Programming Molecular Devices using Nucleic Acid Hairpins

Nucleic Acid hairpins have been a subject of study for the last four decades. They are composed of single strand that is

hybridized to itself, and the central section forming an unhybridized loop. In nature, they stabilize single stranded RNA, serve as nucleation

sites for RNA folding, protein recognition signals, mRNA localization and regulation of mRNA degradation. On the other hand,

DNA hairpins in biological contexts have been studied with respect to forming cruciform structures that can regulate gene expression.

The use of DNA hairpins as fuel for synthetic molecular devices, including locomotion, was proposed and experimental demonstrated in 2003. They

were interesting because they bring to the table an on-demand energy/information supply mechanism.

The energy/information is hidden (from hybridization) in the hairpin’s loop, until required.

The energy/information is harnessed by opening the stem region, and exposing the single stranded loop section.

The loop region is now free for possible hybridization and help move the system into a thermodynamically favourable state.

The hidden energy and information coupled with

programmability provides another functionality, of selectively choosing what reactions to hide and

what reactions to allow to proceed, that helps develop a topological sequence of events.

Hairpins have been utilized as a source of fuel for many different DNA devices. In this thesis, we program four different

molecular devices using DNA hairpins, and experimentally validate them in the

laboratory. 1) The first device: A

novel enzyme-free autocatalytic self-replicating system composed entirely of DNA that operates isothermally. 2) The second

device: Time-Responsive Circuits using DNA have two properties: a) asynchronous: the final output is always correct

regardless of differences in the arrival time of different inputs.

b) renewable circuits which can be used multiple times without major degradation of the gate motifs

(so if the inputs change over time, the DNA-based circuit can re-compute the output correctly based on the new inputs).

3) The third device: Activatable tiles are a theoretical extension to the Tile assembly model that enhances

its robustness by protecting the sticky sides of tiles until a tile is partially incorporated into a growing assembly.

4) The fourth device: Controlled Amplification of DNA catalytic system: a device such that the amplification

of the system does not run uncontrollably until the system runs out of fuel, but instead achieves a finite

amount of gain.

Nucleic acid circuits with the ability

to perform complex logic operations have many potential practical applications, for example the ability to achieve point of care diagnostics.

We discuss the designs of our DNA Hairpin molecular devices, the results we have obtained, and the challenges we have overcome

to make these truly functional.

Ultrastructural and Histological Study of Oogenesis and Oocyte Degeneration in the PenshellAtrina maura(Bivalvia: Pinnidae)

The successive stages of oogenesis and the changes involved in the oocyte degeneration process in the penshell Atrina maura were examined using light and transmission electron microscopy. The ovarian maturation process is asynchronous, as oocytes at different developmental stages can be found simultaneously. Oocytes develop from oogonia and then undergo three distinct stages of oogenesis: previtellogenesis, vitellogenesis and postvitellogenesis with mature oocytes. Atrina maura displays a solitary oogenesis type, in which follicular cells become associated with oocytes from the earliest stages of development and seem to play an integral role in vitellogenesis. The cytoplasm of vitellogenic oocytes contains numerous whorls of rough endoplasmic reticulum and Golgi bodies, suggesting that auto-synthetic vitellogenesis may occur in this species. In addition, the degeneration process of postvitellogenic oocytes triggered by a seasonal increase in water temperature (> 25°C) is described.

Ultrastructural and Histological Study of Oogenesis and Oocyte Degeneration in the PenshellAtrina maura(Bivalvia: Pinnidae)

The successive stages of oogenesis and the changes involved in the oocyte degeneration process in the penshell Atrina maura were examined using light and transmission electron microscopy. The ovarian maturation process is asynchronous, as oocytes at different developmental stages can be found simultaneously. Oocytes develop from oogonia and then undergo three distinct stages of oogenesis: previtellogenesis, vitellogenesis and postvitellogenesis with mature oocytes. Atrina maura displays a solitary oogenesis type, in which follicular cells become associated with oocytes from the earliest stages of development and seem to play an integral role in vitellogenesis. The cytoplasm of vitellogenic oocytes contains numerous whorls of rough endoplasmic reticulum and Golgi bodies, suggesting that auto-synthetic vitellogenesis may occur in this species. In addition, the degeneration process of postvitellogenic oocytes triggered by a seasonal increase in water temperature (> 25°C) is described.

