Synthetic biology in droplet-based microfluidics

Droplet microfluidics is an active multidisciplinary area of research that evolved out of the larger field of microfluidics. It enables the user to handle, process and manipulate micrometer-sized emulsion droplets on a micro- fabricated platform. The capability to carry out a large number of individual experiments per unit time makes the droplet microfluidic technology an ideal high-throughput platform for analysis of biological and biochemical samples. The objective of this thesis was to use such a technology for designing systems with novel implications in the newly emerging field of synthetic biology. Chapter 4, the first results chapter, introduces a novel method of droplet coalescence using a flow-focusing capillary device. In Chapter 5, the development of a microfluidic platform for the fabrication of a cell-free micro-environment for site-specific gene manipulation and protein expression is described. Furthermore, a novel fluorescent reporter system which functions both in vivo and in vitro is introduced in this chapter. Chapter 6 covers the microfluidic fabrication of polymeric vesicles from poly(2-methyloxazoline-b-dimethylsiloxane-b-2-methyloxazoline) tri-block copolymer. The polymersome made from this polymer was used in the next Chapter for the study of a chimeric membrane protein called mRFP1-EstA∗. In Chapter 7, the application of microfluidics for the fabrication of synthetic biological membranes to recreate artificial cell- like chassis structures for reconstitution of a membrane-anchored protein is described.

Ecological effects of flow and temperature regimes on fish communities in temperate rivers

Les organismes aquatiques sont adaptés à une grande variabilité hydrique et thermique des rivières. Malgré ceci, la régulation des eaux suscite des changements aux débits qui peuvent provoquer des impacts négatifs sur la biodiversité et les processus écologiques en rivière. Celle-ci peut aussi causer des modifications au niveau des régimes thermiques et des caractéristiques de l’habitat du poisson. Des données environnementales et biologiques décrivant l’habitat du poisson existent, mais elles sont incomplètes pour plusieurs rivières au Canada et de faible qualité, limitant les relations quantitatives débit-température-poissons à un petit nombre de rivières ou à une région étudiée. La recherche menée dans le cadre de mon doctorat concerne les impacts de la génération d'hydroélectricité sur les rivières; soit les changements aux régimes hydriques et thermiques reliés à la régulation des eaux sur la variation des communautés ichtyologiques qui habitent les rivières régulées et naturelles au Canada. Suite à une comparaison d’échantillonnage de pêche, une méthode constante pour obtenir des bons estimés de poisson (richesse, densité et biomasse des espèces) a été établie pour évaluer la structure de la communauté de poissons pour l’ensemble des rivières ciblées par l’étude. Afin de mieux comprendre ces changements environnementaux, les principales composantes décrivant ces régimes ont été identifiées et l’altération des régimes hydriques pour certaines rivières régulées a été quantifiée. Ces résultats ont servi à établir la relation significative entre le degré de changement biotique et le degré de changement hydrique pour illustrer les différences entre les régimes de régulation. Pour faire un complément aux indices biotiques déjà calculés pour l’ensemble des communautés de poissons (diversité, densité et biomasse des espèces par rivière), les différences au niveau des guildes de poissons ont été quantifiées pour expliquer les divers effets écologiques dus aux changements de régimes hydriques et thermiques provenant de la gestion des barrages. Ces derniers résultats servent à prédire pour quels traits écologiques ou groupes d’espèces de poissons les composantes hydriques et thermiques sont importantes. De plus, ces derniers résultats ont servi à mettre en valeur les variables décrivant les régimes thermiques qui ne sont pas toujours inclues dans les études hydro-écologiques. L’ensemble des résultats de cette thèse ont des retombées importantes sur la gestion des rivières en évaluant, de façon cohérente, l’impact de la régulation des rivières sur les communautés de poissons et en développant des outils de prévision pour la restauration des écosystèmes riverains.

Carrier Selection for Multi-commodity Flow Optimization in Cooperative Environments

Part 18: Optimization in Collaborative Networks

Flow-injection spectrophotometric determination of dipyrone in pharmaceutical formulations using ammonium molybdate as chromogenic reagent

A simple and rapid flow-injection spectrophotometric method is reported for the determination of dipyrone in pharmaceutical formulations. The method is based on the reaction of dipyrone with ammonium molybdate in acidic medium to produce blue molybdenum, which was detected spectrophotometrically at 620 nm. The analyte was determined in a single-line flow system. The calibration curve obtained was linear in the range of 5x10(-4) to 8x10(-3) mol L-1 for dipyrone concentration and the precision ( s r =1.7%) was satisfactory. The method proved to be selective and adequately sensitive. Application of the method to the analysis of pharmaceutical samples resulted in excellent accuracy; the percent mean recoveries were in the range 95.3%-101% and relative errors less than 5.0% for five pharmaceutical formulations were found.

