Die Charakterisierung hochdimensionaler Systeme mit Lyapunov-Instabilität wird durch das Lyapunov-Spektrum und die zugehörigen Lyapunov-Vektoren ermöglicht. Für eine Vielzahl von derartigen Systemen (Coupled-Map-Lattices, Hartkugel-Systeme, Systeme mit ausgedehnten Potentialen ...) konnte durch die Untersuchung der Lyapunov-Vektoren die Existenz von hydrodynamischen Lyapunov-Moden nachgewiesen werden. Diese kollektiven Anregungen zeigen sich in Lyapunov-Vektoren, deren Lyapunov-Exponenten dem Betrage nach am kleinsten sind. Da Lyapunov-Exponenten charakteristische Zeitskalen innerhalb der Systeme repräsentieren, ist durch die Lyapunov-Moden eine Untersuchung des Langzeitverhaltens möglich. In dieser Arbeit werden die hydrodynamischen Lyapunov-Moden durch Molekulardynamiksimulationen von mehrkomponentigen Lennard-Jones-Flüssigkeiten untersucht. Die Charakterisierung der Lyapunov-Moden zeigt im weiteren eine Ähnlichkeit zu Dispersionsrelationen von Phononen.

En nous concentrant sur les valeurs du module de cisaillement l’équilibre Geq pour le modèle bien connu des polymères vitrifiables (echantillionné par le biais de la MD), nous avons adressé la question générale de en quoi les propriétées méchaniques des couches mince diffères de la phase volumique. Il a été démontrè que dans les deux cas Geq de manière non ambigus sèpare l’état fluide (Geq = 0) de l’état vitreux (Geq > 0). Nous avons aussi insisté sur le fait que Geq pour la couche mince dépend de lépaisseur du film h mais aussi de de la pression tangentielle qui est un résultante de la procédure de préparation de la couche mince / Focusing on the equilibrium shear modulus Geq of well-known glass-forming polymer model system (sampled by means of MD), we have addressed the general question of how the mechanical properties of the thin polymer films differs from the bulk. Using ”stress fluctuation” formalism we obtained Geq(T) for the bulk and films. It has been demonstrated that in both cases Geq unambiguously separates the fluid state (Geq = 0) from the glass (Geq > 0). We also stressed that Geq for the film does not only depend on film thickness h, but also on tangential pressure that is a consequence of the film preparation procedure.

Made available in DSpace on 2016-06-02T20:34:43Z (GMT). No. of bitstreams: 1 5238.pdf: 5294587 bytes, checksum: 025b13ac00d18b1830afac47325d6ffe (MD5) Previous issue date: 2013-04-29 / Financiadora de Estudos e Projetos / In this study, our goal was evaluate the interactive forces between the Atomic force microscope tip (AFM tip) and an important enzyme responsible to fatty acids synthesis in all living beings (Acetyl CoA Carboxylase - fic biosensors to detect pesticides molecules used in agriculture. The AFM tip can be functionalized through its oxidation with spacer molecules. In order to simulate computationally this modified AFM tip that was called surface spacer-agent (SSA) using molecular dynamic (MD) simulations, the force field (FF) parameters had to be calculated. The FF parameters were obtained using quantum mechanical calculations and were implemented in an appropriate FF protocol. Three types of geometric molecular orientations of the ACCase were evaluated as a starting point to enzymatic immobilization, but only one was used to MD simulation. The criteria to define xyz orientation were basically based on the active sites from the ACCase enzyme are available to interact with molecules from the bulk and the surface contact area of the enzyme interacting with SSA ensure an strong interaction force to maintain the enzyme immobilized on the tip. Surface contact area, hydrogen bonds and protein stability were the parameters monitored during the MD trajectory as the enzymeherbicide interactions using a combination of molecular docking and molecular dynamics. The clusters formed using docking calculations in different regions along the ACCase enzyme were submitted to MD simulations in order to measure interactive energies of the system. / Neste estudo, o objetivo foi quantificar e analisar as forças de interação entre a ponta do microscópio de força atômica (AFM) modificada quimicamente com moléculas ligantes e uma importante enzima responsável pela síntese de ácidos graxos em todos os seres vivos, a Acetil CoA carboxilase - ACCase. Nosso objetivo é desenvolver biossensores específicos para a detecção de pesticidas usados na agricultura. A fim de simular computacionalmente esta superfície modificada, utilizando a metodologia de dinâmica molecular (MD), os parâmetros campo de força foram desenvolvidos e implementados no modelo computacional aqui proposto. Estes parâmetros foram obtidos utilizando cálculos de mecânica quântica e implementados