Heating the Early Universe : Numerical Methods and Their Analysis

During the epoch when the first collapsed structures formed (6<z<50) our Universe went through an extended period of changes. Some of the radiation from the first stars and accreting black holes in those structures escaped and changed the state of the Intergalactic Medium (IGM). The era of this global phase change in which the state of the IGM was transformed from cold and neutral to warm and ionized, is called the Epoch of Reionization.In this thesis we focus on numerical methods to calculate the effects of this escaping radiation. We start by considering the performance of the cosmological radiative transfer code C2-Ray. We find that although this code efficiently and accurately solves for the changes in the ionized fractions, it can yield inaccurate results for the temperature changes. We introduce two new elements to improve the code. The first element, an adaptive time step algorithm, quickly determines an optimal time step by only considering the computational cells relevant for this determination. The second element, asynchronous evolution, allows different cells to evolve with different time steps. An important constituent of methods to calculate the effects of ionizing radiation is the transport of photons through the computational domain or ``ray-tracing''. We devise a novel ray tracing method called PYRAMID which uses a new geometry - the pyramidal geometry. This geometry shares properties with both the standard Cartesian and spherical geometries. This makes it on the one hand easy to use in conjunction with a Cartesian grid and on the other hand ideally suited to trace radiation from a radially emitting source. A time-dependent photoionization calculation not only requires tracing the path of photons but also solving the coupled set of photoionization and thermal equations. Several different solvers for these equations are in use in cosmological radiative transfer codes. We conduct a detailed and quantitative comparison of four different standard solvers in which we evaluate how their accuracy depends on the choice of the time step. This comparison shows that their performance can be characterized by two simple parameters and that the C2-Ray generally performs best.

OFDM-based schemes for next generation wireless systems

The purpose of this study is to investigate two candidate waveforms for next generation wireless systems, filtered Orthogonal Frequency Division Multiplexing (f-OFDM) and Unified Filtered Multi-Carrier (UFMC). The evaluation is done based on the power spectral density analysis of the signal and performance measurements in synchronous and asynchronous transmission. In f-OFDM we implement a soft truncated filter with length 1/3 of OFDM symbol. In UFMC we use the Dolph-Chebyshev filter, limited to the length of zero padding (ZP). The simulation results demonstrates that both waveforms have a better spectral behaviour compared with conventional OFDM. However, the induced inter-symbol interference (ISI) caused by the filter in f-OFDM, and the inter-carrier interference (ICI) induced in UFMC due to cyclic prefix (CP) reduction , should be kept under control. In addition, in a synchronous transmission case with ideal parameters, f-OFDM and UFMC appear to have similar performance with OFDM. When carrier frequency offset (CFO) is imposed in the transmission, UFMC outperforms OFDM and f-OFDM.

Measuring, Modeling, and Forecasting Volatility and Correlations from High-Frequency Data

