Switchable Genetic Oscillator Operating in Quasi-Stable Mode

Ring topologies of repressing genes have qualitatively different long-term dynamics if the number of genes is odd (they oscillate) or even (they exhibit bistability). However, these attractors may not fully explain the observed behavior in transient and stochastic environments such as the cell. We show here that even repressilators possess quasi-stable, travelling-wave periodic solutions that are reachable, long-lived and robust to parameter changes. These solutions underlie the sustained oscillations observed in even rings in the stochastic regime, even if these circuits are expected to behave as switches. The existence of such solutions can also be exploited for control purposes: operation of the system around the quasi-stable orbit allows us to turn on and off the oscillations reliably and on demand. We illustrate these ideas with a simple protocol based on optical interference that can induce oscillations robustly both in the stochastic and deterministic regimes.Comment: 24 pages, 5 main figure

Integrated radio frequency synthetizers for wireless applications

This thesis consists of six publications and an overview of the research topic, which is also a summary of the work. The research described in this thesis concentrates on the design of phase-locked loop radio frequency synthesizers for wireless applications. In particular, the focus is on the implementation of the prescaler, the phase detector, and the chargepump. This work reviews the requirements set for the frequency synthesizer by the wireless standards, and how these requirements are derived from the system specifications. These requirements apply to both integer-N and fractional-N synthesizers. The work also introduces the special considerations related to the design of fractional-N phase-locked loops. Finally, implementation alternatives for the different building blocks of the synthesizer are reviewed. The presented work introduces new topologies for the phase detector and the chargepump, and improved topologies for high speed CMOS prescalers. The experimental results show that the presented topologies can be successfully used in both integer-N and fractional-N synthesizers with state-of-the-art performance. The last part of this work discusses the additional considerations that surface when the synthesizer is integrated into a larger system chip. It is shown experimentally that the synthesizer can be successfully integrated into a complex transceiver IC without sacrificing the performance of the synthesizer or the transceiver.reviewe

Stochastic analysis of nonlinear dynamics and feedback control for gene regulatory networks with applications to synthetic biology

The focus of the thesis is the investigation of the generalized repressilator model (repressing genes ordered in a ring structure). Using nonlinear bifurcation analysis stable and quasi-stable periodic orbits in this genetic network are characterized and a design for a switchable and controllable genetic oscillator is proposed. The oscillator operates around a quasi-stable periodic orbit using the classical engineering idea of read-out based control. Previous genetic oscillators have been designed around stable periodic orbits, however we explore the possibility of quasi-stable periodic orbit expecting better controllability. The ring topology of the generalized repressilator model has spatio-temporal symmetries that can be understood as propagating perturbations in discrete lattices. Network topology is a universal cross-discipline transferable concept and based on it analytical conditions for the emergence of stable and quasi-stable periodic orbits are derived. Also the length and distribution of quasi-stable oscillations are obtained. The findings suggest that long-lived transient dynamics due to feedback loops can dominate gene network dynamics. Taking the stochastic nature of gene expression into account a master equation for the generalized repressilator is derived. The stochasticity is shown to influence the onset of bifurcations and quality of oscillations. Internal noise is shown to have an overall stabilizing effect on the oscillating transients emerging from the quasi-stable periodic orbits. The insights from the read-out based control scheme for the genetic oscillator lead us to the idea to implement an algorithmic controller, which would direct any genetic circuit to a desired state. The algorithm operates model-free, i.e. in principle it is applicable to any genetic network and the input information is a data matrix of measured time series from the network dynamics. The application areas for readout-based control in genetic networks range from classical tissue engineering to stem cells specification, whenever a quantitatively and temporarily targeted intervention is required

Low power low voltage quadrature RC oscillators for modern RF receivers

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para a obtenção do grau de Mestre em Engenharia Electrotécnica e de ComputadoresThis thesis proposes a study of three different RC oscillators, two relaxation and a ring oscillator. All the circuits are implemented using UMC 130 nm CMOS technology with a supply voltage of 1.2 V. We present a wideband MOS current/voltage controlled quadrature oscillator constituted by two multivibrators. Two different forms of coupling named, soft (traditional)and hard (proposed) are differentiated and investigated. It is found that hard coupling reduces the quadrature error and results in a low phase-noise (about 2 dB improvement) with respect to soft coupling. The behaviour of the singular and coupled multivibrators is investigated, when an external synchronizing harmonic is applied. We introduce a new RC relaxation oscillator with pulse self biasing, to reduce power consumption, and with harmonic ltering and resistor feedback, to reduce phase-noise. The designed circuit has a very low phase-noise, -132.6 dBc/Hz @ 10 MHz offset, and the power consumption is only 1 mW, which leads to a gure of merit (FOM) of -159.1 dBc/Hz. The nal circuit is a two integrator fully implemented in CMOS technology, with low power consumption. The respective layout is made and occupies a total area of5.856x10-3 mm2, post-layout simulation is also done

