Synthetic regulation of eukaryotic gene expression by noncoding RNA

Synthetic biological systems promise to combine the spectacular diversity of biological functionality with engineering principles to design new life to address many pressing needs. As these engineered systems advance in sophistication, there is ever-greater need for customizable, situation-specific expression of desired genes. However, existing gene control platforms are generally not modular, or do not display performance requirements required for robust phenotypic responses to input signals. This work expands the capabilities of eukaryotic gene control in two important directions.

For development of greater modularity, we extend the use of synthetic self-cleaving ribozyme switches to detect changes in input protein levels and convey that information into programmed gene expression in eukaryotic cells. We demonstrate both up- and down-regulation of levels of an output transgene by more than 4-fold in response to rising input protein levels, with maximal output gene expression approaching the highest levels observed in yeast. In vitro experiments demonstrate protein-dependent ribozyme activity modulation. We further demonstrate the platform in mammalian cells. Our switch devices do not depend on special input protein activity, and can be tailored to respond to any input protein to which a suitable RNA aptamer can be developed. This platform can potentially be employed to regulate the expression of any transgene or any endogenous gene by 3’ UTR replacement, allowing for more complex cell state-specific reprogramming.

We also address an important concern with ribozyme switches, and riboswitch performance in general, their dynamic range. While riboswitches have generally allowed for versatile and modular regulation, so far their dynamic ranges of output gene modulation have been modest, generally at most 10-fold. We address this shortcoming by developing a modular genetic amplifier for near-digital control of eukaryotic gene expression. We combine ribozyme switch-mediated regulation of a synthetic TF with TF-mediated regulation of an output gene. The amplifier platform allows for as much as 20-fold regulation of output gene expression in response to input signal, with maximal expression approaching the highest levels observed in yeast, yet being tunable to intermediate and lower expression levels. EC50 values are more than 4 times lower than in previously best-performing non-amplifier ribozyme switches. The system design retains the modular-input architecture of the ribozyme switch platform, and the near-digital dynamic ranges of TF-based gene control.

Together, these developments suggest great potential for the wide applicability of these platforms for better-performing eukaryotic gene regulation, and more sophisticated, customizable reprogramming of cellular activity.

Radio Frequency Superconducting Quantum Interference Device Meta-atoms and Metamaterials: Experiment, Theory, and Analysis

Metamamterials are 1D, 2D or 3D arrays of articial atoms. The articial atoms, called "meta-atoms", can be any component with tailorable electromagnetic properties, such as resonators, LC circuits, nano particles, and so on. By designing the properties of individual meta-atoms and the interaction created by putting them in a lattice, one can create a metamaterial with intriguing properties not found in nature. My Ph. D. work examines the meta-atoms based on radio frequency superconducting quantum interference devices (rf-SQUIDs); their tunability with dc magnetic field, rf magnetic field, and temperature are studied. The rf-SQUIDs are superconducting split ring resonators in which the usual capacitance is supplemented with a Josephson junction, which introduces strong nonlinearity in the rf properties. At relatively low rf magnetic field, a magnetic field tunability of the resonant frequency of up to 80 THz/Gauss by dc magnetic field is observed, and a total frequency tunability of 100% is achieved. The macroscopic quantum superconducting metamaterial also shows manipulative self-induced broadband transparency due to a qualitatively novel nonlinear mechanism that is different from conventional electromagnetically induced transparency (EIT) or its classical analogs. A near complete disappearance of resonant absorption under a range of applied rf flux is observed experimentally and explained theoretically. The transparency comes from the intrinsic bi-stability and can be tuned on/ off easily by altering rf and dc magnetic fields, temperature and history. Hysteretic in situ 100% tunability of transparency paves the way for auto-cloaking metamaterials, intensity dependent filters, and fast-tunable power limiters. An rf-SQUID metamaterial is shown to have qualitatively the same behavior as a single rf-SQUID with regards to dc flux, rf flux and temperature tuning. The two-tone response of self-resonant rf-SQUID meta-atoms and metamaterials is then studied here via intermodulation (IM) measurement over a broad range of tone frequencies and tone powers. A sharp onset followed by a surprising strongly suppressed IM region near the resonance is observed. This behavior can be understood employing methods in nonlinear dynamics; the sharp onset, and the gap of IM, are due to sudden state jumps during a beat of the two-tone sum input signal. The theory predicts that the IM can be manipulated with tone power, center frequency, frequency difference between the two tones, and temperature. This quantitative understanding potentially allows for the design of rf-SQUID metamaterials with either very low or very high IM response.

