CoordenaÃÃo de AperfeiÃoamento de NÃvel Superior / O presente trabalho à divido em duas partes. Na primeira, a utilizaÃÃo do interferÃmetro de Sagnac em informaÃÃo quÃntica à analisada atravÃs da aplicaÃÃo do mesmo em trÃs problemas: MediÃÃo livre de interaÃÃo, distribuiÃÃo quÃntica de chaves e compartilhamento de segredo. Para a mediÃÃo livre de interaÃÃo, dois sistemas usando o Sagnac foram propostos. Considerando detectores ideais e ausÃncia de perdas, um deles apresenta probabilidade de sucesso de 25% por fÃton consumido, enquanto que o segundo apresenta probabilidade de determinar corretamente a presenÃa do objeto prÃxima a 100% por fÃton consumido. Para a distribuiÃÃo quÃntica de chaves foi proposta uma configuraÃÃo diferente das existentes, sendo a principal diferenÃa a ausÃncia de retorno do pulso enviado, como ocorre nos sistemas com Sagnac anteriormente propostos. Isto evita ataques do tipo Cavalo de TrÃia. Por fim, foi proposta uma configuraÃÃo Ãptica que permite que um segredo compartilhado por cinco pessoas, localmente distantes, seja usado apenas quando todos os cinco concordarem. A segunda parte da dissertaÃÃo apresenta um estudo analÃtico e numÃrico da variaÃÃo do entrelaÃamento de estados bipartites de qubits quando da propagaÃÃo dos mesmos em canais quÃnticos ruidosos. Em particular, foi encontrada uma fÃrmula exata que relaciona os entrelaÃamentos dos estados na entrada e saÃda do canal, quando o estado na entrada à puro e o canal à modelado pela interaÃÃo do estado bipartite (sinal) com um qubit (estado do canal) atravÃs de uma operaÃÃo unitÃria canÃnica. / This work is divided into two parts. In the first one, the use of the Sagnac interferometer in quantum information is analyzed applying it in three problems: interaction-free measurement, quantum key distribution, and secret sharing. For the interaction-free measurement two systems using Sagnac interferometer were proposed. Considering ideal detectors and loss less devices, one of them has a success probability of 25% for each photon used while the other presents the probability of getting success to detect the presence of the object close to 100% for each photon used. For quantum key distribution, it was proposed a different setup, where the main difference is that the pulse sent by the transmitter does not come back to him/her as happen with the systems based on Sagnac proposed before. This avoids the Trojan horse attack. Finally, it was proposed an optical configuration where it is possible to share a secret among five users, locally distant, that could be used only when all five persons agreed. The second part of this dissertation presents an analytical and numerical study of the entanglement variation of bipartite states of qubits during propagation in a quantum noisy channel. Particularly, it was found an exactly formula which relates the entanglement of states in the input and output of the channel, when the input state is pure and the channel is modeled by a canonical unitary operation.