This dissertation contains four essays that all share a common purpose: developing new methodologies to exploit the potential of high-frequency data for the measurement, modeling and forecasting of financial assets volatility and correlations. The first two chapters provide useful tools for univariate applications while the last two chapters develop multivariate methodologies. In chapter 1, we introduce a new class of univariate volatility models named FloGARCH models. FloGARCH models provide a parsimonious joint model for low frequency returns and realized measures, and are sufficiently flexible to capture long memory as well as asymmetries related to leverage effects. We analyze the performances of the models in a realistic numerical study and on the basis of a data set composed of 65 equities. Using more than 10 years of high-frequency transactions, we document significant statistical gains related to the FloGARCH models in terms of in-sample fit, out-of-sample fit and forecasting accuracy compared to classical and Realized GARCH models. In chapter 2, using 12 years of high-frequency transactions for 55 U.S. stocks, we argue that combining low-frequency exogenous economic indicators with high-frequency financial data improves the ability of conditionally heteroskedastic models to forecast the volatility of returns, their full multi-step ahead conditional distribution and the multi-period Value-at-Risk. Using a refined version of the Realized LGARCH model allowing for time-varying intercept and implemented with realized kernels, we document that nominal corporate profits and term spreads have strong long-run predictive ability and generate accurate risk measures forecasts over long-horizon. The results are based on several loss functions and tests, including the Model Confidence Set. Chapter 3 is a joint work with David Veredas. We study the class of disentangled realized estimators for the integrated covariance matrix of Brownian semimartingales with finite activity jumps. These estimators separate correlations and volatilities. We analyze different combinations of quantile- and median-based realized volatilities, and four estimators of realized correlations with three synchronization schemes. Their finite sample properties are studied under four data generating processes, in presence, or not, of microstructure noise, and under synchronous and asynchronous trading. The main finding is that the pre-averaged version of disentangled estimators based on Gaussian ranks (for the correlations) and median deviations (for the volatilities) provide a precise, computationally efficient, and easy alternative to measure integrated covariances on the basis of noisy and asynchronous prices. Along these lines, a minimum variance portfolio application shows the superiority of this disentangled realized estimator in terms of numerous performance metrics. Chapter 4 is co-authored with Niels S. Hansen, Asger Lunde and Kasper V. Olesen, all affiliated with CREATES at Aarhus University. We propose to use the Realized Beta GARCH model to exploit the potential of high-frequency data in commodity markets. The model produces high quality forecasts of pairwise correlations between commodities which can be used to construct a composite covariance matrix. We evaluate the quality of this matrix in a portfolio context and compare it to models used in the industry. We demonstrate significant economic gains in a realistic setting including short selling constraints and transaction costs.

Comparative performance analysis of drives for induction motors

The asynchronous polyphase induction motor has been the motor of choice in industrial settings for about the past half century because power electronics can be used to control its output behavior. Before that, the dc motor was widely used because of its easy speed and torque controllability. The two main reasons why this might be are its ruggedness and low cost. The induction motor is a rugged machine because it is brushless and has fewer internal parts that need maintenance or replacement. This makes it low cost in comparison to other motors, such as the dc motor. Because of these facts, the induction motor and drive system have been gaining market share in industry and even in alternative applications such as hybrid electric vehicles and electric vehicles. The subject of this thesis is to ascertain various control algorithms’ advantages and disadvantages and give recommendations for their use under certain conditions and in distinct applications. Four drives will be compared as fairly as possible by comparing their parameter sensitivities, dynamic responses, and steady-state errors. Different switching techniques are used to show that the motor drive is separate from the switching scheme; changing the switching scheme produces entirely different responses for each motor drive.

Signposts in the sand: Key issues for e-moderators

E-learning is a vision that has sparked a wide-ranging enthusiasm for moderators, course designers and learners. Asynchronous conferencing is currently central to this vision. Some educators assume that supporting learners who use this medium is the same as supporting them in the classroom. However, this is not the case. This paper outlines the current research into providing signposts that enable us to improve the training and support offered to new e-moderators and e-course designers. It suggests a classification of roles and tasks that together with an e-course framework will help to maximize the benefits of e-learning and enable all participants to migrate successfully to the new environment.

Asynchronus design for improved EMC behavior of ICs

International audience

Réseau calculant asynchrone dédié à la segmentation d'images

National audience

Metabolite profiling of somatic embryos of Cyclamen persicum in comparison to zygotic embryos, endosperm, and testa

Somatic embryogenesis has been shown to be an efficient in vitro plant regeneration system for many crops such as the important ornamental plant Cyclamen persicum, for which this regeneration pathway of somatic embryogenesis is of interest for the vegetative propagation of parental lines as well as elite plants. However, somatic embryogenesis is not commercially used in many crops due to several unsolved problems, such as malformations, asynchronous development, deficiencies in maturation and germination of somatic embryos. In contrast, zygotic embryos in seeds develop and germinate without abnormalities in most cases. Instead of time-consuming and labor-intensive experiments involving tests of different in vitro culture conditions and plant growth regulator supplements, we follow a more directed approach. Zygotic embryos served as a reference and were compared to somatic embryos in metabolomic analyses allowing the future optimization of the in vitro system. The aims of this study were to detect differences in the metabolite profiles of torpedo stage somatic and zygotic embryos of C. persicum. Moreover, major metabolites in endosperm and testa were identified and quantified. Two sets of extracts of two to four biological replicates each were analyzed. In total 52 metabolites were identified and quantified in the different tissues. One of the most significant differences between somatic and zygotic embryos was that the proline concentration in the zygotic embryos was about 40 times higher than that found in somatic embryos. Epicatechin, a scavenger for reactive oxygen species, was found in highest abundance in the testa. Sucrose, the most abundant metabolite was detected in significantly higher concentrations in zygotic embryos. Also, a yet unknown trisaccharide, was significantly enriched in zygotic embryos.