MANIPULATION OF IONS, ELECTRONS, AND PHOTONS IN 2D MATERIALS BY ION INTERCALATION

2D materials have attracted tremendous attention due to their unique physical and chemical properties since the discovery of graphene. Despite these intrinsic properties, various modification methods have been applied to 2D materials that yield even more exciting results. Among all modification methods, the intercalation of 2D materials provides the highest possible doping and/or phase change to the pristine 2D materials. This doping effect highly modifies 2D materials, with extraordinary electrical transport as well as optical, thermal, magnetic, and catalytic properties, which are advantageous for optoelectronics, superconductors, thermoelectronics, catalysis and energy storage applications. To study the property changes of 2D materials, we designed and built a planar nanobattery that allows electrochemical ion intercalation in 2D materials. More importantly, this planar nanobattery enables characterization of electrical, optical and structural properties of 2D materials in situ and real time upon ion intercalation. With this device, we successfully intercalated Li-ions into few layer graphene (FLG) and ultrathin graphite, heavily dopes the graphene to 0.6 x 10^15 /cm2, which simultaneously increased its conductivity and transmittance in the visible range. The intercalated LiC6 single crystallite achieved extraordinary optoelectronic properties, in which an eight-layered Li intercalated FLG achieved transmittance of 91.7% (at 550 nm) and sheet resistance of 3 ohm/sq. We extend the research to obtain scalable, printable graphene based transparent conductors with ion intercalation. Surfactant free, printed reduced graphene oxide transparent conductor thin film with Na-ion intercalation is obtained with transmittance of 79% and sheet resistance of 300 ohm/sq (at 550 nm). The figure of merit is calculated as the best pure rGO based transparent conductors. We further improved the tunability of the reduced graphene oxide film by using two layers of CNT films to sandwich it. The tunable range of rGO film is demonstrated from 0.9 um to 10 um in wavelength. Other ions such as K-ion is also studied of its intercalation chemistry and optical properties in graphitic materials. We also used the in situ characterization tools to understand the fundamental properties and improve the performance of battery electrode materials. We investigated the Na-ion interaction with rGO by in situ Transmission electron microscopy (TEM). For the first time, we observed reversible Na metal cluster (with diameter larger than 10 nm) deposition on rGO surface, which we evidenced with atom-resolved HRTEM image of Na metal and electron diffraction pattern. This discovery leads to a porous reduced graphene oxide sodium ion battery anode with record high reversible specific capacity around 450 mAh/g at 25mA/g, a high rate performance of 200 mAh/g at 250 mA/g, and stable cycling performance up to 750 cycles. In addition, direct observation of irreversible formation of Na2O on rGO unveils the origin of commonly observed low 1st Columbic Efficiency of rGO containing electrodes. Another example for in situ characterization for battery electrode is using the planar nanobattery for 2D MoS2 crystallite. Planar nanobattery allows the intrinsic electrical conductivity measurement with single crystalline 2D battery electrode upon ion intercalation and deintercalation process, which is lacking in conventional battery characterization techniques. We discovered that with a “rapid-charging” process at the first cycle, the lithiated MoS2 undergoes a drastic resistance decrease, which in a regular lithiation process, the resistance always increases after lithiation at its final stage. This discovery leads to a 2- fold increase in specific capacity with with rapid first lithiated MoS2 composite electrode material, compare with the regular first lithiated MoS2 composite electrode material, at current density of 250 mA/g.

