Desenvolupament computacional de la semblança molecular quàntica

La present Tesi Doctoral, titulada desenvolupament computacional de la semblança molecular quàntica, tracta, fonamentalment, els aspectes de càlcul de mesures de semblança basades en la comparació de funcions de densitat electrònica.El primer capítol, Semblança quàntica, és introductori. S'hi descriuen les funcions de densitat de probabilitat electrònica i llur significança en el marc de la mecànica quàntica. Se n'expliciten els aspectes essencials i les condicions matemàtiques a satisfer, cara a una millor comprensió dels models de densitat electrònica que es proposen. Hom presenta les densitats electròniques, mencionant els teoremes de Hohenberg i Kohn i esquematitzant la teoria de Bader, com magnituds fonamentals en la descripció de les molècules i en la comprensió de llurs propietats.En el capítol Models de densitats electròniques moleculars es presenten procediments computacionals originals per l'ajust de funcions densitat a models expandits en termes de gaussianes 1s centrades en els nuclis. Les restriccions físico-matemàtiques associades a les distribucions de probabilitat s'introdueixen de manera rigorosa, en el procediment anomenat Atomic Shell Approximation (ASA). Aquest procediment, implementat en el programa ASAC, parteix d'un espai funcional quasi complert, d'on se seleccionen variacionalment les funcions o capes de l'expansió, d'acord als requisits de no negativitat. La qualitat d'aquestes densitats i de les mesures de semblança derivades es verifica abastament. Aquest model ASA s'estén a representacions dinàmiques, físicament més acurades, en quant que afectades per les vibracions nuclears, cara a una exploració de l'efecte de l'esmorteïment dels pics nuclears en les mesures de semblança molecular. La comparació de les densitats dinàmiques respecte les estàtiques evidencia un reordenament en les densitats dinàmiques, d'acord al que constituiria una manifestació del Principi quàntic de Le Chatelier. El procediment ASA, explícitament consistent amb les condicions de N-representabilitat, s'aplica també a la determinació directe de densitats electròniques hidrogenoides, en un context de teoria del funcional de la densitat.El capítol Maximització global de la funció de semblança presenta algorismes originals per la determinació de la màxima sobreposició de les densitats electròniques moleculars. Les mesures de semblança molecular quàntica s'identifiquen amb el màxim solapament, de manera es mesuri la distància entre les molècules, independentment dels sistemes de referència on es defineixen les densitats electròniques. Partint de la solució global en el límit de densitats infinitament compactades en els nuclis, es proposen tres nivells de aproximació per l'exploració sistemàtica, no estocàstica, de la funció de semblança, possibilitant la identificació eficient del màxim global, així com també dels diferents màxims locals. Es proposa també una parametrització original de les integrals de recobriment a través d'ajustos a funcions lorentzianes, en quant que tècnica d'acceleració computacional. En la pràctica de les relacions estructura-activitat, aquests avenços possibiliten la implementació eficient de mesures de semblança quantitatives, i, paral·lelament, proporcionen una metodologia totalment automàtica d'alineació molecular. El capítol Semblances d'àtoms en molècules descriu un algorisme de comparació dels àtoms de Bader, o regions tridimensionals delimitades per superfícies de flux zero de la funció de densitat electrònica. El caràcter quantitatiu d'aquestes semblances possibilita la mesura rigorosa de la noció química de transferibilitat d'àtoms i grups funcionals. Les superfícies de flux zero i els algorismes d'integració usats han estat publicats recentment i constitueixen l'aproximació més acurada pel càlcul de les propietats atòmiques. Finalment, en el capítol Semblances en estructures cristal·lines hom proposa una definició original de semblança, específica per la comparació dels conceptes de suavitat o softness en la distribució de fonons associats a l'estructura cristal·lina. Aquests conceptes apareixen en estudis de superconductivitat a causa de la influència de les interaccions electró-fonó en les temperatures de transició a l'estat superconductor. En aplicar-se aquesta metodologia a l'anàlisi de sals de BEDT-TTF, s'evidencien correlacions estructurals entre sals superconductores i no superconductores, en consonància amb les hipòtesis apuntades a la literatura sobre la rellevància de determinades interaccions.Conclouen aquesta tesi un apèndix que conté el programa ASAC, implementació de l'algorisme ASA, i un capítol final amb referències bibliogràfiques.

