Electrostatics interaction plays a very important role in almost all biomolecular systems. The Poisson-Boltzmann equation is widely used to treat this electrostatic effect in an ionic solution. In this work, a simple mixed discrete-continuum model is considered and boundary element method is used to solve for the solution. / Singapore-MIT Alliance (SMA)

Made available in DSpace on 2014-06-11T19:22:55Z (GMT). No. of bitstreams: 0 Previous issue date: 2013-03-22Bitstream added on 2014-06-13T19:49:17Z : No. of bitstreams: 1 bossa_gv_me_sjrp.pdf: 1762827 bytes, checksum: e5ab0758cdec4ff5faee4c416a7cc194 (MD5) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / Proteínas e peptídeos são constituídos por subunidades estruturalmente mais imples chamadas aminoácidos. Uma importante propriedade destes é que, dependendo das características do meio (tais como pH e concentração iônica), os seus grupos onizáveis podem ceder prótons e, assim, adquirir carga elétrica não nula. Tal carga nfluenciará na eficiência da formação de ligações peptídicas e em interações proteína- igante, por exemplo. Partindo da hipótese de que a diferença entre os valores de pK dos rupos ionizáveis isolados e destes como partes constituintes de um aminoácido é devida, principalmente, à interação eletrostática adicional que se atribui à presença de rupos vizinhos, elaborou-se um modelo que emprega a forma linearizada da equação de Poisson-Boltzmann para o estudo de propriedades físico-químicas de moléculas com rês grupos ionizáveis. Neste trabalho tal modelo foi aplicado aos aminoácidos: Aspartato, Glutamato, Cisteína, Tirosina, Arginina, Lisina e Histidina. Calcularam-se os valores de pK e as respectivas cargas elétricas médias de tais moléculas. Como os esultados obtidos concordaram com aqueles oriundos de trabalhos experimentais, o modelo teórico foi expandido para tratar de di, tetra, pentapeptídeos e de resíduos de isina e glutamato da proteína Staphylococcal Nuclease. Os valores do Fator de Correlação de Pearson calculados para ambos proteínas e peptídeos são superiores a 0,99, fato este que evidencia a eficiência e versatilidade do modelo ao reproduzir alores de pK reportados por outros autores / Proteins and peptides are composed of subunits structurally simpler called amino acids. An important property of these is that, depending on the medium characteristics (such pH and ionic concentration), its ionizable groups may provide protons and thereby acquire a nonzero electric charge. Such charge will affect the formation of peptide bond and protein-ligand interactions, for example. Assuming that the difference between pK values of the isolates ionizable groups and of these as constituents parts of an amino acid is mainly due to the extra electrostatic interaction attributed to the presence of neighboring groups, was developed a structure-based model that employs the linearized form of the Poisson-Boltzmann equation for the study of physicochemical properties of molecules with three ionizable groups. In this work it was applied to the amino acids: aspartate, glutamate, cysteine, tyrosine, arginine, lysine and histidine. The pK values and respective mean electric charges were calculated. As the calculated values agreed with those from experimental studies, the theoretical model has been expanded to the treatment of di, tetra, pentapeptides and Staphylococcal Nuclease residues. The Pearson Correlation Factor calculated for both proteins and peptides are above 0.99, what points to the effectiveness and versatility of the model to reproduce pK values reported by other works

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Made available in DSpace on 2014-10-09T12:26:09Z (GMT). No. of bitstreams: 0 / Made available in DSpace on 2014-10-09T14:10:41Z (GMT). No. of bitstreams: 1 01296.pdf: 4114768 bytes, checksum: d4e6cb642ae70a16017316565fe26cab (MD5) / Thesis (Doctor) / IPEN/T / North Caroline State University - NCSU

The present thesis deals with the mathematical treatment of kinetic theory and focuses more precisely on the Boltzmann equation. We investigate several properties of the solutions to the latter equation: their positivity and their hydrodynamical limits for instance. We also study the local Cauchy problem for a quantic version of the Boltzmann equation.

