A variational framework for spectral discretization of the density matrix in Kohn Sham density functional theory

Kohn-Sham density functional theory (KSDFT) is currently the main work-horse of quantum mechanical calculations in physics, chemistry, and materials science. From a mechanical engineering perspective, we are interested in studying the role of defects in the mechanical properties in materials. In real materials, defects are typically found at very small concentrations e.g., vacancies occur at parts per million, dislocation density in metals ranges from $10^{10} m^{-2}$ to $10^{15} m^{-2}$, and grain sizes vary from nanometers to micrometers in polycrystalline materials, etc. In order to model materials at realistic defect concentrations using DFT, we would need to work with system sizes beyond millions of atoms. Due to the cubic-scaling computational cost with respect to the number of atoms in conventional DFT implementations, such system sizes are unreachable. Since the early 1990s, there has been a huge interest in developing DFT implementations that have linear-scaling computational cost. A promising approach to achieving linear-scaling cost is to approximate the density matrix in KSDFT. The focus of this thesis is to provide a firm mathematical framework to study the convergence of these approximations. We reformulate the Kohn-Sham density functional theory as a nested variational problem in the density matrix, the electrostatic potential, and a field dual to the electron density. The corresponding functional is linear in the density matrix and thus amenable to spectral representation. Based on this reformulation, we introduce a new approximation scheme, called spectral binning, which does not require smoothing of the occupancy function and thus applies at arbitrarily low temperatures. We proof convergence of the approximate solutions with respect to spectral binning and with respect to an additional spatial discretization of the domain. For a standard one-dimensional benchmark problem, we present numerical experiments for which spectral binning exhibits excellent convergence characteristics and outperforms other linear-scaling methods.

Catalisadores à base de platina frente a correntes de H2 contendo acetaldeído geradas via reforma do etanol

Devido ao efeito estufa, a produção de hidrogênio a partir da reação de reforma do bioetanol tem se tornado um assunto de grande interesse em catálise heterogênea. Os catalisadores à base de Pt são empregados nos processos de purificação de H2 e também em eletrocatalisadores das células a combustível do tipo membrana polimérica (PEMFC). O hidrogênio obtido a partir da reforma do etanol contém como contaminante o acetaldeído e pequenas quantidades de CO. Assim, pode-se prever que muitas reações podem ocorrer na presença de catalisadores de Pt durante o processo de purificação do H2 e mesmo no próprio eletrocatalisador. Desta forma, este trabalho tem como objetivo descrever o comportamento do acetaldeído na presença de catalisadores de Pt. Para tanto foram preparados dois catalisadores, Pt/SiO2 e Pt/USY, contendo 1,5% de metal em ambos. Também foi estudado um eletrocatalisador (comercial) de Pt suportado em carvão (Pt/C). Os catalisadores foram caracterizados através das técnicas de análise textural, difração de raios X (DRX), quimissorção de H2, reação de desidrogenação do ciclohexano, espectroscopia no infravermelho de piridina adsorvida, dessorção a temperatura programada de n-butilamina (TPD de n-butilamina), dessorção a temperatura programada de CO2 (TPD-CO2), análise termogravimétrica, microscopia eletrônica de varredura (MEV) e espectroscopia de dispersão de energia (EDS). Os testes catalíticos foram realizados entre as temperaturas de 50 e 350 C em corrente contendo acetaldeído, H2 e N2. Foi observado que as propriedades ácido-básicas dos suportes promovem as reações de condensação com formação de éter etílico e acetato de etila. O acetaldeído em catalisadores de Pt sofre quebra das ligações C-C e C=O. A primeira ocorre em uma ampla faixa de temperaturas, enquanto a segunda apenas em temperaturas abaixo de 200 C. A quebra da ligação C-C produz metano e CO. Já a quebra da ligação C=O gera carbono residual nos catalisadores, assim como espécies oxigênio, que por sua vez são capazes de eliminar o CO da superfície dos catalisadores. Nota-se que o tipo de suporte utilizado influencia na distribuição de produtos, principalmente a baixas temperaturas. Além disso, constatou-se que a descarbonilação não é uma reação sensível à estrutura do catalisador. Verificou-se também a presença de resíduos sobre os catalisadores, possivelmente oriundos não somente da quebra da ligação C=O, mas também de reações de polimerização