The counter-propagating Rossby-wave perspective on baroclinic instability. I: Mathematical basis

It is shown that Bretherton's view of baroclinic instability as the interaction of two counter-propagating Rossby waves (CRWs) can be extended to a general zonal flow and to a general dynamical system based on material conservation of potential vorticity (PV). The two CRWs have zero tilt with both altitude and latitude and are constructed from a pair of growing and decaying normal modes. One CRW has generally large amplitude in regions of positive meridional PV gradient and propagates westwards relative to the flow in such regions. Conversely, the other CRW has large amplitude in regions of negative PV gradient and propagates eastward relative to the zonal flow there. Two methods of construction are described. In the first, more heuristic, method a ‘home-base’ is chosen for each CRW and the other CRW is defined to have zero PV there. Consideration of the PV equation at the two home-bases gives ‘CRW equations’ quantifying the evolution of the amplitudes and phases of both CRWs. They involve only three coefficients describing the mutual interaction of the waves and their self-propagation speeds. These coefficients relate to PV anomalies formed by meridional fluid displacements and the wind induced by these anomalies at the home-bases. In the second method, the CRWs are defined by orthogonality constraints with respect to wave activity and energy growth, avoiding the subjective choice of home-bases. Using these constraints, the same form of CRW equations are obtained from global integrals of the PV equation, but the three coefficients are global integrals that are not so readily described by ‘PV-thinking’ arguments. Each CRW could not continue to exist alone, but together they can describe the time development of any flow whose initial conditions can be described by the pair of growing and decaying normal modes, including the possibility of a super-modal growth rate for a short period. A phase-locking configuration (and normal-mode growth) is possible only if the PV gradient takes opposite signs and the mean zonal wind and the PV gradient are positively correlated in the two distinct regions where the wave activity of each CRW is concentrated. These are easily interpreted local versions of the integral conditions for instability given by Charney and Stern and by Fjørtoft.

Boundary integral equations on unbounded rough surfaces: Fredholmness and the finite section method

We consider a class of boundary integral equations that arise in the study of strongly elliptic BVPs in unbounded domains of the form $D = \{(x, z)\in \mathbb{R}^{n+1} : x\in \mathbb{R}^n, z > f(x)\}$ where $f : \mathbb{R}^n \to\mathbb{R}$ is a sufficiently smooth bounded and continuous function. A number of specific problems of this type, for example acoustic scattering problems, problems involving elastic waves, and problems in potential theory, have been reformulated as second kind integral equations $u+Ku = v$ in the space $BC$ of bounded, continuous functions. Having recourse to the so-called limit operator method, we address two questions for the operator $A = I + K$ under consideration, with an emphasis on the function space setting $BC$. Firstly, under which conditions is $A$ a Fredholm operator, and, secondly, when is the finite section method applicable to $A$?

Mersenne numbers

These notes have been issued on a small scale in 1983 and 1987 and on request at other times. This issue follows two items of news. First, WaIter Colquitt and Luther Welsh found the 'missed' Mersenne prime M110503 and advanced the frontier of complete Mp-testing to 139,267. In so doing, they terminated Slowinski's significant string of four consecutive Mersenne primes. Secondly, a team of five established a non-Mersenne number as the largest known prime. This result terminated the 1952-89 reign of Mersenne primes. All the original Mersenne numbers with p < 258 were factorised some time ago. The Sandia Laboratories team of Davis, Holdridge & Simmons with some little assistance from a CRAY machine cracked M211 in 1983 and M251 in 1984. They contributed their results to the 'Cunningham Project', care of Sam Wagstaff. That project is now moving apace thanks to developments in technology, factorisation and primality testing. New levels of computer power and new computer architectures motivated by the open-ended promise of parallelism are now available. Once again, the suppliers may be offering free buildings with the computer. However, the Sandia '84 CRAY-l implementation of the quadratic-sieve method is now outpowered by the number-field sieve technique. This is deployed on either purpose-built hardware or large syndicates, even distributed world-wide, of collaborating standard processors. New factorisation techniques of both special and general applicability have been defined and deployed. The elliptic-curve method finds large factors with helpful properties while the number-field sieve approach is breaking down composites with over one hundred digits. The material is updated on an occasional basis to follow the latest developments in primality-testing large Mp and factorising smaller Mp; all dates derive from the published literature or referenced private communications. Minor corrections, additions and changes merely advance the issue number after the decimal point. The reader is invited to report any errors and omissions that have escaped the proof-reading, to answer the unresolved questions noted and to suggest additional material associated with this subject.