A new method for conditioning stochastic groundwater flow models in fractured media

Many geological formations consist of crystalline rocks that have very low matrix permeability but allow flow through an interconnected network of fractures. Understanding the flow of groundwater through such rocks is important in considering disposal of radioactive waste in underground repositories. A specific area of interest is the conditioning of fracture transmissivities on measured values of pressure in these formations. This is the process where the values of fracture transmissivities in a model are adjusted to obtain a good fit of the calculated pressures to measured pressure values. While there are existing methods to condition transmissivity fields on transmissivity, pressure and flow measurements for a continuous porous medium there is little literature on conditioning fracture networks. Conditioning fracture transmissivities on pressure or flow values is a complex problem because the measurements are not linearly related to the fracture transmissivities and they are also dependent on all the fracture transmissivities in the network. We present a new method for conditioning fracture transmissivities on measured pressure values based on the calculation of certain basis vectors; each basis vector represents the change to the log transmissivity of the fractures in the network that results in a unit increase in the pressure at one measurement point whilst keeping the pressure at the remaining measurement points constant. The fracture transmissivities are updated by adding a linear combination of basis vectors and coefficients, where the coefficients are obtained by minimizing an error function. A mathematical summary of the method is given. This algorithm is implemented in the existing finite element code ConnectFlow developed and marketed by Serco Technical Services, which models groundwater flow in a fracture network. Results of the conditioning are shown for a number of simple test problems as well as for a realistic large scale test case.

Sloshing and slamming oscillations in collapsible channel flow

We consider laminar high-Reynolds-number flow through a finite-length planar channel, where a portion of one wall is replaced by a thin massless elastic membrane that is held under longitudinal tension T and subject to an external pressure distribution. The flow is driven by a fixed pressure drop along the full length of the channel. We investigate the global stability of two-dimensional Poiseuille flow using a method of matched local eigenfunction expansions, which is compared to direct numerical simulations. We trace the neutral stability curve of the primary oscillatory instability of the system, illustrating a transition from high-frequency ‘sloshing’ oscillations at high T to vigorous ‘slamming’ motion at low T . Small-amplitude sloshing at high T can be captured using a low-order eigenmode truncation involving four surface-based modes in the compliant segment of the channel coupled to Womersley flow in the rigid segments. At lower tensions, we show that hydrodynamic modes contribute increasingly to the global instability and we demonstrate a change in the mechanism of energy transfer from the mean flow, with viscous effects being destabilising. Simulations of finite-amplitude oscillations at low T reveal a generic slamming motion, in which the the flexible membrane is drawn close to the opposite rigid wall before rapidly recovering. A simple model is used to demonstrate how fluid inertia in the downstream rigid channel segment, coupled to membrane curvature downstream of the moving constriction, together control slamming dynamics.

Adaptive coatings based on polyaniline for direct 2D observation of diffusion processes in microfluidic systems

[EN] Therefore the understanding and proper evaluation of the flow and mixing behaviour at microscale becomes a very important issue. In this study, the diffusion behaviour of two reacting solutions of HCI and NaOH were directly observed in a glass/polydimethylsiloxane microfluidic device using adaptive coatings based on the conductive polymer polyaniline that are covalently attached to the microchannel walls. The two liquid streams were combined at the junction of a Y-shaped microchannel, and allowed to diffuse into each other and react. The results showed excellent correlation between optical observation of the diffusion process and the numerical results. A numerical model which is based on finite volume method (FVM) discretisation of steady Navier-Stokes (fluid flow) equations and mass transport equations without reactions was used to calculate the flow variables at discrete points in the finite volume mesh element. The high correlation between theory and practical data indicates the potential of such coatings to monitor diffusion processes and mixing behaviour inside microfluidic channels in a dye free environment.

Adaptivity and a posteriori error control for bifurcation problems II: Incompressible fluid flow in open systems with Z_2 symmetry

In this article we consider the a posteriori error estimation and adaptive mesh refinement of discontinuous Galerkin finite element approximations of the bifurcation problem associated with the steady incompressible Navier-Stokes equations. Particular attention is given to the reliable error estimation of the critical Reynolds number at which a steady pitchfork or Hopf bifurcation occurs when the underlying physical system possesses reflectional or Z_2 symmetry. Here, computable a posteriori error bounds are derived based on employing the generalization of the standard Dual-Weighted-Residual approach, originally developed for the estimation of target functionals of the solution, to bifurcation problems. Numerical experiments highlighting the practical performance of the proposed a posteriori error indicator on adaptively refined computational meshes are presented.