no campo de força do programa de MD utilizado. Três tipos de orientações moleculares da ACCase foram avaliadas como ponto de partida para os cálculos de MD, porém, apenas uma posição foi utilizada para a simulação. Os critérios para definir a orientação espacial da enzima na superfície tiveram com base a localização dos sítios ativos da enzima e a área de contato da enzima com a superfície funcionalizada. Este último parâmetro foi levado conta com a intenção de assegurar uma força de interação forte o suficiente para manter a enzima imobilizada na ponta sem que haja o despreendimento da mesma devido a fracas interações. Superfície de contacto, ligações de hidrogênio e estabilidade estrutural da proteína foram os parâmetros avaliados e monitorados. As regiões da enzima expostas para interação com as moléculas do bulk foram avaliadas utilizando uma combinação de docking molecular e dinâmica molecular. Os clusters formados dos cálculos de docking em diferentes regiões da enzima ACCase foram submetidos a simulação por MD para o cálculo das energias envolvidas no sistema.

Submitted by Vinicius de Godoi Contessoto null (vinicius@sjrp.unesp.br) on 2016-09-09T18:11:23Z No. of bitstreams: 1 Tese-Vinícius_Contessoto-Final.pdf: 17297320 bytes, checksum: f601c338b5bf6436dc595bad581418f5 (MD5) / Approved for entry into archive by Juliano Benedito Ferreira (julianoferreira@reitoria.unesp.br) on 2016-09-13T13:26:05Z (GMT) No. of bitstreams: 1 contessoto_vg_dr_sjrp.pdf: 17297320 bytes, checksum: f601c338b5bf6436dc595bad581418f5 (MD5) / Made available in DSpace on 2016-09-13T13:26:05Z (GMT). No. of bitstreams: 1 contessoto_vg_dr_sjrp.pdf: 17297320 bytes, checksum: f601c338b5bf6436dc595bad581418f5 (MD5) Previous issue date: 2016-08-16 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Entender a contribuição das interações eletrostáticas no processo de enovelamento e na estabilidade do estado nativo de proteínas é de grande relevância em biofísica molecular. Este trabalho possui duas frentes de estudos. Na primeira etapa é apresentado o estudo das interações eletrostáticas no processo de enovelamento utilizando modelos baseados em estruturas com cargas em dinâmica molecular com pH constante. O estudo foi realizado na parte N-terminal da proteína ribossomal L9 (NTL9), uma proteína com o mecanismo de enovelamento de 2 estados, reversível e realizado desde pH 1.0 até 12.0. Foi possível comparar os resultados das simulações com os resultados experimentais presentes na literatura e os dados obtidos indicam que o modelo proposto é capaz de capturar informações fundamentais sobre o processo de enovelamento referentes à estabilidade e dependência com pH. Na segunda etapa é apresentado o estudo sobre as interações eletrostáticas na estabilidade de enzimas com interesse na produção de bioetanol de segunda geração. O objetivo final deste trabalho é adequar as enzimas às condições do reator para a produção de bioetanol. Neste trabalho foi utilizada uma metodologia capaz de indicar possíveis mutações, pela otimização da interação carga–carga na superfície da proteína, que levam ao aumento de termostabilidade. Este trabalho conta com a colaboração do grupo experimental do Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE) que realizam os testes experimentais e as validações das mutações propostas. / The understanding of electrostatic interactions in protein folding process and in native state stability is important to molecular biophysics area. This work has two areas of interest. At first step it is presented the study about electrostatic interactions in the protein folding process using structure-based models in a constant pH molecular dynamics. It was used the N-terminal domain of ribosomal protein L9 (NTL9), which folding mechanism is a two-state pathway, fully reversible and foldable in a pH range from 1.0 to 12.0. The simulation results were compared with experimental results from literature and the obtained data indicates that the proposed model is capable of capturing essential features of folding mechanism about stability and pH dependence. At second step, it is presented the study about electrostatic interactions in stability of enzymes related with second generation bioethanol production. The final goal of this work is to adjust the enzymes to reactor conditions of bioethanol production. It was employed a method that can suggest rational mutation, based on optimization of charge-charge interactions, that leads to thermostability increase. This work can count on the collaboration of an experimental group of Brazilian Bioethanol Science and Technology Laboratory (CTBE) that performs the wet lab tests and validates the suggested mutations.