High-resolution, unstructured meshes for hydrodynamic models of the Great Barrier Reef, Australia

Accuracy and mesh generation are key issues for the high-resolution hydrodynamic modelling of the whole Great Barrier Reef. Our objective is to generate suitable unstructured grids that can resolve topological and dynamical features like tidal jets and recirculation eddies in the wake of islands. A new strategy is suggested to refine the mesh in areas of interest taking into account the bathymetric field and an approximated distance to islands and reefs. Such a distance is obtained by solving an elliptic differential operator, with specific boundary conditions. Meshes produced illustrate both the validity and the efficiency of the adaptive strategy. Selection of refinement and geometrical parameters is discussed. (c) 2006 Elsevier Ltd. All rights reserved.

Moving boundary value problems for the wave equation

We study certain boundary value problems for the one-dimensional wave equation posed in a time-dependent domain. The approach we propose is based on a general transform method for solving boundary value problems for integrable nonlinear PDE in two variables, that has been applied extensively to the study of linear parabolic and elliptic equations. Here we analyse the wave equation as a simple illustrative example to discuss the particular features of this method in the context of linear hyperbolic PDEs, which have not been studied before in this framework.

The geometry of optimal control solutions on some six dimensional lie groups

This paper examines optimal solutions of control systems with drift defined on the orthonormal frame bundle of particular Riemannian manifolds of constant curvature. The manifolds considered here are the space forms Euclidean space E-3, the spheres S-3 and the hyperboloids H-3 with the corresponding frame bundles equal to the Euclidean group of motions SE(3), the rotation group SO(4) and the Lorentz group SO(1,3). The optimal controls of these systems are solved explicitly in terms of elliptic functions. In this paper, a geometric interpretation of the extremal solutions is given with particular emphasis to a singularity in the explicit solutions. Using a reduced form of the Casimir functions the geometry of these solutions are illustrated.

Integrating Hamiltonian systems defined on the Lie groups SO(4) and SO(1,3)

This paper examines optimal solutions of control systems with drift defined on the orthonormal frame bundle of particular Riemannian manifolds of constant curvature. The manifolds considered here are the space forms Euclidean space E³, the spheres S³ and the hyperboloids H³ with the corresponding frame bundles equal to the Euclidean group of motions SE(3), the rotation group SO(4) and the Lorentz group SO(1,3). The optimal controls of these systems are solved explicitly in terms of elliptic functions. In this paper, a geometric interpretation of the extremal solutions is given with particular emphasis to a singularity in the explicit solutions. Using a reduced form of the Casimir functions the geometry of these solutions is illustrated.

Exact error estimates and optimal randomized algorithms for integration

Exact error estimates for evaluating multi-dimensional integrals are considered. An estimate is called exact if the rates of convergence for the low- and upper-bound estimate coincide. The algorithm with such an exact rate is called optimal. Such an algorithm has an unimprovable rate of convergence. The problem of existing exact estimates and optimal algorithms is discussed for some functional spaces that define the regularity of the integrand. Important for practical computations data classes are considered: classes of functions with bounded derivatives and Holder type conditions. The aim of the paper is to analyze the performance of two optimal classes of algorithms: deterministic and randomized for computing multidimensional integrals. It is also shown how the smoothness of the integrand can be exploited to construct better randomized algorithms.

Parallel Monte Carlo approach for integration of the rendering equation

This paper is addressed to the numerical solving of the rendering equation in realistic image creation. The rendering equation is integral equation describing the light propagation in a scene accordingly to a given illumination model. The used illumination model determines the kernel of the equation under consideration. Nowadays, widely used are the Monte Carlo methods for solving the rendering equation in order to create photorealistic images. In this work we consider the Monte Carlo solving of the rendering equation in the context of the parallel sampling scheme for hemisphere. Our aim is to apply this sampling scheme to stratified Monte Carlo integration method for parallel solving of the rendering equation. The domain for integration of the rendering equation is a hemisphere. We divide the hemispherical domain into a number of equal sub-domains of orthogonal spherical triangles. This domain partitioning allows to solve the rendering equation in parallel. It is known that the Neumann series represent the solution of the integral equation as a infinity sum of integrals. We approximate this sum with a desired truncation error (systematic error) receiving the fixed number of iteration. Then the rendering equation is solved iteratively using Monte Carlo approach. At each iteration we solve multi-dimensional integrals using uniform hemisphere partitioning scheme. An estimate of the rate of convergence is obtained using the stratified Monte Carlo method. This domain partitioning allows easy parallel realization and leads to convergence improvement of the Monte Carlo method. The high performance and Grid computing of the corresponding Monte Carlo scheme are discussed.

