El control dinámico y determinístico de la luz en una escala espacial por debajo de la longitud de onda es un requisito clave para ampliar los conceptos y las funcionalidades de la macro-óptica hasta la escala nanométrica. Un mayor nivel de control también tendrá implicaciones importantes en nuestra comprensión de los fenómenos ópticos en la nanoescala. Uno de los principales problemas en nano-óptica tiene como objetivo describir cómo y con qué precisión es posible controlar la distribución espacial de la luz de forma dinámica en la nanoescala. Desafortunadamente, un límite fundamental de la física – el límite de difracción de la luz – afecta nuestra capacidad de seleccionar ópticamente puntos separados por menos de media longitud de onda de la luz. El campo de la plasmónica ofrece una oportunidad única para cerrar la brecha entre el límite de difracción y la escala nanométrica. Nanoantenas metálicas pueden acoplarse eficientemente a luz propagante y focalizarla en volúmenes nanométricos, y viceversa. Además, estas nanoantenas prometen mejorar significativamente la eficiencia de procesos como le fotodetección, la emisión de luz, sensores, transferencia de calor, y espectroscopía a la escala nanométrica. Aprender a controlar de forma precisa la respuesta óptica de estas nanoantenas representa un enfoque muy prometedor para controlar la distribución espacial y temporal de la luz a la escala nanométrica. Tradicionalmente, se han desarrollado dos principales estrategias para el control de la respuesta óptica de nanoantenas plasmónicas: la primer estrategia (estrategia estática) tiene como objetivo la optimización del diseño geométrico de las nanoantenas acorde a su aplicación, mientras que la segunda estrategia (estrategia dinámica) tiene como objetivo la modulación reversible del campo cercano de una nanoestructura dada a través de la manipulación de la luz de excitación en el tiempo y el espacio. El trabajo presentado en esta Tesis extiende el estado del arte de estas dos estrategias, y desarrolla nuevas herramientas, tanto experimentales como teóricas, para ampliar el nivel de control que tenemos sobre la distribución espacial de la luz debajo del límite de difracción. Después de presentar una visión general de los principios básicos de nano-óptica y de la óptica de lo plasmones de superficie, el Capítulo 1 repasa los avances en el control de la respuesta óptica de nanoestructuras metálicas – sea por una estrategia estática o dinámica – en el momento en que se inició este trabajo de investigación. La modificación de la geometría y las dimensiones de las nanpartículas metálicas sigue siendo un ingrediente fundamental para controlar las resonancias plasmónicas y los campos de luz a la escala nanométrica. Como ejemplos novedosos de control estático, por lo tanto, los Capítulos 2 y 3 estudian nuevos diseños de estructuras plasmónicas con capacidades sin precedentes de modelar campos de luz a la escala nanométrica, en particular un diseño fractal y una nanoantena unidireccional tipo Yagi-Uda. Los Capítuols 4 y 5 describen una nueva herramienta teórica y experimental para el control dinámico y determinístico de la respuesta óptica de nanoantenas basada en la modulación espacial de la fase de la luz de excitación: el campo óptico cercano, que resulta de la interacción entre la luz y las nanoestructuras plasmónicas, es normalmente determinado por la geometría del sistema metálico y las propiedades de la luz incidente, como su longitud de onda y su polarización; sin embargo, el control exacto y dinámico del campo óptico cercano debajo de límite de difracción de la luz – independientemente de la geometría de la nanoestructura – es también un ingrediente importante para el desarrollo de futuros dispositivos nano-ópticos y para ampliar los conceptos y las funcionalidades de la óptica macroscópica a la escala nanométrica. Finalmente, la Conclusión resume los resultados de este trabajo y ofrece una visión general de algunos estudios paralelos a esta tesis. Algunas de las observaciones finales permiten echar un vistazo a las perspectivas y estrategias futuras para complementar el control estático y el control dinámico en una única herramienta, que podría avanzar enormemente nuestra capacidad de controlar la respuesta óptica de nanoantennas debajo del límite de difracción. / El control dinámico y determinístico de la luz en una escala espacial por debajo de la longitud de onda es un requisito clave para ampliar los conceptos y las funcionalidades de la macro-óptica hasta la escala nanométrica. Un mayor nivel de control también tendrá implicaciones importantes en nuestra comprensión de los fenómenos ópticos en la nanoescala. Uno de los principales problemas en nano-óptica tiene como objetivo describir cómo y con qué precisión es posible controlar la distribución espacial de la luz de forma dinámica en la nanoescala. Desafortunadamente, un límite fundamental de la física – el límite de difracción de la luz – afecta nuestra capacidad de seleccionar ópticamente puntos separados por menos de media longitud de onda de la luz. El campo de la plasmónica ofrece una oportunidad única para cerrar la brecha entre el límite de difracción y la escala nanométrica. Nanoantenas metálicas pueden acoplarse eficientemente a luz propagante y focalizarla en volúmenes nanométricos, y viceversa. Además, estas nanoantenas prometen mejorar significativamente la eficiencia de procesos como le fotodetección, la emisión de luz, sensores, transferencia de calor, y espectroscopía a la escala nanométrica. Aprender a controlar de forma precisa la respuesta óptica de estas nanoantenas representa un enfoque muy prometedor para controlar la distribución espacial y temporal de la luz a la escala nanométrica. Tradicionalmente, se han desarrollado dos principales estrategias para el control de la respuesta óptica de nanoantenas plasmónicas: la primer estrategia (estrategia estática) tiene como objetivo la optimización del diseño geométrico de las nanoantenas acorde a su aplicación, mientras que la segunda estrategia (estrategia dinámica) tiene como objetivo la modulación reversible del campo cercano de una nanoestructura dada a través de la manipulación de la luz de excitación en el tiempo y el espacio. El trabajo presentado en esta Tesis extiende el estado del arte de estas dos estrategias, y desarrolla nuevas herramientas, tanto experimentales como teóricas, para ampliar el nivel de control que tenemos sobre la distribución espacial de la luz debajo del límite de difracción. Después de presentar una visión general de los principios básicos de nano-óptica y de la óptica de lo plasmones de superficie, el Capítulo 1 repasa los avances en el control de la respuesta óptica de nanoestructuras metálicas – sea por una estrategia estática o dinámica – en el momento en que se inició este trabajo de investigación. La modificación de la geometría y las dimensiones de las nanpartículas metálicas sigue siendo un ingrediente fundamental para controlar las resonancias plasmónicas y los campos de luz a la escala nanométrica. Como ejemplos novedosos de control estático, por lo tanto, los Capítulos 2 y 3 estudian nuevos diseños de estructuras plasmónicas con capacidades sin precedentes de modelar campos de luz a la escala nanométrica, en particular un diseño fractal y una nanoantena unidireccional tipo Yagi-Uda. Los Capítuols 4 y 5 describen una nueva herramienta teórica y experimental para el control dinámico y determinístico de la respuesta óptica de nanoantenas basada en la modulación espacial de la fase de la luz de excitación: el campo óptico cercano, que resulta de la interacción entre la luz y las nanoestructuras plasmónicas, es normalmente determinado por la geometría del sistema metálico y las propiedades de la luz incidente, como su longitud de onda y su polarización; sin embargo, el control exacto y dinámico del campo óptico cercano debajo de límite de difracción de la luz – independientemente de la geometría de la nanoestructura – es también un ingrediente importante para el desarrollo de futuros dispositivos nano-ópticos y para ampliar los conceptos y las funcionalidades de la óptica macroscópica a la escala nanométrica. Finalmente, la Conclusión resume los resultados de este trabajo y ofrece una visión general de algunos estudios paralelos a esta tesis. Algunas de las observaciones finales permiten echar un vistazo a las perspectivas y estrategias futuras para complementar el control estático y el control dinámico en una única herramienta, que podría avanzar enormemente nuestra capacidad de controlar la respuesta óptica de nanoantennas debajo del límite de difracción.