As ligações de hidrogênio (LH), fundamentais na determinação da estrutura da água, proteínas, etc., são muito importantes no reconhecimento molecular e nos mecanismos de reações enzimáticas. A determinação da energia das LHs intramoleculares em proteínas e intermoleculares entre uma proteína e o solvente água, porque fornece informações sobre a estrutura secundária, terciária e quaternária das proteínas. Um método para quantificar e qualificar as LHs foi desenvolvido utilizando critérios de distância, geométricos e energéticos a partir das trajetórias obtidas por simulações de dinâmica molecular. O método foi testado com o monômero de uma fosfolipase A2 homodimérica, sem atividade catalítica, isolada do veneno da Bothrops asper(BaspMT-II). No dímero, a análise das LHs mostrou que elas são também essenciais na manutenção da estrutura quaternária. Essa análise permitiu identificar movimentos do tipo dobradiça acompanhados da formação transitória, na interface dimérica, de LHs controladas pelo triptofano na posição 77. Esses movimentos podem estar associados à ação danosa às membranas, uma vez que podem promover a inserção da região C-terminal na membrana. Estudos prévios mostraram que o peptídeo sintético (3Y codificado pelos aminoácidos 115-129 da BaspMT-II) apresenta atividade bactericida e citolítica. Um outro peptídeo (3W), mutante de 3Y, no qual três resíduos tirosina são substituidos por triptofano, apresenta um aumento do dano às membranas e do efeito miotóxico. Os mecanismos de ação desses peptídeos e as suas estruturas foram estudados por dinâmica molecular, dicroísmo circular (DC), microscopia de fluorescência e monocamadas de Langmuir (Mlang). As adsorções dos peptídeos em monocamadas de ácido dimiristoil fosfatídico (DMPA) e dimiristoilfosfatidilcolina (DMPC) se processam por mecanismos diferentes ocasionados pelas diferentes naturezas físico-químicas dos resíduos tirosina e triptofano. A microscopia de fluorescência acoplada a Mlang de DMPA com 3W adsorvido mostra um aumento da fluidez da monocamada, enquanto que o 3Y modifica os domínios do DMPA para pequenas estruturas circulares. Foram realizadas simulações dos peptídeos 3Y e 3W em meio aquoso e nas regiões interfaciais água/n-hexano e água/bicamadas de DMPC. Os resultados confirmam os obtidos por Mlang, demonstrando que os peptídeos interagem diferentemente com as membranas por adotar conformações alternativas definidas previamente. Essas conformações, diferentes das observadas em meio aquoso, dependem da natureza da interface. As estruturas encontradas no final das simulaçoes corroboram o mecanismo proposto por Mlang, assim como as estruturas sugeridas por DC. Isso sugere que a atividade biológica reduzida do peptídeo 3Y ocorre porque os seus dois resíduos Leu se adsorvem na interface sem penetrá-la. Ao contrário de 3W, os resíduos carregados do peptídeo 3Y não estão localizados corretamente para promover uma interação suficientemente atrativa para permitir a sua inserção na membrana celular. / Hydrogen bonds (HB) are highly important in the determination of the structure of the water and proteins. They also play a important role in molecular recognition and in enzyme reaction mechanisms. The determination of protein/water intermolecular and protein intramolecular HB energies provide information with respect to the formation and stabilization of secondary, tertiary and quaternary protein structure. A method that quantifies and qualifies the properties of HB was developed using distance, geometric and energy criteria as applied to data obtained from the atomic trajectories generated by molecular dynamics simulations. The method was tested with a monomer of a catalytically inactive homodimeric phospholipase A2 from Bothrops asper(BaspMT-II) venom. HBs at dimmer interface are essential for maintaining the quaternary structure, and are highly conserved during hinge-like