In the study of kinetic theory and especially in the study of rarefied gas dynamics one often turns to the Boltzmann equation. The mathematical theory developed by Ludwig Boltzmann was at first sight applicable in aerospace engineering and fluid mechanics. As of today, the methods in kinetic theory are extended to other fields, for instance, molecular biology and socioeconomics, which makes the need of finding efficient solution methods still important. In this thesis, we study the underlying theory of the continuous and discrete Boltzmann equation for monatomic gases. We extend the theory where needed, such that, we cover the case of colliding molecules that possess different levels of internal energy. Mainly, we discuss discrete velocity models and present explicit calculations for a model of a gas consisting of polyatomic molecules modelled with two levels of internal energy. / I studiet av kinetisk teori och speciellt i studiet av dynamik för tunna gaser vänder man sig ofta till Boltzmannekvationen. Den matematiska teorien utvecklad av Ludwig Boltzmann var vid första anblicken tillämpbar i flyg- och rymdteknik och strömningsmekanik. Idag generaliseras metoder i kinetisk teori till andra områden, till exempel inom molekylärbiologi och socioekonomi, vilket gör att vi har ett fortsatt behov av att finna effektiva lösningsmetoder. Vi studerar i denna uppsats den underliggande teorin av den kontinuerliga och diskreta Boltzmannekvationen för monatomiska gaser. Vi utvidgar teorin där det behövs för att täcka fallet då kolliderande molekyler innehar olika nivåer av intern energi. Vi diskuterar huvudsakligen diskreta hastighetsmodeller och presenterar explicita beräkningar för en modell av en gas bestående av polyatomiska molekyler modellerad med två lägen av intern energi.

京都大学 / 0048 / 新制・課程博士 / 博士(人間・環境学) / 甲第20455号 / 人博第805号 / 新制||人||194(附属図書館) / 28||人博||805(吉田南総合図書館) / 京都大学大学院人間・環境学研究科共生人間学専攻 / (主査)教授 清水 扇丈, 教授 足立 匡義, 准教授 木坂 正史, 教授 森本 芳則 / 学位規則第4条第1項該当 / Doctor of Human and Environmental Studies / Kyoto University / DFAM

The use of moment-closure methods to predict continuum and moderately rarefied flow offers many modelling and numerical advantages over traditional methods. The maximum-entropy family of moment closures offers models described by hyperbolic systems of balance laws. In particular, the twenty-one moment model of the maximum-entropy hierarchy offers a hyperbolic treatment of viscous flows exhibiting heat transfer. This twenty-one moment model has the ability to provide accurate solutions where the Navier-Stokes equations lose physical validity due to the solution being too far from local equilibrium. Furthermore, its first-order hyperbolic nature offers the potential for improved numerical accuracy as well as a decreased sensitivity to mesh quality. Unfortunately, higher-order maximum-entropy closures cannot be expressed in closed form. The only known affordable option is to propose approximations. Previous approximations to the fourteen-moment maximum-entropy model have been proposed [McDonald and Torrilhon, 2014]. Although this fourteen-moment model also predicts viscous flow with heat transfer, the necessary moments to close the system renders it more difficult to approximate accurately than the twenty-one moment model. The proposed approximation for the fourteen-moment model also has realizable states for which hyperbolicity is lost. Unfortunately, the velocity distribution function associated with the twenty-one moment model is an exponential of a fourth-order polynomial. Such a function cannot be integrated in closed form, resulting in closing fluxes that can only be obtained through complex numerical methods. The goal of this work is to present a new approximation to the closing fluxes that respect the maximum-entropy philosophy as closely as possible. Preliminary results show that a proposed approximation is able to provide shock predictions that are in good agreement with the Boltzmann equation and surpassing the prediction of the Navier-Stokes equations. Furthermore, Couette flow results as well as lid-driven cavity flows are computed using a novel approach to Knudsen layer boundary conditions. A dispersion analysis as well as an investigation of the hyperbolicity of the model is also shown. The Couette flow results are compared against Navier-Stokes and the free-molecular analytical solutions for a varying Knudsen number, for which the twenty-one moment model show good agreement over the domain. The shock-tube problem is also computed for different Knudsen numbers. The results are compared with the one obtained by directly solving the BGK equation. Finally, the lid-driven cavity flow computed with the twenty-one moment model shows good agreement with the direct simulation Monte-Carlo (DSMC) solution.