A química computacional, uma importante e crescente área da química teórica, vem sendo empregada com grande sucesso no entendimento dos mais variados tipos de sistemas químicos. Focando na interação entre arsênio e carbono, o presente trabalho apresenta duas situações distintas: uma que engloba o menor sistema formado entre eles, o radical CAs, e outra que traz a interação da superfície C(100) do diamante com o átomo de arsênio e a sua forma hidreto, ou seja, os sistemas C(100)+As e C(100)+AsH3. No primeiro caso, um tratamento de alto nível de correlação eletrônica (MRCI/aV5Z) é feito, permitindo se obter as propriedades espectroscópicas associados aos estados eletrônicos de mais baixa energia do radical. No estudo envolvendo a superfície C(100), dois modelos distintos de aglomerados foram adotados na representação do sólido: o modelo QM (C15H16) e o QM/MM (C292H120). A aproximação híbrida é baseada no método SIMOMM que é indicado para o tratamento de superfícies sólidas. Os dados estruturais e energéticos dos pontos de mínimos identificados nas duas diferentes aproximações foram contrastados, sugerindo que o modelo de aglomerado QM/MM é capaz de representar melhor o problema real. / Computational chemistry, a growing and important area in theoretical chemistry, has been successfully employed to understand many types of chemical systems. Focusing on the interaction between carbon and arsenic, this work presents two distinct situations: one is the study of the smallest system formed between them, the CAs radical, and another one where the diamond C(100) surface interacts with an arsenic atom and its hydride form, i.e. , the C(100)+As and C(100)+AsH3 systems. In the first case, a high-level (MRCI/aV5Z ) calculation was performed, allowing us to obtain the spectroscopic properties of the low-lying electronic states. In the study of the diamond C(100) surface, two different cluster models were used to represent the solid: one QM (C15H16) and the other QM/MM (C292H120). The hybrid approach is based on the SIMOMM method, that is recommended for dealing with solid surfaces. Energetic and structural aspects associated with the minimum energy species were contrasted for both a pproaches, suggesting that the QM/MM model is able to better represent the real problem.

Nesta tese estudamos dois problemas diferentes na área de átomos ultra frios: Ondas de choque em condensados de Bose-Einstein e Espalhamento inelástico de átomos em um potencial de dois poços. No primeiro problema, estudamos o fluxo supersônico de um condensado de Bose-Einstein (BEC) através de um obstáculo macroscópico impenetrável delgado no sistema da equação de Schrödinger não-linear (NLS) bidimensional. Assumindo-se que a velocidade do fluxo é suficientemente alta, reduzimos assintoticamente o problema bidimensional original de valor de contorno para o fluxo estacionário através de um obstáculo alongado ao problema do pistão dispersivo unidimensional descrito pela NLS 1D dependente do tempo, no qual a coordenada original x reescalonada faz o papel de tempo e o movimento do pistão está vinculado à geometria do obstáculo. Duas ondas de choque dispersivas (DSWs) são geradas no fluxo, cada uma sendo formada em uma extremidade (frontal e traseira) do obstáculo. A DSW frontal é descrita analiticamente construindo-se soluções de modulação exatas para as equações de Whitham e a para a DSW traseira, empregamos a regra de quantização de Bohr-Sommerfeld generalizada para descrever a distribuição dos sólitons escuros. Propomos uma extensão da solução de modulação tradicional, a fim de incluir o padrão de ship-wave linear formado fora da região da DSW frontal. Realizamos simulações numéricas 2D completas e verificamos a validade das previsões analíticas. Os resultados deste problema podem ser relevantes para experimentos recentes sobre o fluxo de BECs através de obstáculos. No segundo problema, estudamos uma mistura atômica de dois átomos fermiônicos leves de spin 1/2 e dois átomos pesados em um potencial de dois poços. Processos de espalhamento inelástico entre ambas as espécies atômicas excitam os átomos pesados e renormalizam a taxa de tunelamento e a interação entre os átomos leves (efeito polarônico). A interação efetiva dos átomos leves muda de sinal e se torna atrativa quando o espalhamento inelástico é forte. Observamos também o cruzamento de níveis de energia, de um estado onde cada poço contém apenas um férmion (espalhamento inelástico fraco) para um estado onde um poço contém um par de férmions e ou outra está vazio (espalhamento inelástico forte). Identificamos o efeito polarônico e o cruzamento dos níveis de energia estudando-se a dinâmica quântica do sistema. / In this thesis we study two different problems in the field of ultracold atoms: Shock waves in Bose-Einstein condensates and Inelastic scattering of atoms in a double well. In