movements of the dimmer. HB formed by tryptophan residue at position 77 controls this movement. These motions can be associated to the membrane damaging action since they facilitate the insertion of the C-terminus into the cellular membrane. Previous studies have shown that synthetic peptide (3Y, coding the amino acids 115-129 of BaspMT-II ) presents bactericidal and cytolitic activities. A peptide variant ( 3W ), in which tyrosine residues were substituted by tryptophan residues, presents an enhanced membrane damaging activity increased miotoxic effect. The mechanism of action of the peptides and their structures were studied by molecular dynamics simulations, circular dichroism (CD), fluorescence microscopy and Langmuir monolayers (Mlang). The adsorption of the peptides on a monolayer composed of dimiristoyl phosphatidic acid (DMPA) and dimiristoylphosphatidyl choline (DMPC) occurs through different processes due to the differences in the physic-chemical nature of the tyrosine and tryptophan residues. Fluorescence microscopy together with Mlang of DMPA with adsorbed 3W indicates an increase of the membrane fluidity while small circular domains are formed with DMPA. Simulations were conducted with the 3Y and 3W peptides in aqueous media, is a water/n-hexane and water/DMPC bilayers. The results confirm the Mlang results, showing that the peptides interact differently with the membranes by adopting alternative previously defined conformations. These two conformations, both of which are different to those observed in water, are dependent of the nature of the interfaces. The final simulated configurations confirm the mechanism proposed by Mlang and the structures proposed by CD. It is suggest that the reduced biological activity of the 3Y peptide is due to the two Leu residues that only adsorb to the cellular membrane without penetrating the bilayer. In contrast to the 3W peptide, no charged residue is correctly located to promote the interaction and insertion of the 3Y peptide into the membrane.

Comprendre l’origine microscopique du ralentissement de la dynamique au voisinage de la transition vitreuse reste l’un des problèmes fondamentaux de la physique de la matière condensée. Au cours de ce travail, nous introduisons un nouveau modèle de liquide, appelé liquide de Voronoï, et dont les interactions sont directement reliées aux propriétés géométriques des tessellations de Voronoï. Pour cette classe de liquides, les interactions sont à plusieurs corps et agissent de telle sorte que le système est toujours sous tension tout en restant stable. Le but de ce travail est d’étudier un mélange binaire du liquide de Voronoï et de voir de quelles façons ces interactions exotiques affectent le scénario habituel de la transition vitreuse. Tout au long de ce travail, nous caractérisons le liquide de Voronoï bidisperse théoriquement et par le biais des simulations numériques. Nous proposons également des comparaisons avec des liquides de Lennard-Jones surfondus bien décrit dans la littérature. / Understanding the origin of the important slowing down of the dynamics near glass transition is still one of the remaining fundamental problems of condensed matter physics. During this work we introduced a brand-new model of liquids named Voronoi liquid, whose interactions are directly related to the geometrical properties of Voronoi tessellations. For these class of liquids interactions are intrinsically manybody and act in such a way that the liquid is always under tension but remains stable. The aim of this work is to use a binary mixture of the Voronoi liquid to see to what extend these exotic interactions may affect the classical scenario of glass transition. Throughout this work we characterize theoretically and by mean of numerical simulation the bidisperse Voronoi liquid. Comparisons with well-known Lennard-Jones glass formers are systematically performed.

