Single-Molecule Carbon Nanotube Field-Effect Transistors for Genomic Applications

Single-molecule carbon nanotube-based field-effect transistors are promising all-electronic devices for probing interactions of various biological and chemical molecules at the single- molecule level. Such devices consist of point-functionalized carbon nanotubes which are charge sensitive in the vicinity of a generated defect on the nanotube sidewall. Of particular interest is the characterization of the kinetic rates and thermodynamics of DNA duplex formation through repeated association (hybridization) and dissociation (melting) events on timescales unmatched by conventional single-molecule methods. In this work, we study the kinetics and thermodynamics of DNA duplex formation with two types of single-walled nanotubes: CVD-grown and solution-processed. In both assessments, we are able to extract kinetic and thermodynamic parameters governing the hybridization and melting of DNA oligonucleotides. In the latter case, devices are spun onto a wafer surface from an organic suspension, revealing consistent electrical characteristics. Significant effort is made to expand this work to wafer-level, in an effort to make the fabrication manufacturable

DNA Matrix Operation Based on the Mechanism of the DNAzyme Binding to Auxiliary Strands to Cleave the Substrate

Numerical computation is a focus of DNA computing, and matrix operations are among the most basic and frequently used operations in numerical computation. As an important computing tool, matrix operations are often used to deal with intensive computing tasks. During calculation, the speed and accuracy of matrix operations directly affect the performance of the entire computing system. Therefore, it is important to find a way to perform matrix calculations that can ensure the speed of calculations and improve the accuracy. This paper proposes a DNA matrix operation method based on the mechanism of the DNAzyme binding to auxiliary strands to cleave the substrate. In this mechanism, the DNAzyme binding substrate requires the connection of two auxiliary strands. Without any of the two auxiliary strands, the DNAzyme does not cleave the substrate. Based on this mechanism, the multiplication operation of two matrices is realized; the two types of auxiliary strands are used as elements of the two matrices, to participate in the operation, and then are combined with the DNAzyme to cut the substrate and output the result of the matrix operation. This research provides a new method of matrix operations and provides ideas for more complex computing systems

Integrated Electronics for Molecular Biosensing

This thesis, Integrated electronics for molecular biosensing, focuses on different approaches to sense the presence and activity of a specific analyte by using integrated electronic platforms. The aim of the first platform is to detect the enzyme telomerase. Telomerase causes the elongation of telomeres, which are part of the chromosomes, and determines the lifespan of cells. Telomerase expression is a marker of malignity in tumoral cells and its evaluation can be exploited for early diagnosis of many types of cancer cells. To detect the telomerase enzyme, a CMOS (complementary metal-oxide semiconductor) biosensor based on CMFET (Charge-Modulated Field Effect Transistor) able to measure kinetics of DNA replication and telomerase reaction was developed. The sensor can be functionalized by immobilizing single strands of DNA that contain the telomeric sequence, used as probes. If telomerase is present, the probes will be elongated by the enzyme and the charge on the sensing area will change, which reflects in a variation of the output current or voltage. The chip includes three different readout schemes (voltage, current- and time-based), each of which has different measuring ranges and operating conditions. The measured data is then digitized, stored, and can be sent off-chip through SPI (Serial Peripheral Interface) protocol. A total of 1024 biosensors have been integrated in a single chip with a size of 10x10 mm2. Each sensor can be independently addressed and functionalized by an electrochemical procedure using an integrated potentiostat, thus requiring no external equipment. Although the sensors have been tailored and optimized to perform telomerase detection, the sensing areas can be functionalized to be used with different analytes. This feature turns the chip into a complete bioassay platform. The second part of this work rises from the idea that bacteria, like Escherichia coli, can detect analytes in solution even at extremely low concentrations and change their movement through a process called chemotaxis, to move towards chemical gradients in the solution. E. coli moves by rotating its flagella either clockwise (for random tumbles) or counterclockwise (for straight runs, when it senses a chemical it is attracted to). Therefore, observing bacteria flagellar rotation can give enough information on the presence of a specific analyte in the solution. To electronically detect bacteria movement, an active surface covered in electrodes has been designed. By measuring the impedance between each pair of electrodes through an integrated LIA (lock-in amplifier), it is possible to know how a single bacterium is moving. By that, the presence or absence of the analyte can be deduced, thus effectively turning bacteria into chemical sensors