'Flat phase' PID controllers

Flat Phase PID Controllers have the property that the phase of the transfer function round the associated feedback loop is constant or flat around the design frequency, with the aim that the phase margin and overshoot to a step response is unaffected when the gain of the device under control changes. Such designs have been achieved using Bode Integrals and by ensuring the phase is the same at two frequencies. This paper extends the ‘two frequency’ controller and describes a novel three frequency controller. The different design strategies arc compared.

Singularities of optimal control problems on some 6-D lie groups

This paper considers the motion planning problem for oriented vehicles travelling at unit speed in a 3-D space. A Lie group formulation arises naturally and the vehicles are modeled as kinematic control systems with drift defined on the orthonormal frame bundles of particular Riemannian manifolds, specifically, the 3-D space forms Euclidean space E-3, the sphere S-3, and the hyperboloid H'. The corresponding frame bundles are equal to the Euclidean group of motions SE(3), the rotation group SO(4), and the Lorentz group SO (1, 3). The maximum principle of optimal control shifts the emphasis for these systems to the associated Hamiltonian formalism. For an integrable case, the extremal curves are explicitly expressed in terms of elliptic functions. In this paper, a study at the singularities of the extremal curves are given, which correspond to critical points of these elliptic functions. The extremal curves are characterized as the intersections of invariant surfaces and are illustrated graphically at the singular points. It. is then shown that the projections, of the extremals onto the base space, called elastica, at these singular points, are curves of constant curvature and torsion, which in turn implies that the oriented vehicles trace helices.

Electron spin resonance study of puff-resolved free radical formation in mainstream cigarette smoke

Puff-by-puff resolved gas phase free radicals were measured in mainstream smoke from Kentucky 2R4F reference cigarettes using ESR spectroscopy. Three spin-trapping reagents were evaluated: PBN, DMPO and DEPMPO. Two procedures were used to collect gas phase smoke on a puff-resolved basis: i) the accumulative mode, in which all the gas phase smoke up to a particular puff was bubbled into the trap (i.e., the 5th puff corresponded to the total smoke from the 1st to 5th puffs). In this case, after a specified puff, an aliquot of the spin trap was taken and analysed; or, ii) the individual mode, in which the spin trap was analysed and then replaced after each puff. Spin concentrations were determined by double-integration of the first derivative of the ESR signal. This was compared with the integrals of known standards using the TEMPO free radical. The radicals trapped with PBN were mainly carbon-centred, whilst the oxygen-centred radicals were identified with DMPO and DEPMPO. With each spin trap, the puff-resolved radical concentrations showed a characteristic pattern as a function of the puff number. Based on the spin concentrations, the DMPO and DEPMPO spin traps showed better trapping efficiencies than PBN. The implication for gas phase free radical analysis is that a range of different spin traps should be used to probe complex free radical reactions in cigarette smoke.

Analytic Benchmark Solutions for Open-Channel Flows

An important test of the quality of a computational model is its ability to reproduce standard test cases or benchmarks. For steady open–channel flow based on the Saint Venant equations some benchmarks exist for simple geometries from the work of Bresse, Bakhmeteff and Chow but these are tabulated in the form of standard integrals. This paper provides benchmark solutions for a wider range of cases, which may have a nonprismatic cross section, nonuniform bed slope, and transitions between subcritical and supercritical flow. This makes it possible to assess the underlying quality of computational algorithms in more difficult cases, including those with hydraulic jumps. Several new test cases are given in detail and the performance of a commercial steady flow package is evaluated against two of them. The test cases may also be used as benchmarks for both steady flow models and unsteady flow models in the steady limit.

On the Convergence of Two-Stage Iterative Processes for Solving Linear Equations

This paper considers two-stage iterative processes for solving the linear system $Af = b$. The outer iteration is defined by $Mf^{k + 1} = Nf^k + b$, where $M$ is a nonsingular matrix such that $M - N = A$. At each stage $f^{k + 1} $ is computed approximately using an inner iteration process to solve $Mv = Nf^k + b$ for $v$. At the $k$th outer iteration, $p_k $ inner iterations are performed. It is shown that this procedure converges if $p_k \geqq P$ for some $P$ provided that the inner iteration is convergent and that the outer process would converge if $f^{k + 1} $ were determined exactly at every step. Convergence is also proved under more specialized conditions, and for the procedure where $p_k = p$ for all $k$, an estimate for $p$ is obtained which optimizes the convergence rate. Examples are given for systems arising from the numerical solution of elliptic partial differential equations and numerical results are presented.