光合放氧结构与机理的理论探索

光合放氧研究近十年来已有重要进展，但在该领域仍有很多重要问题待研究。本论文工作主要是对光系统氧化侧与光合放氧密切相关的组分的结构和性能进行理论和模拟研究，工作可概括如下： (一)、放氧中心结构和性能的探索。 1、对放氧中心Mn202单元与配体组氨酸、H2O和Cl等结合方式的理论研究显示：(a)、组氨酸和H20分子均可能与Mn202平面垂直，彼此保持较大的距离，且结合在不同的Mn离子上;(b)、2个H2O分子可能结合在不同Mn202单元上。 2、对Mn簇核心骨架的理论研究显示有必要引入新的Ca、Cl结合方式，以防止因两个Mn202单元线性化而导致2个H2O分子结合位点远离。 (二)、次级电子给体Tyr_z和Tyr_D的结构与功能。 对次级电子给体Tyr_z和Tyr_D进行精确量子化学研究显示：(a)、在中性条件下，Tyr_D和Tyr_z均只与组氨酸通过氢键作用;(b)、当失去电子后，结构发生明显变化，导致正电荷主要集中在组氨酸上，自由基主要集中在Tyr上;(c)、第三组分(H_20分子或羧基等)的引入使中性体系不容易给出电子;(d)、结合最新文献报导，推测Tyr_D~+和Tyr_z~+除与组氨酸作用外还可能分别与水和羧基作用。 (三)、原初电子给体的理论和模拟研究。 1、对紫细菌原初电子给体P_(870)的理论研究显示：(a)、双分子结构比单分子结构稳定;(b)、电荷分离之后，原初电子给体原有的空间结构不再是稳定的构型，它会向能量和化学活性均更低的构型转变。在光合细菌的原初电子给体P870中，这种转变可通过C3位的乙酰基旋转使其氧原子与另一个细菌叶绿素分子的镁原子相互作用使P870+•的总能量和化学活性明显降低。推测这种构型转变对于防止原初反应过程中的电荷重组、维持光能的高效转化有重要意义。提出了原初反应过程中结构动态变化的新观点，利用这一观点可对光合细菌原初反应动力学研究所观测到的慢过程及蛋白质微环境对原初电子给体和原初反应都有重要影响等实验现象给予较好的解释。 2、对光系统II原初电子给体P680的结构进行理论探讨，提出了两个叶绿素a分子平面间夹角为50.0±2.5°时能量最低的夹角模型。 3、采用N-甲基咪唑(C4H6N2)模拟生物体内的组氨酸，通过观测CCL4中的Chla与C4H6N2反应的吸收、CD和MCD光谱得到以下结论：(a)、在纯CCL4中，每个Chla处于5配位状态，Chla形成不对称的双聚体，彼此之间存在较强的偶合作用。提出两个Chla通过不等价的2个Mg-O配位键(O分别来自于C131位的酮基和C17位酯基的C=O)连接为紧密双体结构;(b)、当C4H6N2／Chla = 0.5和1时，其吸收、CD和MCD光谱均发生明显变化，两个Chla之间的偶合作用明显减弱，但此时仍为双聚体。推测C4H6N2首先取代原紧密双体结构中Mg-O酯键，进而取代Mg-O酮键，最后两个Chla分子通过两个Mg…O弱相互作用连接为松弛的双体结构，该模型与理论获得的P_(680)的结构相似。 在上述研究的基础上，提出了包括放氧中心外围配体和TyrZ在内的放氧中心结构新模型。在新结构模型中，2个H2O分子不对称地结合于“C”形结构开口端两个低价的Mn1II和Mn4III上，并保持较大距离;两个组氨酸的咪唑环通过N原子与两个高价的Mn2IV、Mn3IV结合;Cl结合于MB4TM，并与Ca相连;Ca通过O桥和COO-相连使两个Mn202单元保持特定空间构型。TyrZ通过组氨酸(D1-His190)与Mn簇作用。此外，新模型尝试着在O桥上引入质子。放氧中心结构及其邻近环境(包括TyrZ和TyrD)整体处于中性状态。 同时还提出了新的放氧机理，认为电子和质子的释放非同步进行，并首次明确提出两个水分子的不对称氧化和结构动态变化等观点。认为Ca在维持放氧中心的结构方面担负重要作用，C1与Mn离子之间的亲核作用变化是放氧中心结构变化的关键。

Twin-spot launch for enhancement of multimode-fiber communication links

A novel twin-spot launch is proposed for multimode-fiber (MMF) links. Experimental and theoretical investigation of the launch indicates a penalty reduction of ≈50% of the 10 Gigabit Ethernet allocation for EDC-enabled links over worst-case MMF. © 2007 Optical Society of America.

