Genomic mining of prokaryotic repressors for orthogonal logic gates

Genetic circuits perform computational operations based on interactions between freely diffusing molecules within a cell. When transcription factors are combined to build a circuit, unintended interactions can disrupt its function. Here, we apply 'part mining' to build a library of 73 TetR-family repressors gleaned from prokaryotic genomes. The operators of a subset were determined using an in vitro method, and this information was used to build synthetic promoters. The promoters and repressors were screened for cross-reactions. Of these, 16 were identified that both strongly repress their cognate promoter (5- to 207-fold) and exhibit minimal interactions with other promoters. Each repressor-promoter pair was converted to a NOT gate and characterized. Used as a set of 16 NOT/NOR gates, there are >10[superscript 54] circuits that could be built by changing the pattern of input and output promoters. This represents a large set of compatible gates that can be used to construct user-defined circuits.United States. Air Force Office of Scientific Research (Award FA9550-11-C-0028)American Society for Engineering Education. National Defense Science and Engineering Graduate Fellowship (32 CFR 168a)United States. Defense Advanced Research Projects Agency. Chronical of Lineage Indicative of Origins (N66001-12-C-4016)United States. Office of Naval Research (N00014-13-1-0074)National Institutes of Health (U.S.) (GM095765)National Science Foundation (U.S.). Synthetic Biology Engineering Research Center (SA5284-11210

Synthesis of 2-level combinatorial circuits with PKmin

In this paper a new design tool is presented that is useful in automated synthesis of combinatorial logic. PKmin program is devoted for synthesis of 2-level circuits composed of gates and PLAs, multi-level circuits and a functional decomposition of logical functions for LUT-based logic implementations in FPGA. It has been built on the basis of the research conducted at Cracow University of Technology. In the paper design algorithms implemented in PKmin are mutually compared. Then, an experimental efficiency comparison of gate and PLA-based 2-level synthesis with PKmin and Espresso design tools is reported

Digital Circuit Design Using Floating Gate Transistors

Floating gate (flash) transistors are used exclusively for memory applications today. These applications include SD cards of various form factors, USB flash drives and SSDs. In this thesis, we explore the use of flash transistors to implement digital logic circuits. Since the threshold voltage of flash transistors can be modified at a fine granularity during programming, several advantages are obtained by our flash-based digital circuit design approach. For one, speed binning at the factory can be controlled with precision. Secondly, an IC can be re-programmed in the field, to negate effects such as aging, which has been a significant problem in recent times, particularly for mission-critical applications. Thirdly, unlike a regular MOSFET, which has one threshold voltage level, a flash transistor can have multiple threshold voltage levels. The benefit of having multiple threshold voltage levels in a flash transistor is that it allows the ability to encode more symbols in each device, unlike a regular MOSFET. This allows us to implement multi-valued logic functions natively. In this thesis, we evaluate different flash-based digital circuit design approaches and compare their performance with a traditional CMOS standard cell-based design approach. We begin by evaluating our design approach at the cell level to optimize the design’s delay, power energy and physical area characteristics. The flash-based approach is demonstrated to be better than the CMOS standard cell approach, for these performance metrics. Afterwards, we present the performance of our design approach at the block level. We describe a synthesis flow to decompose a circuit block into a network of interconnected flash-based circuit cells. We also describe techniques to optimize the resulting network of flash-based circuit cells using don’t cares. Our optimization approach distinguishes itself from other optimization techniques that use don’t cares, since it a) targets a flash-based design flow, b) optimizes clusters of logic nodes at once instead of one node at a time, c) attempts to reduce the number of cubes instead of reducing the number of literals in each cube and d) performs optimization on the post-technology mapped netlist which results in a direct improvement in result quality, as compared to pre-technology mapping logic optimization that is typically done in the literature. The resulting network characteristics (delay, power, energy and physical area) are presented. These results are compared with a standard cell-based realization of the same block (obtained using commercial tools) and we demonstrate significant improvements in all the design metrics. We also study flash-based FPGA designs (both static and dynamic), and present the tradeoff of delay, power dissipation and energy consumption of the various designs. Our work differs from previously proposed flash-based FPGAs, since we embed the flash transistors (which store the configuration bits) directly within the logic and interconnect fabrics. We also present a detailed description of how the programming of the configuration bits is accomplished, for all the proposed designs

