Hydrothermal waves and corotating rolls in laterally heated convection in simple liquids.

The stability of a liquid layer with an undeformable interface open to the atmo- sphere, subjected to a horizontal temperature gradient, is theoretically analysed. Buoyancy and surface tension forces give rise to a basic flow for any temperature dif- ference applied on the system. Depending on the liquid depth, this basic flow is desta- bilised either by an oscillatory instability, giving rise to the so-called hydrothermal waves, or by a stationary instability leading to corotating rolls. Oscillatory perturba- tions are driven by the basic flow and therefore one must distinguish between convec- tive and absolute thresholds. The instability mechanisms as well as the di¿erent re- gimes observed in experiments are discussed. The calculations are performed for a fluid used in recent experiments, namely silicone oil of 0.65 cSt ðPr 1?4 10Þ. In partic- ular, it is shown that two branches of absolute instability exist, which may be related to the two types of hydrothermal waves observed experimentally

On the onset of turbulence in natural convection on inclined plates

The problem of determination of the turbulence onset in natural convection on heated inclined plates in an air environment has been experimentally revisited. The transition has been detected by using hot wire velocity measurements. The onset of turbulence has been considered to take place where velocity fluctuations (measured through turbulence intensity) start to grow. Experiments have shown that the onset depends not only on the Grashof number defined in terms of the temperature difference between the heated plate and the surrounding air. A correlation between dimensionless Grashof and Reynolds numbers has been obtained, fitting quite well the experimental data.

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.

Measurement of transmitted power in untapered multifibre unions oscillatory spectral behaviour

Shows a new structure, the untapered multifibre union, with similar oscillation behaviour to that of tapered single-mode fibres. As a consequences conical regions are not relevant to the final results. This oscillatory behaviour opens the way to low-cost all-fibre devices such as optical filters

Reentrant and whirling hexagons in non-Boussinesq convection

We review recent computational results for hexagon patterns in non- Boussinesq convection. For sufficiently strong dependence of the fluid parameters on the temperature we find reentrance of steady hexagons, i.e. while near onset the hexagon patterns become unstable to rolls as usually, they become again stable in the strongly nonlinear regime. If the convection apparatus is rotated about a vertical axis the transition from hexagons to rolls is replaced by a Hopf bifurcation to whirling hexagons. For weak non-Boussinesq effects they display defect chaos of the type described by the two-dimensional (2D) complex Ginzburg-andau equation. For stronger non-Boussinesq effects the Hopf bifurcation becomes subcritical and localized bursting of the whirling amplitude is found. In this regime the cou- pling of the whirling amplitude to (small) deformations of the hexagon lattice becomes important. For yet stronger non-Boussinesq effects this coupling breaks up the hexagon lattice and strongly disordered states characterized by whirling and lattice defects are obtained.

Hexagonal patterns in a model for rotating convection

We study a model equation that mimics convection under rotation in a fluid with temperature- dependent properties (non-Boussinesq (NB)), high Prandtl number and idealized boundary conditions. It is based on a model equation proposed by Segel [1965] by adding rotation terms that lead to a Kuppers-Lortz instability [Kuppers & Lortz, 1969] and can develop into oscillating hexagons. We perform a weakly nonlinear analysis to find out explicitly the coefficients in the amplitude equation as functions of the rotation rate. These equations describe hexagons and os- cillating hexagons quite well, and include the Busse?Heikes (BH) model [Busse & Heikes, 1980] as a particular case. The sideband instabilities as well as short wavelength instabilities of such hexagonal patterns are discussed and the threshold for oscillating hexagons is determined.

Hexagons and spiral defect chaos in non-Boussinesq convection at low Prandtl numbers

We study the stability and dynamics of non-Boussinesq convection in pure gases ?CO2 and SF6? with Prandtl numbers near Pr? 1 and in a H2-Xe mixture with Pr= 0.17. Focusing on the strongly nonlinear regime we employ Galerkin stability analyses and direct numerical simulations of the Navier-Stokes equations. For Pr ? 1 and intermediate non-Boussinesq effects we find reentrance of stable hexagons as the Rayleigh number is increased. For stronger non-Boussinesq effects the usual, transverse side-band instability is superseded by a longitudinal side-band instability. Moreover, the hexagons do not exhibit any amplitude instability to rolls. Seemingly, this result contradicts the experimentally observed transition from hexagons to rolls. We resolve this discrepancy by including the effect of the lateral walls. Non-Boussinesq effects modify the spiral defect chaos observed for larger Rayleigh numbers. For convection in SF6 we find that non-Boussinesq effects strongly increase the number of small, compact convection cells and with it enhance the cellular character of the patterns. In H2-Xe, closer to threshold, we find instead an enhanced tendency toward roll-like structures. In both cases the number of spirals and of targetlike components is reduced. We quantify these effects using recently developed diagnostics of the geometric properties of the patterns.

Defect chaos and bursts: Hexagonal rotating convection and the complex Ginzburg-Landau equation

We employ numerical computations of the full Navier-Stokes equations to investigate non-Boussinesq convection in a rotating system using water as the working fluid. We identify two regimes. For weak non- Boussinesq effects the Hopf bifurcation from steady to oscillating (whirling) hexagons is supercritical and typical states exhibit defect chaos that is systematically described by the cubic complex Ginzburg-Landau equation. For stronger non-Boussinesq effects the Hopf bifurcation becomes subcritical and the oscil- lations exhibit localized chaotic bursting, which is modeled by a quintic complex Ginzburg-Landau equation.