Evaluating the effect of dislocation on the photovoltaic performance of metamorphic tandem solar cells

The photovoltaic conversion efficiency for monolithic GaInP/GaInAs/Ge triple-junction cell with various bandgap combination (300 suns, AM1.5d) was theoretically calculated. An impressive improvement on conversion efficiency was observed for a bandgap combination of 1.708, 1.194, and 0.67 eV. A theoretical investigation was carried out on the effect of dislocation on the metamorphic structure's efficiency by regarding dislocation as minority-carrier recombination center. The results showed that only when dislocation density was less than 1.6x10(6) cm(-2), can this metamorphic combination exhibit its efficiency advantage over the fully-matched combination. In addition, we also briefly evaluated the lattice misfit dependence of the dislocation density for a group of metamorphic triple-junction system, and used it as guidance for the choice of the proper cell structure.

Chirped fiber Bragg gratings for optical fiber dispersion compensation

The use of alpha-power chirped fiber Bragg gratings for dispersion cancellation in an optical fiber link is discussed. Numerical and theoretical investigation of recompressing the dispersion-broadened pulse by using alpha-power chirped gratings is made, which shows that, the dispersion-broadened Gaussian pulse after 100 km standard fiber (with zero dispersion at lambda = 1.3 mu m) trnasmission at lambda = 1.55 mu m with initial width of T-FWHM = 33ps (full width at half maximum) can be perfectly recompressed with the peak reflectivity of 82% by using a 30 mm long alpha-power chirped fiber grating with proper a value and optimal grating parameters.

Influence of the lateral confining potential on the ballistic electron transport in a quantum wire

A theoretical investigation of ballistic electron transport in a quantum wire with soft wall confinement is presented. A general method of the electron transmission calculation is proposed for structures with complicated geometries. The effects of the lateral guiding potential on ballistic transport are investigated using three soft wall confinement models and the results are compared with those obtained from the hard wall confinement approximation. It is shown that the calculated transmission coefficients are notably dependent on the lateral confining potential especially when the incident electron energy is larger than the energy of the second transverse mode. It is found that the transmission profile obtained from soft wall confinement models exhibits simpler resonance structures than that obtained from the hard wall confinement approximation. Our results suggest that only in the single-channel regime the hard wall confinement approximation can give reasonable results.

Design of a Tapered Lens for Semiconductor Laser to Single-Mode Fiber Coupling

The theoretical investigation of the coupling efficiency of a laser diode to a single mode fiber via a hemispherical lens on the tip of the tapered fiber in the presence of possible transverse offset and angular mismatch is reported.Without the misalignment,coupling efficiency increases with the decreasing of taper length.With the misalignment,this relation is that the coupling efficiency decreases with each kind of offset.

Photoionization of 1s electron and corresponding shake-up process in ground and excited lithium atoms

The cross sections of the 18 electron photoionization and corresponding shake-up processes for Li atoms in the ground state 1s(2)2s and excited states 1s(2)2p, 1s(2)3p, 1s(2)3p and 1s(2)3d are calculated using the multi-configuration Dirac-Fock method. The latest experimental photoelectron spectrum at hv = 100 eV [Cubaynes D et al. Phys. Rev. Lett. 99 (2007) 213004] has been reproduced by the present theoretical investigation excellently. The relative intensity of the shake-up satellites shows that the effects of correlation and relaxation become more important for the higher excited states of the lithium atom, which are explained very well by the spatial overlap of the initial and final state wavefunctions. In addition, strong dependence of the cross section on the atomic orbitals of the valence electrons are found, especially near the threshold.

Chemistry of B1- and B10- boranes containing halogen or pseudohalogen groups

The research described in this thesis involved the chemistry of borane-species which contain one or more halide or pseudohalide groups. Both monoboron species e.g. [BH3X]- and "cluster" borane species e.g. [B10H9X]2- and I-Se B11H10 were studied. The first chapter is a review of the syntheses, properties and reactions of halide and pseudohalide species containing from one to ten boron atoms. Chapter Two is a theoretical investigation of' the electronic and molecular structures of two series of boranes i. e. [BH3X]- and [B10H9X]2- where X = H, CI, CN, NCS, SCN and N3. The calculational method used was the Modified Neglect of Differential Overlap (MNDO) method of Dewar et al. The results were compared where possible with experimental results such as the X-ray crystallographically determined structures of [BH3CI]- and [B10H10]2-. Chapter Three concerns halogenated selenaborane clusters and reports an improved synthesis of 12-Br-SeB11H10 and the first structural data for a simple non-metal containing selenaborane cage with the X-ray crystallographically determined structure of 12-1-SeB11H10. Finally, an indepth n.m.r. study of Se2B9H9 is also reported together with attempts to halogenate this compound. The last two chapters are based on single boron systems. Chapter Four concerns the synthetic routes to amine-boranes and -cyanoboranes from [BH4]- and [BH3CN]- substrates. This chapter discusses some difficulties encountered when polyamines were used in these reactions. The characterisation of an unusual ketone isolated from some of these reactions, the X-ray crystallographically determined structure of 4-dimethylamino-pyridine-cyanoborane and a new route to pyrazabole dimeric species are also discussed. The final chapter reports on work carried out at producing BH2X (X = H, CN) adducts of aminophosphines. Three routes were attempted to generate P-B and N-B bonded species with varying degrees of success. Some unusual products of these reactions are discussed including [Ph2(O) PPPh2 ] [Ph2NH]2, the structure of which was determined by X-ray crystallography.

