Coupled effects of mechanics, geometry, and chemistry on bio-membrane behavior

Lipid bilayer membranes are models for cell membranes--the structure that helps regulate cell function. Cell membranes are heterogeneous, and the coupling between composition and shape gives rise to complex behaviors that are important to regulation. This thesis seeks to systematically build and analyze complete models to understand the behavior of multi-component membranes.

We propose a model and use it to derive the equilibrium and stability conditions for a general class of closed multi-component biological membranes. Our analysis shows that the critical modes of these membranes have high frequencies, unlike single-component vesicles, and their stability depends on system size, unlike in systems undergoing spinodal decomposition in flat space. An important implication is that small perturbations may nucleate localized but very large deformations. We compare these results with experimental observations.

We also study open membranes to gain insight into long tubular membranes that arise for example in nerve cells. We derive a complete system of equations for open membranes by using the principle of virtual work. Our linear stability analysis predicts that the tubular membranes tend to have coiling shapes if the tension is small, cylindrical shapes if the tension is moderate, and beading shapes if the tension is large. This is consistent with experimental observations reported in the literature in nerve fibers. Further, we provide numerical solutions to the fully nonlinear equilibrium equations in some problems, and show that the observed mode shapes are consistent with those suggested by linear stability. Our work also proves that beadings of nerve fibers can appear purely as a mechanical response of the membrane.

Atom localization in a four-level alkaline earth atomic system

We propose an atom localization scheme for a four-level alkaline earth atom via a classical standing-wave field, and give the analytical expressions of the localization peak positions as well as the widths versus the parameters of the optical fields. We show that the probability of finding the atom at a particular position can be increased from 1/4 to 1/3 or 1/2 by adjusting the detuning of the probe field and the Rabi frequencies of the optical fields. Furthermore, the localization precision can be dramatically enhanced by increasing the intensity of the standing-wave field or decreasing the detuning of the probe field. The analytical results are quite accordant to the numerical solutions.

The accuracy of Kirchhoff's approximation in describing the far field speckles produced by random self-affine fractal surfaces

Based on the rigorous formulation of integral equations for the propagations of light waves at the medium interface, we carry out the numerical solutions of the random light field scattered from self-affine fractal surface samples. The light intensities produced by the same surface samples are also calculated in Kirchhoff's approximation, and their comparisons with the corresponding rigorous results show directly the degree of the accuracy of the approximation. It is indicated that Kirchhoff's approximation is of good accuracy for random surfaces with small roughness value w and large roughness exponent alpha. For random surfaces with larger w and smaller alpha, the approximation results in considerable errors, and detailed calculations show that the inaccuracy comes from the simplification that the transmitted light field is proportional to the incident field and from the neglect of light field derivative at the interface.

Approximate theory for the flow through a cascade of cambered airfoils

An approximate theory for steady irrotational flow through a cascade of thin cambered airfoils is developed. Isolated thin airfoils have only slight camber is most applications, and the well known methods that replace the source and vorticity distributions of the curved camber line by similar distributions on the straight chord line are adequate. In cascades, however, the camber is usually appreciable, and significant errors are introduced if the vorticity and source distributions on the camber line are approximated by the same distribution on the chord line.

The calculation of the flow field becomes very clumsy in practice if the vorticity and source distributions are not confined to a straight line. A new method is proposed and investigated; in this method, at each point on the camber line, the vorticity and sources are assumed to be distributed along a straight line tangent to the camber line at that point, and corrections are determined to account for the deviation of the actual camber line from the tangent line. Hence, the basic calculation for the cambered airfoils is reduced to the simpler calculation of the straight line airfoils, with the equivalent straight line airfoils changing from point to point.

The results of the approximate method are compared with numerical solutions for cambers as high as 25 per cent of the chord. The leaving angles of flow are predicted quite well, even at this high value of the camber. The present method also gives the functional relationship between the exit angle and the other parameters such as airfoil shape and cascade geometry.

