Oscillatory genetic circuits: new designs and mathematical models

Introduction and motivation: A wide variety of organisms have developed in-ternal biomolecular clocks in order to adapt to cyclic changes of the environment. Clock operation involves genetic networks. These genetic networks have to be mod¬eled in order to understand the underlying mechanism of oscillations and to design new synthetic cellular clocks. This doctoral thesis has resulted in two contributions to the fields of genetic clocks and systems and synthetic biology, generally. The first contribution is a new genetic circuit model that exhibits an oscillatory behav¬ior through catalytic RNA molecules. The second and major contribution is a new genetic circuit model demonstrating that a repressor molecule acting on the positive feedback of a self-activating gene produces reliable oscillations. First contribution: A new model of a synthetic genetic oscillator based on a typical two-gene motif with one positive and one negative feedback loop is pre¬sented. The originality is that the repressor is a catalytic RNA molecule rather than a protein or a non-catalytic RNA molecule. This catalytic RNA is a ribozyme that acts post-transcriptionally by binding to and cleaving target mRNA molecules. This genetic clock involves just two genes, a mRNA and an activator protein, apart from the ribozyme. Parameter values that produce a circadian period in both determin¬istic and stochastic simulations have been chosen as an example of clock operation. The effects of the stochastic fluctuations are quantified by a period histogram and autocorrelation function. The conclusion is that catalytic RNA molecules can act as repressor proteins and simplify the design of genetic oscillators. Second and major contribution: It is demonstrated that a self-activating gene in conjunction with a simple negative interaction can easily produce robust matically validated. This model is comprised of two clearly distinct parts. The first is a positive feedback created by a protein that binds to the promoter of its own gene and activates the transcription. The second is a negative interaction in which a repressor molecule prevents this protein from binding to its promoter. A stochastic study shows that the system is robust to noise. A deterministic study identifies that the oscillator dynamics are mainly driven by two types of biomolecules: the protein, and the complex formed by the repressor and this protein. The main conclusion of this study is that a simple and usual negative interaction, such as degradation, se¬questration or inhibition, acting on the positive transcriptional feedback of a single gene is a sufficient condition to produce reliable oscillations. One gene is enough and the positive transcriptional feedback signal does not need to activate a second repressor gene. At the genetic level, this means that an explicit negative feedback loop is not necessary. Unlike many genetic oscillators, this model needs neither cooperative binding reactions nor the formation of protein multimers. Applications and future research directions: Recently, RNA molecules have been found to play many new catalytic roles. The first oscillatory genetic model proposed in this thesis uses ribozymes as repressor molecules. This could provide new synthetic biology design principles and a better understanding of cel¬lular clocks regulated by RNA molecules. The second genetic model proposed here involves only a repression acting on a self-activating gene and produces robust oscil¬lations. Unlike current two-gene oscillators, this model surprisingly does not require a second repressor gene. This result could help to clarify the design principles of cellular clocks and constitute a new efficient tool for engineering synthetic genetic oscillators. Possible follow-on research directions are: validate models in vivo and in vitro, research the potential of second model as a genetic memory, investigate new genetic oscillators regulated by non-coding RNAs and design a biosensor of positive feedbacks in genetic networks based on the operation of the second model Resumen Introduccion y motivacion: Una amplia variedad de organismos han desarro-llado relojes biomoleculares internos con el fin de adaptarse a los cambios ciclicos del entorno. El funcionamiento de estos relojes involucra redes geneticas. El mo delado de estas redes geneticas es esencial tanto para entender los mecanismos que producen las oscilaciones como para diseiiar nuevos