<p>This study is focused on designing and characterizing protein-based building blocks in order to construct self-assembled nano-structured biomaterials. In detail, this research aims to: (1) investigate a new class of proteins that possess nanospring behaviors at a single-molecule level, and utilize these proteins along with currently characterized elastomeric proteins as building blocks for nano-structured biomaterials; (2) develop a new method to accurately measure intermolecular interactions of self-assembling two or more arbitrary (poly)peptides, and select some of them which have appropriate tensile strength for crosslinking the proteins to construct elastomeric biomaterials; (3) construct well-defined protein building blocks which are composed of elastomeric proteins terminated with self-oligomerizing crosslinkers, and characterize self-assembled structures created by the building blocks to determine whether the elasticity of proteins at single-molecule level can be maintained.</p><p>Primary experimental methods of this research are (1) atomic force microscope (AFM) based single-molecule force spectroscopy (SMFS) that allows us to manipulate single molecules and to obtain their mechanical properties such as elasticity, unfolding and refolding properties, and force-induced conformational changes, (2) AFM imaging that permits us to identify topology of single molecules and supramolecular structures, and (3) protein engineering that allows us to genetically connect elastomeric proteins and self-assembling linkers together to construct well-defined protein building blocks.</p><p>Nanospring behavior of á-helical repeat proteins: We revealed that á-helical repeat proteins, composed of tightly packed á-helical repeats that form spiral-shaped protein structures, unfold and refold in near equilibrium, while they are stretched and relaxed during AFM based SMFS measurements. In addition to minimal energy dissipation by the equilibrium process, we also found that these proteins can yield high stretch ratios (>10 times) due to their packed initial forms. Therefore, we, for the first time, recognized a new class of polypeptides with nanospring behaviors. </p><p>Protein-based force probes for gauging molecular interactions: We developed protein-based force probes for simple, robust and general AFM assays to accurately measure intermolecular forces between self-oligomerization of two or more arbitrary polypeptides that potentially can serve as molecular crosslinkers. For demonstration, we genetically connected the force probe to the Strep-tag II and mixed it with its molecular self-assembling partner, the Strep-Tactin. Clearly characterized force fingerprints by the force probe allowed identification of molecular interactions of the single Strep-tag II and Strep-Tactin complex when the complex is stretched by AFM. We found a single energy barrier exists between Strep-tag II and Strep-Tactin in our given loading rates. Based upon our demonstration, the use of the force probe can be expanded to investigate the strength of interactions within many protein complexes composed of homo- and hetero-dimers, and even higher oligomeric forms. Obtained information can be used to choose potential self-assembling crosslinkers which can connect elastomeric proteins with appropriate strength in higher-order structures. </p><p>Self-assembled nano-structured biomaterials with well-defined protein-based building blocks: We constructed well-defined protein building blocks with tailored mechanical properties for self-assembled nano-structured materials. We engineered protein constructs composed of tandem repeats of either a I27-SNase dimer or a I27 domain alone and terminated them with a monomeric streptavidin which is known to form extremely stable tetramers naturally. By using molecular biology and AFM imaging techniques, we found that these protein building blocks transformed into stable tetrameric complexes. By using AFM based SMFS, we measured, to our knowledge for the first time, the mechanical strength of the streptavidin tetramer at a single-molecule level and captured its mechanical anisotropy. Using streptavidin tetramers as crosslinkers offers a unique opportunity to create well-defined protein based self-assembled materials that preserve the molecular properties of their building blocks.</p> / Dissertation