the first problem, we study the supersonic flow of a Bose-Einstein condensate (BEC) past a slender impenetrable macroscopic obstacle in the framework of the twodimensional (2D) defocusing nonlinear Schr¨odinger equation (NLS). Assuming the oncoming flow speed sufficiently high, we asymptotically reduce the original boundary-value problem for a steady flow past a slender body to the one-dimensional dispersive piston problem described by the nonstationary NLS equation, in which the role of time is played by the stretched x-coordinate and the piston motion curve is defined by the spatial body profile. Two steady oblique spatial dispersive shock waves (DSWs) spreading from the pointed ends of the body are generated in both half-planes. These are described analytically by constructing appropriate exact solutions of the Whitham modulation equations for the front DSW and by using a generalized Bohr-Sommerfeld quantization rule for the oblique dark soliton fan in the rear DSW. We propose an extension of the traditional modulation description of DSWs to include the linear ship-wave pattern forming outside the nonlinear modulation region of the front DSW. Our analytic results are supported by direct 2D unsteady numerical simulations and are relevant to recent experiments on Bose-Einstein condensates freely expanding past obstacles. In the second problem, we study a mixture of two light spin-1/2 fermionic atoms and two heavy atoms in a double well potential. Inelastic scattering processes between both atomic species excite the heavy atoms and renormalize the tunneling rate and the interaction of the light atoms (polaron effect). The effective interaction of the light atoms changes its sign and becomes attractive for strong inelastic scattering. This is accompanied by a crossing of the energy levels from singly occupied sites at weak inelastic scattering to a doubly occupied and an empty site for stronger inelastic scattering. We are able to identify the polaron effect and the level crossing in the quantum dynamics.

Este trabalho descreve a utilização de um software livre educacional do interferômetro de Mach-Zehnder (IMZ), em português, como instrumento motivador, ilustrativo, de fácil manuseio e compreensão, para ajudar no ensino e aprendizagem de Física. Salientamos que este software educacional foi desenvolvido através de um projeto coordenado pelas professoras Fernanda Ostermann e Flávia Rezende, do Instituto de Física da Universidade Federal do Rio Grande do Sul (UFRGS) e da Universidade Federal do Rio de Janeiro (UFRJ) e foi utilizado como principal instrumento para introduzir conceitos fundamentais de física quântica em uma disciplina do curso Mestrado Profissional de Ensino de Física. No entanto, podemos dizer que esta foi a primeira vez que o IMZ foi aplicado a uma turma de professores não ligados profissionalmente à UFRGS. Em acréscimo ao software, foram elaborados e remodelados como produtos educacionais, textos de apoio e guias experimentais que poderão ser usados tanto por professores, como por alunos do Ensino Médio. Fenômenos ondulatórios foi o assunto explorado e um de seus subtemas, a interferência da luz, foi bastante enfatizada. Colocamos à disposição dos professores um material didático de fácil interpretação, podendo, também, ser utilizado com alunos do Ensino Médio. O desenvolvimento desse material tem caráter estratégico para que sirva de base a futuras transposições de temas da física quântica, em particular, o fenômeno da dualidade onda-partícula, para este nível de ensino. Este material de apoio e o software compreendem um curso de quarenta horas, para um grupo de seis professores da rede estadual, mais especificamente para os professores que lecionam Física, nas escolas que representam a 6ª Coordenadoria Regional de Educação (6ª CRE), com o apoio da mesma. O curso aconteceu em 2006, na Escola Estadual de Ensino Médio “Ernesto Alves de Oliveira”, em Santa Cruz do Sul, RS. Embasado na Teoria de Aprendizagem Significativa de Ausubel, o material servirá, também, como base ou conhecimento prévio para futuras investidas em outros temas relacionados à física quântica. O conteúdo da teoria ondulatória da luz, trabalhado sobre o aparato do interferômetro virtual de Mach-Zehnder proporcionou a interação entre o conhecimento novo (física quântica e dualidade ondapartícula, desenvolvida sobre o interferômetro virtual de Mach-Zehnder no regime quântico) e o prévio (teoria ondulatória da luz desenvolvida sobre o interferômetro virtual de Mach- Zehnder clássico), possibilitando uma aprendizagem significativa e dando sentido às novas informações. No decorrer do curso, ao analisarmos o comportamento e as atitudes dos professores, pudemos perceber que este assunto não é trabalhado no Ensino Médio, e que eles apresentam dificuldades em relação aos conceitos fundamentais da teoria. Entretanto, parte