Reconstruction of the Disassembly Pathway of an Icosahedral Viral Capsid and Shape Determination of Two Successive Intermediates

Viral capsids derived from an icosahedral plant virus widely used in physical and nanotechnological investigations were fully dissociated into dimers by a rapid change of pH. The process was probed in vitro at high spatiotemporal resolution by time-resolved small-angle X-ray scattering using a high brilliance synchrotron source. A powerful custom-made global fitting algorithm allowed us to reconstruct the most likely pathway parametrized by a set of stoichiometric coefficients and to determine the shape of two successive intermediates by ab initio calculations. None of these two unexpected intermediates was previously identified in self-assembly experiments, which suggests that the disassembly pathway is not a mirror image of the assembly pathway. These findings shed new light on the mechanisms and the reversibility of the assembly/disassembly of natural and synthetic virus-based systems. They also demonstrate that both the structure and dynamics of an increasing number of intermediate species become accessible to experiments.

Folding of Protein L with Implications for Collapse in the Denatured State Ensemble

A fundamental question in protein folding is whether the coil to globule collapse transition occurs during the initial stages of folding (burst phase) or simultaneously with the protein folding transition. Single molecule fluorescence resonance energy transfer (FRET) and small-angle X-ray scattering (SAXS) experiments disagree on whether Protein L collapse transition occurs during the burst phase of folding. We study Protein L folding using a coarse-grained model and molecular dynamics simulations. The collapse transition in Protein L is found to be concomitant with the folding transition. In the burst phase of folding, we find that FRET experiments overestimate radius of gyration, R-g, of the protein due to the application of Gaussian polymer chain end-to-end distribution to extract R-g from the FRET efficiency. FRET experiments estimate approximate to 6 angstrom decrease in R-g when the actual decrease is approximate to 3 angstrom on guanidinium chloride denaturant dilution from 7.5 to 1 M, thereby suggesting pronounced compaction in the protein dimensions in the burst phase. The approximate to 3 angstrom decrease is close to the statistical uncertainties of the R-g data measured from SAXS experiments, which suggest no compaction, leading to a disagreement with the FRET experiments. The transition-state ensemble (TSE) structures in Protein L folding are globular and extensive in agreement with the Psi-analysis experiments. The results support the hypothesis that the TSE of single domain proteins depends on protein topology and is not stabilized by local interactions alone.

Biochemical and Biophysical Characterization of Huntingtin

Huntington’s disease (HD) is a fatal autosomal dominant neurodegenerative disease. HD has no cure, and patients pass away 10-20 years after the onset of symptoms. The causal mutation for HD is a trinucleotide repeat expansion in exon 1 of the huntingtin gene that leads to a polyglutamine (polyQ) repeat expansion in the N-terminal region of the huntingtin protein. Interestingly, there is a threshold of 37 polyQ repeats under which little or no disease exists; and above which, patients invariably show symptoms of HD. The huntingtin protein is a 350 kDa protein with unclear function. As the polyQ stretch expands, its propensity to aggregate increases with polyQ length. Models for polyQ toxicity include formation of aggregates that recruit and sequester essential cellular proteins, or altered function producing improper interactions between mutant huntingtin and other proteins. In both models, soluble expanded polyQ may be an intermediate state that can be targeted by potential therapeutics.

In the first study described herein, the conformation of soluble, expanded polyQ was determined to be linear and extended using equilibrium gel filtration and small-angle X-ray scattering. While attempts to purify and crystallize domains of the huntingtin protein were unsuccessful, the aggregation of huntingtin exon 1 was investigated using other biochemical techniques including dynamic light scattering, turbidity analysis, Congo red staining, and thioflavin T fluorescence. Chapter 4 describes crystallization experiments sent to the International Space Station and determination of the X-ray crystal structure of the anti-polyQ Fab MW1. In the final study, multimeric fibronectin type III (FN3) domain proteins were engineered to bind with high avidity to expanded polyQ tracts in mutant huntingtin exon 1. Surface plasmon resonance was used to observe binding of monomeric and multimeric FN3 proteins with huntingtin.

