The use of polymers as flocculating additives is a common practice in many manufacturing environments. However, exactly how these polymers interact with surfaces is relatively unknown. One specific topic which is thought to be very important to flocculation is an adsorbed polymer's conformation. Substantial amounts of previous work, mainly using simulations, have been performed to elucidate the theory surrounding adsorbed polymer conformations. Yet, there is little experimental work which directly verifies current theory. In order to optimize the use of polymer flocculants in industrial applications, a better understanding of an adsorbed polymer's conformation on a surface beyond theoretical simulations is necessary. This work looks specifically at site blocking, which has a broad impact on flocculation, adsorption, and surface modification, and investigated its effects on the resulting adsorbed polymer conformation. Experimental methods which would allow direct determination of adsorbed polymer conformational details and be comparable with previous experimental results were first determined or developed. Characterization of an adsorbed polymer's conformation was then evaluated using dynamic light scattering, a currently accepted experimental technique to examine this. This commonly used technique was performed to allow the comparison of this works results with past literature. Next, a new technique using atomic force microscopy was developed, building on previous experimental techniques, to allow the direct determination of an adsorbed polymer's loop lengths. This method also was able to quantify changes in the length of adsorbed polymer tails. Finally, mesoscopic simulation was attempted using dissipative particle dynamics. In order to determine more information about an adsorbed polymer's conformation, three different environmental factors were analyzed: an adsorbed polymer on a surface in water, an adsorbed polymer on a surface in aqueous solutions of varying ionic strength, and an adsorbed polymer on a surface functionalized with site blocking additives. This work investigated these scenarios using a low charge density high molecular weight cationic polyacrylamide. Three different substrates, for polymer adsorption were analyzed: mica, anionic latex, and glass. It was determined that, similar to previous studies, the adsorbed polymer layer thickness in water is relatively small even for high molecular weight polymers, on the order of tens of nanometers. The loop length distribution of a single polymer, experimentally verified for the first time, revealed a broad span of loop lengths as high as 1.5 microns. However, the bulk of the distribution was found between 40 and 260 nanometers. For the first time, previous theoretical predictions regarding the salt effect on adsorbed polymer conformation were confirmed experimentally. It was determined that the adsorbed polymer layer thickness expanded with increasing ionic strength of the solvent. Using atomic force microscopy, it was determined that the adsorbed polymer loop lengths and tail lengths increased with increasing ionic strength, supporting the results found using dynamic light scattering. The effect of the addition of site blocking additives on a single polymer's conformation was investigated for the first time. It was determined that the addition of site blocking additives caused strikingly similar results as the addition of salt to the medium. The changes in an adsorbed polymer's loop lengths was found to be inconsistent and minimal. However, the changes in an adsorbed polymer's free tail length was found to increase with increasing site blocking additive levels. These results were obtained using either PDADMAC or cationic nanosilica as site blocking additives.

Diss. (sammanfattning) Stockholm : Karol. inst., 2006. / Härtill 5 uppsatser.

Submitted by Milena Rubi (milenarubi@ufscar.br) on 2017-08-16T14:34:16Z No. of bitstreams: 1 ZANCHETTA_Bianca_2017.pdf: 6817373 bytes, checksum: 19faa9d0aa5279e71d08211f9d262c35 (MD5) / Approved for entry into archive by Milena Rubi (milenarubi@ufscar.br) on 2017-08-16T14:34:26Z (GMT) No. of bitstreams: 1 ZANCHETTA_Bianca_2017.pdf: 6817373 bytes, checksum: 19faa9d0aa5279e71d08211f9d262c35 (MD5) / Approved for entry into archive by Milena Rubi (milenarubi@ufscar.br) on 2017-08-16T14:34:35Z (GMT) No. of bitstreams: 1 ZANCHETTA_Bianca_2017.pdf: 6817373 bytes, checksum: 19faa9d0aa5279e71d08211f9d262c35 (MD5) / Made available in DSpace on 2017-08-16T14:34:44Z (GMT). No. of bitstreams: 1 ZANCHETTA_Bianca_2017.pdf: 6817373 bytes, checksum: 19faa9d0aa5279e71d08211f9d262c35 (MD5) Previous issue date: 2017-04-27 / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) / Aluminum sheets are produced by rolling followed by annealing. However when submitted to deep drawing earing appears, caused by the plastic anisotropy resulting from the production process. After annealing the main texture is cube {001} , that is recognized as being the cause of this heterogeneity during deep drawing. The literature shows that when shear stress is applied in the deformation process, it leads to texture changes. In this study asymmetric rolling (AR) was used as a technique to produce shear. The shear stress is introduced by the different velocities between the upper and bottom rolls and in this study this was achieved by using roll radius relations (r1/r2) of 1,5 and 2. Rolling reductions of 50% in thickness were applied to aluminum AA1050 sheets. The conventional