Digital Circuit Design Using Floating Gate Transistors

Floating gate (flash) transistors are used exclusively for memory applications today. These applications include SD cards of various form factors, USB flash drives and SSDs. In this thesis, we explore the use of flash transistors to implement digital logic circuits. Since the threshold voltage of flash transistors can be modified at a fine granularity during programming, several advantages are obtained by our flash-based digital circuit design approach. For one, speed binning at the factory can be controlled with precision. Secondly, an IC can be re-programmed in the field, to negate effects such as aging, which has been a significant problem in recent times, particularly for mission-critical applications. Thirdly, unlike a regular MOSFET, which has one threshold voltage level, a flash transistor can have multiple threshold voltage levels. The benefit of having multiple threshold voltage levels in a flash transistor is that it allows the ability to encode more symbols in each device, unlike a regular MOSFET. This allows us to implement multi-valued logic functions natively. In this thesis, we evaluate different flash-based digital circuit design approaches and compare their performance with a traditional CMOS standard cell-based design approach. We begin by evaluating our design approach at the cell level to optimize the design’s delay, power energy and physical area characteristics. The flash-based approach is demonstrated to be better than the CMOS standard cell approach, for these performance metrics. Afterwards, we present the performance of our design approach at the block level. We describe a synthesis flow to decompose a circuit block into a network of interconnected flash-based circuit cells. We also describe techniques to optimize the resulting network of flash-based circuit cells using don’t cares. Our optimization approach distinguishes itself from other optimization techniques that use don’t cares, since it a) targets a flash-based design flow, b) optimizes clusters of logic nodes at once instead of one node at a time, c) attempts to reduce the number of cubes instead of reducing the number of literals in each cube and d) performs optimization on the post-technology mapped netlist which results in a direct improvement in result quality, as compared to pre-technology mapping logic optimization that is typically done in the literature. The resulting network characteristics (delay, power, energy and physical area) are presented. These results are compared with a standard cell-based realization of the same block (obtained using commercial tools) and we demonstrate significant improvements in all the design metrics. We also study flash-based FPGA designs (both static and dynamic), and present the tradeoff of delay, power dissipation and energy consumption of the various designs. Our work differs from previously proposed flash-based FPGAs, since we embed the flash transistors (which store the configuration bits) directly within the logic and interconnect fabrics. We also present a detailed description of how the programming of the configuration bits is accomplished, for all the proposed designs

Deterministic, Efficient Variation of Circuit Components to Improve Resistance to Reverse Engineering

This research proposes two alternative methods for generating semantically equivalent circuit variants which leave the circuit\u27s internal structure pseudo-randomly determined. Component fusion deterministically selects subcircuits using a component identification algorithm and replaces them using a deterministic algorithm that generates canonical logic forms. Component encryption seeks to alter the semantics of individual circuit components using an encoding function, but preserves the overall circuit semantics by decoding signal values later in the circuit. Experiments were conducted to examine the performance of component fusion and component encryption against representative trials of subcircuit selection-and-replacement and Boundary Blurring, two previously defined methods for circuit obfuscation. Overall, results support the conclusion that both component fusion and component encryption generate more secure variants than previous methods and that these variants are more efficient in terms of required circuit delay and the power and area required for their implementation

Scaling silicon-based quantum computing using CMOS technology: State-of-the-art, Challenges and Perspectives

Complementary metal-oxide semiconductor (CMOS) technology has radically reshaped the world by taking humanity to the digital age. Cramming more transistors into the same physical space has enabled an exponential increase in computational performance, a strategy that has been recently hampered by the increasing complexity and cost of miniaturization. To continue achieving significant gains in computing performance, new computing paradigms, such as quantum computing, must be developed. However, finding the optimal physical system to process quantum information, and scale it up to the large number of qubits necessary to build a general-purpose quantum computer, remains a significant challenge. Recent breakthroughs in nanodevice engineering have shown that qubits can now be manufactured in a similar fashion to silicon field-effect transistors, opening an opportunity to leverage the know-how of the CMOS industry to address the scaling challenge. In this article, we focus on the analysis of the scaling prospects of quantum computing systems based on CMOS technology.Comment: Comments welcom

Low-power CMOS digital-pixel Imagers for high-speed uncooled PbSe IR applications