Multipole moments in general relativity and dynamical perturbations of black-hole magnetospheres

This thesis consists of two parts. In Part I, we develop a multipole moment formalism in general relativity and use it to analyze the motion and precession of compact bodies. More specifically, the generic, vacuum, dynamical gravitational field of the exterior universe in the vicinity of a freely moving body is expanded in positive powers of the distance r away from the body's spatial origin (i.e., in the distance r from its timelike-geodesic world line). The expansion coefficients, called "external multipole moments,'' are defined covariantly in terms of the Riemann curvature tensor and its spatial derivatives evaluated on the body's central world line. In a carefully chosen class of de Donder coordinates, the expansion of the external field involves only integral powers of r ; no logarithmic terms occur. The expansion is used to derive higher-order corrections to previously known laws of motion and precession for black holes and other bodies. The resulting laws of motion and precession are expressed in terms of couplings of the time derivatives of the body's quadrupole and octopole moments to the external moments, i.e., to the external curvature and its gradient.

In part II, we study the interaction of magnetohydrodynamic (MHD) waves in a black-hole magnetosphere with the "dragging of inertial frames" effect of the hole's rotation - i.e., with the hole's "gravitomagnetic field." More specifically: we first rewrite the laws of perfect general relativistic magnetohydrodynamics (GRMHD) in 3+1 language in a general spacetime, in terms of quantities (magnetic field, flow velocity, ...) that would be measured by the ''fiducial observers” whose world lines are orthogonal to (arbitrarily chosen) hypersurfaces of constant time. We then specialize to a stationary spacetime and MHD flow with one arbitrary spatial symmetry (e.g., the stationary magnetosphere of a Kerr black hole); and for this spacetime we reduce the GRMHD equations to a set of algebraic equations. The general features of the resulting stationary, symmetric GRMHD magnetospheric solutions are discussed, including the Blandford-Znajek effect in which the gravitomagnetic field interacts with the magnetosphere to produce an outflowing jet. Then in a specific model spacetime with two spatial symmetries, which captures the key features of the Kerr geometry, we derive the GRMHD equations which govern weak, linealized perturbations of a stationary magnetosphere with outflowing jet. These perturbation equations are then Fourier analyzed in time t and in the symmetry coordinate x, and subsequently solved numerically. The numerical solutions describe the interaction of MHD waves with the gravitomagnetic field. It is found that, among other features, when an oscillatory external force is applied to the region of the magnetosphere where plasma (e⁺e^-) is being created, the magnetosphere responds especially strongly at a particular, resonant, driving frequency. The resonant frequency is that for which the perturbations appear to be stationary (time independent) in the common rest frame of the freshly created plasma and the rotating magnetic field lines. The magnetosphere of a rotating black hole, when buffeted by nonaxisymmetric magnetic fields anchored in a surrounding accretion disk, might exhibit an analogous resonance. If so then the hole's outflowing jet might be modulated at resonant frequencies ω=(m/2) Ω_H where m is an integer and Ω_H is the hole's angular velocity.

Turbulent buoyant jets into stratified or flowing ambient fluids

Theoretical and experimental studies were made on two classes of buoyant jet problems, namely:

1) an inclined, round buoyant yet in a stagnant environment with linear density-stratification;

2) a round buoyant jet in a uniform cross stream of homogenous density.

Using the integral technique of analysis, assuming similarity, predictions can be made for jet trajectory, widths, and dilution ratios, in a density-stratified or flowing environment. Such information is of great importance in the design of disposal systems for sewage effluent into the ocean or waste gases into the atmosphere.

The present study of a buoyant jet in a stagnant environment has extended the Morton type of analysis to cover the effect of the initial angle of discharge. Numerical solutions have been presented for a range of initial conditions. Laboratory experiments were conducted for photographic observations of the trajectories of dyed jets. In general the observed jet forms agreed well with the calculated trajectories and nominal half widths when the value of the entrainment coefficient was taken to be α = 0.082, as previously suggested by Morton.

The problem of a buoyant jet in a uniform cross stream was analyzed by assuming an entrainment mechanism based upon the vector difference between the characteristic jet velocity and the ambient velocity. The effect of the unbalanced pressure field on the sides of the jet flow was approximated by a gross drag term. Laboratory flume experiments with sinking jets which are directly analogous to buoyant jets were performed. Salt solutions were injected into fresh water at the free surface in a flume. The jet trajectories, dilution ratios and jet half widths were determined by conductivity measurements. The entrainment coefficient, α, and drag coefficient, C_d, were found from the observed jet trajectories and dilution ratios. In the ten cases studied where jet Froude number ranged from 10 to 80 and velocity ratio (jet: current) K from 4 to 16, α varied from 0.4 to 0.5 and C_d from 1.7 to 0.1. The jet mixing motion for distance within 250D was found to be dominated by the self-generated turbulence, rather than the free-stream turbulence. Similarity of concentration profiles has also been discussed.

