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Nous menons une étude en simulations atomiques des propriétés des dislocations vis <a> dans le zirconium et le titane pur, et de l'effet durcissant de l'oxygène dans ces deux métaux de transition de structure hexagonale compacte. Nous utilisons deux modèles énergétiques : les calculs ab initio, basés sur la théorie de la fonctionnelle de la densité, et les calculs en potentiel empirique.Ce travail permet d'abord d'établir le profil énergétique complet de la dislocation vis dans le Zr pur au cours de ses différents modes de glissement. Nos calculs révèlent l'existence d'une configuration métastable de la dislocation vis partiellement étalée dans le plan pyramidal de première espèce. Cette configuration est responsable du glissement dévié de la dislocation vis du plan prismatique, plan principal de glissement, vers le plan pyramidal ou le plan basal. Ce profil énergétique est modifié par l'ajout d'atomes d'oxygène en impureté. L'oxygène favorise le glissement dévié dans le plan pyramidal ce qui entraine un durcissement du glissement prismatique, et il piège la dislocation dans la configuration métastable sessile.La même démarche de modélisation est ensuite appliquée au titane. Dans le Ti pur, les mêmes configurations de la dislocation vis dans le Zr sont obtenues, mais avec des niveaux énergétiques différents. Ceci conduit à un mécanisme de glissement différent. Tout comme dans le Zr, l'oxygène favorise le glissement pyramidal dans le Ti en affectant la structure de cœur de la dislocation. De plus, la présence de l'oxygène fait baisser l'énergie de la configuration métastable mais pas suffisamment pour la piéger. / We performed atomistic simulations to determine screw dislocations properties in pure zirconium and titanium and to explain the hardening effect attributed to oxygen alloying in both hexagonal close-packed transition metals. We used two energetic models: ab initio calculations based on the density functional theory and calculations with an empirical potential.The complete energetic profile of the screw dislocation when gliding in the different slip planes is obtained in pure Zr. Our calculations reveal the existence of a metastable configuration of the screw dislocation partially spread in the first order pyramidal plane. This configuration is responsible for the cross slip of screw dislocations from prismatic planes, the easiest glide planes, to pyramidal or basal planes. This energy profile is affected by oxygen addition. Ab initio calculations reveal two main effects: oxygen enhances pyramidal cross slip by modifying the dislocation core structure, and pins the dislocation in its metastable sessile configuration.The same modeling approach is applied to titanium. In pure Ti, the same configurations of the screw dislocation in Zr are obtained, but with different energy levels. This leads to a different gliding mechanism. The same way as in Zr, oxygen enhances pyramidal glide in Ti by modifying the dislocation core structure. Besides, oxygen atom lowers the energy of the metastable configuration but not enough to pin the dislocation in this sessile configuration.