ENGINEERING HIERARCHICAL MESO-/MICROPOROUS LAMELLAR ZEOLITES WITH VARIABLE TEXTURAL AND CATALYTIC PROPERTIES

Meso-/microporous zeolites combine the charactersitics of well-defined micropores of zeolite with efficient mass transfer consequences of mesopores to increase the efficiency of the catalysts in reactions involving bulky molecules. Different methods such as demetallation and templating have been explored for the synthesis of meso-/microporous zeolites. However, they all have limitations in production of meso-/microporous zeolites with tunable textural and catalytic properties using few synthesis steps. To address this challenge, a simple one-step dual template synthesis approach has been developed in this work to engineer lamellar meso-/microporous zeolites structures with tunable textural and catalytic properties. First, one-step dual template synthesis of meso-/microporous mordenite framework inverted (MFI) zeolite structures was investigated. Tetrapropyl ammonium hydroxide (TPAOH) and diquaternary ammonium surfactant ([C22H45-N+(CH3)2-C6H12-N+(CH3)2-C6H13]Br2, C22-6-6) were used as templates to produce micropores and mesopores, respectively. The variation in concentration ratios of dual templates and hydrothermal synthesis conditions resulted in production of multi-lamellar MFI and the hybrid lamellar-bulk MFI (HLBM) zeolite structures. The relationship between the morphology, porosity, acidity, and catalytic properties of these catalysts was systematically studied. Then, the validity of the proposed synthesis approach for production of other types of zeolites composites was examined by creating a meso-/microporous bulk polymorph A (BEA)-lamellar MFI (BBLM) composite. The resulted composite samples showed higher catalytic stability compared to their single component zeolites. The studies demonstrated the high potential of the one-step dual template synthesis procedure for engineering the textural and catalytic properties of the synthesized zeolites.

Holistic Design In High-Speed Optical Interconnects

Integrated circuit scaling has enabled a huge growth in processing capability, which necessitates a corresponding increase in inter-chip communication bandwidth. As bandwidth requirements for chip-to-chip interconnection scale, deficiencies of electrical channels become more apparent. Optical links present a viable alternative due to their low frequency-dependent loss and higher bandwidth density in the form of wavelength division multiplexing. As integrated photonics and bonding technologies are maturing, commercialization of hybrid-integrated optical links are becoming a reality. Increasing silicon integration leads to better performance in optical links but necessitates a corresponding co-design strategy in both electronics and photonics. In this light, holistic design of high-speed optical links with an in-depth understanding of photonics and state-of-the-art electronics brings their performance to unprecedented levels. This thesis presents developments in high-speed optical links by co-designing and co-integrating the primary elements of an optical link: receiver, transmitter, and clocking.

In the first part of this thesis a 3D-integrated CMOS/Silicon-photonic receiver will be presented. The electronic chip features a novel design that employs a low-bandwidth TIA front-end, double-sampling and equalization through dynamic offset modulation. Measured results show -14.9dBm of sensitivity and energy efficiency of 170fJ/b at 25Gb/s. The same receiver front-end is also used to implement source-synchronous 4-channel WDM-based parallel optical receiver. Quadrature ILO-based clocking is employed for synchronization and a novel frequency-tracking method that exploits the dynamics of IL in a quadrature ring oscillator to increase the effective locking range. An adaptive body-biasing circuit is designed to maintain the per-bit-energy consumption constant across wide data-rates. The prototype measurements indicate a record-low power consumption of 153fJ/b at 32Gb/s. The receiver sensitivity is measured to be -8.8dBm at 32Gb/s.

Next, on the optical transmitter side, three new techniques will be presented. First one is a differential ring modulator that breaks the optical bandwidth/quality factor trade-off known to limit the speed of high-Q ring modulators. This structure maintains a constant energy in the ring to avoid pattern-dependent power droop. As a first proof of concept, a prototype has been fabricated and measured up to 10Gb/s. The second technique is thermal stabilization of micro-ring resonator modulators through direct measurement of temperature using a monolithic PTAT temperature sensor. The measured temperature is used in a feedback loop to adjust the thermal tuner of the ring. A prototype is fabricated and a closed-loop feedback system is demonstrated to operate at 20Gb/s in the presence of temperature fluctuations. The third technique is a switched-capacitor based pre-emphasis technique designed to extend the inherently low bandwidth of carrier injection micro-ring modulators. A measured prototype of the optical transmitter achieves energy efficiency of 342fJ/bit at 10Gb/s and the wavelength stabilization circuit based on the monolithic PTAT sensor consumes 0.29mW.