circuitos sinteticos en celulas. Esta tesis doctoral ha dado lugar a dos contribuciones dentro de los campos de los circuitos geneticos en particular, y biologia de sistemas y sintetica en general. La primera contribucion es un nuevo modelo de circuito genetico que muestra un comportamiento oscilatorio usando moleculas de ARN cataliticas. La segunda y principal contribucion es un nuevo modelo de circuito genetico que demuestra que una molecula represora actuando sobre el lazo de un gen auto-activado produce oscilaciones robustas. Primera contribucion: Es un nuevo modelo de oscilador genetico sintetico basado en una tipica red genetica compuesta por dos genes con dos lazos de retroa-limentacion, uno positivo y otro negativo. La novedad de este modelo es que el represor es una molecula de ARN catalftica, en lugar de una protefna o una molecula de ARN no-catalitica. Este ARN catalitico es una ribozima que actua despues de la transcription genetica uniendose y cortando moleculas de ARN mensajero (ARNm). Este reloj genetico involucra solo dos genes, un ARNm y una proteina activadora, aparte de la ribozima. Como ejemplo de funcionamiento, se han escogido valores de los parametros que producen oscilaciones con periodo circadiano (24 horas) tanto en simulaciones deterministas como estocasticas. El efecto de las fluctuaciones es-tocasticas ha sido cuantificado mediante un histograma del periodo y la función de auto-correlacion. La conclusion es que las moleculas de ARN con propiedades cataliticas pueden jugar el misnio papel que las protemas represoras, y por lo tanto, simplificar el diseno de los osciladores geneticos. Segunda y principal contribucion: Es un nuevo modelo de oscilador genetico que demuestra que un gen auto-activado junto con una simple interaction negativa puede producir oscilaciones robustas. Este modelo ha sido estudiado y validado matematicamente. El modelo esta compuesto de dos partes bien diferenciadas. La primera parte es un lazo de retroalimentacion positiva creado por una proteina que se une al promotor de su propio gen activando la transcription. La segunda parte es una interaction negativa en la que una molecula represora evita la union de la proteina con el promotor. Un estudio estocastico muestra que el sistema es robusto al ruido. Un estudio determinista muestra que la dinamica del sistema es debida principalmente a dos tipos de biomoleculas: la proteina, y el complejo formado por el represor y esta proteina. La conclusion principal de este estudio es que una simple y usual interaction negativa, tal como una degradation, un secuestro o una inhibition, actuando sobre el lazo de retroalimentacion positiva de un solo gen es una condition suficiente para producir oscilaciones robustas. Un gen es suficiente y el lazo de retroalimentacion positiva no necesita activar a un segundo gen represor, tal y como ocurre en los relojes actuales con dos genes. Esto significa que a nivel genetico un lazo de retroalimentacion negativa no es necesario de forma explicita. Ademas, este modelo no necesita reacciones cooperativas ni la formation de multimeros proteicos, al contrario que en muchos osciladores geneticos. Aplicaciones y futuras lineas de investigacion: En los liltimos anos, se han descubierto muchas moleculas de ARN con capacidad catalitica. El primer modelo de oscilador genetico propuesto en esta tesis usa ribozimas como moleculas repre¬soras. Esto podria proporcionar nuevos principios de diseno en biologia sintetica y una mejor comprension de los relojes celulares regulados por moleculas de ARN. El segundo modelo de oscilador genetico propuesto aqui involucra solo una represion actuando sobre un gen auto-activado y produce oscilaciones robustas. Sorprendente-mente, un segundo gen represor no es necesario al contrario que en los bien conocidos osciladores con dos genes. Este resultado podria ayudar a clarificar los principios de diseno de los relojes celulares naturales y constituir una nueva y eficiente he-rramienta para crear osciladores geneticos sinteticos. Algunas de las futuras lineas de investigation abiertas tras esta tesis son: (1) la validation in vivo e in vitro de ambos modelos, (2) el estudio del potential del segundo modelo como circuito base para la construction de una memoria genetica, (3) el estudio de nuevos osciladores geneticos regulados por ARN no codificante y, por ultimo, (4) el rediseno del se¬gundo modelo de oscilador genetico para su uso como biosensor capaz de detectar genes auto-activados en redes geneticas.

