Topology of toroidal helical fields in non-circular cross-sectional tokamaks

The ordinary differential magnetic field line equations are solved numerically; the tokamak magnetic structure is studied on Hefei Tokamak-7 Upgrade (HT-7U) when the equilibrium field with a monotonic q-profile is perturbed by a helical magnetic field. We find that a single mode (m, n) helical perturbation can cause the formation of islands on rational surfaces with q = m/n and q = (m +/- 1, +/- 2, +/- 3,...)/n due to the toroidicity and plasma shape (i.e. elongation and triangularity), while there are many undestroyed magnetic surfaces called Kolmogorov-Arnold-Moser (KAM) barriers on irrational surfaces. The islands on the same rational surface do not have the same size. When the ratio between the perturbing magnetic field B-r(r) and the toroidal magnetic field amplitude B(phi)0 is large enough, the magnetic island chains on different rational surfaces will overlap and chaotic orbits appear in the overlapping area, and the magnetic field becomes stochastic. It is remarkable that the stochastic layer appears first in the plasma edge region.

Investigation of the influence of the aberration induced by a plane interface on STED microscopy

The structure of the inhibition patterns is important to the stimulated emission depletion (STED) microscopy. Usually, Laguerre-Gaussian (LG) beam and the central zero-intensity patterns created by inserting phase masks in Gaussian beams are used as the erase beam in STED microscopy. Aberration is generated when focusing beams through an interface between the media of the mismatched refractive indices. By use of the vectorial integral, the effects of such aberration on the shape of depletion patterns and the size of fluorescence emission spot in the STED microscopy are studied. Results are presented as a comparison between the aberration-free case and the aberrated cases. (C) 2009 Optical Society of America

Baryon and lepton numbers in particle physics beyond the standard model

The works presented in this thesis explore a variety of extensions of the standard model of particle physics which are motivated by baryon number (B) and lepton number (L), or some combination thereof. In the standard model, both baryon number and lepton number are accidental global symmetries violated only by non-perturbative weak effects, though the combination B-L is exactly conserved. Although there is currently no evidence for considering these symmetries as fundamental, there are strong phenomenological bounds restricting the existence of new physics violating B or L. In particular, there are strict limits on the lifetime of the proton whose decay would violate baryon number by one unit and lepton number by an odd number of units.

The first paper included in this thesis explores some of the simplest possible extensions of the standard model in which baryon number is violated, but the proton does not decay as a result. The second paper extends this analysis to explore models in which baryon number is conserved, but lepton flavor violation is present. Special attention is given to the processes of μ to e conversion and μ → eγ which are bound by existing experimental limits and relevant to future experiments.

The final two papers explore extensions of the minimal supersymmetric standard model (MSSM) in which both baryon number and lepton number, or the combination B-L, are elevated to the status of being spontaneously broken local symmetries. These models have a rich phenomenology including new collider signatures, stable dark matter candidates, and alternatives to the discrete R-parity symmetry usually built into the MSSM in order to protect against baryon and lepton number violating processes.

Development and Application of Embedding Methods for the Simulation of Large Chemical Systems

The high computational cost of correlated wavefunction theory (WFT) calculations has motivated the development of numerous methods to partition the description of large chemical systems into smaller subsystem calculations. For example, WFT-in-DFT embedding methods facilitate the partitioning of a system into two subsystems: a subsystem A that is treated using an accurate WFT method, and a subsystem B that is treated using a more efficient Kohn-Sham density functional theory (KS-DFT) method. Representation of the interactions between subsystems is non-trivial, and often requires the use of approximate kinetic energy functionals or computationally challenging optimized effective potential calculations; however, it has recently been shown that these challenges can be eliminated through the use of a projection operator. This dissertation describes the development and application of embedding methods that enable accurate and efficient calculation of the properties of large chemical systems.

Chapter 1 introduces a method for efficiently performing projection-based WFT-in-DFT embedding calculations on large systems. This is accomplished by using a truncated basis set representation of the subsystem A wavefunction. We show that naive truncation of the basis set associated with subsystem A can lead to large numerical artifacts, and present an approach for systematically controlling these artifacts.