do grupo mostrou interesse em obter novos conhecimentos, pois em todos os encontros havia questionamentos relacionando novos conceitos com os pré-existentes. Enfim, o software gerou visível entusiasmo com as novas possibilidades de aulas “práticas”, com a aprendizagem dos novos conceitos e também a proposta de se avaliar com a utilização de mapas conceituais, estratégia desenvolvida por Novak. / In this work it is shown how the utilization of a free educational software can be useful as a motivating and illustrative tool to help the teaching and understanding of fundamental concepts on quantum mechanics. Besides being available also in Portuguese, the virtual Mach-Zehnder Interferometer (MZI) is easy to handle. The software has been developed under a project coordinated by Professor Ostermann (UFRGS) and Professor Rezende (UFRJ) and has been used as a main tool to introduce students from Mestrado Profissional em Ensino de Física to fundamental concepts on quantum physics. Here, it is reported the first time the software was used in an environment that is not university. Concepts of quantum physics were discussed in a 40 hours course given to a group of six secondary level school teachers in 2006. They were teachers working under the 6ª Coordenadoria Regional de Educação (6ª CRE). The course took place in Santa Cruz do Sul (RS) at Escola Estadual de Ensino Médio “Ernesto Alves de Oliveira”. In order to help the students with the software itself and physical concepts that could help the understanding of the simulations results, supporting materials like helping texts and experimental guides were prepared based on Ausubel framework. We were also concerned about an educational product that could also be helpful to secondary level school students. The texts are available in an easy language and straightforward physics. Although the number of students were relatively small, the group was representative in the sense it reproduces the reality of public secondary schools in Brazil. Physics is not, in general, taught by people that are graduated in Licenciatura em Física and the ones that are, are in general, not very well prepared. It was clear that no one in the group had enough confidence “to touch” subjects related to quantum physics in classes having the excuse this is a very difficult topic to overcome. Using optical physics as basis and the virtual MZI, we could see some enthusiasm when the students realize it is possible, for example, to discuss some concepts related to wave-particle duality without unreachable mathematics.

Efeitos de solventes tem sido um tema de grande interesse científco. Em particular, o estudo dos efeitos de solventes no espectro eletrônico de absorção tem sua própria motivação e complexidade. Neste trabalho, nós estudamos os efeitos da solução aquosa na estabilidade conformacional e no espectro eletrônico de absorção da molécula Óxido Mesitil (OM). Essa molécula pertence a família das cetonas ,-insaturadas e, semelhantemente aos outros membros da família, ela apresenta transições eletrônicas sensíveis ao solvente. Inicialmente, estudamos os isômeros syn e anti do OM isoladamente usando cálculos quânticos para determinar a energia livre relativa, a barreira de rotação, os momentos de dipolo e as transições eletrônicas de absorção. Nosso melhor resultado mostra que o isômero syn do OM é a conformação mais estável, por cerca de 1.3 kcal/- mol calculado com nível MP2/aug-cc-pVDZ. Com o mesmo nível de cálculo, obtivemos os momentos de dipolo de 2.80 e 3.97 D para os isômeros syn e anti respectivamente, que estão em boa concordância com os valores experimentais de 2.8 e 3.7 D. Para o espectro eletrônico de absorção, analisamos a banda mais intensa, -*, com diferentes funcionais de densidade e funções base. Obtivemos o comprimento de transição de 229 nm calculado com nível TD-B3LYP/6-311++G** para o isômero syn em muito boa concordância com o valor experimental de 231 nm medido em solução de iso-octano (solvente de baixa polaridade). Para realizar os estudos em solução, geramos estruturas supermoleculares dos isômeros do OM em solução aquosa usando simulações computacionais com o método Monte Carlo. Usamos os potenciais Lennard-Jones e Coulomb para descrever as interações intermoleculares com os parâmetros do campo de força OPLS. Verifcamos que as cargas atômicas OPLS não descrevem bem o potencial eletrostático do OM. Portanto, realizamos um processo iterativo para incluir a polarização do soluto na presença do solvente para descrever melhor as interações entre o OM e as moléculas de água. Assim, obtivemos um aumento de cerca de 80% nos momentos de dipolo dos isômeros isolados. Adicionalmente, calculamos a energia livre relativa entre os isômeros em solução aquosa usando teoria de perturbação termodinâmica. Obtivemos que o isômero anti do OM é a conformação mais