Cell matrix methodologies for integrated circuit design

Journal ArticleA class of integrated circuit design and implementation methodologies is described. These techniques are unique in that they simultaneously model both function and interconnect using cells. These cells are designed such that cell adjacency normally implies interconnection. The absence of an interconnection is explicitly modeled as a wire break between adjacent cells. These methodologies have the potential to greatly simplify and shorten the design process since some design steps are either eliminated or merged with others. They permit near custom layout density while reducing design time over full custom design by up to thirty times and over gate array design by up to four times

VLSI Architecture and Design

Integrated circuit technology is rapidly approaching a state where feature sizes of one micron or less are tractable. Chip sizes are increasing slowly. These two developments result in considerably increased complexity in chip design. The physical characteristics of integrated circuit technology are also changing. The cost of communication will be dominating making new architectures and algorithms both feasible and desirable. A large number of processors on a single chip will be possible. The cost of communication will make designs enforcing locality superior to other types of designs. Scaling down feature sizes results in increase of the delay that wires introduce. The delay even of metal wires will become significant. Time tends to be a local property which will make the design of globally synchronous systems more difficult. Self-timed systems will eventually become a necessity. With the chip complexity measured in terms of logic devices increasing by more than an order of magnitude over the next few years the importance of efficient design methodologies and tools become crucial. Hierarchical and structured design are ways of dealing with the complexity of chip design. Structered design focuses on the information flow and enforces a high degree of regularity. Both hierarchical and structured design encourage the use of cell libraries. The geometry of the cells in such libraries should be parameterized so that for instance cells can adjust there size to neighboring cells and make the proper interconnection. Cells with this quality can be used as a basis for "Silicon Compilers"

A modular and interactive OLED-based lighting system

The concept of a flexible, large-area, organic light emitting diode (OLED)-based lighting system with a modular structure and built-in intelligent light management is introduced. Such a flexible, thin, portable lighting system with discreetly integrated electronics is important in order to allow the implementation of the lighting system into a variety of places, such as cars and temporary expedition areas. A modular construction of an OLED lighting panel makes it possible to control each OLED cell individually. This not only enables us to counteract aging or degradation effects in the OLED cells but it also allows individual OLED module brightness control to support human or ambient interaction based on integrated or centralized sensors. Moreover, integrating the driving electronics in the backplane of an OLED module improves the energy efficiency of operating large OLED panels. The thin, modular construction and individual, dynamic control are successfully demonstrated

Reduced order modeling of delayed PEEC circuits

We propose a novel model order reduction technique that is able to accurately reduce electrically large systems with delay elements, which can be described by means of neutral delayed differential equations. It is based on an adaptive multipoint expansion and model order reduction of equivalent first order systems. The neutral delayed differential formulation is preserved in the reduced model. Pertinent numerical results validate the proposed model order reduction approach

Path-programmable logic

Journal ArticlePath-Programmable Logic (PPL) is a structured IC design methodology under development at the University of Utah. PPL employs a sea-of-wires approach to design. In PPL, design is done entirely using cells for both functionality and interconnect. PPL cells may have modifiers that change either their connections or functionality. Wires in the PPL design plane are segmentable at any cell boundary. PPL is implemented as a set of cell libraries (NMOS, CMOS, and GaAs) and a suite of tools that permit the designer to create, modify, simulate and check PPL circuit designs and to generate mask data for them. PPL exhibits little or no area penalty with respect to full custom densities while permitting system design to be done more rapidly than with gate arrays or standard cells. PPL may be implemented as a sea-of-gates gate array to provide fast turnaround

Development of novel orthogonal genetic circuits, based on extracytoplasmic function (ECF) σ factors