rolling (CR) was compared to the asymmetric rolling (AR), at two different reduction rates: 5% and 10%. The crystallographic textures were obtained by xray diffraction. Finite element analysis, using the DEFORM software, was used to analyze the effective strain distribution throughout the thickness as well as its components: normal strain, shear strain and rigid body rotation. The samples were annealed in a furnace with 350°C for 05, 10, 15, 20 and 60 minutes. The microstructure was characterized by optical microscopy, electron back scatter diffraction and x-ray diffraction. The plastic anisotropy (Lankford Parameter) was measured by tensile experiments at three different sheet directions and by the Erichsen test. The deformed samples’ microstructure was analyzed at the surface near to the upper roll and at half of the thickness. For the CR the main components were brass (Bs) {011} , Goss (Gs) {011} and copper (Cu) {112} , with 8.8 intensity at the central layer, and 4.5 at the surface. For AR samples the was more random at the surface of the samples with 5% of reduction per pass, added to a component of rotation in the normal direction, what resulted in cube and rotated cube textures or near to these orientations, generating a type of fiber {100}//ND. The maximum intensities for the (r1/r2) of 1,5 and 2 were 3 and 4, respectively. For the samples with 10% of reduction per pass the rolled texture was still presented, with a more intense rotation in the transversal direction related to the rolling direction and shear texture components {100}//ND and . The maximum intensities were 3 and 3.5 , for the (r1/r2) of 1,5 and 2, respectively. In the center layer of the samples with 5% of reduction per pass for (r1/r2) of 1,5 and 2 showed a intensity of 5.26 and 6.56, respectively and the strongest shear texture was rotated Goss (C). (011)[0-1- 1] The samples with 10% reduction per pass showed the greatest reduction of intensity with 3.05 and 3.63, for the (r1/r2) of 1,5 and 2 respectively, and the highest intensity was related to rotate the Goss (011)[0-1-1] component. In the pole figures rotations around the transversal direction (TD) and the normal direction (ND) were observed. Using the finite element analysis the rotation around the TD and ND were quantified and its variation across the thickness were analyzed. The rigid body rotation is superposed to shear , which leads to the observed texture gradients. The rotation around TD is imposed by the velocity difference between top and bottom roll, whereas the ND rotation is imposed by the experimental configuration, which permit variation of the sample alignment at the roll mill entrance. This was stronger for the 5% reduction rate and more concentrated at the samples surface. After 05 minutes the annealed samples were already recrystallized , after 60 minutes the grain average size was 30µm, and hardness 21HV. The annealed texture for the CR sample showed the greatest concentration off Cube texture {001} and intensity of 8.08 times the random. For the AR samples with 5% reduction per pass the intensities for the (r1/r2) of 1,5 and 2 was 5.88 and 6.56, respectively, and for the 10% reduction per pass 2.96 and 2.85, respectively. The AR decreases the annealed texture. In the samples of 5% reduction per pass the most intense shear texture was rotated Goss, the 10% reduction per pass did not have a predominant component. The Lankford parameters showed less anisotropy for the annealed samples with 10% reduction per pass. Based on the values of anisotropy and hardening exponent for each sample, the Limiting Rate of Drawing was calculated. The AR got a superior values than the CR ones, indicating an improvement of the drawability. / Chapas de Alumínio são comumente produzidas por laminação seguida de recozimento. Entretanto, ao serem submetidas à estampagem profunda apresentam problemas de orelhamento, devido à anisotropia plástica. Durante o recozimento a textura predominante é a cubo {001} , esta textura é reconhecida como sendo a causadora da má estampabilidade. A literatura indica que é possível alterar a textura final aplicando cisalhamento durante o processamento do material, neste trabalho aplicamos a Laminação Assimétrica (LA) como forma de produzir cisalhamento sobre a chapa. Utilizando o alumínio AA1050 até atingir um total de 50% de redução em espessura, com relações de assimetria (LA) de (r1/r2) de 1,5 e 2 com 5% e 10% de redução por passe e Laminação Convencional (LC) com taxa de 10% de redução por passe. A deformação experimental foi comparada à simulação de elementos finitos utilizando o software DEFORM, e a distribuição de deformação equivalente foi analisada ao longo da espessura da chapa. As amostras passaram por recozimento em forno tipo MUFLA, a 350°C por 05, 10, 15, 20 e 60 minutos. As amostras deformadas foram caracterizadas por microscopia óptica e sua textura cristalográfica foi obtida por difração de raios-x. As amostras recozidas passaram por caracterização microestrutural por microscopia óptica, difração de elétrons retroespalhados (EBSD) e difração de raios-x. A caracterização mecânica foi feita por ensaios de dureza, de tração e pelo ensaio de embutimento Erichsen. A microestrutura das amostras deformadas foi analisada próxima a superfície do rolo superior e no plano central a espessura. Para a LC foram encontradas concentrações maiores de Bs {011} , Gs {011} , Cu {112} , com intensidade máxima de 8,8 para o centro da chapa e de 4,5 na superfície. Para as