Orientador: Iris Concepcion Lineares de Torriani / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Fisica "Gleb Wataghin" / Made available in DSpace on 2018-08-04T15:02:02Z (GMT). No. of bitstreams: 1 Oliveira_CristianoLuisPintode_D.pdf: 31759545 bytes, checksum: a92d80aac97e4e41bdf268c343cbd43e (MD5) Previous issue date: 2005 / Resumo: Apresentamos nesta tese estudos relacionados à obtenção de parâmetros estruturais e modelagem ab initio para macromoléculas biológicas e sistemas densos de partículas elipsoidais a partir de dados de espalhamento de raios X a baixos ângulos. Aspectos teóricos e experimentais são discutidos, complementados por simulações computacionais e pela apresentação de resultados experimentais que exemplificam a aplicação dos métodos de cálculo revelando assim os alcances e limites da técnica. Progressos recentes em biologia molecular estrutural revelam que a correlação entre a forma e a função de macromoléculas biológicas é crucial para a compreensão dos processos biológicos. Além disso, diversos estudos associam várias doenças a defeitos estruturais em proteínas, aumentando ainda mais o interesse na determinação das estruturas protéicas. A técnica de espalhamento de raios X a baixos ângulos permite a obtenção de parâmetros estruturais de proteínas, apresentando diversas vantagens sobre a cristalografia de proteínas e a ressonância magnética nuclear, mesmo não atingindo alta resolução. Trataremos, portanto, dois assuntos principais: estudos de sistemas diluídos e estudos de sistemas densos. Para o estudo de sistemas diluídos o enfoque principal será na modelagem estrutural de proteínas em solução, onde são apresentados e discutidos diversos métodos de simulação tanto da estrutura das macromoléculas quanto de seus parâmetros hidrodinâmicos. Estes métodos foram aplicados ao estudo de diversos problemas, tais como: (i) as estruturas das hemoglobinas extracelulares de Biomphalaria glabrata e Glossoscolex paulistus, proteínas gigantes com elevada cooperatividade funcional entre suas subunidades; (ii) as diferenças estruturais entre as formas livres e ligadas a lipídeos da proteína básica de mielina, uma das proteínas principais do axônio nervoso e cujo mal funcionamento leva a doenças neuronais; (iii) a interação entre proteínas e polímeros, tema relevante para processos de cristalização e construção de sistemas bio-poliméricos; e (iv) a estrutura da proteína precursora amilóide, proteína transmembrana que, apesar de diversas funções conhecidas, é uma das precursoras principais do Mal de Alzheimer. Já no estudo de sistemas densos é apresentada uma nova metodologia baseada em simulações de Monte Carlo para elipsóides de revolução. Como elipsóides podem servir de sistemas modelos para diversos sistemas reais, simulações de propriedades de soluções concentradas destes sistemas são de grande interesse. Com base nestas simulações, funções de espalhamento e funções de correlação puderam ser calculadas para um grande intervalo de anisotropias e concentrações, permitindo a obtenção de funções numéricas que podem ser utilizadas no estudo de sistemas reais uma vez que não existem expressões analíticas para este tipo de sistema. Como aplicação, este método foi utilizado no estudo de nanopartículas de ferro em matriz de silício, fornecendo parâmetros estruturais do sistema. / Abstract: In this dissertation, theoretical and experimental aspects of the calculation of structural parameters and ab-initio modeling for biological macromolecules and condensed particle systems are being discussed. Two main applications will be presented, complemented by computational simulations and many experimental results. For dilute systems the focus will be on the structural modeling of several proteins in solutions, including the calculation of hydrodynamic parameters. Recent developments in structural molecular biology reveal that knowledge about the correlation existing between the structure and function of biological macromolecules is crucial for the understanding of biological processes. Many studies have proved that structural defects detected in certain proteins are responsible for serious diseases. Small angle X-ray scattering has proved to be very useful in the determination of the low resolution structure of macromolecules in solution. This technique offers clear advantages with respect to other techniques, like singlecrystal X-ray crystallography and nuclear magnetic resonance. The low resolution structural studies of proteins included: (i) the 3D solution structure of the extracellular hemoglobin from the species Biomphalaria glabrata and Glossoscolex paulistus, giant proteins with high functional cooperativity between their subunits; (ii) the determination of the structural differences between the lipid free and lipid bound forms of myelin basic protein (MBP), one of the most important proteins of the axon sheath whose bad functioning leads to neural diseases; (iii) the study of protein-polymer interactions, relevant subject for crystallization processes and development of bio-polymeric systems; (iv) the 3D solution structure of the amyloid precursor protein, APP, transmembrane protein which is related to the Alzheimer disease. For the study of dense systems, a Monte Carlo based method for the simulation of a system of hard ellipsoids of revolution was developed. Ellipsoidal particles can be used as model systems for many real problems and simulations of the properties of concentrated solutions are of great interest. As a result of these simulations, scattering functions and correlation functions could be derived for a wide interval of anisotropies, permitting the calculation of numerical functions that can be used in real systems. As an example, this method was used for the study of iron nanoparticles in a silica matrix, leading to the determination of mean radius and size distribution of the particles. / Doutorado / Física da Matéria Condensada / Doutor em Ciências

