The implicit-solvent model uses continuum electrostatic theory to represent the salt solution around dissolved biomolecules, leading to a coupled system of the Poisson-Boltzmann and Poisson equations. This thesis uses the implicit-solvent model to study solvation, binding and adsorption of proteins. We developed an implicit-solvent model solver that uses the boundary element method (BEM), called PyGBe. BEM numerically solves integral equations along the biomolecule-solvent interface only, therefore, it does not need to discretize the entire domain. PyGBe accelerates the BEM with a treecode algorithm and runs on graphic processing units. We performed extensive verification and validation of the code, comparing it with experimental observations, analytical solutions, and other numerical tools. Our results suggest that a BEM approach is more appropriate than volumetric based methods, like finite-difference or finite-element, for high accuracy calculations. We also discussed the effect of features like solvent-filled cavities and Stern layers in the implicit-solvent model, and realized that they become relevant in binding energy calculations. The application that drove this work was nano-scale biosensors-- devices designed to detect biomolecules. Biosensors are built with a functionalized layer of ligand molecules, to which the target molecule binds when it is detected. With our code, we performed a study of the orientation of proteins near charged surfaces, and investigated the ideal conditions for ligand molecule adsorption. Using immunoglobulin G as a test case, we found out that low salt concentration in the solvent and high positive surface charge density leads to favorable orientations of the ligand molecule for biosensing applications. We also studied the plasmonic response of localized surface plasmon resonance (LSPR) biosensors. LSPR biosensors monitor the plasmon resonance frequency of metallic nanoparticles, which shifts when a target molecule binds to a ligand molecule. Electrostatics is a valid approximation to the LSPR biosensor optical phenomenon in the long-wavelength limit, and BEM was able to reproduce the shift in the plasmon resonance frequency as proteins approach the nanoparticle.

No description available.

In this research project, the Boundary Element Method (BEM) is developed and formulated for the solution of two-dimensional convection-diffusion-reaction problems. A combined approach with the dual reciprocity boundary element method (DRBEM) has been applied to solve steady-state problems with variable velocity and transient problems with constant and variable velocity fields. Further, the radial integration boundary element method (RIBEM) is utilised to handle non-homogeneous problems with variable source term. For all cases, a boundary-only formulation is produced. Initially, the steady-state case with constant velocity is considered, by employing constant boundary elements and a fundamental solution of the adjoint equation. This fundamental solution leads to a singular integral equation. The conservation laws, usually applied to avoid this integration, do not hold when a chemical reaction is taking place. Then, the integrals are successfully computed using Telles' technique. The application of the BEM for this particular equation is discussed in detail in this work. Next, the steady-state problem for variable velocity fields is presented and investigated. The velocity field is divided into an average value plus a perturbation. The perturbation is taken to the right-hand-side of the equation generating a non-homogeneous term. This nonhomogeneous equation is treated by utilising the DRM approach resulting in a boundary-only equation. Then, an integral equation formulation for the transient problem with constant velocity is derived, based on the DRM approach utilising the fundamental solution of the steady-state case. Therefore, the convective terms will be encompassed by the fundamental solution and lie within the boundary integral after application of Greens's second identity, leaving on the right-hand-side of the equation a domain integral involving the time-derivative only. The proposed DRM method needs the time-derivative to be expanded as a series of functions that will allow the domain integral to be moved to the boundary. The expansion required by the DRM uses functions which take into account the geometry and physics of the problem, if velocity-dependent terms are used. After that, a novel DRBEM model for transient convection-diffusion-reaction problems with variable velocity field is investigated and validated. The fundamental solution for the corresponding steady-state problem is adopted in this formulation. The variable velocity is decomposed into an average which is included into the fundamental solution of the corresponding equation with constant coefficients, and a perturbation which is treated using the DRM approximation. The mathematical formulation permits the numerical solution to be represented in terms of boundary-only integrals. Finally, a new formulation for non-homogeneous convection-diffusion-reaction problems with variable source term is achieved using RIBEM. The RIM is adopted to convert the domain integrals into boundary-only integrals. The proposed technique shows very good solution behaviour and accuracy in all cases studied. The convergence of the methods has been examined by implementing different error norm indicators and increasing the number of boundary elements in all cases. Numerical test cases are presented throughout this research work. Their results are sufficiently encouraging to recommend the use of the techniques developed for solution of general convection-diffusion-reaction problems. All the simulated solutions for several examples showed very good agreement with available analytical solutions, with no numerical problems of oscillation and damping of sharp fronts.