Fundamentals and applications of spatial dissipative solitons in photonic devices : [Chapter 6]

We review the properties of optical spatial dissipative solitons (SDS). These are stable, self‐localized optical excitations sitting on a uniform, or quasi‐uniform, background in a dissipative environment like a nonlinear optical cavity. Indeed, in optics they are often termed “cavity solitons.” We discuss their dynamics and interactions in both ideal and imperfect systems, making comparison with experiments. SDS in lasers offer important advantages for applications. We review candidate schemes and the tremendous recent progress in semiconductor‐based cavity soliton lasers. We examine SDS in periodic structures, and we show how SDS can be quantitatively related to the locking of fronts. We conclude with an assessment of potential applications of SDS in photonics, arguing that best use of their particular features is made by exploiting their mobility, for example in all‐optical delay lines

An Analog Multiphase Self-Calibrating DLL to Minimize the Effects of Process, Supply Voltage, and Temperature Variations

Delay locked loops have been found to be useful tools in such applications as computing, TDCs, and communications. These system can be found in space exploration vehicles and satellites, which operate in extreme environments. Unfortunately, in these environments supply voltage and temperature will not be constant, therefore they must be under consideration when designing a DLL. Furthermore, solar radiation in conjunction with the varying environmental aspects, could cause the delay locked loop to lose it locked state. Delay locked loops are inherently good at tracking these environmental aspects, but in order to do so, the voltage controlled delay line must exhibit a very large gain, which translates to a large capture range. Assuming charged particles hit a key node in the DLL (e.g. the control voltage), the DLL would lose lock and would have to recapture it. Depending on the severity of the uctuation, this relocking process could easily take on the order of many microseconds assuming the bandwidth was kept low to minimize jitter. To date, no delay locked loops have been published for extreme environment applications. In many other extreme environment circuits, calibration techniques have been applied to minimize the environmental effects. Whereas there have been multiple calibration methods published related to delay locked loops, none of them were intended for extreme environments. Furthermore, none of these methods are directly suitable for an analog multiphase delay locked loop. The self-calibrating DLL in this work includes an all digital calibration circuit, as well as a system transient monitor. The coarse calibration helps minimize global process, voltage, and temperature errors for an analog multiphase DLL. The system monitor is used to detect any transients that might cause the DLL to unlock, which could be used to allow the DLL to be recalibrated to the new environmental conditions. The presented measurement results will demonstrate that the DLL can be used in extreme environments such as space, or other extreme environment applications

Optimising the efficiency of coherent optical packet switched networks

There is a continuing need to increase throughput in optical networks to satisfy the demands of internet applications. However, the non-linear Shannon capacity of standard single mode fibre is being approached. Also, almost all of the power used in optical networks is used by electronic routers. One possible solution to deal with both problems is to use optical packet switching. Optical packet switching uses fast switching tuneable lasers, which can change wavelength in the order of a several nanoseconds, to dynamically vary wavelength assignments in a network, and thus achieve routing in the network without electronic routers. In addition, fast wavelength assignment reduces waiting times, resulting in better utilization of network resources. However, the frequency dynamics of the tuneable lasers after switching wavelengths increases the waiting times required to successfully transmit data packets. In this thesis, frequency and phase dynamics of a tuneable laser transmitter, after a wavelength switching event, are initially characterised accurately using a novel technique. The effects that the frequency dynamics have on the transmission of coherent optical communication signals are mitigated using doubly differential decoding, a new approach proposed in this work for application in optical packet switched networks. This technique reduces the waiting times required to successfully transmit data after a wavelength switching event, and this enhances overall network efficiency and throughput. In addition, this work proposes and demonstrates the use of a least-mean squares algorithm to overcome polarisation demultiplexing issues which are present in these networks, which also decreases waiting times, increases network efficiency, and improves system robustness