Heterogeneous electrocatalysis is the usage of solid materials to decrease the amount of energy needed to produce chemicals using electricity. It is of core importance for modern life, as it enables production of chemicals, such as chlorine gas and sodium chlorate, needed for e.g. materials and pharmaceuticals production. Furthermore, as the need to make a transition to usage of renewable energy sources is growing, the importance for electrocatalysis used for electrolytic production of clean fuels, such as hydrogen, is rising. In this thesis, work aimed at understanding and improving electrocatalysts used for these purposes is presented. A main part of the work has been focused on the selectivity between chlorine gas, or sodium chlorate formation, and parasitic oxygen evolution. An activation of anode surface Ti cations by nearby Ru cations is suggested as a reason for the high chlorine selectivity of the “dimensionally stable anode” (DSA), the standard anode used in industrial chlorine and sodium chlorate production. Furthermore, theoretical methods have been used to screen for dopants that can be used to improve the activity and selectivity of DSA, and several promising candidates have been found. Moreover, the connection between the rate of chlorate formation and the rate of parasitic oxygen evolution, as well as the possible catalytic effects of electrolyte contaminants on parasitic oxygen evolution in the chlorate process, have been studied experimentally. Additionally, the properties of a Co-doped DSA have been studied, and it is found that the doping makes the electrode more active for hydrogen evolution. Finally, the hydrogen evolution reaction on both RuO2 and the noble-metal-free electrocatalyst material MoS2 has been studied using a combination of experimental and theoretically calculated X-ray photoelectron chemical shifts. In this way, insight into structural changes accompanying hydrogen evolution on these materials is obtained. / Heterogen elektrokatalys innebär användningen av fasta material för att minska energimängden som krävs för produktion av kemikalier med hjälp av elektricitet. Heterogen elektrokatalys har en central roll i det moderna samhället, eftersom det möjliggör produktionen av kemikalier såsom klorgas och natriumklorat, som i sin tur används för produktion av t ex konstruktionsmaterial och läkemedel. Vikten av användning av elektrokatalys för produktion av förnybara bränslen, såsom vätgas, växer dessutom i takt med att en övergång till användning av förnybar energi blir allt nödvändigare. I denna avhandling presenteras arbete som utförts för att förstå och förbättra sådana elektrokatalysatorer. En stor del av arbetet har varit fokuserat på selektiviteten mellan klorgas och biprodukten syrgas i klor-alkali och kloratprocesserna. Inom ramen för detta arbete har teoretisk modellering av det dominerande anodmaterialet i dessa industriella processer, den så kallade “dimensionsstabila anoden” (DSA), använts för att föreslå en fundamental anledning till att detta material är speciellt klorselektivt. Vi föreslår att klorselektiviteten kan förklaras av en laddningsöverföring från ruteniumkatjoner i materialet till titankatjonerna i anodytan, vilket aktiverar titankatjonerna. Baserat på en bred studie av ett stort antal andra dopämnen föreslår vi dessutom vilka dopämnen som är bäst lämpade för produktion av aktiva och klorselektiva anoder. Med hjälp av experimentella studier föreslår vi dessutom en koppling mellan kloratbildning och oönskad syrgasbildning i kloratprocessen, och vidare har en bred studie av tänkbara elektrolytföroreningar utförts för att öka förståelsen för syrgasbildningen i denna process. Två studier relaterade till elektrokemisk vätgasproduktion har också gjorts. En experimentell studie av Co-dopad DSA har utförts, och detta elektrodmaterial visade sig vara mer aktivt för vätgasutveckling än en standard-DSA. Vidare har en kombination av experimentell och teoretisk röntgenfotoelektronspektroskopi använts för att öka förståelsen för strukturella förändringar som sker i RuO2 och i det ädelmetallfria elektrodmaterialet MoS2 under vätgasutveckling. / <p>QC 20151119</p>

This work describes the three dimensional structure of protein molecules and biological databases used to store information about this structure or its hierarchical classification. Current methods of computational structure prediction are overviewed with an emphasis on comparative modeling. This particular method is also implemented in a proof-of-concept program and finally, the implementation is analysed.

No description available.

In the first part of the thesis, the molecular structure and electronic properties of phospholipids at the single molecule level and also for a monolayer structure are investigated via ab initio calculations under different degrees of hydration. The focus of the study is on phosphatidylcholines, in particular dipalmitoylphosphatidylcholine (DPPC), which are the most abundant phospholipids in biological membranes. Upon hydration, the phospholipid shape into a sickle-like structure. The hydration dramatically alters the surface potential, dipole and quadrupole moments of the lipids, and probably guides the interactions of the lipids with other molecules and the communication between cells. The vibrational spectrum of DPPC and DPPC-water complexes are completely assigned and it is shown that water hydrating the lipid head groups enables efficient energy transfer across membrane leaflets on sub-picosecond time scales. Moreover, the vibrational modes and lifetimes of pure and hydrated DPPC lipids, at human body temperature, are estimated by performing ab initio molecular dynamics simulations. The vibrational modes of the water molecules close to the head group of DPPC are active in the frequency range between 0.5 - 55 THz, with a peak at 2.80 THz in the energy spectrum. The computed lifetimes for the high-frequency modes agree well with recent data measured at room temperature, where high-order phonon scattering is not negligible. The structure and auto-ionization of water at the water-phospholipid interface are investigated by ab initio molecular dynamics and ab initio Monte Carlo simulations using local density approximation and generalized gradient approximation for the exchange-correlation energy functional. Depending on the lipid head group, strongly enhanced ionization is observed, leading to dissociation of several water molecules into H+ and OH- per lipid. The results can shed light on the phenomena of the high proton conductivity along membranes that has been reported experimentally. In the second part of the thesis, Monte Carlo simulations of the lipid bilayer, on the basis of a coarse grained model, are performed to gain insight into the mechanical properties of planar lipid bilayers. By using a rescaling method, the Poisson's ratio is calculated for different phases. Additional information on the bending rigidity, determined from height fluctuations on the basis of the Helfrich Hamiltonian, allows for calculation of the Young's modulus for each phase. In addition, the free energy barrier for lipid flip-flop process in the fluid and gel phases are estimated. The main rate-limiting step to complete a flip-flop process is related to a free energy barrier that has to be crossed in order to reach the center of the bilayer. The free energy cost for performing a lipid flip-flop in the gel phase is found to be five times greater than in the fluid phase, demonstrating the rarity of such events in the gel phase. Moreover, an energy barrier is estimated for formation of transient water pores that often precedes lipid translocation events and accounts for the rate-limiting step of these pore-associated lipid translocation processes.