Triple-junction solar cell performance under Fresnel-based concentrators taking into account chromatic aberration and off-axis operation

Concentration photovoltaic (CPV) systems might produce quite uneven irradiance distributions (both on their level and on their spectral distribution) on the solar cell. This effect can be even more evident when the CPV system is slightly off-axis, since they are often designed to assure good uniformity only at normal incidence. The non-uniformities both in absolute irradiance and spectral content produced by the CPV systems, can originate electrical losses in multi-junction solar cells (MJSC). This works is focused on the integration of ray-tracing methods for simulating the irradiance and spectrum maps produced by different optic systems throughout the solar cell surface, with a 3D fully distributed circuit model which simulates the electrical behavior of a state-of-the-art triple-junction solar cell under the different light distributions obtained with ray-tracing. In this study four different CPV system (SILO, XTP, RTP, and FK) comprising Fresnel lenses concentrating sunlight onto the same solar cell are modeled when working on-axis and 0.6 degrees off-axis. In this study the impact of non-uniformities on a CPV system behavior is revealed. The FK outperforms other Fresnel-based CPV systems in both on-axis and off-axis conditions.

Experimental confirmation of FK concentrator insensitivity to chromatic aberrations

The FK concentrator has demonstrated during the last years that compares very well with other Fresnel-based concentrator optics for CPV. There are several features that provide the FK high performance: (1) high optical efficiency; (2) large tolerance to tracking misalignment and manufacturing errors, thanks to a high CAP (Concentration-Acceptance Product); (3) good irradiance uniformity and low chromatic dispersion on the cell surface. Non-uniformities in terms of absolute irradiance and spectral content produced by conventional CPV systems can originate electrical losses in multi-junction (MJ) solar cells. The aim of this work is to analyze the influence of these non-uniformities in the FK concentrator performance and how FK concentrator provides high electrical efficiencies thanks to its insensitivity to chromatic aberrations, especially when components move away from the module nominal position due to manufacturing misalignments. This analysis has been done here by means of both, experimental on-sun measurements and simulations based on 3D fully distributed circuit model for MJ cells.

New method for analytical photovoltaic parameter extraction

Correct modeling of the equivalent circuits regarding solar cell and panels is today an essential tool for power optimization. However, the parameter extraction of those circuits is still a quite difficult task that normally requires both experimental data and calculation procedures, generally not available to the normal user. This paper presents a new analytical method that easily calculates the equivalent circuit parameters from the data that manufacturers usually provide. The analytical approximation is based on a new methodology, since methods developed until now to obtain the aforementioned equivalent circuit parameters from manufacturer's data have always been numerical or heuristic. Results from the present method are as accurate as the ones resulting from other more complex (numerical) existing methods in terms of calculation process and resources.

Circuitos equivalentes en bandas milimétricas

The use of ideal equivalent circuits which represent the electrical response of a physical device is a very common practice in microwave and millimeter wave circuit design. However, these equivalent circuit models only get accurate results in a certain frequency range. In this document, some basic devices have been analyzed, with several equivalent circuit models for each one. Physical devices have been manufactured and measured, and measurements have been compared with the responses obtained from the equivalent models. From this comparison, it?s possible to see what equivalent models are more advisable in each case and which are their limitations.

Uso de circuitos equivalentes y teoría de filtros para el diseño de superficies selectivas en frecuencia

Frequency selective surfaces (FSS) and reflect/trasmitarrays are mostly designed on the basis ot optimization using an electromagnetic simulator. That is a time consuming method and some decisions have to be taken using simply intuition. The use of equivalent circuits of the scatterers selected for the design allows the substitution of the intuition and most part of the optimization process by the application of the classic rules of filter design. This communication presents all the steps necessary to obtain the equivalent circuit of different square scatterers in a periodic lattice and to implement the desired FSS frequency behaviour calculating the number of layers and the dimensions of the periodic cells. Several examples are included to evaluate the results.

The peculiar electrical response of liquid crystal-carbon nanotube systems as seen by impedance spectroscopy

Conductive nanoparticles, especially elongated ones such as carbon nanotubes, dramatically modify the electrical behavior of liquid crystal cells. These nanoparticles are known to reorient with liquid crystals in electric fields, causing significant variations of conductivity at minute concentrations of tens or hundreds ppm. The above notwithstanding, impedance spectroscopy of doped cells in the frequency range customarily employed by liquid crystal devices, 100 Hz?10 kHz, shows a relatively simple resistor/capacitor response where the components of the cell can be univocally assigned to single components of the electrical equivalent circuit. However, widening the frequency range up to 1 MHz or beyond reveals a complex behavior that cannot be explained with the same simple EEC. Moreover, the system impedance varies with the application of electric fields, their effect remaining after removing the field. Carbon nanotubes are reoriented together with liquid crystal reorientation when applying voltage, but barely reoriented back upon liquid crystal relaxation once the voltage is removed. Results demonstrate a remarkable variation in the impedance of the dielectric blend formed by liquid crystal and carbon nanotubes, the irreversible orientation of the carbon nanotubes and possible permanent contacts between electrodes.

Numerical modeling of electromagnetic coupling phenomena in the vicinities of overhead power transmission lines.

Electromagnetic coupling phenomena between overhead power transmission lines and other nearby structures are inevitable, especially in densely populated areas. The undesired effects resulting from this proximity are manifold and range from the establishment of hazardous potentials to the outbreak of alternate current corrosion phenomena. The study of this class of problems is necessary for ensuring security in the vicinities of the interaction zone and also to preserve the integrity of the equipment and of the devices there present. However, the complete modeling of this type of application requires the three- -dimensional representation of the region of interest and needs specific numerical methods for field computation. In this work, the modeling of problems arising from the flow of electrical currents in the ground (the so-called conductive coupling) will be addressed with the finite element method. Those resulting from the time variation of the electromagnetic fields (the so-called inductive coupling) will be considered as well, and they will be treated with the generalized PEEC (Partial Element Equivalent Circuit) method. More specifically, a special boundary condition on the electric potential is proposed for truncating the computational domain in the finite element analysis of conductive coupling problems, and a complete PEEC formulation for modeling inductive coupling problems is presented. Test configurations of increasing complexities are considered for validating the foregoing approaches. These works aim to provide a contribution to the modeling of this class of problems, which tend to become common with the expansion of power grids.