Au nanorods-semiconductor nanowire hybrid nanostructures : nanofabrication techniques and optoelectronic properties

The objective of this thesis is the exploration and characterization of novel Au nanorod-semiconductor nanowire hybrid nanostructures. I provide a comprehensive bottom-up approach in which, starting from the synthesis and theoretical investigation of the optical properties of Au nanorods, I design, nanofabricate and characterize Au nanorods-semiconductor nanowire hybrid nanodevices with novel optoelectronic capabilities compared to the non-hybrid counterpart. In this regards, I first discuss the seed-mediated protocols to synthesize Au nanorods with different sizes and the influence of nanorod geometries and non-homogeneous surrounding medium on the optical properties investigated by theoretical simulation. Novel methodologies for assembling Au nanorods on (i) a Si/SiO2 substrate with highly-ordered architecture and (ii) on semiconductor nanowires with spatial precision are developed and optimized. By exploiting these approaches, I demonstrate that Raman active modes of an individual ZnO nanowire can be detected in non-resonant conditions by exploring the longitudinal plasmonic resonance mediation of chemical-synthesized Au nanorods deposited on the nanowire surface otherwise not observable on bare ZnO nanowire. Finally, nanofabrication and detailed electrical characterization of ZnO nanowire field-effect transistor (FET) and optoelectronic properties of Au nanorods - ZnO nanowire FET tunable near-infrared photodetector are investigated. In particular we demonstrated orders of magnitude enhancement in the photocurrent intensity in the explored range of wavelengths and 40 times faster time response compared to the bare ZnO FET detector. The improved performance, attributed to the plasmonicmediated hot-electron generation and injection mechanism underlying the photoresponse is investigated both experimentally and theoretically. The miniaturized, tunable and integrated capabilities offered by metal nanorodssemicondictor nanowire device architectures presented in this thesis work could have an important impact in many application fields such as opto-electronic sensors, photodetectors and photovoltaic devices and open new avenues for designing of novel nanoscale optoelectronic devices.

Comparison of the experimental, semi-experimental and ab initio equilibrium structures of acetylene: Influence of relativisitic effects and of the diagonal Born-Oppenheimer corrections

The equilibrium structure of acetylene (also named ethyne) has been reinvestigated to resolve the small discrepancies noted between different determinations. The size of the system as well as the large amount of available experimental data provides the quite unique opportunity to check the magnitude and relevance of various contributions to equilibrium structure as well as to verify the accuracy of experimental results. With respect to pure theoretical investigation, quantum-chemical calculations at the coupled-cluster level have been employed together with extrapolation to the basis set limit, consideration of higher excitations in the cluster operator, inclusion of core correlation effects as well as relativistic and diagonal Born-Oppenheimer corrections. In particular, it is found that the extrapolation to the complete basis set limit, the inclusion of higher excitations in the electronic-correlation treatment and the relativistic corrections are of the same order of magnitude. It also appears that a basis set as large as a core-valence quintuple-zeta set is required for accurately accounting for the inner-shell correlation contribution. From a pure experimental point of view, the equilibrium structure has been determined using very accurate rotational constants recently obtained by a global analysis (that is to say that all non-negligible interactions are explicitely included in the Hamiltonian matrix) of rovibrational spectra. Finally, a semi-experimental equilibrium structure (where the equilibrium rotational constants are obtained from the experimental ground state rotational constants and computed rovibrational corrections) has been obtained from the available experimental ground-state rotational constants for ten isotopic species corrected for computed vibrational corrections. Such a determination led to the revision of the ground-state rotational constants of two isotopologues, thus showing that structural determination is a good method to identify errors in experimental rotational constants. The three structures are found in a very good agreement, and our recommended values are rCC 120.2958(7) pm and rCH 106.164(1) pm. © 2011 American Institute of Physics.