Cold vapour generation electrothermal atomic absorption spectrometry and solid phase extraction based on a new nanosorbent for sensitive HG determination in environmental samples (sea water and river water)

Mercury is not an essential element for plant or animal life and it is a potential environmental toxic because of its tendency to form covalent bonds with organic molecules and the high stability of the Hg-C bond. Reports estimate a total mercury concentration in natural waters ranging from 0.2 to 100 ng L-1. Due to this fact, highly sensitive methods are required for direct determination of such extremely low levels. In this work, a rapid and simple method was developed for separation and preconcentration of mercury by flow injection solid phase extraction coupled with on-line chemical vapour generation electrothermal atomic absorption spectrometry. The system is based on chelating retention of the analyte onto the mini column filled with a mesoporous silica functionalized with 1,5 bis (di-2-pyridyl) methylene thiocarbohydrazide. The main aim of this work was to develop a precise and accurate method for the determination of the Hg. Under the optima conditions and 120 s preconcentration time, the detection limit obtained was 0.009 μg L-1, with RSDs 3.7 % for 0.2 μg L-1, 4.8 % for 1 μg L-1 and enrichment factor 4, Furthermore, the method proposed has permitted the determination of Hg with a reduction in the analysis time, the sample throughput was about 18 h-1, low consumption of reagents and sample volume. The method was applied to the determination of Hg in sea water and river water. For the quality control of the analytical performance and the validation of the newly developed method, the analysis of two certified samples, TMDA 54.4 Fortified Lake, and LGC6187 River sediment was addressed. The results showed good agreement with the certified values.

Processing of laser Doppler flowmetry signals from healthy subjects and patients with varicose veins: information categorization approach based on intrinsic mode functions and entropy computation

International audience

Experimental characterization of wingtip vortices using smoke flow visualizations

In order to predict the axial development of the wingtip vortices strength an accurate theoretical model is required. Several experimental techniques have been used to that end, e.g. PIV or hotwire anemometry, but they imply a significant cost and effort. For this reason, we have carried out experiments using the smoke-wire technique to visualize smoke streaks in six planes perpendicular to the main stream flow direction. Using this visualization technique, we obtained quantitative information regarding the vortex velocity field by means of Batchelor's model~\cite{batchelor}, which only depends on two free parameters, i.e. the vortex strength, $S$, and the virtual origin, $z_0$. Results for two chord based Reynolds numbers have been compared with those provided by del Pino et at. (2011), finding good agreement.

AN ASSESSMENT OF FLOW REGIME MAPS AND A NUMERICAL HEAT TRANSFER CORRELATION FOR THE STRATIFIED/ANNULAR REGIME OF SHEAR-DRIVEN INTERNAL CONDENSING FLOWS

Several modern-day cooling applications require the incorporation of mini/micro-channel shear-driven flow condensers. There are several design challenges that need to be overcome in order to meet those requirements. The difficulty in developing effective design tools for shear-driven flow condensers is exacerbated due to the lack of a bridge between the physics-based modelling of condensing flows and the current, popular approach based on semi-empirical heat transfer correlations. One of the primary contributors of this disconnect is a lack of understanding caused by the fact that typical heat transfer correlations eliminate the dependence of the heat transfer coefficient on the method of cooling employed on the condenser surface when it may very well not be the case. This is in direct contrast to direct physics-based modeling approaches where the thermal boundary conditions have a direct and huge impact on the heat transfer coefficient values. Typical heat transfer correlations instead introduce vapor quality as one of the variables on which the value of the heat transfer coefficient depends. This study shows how, under certain conditions, a heat transfer correlation from direct physics-based modeling can be equivalent to typical engineering heat transfer correlations without making the same apriori assumptions. Another huge factor that raises doubts on the validity of the heat-transfer correlations is the opacity associated with the application of flow regime maps for internal condensing flows. It is well known that flow regimes influence heat transfer rates strongly. However, several heat transfer correlations ignore flow regimes entirely and present a single heat transfer correlation for all flow regimes. This is believed to be inaccurate since one would expect significant differences in the heat transfer correlations for different flow regimes. Several other studies present a heat transfer correlation for a particular flow regime - however, they ignore the method by which extents of the flow regime is established. This thesis provides a definitive answer (in the context of stratified/annular flows) to: (i) whether a heat transfer correlation can always be independent of the thermal boundary condition and represented as a function of vapor quality, and (ii) whether a heat transfer correlation can be independently obtained for a flow regime without knowing the flow regime boundary (even if the flow regime boundary is represented through a separate and independent correlation). To obtain the results required to arrive at an answer to these questions, this study uses two numerical simulation tools - the approximate but highly efficient Quasi-1D simulation tool and the exact but more expensive 2D Steady Simulation tool. Using these tools and the approximate values of flow regime transitions, a deeper understanding of the current state of knowledge in flow regime maps and heat transfer correlations in shear-driven internal condensing flows is obtained. The ideas presented here can be extended for other flow regimes of shear-driven flows as well. Analogous correlations can also be obtained for internal condensers in the gravity-driven and mixed-driven configuration.