L’objectif de ce travail consiste à développer un nouveau potentiel SMTB-Q, puis à l’incorporer dans un code de dynamique moléculaire (DM) afin d’étudier les premiers stades de l’oxydation de l’aluminium. Le potentiel peut modéliser les différents polymorphes de l’alumine ainsi qu’une transition de la phase amorphe vers une phase cristalline. Notre approche couple un terme covalent avec la charge. Il utilise le schéma de Rappé et Goddard pour la partie électrostatique et le modèle du réseau alterné de C. Noguera pour la partie covalente. Le potentiel SMTB-Q obtenu est validé par une approche Monte Carlo. Nous y présentons les outils utilisés pour l’optimisation du potentiel ou analyser les résultats obtenus pour les situations hétérogènes. Cette étude permet de montrer que le potentiel SMTB-Q donne une description satisfaisante de la liaison Al-O dans différentes configurations atomiques. Cette liaison résulte de la compétition entre trois contributions énergétiques : électrostatique, covalente et répulsion de Pauli entre les oxygènes. Après son incorporation dans le logiciel LAMMPS, le potentiel SMTB-Q est utilisé en DM pour l'étude d'oxydes à stœchiométrie constante. Les transitions de phases de l’alumine sont étudiées sous haute pression et en température. Le problème du changement de stœchiométrie de l’oxyde est traité à partir de l'étude de diverses structures de différentes stœchiométries. Nous introduirons la liaison métallique dans le potentiel. La superposition des liaisons iono-covalentes et métalliques sera étudiée pour des systèmes métal/oxyde. Enfin, nous discuterons du formalisme du potentiel SMTB-Q face au changement de stœchiométrie dans l’oxyde. / The goal of this work is to develop a new SMTB-Q potential in order to study the early stages of the oxidation of aluminium by molecular dynamics (MD).Our potential is able to model different alumina polymorphs as well as transitions from the amorphous state to a crystalline phase. Our approach couples a covalent term with the charge. It uses Rapp_ and Goddard scheme for the electrostatic part and the model of alternating network developed by C. Noguera for the covalent part.The SMTB-Q potential was validated with a Monte Carlo approach. This study shows that the potential SMTB-Q gives satisfactory results for the Al-O bonding in different atomic configurations. The bonding results from the competition between three energy contributions: electrostatic, covalent and Pauli repulsion between the oxygens.After implementation in the LAMMPS software, the potential SMTB-Q is used to study by DM constant stoichiometry oxides. Alumina phase transitions are observed under high pressure and temperature. We also introduce the metallic bonding in the potential. The superposition of the iono-covalent and metallic bonds was investigated for metal / oxide systems. Finally, we discuss the formalism of the SMTB-Q potential to take into account the change of stoichiometry in the oxide.

La présente étude est une approche holistique axée sur l'étude des effets spécifiques d'ions sur les propriétés d'auto-assemblage de tensioactifs cationiques gemini. Notre objectif principal étant l’étude de l'effet de divers contre-ions sur les caractéristiques d’auto-assemblage de tensioactifs cationiques en solution aqueuse. Afin d'obtenir une vision plus complète de l'effet des interactions ioniques et moléculaires à l’interface sur les propriétés globales, nous avons utilisé des approches différentes. Nous avons combiné une étude expérimentale portant sur les propriétés en solution (concentration micellaire critique, degré d'ionisation, nombre d'agrégation, etc.), avec des approches centrées sur l'étude des propriétés micellaires interfaciales en analysant les concentrations des contre-ions et de l'eau de façon expérimentale (piégeage chimique) et informatique (simulations de dynamique moléculaire). En outre, nous avons étudié l'impact de la nature des contre-ions sur la croissance des micelles géantes par rhéologie. En plus de l'examen des propriétés de tensio-actifs en solution, les effets spécifiques d'ions sur les structures cristallines des agents tensioactifs gémini ont été étudiés.Nous avons trouvé que les effets d'ions spécifiques qui déterminent le comportement des agrégats micellaires de gemini cationiques d'ammonium quaternaire dans des solutions aqueuses dépendent fortement de l'énergie libre d'hydratation des contre-ions, en d'autres termes, sur leur propriétés hydrophile /hydrophobe. Contrairement à la solution aqueuse, dans les cristaux, la taille de l'ion devient le facteur déterminant. La comparaison des résultats obtenus pour un même système en solution aqueuse et à l'état solide a montré l'importance des interactions ion-eau dans les effets spécifiques d'ions. Cependant, il faut noter que les propriétés du substrat (les gemini dans notre cas) doivent être prises en compte non moins soigneusement afin de prédire complétement les effets Hofmeister. / The present study is a holistic approach focused on the investigation of ion specific effects on the self-assembly properties of cationic gemini surfactants. Our main focus was on the effect of various counterions on the self-organization features of cationic surfactants in aqueous solution. In order to obtain amore comprehensive understanding of the effect of interfacial ionic and molecular interactions on aggregate properties we used different approaches. We combined an experimental study focused on the bulk solution properties (critical micelle concentration, ionization degree, aggregation number, etc.), with approaches focused on investigating the interfacial micellar properties by analyzing the interfacial counterion and waterconcentrations, experimentally (chemical trapping) and computationally (molecular dynamic simulations). Moreover, the impact of counterion nature was investigated by studying the growth of wormlike micelles using rheology. Besides the examination of the surfactants properties in solution, the ion specific effects onthe crystalline structures of gemini surfactants were studied.We found that ion specific effects which determine the behavior of micellar aggregates of cationic quaternary ammonium gemini in aqueous solutions strongly depend on the free energy of hydration of the counterions, in others words, on their hydrophilic/hydrophobic properties. Contrarily to aqueous solution, in crystals, the size of the ion becomes the determining factor. Comparison of the results obtained for the same system in aqueous solution and in solid state showed the importance of ion-water interactions in ion specific effects. However, one should note that the properties of substrate (the gemini in our case) should be taken into account not less carefully in order to fully predict Hofmeister effects.

In this thesis, we start with the description of the biophysical properties of the plasma membrane models upon signaling processess such as the increased cytoso- lic concentration of calcium ions, or posttranslational modifications of membrane proteins. Calcium signaling is characterized by a rapid increase of its cytosolic concentration. We identify calcium binding sites and characterize the binding in the plasma membrane models of increasing complexity from pure phospholipid bilayers, through cholesterol and peptide rich lipid membranes, to membranes ex- tracted from HEK293 cells. We use Time-Dependent Fluorescent Shift method, which provides direct information on hydration and mobility in defined regions of a lipid bilayer, accompanied with molecular dynamic (MD) simulations, which give molecular details of the studied interactions. The initial step of signaling mediated by PAG protein is its double palmi- toylation. We investigate changes of the biophysical properties of both the lipid membrane and the peptide itself upon the incorporation of the palmitoyls. Em- ploying all atom MD simulations, we study inter- and intramolecular interactions as well as changes in membrane hydration, thickness, or lipid ordering. The second part of the thesis, realized in a direct collaboration with a phar- macological...

We employ the empirical potential function Airebo to computationally model free-standing Carbon-12 graphene in a classical setting. Our objective is to measure the mean square displacement (MSD) of atoms in the system for different average temperatures and Carbon-13 isotope concentrations. From results of the MSD we aim to develop a technique that employs Transmission Electron Microscopy (TEM), using high-angle annular dark filed (HAADF) detection, to obtain atomic-resolution images. From the thermally diffusive images, produced by the vibrations of atoms, we intent to resolve isotopes types in graphene. For this, we establish a relationship between the full width half maximum (FWHM) of real-space intensity images and MSD for temperature and isotope concentration changes. For the case of changes in the temperature of the system, simulation results show a linear relationship between the MSD as a function of increased temperature in the system, with a slope of 7.858×10-6 Å2/K. We also note a power dependency for the MSD in units of [Å2] with respect to the FWHM in units of [Å] given by FWHM(MSD)=0.20MSD0.53+0.67. For the case of increasing isotope concentration, no statistically significant changes to the MSD of 12C and 13C are noted for graphene systems with 2,000 atoms or more. We note that for the experimental replication of results, noticeable differences in the MSD for systems with approximately 320,000 atoms must be observable. For this, we conclude that isotopes in free-standing graphene cannot be distinguished using TEM.