Desenvolvem-se a formulação do Método dos Elementos de Contorno e correspondente algoritmo (para implementação em microcomputador) para a análise de propagação de fraturas em domínios bidimensionais. São utilizados elementos lineares isoparamétricos, tanto para discretizar o contorno quanto para simular a fratura. Os elementos de fratura são descontínuos. A formulação é baseada em equações integrais de tensões e de deslocamentos, onde o termo que considera tensões iniciais concentradas na linha de fratura é formulado a partir da definição de dipolos. O critério adotado é o modelo de fratura coesiva. Os termos singulares e hiper-singulares da formulação são tratados analiticamente e os termos quase-singulares são calculados através de um esquema numérico baseado na utilização de sub-elementos. Os valores dos dipolos são estimados ponto a ponto. Ao longo das fraturas, o valor máximo da tensão normal de tração permite definir novos elementos. As tensões de cisalhamento são removidas para manter a direção principal durante o processo. / The Boundary Element Method formulation and corresponding algorithrn (for microcomputer implementation) are developed for crack growth analysis in two-dimensional domains. Linear isoparametric elements are used to discretize both boundary and crack path. Fracture elements are assumed to be discontinuous. The formulation is based on stress and displacement integral equations, where the term that takes into account initial stresses concentrated along fracture line is formulated from dipoles definition. The coesive fracture rnodel is the criterium adopted. Singular and hipersingular formulation terms are anallitically treated and quasi-singular terms are computed by a numerical scheme based on element subdivision. Dipole values are estirnated point by point. Along fractures, the maximum normal tensile strenght is used to define new elements. Shear stresses are also removed to maintain the principal direction during the process.

Neste trabalho, estudam-se problemas bidimensionais de propagação de ondas acústicas e elásticas, no domínio da freqüência, formulados através do Método dos Elementos de Contorno. A formulação é baseada nas representações integrais das equações diferenciais que governam os fenômenos de propagação de ondas acústicas num meio fluido e de ondas elásticas numa estrutura elástica. Analisa-se também a interação entre o fluido e a estrutura com o uso de sistemas de equações acoplados. As soluções fundamentais utilizadas são expressões exatas e não há necessidade de subdivisão dos domínios em células de integração. São aplicadas técnicas de integração alternativas na escolha das equações algébricas no domínio do fluido, visando a melhora das respostas globais do conjunto. Apresentam-se ainda exemplos numéricos, com o objetivo de possibilitar a modelagem numérica de problemas de acoplamento fluido-estrutura e de radiação e difusão acústica. / In this work, acoustic and elastic wave propagation problems in 2D, in frequency domain, are studied and formulated with the Boundary Element Methods. The formulation is based on the integral representations derived from the differential equations that govern the phenomena of acoustic wave propagation in a fluid medium and elastic wave propagation inside an elastic domain. The fluid-structure interaction is also formulated by coupling appropriately the corresponding systems of equations. The fundamental solutions adopted in this work are conveniently chosen to avoid the mass integral terms in the elastic wave integral representation and the equivalent terms in the acoustic integral equation. Thus, the algebraic representations of both problems are written only in terms of boundary values. Subdivisions of the domain to perform integrals over cells are not required. In an attempt to improve the global answers of the fluid problem, several integration techniques have been experimented to build alternative algebraic matrix equations. Numerical examples are presented in order to shown the accuracy of the studied acoustic radiation and scattering problems and also to verify the proposed fluid-structure coupling.

O objetivo deste trabalho é apresentar uma nova formulação direta do Método dos Elementos de Contorno (M.E.C.) para análise de placas, utilizando a teoria de Kirchhoff, admitindo três parâmetros nodais de deslocamentos para sua representação integral: deslocamento transversal e suas derivadas nas direções normal e tangencial ao contorno. Dois valores nodais são usados para os esforços, momento fletor normal mn e força cortante equivalente Vn. Desta forma são escritas três equações integrais de contorno por nó, obtidas a partir da discretização da placa, segundo a forma usual do método. A vantagem mais perceptível desta formulação é a possibilidade de se fazer a ligação da placa analisada pelo M.E.C. com elementos lineares, representados por três valores nodais de deslocamentos que passam a ser compatibilizados diretamente, para a análise de edifícios. São apresentados exemplos numéricos da formulação e das ligações para comprovação da formulação. / The aim of this work is to present an alternative formulation for plate bending analysis, using Kirchhoff\'s theory, in wich the boundary equation for displacements and its derivative in tangential and normal directions to the boundary for each boundary node are used. The efforts, according to Kirchhoff\'s theory, are the normal bending mn and the equivalent shear force Vn. This formulation is adequate for the analysis of plates coupled with flexible colunms and beams because these structural elements have three nodal displacement values at its nodes. Many examples of single plates and buildings slab are presented using the formulation proposed in this work.