Caracterização de filmes formados por dispersões aquosas de poli(uretano-uréia)s para aplicação em membranas para permeação de gases

Entre os polímeros considerados promissores para a remoção seletiva de CO2, destacam-se aqueles que contêm os grupos glicol etilênico (EG). Nesta dissertação, foram obtidos filmes a partir de dispersões aquosas de poliuretano (PU), sintetizadas em trabalho anterior, à base de poli(glicol propilênico) (PPG), copolímero em bloco à base de poli(glicol etilênico) (PEG) e PPG (EG-b-PG), ácido dimetilolpropiônico (DMPA), diisocianato de isoforona (IPDI) e etilenodiamina (EDA). PPG, EG-b-PG e DMPA formaram as regiões flexíveis nas proporções de: PPG 100% e 0% EG-b-PG, PPG 75% e 25% EG-b-PG, PPG 50% e 50% EG-b-PG e PPG 25% e 75% EG-b-PG em termos de equivalentes-gramas. A influência da quantidade dos segmentos de PEG foi avaliada por ensaios de permeação com os gases CO2, CH4 e N2. Os filmes obtidos das dispersões foram caracterizados por espectrometria de infravermelho com transformadas de Fourier (FTIR), análise termogravimétrica (TGA), difração de raios x (DRX) e espalhamento de raios X a baixo ângulo (SAXS). Espectros de FTIR mostraram que os segmentos de EG influenciaram a frequência da banda de carbonila. Curvas de perda de massa (TG) mostraram perfis semelhantes de degradação, enquanto que as curvas derivadas apresentaram diferenças. DRX e SAXS mostraram que os segmentos de PEG promoveram uma maior ordenação na estrutura da membrana. Testes de permeação de gases mostraram que o aumento do teor de PEG aumentou o valor da permeabilidade para o CO2, indicando que os segmentos de PEG interagiram favoravelmente com este gás. Em relação ao CH4 e N2, houve uma diminuição na permeabilidade quando comparados com os valores encontrados para o CO2, sendo atribuído a perda de mobilidade segmental. Em termos de seletividade, para o par CO2/CH4 foi obtido um valor médio de 61,7 para a membrana contendo o maior teor de PEG, e o par CO2/N2 um valor médio de 121,5, sendo superior aos valores encontrados na literatura, tornando o material promissor

New (1R,4R)-2-arylidene-p-menthan-3-ones with a bridging ester group in the arylidene fragment. Synthesis and behavior in liquid-crystalline systems

(1R,4R)-2-(4-Hydroxybenzylidene)- and (1R,4R)-2-(4′-hydroxybiphenyl- 4-yl)methylene-p-menthan-3-ones were synthesized by condensation of (-)-menthone with O-tetrahydropyran-2-yl derivatives of 4-hydroxybenzaldehyde and 4′-hydroxy-4-formylbiphenyl, respectively, in a DMSO - base medium followed by the removal of the protective group. The reactions of these hydroxy derivatives with 4-alkylbenzoic, 4-alkyloxybenzoic, trans-4-alkylcyclohexane-4- carboxylic, and 4′-alkylbiphenyl-4-carboxylic acids afforded three series of new chiral esters. Compounds containing the arylidene moiety with three benzene rings were found to exhibit liquid-crystalline properties. The characteristic features of these compounds are discussed based on the results of studies by polarizing microscopy, differential scanning calorimetry, and small-angle X-ray scattering. It was found that the mesomorphic compounds under study can form a smectic A mesophase, twist grain boundary mesophases (TGBA), and blue phases in a wide temperature range. Upon dissolution of certain of chiral compounds in 4′-cyano-4-pentylbiphenyl, a rather high twisting power and the thermal stabilizing effect on mesophases were observed.