In this dissertation, an innovative approach combining continuum mechanics and atomistic simulations is exposed to develop a nanomechanics theory for modeling and predicting the macroscopic behavior of nanomaterials. This nanomechanics theory exhibits the simplicity of the continuum formulation while taking into account the discrete atomic structure and interaction near surfaces/interfaces. There are four primary objectives to this dissertation. First, theory of interfaces is revisited to better understand its behavior and effects on the overall behavior of nanostructures. Second, atomistic tools are provided in order to efficiently determine the properties of free surfaces and interfaces. Interface properties are reported in this work, with comparison to both theoretical and experimental characterizations of interfaces. Specifically, we report surface elastic properties of groups 10 11 transition metals as well as properties for low-CSL grain boundaries in copper. Third, we propose a continuum framework that casts the atomic level information into continuum quantities that can be used to analyze, model and simulate macroscopic behavior of nanostructured materials. In particular, we study the effects of surface free energy on the effective modulus of nano-particles, nanowires and nano-films as well as nanostructured crystalline materials and propose a general framework valid for any shape of nanostructural elements / nano-inclusions (integral forms) that characterizes the size-dependency of the elastic properties. This approach bridges the gap between discrete systems (atomic level interactions) and continuum mechanics. Finally this continuum outline is used to understand the effects of surfaces on the overall behavior of nano-size structural elements (particles, films, fibers, etc.) and nanostructured materials. More specifically we will discuss the impact of surface relaxation, surface elasticity and non-linearity of the underlying bulk on the properties nanostructured materials.

This dissertation focuses on quantitative subsurface and mechanical properties imaging potential of AFM probes. Extensive modeling of AFM probes are presented for thorough understanding of capabilities and limitations of current techniques, these models are verified by various experiments, and different methods are developed by utilizing force-sensing integrated read-out active tip (FIRAT), which is an active AFM probe with broad bandwidth. For quantitative subsurface imaging, a 3-D FEA model of AFM tip-sample contact is developed and this model can simulate AFM tip scan on nanoscale-sized buried structures. FIRAT probe, which is active and broadband, is utilized for interaction forces imaging during intermittent contact mode and mechanical characterization capability of this probe is investigated. It is shown that probe dynamics, stiffness, stiffness ambiguity, assumed contact mechanics, and noise are important parameters for the accuracy of mechanical properties imaging. An active tip control mechanism is introduced to limit contact forces during intermittent contact mode. In addition to these, a combined ultrasonic AFM and interaction forces imaging method is developed and modeled to solve the reduced elasticity measurement sensitivity on composite materials. This method is capable of imaging a broader range of elasticity on combination samples such as metal nanoparticles in polymers at nanoscale.