Lastly, a first-order frequency synthesizer that is suitable for high-speed on-chip clock generation will be discussed. The proposed design features an architecture combining an LC quadrature VCO, two sample-and-holds, a PI, digital coarse-tuning, and rotational frequency detection for fine-tuning. In addition to an electrical reference clock, as an extra feature, the prototype chip is capable of receiving a low jitter optical reference clock generated by a high-repetition-rate mode-locked laser. The output clock at 8GHz has an integrated RMS jitter of 490fs, peak-to-peak periodic jitter of 2.06ps, and total RMS jitter of 680fs. The reference spurs are measured to be –64.3dB below the carrier frequency. At 8GHz the system consumes 2.49mW from a 1V supply.

Análise de conversores de frequência óptica baseados em amplificadores ópticos semicondutores

Dissertação de mest. em Engenharia de Sistemas e Computação, Faculdade de Ciências e Tecnologia, Univ. do Algarve, 2002

Design, Fabrication, and Mechanical Property Analysis of 3D Nanoarchitected Materials

Recent developments in micro- and nanoscale 3D fabrication techniques have enabled the creation of materials with a controllable nanoarchitecture that can have structural features spanning 5 orders of magnitude from tens of nanometers to millimeters. These fabrication methods in conjunction with nanomaterial processing techniques permit a nearly unbounded design space through which new combinations of nanomaterials and architecture can be realized. In the course of this work, we designed, fabricated, and mechanically analyzed a wide range of nanoarchitected materials in the form of nanolattices made from polymer, composite, and hollow ceramic beams. Using a combination of two-photon lithography and atomic layer deposition, we fabricated samples with periodic and hierarchical architectures spanning densities over 4 orders of magnitude from ρ=0.3-300kg/m³ and with features as small as 5nm. Uniaxial compression and cyclic loading tests performed on different nanolattice topologies revealed a range of novel mechanical properties: the constituent nanoceramics used here have size-enhanced strengths that approach the theoretical limit of materials strength; hollow aluminum oxide (Al₂O₃) nanolattices exhibited ductile-like deformation and recovered nearly completely after compression to 50% strain when their wall thicknesses were reduced below 20nm due to the activation of shell buckling; hierarchical nanolattices exhibited enhanced recoverability and a near linear scaling of strength and stiffness with relative density, with E∝ρ^1.04 and σy∝ρ^1.17 for hollow Al₂O₃ samples; periodic rigid and non-rigid nanolattice topologies were tested and showed a nearly uniform scaling of strength and stiffness with relative density, marking a significant deviation from traditional theories on “bending” and “stretching” dominated cellular solids; and the mechanical behavior across all topologies was highly tunable and was observed to strongly correlate with the slenderness λ and the wall thickness-to-radius ratio t/a of the beams. These results demonstrate the potential of nanoarchitected materials to create new highly tunable mechanical metamaterials with previously unattainable properties.

Synthesis of porous graphene/TiO2 by use of recycled graphite

Graphene-based nanomaterials are a kind of new technological materials with high interest for physicists, chemists and materials scientists. Graphene is a two-dimensional (2-D) sheet of carbon atoms in a hexagonal configuration with atoms bonded by sp2 bonds. These bonds and this electron configuration provides the extraordinary properties of graphene, such as very large surface area, a tunable band gap, high mechanical strength and high elasticity and thermal conductivity [1]. Graphene has also been investigated for preparation of composites with various semiconductors like TiO2, ZnO, CdS aiming at enhanced photocatalytic activity for their use for photochemical reaction as water splitting or CO2 to methanol conversion [2-3]. In this communication, the synthesis of porous graphene@TiO2 obtained from a powder graphite recycled, supplied by ECOPIBA, is presented. This graphite was exfoliated, using a nonionic surfactant (Triton X-100) and sonication. Titanium(IV) isopropoxide was used as TiO2 source. After removing the surfactant with a solution HCl/n-propanol, a porous solid is obtained with a specific area of 358 m2g-1. The solid was characterized by XRD, FTIR, XPS, EDX and TEM. Figure 1 shows the graphene 2D layer bonded with nanoparticles of TiO2. When a water suspension of this material is exposed with UV-vis radiation, water splitting reaction is carried out and H2/O2 bubbles are observed (Figure 2)