Identifying Robust Proxies of Gonad Maturation for the Protandrous Hermaphrodite Tridacna maxima (Röding, 1798, Bivalvia) from Individual to Population Scale

Monitoring gonadmaturation for protandrous and functional hermaphrodite species such as the giant clamTridacna maxima is difficult due to the juxtaposition and relative proportion ofmale and female tissues in the gonad [gonadal sex ratio (GSR)]. Here, the relevance of the widely used gonadosomatic index (GSI) as proxy of giant clam gonad maturation is tested with a large dataset (n = 265). Gonadosomatic index is compared with other indices, namely the proportion of the male part harboring spermatozoids, the proportion of empty oocyte follicles, the mean oocyte diameter, and the oocyte elongation. At gonad scale, high index variability highlighted partial spawning. At individual scale, male and female maturation proxies were contrasted, showing either asynchronous emissions of male and female gametes or contrasted spermatogenesis and oogenesis duration. The GSI was mostly driven by the number and diameter of oocytes and therefore it is recommended here as primary proxy for female maturity. Except for the oocyte elongation, all indices were affected by the GSR, which ruled out drawing conclusions at population scale. These results highlight the need for maturation stage proxies that are optimized for functional hermaphrodite species.

Gap junctions and emergent rhythms

Gap junction coupling is ubiquitous in the brain, particularly between the dendritic trees of inhibitory interneurons. Such direct non-synaptic interaction allows for direct electrical communication between cells. Unlike spike-time driven synaptic neural network models, which are event based, any model with gap junctions must necessarily involve a single neuron model that can represent the shape of an action potential. Indeed, not only do neurons communicating via gaps feel super-threshold spikes, but they also experience, and respond to, sub-threshold voltage signals. In this chapter we show that the so-called absolute integrate-and-fire model is ideally suited to such studies. At the single neuron level voltage traces for the model may be obtained in closed form, and are shown to mimic those of fast-spiking inhibitory neurons. Interestingly in the presence of a slow spike adaptation current the model is shown to support periodic bursting oscillations. For both tonic and bursting modes the phase response curve can be calculated in closed form. At the network level we focus on global gap junction coupling and show how to analyze the asynchronous firing state in large networks. Importantly, we are able to determine the emergence of non-trivial network rhythms due to strong coupling instabilities. To illustrate the use of our theoretical techniques (particularly the phase-density formalism used to determine stability) we focus on a spike adaptation induced transition from asynchronous tonic activity to synchronous bursting in a gap-junction coupled network.

Design, construction, and applications of a high-resolution terahertz time-domain spectrometer

This thesis reports on the design, construction, and initial applications of a high-resolution terahertz time-domain ASOPS spectrometer. The instrument employs asynchronous optical sampling (ASOPS) between two Ti:sapphire ultrafast lasers operating at a repetition rate of approximately 80 MHz, and we thus demonstrate a THz frequency resolution approaching the limit of that repetition rate. This is an order of magnitude improvement in resolution over typical THz time-domain spectrometers. The improved resolution is important for our primary effort of collecting THz spectra for far-infrared astronomy. We report on various spectroscopic applications including the THz rotational spectrum of water, where we achieve a mean frequency error, relative to established line centers, of 27.0 MHz. We also demonstrate application of the THz system to the long-duration observation of a coherent magnon mode in a anti-ferromagnetic yttrium iron oxide (YFeO3) crystal. Furthermore, we apply the all-optical virtual delay line of ASOPS to a transient thermoreflectance experiment for quickly measuring the thermal conductivity of semiconductors.