Reentrant hexagons in non-Boussinesq convection.

While non-Boussinesq hexagonal convection patterns are known to be stable close to threshold (i.e. for Rayleigh numbers R ? Rc ), it has often been assumed that they are always unstable to rolls for slightly higher Rayleigh numbers. Using the incompressible Navier?Stokes equations for parameters corresponding to water as the working fluid, we perform full numerical stability analyses of hexagons in the strongly nonlinear regime ( ? (R ? Rc )/Rc = O(1)). We find ?re-entrant? behaviour of the hexagons, i.e. as is increased they can lose and regain stability. This can occur for values of as low as = 0.2. We identify two factors contributing to the re-entrance: (i) far above threshold there exists a hexagon attractor even in Boussinesq convection as has been shown recently and (ii) the non-Boussinesq effects increase with . Using direct simulations for circular containers we show that the re-entrant hexagons can prevail even for sidewall conditions that favour convection in the form of competing stable rolls. For sufficiently strong non-Boussinesq effects hexagons even become stable over the whole -range considered, 0 6 6 1.5.

Metodología de simulación numérica de la transferencia de calor por ebullición en película en torno a superficies esféricas refrigeradas por líquido saturado en convección libre: aplicación a reactores nucleares de lecho de bolas (PBR)

En la presente Tesis se realizó un análisis numérico, usando el código comercial Ansys-Fluent, de la refrigeración de una bola de combustible de un reactor de lecho de bolas (PBR, por sus siglas en inglés), ante un escenario de emergencia en el cual el núcleo sea desensamblado y las bolas se dejen caer en una piscina de agua, donde el mecanismo de transferencia de calor inicialmente sería la ebullición en película, implicando la convección y la radiación al fluido. Previamente se realizaron pruebas de validación, comparando los resultados numéricos con datos experimentales disponibles en la literatura para tres geometrías diferentes, lo cual permitió seleccionar los esquemas y modelos numéricos con mejor precisión y menor costo computacional. Una vez identificada la metodología numérica, todas las pruebas de validación fueron ampliamente satisfactorias, encontrándose muy buena concordancia en el flujo de calor promedio con los datos experimentales. Durante estas pruebas de validación se lograron caracterizar numéricamente algunos parámetros importantes en la ebullición en película con los cuales existen ciertos niveles de incertidumbre, como son el factor de acoplamiento entre convección y radiación, y el factor de corrección del calor latente de vaporización. El análisis térmico de la refrigeración de la bola del reactor por ebullición en película mostró que la misma se enfría, a pesar del calor de decaimiento, con una temperatura superficial de la bola que desciende de forma oscilatoria, debido al comportamiento inestable de la película de vapor. Sin embargo, la temperatura de esta superficie tiene una buena uniformidad, notándose que las áreas mejor y peor refrigeradas están localizadas en la parte superior de la bola. Se observó la formación de múltiples domos de vapor en diferentes posiciones circunferenciales, lo cual causa que el área más caliente de la superficie se localice donde se forman los domos más grandes. La separación entre los domos de vapor fue consistente con la teoría hidrodinámica, con la adición de que la separación entre domos se reduce a medida que evolucionan y crecen, debido a la curvatura de la superficie. ABSTRACT A numerical cooling analysis of a PBR fuel pebble, after an emergency scenario in which the nucleus disassembly is made and the pebbles are dropped into a water pool, transmitting heat by film boiling, involving convection and radiation to the fluid, is carried out in this Thesis. First, were performed validation tests comparing the numerical results with experimental works available for three different geometries, which allowed the selection of numerical models and schemes with better precision and lower computational cost. Once identified the numerical methodology, all validation tests were widely satisfactory, finding very good agreement with experimental works in average heat flux. During these validation tests were achieved numerically characterize some important parameters in film boiling with which there are certain levels of uncertainty, such as the coupling factor between convection and radiation, and the correction factor of the latent heat of vaporization. The thermal analysis of pebble cooling by film boiling shows that despite its decay heat, cooling occurs, with pebble surface temperature descending from an oscillatory manner, due to the instability of the vapor film. However, the temperature of this surface has a good uniformity, noting that the best and worst refrigerated area is located at the top of the pebble. The formation of multiple vapor domes at different circumferential positions is observed, which cause that the hottest area of the surface was located where biggest vapor domes were formed. The separation between vapor domes was consistent with the hydrodynamic theory, with the addition that the separation is reduced as the vapor dome evolves and grows, due to the surface curvature.

A subgrid viscosity Lagrance-Galerkin method for convection-diffusion problems

We present and analyze a subgrid viscosity Lagrange-Galerk in method that combines the subgrid eddy viscosity method proposed in W. Layton, A connection between subgrid scale eddy viscosity and mixed methods. Appl. Math. Comp., 133: 14 7-157, 2002, and a conventional Lagrange-Galerkin method in the framework of P1⊕ cubic bubble finite elements. This results in an efficient and easy to implement stabilized method for convection dominated convection diffusion reaction problems. Numerical experiments support the numerical analysis results and show that the new method is more accurate than the conventional Lagrange-Galerkin one.