This PhD dissertation describes the research and development of a new low-cost medium wavelength infrared MWIR monolithic imager technology for high-speed uncooled industrial applications. It takes the baton on the latest technological advances in the field of vapour phase deposition (VPD) PbSe-based medium wavelength IR (MWIR) detection accomplished by the industrial partner NIT S.L., adding fundamental knowledge on the investigation of novel VLSI analog and mixed-signal design techniques at circuit and system levels for the development of the readout integrated device attached to the detector. The work supports on the hypothesis that, by the use of the preceding design techniques, current standard inexpensive CMOS technologies fulfill all operational requirements of the VPD PbSe detector in terms of connectivity, reliability, functionality and scalability to integrate the device. The resulting monolithic PbSe-CMOS camera must consume very low power, operate at kHz frequencies, exhibit good uniformity and fit the CMOS read-out active pixels in the compact pitch of the focal plane, all while addressing the particular characteristics of the MWIR detector: high dark-to-signal ratios, large input parasitic capacitance values and remarkable mismatching in PbSe integration. In order to achieve these demands, this thesis proposes null inter-pixel crosstalk vision sensor architectures based on a digital-only focal plane array (FPA) of configurable pixel sensors. Each digital pixel sensor (DPS) cell is equipped with fast communication modules, self-biasing, offset cancellation, analog-to-digital converter (ADC) and fixed pattern noise (FPN) correction. In-pixel power consumption is minimized by the use of comprehensive MOSFET subthreshold operation. The main aim is to potentiate the integration of PbSe-based infra-red (IR)-image sensing technologies so as to widen its use, not only in distinct scenarios, but also at different stages of PbSe-CMOS integration maturity. For this purpose, we posit to investigate a comprehensive set of functional blocks distributed in two parallel approaches: • Frame-based “Smart” MWIR imaging based on new DPS circuit topologies with gain and offset FPN correction capabilities. This research line exploits the detector pitch to offer fully-digital programmability at pixel level and complete functionality with input parasitic capacitance compensation and internal frame memory. • Frame-free “Compact”-pitch MWIR vision based on a novel DPS lossless analog integrator and configurable temporal difference, combined with asynchronous communication protocols inside the focal plane. This strategy is conceived to allow extensive pitch compaction and readout speed increase by the suppression of in-pixel digital filtering, and the use of dynamic bandwidth allocation in each pixel of the FPA. In order make the electrical validation of first prototypes independent of the expensive PbSe deposition processes at wafer level, investigation is extended as well to the development of affordable sensor emulation strategies and integrated test platforms specifically oriented to image read-out integrated circuits. DPS cells, imagers and test chips have been fabricated and characterized in standard 0.15μm 1P6M, 0.35μm 2P4M and 2.5μm 2P1M CMOS technologies, all as part of research projects with industrial partnership. The research has led to the first high-speed uncooled frame-based IR quantum imager monolithically fabricated in a standard VLSI CMOS technology, and has given rise to the Tachyon series [1], a new line of commercial IR cameras used in real-time industrial, environmental and transportation control systems. The frame-free architectures investigated in this work represent a firm step forward to push further pixel pitch and system bandwidth up to the limits imposed by the evolving PbSe detector in future generations of the device.La present tesi doctoral descriu la recerca