Inverse symmetric Dammann gratings

Inverse symmetric Dammann grating is a special grating, whose transition points are reflection symmetric about the midpoint with inverse phase offset in one period. It can produce even-numbered or odd-numbered array illumination when the phase modulations are pi or a specific value. Numerical solutions optimized by the steepest-descent algorithm for binary phase and multilevel phases with splitting ratio from I x 4 to 1 x 14 are given. Fabrication of 1 x 6 array without the zero-order intensity and 1 x 7 array with the zero-order intensity are made from the same amplitude mask. A 6 x 6 output without the crossed zero-orders was achieved by crossing two one-dimensional 1 x 6 inverse symmetric Dammann gratings. This grating may have potential value for practical applications. (C) 2008 Elsevier B.V. All rights reserved.

Fast Lattice Green's Function Methods for Viscous Incompressible Flows on Unbounded Domains

In this thesis, a collection of novel numerical techniques culminating in a fast, parallel method for the direct numerical simulation of incompressible viscous flows around surfaces immersed in unbounded fluid domains is presented. At the core of all these techniques is the use of the fundamental solutions, or lattice Green’s functions, of discrete operators to solve inhomogeneous elliptic difference equations arising in the discretization of the three-dimensional incompressible Navier-Stokes equations on unbounded regular grids. In addition to automatically enforcing the natural free-space boundary conditions, these new lattice Green’s function techniques facilitate the implementation of robust staggered-Cartesian-grid flow solvers with efficient nodal distributions and fast multipole methods. The provable conservation and stability properties of the appropriately combined discretization and solution techniques ensure robust numerical solutions. Numerical experiments on thin vortex rings, low-aspect-ratio flat plates, and spheres are used verify the accuracy, physical fidelity, and computational efficiency of the present formulations.

Um método sintético de difusão para aceleração do esquema de fonte de espalhamento em cálculos SN unidimensionais de fonte fixa

O esquema iterativo de fonte de espalhamento (SI) é tradicionalmente aplicado para a convergência da solução numérica de malha fina para problemas de transporte de nêutrons monoenergéticos na formulação de ordenadas discretas com fonte fixa. O esquema SI é muito simples de se implementar sob o ponto de vista computacional; porém, o esquema SI pode apresentar taxa de convergência muito lenta, principalmente para meios difusivos (baixa absorção) com vários livres caminhos médios de extensão. Nesta dissertação descrevemos uma técnica de aceleração baseada na melhoria da estimativa inicial para a distribuição da fonte de espalhamento no interior do domínio de solução. Em outras palavras, usamos como estimativa inicial para o fluxo escalar médio na grade de discretização de malha fina, presentes nos termos da fonte de espalhamento das equações discretizadas SN usadas nas varreduras de transporte, a solução numérica da equação da difusão de nêutrons em grade espacial de malha grossa com condições de contorno especiais, que aproximam as condições de contorno prescritas que são clássicas em cálculos SN, incluindo condições de contorno do tipo vácuo. Para aplicarmos esta solução gerada pela equação da difusão em grade de discretização de malha grossa nas equações discretizadas SN de transporte na grade de discretização de malha fina, primeiro implementamos uma reconstrução espacial dentro de cada nodo de discretização, e então determinamos o fluxo escalar médio em grade de discretização de malha fina para usá-lo nos termos da fonte de espalhamento. Consideramos um número de experimentos numéricos para ilustrar a eficiência oferecida pela presente técnica (DSA) de aceleração sintética de difusão.

Um método de matriz resposta com esquema iterativo de inversão parcial por região para problemas unidimensionais de transporte de nêutrons monoenergéticos na formulação de ordenadas discretas

Um método de matriz resposta (RM) é descrito para gerar soluções numéricas livres de erros de truncamento espacial para problemas de transporte de nêutrons monoenergéticos e com fonte fixa, em geometria unidimensional na formulação de ordenadas discretas (SN). O método RM com esquema iterativo de inversão parcial por região (RBI) converge valores numéricos para os fluxos angulares nas fronteiras das regiões que coincidem com os valores da solução analítica das equações SN, afora os erros de arredondamento da aritmética finita computacional. Desenvolvemos um esquema numérico de reconstrução espacial, que fornece a saída para os fluxos escalares de nêutrons em qualquer ponto do domínio definido pelo usuário, com um passo de avanço também escolhido pelo usuário. Resultados numéricos são apresentados para ilustrar a precisão do presente método em cálculos de malha grossa.