Biological Activity of Rhodium Metalloinsertors and the Design of Bifunctional Conjugates

The Barton laboratory has established that octahedral rhodium complexes bearing the sterically expansive 5,6-chrysene diimine ligand can target thermodynamically destabilized sites, such as base pair mismatches, in DNA with high affinity and selectivity. These complexes approach DNA from the minor groove, ejecting the mismatched base pairs from the duplex in a binding mode termed metalloinsertion. In recent years, we have shown that these metalloinsertor complexes also exhibit cytotoxicity preferentially in cancer cells that are deficient in the mismatch repair (MMR) machinery.

Here, we establish that a sensitive structure-activity relationship exists for rhodium metalloinsertors. We studied the relationship between the chemical structures of metalloinsertors and their effect on biological activity for ten complexes with similar DNA binding affinities, but wide variation in their lipophilicity. Drastic differences were observed in the selectivities of the complexes for MMR-deficient cells. Compounds with hydrophilic ligands were highly selective, exhibiting preferential cytotoxicity in MMR-deficient cells at low concentrations and short incubation periods, whereas complexes with lipophilic ligands displayed poor cell-selectivity. It was discovered that all of the complexes localized to the nucleus in concentrations sufficient for mismatch binding; however, highly lipophilic complexes also exhibited high mitochondrial uptake. Significantly, these results support the notion that mitochondrial DNA is not the desired target for our metalloinsertor complexes; instead, selectivity stems from targeting mismatches in genomic DNA.

We have also explored the potential for metalloinsertors to be developed into more complex structures with multiple functionalities that could either enhance their overall potency or impart mismatch selectivity onto other therapeutic cargo. We have constructed a family of bifunctional metalloinsertor conjugates incorporating cis-platinum, each unique in its chemical structure, DNA binding interactions, and biological activity. The study of these complexes in MMR-deficient cells has established that the cell-selective biological activity of rhodium metalloinsertors proceeds through a critical cellular pathway leading to necrosis.

We further explored the underlying mechanisms surrounding the biological response to mismatch recognition by metalloinsertors in the genome. Immunofluorescence assays of MMR-deficient and MMR-proficient cells revealed that a critical biomarker for DNA damage, phosphorylation of histone H2AX (γH2AX) rapidly accumulates in response to metalloinsertor treatment, signifying the induction of double strand breaks in the genome. Significantly, we have discovered that our metalloinsertor complexes selectively inhibit transcription in MMR-deficient cells, which may be a crucial checkpoint in the eventual breakdown of the cell via necrosis. Additionally, preliminary in vivo studies have revealed the capability of these compounds to traverse the complex environments of multicellular organisms and accumulate in MMR-deficient tumors. Our ever-increasing understanding of metalloinsertors, as well as the development of new generations of complexes both monofunctional and bifunctional, enables their continued progress into the clinic as promising new chemotherapeutic agents.

A Continuum Model for Slip-Twinning Interactions in Magnesium and Magnesium Alloys

Due to their high specific strength and low density, magnesium and magnesium-based alloys have gained great technological importance in recent years. However, their underlying hexagonal crystal structure furnishes Mg and its alloys with a complex mechanical behavior because of their comparably smaller number of energetically favorable slip systems. Besides the commonly studied slip mechanism, another way to accomplish general deformation is through the additional mechanism of deformation-induced twinning. The main aim of this thesis research is to develop an efficient continuum model to understand and ultimately predict the material response resulting from the interaction between these two mechanisms.

The constitutive model we present is based on variational constitutive updates of plastic slips and twin volume fractions and accounts for the related lattice reorientation mechanisms. The model is applied to single- and polycrystalline pure magnesium. We outline the finite-deformation plasticity model combining basal, pyramidal, and prismatic dislocation activity as well as a convexification based approach for deformation twinning. A comparison with experimental data from single-crystal tension-compression experiments validates the model and serves for parameter identification. The extension to polycrystals via both Taylor-type modeling and finite element simulations shows a characteristic stress-strain response that agrees well with experimental observations for polycrystalline magnesium. The presented continuum model does not aim to represent the full details of individual twin-dislocation interactions, yet it is sufficiently efficient to allow for finite element simulations while qualitatively capturing the underlying microstructural deformation mechanisms.