Chapter 2 describes the application of the projection-based embedding method to investigate the oxidative stability of lithium-ion batteries. We study the oxidation potentials of mixtures of ethylene carbonate (EC) and dimethyl carbonate (DMC) by using the projection-based embedding method to calculate the vertical ionization energy (IE) of individual molecules at the CCSD(T) level of theory, while explicitly accounting for the solvent using DFT. Interestingly, we reveal that large contributions to the solvation properties of DMC originate from quadrupolar interactions, resulting in a much larger solvent reorganization energy than that predicted using simple dielectric continuum models. Demonstration that the solvation properties of EC and DMC are governed by fundamentally different intermolecular interactions provides insight into key aspects of lithium-ion batteries, with relevance to electrolyte decomposition processes, solid-electrolyte interphase formation, and the local solvation environment of lithium cations.

Investigations of DNA-mediated protein oxidation

DNA charge transport (CT) involves the efficient transfer of electrons or electron holes through the DNA π-stack over long molecular distances of at least 100 base-pairs. Despite this shallow distance dependence, DNA CT is sensitive to mismatches or lesions that disrupt π-stacking and is critically dependent on proper electronic coupling of the donor and acceptor moieties into the base stack. Favorable DNA CT is very rapid, occurring on the picosecond timescale. Because of this speed, electron holes equilibrate along the DNA π-stack, forming a characteristic pattern of DNA damage at low oxidation potential guanine multiplets. Furthermore, DNA CT may be used in a biological context. DNA processing enzymes with 4Fe4S clusters can perform DNA-mediated electron transfer (ET) self-exchange reactions with other 4Fe4S cluster proteins, even if the proteins are quite dissimilar, as long as the DNA-bound [4Fe4S]^3+/2+ redox potentials are conserved. This mechanism would allow low copy number DNA repair proteins to find their lesions efficiently within the cell. DNA CT may also be used biologically for the long-range, selective activation of redox-active transcription factors. Within this work, we pursue other proteins that may utilize DNA CT within the cell and further elucidate aspects of the DNA-mediated ET self-exchange reaction of 4Fe4S cluster proteins.

Dps proteins, bacterial mini-ferritins that protect DNA from oxidative stress, are implicated in the survival and virulence of pathogenic bacteria. One aspect of their protection involves ferroxidase activity, whereby ferrous iron is bound and oxidized selectively by hydrogen peroxide, thereby preventing formation of damaging hydroxyl radicals via Fenton chemistry. Understanding the specific mechanism by which Dps proteins protect the bacterial genome could inform the development of new antibiotics. We investigate whether DNA-binding E. coli Dps can utilize DNA CT to protect the genome from a distance. An intercalating ruthenium photooxidant was employed to generate oxidative DNA damage via the flash-quench technique, which localizes to a low potential guanine triplet. We find that Dps loaded with ferrous iron, in contrast to Apo-Dps and ferric iron-loaded Dps which lack available reducing equivalents, significantly attenuates the yield of oxidative DNA damage at the guanine triplet. These data demonstrate that ferrous iron-loaded Dps is selectively oxidized to fill guanine radical holes, thereby restoring the integrity of the DNA. Luminescence studies indicate no direct interaction between the ruthenium photooxidant and Dps, supporting the DNA-mediated oxidation of ferrous iron-loaded Dps. Thus DNA CT may be a mechanism by which Dps efficiently protects the genome of pathogenic bacteria from a distance.

Further work focused on spectroscopic characterization of the DNA-mediated oxidation of ferrous iron-loaded Dps. X-band EPR was used to monitor the oxidation of DNA-bound Dps after DNA photooxidation via the flash-quench technique. Upon irradiation with poly(dGdC)₂, a signal arises with g = 4.3, consistent with the formation of mononuclear high-spin Fe(III) sites of low symmetry, the expected oxidation product of Dps with one iron bound at each ferroxidase site. When poly(dGdC)₂ is substituted with poly(dAdT)₂, the yield of Dps oxidation is decreased significantly, indicating that guanine radicals facilitate Dps oxidation. The more favorable oxidation of Dps by guanine radicals supports the feasibility of a long-distance protection mechanism via DNA CT where Dps is oxidized to fill guanine radical holes in the bacterial genome produced by reactive oxygen species.

We have also explored possible electron transfer intermediates in the DNA-mediated oxidation of ferrous iron-loaded Dps. Dps proteins contain a conserved tryptophan residue in close proximity to the ferroxidase site (W52 in E. coli Dps). In comparison to WT Dps, in EPR studies of the oxidation of ferrous iron-loaded Dps following DNA photooxidation, W52Y and W52A mutants were deficient in forming the characteristic EPR signal at g = 4.3, with a larger deficiency for W52A compared to W52Y. In addition to EPR, we also probed the role of W52 Dps in cells using a hydrogen peroxide survival assay. Bacteria containing W52Y Dps survived the hydrogen peroxide challenge more similarly to those containing WT Dps, whereas cells with W52A Dps died off as quickly as cells without Dps. Overall, these results suggest the possibility of W52 as a CT hopping intermediate.