i el desenvolupament d'una nova tecnologia monolítica d'imatgeria infraroja de longitud d'ona mitja (MWIR), no refrigerada i de baix cost, per a usos industrials d'alta velocitat. El treball pren el relleu dels últims avenços assolits pel soci industrial NIT S.L. en el camp dels detectors MWIR de PbSe depositats en fase vapor (VPD), afegint-hi coneixement fonamental en la investigació de noves tècniques de disseny de circuits VLSI analògics i mixtes pel desenvolupament del dispositiu integrat de lectura unit al detector pixelat. Es parteix de la hipòtesi que, mitjançant l'ús de les esmentades tècniques de disseny, les tecnologies CMOS estàndard satisfan tots els requeriments operacionals del detector VPD PbSe respecte a connectivitat, fiabilitat, funcionalitat i escalabilitat per integrar de forma econòmica el dispositiu. La càmera PbSe-CMOS resultant ha de consumir molt baixa potència, operar a freqüències de kHz, exhibir bona uniformitat, i encabir els píxels actius CMOS de lectura en el pitch compacte del pla focal de la imatge, tot atenent a les particulars característiques del detector: altes relacions de corrent d'obscuritat a senyal, elevats valors de capacitat paràsita a l'entrada i dispersions importants en el procés de fabricació. Amb la finalitat de complir amb els requisits previs, es proposen arquitectures de sensors de visió de molt baix acoblament interpíxel basades en l'ús d'una matriu de pla focal (FPA) de píxels actius exclusivament digitals. Cada píxel sensor digital (DPS) està equipat amb mòduls de comunicació d'alta velocitat, autopolarització, cancel·lació de l'offset, conversió analògica-digital (ADC) i correcció del soroll de patró fixe (FPN). El consum en cada cel·la es minimitza fent un ús exhaustiu del MOSFET operant en subllindar. L'objectiu últim és potenciar la integració de les tecnologies de sensat d'imatge infraroja (IR) basades en PbSe per expandir-ne el seu ús, no només a diferents escenaris, sinó també en diferents estadis de maduresa de la integració PbSe-CMOS. En aquest sentit, es proposa investigar un conjunt complet de blocs funcionals distribuïts en dos enfocs paral·lels: - Dispositius d'imatgeria MWIR "Smart" basats en frames utilitzant noves topologies de circuit DPS amb correcció de l'FPN en guany i offset. Aquesta línia de recerca exprimeix el pitch del detector per oferir una programabilitat completament digital a nivell de píxel i plena funcionalitat amb compensació de la capacitat paràsita d'entrada i memòria interna de fotograma. - Dispositius de visió MWIR "Compact"-pitch "frame-free" en base a un novedós esquema d'integració analògica en el DPS i diferenciació temporal configurable, combinats amb protocols de comunicació asíncrons dins del pla focal. Aquesta estratègia es concep per permetre una alta compactació del pitch i un increment de la velocitat de lectura, mitjançant la supressió del filtrat digital intern i l'assignació dinàmica de l'ample de banda a cada píxel de l'FPA. Per tal d'independitzar la validació elèctrica dels primers prototips respecte a costosos processos de deposició del PbSe sensor a nivell d'oblia, la recerca s'amplia també al desenvolupament de noves estratègies d'emulació del detector d'IR i plataformes de test integrades especialment orientades a circuits integrats de lectura d'imatge. Cel·les DPS, dispositius d'imatge i xips de test s'han fabricat i caracteritzat, respectivament, en tecnologies CMOS estàndard 0.15 micres 1P6M, 0.35 micres 2P4M i 2.5 micres 2P1M, tots dins el marc de projectes de recerca amb socis industrials. Aquest treball ha conduït a la fabricació del primer dispositiu quàntic d'imatgeria IR d'alta velocitat, no refrigerat, basat en frames, i monolíticament fabricat en tecnologia VLSI CMOS estàndard, i ha donat lloc a Tachyon, una nova línia de càmeres IR comercials emprades en sistemes de control industrial, mediambiental i de transport en temps real.Postprint (published version