estável, por cerca de 2.8 kcal/mol. Examinando os efeitos de solvente no espectro eletrônico de absorção do OM, identificamos que existem duas contribuições competindo para o deslocamento da banda -*. Uma contribuição vem da mudança conformacional syn anti do OM devido a mudança de polaridade, baixa alta, do solvente. Essa mudança conformacional provoca um deslocamento para o azul de 1210 cm-1 na transição -*. A outra contribuição vem do efeito do solvente na estrutura eletrônica do OM, que provoca um deslocamento para o vermelho de - 4460 cm-1 nessa transição. Adicionando essas duas contribuições, temos o efeito do solvente total no espectro eletrônico de absorção do OM em solução aquosa. Nosso melhor resultado é um valor médio de 248 nm obtido com 75 cálculos TD-B3LYP/6-311++G** de estruturas supermoleculares estatisticamente descorrelacionadas compostas por um anti-OM rodeado por 14 moléculas de água explícitas embebidas no campo eletrostático de 236 moléculas de água tratadas como cargas pontuais simples. Esse resultado está em muito boa concordância com o resultado experimental de 243 nm em solução aquosa. Sendo assim, este trabalho demonstra que a mudança conformacional syn anti é essencial para entender o deslocamento espectral da transição -* do OM em água. / Solvent effects have been the subject of considerable scientifc interest. In particular, the study of solvent effects in electronic absorption spectroscopy has its own motivation and complexities. In this work we study the effects of the aqueous solution in the conformational stability and the electronic absorption spectrum of the Mesityl Oxide (OM) molecule. This molecule belongs to the family of the ,-unsaturated ketones and, like other members of the family, presents sensitivity to solvent in the absorption transitions. Initially we studied the isolated syn and anti isomers of OM by performing quantum mechanical calculations to obtain the relative free energy, the rotational barrier, the dipole moments and the electronic absorption transitions. Our best result showed that the OM syn isomer is the most stable conformer, by approximately 1.3 kcal/mol calculated with the MP2/aug-cc-pVDZ level. With the same level of calculation, we obtained the dipole moments of 2.80 and 3.97 D for the syn and anti isomers respectively, which are in good agreement with the experimental values of 2.8 and 3.7 D. For the electronic absorption spectrum, we analyzed the most intense band, -*, with different density functional and basis sets. We obtained a transition wavelength of 229 nm calculated with TD-B3LYP/6-311++G** level for the syn isomer in good agreement with the experimental value of 231 nm measured in iso-octane (solvent of low polarity). For performing the in-solution studies, we generated supermolecular structures of the OM isomers in aqueous solution using computer simulations with the Monte Carlo method. We used the Lennard-Jones and Coulomb potentials to describe the intermolecular interactions with the OPLS force field parameters. We found that the OPLS atomic charges do not describe well the electrostatic potential of OM. Therefore we performed an iterative process for including the solute polarization in the presence of the solvent to better describe the interactions between the OM and the water molecules. We obtained an increase of about 80% in the dipole moments of the isolated isomers. Additionally, we calculated the relative free energy between the isomers in aqueous solution using thermodynamic perturbation theory. We found that the anti isomer is the most stable conformer in aqueous solution, by about 2.8 kcal/mol. Examining the solvent effects in the electronic absorption spectrum of OM, we found that there are two competing contributions to the -* band shift. One contribution is due to the syn anti conformational change of OM caused by the low high polarity change of the solvent. This conformational change led to a blue shift of 1210 cm-1 in the * band. The remaining contribution is due to the solvent effect in the electronic structure of OM, which led to a red shift of -4460 cm-1. Adding these two contributions, we obtained the total solvent effect in the electronic absorption spectrum of OM in aqueous solution. Our best result was an average wavelength transition of 248 nm obtained using 75 TD-B3LYP/6-311++G** quantum calculations on statistically uncorrelated supermolecular structures composed by one anti-OM surrounded by 14 explicit water molecules in the electrostatic embedding composed of 236 water molecules described as simple point charges. This result is in very good agreement with the experimental result of 243 nm in aqueous solution. Thus, this work demonstrates that the syn anti conformational change is the essential ingredient to understand the spectral shift of the - * absorption transition of OM in water.