Large silencers used in the power generation industry usually have a very large cross section at the inlet and outlet. Higher-order modes will populate the inlet and outlet even at very low frequencies. Although the silencer itself is often modeled by a three-dimensional analysis tool such as the boundary element method (BEM) or finite element method (FEM), a direct computation of the transmission loss (TL) from the BEM or FEM model can be challenging without incorporating certain forms of modal expansion. A so-called “impedance-to-scattering matrix method” is proposed to extract the modes at the inlet and outlet from the BEM impedance matrix based on the point collocation method. The BEM impedance matrix relates the sound pressures at the inlet and outlet to the corresponding particle velocities, while the scattering matrix relates the modes at the inlet and outlet. Normally there are more boundary elements than the total number of modes at the inlet and outlet, and a least-squares procedure is used to condense the element-based impedance matrix to the mode-based scattering matrix. The TL computation will follow if a certain form of the incident wave is assumed and the outlet is non-reflective. Several commonly used inlet/outlet configurations are considered in this dissertation, which include axisymmetric, non-axisymmetric circular, and rectangular inlet/outlet shapes. In addition to the single inlet and outlet silencers, large multi-inlet and multi-outlet silencers are also investigated. Besides the collocation-based impedance-to-scattering matrix method, an integral-based impedance-to-scattering matrix method based on the reciprocal identity is also proposed for large silencer analysis. Although it may be more time-consuming to perform the additional numerical integration, an integral-based method is free of any uncertainties associated with collocation points. The computational efficiency, accuracy and stability are compared between two proposed methods. One bonus effect of producing the scattering matrix is that it can also be used to combine subsystems in series connection. The Redheffer’s star product is introduced to combine scattering matrices of subsystems. In the design stage, rapid assessment of the silencer performance is always preferred. However, the existing analytical approaches are only suitable for simple dissipative silencers such as straight lined ducts. A two-dimensional first-mode semi-analytical solution is developed to quickly evaluate the performance of tuned dissipative silencers below the cut-off frequency. The semi-analytical solution can also serve as a validation tool for the BEM.

This thesis presents the development of a reliable and efficient technique for the numerical simulation of dynamic soil-structure interaction problems in anisotropic and nonhomogeneous unbounded soils of arbitrary geometry. Such a technique is indispensable in the seismic analysis of large-scale engineering constructions and, to my best knowledge, does not exist at present. The theoretical framework of the research is based on the scaled boundary finite-element method. The following advances are achieved: The scaled boundary finite-element method is extended to simulate the dynamic response of non-homogeneous unbounded domains. The scaled boundary finite element equations in the frequency and time domains are derived for power-type non-homogeneity frequently employed in geotechnical engineering. A high-frequency asymptotic expansion of the dynamic-stiffness matrix is developed. The frequency domain analysis is performed by integrating the scaled boundary finite-element equation in dynamic stiffness. In the time domain, the scaled boundary finite-element equation including convolution integrals is solved for the unit-impulse response at discrete time stations. A Pad?? series solution for the scaled boundary finite-element equation in dynamic stiffness is developed. It converges over the whole frequency range as the order of the approximation increases. The computationally expensive task of numerically integrating the scaled boundary finite-element equation is circumvented. Exploiting the sparsity of the coefficientmatrices in the scaled boundary finite-element equation leads to a significant reduction in computer time and memory requirements for solving large-scale problems. Furthermore, lumped coefficient matrices are obtained by adopting the auss-Lobatto-Legendre shape functions with nodal quadrature, which avoids the eigenvalue problem in determining the asymptotic expansion. A high-order local transmitting boundary constructed from a continued-fraction solution of the dynamic-stiffness matrix is developed. An equation of motion as occurring in standard structural dynamics with symmetric and frequency-independent coefficient matrices is obtained. This transmitting boundary condition can be coupled seamlessly with standard finite elements. Transient responses are evaluated by using a standard timeintegration scheme. The expensive task of evaluating convolution integrals is circumvented. The advances developed in this thesis are applicable in other disciplines of engineering and science to the analysis of scalar and vector waves in unbounded media.

No description available.

In this dissertation, we introduce and analyse a scheme for the fast evaluation of integrals stemming from boundary element methods including discretisations of the classical single and double layer potential operators. Our method is based on the parametrisation of boundary elements in terms of a d-dimensional parameter tuple. We interpret the integral as a real-valued function f depending on d parameters and show that f is smooth in a d-dimensional box. A standard interpolation of f by polynomials leads to a d-dimensional tensor which is given by the values of f at the interpolation points. This tensor may be approximated in a low rank tensor format like the canonical format or the hierarchical format. The tensor approximation has to be done only once and allows us to evaluate interpolants in O(dr(m+1)) operations in the canonical format, or O(dk³ + dk(m + 1)) operations in the hierarchical format, where m denotes the interpolation order and the ranks r, k are small integers. In particular, we apply an efficient black box scheme in the hierarchical tensor format in order to adaptively approximate tensors even in high dimensions d with a prescribed (but heuristic) target accuracy. By means of detailed numerical experiments, we demonstrate that highly accurate integral values can be obtained at very moderate costs.