I. Anisotropy and crystal structure of ferromagnetic thin films. II. Investigations into magnetic microstructure by Lorentz microscopy

The induced magnetic uniaxial anisotropy of Ni-Fe alloy films has been shown to be related to the crystal structure of the film. By use of electron diffraction, the crystal structure or vacuum-deposited films was determined over the composition range 5% to 85% Ni, with substrate temperature during deposition at various temperatures in the range 25° to 500° C. The phase diagram determined in this way has boundaries which are in fair agreement with the equilibrium boundaries for bulk material above 400°C. The (α+ ɤ) mixture phase disappears below 100°C.

The measurement of uniaxial anisotropy field for 25% Ni-Fe alloy films deposited at temperatures in the range -80°C to 375°C has been carried out. Comparison of the crystal structure phase diagram with the present data and those published by Wilts indicates that the anisotropy is strongly sensitive to crystal structure. Others have proposed pair ordering as an important source of anisotropy because of an apparent peak in the anisotropy energy at about 50% Ni composition. The present work shows no such peak, and leads to the conclusion that pair ordering cannot be a dominant contributor.

Width of the 180° domain wall in 76% Ni-Fe alloy films as a function of film thickness up to 1800 Å was measured using the defocused mode of Lorentz microscopy. For the thinner films, the measured wall widths are in good agreement with earlier data obtained by Fuchs. For films thicker than 800 Å, the wall width increases with film thickness to about 9000 Å at 1800 Å film thickness. Similar measurements for polycrystalline Co films with thickness from 200 to 1500 Å have been made. The wall width increases from 3000 Å at 400 Å film thickness to about 6000 Å at 1500 Å film thickness. The wall widths for Ni-Fe and Co films are much greater than predicted by present theories. The validity of the classical determination of wall width is discussed, and the comparison of the present data with theoretical results is given.

Finally, an experimental study of ripple by Lorentz microscopy in Ni-Fe alloy films has been carried out. The following should be noted: (1) the only practical way to determine experimentally a meaningful wavelength is to find a well-defined ripple periodicity by visual inspection of a photomicrograph. (2) The average wavelength is of the order of 1µ. This value is in reasonable agreement with the main wavelength predicted by the theories developed by others. The dependence of wavelength on substrate deposition temperature, alloy composition and the external magnetic field has been also studied and the results are compared with theoretical predictions. (3) The experimental fact that the ripple structure could not be observed in completely epitaxial films gives confirmation that the ripple results from the randomness of crystallite orientation. Furthermore, the experimental observation that the ripple disappeared in the range 71 and 75% Ni supports the theory that the ripple amplitude is directly dependent on the crystalline anisotropy. An attempt to experimentally determine the order of magnitude of the ripple angle was carried out. The measured angle was about 0.02 rad. The discrepancy between the experimental data and the theoretical prediction is serious. The accurate experimental determination of ripple angle is an unsolved problem.

Estimation of catalyst activity profiles and deactivation parameters from reactor operating data with applications to naphtha reforming

Techniques are developed for estimating activity profiles in fixed bed reactors and catalyst deactivation parameters from operating reactor data. These techniques are applicable, in general, to most industrial catalytic processes. The catalytic reforming of naphthas is taken as a broad example to illustrate the estimation schemes and to signify the physical meaning of the kinetic parameters of the estimation equations. The work is described in two parts. Part I deals with the modeling of kinetic rate expressions and the derivation of the working equations for estimation. Part II concentrates on developing various estimation techniques.

Part I: The reactions used to describe naphtha reforming are dehydrogenation and dehydroisomerization of cycloparaffins; isomerization, dehydrocyclization and hydrocracking of paraffins; and the catalyst deactivation reactions, namely coking on alumina sites and sintering of platinum crystallites. The rate expressions for the above reactions are formulated, and the effects of transport limitations on the overall reaction rates are discussed in the appendices. Moreover, various types of interaction between the metallic and acidic active centers of reforming catalysts are discussed as characterizing the different types of reforming reactions.