ELECTRON TRANSPORT IN LOW-DIMENSIONAL NANOSTRUCTURES - THEORETICAL STUDY WITH APPLICATION

Graphene as a carbon monolayer has attracted extensive research interest in recent years. My research work within the frame of density functional theory has suggested that positioning graphene in proximity to h-BN may induce a finite energy gap in graphene, which is important for device applications. For an AB-stacked graphene/BN bilayer, a finite gap is induced at the equilibrium configuration. This induced gap shows a linear relationship with the applied strain. For a graphene/BN/graphene trilayer, a negligible gap is predicted in the ground state due to the overall symmetry of the system. When an electric field is applied, a tunable gap can be obtained for both AAA and ABA stackings. Enhanced tunneling current in the AA-stacked bilayer nanoribbons is predicted compared to either single-layer or AB-stacked bilayer nanoribbons. Interlayer separation between the nanoribbons is shown to have a profound impact on the conducting features. The effect of boron or nitrogen doping on the electronic transport properties of C60 fullerene is studied. The BC59 fullerene exhibits a considerably higher current than the pristine or nitrogen doped fullerenes beyond the applied bias of 1 V, suggesting it can be an effective semiconductor in p-type devices. The interaction between nucleic acid bases - adenine (A), guanine (G), cytosine (C), thymine (T) and uracil (U) - and a hydrogen-passivated silicon nanowire (SiNW) is investigated. The binding energy of the bases with the SiNW shows the order: G > A~C~T~U. This suggests that the interaction strength of a hydrogen passivated SiNW with the nucleic acid bases is nearly the same-G being an exception. The nature of the interaction is suggested to be electrostatic.

Disorder-induced light localisation:from random to artificial

Light localisation in one-dimensional (1D) randomly disordered medium is usually characterized by randomly distributed resonances with fluctuating transmission values, instead of selectively distributed resonances with close-to-unity transmission values that are needed in real application fields. By a resonance tuning scheme developed recently, opening of favorable resonances or closing of unfavorable resonances are achieved by disorder micro-modification, both on the layered medium and the fibre Bragg grating (FBG) array. And furthermore, it is shown that those disorder-induced resonances are independently tunable. Therefore, selected resonances and arranged light localisation can be achieved via artificial disorder, and thus meet the demand of various application fields.

Weakly-constrained codes for suppression of patterning effects in digital communications

We propose weakly-constrained stream and block codes with tunable pattern-dependent statistics and demonstrate that the block code capacity at large block sizes is close to the the prediction obtained from a simple Markov model published earlier. We demonstrate the feasibility of the code by presenting original encoding and decoding algorithms with a complexity log-linear in the block size and with modest table memory requirements. We also show that when such codes are used for mitigation of patterning effects in optical fibre communications, a gain of about 0.5dB is possible under realistic conditions, at the expense of small redundancy (≈10%). © 2010 IEEE

Influence of combined fundamental potentials in a nonlinear vibration energy harvester

Ambient mechanical vibrations have emerged as a viable energy source for low-power wireless sensor nodes aiming the upcoming era of the ‘Internet of Things’. Recently, purposefully induced dynamical nonlinearities have been exploited to widen the frequency spectrum of vibration energy harvesters. Here we investigate some critical inconsistencies between the theoretical formulation and applications of the bistable Duffing nonlinearity in vibration energy harvesting. A novel nonlinear vibration energy harvesting device with the capability to switch amidst individually tunable bistable-quadratic, monostable-quartic and bistable-quartic potentials has been designed and characterized. Our study highlights the fundamentally different large deflection behaviors of the theoretical bistable-quartic Duffing oscillator and the experimentally adapted bistable-quadratic systems, and underlines their implications in the respective spectral responses. The results suggest enhanced performance in the bistable-quartic potential in comparison to others, primarily due to lower potential barrier and higher restoring forces facilitating large amplitude inter-well motion at relatively lower accelerations.