Simulações de problemas inversos com aplicações em engenharia nuclear usando técnicas de transporte de partículas neutras monoenergéticas na formulação unidimensional de ordenadas discretas

Neste trabalho, três técnicas para resolver numericamente problemas inversos de transporte de partículas neutras a uma velocidade para aplicações em engenharia nuclear são desenvolvidas. É fato conhecido que problemas diretos estacionários e monoenergéticos de transporte são caracterizados por estimar o fluxo de partículas como uma função-distribuição das variáveis independentes de espaço e de direção de movimento, quando os parâmetros materiais (seções de choque macroscópicas), a geometria, e o fluxo incidente nos contornos do domínio (condições de contorno), bem como a distribuição de fonte interior são conhecidos. Por outro lado, problemas inversos, neste trabalho, buscam estimativas para o fluxo incidente no contorno, ou a fonte interior, ou frações vazio em barras homogêneas. O modelo matemático usado tanto para os problemas diretos como para os problemas inversos é a equação de transporte independente do tempo, a uma velocidade, em geometria unidimensional e com o espalhamento linearmente anisotrópico na formulação de ordenadas discretas (SN). Nos problemas inversos de valor de contorno, dado o fluxo emergente em um extremo da barra, medido por um detector de nêutrons, por exemplo, buscamos uma estimativa precisa para o fluxo incidente no extremo oposto. Por outro lado, nos problemas inversos SN de fonte interior, buscamos uma estimativa precisa para a fonte armazenada no interior do domínio para fins de blindagem, sendo dado o fluxo emergente no contorno da barra. Além disso, nos problemas inversos SN de fração de vazio, dado o fluxo emergente em uma fronteira da barra devido ao fluxo incidente prescrito no extremo oposto, procuramos por uma estimativa precisa da fração de vazio no interior da barra, no contexto de ensaios não-destrutivos para aplicações na indústria. O código computacional desenvolvido neste trabalho apresenta o método espectronodal de malha grossa spectral Greens function (SGF) para os problemas diretos SN em geometria unidimensional para gerar soluções numéricas precisas para os três problemas inversos SN descritos acima. Para os problemas inversos SN de valor de contorno e de fonte interior, usamos a propriedade da proporcionalidade da fuga de partículas; ademais, para os problemas inversos SN de fração de vazio, oferecemos a técnica a qual nos referimos como o método físico da bissecção. Apresentamos resultados numéricos para ilustrar a precisão das três técnicas, conforme descrito nesta tese.

Métodos espectronodais para cálculos de transporte de partículas neutras com fonte fixa na formulação de ordenadas discretas e multigrupo de energia

Um método espectronodal é desenvolvido para problemas de transporte de partículas neutras de fonte fixa, multigrupo de energia em geometria cartesiana na formulação de ordenadas discretas (SN). Para geometria unidimensional o método espectronodal multigrupo denomina-se método spectral Greens function (SGF) com o esquema de inversão nodal (NBI) que converge solução numérica para problemas SN multigrupo em geometria unidimensional, que são completamente livre de erros de truncamento espacial para ordem L de anisotropia de espalhamento desde que L < N. Para geometria X; Y o método espectronodal multigrupo baseia-se em integrações transversais das equações SN no interior dos nodos de discretização espacial, separadamente nas direções coordenadas x e y. Já que os termos de fuga transversal são aproximados por constantes, o método nodal resultante denomina-se SGF-constant nodal (SGF-CN), que é aplicado a problemas SN multigrupo de fonte fixa em geometria X; Y com espalhamento isotrópico. Resultados numéricos são apresentados para ilustrar a eficiência dos códigos SGF e SGF-CN e a precisão das soluções numéricas convergidas em cálculos de malha grossa.