The synthetic biology field aims to apply the engineering 'design-build-test-learn' cycle for the implementation of synthetic genetic circuits modifying the behavior of biological systems. In order to reach this goal, synthetic biology projects use a set of fully characterized biological parts that subsequently are assembled into complex synthetic circuits following a rational, model-driven design. However, even though the bottom-up design approach represents an optimal starting point to assay the behavior of the synthetic circuits under defined conditions, the rational design of such circuits is often restricted by the limited number of available DNA building blocks. These usually consist only of a handful of transcriptional regulators that additionally are often borrowed from natural biological systems. This, in turn, can lead to cross-reactions between the synthetic circuit and the host cell and eventually to loss of the original circuit function. Thus, one of the challenges in synthetic biology is to design synthetic circuits that perform the designated functions with minor cross-reactions (orthogonality). To overcome the restrictions of the widely used transcriptional regulators, this project aims to apply extracytoplasmic function (ECF) σ factors in the design novel orthogonal synthetic circuits. ECFs are the smallest and simplest alternative σ factors that recognize highly specific promoters. ECFs represent one of the most important mechanisms of signal transduction in bacteria, indeed, their activity is often controlled by anti-σ factors. Even though it was shown that the overexpression of heterologous anti-σ factors can generate an adverse effect on cell growth, they represent an attractive solution to control ECF activity. Finally, to date, we know thousands of ECF σ factors, widespread among different bacterial phyla, that are identifiable together with the cognate promoters and anti-σ factors, using bioinformatic approaches. All the above-mentioned features make ECF σ factors optimal candidates as core orthogonal regulators for the design of novel synthetic circuits. In this project, in order to establish ECF σ factors as standard building blocks in the synthetic biology field, we first established a high throughput experimental setup. This relies on microplate reader experiments performed using a highly sensitive luminescent reporter system. Luminescent reporters have a superior signal-to-noise ratio when compared to fluorescent reporters since they do not suffer from the high auto-fluorescence background of the bacterial cell. However, they also have a drawback represented by the constant light emission that can generate undesired cross-talk between neighboring wells on a microplate. To overcome this limitation, we developed a computational algorithm that corrects for luminescence bleed-through and estimates the “true” luminescence activity for each well of a microplate. We show that the correcting algorithm preserves low-level signals close to the background and that it is universally applicable to different experimental conditions. In order to simplify the assembly of large ECF-based synthetic circuits, we designed an ECF toolbox in E. coli. The toolbox allows for the combinatorial assembly of circuits into expression vectors, using a library of reusable genetic parts. Moreover, it also offers the possibility of integrating the newly generated synthetic circuits into four different phage attachment (att) sites present in the genome of E. coli. This allows for a flawless transition between plasmid-encoded and chromosomally integrated genetic circuits, expanding the possible genetic configurations of a given synthetic construct. Moreover, our results demonstrate that the four att sites are orthogonal in terms of the gene expression levels of the synthetic circuits. With the purpose of rationally design ECF-based synthetic circuits and taking advantage of the ECF toolbox, we characterized the dynamic behavior of a set of 15 ECF σ factors, their cognate promoters, and relative anti-σs. Overall, we found that ECFs are non-toxic and functional and that they display different binding affinities for the cognate target promoters. Moreover, our results show that it is possible to optimize the output dynamic range of the ECF-based switches by changing the copy number of the ECFs and target promoters, thus, tuning the input/output signal ratio. Next, by combining up to three ECF-switches, we generated a set of “genetic-timer circuits”, the first synthetic circuits harboring more than one ECF. ECF-based timer circuits sequentially activate a series of target genes with increasing time delays, moreover, the behavior of the circuits can be predicted by a set of mathematical models. In order to improve the dynamic response of the ECF-based constructs, we introduced anti-σ factors in our synthetic circuits. By doing so we first confirmed that anti-σ factors can exert an adverse effect on the growth of E. coli, thus we explored possible solutions. Our results demonstrate that anti-σ factors toxicity can be partially alleviated by generating truncated, soluble variants of the anti-σ factors and, eventually, completely abolished via chromosomal integration of the anti-σ factor-based circuits. Finally, after demonstrating that anti-σ factors can be used to generate a tunable time delay among ECF expression and target promoter activation, we designed ECF/AS-suicide circuits. Such circuits allow for the time-delayed cell-death of E. coli and will serve as a prototype for the further development of ECF/AS-based lysis circuits

Column-row addressing of thermo-optic phase shifters for controlling large silicon photonic circuits

We demonstrate a time-multiplexed row-column addressing scheme to drive thermo-optic phase shifters in a silicon photonic circuit. By integrating a diode in series with the heater, we can connect $N \times M$ heaters in an matrix topology to $N$ row and $M$ column lines. The heaters are digitally driven with pulse-width modulation, and time-multiplexed over different channels. This makes it possible to drive the circuit without digital-to-analog converters, and using only $M+N$ wires. We demonstrate this concept with a $1 \times 16$ power splitter tree with 15 thermo-optic phase shifters that are controlled in a $3 \times 5$ matrix, connected through 8 bond pads. This technique is especially useful in silicon photonic circuits with many tuners but limited space for electrical connections