Activated carbons with high nitrogen content by a combination of hydrothermal carbonization with activation

This paper reports the production of carbons materials with a nitrogen content around 8%(w/w) and a well-developed porous structure, with BET surface area and pore volume up to 2130 m2 g−1 and 1.12 cm3 g−1, respectively, produced by a combination of hydrothermal carbonization, an environmental friendly method in the production of sustainable tunable carbon materials, with traditional activation methods. The porosity was developed through an activation process according to different routes, namely activation with CO2 and chemical activation using CaCO3 and K2CO3. The successful production of activated carbons using chitosan as a nitrogen source revealed to be a good alternative to post-synthesis methods.

Resonant metamaterials for the control of Rayleigh waves

Since their emergence, locally resonant metamaterials have found several applications for the control of surface waves, from micrometer-sized electronic devices to meter-sized seismic barriers. The interaction between Rayleigh-type surface waves and resonant metamaterials has been investigated through the realization of locally resonant metasurfaces, thin elastic interfaces constituted by a cluster of resonant inclusions or oscillators embedded near the surface of an elastic waveguide. When such resonant metasurfaces are embedded in an elastic homogeneous half-space, they can filter out the propagation of Rayleigh waves, creating low-frequency bandgaps at selected frequencies. In the civil engineering context, heavy resonating masses are needed to extend the bandgap frequency width of locally resonant devices, a requirement that limits their practical implementations. In this dissertation, the wave attenuation capabilities of locally resonant metasurfaces have been enriched by proposing (i) tunable metasurfaces to open large frequency bandgaps with small effective inertia, and by developing (ii) an analytical framework aimed at studying the propagation of Rayleigh waves propagation in deep resonant waveguides. In more detail, inertial amplified resonators are exploited to design advanced metasurfaces with a prescribed static and a tunable dynamic response. The modular design of the tunable metasurfaces allows to shift and enlarge low-frequency spectral bandgaps without modifying the total inertia of the metasurface. Besides, an original dispersion law is derived to study the dispersive properties of Rayleigh waves propagating in thick resonant layers made of sub-wavelength resonators. Accordingly, a deep resonant wave barrier of mechanical resonators embedded inside the soil is designed to impede the propagation of seismic surface waves. Numerical models are developed to confirm the analytical dispersion predictions of the tunable metasurface and resonant layer. Finally, a medium-size scale resonant wave barrier is designed according to the soil stratigraphy of a real geophysical scenario to attenuate ground-borne vibration.

Nanostructured Systems for Electrocatalysis of Reduction Reactions for Energy Conversion Applications

Oxygen Reduction Reaction (ORR) requires a platinum-based catalyst to reduce the activation barrier. One of the most promising materials as alternative catalysts are carbon-based, graphene and carbon nanotubes (CNT) derivatives. ORR on a carbon-based substrate involves the less efficient two electrons process and the optimal four electrons process. New synthetic strategies to produce tunable graphene-based materials utilizing graphene oxide (GO) as a base inspired the first part of this work. Hydrogen Evolution Reaction (HER) is a slow process requiring also platinum or palladium as catalyst. In the second part of this work, we develop and use a technique for Ni nanoparticles electrodeposition using NiCl2 as precursor in the presence of ascorbate ligands. Electrodeposition of nano-nickel onto flat glassy carbon (GC) and onto nitrogen-doped reduced graphene oxide (rGO-N) substrates are studied. State of the art catalysts for CO2RR requires rare metals rhenium or rhodium. In recent years significant research has been done on non-noble metals and molecular systems to use as electro and photo-catalysts (artificial photosynthesis). As Cu-Zn alloys show good CO2RR performance, here we applied the same nanoparticle electrosynthesis technique using as precursors CuCl2 and Cl2Zn and observed successful formation of the nanoparticles and a notable activity in presence of CO2. Using rhenium complexes as catalysts is another popular approach and di-nuclear complexes have a positive cooperative effect. More recently a growing family of pre-catalysts based on the earth-abundant metal manganese, has emerged as a promising, cheaper alternative. Here we study the cooperative effects of di-nuclear manganese complexes derivatives when used as homogeneous electrocatalysts, as well as a rhenium functionalized polymer used as heterogeneous electrocatalyst.