A química computacional, uma importante e crescente área da química teórica, vem sendo empregada com grande sucesso no entendimento dos mais variados tipos de sistemas químicos. Focando na interação entre arsênio e carbono, o presente trabalho apresenta duas situações distintas: uma que engloba o menor sistema formado entre eles, o radical CAs, e outra que traz a interação da superfície C(100) do diamante com o átomo de arsênio e a sua forma hidreto, ou seja, os sistemas C(100)+As e C(100)+AsH3. No primeiro caso, um tratamento de alto nível de correlação eletrônica (MRCI/aV5Z) é feito, permitindo se obter as propriedades espectroscópicas associados aos estados eletrônicos de mais baixa energia do radical. No estudo envolvendo a superfície C(100), dois modelos distintos de aglomerados foram adotados na representação do sólido: o modelo QM (C15H16) e o QM/MM (C292H120). A aproximação híbrida é baseada no método SIMOMM que é indicado para o tratamento de superfícies sólidas. Os dados estruturais e energéticos dos pontos de mínimos identificados nas duas diferentes aproximações foram contrastados, sugerindo que o modelo de aglomerado QM/MM é capaz de representar melhor o problema real. / Computational chemistry, a growing and important area in theoretical chemistry, has been successfully employed to understand many types of chemical systems. Focusing on the interaction between carbon and arsenic, this work presents two distinct situations: one is the study of the smallest system formed between them, the CAs radical, and another one where the diamond C(100) surface interacts with an arsenic atom and its hydride form, i.e. , the C(100)+As and C(100)+AsH3 systems. In the first case, a high-level (MRCI/aV5Z ) calculation was performed, allowing us to obtain the spectroscopic properties of the low-lying electronic states. In the study of the diamond C(100) surface, two different cluster models were used to represent the solid: one QM (C15H16) and the other QM/MM (C292H120). The hybrid approach is based on the SIMOMM method, that is recommended for dealing with solid surfaces. Energetic and structural aspects associated with the minimum energy species were contrasted for both a pproaches, suggesting that the QM/MM model is able to better represent the real problem.