Part II: In catalytic reactor operation, the activity distribution along the reactor determines the kinetics of the main reaction and is needed for predicting the effect of changes in the feed state and the operating conditions on the reactor output. In the case of a monofunctional catalyst and of bifunctional catalysts in limiting conditions, the cumulative activity is sufficient for predicting steady reactor output. The estimation of this cumulative activity can be carried out easily from measurements at the reactor exit. For a general bifunctional catalytic system, the detailed activity distribution is needed for describing the reactor operation, and some approximation must be made to obtain practicable estimation schemes. This is accomplished by parametrization techniques using measurements at a few points along the reactor. Such parametrization techniques are illustrated numerically with a simplified model of naphtha reforming.

To determine long term catalyst utilization and regeneration policies, it is necessary to estimate catalyst deactivation parameters from the the current operating data. For a first order deactivation model with a monofunctional catalyst or with a bifunctional catalyst in special limiting circumstances, analytical techniques are presented to transform the partial differential equations to ordinary differential equations which admit more feasible estimation schemes. Numerical examples include the catalytic oxidation of butene to butadiene and a simplified model of naphtha reforming. For a general bifunctional system or in the case of a monofunctional catalyst subject to general power law deactivation, the estimation can only be accomplished approximately. The basic feature of an appropriate estimation scheme involves approximating the activity profile by certain polynomials and then estimating the deactivation parameters from the integrated form of the deactivation equation by regression techniques. Different bifunctional systems must be treated by different estimation algorithms, which are illustrated by several cases of naphtha reforming with different feed or catalyst composition.

Electronic properties of graphene grain boundaries

Grain boundaries and defect lines in graphene are intensively studied for their novel electronic and magnetic properties. However, there is not a complete comprehension of the appearance of localized states along these defects. Graphene grain boundaries are herein seen as the outcome of matching two semi-infinite graphene sheets with different edges. We classify the energy spectra of grain boundaries into three different types, directly related to the combination of the four basic classes of spectra of graphene edges. From the specific geometry of the grains, we are able to obtain the band structure and the number of localized states close to the Fermi energy. This provides a new understanding of states localized at grain boundaries, showing that they are derived from the edge states of graphene. Such knowledge is crucial for the ultimate tailoring of electronic and optoelectronic applications.

5.5W CWYb3+ : Y2O3 ceramic laser pumped with 970 nm laser diode

CW laser output has been demonstrated for polycrystalline transparent 10 at.% Yb3+-doped Y2O3 ceramics. End-pumped with 970 nm laser diode, a maximum output power of 5.5 W has been obtained with absorbed pump power of 31.1 W. The slope efficiency is 25% while the threshold pump power is 5.6 W. Saturation is not observed in our experiments, indicating higher laser output can be expected with higher pump power. (C) 2004 Elsevier B.V. All rights reserved.

Síntese e estudo das propriedades luminescentes do SrGa2O4 dopado com íons de Cr3+

Amostras policristalinas de Sr(Ga1-xCrx)2O4 com x = 0,01 foram estequiometricamente preparadas pela mistura dos materiais em pó SrCO3, Ga2O3 e Cr2O3. A estrutura cristalina da amostra dopada foi analisada pelas medidas de difração de raios-X. O padrão de difração revelou uma única fase relacionada a fase monoclínica do SrGa2O4. Os dados foram ajustados usando o Método de Rietveld para refinamento de estruturas e os parâmetros da rede foram determinados. A luminescência do íon de Cr3+ na rede do SrGa2O4 foi investigada pelas espectroscopias de excitação e emissão a temperatura ambiente, através das quais verificamos que os íons de Cr3+ estão localizados em dois sítios diferentes. Os espectros de emissão apresentam bandas largas associadas à transição eletrônica 4T2(4F) → 4A2(4F) para ambos os sítios. Estes resultados são analisados pela teoria de campo cristalino e o parâmetro de campo cristalino Dq e os parâmetros de Racah B e C são determinados pelas posições das bandas de excitação. A partir destes parâmetros determinamos um campo cristalino forte para ambos os sítios. Além disto, foram realizadas medidas de espectroscopia fotoacústica que confirmaram as transições identificadas e estimadas nos espectros de excitação.