Non-destructive characterization of structural hierarchy within aligned carbon nanotube assemblies

Understanding and controlling the hierarchical self-assembly of carbon nanotubes (CNTs) is vital for designing materials such as transparent conductors, chemical sensors, high-performance composites, and microelectronic interconnects. In particular, many applications require high-density CNT assemblies that cannot currently be made directly by low-density CNT growth, and therefore require post-processing by methods such as elastocapillary densification. We characterize the hierarchical structure of pristine and densified vertically aligned multi-wall CNT forests, by combining small-angle and ultra-small-angle x-ray scattering (USAXS) techniques. This enables the nondestructive measurement of both the individual CNT diameter and CNT bundle diameter within CNT forests, which are otherwise quantified only by delicate and often destructive microscopy techniques. Our measurements show that multi-wall CNT forests grown by chemical vapor deposition consist of isolated and bundled CNTs, with an average bundle diameter of 16 nm. After capillary densification of the CNT forest, USAXS reveals bundles with a diameter 4 m, in addition to the small bundles observed in the as-grown forests. Combining these characterization methods with new CNT processing methods could enable the engineering of macro-scale CNT assemblies that exhibit significantly improved bulk properties. © 2011 American Institute of Physics.

A novel method of extraction of blend component structure from SANS measurements of homopolymer bimodal blends

A new method is presented for the extraction of single-chain form factors and interchain interference functions from a range of small-angle neutron scattering (SANS) experiments on bimodal homopolymer blends. The method requires a minimum of three blends, made up of hydrogenated and deuterated components with matched degree of polymerization at two different chain lengths, but with carefully varying deuteration levels. The method is validated through an experimental study on polystyrene homopolymer bimodal blends with M A≈1/2MB. By fitting Debye functions to the structure factors, it is shown that there is good agreement between the molar mass of the components obtained from SANS and from chromatography. The extraction method also enables, for the first time, interchain scattering functions to be produced for scattering between chains of different lengths. © 2014 The Authors. Published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Photoluminescence and Raman scattering of silicon nanocrystals prepared by silicon ion implantion into SiO2 films

Photoluminescence (PL) and Raman spectra of silicon nanocrystals prepared by Si ion implantion into SiO2 layers on Si substrate have been measured at room temperature. Their dependence on annealing temperature was investigated in detail. The PL peaks observed in the as-implanted sample originate from the defects in SiO2 layers caused by ion implantation. They actually disappear after thermal annealing at 800 degrees C. The PL peak from silicon nanocrystals was observed when thermal annealing temperatures are higher than 900 degrees C. The PL peak is redshifted to 1.7 eV and the intensity reaches maximum at the thermal annealing temperature of 1100 degrees C. The characterized Raman scattering peak of silicon nanocrystals was observed by using a right angle scattering configuration. The Raman signal related to the silicon nanocrystals appears only in the samples annealed at temperature above 900 degrees C. It further proves the formation of silicon nanocrystals in these samples. (C) 2000 American Institute of Physics. [S0021-8979(00)00215-2].

Microstructures of microcrystalline silicon thin films prepared by hot wire chemical vapor deposition

Undoped hydrogenated microcrystalline silicon (mu c-Si:H) thin films were prepared at low temperature by hot wire chemical vapor deposition (HWCVD). Microstructures of the mu c-Si:H films with different H-2/SiH4 ratios and deposition pressures have been characterized by infrared spectroscopy X-ray diffraction (XRD), Raman scattering, Fourier transform (FTIR), cross-sectional transmission electron microscopy (TEM) and small angle X-ray scattering (SAX). The crystallization of silicon thin film was enhanced by hydrogen dilution and deposition pressure. The TEM result shows the columnar growth of mu c-Si:H thin films. An initial microcrystalline Si layer on the glass substrate, instead of the amorphous layer commonly observed in plasma enhanced chemical vapor deposition (PECVD), was observed from TEM and backside incident Raman spectra. The SAXS data indicate an enhancement of the mass density of mu c-Si:H films by hydrogen dilution. Finally, combining the FTIR data with the SAXS experiment suggests that the Si--H bonds in mu c-Si:H and in polycrystalline Si thin films are located at the grain boundaries. (C) 2000 Elsevier Science S.A. All rights reserved.