REALIZATION OF A DC MICROGRID USING A HAMILTONIAN BASED CONTROLS SOLUTION

Future power grids are envisioned to be serviced by heterogeneous arrangements of renewable energy sources. Due to their stochastic nature, energy storage distribution and management are pivotal in realizing microgrids serviced heavily by renewable energy assets. Identifying the required response characteristics to meet the operational requirements of a power grid are of great importance and must be illuminated in order to discern optimal hardware topologies. Hamiltonian Surface Shaping and Power Flow Control (HSSPFC) presents the tools to identify such characteristics. By using energy storage as actuation within the closed loop controller, the response requirements may be identified while providing a decoupled controller solution. A DC microgrid servicing a fixed RC load through source and bus level storage managed by HSSPFC was realized in hardware. A procedure was developed to calibrate the DC microgrid architecture of this work to the reduced order model used by the HSSPFC law. Storage requirements were examined through simulation and experimental testing. Bandwidth contributions between feed forward and PI components of the HSSPFC law are illuminated and suggest the need for well-known system losses to prevent the need for additional overhead in storage allocations. The following work outlines the steps taken in realizing a DC microgrid and presents design considerations for system calibration and storage requirements per the closed loop controls for future DC microgrids.

Development of an innovative non rule-based energy management strategy for a Hybrid Electric Vehicle, structured for predictive driving controls based on external information knowledge

Recently, the interest of the automotive market for hybrid vehicles has increased due to the more restrictive pollutants emissions legislation and to the necessity of decreasing the fossil fuel consumption, since such solution allows a consistent improvement of the vehicle global efficiency. The term hybridization regards the energy flow in the powertrain of a vehicle: a standard vehicle has, usually, only one energy source and one energy tank; instead, a hybrid vehicle has at least two energy sources. In most cases, the prime mover is an internal combustion engine (ICE) while the auxiliary energy source can be mechanical, electrical, pneumatic or hydraulic. It is expected from the control unit of a hybrid vehicle the use of the ICE in high efficiency working zones and to shut it down when it is more convenient, while using the EMG at partial loads and as a fast torque response during transients. However, the battery state of charge may represent a limitation for such a strategy. That’s the reason why, in most cases, energy management strategies are based on the State Of Charge, or SOC, control. Several studies have been conducted on this topic and many different approaches have been illustrated. The purpose of this dissertation is to develop an online (usable on-board) control strategy in which the operating modes are defined using an instantaneous optimization method that minimizes the equivalent fuel consumption of a hybrid electric vehicle. The equivalent fuel consumption is calculated by taking into account the total energy used by the hybrid powertrain during the propulsion phases. The first section presents the hybrid vehicles characteristics. The second chapter describes the global model, with a particular focus on the energy management strategies usable for the supervisory control of such a powertrain. The third chapter shows the performance of the implemented controller on a NEDC cycle compared with the one obtained with the original control strategy.

Feasibility study and flow scheduling optimization of a multi-product pipeline system

The first goal of this study is to analyse a real-world multiproduct onshore pipeline system in order to verify its hydraulic configuration and operational feasibility by constructing a simulation model step by step from its elementary building blocks that permits to copy the operation of the real system as precisely as possible. The second goal is to develop this simulation model into a user-friendly tool that one could use to find an “optimal” or “best” product batch schedule for a one year time period. Such a batch schedule could change dynamically as perturbations occur during operation that influence the behaviour of the entire system. The result of the simulation, the ‘best’ batch schedule is the one that minimizes the operational costs in the system. The costs involved in the simulation are inventory costs, interface costs, pumping costs, and penalty costs assigned to any unforeseen situations. The key factor to determine the performance of the simulation model is the way time is represented. In our model an event based discrete time representation is selected as most appropriate for our purposes. This means that the time horizon is divided into intervals of unequal lengths based on events that change the state of the system. These events are the arrival/departure of the tanker ships, the openings and closures of loading/unloading valves of storage tanks at both terminals, and the arrivals/departures of trains/trucks at the Delivery Terminal. In the feasibility study we analyse the system’s operational performance with different Head Terminal storage capacity configurations. For these alternative configurations we evaluated the effect of different tanker ship delay magnitudes on the number of critical events and product interfaces generated, on the duration of pipeline stoppages, the satisfaction of the product demand and on the operative costs. Based on the results and the bottlenecks identified, we propose modifications in the original setup.