The understanding of molecular effects in nanoscale environments is becoming increasingly relevant for various emerging fields. These include spectroscopy for molecular identification as well as in finding molecules for energy harvesting. Theoretical quantum chemistry has been increasingly useful to address these phenomena to yield an understanding of these effects. In the first part of this dissertation, we study the chemical effect of surface-enhanced Raman scattering (SERS). We use quantum chemistry simulations to study the metal-molecule interactions present in these systems. We find that the excitations that provide a chemical enhancement contain a mixed contribution from the metal and the molecule. Moreover, using atomistic studies we propose an additional source of enhancement, where a transition metal dopant surface could provide an additional enhancement. We also develop methods to study the electrostatic effects of molecules in metallic environments. We study the importance of image-charge effects, as well as field-bias to molecules interacting with perfect conductors. The atomistic modeling and the electrostatic approximation enable us to study the effects of the metal interacting with the molecule in a complementary fashion, which provides a better understanding of the complex effects present in SERS. In the second part of this dissertation, we present the Harvard Clean Energy project, a high-throughput approach for a large-scale computational screening and design of organic photovoltaic materials. We create molecular libraries to search for candidates structures and use quantum chemistry, machine learning and cheminformatics methods to characterize these systems and find structure-property relations. The scale of this study requires an equally large computational resource. We rely on distributed volunteer computing to obtain these properties. In the third part of this dissertation we present our work related to the acceleration of electronic structure methods using graphics processing units. This hardware represents a change of paradigm with respect to the typical CPU device architectures. We accelerate the resolution-of-the-identity Moller-Plesset second-order perturbation theory algorithm using graphics cards. We also provide detailed tools to address memory and single-precision issues that these cards often present.

Observing and controlling solid state quantum systems is an area of intense research in quantum science today. Such systems offer the natural advantage of being bound into a solid device, eliminating the need for laser cooling and trapping of atoms in free space. These solid state "atoms" can interface directly with photonic channels designed to efficiently couple into larger networks of interacting quantum systems. With all of the tools of semiconductor fabrication technology available, the idea of scalable, chip-based quantum networks is a tantalizing prospect. / Physics

No description available.

Shape memory alloys (SMAs) are widely used in a broad variety of applications in multiscale devices ranging from nano-actuators used in nano-electrical-mechanical systems (NEMS) to large energy absorbing elements in civil engineering applications. This research introduces a multiscale analysis for SMAs, particularly Nickel-Titanium alloys (NiTi). SMAs are studied in a variety of length scales ranging from macroscale to nanoscale. In macroscale, a phenomenological constitutive framework is adopted and developed by adding the effect of phase transformation latent heat. Analytical closed-form solutions are obtained for modeling the coupled thermomechanical behavior of various large polycrystalline SMA devices subjected to different loadings, including uniaxial loads, torsion, and bending. Thermomechanical responses of several SMA devices are analyzed using the introduced solutions and the results are validated by performing various experiments on some large SMA elements. In order to study some important properties of polycrystalline SMAs that the macroscopic phenomenological frameworks cannot capture, including the texture and intergranular effects in polycrystalline SMAs, a micromechanical framework with a realistic modeling of the grains based on Voronoi tessellations is used. The local form of the first law of thermodynamics is used and the energy balance relations for the polycrystalline SMAs are obtained. Generalized coupled thermomechanical governing equations considering the phase transformation latent heat are derived for polycrystalline SMAs. A three-dimensional finite element framework is used and different polycrystalline samples are modeled. By considering appropriate distributions of crystallographic orientations in the grains obtained from experimental texture measurements of NiTi samples the effects of texture and the tension-compression asymmetry on the thermomechanical response of polycrystalline SMAs are studied. The interaction between the stress state (tensile or compressive), number of grains, and the texture on the thermomechanical response of polycrystalline SMAs is also studied. For studying some aspects of the thermomechanical properties of SMAs that cannot be studied neither by the phenomenological constitutive models nor by the micromechanical models, molecular dynamics simulations are used to explore the martensitic phase transformation in NiTi alloys at the atomistic level. The martensite reorientation, austenite to martensite phase transformation, and twinning mechanisms in NiTi nanostructures are analyzed and the effect of various parameters including the temperature and size on the phase transformation at the atomistic level is studied. Results of this research provide insight into studying pseudoelasticity and shape memory response of NiTi alloys at different length scales and are useful for better understanding the solid-to-solid phase transformation at the atomistic level, and the effects of this transformation on the microstructure of polycrystal SMAs and the macroscopic response of these alloys.