Raman scattering in hexagonal GaN epitaxial layer grown on MgAl2O4 substrate

The room temperature Raman spectra of the hexagonal GaN epilayer grown on [111]- oriented MgAl2O4 substrate were measured in various backscattering and right angle scattering geometries. All of the symmetry-allowed optical phonon modes were observed except the E-2 (low frequency) mode. The quasitransverse and quasilongitudinal modes were also observed in the x(zx)z and x(yy)z configurations, which are the mixed modes of pure transverse and longitudinal modes with A(1) and E-1 symmetry, respectively. (C) 1999 American Institute of Physics. [S0021-8979(99)01416-4].

Analysis of the interfaces of [NiFe/Mo](30) and [Fe/Mo](30) multilayers

The interface states of [NiFe/Mo](30) and [Fe/Mo](30) multilayers have been investigated by x-ray small angle reflection and diffuse scattering. Significant interface roughness correlation was observed in both ultrathin [NiFe/Mo](30) and [Fe/Mo](30) multilayers. An uncorrelated roughness of about 27-3.1 Angstrom was revealed in the [NiPe/Mo](30) multilayers, which is explained as originating from a transition layer between the NiFe and the Mo layers. By the technique of diffuse scattering, it is clearly indicated that the interfacial roughness of NiFe/Mo is much smaller than that of Fe/Mo although the lattice mismatch is the same in both multilayers.