脉冲激光晶化非晶硅薄膜的有限差分模拟

根据热传导原理，建立了脉冲激光晶化非晶硅薄膜的理论模型。运用有限差分方法研究了不同激光波长、能量密度等因素对薄膜温度变化及相变过程的影响。计算了不同波长激光器对厚度500nm非晶硅晶化的阈值能量密度。结果发现，准分子晶化的阈值能量密度最低，但是在同样的能量密度下，熔融深度却不及使用更长波长的激光器。计算并分析了升高衬底温度对结晶速度和晶粒尺寸的影响，模拟结果较好地验证了实验结论和规律。

Numerical and experimental analysis on green laser crystallization of amorphous silicon thin films

The effect of laser fluence on the crystallization of amorphous silicon irradiated by a frequency-doubled Nd:YAG laser is studied both theoretically and experimentally. An effective numerical model is set up to predict the melting threshold and the optimized laser fluence for the crystallization of 200-nm-thick amorphous silicon. The variation of the temperature distribution with time and the melt depth is analyzed. Besides the model, the Raman spectra of thin films treated with different fluences are measured to confirm the phase transition and to determine the optimized fluence. The calculating results accord well with those obtained from the experimental data in this research. (C) 2008 Elsevier Ltd. All rights reserved.

熔制条件对铋酸盐玻璃性质的影响

采用传统的玻璃熔融法制备了组成为60Bi2O3-20B2O3-15SiO2-5La2O3(mol%)的铋酸盐玻璃， 系统研究了不同工艺过程对玻璃性能的影响. 分析了样品ICP的成分，扫描电镜，X-射线衍射谱， 差热分析和紫外-可见-近红外透过光谱测试. 结果表明：使用刚玉坩埚能提高玻璃的抗析晶稳定性 和透过率，陶瓷坩埚和白金坩埚均受到严重腐蚀，玻璃组分也随之发生很大变化. 当熔制温度从1 100 ℃变化到1 300 ℃时，玻璃的颜色从浅黄色变到深红棕色. 尤其是白金粒子被腐蚀进入玻璃液 后，玻璃中很容易形成纳米颗粒或者团聚形成胶体粒子，在玻璃中形成色散源，加深玻璃的颜色， 降低透过率. 1 300 ℃下，白金粒子起到晶核剂的作用，生成Bi2Pt2O7和BiB3O6晶相，导致玻璃失透.

不同退火气氛下γ-LiAlO2形貌和结构研究

研究了温度梯度法生长的γ-LiAlO2晶体在1100℃下富Li气氛和空气中退火处理后的表面形貌、表面结构以及吸收光谱。发现γ-LiAlO2晶体的抛光面在1100℃空气中退火后变为粗糙面，X射线衍射(XRD)分析表明此粗糙面为单相的LiAl5O8。而γ-LiAlO2晶体的抛光面在1100℃富Li气氛中处理后几乎没有变化。同时对不同气氛下热处理的γ-LiAlO2晶体进行了光谱分析，确认了晶片中196nm的吸收峰是由Li空位引起的。

用VTE方法在蓝宝石衬底上生长γ-LiAlO2薄膜

利用气相传输平衡技术(VTE)和后退火处理工艺在(0001)蓝宝石衬底上获得了高度[100]取向的γ-LiAlO2薄膜．X射线衍射表明是由单相的γ-LiAlO2所组成,此薄膜经850～900℃／120h空气中退火处理后显示出高度的[100]取向,这一实验结果意味着有望通过VTE方法制备用于GaN基器件外延生长的γ-LiAlO2(100)-Al2O3(0001)复合衬底.

Cr^3＋：Al2O3透明多晶陶瓷光谱特性分析

对透光性良好的Cr^3＋：Al2O3透明多晶陶瓷的光谱性能进行了研究，其吸收光谱中吸收峰与单晶红宝石相一致，按吸收光谱和Tanabe-Sugano能级图，算出其晶场强度参数Dq及Racah参数B分别为1792cm^-1，689cm^-1，Dq／B=2．6，陶瓷中Cr^3＋离子所处格位的晶体场强比单晶弱一些，但Cr^3＋：Al2O3透明陶瓷仍属于强场晶体材料；当Cr^3＋掺杂浓度到达0．8wt％时，陶瓷的发射谱仍保持较好的R线发射；随Cr^3＋掺杂浓度的增大，激发峰位发生“红移”．在Cr^3＋：Al2O3透