Nucleic Acid Architectures for Therapeutics, Diagnostics, Devices and Materials

Nucleic acids (RNA and DNA) and their chemical analogs have been utilized as building materials due to their biocompatibility and programmability. RNA, which naturally possesses a wide range of different functions, is now being widely investigated for its role as a responsive biomaterial which dynamically reacts to changes in the surrounding environment. It is now evident that artificially designed self-assembling RNAs, that can form programmable nanoparticles and supra-assemblies, will play an increasingly important part in a diverse range of applications, such as macromolecular therapies, drug delivery systems, biosensing, tissue engineering, programmable scaffolds for material organization, logic gates, and soft actuators, to name but a few. The current exciting Special Issue comprises research highlights, short communications, research articles, and reviews that all bring together the leading scientists who are exploring a wide range of the fundamental properties of RNA and DNA nanoassemblies suitable for biomedical applications

New Logic Synthesis As Nanotechnology Enabler (invited paper)

Nanoelectronics comprises a variety of devices whose electrical properties are more complex as compared to CMOS, thus enabling new computational paradigms. The potentially large space for innovation has to be explored in the search for technologies that can support large-scale and high- performance circuit design. Within this space, we analyze a set of emerging technologies characterized by a similar computational abstraction at the design level, i.e., a binary comparator or a majority voter. We demonstrate that new logic synthesis techniques, natively supporting this abstraction, are the technology enablers. We describe models and data-structures for logic design using emerging technologies and we show results of applying new synthesis algorithms and tools. We conclude that new logic synthesis methods are required to both evaluate emerging technologies and to achieve the best results in terms of area, power and performance

On-chip ultra low power optical wake-up receiver for wireless sensor nodes targeting structural health monitoring

Wireless sensor network (WSN) consists of distributed nodes deployed for monitoring the physical conditions and organizing collected data at the central control unit. Power consumption is the challenges in WSN as the network consists of wireless sensor nodes becomes denser. By utilizing WSN and visible light technology, a simple health monitoring system design can be approached that are smaller in size, faster and lower power consumption. This work focuses on design a low power optical wake-up receiver to reduce the energy consumption of each node in WSN. A wake-up receiver is designed to be always-on for detecting incoming signal and switches on the stand by protocol controller and WSN network for data transmission process. The characteristic of optical transmission and functional circuit of a wake-up receiver has been investigated. A low power optical wake-up receiver has been designed in 180nm Silterra CMOS process technology. The proposed wake-up receiver consumes only 443pW in standby mode and 1.89nW in active mode. The proposed optical wake-up receiver drastically reduces the power consumption by more than one third compared to other wake-up receivers which could be a milestone in the medical field if successfully conducted

Multiplexing Techniques and Design-Automation Tools for FRET-Enabled Optical Computing

<p>FRET-enabled optical computing is a new computing paradigm that uses the energy of incident photons to perform computation in molecular-scale circuits composed of inter-communicating photoactive molecules. Unlike conventional computing approaches, computation in these circuits does not require any electric current; instead, it relies on the controlled-migration of energy in the circuit through a phenomenon called Förster Resonance Energy Transfer (FRET). This, coupled with other unique features of FRET circuits can enable computing in new domains that are unachievable by the conventional semiconductor-based computing, such as in-cell computing or targeted drug delivery. In this thesis, we explore novel FRET-based multiplexing techniques to significantly increase the storage density of optical storage media. Further, we develop analysis algorithms, and computer-aided design tools for FRET circuits.</p><p>Existing computer-aided design tools for FRET circuits are predominantly ad hoc and specific to particular functionalities. We develop a generic design-automation framework for FRET-circuit optimization that is not limited to any particular functionality. We also show that within a fixed time-budget, the low-speed of Monte-Carlo-based FRET-simulation (MCS) algorithms can have a potentially-significant negative impact on the quality of the design process, and to address this issue, we design and implement a fast FRET-simulation algorithm which is up to several million times faster than existing MCS algorithms. We finally exploit the unique features of FRET-enabled optical computing to develop novel multiplexing techniques that enable orders of magnitude higher storage density compared to conventional optical storage media, such as DVD or Blu-Ray.</p>Dissertatio