<p>Human Immunodeficiency Virus (HIV) is the causative agent of the pandemic disease Acquired Immune Deficiency Syndrome (AIDS). HIV acts to disrupt the immune system which makes the body susceptible to opportunistic infections. Untreated, AIDS is generally fatal. Twenty years of research by countless scientists around the world has led to the discovery and exploitation of several targets in the replication cycle of HIV. Many lives have been saved, prolonged and improved as a result of this massive effort. One particularly successful target has been the inhibition of HIV protease. In combination with the inhibition of HIV reverse transcriptase, protease inhibitors have helped to reduce viral loads and partially restore the immune system. Unfortunately, viral mutations leading to drug resistance and harmful side-effects of the current medicines have identified the need for new drugs to combat HIV.</p><p>This study presents computational efforts to understand the interaction of inhibitors to HIV protease. The first part of this study has used molecular modelling and Comparative Molecular Field Analysis (CoMFA) to help explain the structure-active relationship of a novel series of protease inhibitors. The inhibitors are sulfamide derivatives structurally similar to the cyclic urea candidate drug mozenavir (DMP-450). The central ring of the sulfamides twists to adopt a nonsymmetrical binding mode distinct from that of the cyclic ureas. The energetics of this twist has been studied with <i>ab initio</i> calculations to develop improved empirical force field parameters for use in molecular modelling.</p><p>The second part of this study has focused on an analysis of the association and dissociation kinetics of a broad collection of HIV protease inhibitors. Quantitative models have been derived using CoMFA which relate the dissociation rate back to the chemical structures. Efforts have also been made to improve the models by systematically varying the parameters used to generate them.</p>

Quantum computation has attracted a great deal of attention from the scientific community in recent years. By using the quantum mechanical phenomena of superposition and entanglement, a quantum computer can solve certain problems much faster than classical computers. Several quantum algorithms have been developed to demonstrate this quantum speedup. Two important examples are Shor’s algorithm for the factorization problem, and Grover’s algorithm for the search problem. Significant efforts are on to build a large scale quantum computer for implementing these quantum algorithms. This thesis deals with Grover’s search algorithm, and presents its several generalizations that perform better in specific contexts. While writing the thesis, we have assumed the familiarity of readers with the basics of quantum mechanics and computer science. For a general introduction to the subject of quantum computation, see [1]. In Chapter 1, we formally define the search problem as well as present Grover’s search algorithm [2]. This algorithm, or more generally the quantum amplitude amplification algorithm [3, 4], drives a quantum system from a prepared initial state (s) to a desired target state (t). It uses O(α-1 = | (t−|s)| -1) iterations of the operator g = IsIt on |s), where { IsIt} are selective phase inversions selective phase inversions of the corresponding states. That is a quadratic speedup over the simple scheme of O(α−2) preparations of |s) and subsequent projective measurements. Several generalizations of Grover’s algorithm exist. In Chapter 2, we study further generalizations of Grover’s algorithm. We analyse the iteration of the search operator S = DsI t on |s) where Ds is a more general transformation than Is, and I t is a selective phase rotation of |t) by angle . We find sufficient conditions for S to produce a successful quantum search algorithm. In Chapter 3, we demonstrate that our general framework encapsulates several previous generalizations of Grover’s algorithm. For example, the phase-matching condition for the search operator requires the angles and and to be almost equal for a successful quantum search. In Kato’s algorithm, the search operator is where Ks consists of only single-qubit gates, which are easier to implement physically than multi-qubit gates. The spatial search algorithms consider the search operator where is a spatially local operator and provides implementation advantages over Is. The analysis of Chapter 2 provides a simpler understanding of all these special cases. In Chapter 4, we present schemes to improve our general quantum search algorithm, by controlling the operators through an ancilla qubit. For the case of two dimensional spatial search problem, these schemes yield an algorithm with time complexity . Earlier algorithms solved this problem in time steps, and it was an open question to design a faster algorithm. The schemes can also be used to find, for a given unitary operator, an eigenstate corresponding to a specified eigenvalue. In Chapter 5, we extend the analysis of Chapter 2 to general adiabatic quantum search. It starts with the ground state |s) of an initial Hamiltonian Hs and evolves adiabatically to the target state |t) that is the ground state of the final Hamiltonian The evolution uses a time dependent Hamiltonian HT that varies linearly with time . We show that the minimum excitation