DNA-modified electrodes have become an essential tool for the study of the redox chemistry of DNA processing enzymes with 4Fe4S clusters. In many cases, it is necessary to investigate different complex samples and substrates in parallel in order to elucidate this chemistry. Therefore, we optimized and characterized a multiplexed electrochemical platform with the 4Fe4S cluster base excision repair glycosylase Endonuclease III (EndoIII). Closely packed DNA films, where the protein has limited surface accessibility, produce EndoIII electrochemical signals sensitive to an intervening mismatch, indicating a DNA-mediated process. Multiplexed analysis allowed more robust characterization of the CT-deficient Y82A EndoIII mutant, as well as comparison of a new family of mutations altering the electrostatics surrounding the 4Fe4S cluster in an effort to shift the reduction potential of the cluster. While little change in the DNA-bound midpoint potential was found for this family of mutants, likely indicating the dominant effect of DNA-binding on establishing the protein redox potential, significant variations in the efficiency of DNA-mediated electron transfer were apparent. On the basis of the stability of these proteins, examined by circular dichroism, we proposed that the electron transfer pathway in EndoIII can be perturbed not only by the removal of aromatic residues but also through changes in solvation near the cluster.

While the 4Fe4S cluster of EndoIII is relatively insensitive to oxidation and reduction in solution, we have found that upon DNA binding, the reduction potential of the [4Fe4S]^3+/2+ couple shifts negatively by approximately 200 mV, bringing this couple into a physiologically relevant range. Demonstrated using electrochemistry experiments in the presence and absence of DNA, these studies do not provide direct molecular evidence for the species being observed. Sulfur K-edge X-ray absorbance spectroscopy (XAS) can be used to probe directly the covalency of iron-sulfur clusters, which is correlated to their reduction potential. We have shown that the Fe-S covalency of the 4Fe4S cluster of EndoIII increases upon DNA binding, stabilizing the oxidized [4Fe4S]³⁺ cluster, consistent with a negative shift in reduction potential. The 7% increase in Fe-S covalency corresponds to an approximately 150 mV shift, remarkably similar to DNA electrochemistry results. Therefore we have obtained direct molecular evidence for the shift in 4Fe4S reduction potential of EndoIII upon DNA binding, supporting the feasibility of our model whereby these proteins can utilize DNA CT to cooperate in order to efficiently find DNA lesions inside cells.

In conclusion, in this work we have explored the biological applications of DNA CT. We discovered that the DNA-binding bacterial ferritin Dps can protect the bacterial genome from a distance via DNA CT, perhaps contributing to pathogen survival and virulence. Furthermore, we optimized a multiplexed electrochemical platform for the study of the redox chemistry of DNA-bound 4Fe4S cluster proteins. Finally, we have used sulfur K-edge XAS to obtain direct molecular evidence for the negative shift in 4Fe4S cluster reduction potential of EndoIII upon DNA binding. These studies contribute to the understanding of DNA-mediated protein oxidation within cells.

Effect of absorption on the diffraction efficiency in Fe : LiNbO3 crystal with 90 degrees recording geometry

In this paper the saturated diffraction efficiency has been optimized by considering the effect of the absorption of the recording light on a crossed-beam grating with 90 degrees recording geometry in Fe:LiNbO3 crystals. The dependence of saturated diffraction efficiency on the doping levels with a known oxidation-reduction state, as well as the dependence of saturated diffraction efficiency on oxidation-reduction state with known doping levels, has been investigated. Two competing effects on the saturated diffraction efficiency were discussed, and the intensity profile of the diffracted beam at the output boundary has also been investigated. The results show that the maximal saturated diffraction efficiency can be obtained in crystals with moderate doping levels and modest oxidation state. An experimental verification is performed and the results are consistent with those of the theoretical calculation.