34th Midwest Symposium on Circuits and Systems-Final Program

Organized by the Naval Postgraduate School Monterey California. Cosponsored by the IEEE Circuits and Systems Society. Symposium Organizing Committee: General Chairman-Sherif Michael, Technical Program-Roberto Cristi, Publications-Michael Soderstrand, Special Sessions- Charles W. Therrien, Publicity: Jeffrey Burl, Finance: Ralph Hippenstiel, and Local Arrangements: Barbara Cristi

Synthesis of variability-tolerant circuits with adaptive clocking

Improvements in circuit manufacturing have allowed, along the years, increasingly complex designs. This has been enabled by the miniaturization that circuit components have undergone. But, in recent years, this scaling has shown decreasing benefits as we approach fundamental limits. Furthermore, the decrease in size is nowadays producing an increase in variability: unpredictable differences and changes in the behavior of components. Historically, this has been addressed by establishing guardband margins at the design stage. Nonetheless, as variability grows, the amount of pessimism introduced by these margins is taking an ever-increasing cost on performance and power consumption. In recent years, several approaches have been proposed to lower the impact of variability and reduce margins. One such technique is the substitution of a classical PLL clock by a Ring Oscillator Clock. The design of the Ring Oscillator Clock is done in such a way that its variability is highly correlated to that of the circuit. One of the contributions of this thesis is in the automatic design of such circuits. In particular, we propose a novel method to design digital delay lines with variability-tracking properties. Those designs are also suitable for other purposes, such as bundled-data circuits or performance monitors. The advantage of the proposed technique is based on the exclusive use of cells from a standard cell library, which lowers the design cost and complexity. The other focus of this thesis is on state encoding for asynchronous controllers. One of the main properties of asynchronous circuits is their ability to, implicitly, work under variable conditions. In the near future, this advantage might increase the relevance of this class of circuits. One of the hardest stages for the synthesis of these circuits is the state encoding. This thesis presents a SAT-based algorithm for solving the state encoding at the state level. It is shown, by means of a comprehensive benchmark suite, that results obtained by this technique improve significantly compared to results from similar approaches. Nonetheless, the main limitation of techniques at the state level is the state explosion problem, to which the sequential modeling of concurrency is often subject to. The last contribution of this thesis is a method to process asynchronous circuits in order to allow the use of state-based techniques for large instances. In particular, the process is divided into three stages: projection, signal insertion and re-composition. In the projection step, the behavior of the controller is simplified until the signal insertion can be performed by state-based techniques. Afterwards, the re-composition generalizes the insertion of the signal into the original controller. Experimental results show that this process enables the resolution of large controllers, in the order of 10 6 states, by state-based techniques. At the same time, only a minor impact in solution quality is observed, preserving one of the main advantages for state-based approaches.A lo largo de los años, mejoras en la fabricación de circuitos han permitido diseños cada vez más complejos. Esta tendencia, que ha tenido lugar gracias a la miniaturización de los componentes que forman estos circuitos, recientemente está mostrando beneficios decrecientes a medida que nos acercamos a ciertas limitaciones fundamentales. Además de estos beneficios decrecientes, la reducción en tamaño está produciendo un aumento, cada vez mayor, en la variabilidad: diferencias impredecibles y cambios en el comportamiento de los componentes. Esto se ha compensado históricamente con el uso de márgenes de seguridad en la fase de diseño. No obstante, a medida que la variabilidad crece, la cantidad de pesimismo que estos márgenes introducen está afectando significativamente el coste en rendimiento y consumo energético. En los últimos años se han propuesto diferentes técnicas para limitar el impacto de la variabilidad y reducir márgenes de seguridad. Una de estas técnicas consiste en substituir un reloj PLL clásico por un Ring Oscillator Clock. El diseño de un Ring Oscillator Clock se realiza de manera que su variabilidad este altamente correlacionada con la del circuito. Una de las contribuciones de esta tesis consiste en el diseño automático de estos relojes. Concretamente, se propone un nuevo método para diseñar líneas de retardo digitales (digital delay lines) que tengan como propiedad la capacidad de imitar la variabilidad de un circuito dado. Estos diseños son también apropiados para otros propósitos, tal y como circuitos con ?bundled-data? o monitorizadores de rendimiento. La ventaja del método propuesto con respecto a otras técnicas similares radica en el uso exclusivo de celdas provenientes de una librería de celdas estándar, lo que reduce considerablemente el coste de diseño y su complejidad. Por otro lado, esta tesis también se centra en la codificación de estados de circuitos asíncronos. Una de las principales propiedades de estos circuitos reside en su capacidad implícita para trabajar bajo condiciones de variabilidad. Es previsible que, en un futuro próximo, esta ventaja se vuelva aún más relevante. La síntesis de circuitos asíncronos consta de varias etapas, una de las cuales es la codificación de estados. Este trabajo presenta un algoritmo basado en SAT que permite resolver la codificación de estados a nivel de estado. Mediante el uso de un exhaustivo banco de pruebas, esta tesis muestra como resultados obtenidos por esta técnica mejoran significativamente en comparación con otros métodos similares. A pesar de ello, técnicas que trabajan a nivel de estado tienen como principal limitación el problema conocido como "explosión de estados" que aparece habitualmente cuando se modelan elementos concurrentes de manera secuencial. Así pues, la última contribución de esta tesis es la propuesta de un método para procesar circuitos asíncronos de manera que técnicas a nivel de estado sean usables para instancias grandes. En concreto, el proceso está dividido en tres fases: proyección, inserción de señal y re-composición. En la etapa de proyección, el comportamiento del controlador es simplificado suficientemente como para que la inserción de la señal se pueda realizar con técnicas a nivel de estado. A continuación, la re-composición generaliza esta inserción en el controlador original. Resultados experimentales muestran que este proceso permite la resolución de grandes controladores, del orden de 10^6 estados, mediante el uso de técnicas a nivel de estado. Al mismo tiempo, solo se observa un impacto mínimo en la calidad de las soluciones, preservando una de las mayores ventajas de los métodos a nivel de estado