Numerical evaluation of the fields induced by body motion in or near high-field MRI scanners

In modern magnetic resonance imaging, both patients and health care workers are exposed to strong. non-uniform static magnetic fields inside and outside of the scanner. In which body movement may be able to induce electric currents in tissues which could be potentially harmful. This paper presents theoretical investigations into the spatial distribution of induced E-fields in a tissue-equivalent human model when moving at various positions around the magnet. The numerical calculations are based on an efficient. quasi-static, finite-difference scheme. Three-dimensional field profiles from an actively shielded 4 T magnet system are used and the body model projected through the field profile with normalized velocity. The simulation shows that it is possible to induce E-fields/currents near the level of physiological significance under some circumstances and provides insight into the spatial characteristics of the induced fields. The methodology presented herein can be extrapolated to very high field strengths for the evaluation of the effects of motion at a variety of field strengths and velocities. (C) 2004 Elsevier Ltd. All rights reserved.

Loss-tolerant optical qubits

We present a linear optics quantum computation scheme that employs a new encoding approach that incrementally adds qubits and is tolerant to photon loss errors. The scheme employs a circuit model but uses techniques from cluster-state computation and achieves comparable resource usage. To illustrate our techniques we describe a quantum memory which is fault tolerant to photon loss.

Dielectric transition of polyacrylonitrile derived carbon nanofibers

The dielectric behavior of polyacrylonitrile derived carbon nanofibers formed at different carbonization temperatures was investigated using impedance spectroscopy. The impedance data are presented in the form of Cole-Cole plots and four equivalent electrical circuits are derived. It is found that by increasing carbonization temperature from 500 to 800 °C, a strong capacitive element in the parallel equivalent circuit is transformed into an inductive element, while the contact resistance and parallel resistance are significantly decreased. Along with the morphological and chemical structural evolution, respectively witnessed by scanning electron microscopy and Raman spectroscopy, the dielectric transition deduced from the transformation of electrical circuits can be correlated to the proposed microstructural changes of polyacrylonitrile derived carbon nanofibers and the interaction/interference among them.

Electromagnetic interference from variable speed motor drives

A methodology is presented which can be used to produce the level of electromagnetic interference, in the form of conducted and radiated emissions, from variable speed drives, the drive that was modelled being a Eurotherm 583 drive. The conducted emissions are predicted using an accurate circuit model of the drive and its associated equipment. The circuit model was constructed from a number of different areas, these being: the power electronics of the drive, the line impedance stabilising network used during the experimental work to measure the conducted emissions, a model of an induction motor assuming near zero load, an accurate model of the shielded cable which connected the drive to the motor, and finally the parasitic capacitances that were present in the drive modelled. The conducted emissions were predicted with an error of +/-6dB over the frequency range 150kHz to 16MHz, which compares well with the limits set in the standards which specify a frequency range of 150kHz to 30MHz. The conducted emissions model was also used to predict the current and voltage sources which were used to predict the radiated emissions from the drive. Two methods for the prediction of the radiated emissions from the drive were investigated, the first being two-dimensional finite element analysis and the second three-dimensional transmission line matrix modelling. The finite element model took account of the features of the drive that were considered to produce the majority of the radiation, these features being the switching of the IGBT's in the inverter, the shielded cable which connected the drive to the motor as well as some of the cables that were present in the drive.The model also took account of the structure of the test rig used to measure the radiated emissions. It was found that the majority of the radiation produced came from the shielded cable and the common mode currents that were flowing in the shield, and that it was feasible to model the radiation from the drive by only modelling the shielded cable. The radiated emissions were correctly predicted in the frequency range 30MHz to 200MHz with an error of +10dB/-6dB. The transmission line matrix method modelled the shielded cable which connected the drive to the motor and also took account of the architecture of the test rig. Only limited simulations were performed using the transmission line matrix model as it was found to be a very slow method and not an ideal solution to the problem. However the limited results obtained were comparable, to within 5%, to the results obtained using the finite element model.