透镜自重变形引起波像差的有限元分析

在用大口径、长焦距平行光管模拟激光远场特性时，其光组透镜在重力作用下的变形不能忽略，为了分析对出射光束质量的影响，采用有限元分析软件“ANSYS”建立了平行光管光组中声400mm平凸透镜的有限元模型，给出一种分析透镜轴向变形引起的波像差的方法，在不同工况下，计算了平凸透镜在重力作用下轴向变形的峰谷值和均方根值，对轴向变形量均方根值最小工况画出了透镜表面变形的等值线图，计算了声350mm通光口径内的波像差峰谷值和均方根值，对平行光管光组的波像差做出估计，验证了设计的合理性。

沢吨染料的光化漂白动力学及全息特性研究

研究了以三乙醇胺作为引发剂,五种沢吨染料的光化漂白过程.实验结果表明五种染料的光化漂白速率大小顺序是藻红B（ErB）＞曙红Y（EY）＞孟加拉玫瑰红B（RsB）＞罗丹明B（RoB）＞荧光素（F）.并研究了曝光强度及染料浓度对漂白过程的影响,以及这五种染料的全息记录性能.

Comparison of fluorescence spectra of Yb : Y3Al5O12 and Yb : YALO(3) single crystals

Yb:Y3Al5O12 (Yb:YAG) single crystals with Yb doping concentration 0.5 at.%, 5 at.%, 15 at.%, 25 at.%, 50 at.%, 100 at.% and Yb:YAlO3 (Yb:YAP) single crystals with Yb doping concentration 0.5 at.%, 5 at.%, 15 at.%, 30 at.% were grown by the Czochralski process. The fluorescence spectra of these crystals and the effects of self-absorption on the shape of the fluorescence spectra were studied. Through comparing the fluorescence spectra of Yb:YAG and Yb:YAP, all results indicate that the effects of self-absorption on the fluorescence spectra of Yb:YAP are remarkably stronger than that of Yb:YAG at the same Yb concentration. (c) 2006 Elsevier B.V. All rights reserved.

A voz e a invocação para musicar a vida: ressonâncias entre música e psicanálise

A articulação entre a psicanálise e a música, mais especificamente a produzida a partir do paradigma de Arnold Schönberg, renovado por John Cage, se mostra emblemática para pensar a constituição do sujeito em Sigmund Freud e Jacques Lacan, bem como para refletir sobre a escuta clínica, o ato analítico enquanto poético, e a escrita pulsional do sujeito como resposta à invocação da voz. O momento de estruturação do sujeito implica a dimensão de musicalidade da linguagem que permite o ato da fala. O sujeito nasce em um ponto em que o significante (simbólico) escreve no real do corpo um possível, um começo, uma marca que invoca uma nota e uma letra, sendo estes os dois aspectos da linguagem: a musicalidade (continuidade) e a fala (descontinuidade em movimento). Este ponto escreve e cria um vazio no sujeito que está e estará sempre em pulsação. Se o real grita caoticamente, é possível que se cante e se musique a vida com a criação de notas singulares, efeito do movimento desejante e de uma escrita pelo circuito da pulsão invocante na partitura já dada pelo Outro e face aos encontros com pedaços de real. A música tem a capacidade de retirar o sujeito de uma surdez de seu próprio desejo, o convocando a recriar a linguagem por seus atos. O paradigma de Schönberg, bem como a música criada a partir deste momento, nos dá a ouvir um saber-fazer com a voz no qual a dimensão equivocante (de equivoco e de invocação) da linguagem pode ressurgir por uma via nova. A transmissão de um saber-fazer com o objeto voz por ele efetuado se apresenta como uma radicalização do efeito de verdade do real, ressoando borromeanamente sobre o simbólico e o imaginário, invocando o momento originário do sujeito, de um começo sempre a recomeçar, que se faz ouvir como uma invocação de musicar a vida de uma maneira ética, estética e poética. É através dos eixos acima expostos que nos é possível sustentar, com Lacan, uma prática clínica orientada para além da repetição em direção a um significante novo. Trata-se de uma orientação que parte dos encontros com o real aos quais o sujeito é confrontado ao acaso visando o movimento renascente pelo qual ele pode re-escutar o inaudito do real contínuo perdido, o que faz com que seu ritmo singular possa ser, uma vez mais e de modo inédito, reinventado. A psicanálise pode ser, portanto, entendida como uma prática invocante, como uma abertura para que o sujeito possa, com entusiasmo, musicar a vida.