Uma formulação implícita para o método Smoothed Particle Hydrodynamics

Em uma grande gama de problemas físicos, governados por equações diferenciais, muitas vezes é de interesse obter-se soluções para o regime transiente e, portanto, deve-se empregar técnicas de integração temporal. Uma primeira possibilidade seria a de aplicar-se métodos explícitos, devido à sua simplicidade e eficiência computacional. Entretanto, esses métodos frequentemente são somente condicionalmente estáveis e estão sujeitos a severas restrições na escolha do passo no tempo. Para problemas advectivos, governados por equações hiperbólicas, esta restrição é conhecida como a condição de Courant-Friedrichs-Lewy (CFL). Quando temse a necessidade de obter soluções numéricas para grandes períodos de tempo, ou quando o custo computacional a cada passo é elevado, esta condição torna-se um empecilho. A fim de contornar esta restrição, métodos implícitos, que são geralmente incondicionalmente estáveis, são utilizados. Neste trabalho, foram aplicadas algumas formulações implícitas para a integração temporal no método Smoothed Particle Hydrodynamics (SPH) de modo a possibilitar o uso de maiores incrementos de tempo e uma forte estabilidade no processo de marcha temporal. Devido ao alto custo computacional exigido pela busca das partículas a cada passo no tempo, esta implementação só será viável se forem aplicados algoritmos eficientes para o tipo de estrutura matricial considerada, tais como os métodos do subespaço de Krylov. Portanto, fez-se um estudo para a escolha apropriada dos métodos que mais se adequavam a este problema, sendo os escolhidos os métodos Bi-Conjugate Gradient (BiCG), o Bi-Conjugate Gradient Stabilized (BiCGSTAB) e o Quasi-Minimal Residual (QMR). Alguns problemas testes foram utilizados a fim de validar as soluções numéricas obtidas com a versão implícita do método SPH.

Simplifying mooring analysis for deepwater systems using truncation

Over recent years academia and industry have engaged with the challenge of model testing deepwater structures at conventional scales. One approach to the limited depth problem has been to truncate the lines. This concept will be introduced, highlighting the need to better understand line dynamic processes. The type of line truncation developed here models the upper sections of each line in detail, capturing wave action and all coupling effects with the vessel, terminating to an approximate analytical model that aims to simulate the remainder of the line. A rationale for this is that in deep water transverse elastic waves of a line are likely to decay before they are reflected at the seabed because of nonlinear hydrodynamic drag forces. The first part of this paper is centered on verification of this rationale. A simplified model of a mooring line that describes the transverse dynamics in wave frequency is used, adopting the equation of motion of an inextensible taut string. The line is submerged in still water, one end fixed at the bottom the other assumed to follow the vessel response, which can be harmonic or random. A dimensional analysis, supported by exact benchmark numerical solutions, has shown that it is possible to produce a universal curve for the decay of transverse vibrations along the line, which is suitable for any kind of line with any top motion. This has a significant engineering benefit, allowing for a rapid assessment of line dynamics - it can be useful in deciding whether a truncated line model is appropriate, and if so, at which point truncation might be applied. This is followed by developing a truncation mechanism, formulating an end approximation that can reproduce the correct impedance, had the line been continuous to full depth. It has been found that below a certain length criterion, which is also universal, the transverse vibrational characteristics for each line are inertia driven. As such the truncated model can assume a linear damper whose coefficient depends on the line properties and frequency of vibration. Copyright © 2011 by the International Society of Offshore and Polar Engineers (ISOPE).

Decay of vibrations along deepwater mooring lines

Model tests for global design verification of deepwater floating structures cannot be made at reasonable scales. An overview of recent research efforts to tackle this challenge is given first, introducing the concept of line truncation techniques. In such a method the upper sections of each line are modelled in detail, capturing the wave action zone and all coupling effects with the vessel. These terminate to an approximate analytical model, that aims to simulate the remainder of the line. The rationale for this is that in deep water the transverse elastic waves of a line are likely to decay before they are reflected at the seabed. The focus of this paper is the verification of this rationale and the ongoing work, which is considering ways to produce a truncation model. Transverse dynamics of a mooring line are modelled using the equations of motion of an inextensible taut string, submerged in still water, one end fixed at the bottom the other assumed to follow the vessel response, which can be harmonic or random. Nonlinear hydrodynamic damping is included; bending and VIV effects are neglected. A dimensional analysis, supported by exact benchmark numerical solutions, has shown that it is possible to produce a universal curve for the decay of transverse vibrations along the line, which is suitable for any kind of line with any top motion. This has a significant engineering benefit, allowing for a rapid assessment of line dynamics - it is very useful in deciding whether a truncated line model is appropriate, and if so, at which point truncation might be applied. Initial efforts in developing a truncated model show that a linearized numerical solution in the frequency domain matches very closely the exact benchmark. Copyright © 2011 by ASME.