gap of HT is proportional to α. Also, the ground state of HT changes significantly only within a very narrow interval of width around the transition point, where the excitation gap has its minimum. This feature can be used to reach the target state (t) using adiabatic evolution for time In Chapter 6, we present a robust quantum search algorithm that iterates the operator on |s) to successfully reach |t), whereas Grover’s algorithm fails if as per the phase-matching condition. The robust algorithm also works when is generalized to multiple target states. Moreover, the algorithm provides a new search Hamiltonian that is robust against certain systematic perturbations. In Chapter 7, we look beyond the widely studied scenario of iterative quantum search algorithms, and present a recursive quantum search algorithm that succeeds with transformations {Vs,Vt} sufficiently close to {Is,It.} Grover’s algorithm generally fails if while the recursive algorithm is nearly optimal as long as , improving the error tolerance of the transformations. The algorithms of Chapters 6-7 have applications in quantum error-correction, when systematic errors affect the transformations The algorithms are robust as long as the errors are small, reproducible and reversible. This type of errors arise often from imperfections in apparatus setup, and so the algorithms increase the flexibility in physical implementation of quantum search. In Chapter 8, we present a fixed-point quantum search algorithm. Its state evolution monotonically converges towards |t), unlike Grover’s algorithm where the evolution passes through |t) under iterations of the operator . In q steps, our algorithm monotonically reduces the failure probability, i.e. the probability of not getting |t), from . That is asymptotically optimal for monotonic convergence. Though the fixed-point algorithm is of not much use for , it is useful when and each oracle query is highly expensive. In Chapter 9, we conclude the thesis and present an overall outlook.

Human Immunodeficiency Virus (HIV) is the causative agent of the pandemic disease Acquired Immune Deficiency Syndrome (AIDS). HIV acts to disrupt the immune system which makes the body susceptible to opportunistic infections. Untreated, AIDS is generally fatal. Twenty years of research by countless scientists around the world has led to the discovery and exploitation of several targets in the replication cycle of HIV. Many lives have been saved, prolonged and improved as a result of this massive effort. One particularly successful target has been the inhibition of HIV protease. In combination with the inhibition of HIV reverse transcriptase, protease inhibitors have helped to reduce viral loads and partially restore the immune system. Unfortunately, viral mutations leading to drug resistance and harmful side-effects of the current medicines have identified the need for new drugs to combat HIV. This study presents computational efforts to understand the interaction of inhibitors to HIV protease. The first part of this study has used molecular modelling and Comparative Molecular Field Analysis (CoMFA) to help explain the structure-active relationship of a novel series of protease inhibitors. The inhibitors are sulfamide derivatives structurally similar to the cyclic urea candidate drug mozenavir (DMP-450). The central ring of the sulfamides twists to adopt a nonsymmetrical binding mode distinct from that of the cyclic ureas. The energetics of this twist has been studied with ab initio calculations to develop improved empirical force field parameters for use in molecular modelling. The second part of this study has focused on an analysis of the association and dissociation kinetics of a broad collection of HIV protease inhibitors. Quantitative models have been derived using CoMFA which relate the dissociation rate back to the chemical structures. Efforts have also been made to improve the models by systematically varying the parameters used to generate them.

Multilayer epitaxial graphene has been shown to contain "massless Dirac fermions" and is believed to provide a possible route to industrial-scale graphene electronics. We used scanning tunneling microscopy (STM) and spectroscopy (STS) in high magnetic fields to obtain local information on these fermions. A new STS technique was developed to directly measure graphene's energy-momentum relationship and resulted in the highest precision measurement of graphene's Dirac cone. STS spectra similar to ideal graphene were observed, but additional anomalies were also found. Extra peaks and an asymmetry between electron and hole states were shown to be caused by the work function difference between the Iridium STM tip and graphene. This tip effect was extracted using modeled potentials and performing a least square fit using degenerate perturbation theory on graphene's eigenstates solved in the symmetric gauge. Defects on graphene were then investigated and magnetic field effects were shown to be due to a mixture of potential effect from defects and the tip potential. New defect states were observed to localize around specific defects, and are believed to interact with the STM tip by Stark shifting in energy. This Stark shift gives a direct measurement of the capacitive coupling between the tip and graphene and agrees with the modeled results found when extracting the tip potential.