Sobre o gozo na clínica psicanalítica com mulheres devastadas

A presente pesquisa sobre o gozo na clínica com mulheres devastadas teve como foco o lugar ocupado pelo gozo em seu aspecto mortífero, de excesso e falta de medida, que se manifesta no âmbito das parcerias amorosas. Partindo das experiências relatadas por algumas analisandas, que as descrevem como "sair do corpo", "ficar louca", "descontrolada" ou "fora de si", e das formulações psicanalíticas a respeito do gozo feminino, buscou-se discutir a questão a partir dos referenciais propostos por Freud e Lacan no que diz respeito à constituição da feminilidade e do feminino, tais como a catástrofe e a devastação na ligação com a mãe e com o parceiro, a forma erotomaníaca de amar, além das duas formas de gozo nas mulheres. Entre os temas abordados nesta dissertação destacam-se as operações da castração e do Complexo de Édipo, juntamente com o seu elemento central, o falo, que permitem trazer à discussão algumas consequências para as mulheres, sobretudo as posições implicadas, a saber: o falo e a mascarada. O conceito de gozo é examinado através de três ser mascarada articulações principais. Primeiramente, a tentativa de Freud, que parece a mais antiga na psicanálise, de circunscrever um gozo propriamente feminino, ligado à satisfação da pulsão pela via da zona vaginal; em segundo lugar, o pensamento de Lacan em Diretrizes para um congresso sobre a sexualidade feminina (1958), em que ele recupera a questão freudiana do congresso sobre a sexualidade feminina gozo feminino, e posteriormente no Seminário 7:a ética da psicanálise (1959-1960), desenvolvido durante o período de preparação para o referido congresso, no qual Lacan eleva o gozo ao estatuto de conceito. Como desdobramento, encontram-se algumas articulações clínicas acerca do gozo devastador nos relacionamentos amorosos, tomando como referência a personagem da Erwartung, op. 17 , de Arnold Schoenberg e as mulheres que encontramos no dia a dia da clínica.

A relação entre o principio de razão suficiente e o principio da contradição em Leibniz

De acordo com Leibniz, nossos raciocínios estão fundados em dois grandes princípios, o Princípio de Razão Suficiente e o Princípio de Contradição. Apesar da reconhecida relevância de tais princípios para sua filosofia, muitas são as interpretações sobre o real papel que eles desempenham dentro dela e sobre a relação deles entre si. Nosso estudo pauta-se não só pela interpretação de Leibniz como pela visão de alguns de seus comentadores, especialmente três deles: Russell, Couturat e Deleuze. Iremos pesquisar, entre outras coisas, se tais princípios são independentes um do outro; se são aplicáveis a todo tipo de verdade; se o Princípio de Perfeição é uma particularização do Princípio de Razão Suficiente ou se é irredutível a ele; e se as verdades da razão são regidas pelo Princípio de Contradição e as verdades de fato são regidas pelo Princípio de Razão Suficiente. A articulação entre tais princípios remete a um terceiro ponto: a concepção da verdade como inclusão do conceito do predicado no sujeito, tema este que iremos analisar com base nos diferentes pontos de vista acerca das proposições essenciais e existenciais. Em relação a esta última, investigaremos se representam ou não uma exceção ao caráter analítico de todas as proposições verdadeiras.

Regional and seasonal patterns of epipelagic fish assemblages from the central California Current

The coastal Pacific Ocean off northern and central California encompasses the strongest seasonal upwelling zone in the California Current ecosystem. Headlands and bays here generate complex circulation features and confer unusual oceanographic complexity. We sampled the coastal epipelagic fish community of this region with a surface trawl in the summer and fall of 2000–05 to assess patterns of spatial and temporal community structure. Fifty-three species of fish were captured in 218 hauls at 34 fixed stations, with clupeiform species dominating. To examine spatial patterns, samples were grouped by location relative to a prominent headland at Point Reyes and the resulting two regions, north coast and Gulf of the Farallones, were plotted by using nonmetric multidimensional scaling. Seasonal and interannual patterns were also examined, and representative species were identified for each distinct community. Seven oceanographic variables measured concurrently with trawling were plotted by principal components analysis and tested for correlation with biotic patterns. We found significant differences in community structure by region, year, and season, but no interaction among main effects. Significant differences in oceanographic conditions mirrored the biotic patterns, and a match between biotic and hydrographic structure was detected. Dissimilarity between assemblages was mostly the result of differences in abundance and frequency of occurrence of about twelve common species. Community patterns were best described by a subset of hydrographic variables, including water depth, distance from shore, and any one of several correlated variables associated with upwelling intensity. Rather than discrete communities with clear borders and distinct member species, we found gradients in community structure and identified stations with similar fish communities by region and by proximity to features such as the San Francisco Bay.