高分子溶液中物理凝胶化的Monte Carlo模拟和小角中子散射研究

高分子凝胶广泛地存在于自然界以及日常生活中，按其形成作用力不同分为化学凝胶和物理凝胶两大类。由于高分子物理凝胶具有凝胶化的可逆性及其对环境条件强烈的响应性，因此，在近半个世纪的研究与应用中受到极大的关注。高分子溶液中的物理凝胶因其结构及形成机制复杂，在实验方面，除了散射技术及流变技术能够有效地揭示它的部分信息外，其它的实验手段很难用于这个领域的研究；在理论方面，化学凝胶的理论已经比较成熟，而物理凝胶的粘弹性质以及凝胶化是一个远离平衡态的松弛过程，除了一些特征的标度指数外，人们还没有得到适用于高分子物理凝胶的普适规律。当前，由于计算机模拟理论及模拟方法的发展，使得计算机模拟成为除了实验和理论研究方法之外的第三个重要的研究方法。但是，由于物理凝胶化行为的复杂性，用实验和理论获得的信息很难较好地描述凝胶化过程，而计算机模拟的高度透明性及反映信息的完整性，有助于理解这一复杂过程中所涉及的物理本质。因此，利用计算机模拟结合实验及理论方法深入研究高分子物理凝胶的形成机制、结构与性能关系已成为目前最有效的手段之一。 本论文主要运用Monte Carlo模拟方法，并结合小角中子散射（Small-Angle Neutron Scattering, SANS）和流变（Rheology）等实验手段从多个角度探讨了以下几类典型的高分子溶液物理凝胶化行为。 1. 温度对遥爪型三嵌段共聚物在选择性溶剂中的自组装及凝胶化行为影响的研究：采用二维简单方格子Monte Carlo模拟方法，结合逾渗（Percolation）理论，建立了溶胶－凝胶转变相图在统计热力学中的确定方法；甄别了具有特征构象的链，讨论了链及胶束的聚集，明晰了相互作用（体现为约化温度）、构象转变、聚集与凝胶化的一致的关联关系；提出了构象转变模型，进而明确了此体系的凝胶化过程，在微观尺度上表现为桥型链和环型链之间的竞争。 2. 模拟模型改进及其应用到持续长度对稀溶液中高分子链构象影响的研究：考虑到原始八位置键涨落模型效率低，实现复杂且不能应用到复杂的高分子体系，对该模型进行了改进，使其实现简单、效率高，并拓宽了该模型的应用范围。然后，以刚性对均聚物构象的影响为例，发现随着刚性增加，均聚物构象从球形椭球到棒状椭球的转变，并对比了自由连接链（Free Joint Chain, FJC）模型和蠕虫链（Wormlike Chain, WLC）模型在不同刚性范围内对高分子链末端距预测的偏差，首次给出了这两个经典模型的半定量的适用边界。 3. 溶剂尺寸对遥爪型三嵌段共聚物在选择性溶剂中的自组装及凝胶化行为影响的研究：用改进后的八位置键涨落Monte Carlo模型，研究了遥爪型三嵌段共聚物在选择性溶剂条件下的聚集和凝胶化对溶剂尺寸的依赖性，发现溶剂尺寸效应对凝胶化的作用是非单调的。由一个均聚物体系的对比模拟证明这种作用主要是由熵驱动的，并给出了中分子溶剂的半定量定义。在均聚物和嵌段共聚物溶液中，不同尺寸的溶剂分子可以使溶液由于高分子聚集不同而具有不同的微结构，并影响高分子链构象和溶液的性质。从多个角度研究了三嵌段共聚物在不同尺寸溶剂的溶液中所遵循的三种不同的凝胶化机理。 4. 聚氧化乙烯－氧化丙稀－氧化乙烯三嵌段共聚物（poly(ethylene oxide)-poly (propylene oxide)-poly-(ethylene oxide), PEO-PPO-PEO）重水溶液凝胶化的小角中子散射（SANS）和Monte Carlo研究：结合Pluronic F127（EO65PO99EO65）/D2O三嵌段共聚物溶液的特征，对照SANS数据，用改进后的八位置键涨落模型成功地从模拟中获得了F127/D2O的溶胶－凝胶转变相图。详细地考察了体系的微观结构，提出此类高分子溶液中形成的物理凝胶包含高分子逾渗网络的生成，以及被束缚溶剂（Bound Solvent）必须超过离散组分体系逾渗的临界体积分数的机理。着重研究了一定浓度的F127水溶液随温度升高引起的溶胶－凝胶转变以及凝胶－溶胶转变的Reentrant相行为，发现体系在低温区域的溶胶－凝胶转变遵循相同的机理，而在中等温度和较高温度以及不同浓度区域中的凝胶－溶胶转变遵循不同的机理。 5. 极性基团饱和度和溶剂条件对两亲性聚合物在溶液中的聚集行为和凝胶化影响的研究：用改进后的八位置键涨落模型，针对两亲性聚合物在不同溶剂条件的溶液建立了粗粒化模型，以两亲性聚合物中极性基团的饱和度，溶剂条件和高分子浓度为变量，考察了其对链构象、聚集及其凝胶化的影响。 6. 多糖水溶液凝胶化的流变和小角中子散射研究：用流变和SANS考察了两个多糖水溶液中物理凝胶化过程，针对由氢键主导的水基凝胶体系的典型特征进行了讨论，从分子链构象，聚集体结构及其关联以及流变特征等方面对聚强电解质角叉胶（Carrageenan）水溶液和聚弱电解质明胶（Pectin）水溶液进行了详细的讨论。考察了不同多糖的种类（聚合物链的电荷密度），盐的种类和浓度，溶液温度等对凝胶化和凝胶结构的影响，分析了不同多糖溶液的凝胶化机理。

Time-resolved synchrotron SAXS observations on sheared syndiotactic poly(propylene) crystallization process

The in situ crystallization kinetics of syndiotactic poly(propylene) (sPP) has been investigated by synchrotron small-angle X-ray scattering (SAXS). The structure evolutions during the isothermal crystallization of sPP with different shear rates have been observed. The results show that shear accelerates the process of crystallization kinetics. Even under low shear rate, the lamellae can be distinctly oriented. In contrast, the lamellar parameters such as the long period, lamellar thickness, and the scattering invariant 0 can change obviously only under high shear rate.