An Experimental and Predictive Evaluation of Unsteady Gas Flow through Automotive Catalyst Elements

The incorporation of one-dimensional simulation codes within engine modelling applications has proved to be a useful tool in evaluating unsteady gas flow through elements in the exhaust system. This paper reports on an experimental and theoretical investigation into the behaviour of unsteady gas flow through catalyst substrate elements. A one-dimensional (1-D) catalyst model has been incorporated into a 1-D simulation code to predict this behaviour.

Experimental data was acquired using a ‘single pulse’ test rig. Substrate samples were tested under ambient conditions in order to investigate a range of regimes experienced by the catalyst during operation. This allowed reflection and transmission characteristics to be quantified in relation to both geometric and physical properties of substrate elements. Correlation between measured and predicted results is demonstrably good and the model provides an effective analysis tool for evaluating unsteady gas flow through different catalytic converter designs.

Clustering-Based Ensemble Method as an Alternative to Stacking

One of the most popular techniques of generating classifier ensembles is known as stacking which is based on a meta-learning approach. In this paper, we introduce an alternative method to stacking which is based on cluster analysis. Similar to stacking, instances from a validation set are initially classified by all base classifiers. The output of each classifier is subsequently considered as a new attribute of the instance. Following this, a validation set is divided into clusters according to the new attributes and a small subset of the original attributes of the instances. For each cluster, we find its centroid and calculate its class label. The collection of centroids is considered as a meta-classifier. Experimental results show that the new method outperformed all benchmark methods, namely Majority Voting, Stacking J48, Stacking LR, AdaBoost J48, and Random Forest, in 12 out of 22 data sets. The proposed method has two advantageous properties: it is very robust to relatively small training sets and it can be applied in semi-supervised learning problems. We provide a theoretical investigation regarding the proposed method. This demonstrates that for the method to be successful, the base classifiers applied in the ensemble should have greater than 50% accuracy levels.

Interacção entre estruturas intervalares e estruturas espectrais, na música instrumental/vocal

A presente tese apresenta-se num formato bipartido, sendo a primeira parte uma investigação teórica e a segunda parte um conjunto de composições originais que procuram estabelecer, directa e indirectamente, uma relação com a temática investigada. A investigação incide sobre as diferentes relações que se podem estabelecer entre estruturas intervalares e estruturas espectrais, a partir de um conjunto representativo de obras de diferentes compositores. As obras originais da segunda parte configuram um objecto final de análise e reflexão. As composições que integram a segunda parte da tese são: Inês – sete miniaturas sobre A Castro, para soprano e orquestra, sobre excertos de “Castro”, de António Ferreira; Um sino contra o tempo, para flauta, clarinete, percussão e piano; Terra, para orquestra de cordas; Dor e Amor, para voz, flauta, clarinete, percussão, harpa, piano, violino, viola e violoncelo, sobre poemas de Nuno Júdice; e Ode a Gaia, para soprano solo, coro misto e electrónica, a partir de textos de diversos autores e épocas, desde Homero a Fernando Pessoa. Esta investigação surge a partir da convicção de que é possível e enriquecedor para a composição a coexistência e o estabelecimento de uma relação entre estruturas que valorizam as qualidades dos intervalos que as constituem e estruturas de tipo espectral. Se o pensamento intervalar pode ser relacionado com princípios de estruturação ligados a toda uma tradição musical, desde a música modal, à tonal e à atonal, o pensamento espectral relaciona-se com o estudo do fenómeno sonoro e do timbre e é integrado mais tardiamente no séc. XX como um possível modelo estruturante na composição. A investigação sobre as obras seleccionadas, sobretudo de compositores que colocam o fenómeno da percepção num plano central, procura diferentes interacções entre os dois tipos de estrutura, interrogando-se sobre em que medida é que essa interacção influencia ou é mesmo determinante para o resultado musical final. São analisadas diferentes aplicações, tais como: a procura de qualidades acústicas na criação de estruturas intervalares, a criação de timbres particulares para linhas estruturantes, a manipulação tímbrica de estruturas verticais, a inter-relação de camadas intervalares e espectrais na textura musical de forma sincrónica e diacrónica, e o surgimento de material intervalar a partir de estruturas espectrais. Os principais resultados passam pela confirmação de que o pensamento intervalar é compatível com o pensamento espectral e vice-versa, podendo-se concluir que são essenciais diferentes funções para os dois tipos de estrutura na textura musical e que quer as estruturas intervalares quer as espectrais se relacionam com diferentes aspectos da percepção, tendo, assim, uma influência determinante no resultado musical final, na eficácia da escuta e na sua fruição.