In this thesis, I present a microscopic theory of quantum circuits based on interacting electron spins in quantum dot molecules. We use the Linear Combination of Harmonic Orbitals-Configuration Interaction (LCHO-CI) formalism for microscopic calculations. We then derive effective Hubbard, t-J, and Heisenberg models. These models are used to predict the electronic, spin and transport properties of a triple quantum dot molecule (TQDM) as a function of topology, gate configuration, bias and magnetic field. With these theoretical tools and fully characterized TQDMs, we propose the following applications: 1. Voltage tunable qubit encoded in the chiral states of a half-filled TQDM. We show how to perform single qubit operations by pulsing voltages. We propose the "chirality-to-charge" conversion as the measurement scheme and demonstrate the robustness of the chirality-encoded qubit due to charge fluctuations. We derive an effective qubit-qubit Hamiltonian and demonstrate the two-qubit gate. This provides all the necessary operations for a quantum computer built with chirality-encoded qubits. 2. Berry's phase. We explore the prospect of geometric quantum computing with chirality-encoded qubit. We construct a Herzberg circuit in the voltage space and show the accumulation of Berry's phase. 3. Macroscopic quantum states on a semiconductor chip. We consider a linear chain of TQDMs, each with 4 electrons, obtained by nanostructuring a metallic gate in a field effect transistor. We theoretically show that the low energy spectrum of the chain maps onto that of a spin-1 chain. Hence, we show that macroscopic quantum states, protected by a Haldane gap from the continuum, emerge. In order to minimize decoherence of electron spin qubits, we consider using electron spins in the p orbitals of the valence band (valence holes) as qubits. We develop a theory of valence hole qubit within the 4-band k.p model. We show that static magnetic fields can be used to perform single qubit operations. We also show that the qubit-qubit interactions are sensitive to the geometry of a quantum dot network. For vertical qubit arrays, we predict that there exists an optimal qubit separation suitable for the voltage control of qubit-qubit interactions.

Naturally occurring food antimicrobials such as plant essential oils are receiving tremendous interest as intervention systems to enhance microbiological safety and quality. Poor water solubility of essential oils makes it difficult to incorporate them in foods, impacting visual appearance, antimicrobial effectiveness, and possibly organoleptic properties. Engineered nanoscale delivery systems can principally solve these challenges, but those based on low-cost food ingredients and inexpensive and scalable processes are currently scarce. This dissertation presents a simple and scalable two-step technology to prepare nano-delivery systems. The first encapsulation step, based on emulsion-evaporation, involves preparing emulsions composed of an oil phase with thymol or eugenol, major compounds in extracts from thyme and clove respectively, in hexane and an aqueous phase with conjugates of whey protein isolate and maltodextrin, followed by evaporation of hexane by spray drying. The second step is to hydrate spray dried capsules to enable the formation of nanoscale particles. The encapsulation performance and dispersion characteristics were affected by amounts and types of conjugates (ratio of protein: maltodextrin and maltodextrin chain length), volume fraction and composition of the oil phase. The optimal conditions corresponded to 55.8 % encapsulation efficiency and 12.6 % loading for thymol and 47.9 % encapsulation efficiency and 7.9 % loading for eugenol. Dispersions prepared from the identified capsules contained particles smaller than 100 nm and were transparent at pH 3.0-7.0 and 0-50 mM before and after heating at 80°C for 15 min. Nano-dispersions and free oil were tested for antimicrobial activity against Escherichia coli O157:H7, Listeria monocytogenes, Staphylococcus aureus, and Salmonella typhimurium. Nano-dispersed and free antimicrobials had similar effectiveness at various pH and temperatures in tryptic soy broth and apple cider, while in 2 % reduced fat milk, nano-dispersed antimicrobials were consistently more effective than unencapsulated ones. Therefore, the commercially viable nanoscale technology presented in this study enables the delivery of lipophilic antimicrobials for enhanced microbial safety and quality, without compromising visual appearance of foods, especially clear beverages.