorganic QDLEDs have shown great promise. We have demonstrated designs and fabrication strategies for creating QDLEDs with enhanced performance. In particular: (I) We introduce a sandwich structure with a spin coated inorganic hole transporting layer of nickel oxide underlying the QD layer and with a spin coated zinc oxide electron transporting layer, with patterning of anode and cathode on the substrate. Compared to the use of sputtered thin films, solution processed charge transporting layers (CTLs) improve robustness of the device, as crystalline ZnO shows low CB and VB edge energy levels, efficiently suppressing hole leakage current resulting in LEDs with longer lifetimes. We also use Atomic Layer Deposition to deposit an additional hole injecting layer to protect the QDs from direct contact with the anode. With this device design, we demonstrate a working lifetime of more than 12 hours and a shelf-life of more than 240 days for the devices. Our solution based process is applicable to micro-contact printed and also spin-coated QD films. QDLEDs with spin-coated CTLs show a lifetime increase of more than three orders of magnitude compared to devices made using sputtered CTLs. (II) We implement strategies of the enhancement of light extraction from the fabricated QDLEDs. We discuss the integration of a two dimensional grating structure based on a metal-dielectric-metal plasmonic waveguide with the metal electrode of a QDLED, with the aim of enhancing the light intensity by resonant suppression of transmitted light. The grating structure reflects the light coupled with the metal electrode in the QDLED and we found an increase of 34.72% in the electroluminescence intensity from the area of the pattern and an increase of 32.63% from photoluminescence of QDs deposited on a metal surface. (III) We demonstrate the capability of our fabricated devices as a light source by measuring intensity across stained cells with QDLEDs of two different wavelengths and show the correlation as expected with the absorption profile of the fluorescent dye. We measure the absorption from the biological samples using QDLEDs fabricated with various design modifications, as a quantification of the improvements in device performance, directly affecting to our target application.
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Thesis (M.S.C.S.E.)--University of Notre Dame, 2005.
Thesis directed by Peter Kogge for the Department of Computer Science and Engineering. "March 2005." Includes bibliographical references (leaves 129-133).

Thesis (Ph. D.)--University of Notre Dame, 2004.
Thesis directed by Gregory L. Snider for the Department of Electrical Engineering. "April 2004." Includes bibliographical references (leaves 135-139).