Synthesis, characterisation and applications of diamond materials

This thesis presented a detailed research work on diamond materials. Chapter 1 is an overall introduction of the thesis. In the Chapter 2, the literature review on the physical, chemical, optical, mechanical, as well as other properties of diamond materials are summarised. Followed by this chapter, several advanced diamond growth and characterisation techniques used in experimental work are also introduced. Then, the successful installation and applications of chemical vapour deposition system was demonstrated in Chapter 4. Diamond growth on a variety of different substrates has been investigated such as on silicon, diamond-like carbon or silica fibres. In Chapter 5, the single crystalline diamond substrate was used as the substrate to perform femtosecond laser inscription. The results proved the potentially feasibility of this technique, which could be utilised in fabricating future biochemistry microfluidic channels on diamond substrates. In Chapter 6, the hydrogen-terminated nanodiamond powder was studied using impedance spectroscopy. Its intrinsic electrical properties and its thermal stability were presented and analysed in details. As the first PhD student within Nanoscience Research Group at Aston, my initial research work was focused on the installation and testing of the microwave plasma enhanced chemical vapour deposition system (MPECVD), which will be beneficial to all the future researchers in the group. The fundamental of the on MPECVD system will be introduced in details. After optimisation of the growth parameters, the uniform diamond deposition has been achieved with a good surface coverage and uniformity. Furthermore, one of the most significant contributions of this work is the successful pattern inscription on diamond substrates by femtosecond laser system. Previous research of femtosecond laser inscription on diamond was simple lines or dots, with little characterisation techniques were used. In my research work, the femtosecond laser has been successfully used to inscribe patterns on diamond substrate and fully characterisation techniques, e.g. by SEM, Raman, XPS, as well as AFM, have been carried out. After the femtosecond laser inscription, the depth of microfluidic channels on diamond film has been found to be 300~400 nm, with a graphitic layer thickness of 165~190 nm. Another important outcome of this work is the first time to characterise the electrical properties of hydrogenterminated nanodiamond with impedance spectroscopy. Based on the experimental evaluation and mathematic fitting, the resistance of hydrogen-terminated nanodiamond reduced to 0.25 MO, which were four orders of magnitude lower than untreated nanodiamond. Meanwhile, a theoretical equivalent circuit has been proposed to fit the results. Furthermore, the hydrogenterminated nanodiamond samples were annealed at different temperature to study its thermal stability. The XPS and FTIR results indicate that hydrogen-terminated nanodiamond will start to oxidize over 100ºC and the C-H bonds can survive up to 400ºC. This research work reports the fundamental electrical properties of hydrogen-terminated nanodiamond, which can be used in future applications in physical or chemical area.

Universality in the merging dynamics of parametric active contours:a study in MRI based lung segmentation

Measurement of lung ventilation is one of the most reliable techniques in diagnosing pulmonary diseases. The time-consuming and bias-prone traditional methods using hyperpolarized H 3He and 1H magnetic resonance imageries have recently been improved by an automated technique based on 'multiple active contour evolution'. This method involves a simultaneous evolution of multiple initial conditions, called 'snakes', eventually leading to their 'merging' and is entirely independent of the shapes and sizes of snakes or other parametric details. The objective of this paper is to show, through a theoretical analysis, that the functional dynamics of merging as depicted in the active contour method has a direct analogue in statistical physics and this explains its 'universality'. We show that the multiple active contour method has an universal scaling behaviour akin to that of classical nucleation in two spatial dimensions. We prove our point by comparing the numerically evaluated exponents with an equivalent thermodynamic model. © IOP Publishing Ltd and Deutsche Physikalische Gesellschaft.

Hydrogen-terminated detonation nanodiamond:impedance spectroscopy and thermal stability studies

In this paper, we investigated the effect of hydrogen termination on the electrical properties and impedance spectra of detonation nanodiamond. The impedance spectra revealed that the hydrogen-termination process increases the electrical conductivity by four orders of magnitude at room temperature. An equivalent circuit has been proposed to correlate with the conduction mechanism. Arrhenius plot showed that there were two different activation energy levels located at 0.089 eV and 0.63 eV between 50 °C and 400 °C. The possible physical mechanism corresponding to these activation energy levels has been discussed. Hydrogen-terminated detonation nanodiamond has been further annealed at different temperatures prior to FTIR and XPS measurements in order to understand their thermal stability. The results demonstrated that the surface oxidization occurred between 100 °C and 150 °C. However, the C-H bonds could partially survive when the temperature reaches 400 °C in air. © 2013 American Institute of Physics.