amostras LA houve uma maior aleatoriedade das texturas tanto na superfície quanto no plano central. As amostras com 5% de redução por passe apresentaram as melhores reduções de intensidades máximas, somada a uma componente de rotação na direção normal (DN) da chapa, as intensidades máximas para (r1/r2) 1,5 e 2 foram de 3 e 4 respectivamente. Nas amostras de 10% de redução por passe ainda estavam presentes as componentes de laminação com uma rotação mais acentuada ao redor da direção transversal (DT) a direção de laminação as intensidades máximas foram de 3 e 3,5 para (r1/r2) 1,5 e 2 respectivamente. No centro da chapa as amostras de 5% de redução por passe para (r1/r2) 1,5 e 2 apresentam intensidades de 5,26 e 6,56 respectivamente e a textura de cisalhamento mais forte foi a Goss rodado (011) [0 1 1 ] (C). Já as amostras de 10% de redução apresentam as maiores reduções de intensidade com 3,05 e 3,63, para (r1/r2) 1,5 e 2 respectivamente, e uma proporção maior de intensidade Goss rodado (C). A simulação numérica foi utilizada para quantificar as rotações de corpo rígido impostas pela deformação, indicadas nas figuras de pólo pelas rotações ao redor da DN e da DT. Quanto às rotações ao redor da DT, para as reduções de 5% o cisalhamento se concentra na superfície e a rotação de corpo rígido é relativamente mais intensa no centro da amostra; nas reduções de 10% uma contribuição mais intensa tanto da rotação quanto do cisalhamento foi obtida. Quanto à rotação ao redor de DN ela foi mais intensa na superfície da chapa e para a redução de 5%. Após 05 minutos de tratamento as amostras já se encontravam recozidas atingindo um tamanho de grão médio de cerca de 30µm, e dureza em torno de 21HV. A textura de recozimento da amostra LC apresentou maiores concentrações das texturas cubo {001} e intensidade de 8,08. Para a LA com 5% de redução por passe as intensidades são máximas para r1/r2 1,5 e 2 foram 5,88 e 6,56, respectivamente, já para as com 10% de redução por passe, 2,96 e 2,85, respectivamente, apresentando a maior redução de concentração de texturas, assim como no material deformado. A LA promoveu, portanto a redução da intensidade de textura de recozimento Nas amostras de 5% de redução por passe a textura de cisalhamento mais intensa foi a Goss rodado, já para as amostras de 10% não houve uma componente predominante. O ensaio de tração nas três direções apresentou uma menor anisotropia para as amostras recozidas com 10% de redução por passe. Baseado nos valores de anisotropia e encruamento para cada amostra foi calculado a taxa de limite de embutimento, na qual as amostras LA obtiveram um valor superior a LC, indicando possuírem um melhor comportamento ao ensaio.

How proteins undergo conformational changes to bind a ligand is one of the most fundamental questions of protein biology. MD simulations provide a useful computational tool for studying the theoretical movements of protein in solution on nanosecond timescales. The results of these simulations can be used to guide experimental design. By correlating the theoretical models with the results of experimental studies, we can obtain a significant amount of information about protein dynamics. This study represents the application of both computational and traditional experimental techniques to study protein dynamics in HIV-1 protease. The results provide a novel mechanism for the conformational changes in proteins and address the role of residues outside the active site in protein dynamics. Additionally, these results are applied to the complex role of non-active site mutations in the development of drug resistance. Chapter II examines an invariant Thr80 at the apex of the P1 loop of HIV-1, HIV-2, and simian immunodeficiency virus protease. Sequence variability associated with human immunodeficiency virus type 1 (HIV-1) is useful for inferring structural and/or functional constraints at specific residues within the viral protease. Positions that are invariant even in the presence of drug selection define critically important residues for protease function. Three protease variants (T80V, T80N, and T80S) were examined for changes in structure, dynamics, enzymatic activity, affinity for protease inhibitors, and viral infectivity. While all three variants were structurally similar to the wild type, only T80S was functionally similar. T80V significantly decreased the ability of the enzyme to cleave a peptide substrate but maintained infectivity, while T80N abolished both activity and viral infectivity. Additionally, T80N decreased the conformational flexibility of the flap region, as observed by simulations of molecular dynamics. Taken together, these data indicate that HIV-1 protease functions best when residue 80 is a small polar residue and that mutations to other amino acids significantly impair enzyme function, possibly by affecting the flexibility of the flap domain. Chapter III focuses on residues within the hydrophobic core of each monomer in HIV-1 protease. Many hydrophobic residues located in the core of this dimeric enzyme frequently mutate in patients undergoing protease inhibitor therapy. The mechanism by which these mutations aid the development of drug resistance is not well understood. Using MD simulations, this study suggests that the hydrophobic residues outside the active site facilitate the conformational change that occurs in HIV-1 protease upon binding substrates and inhibitors. In these simulations, the core of each monomer significantly rearranges to assist in the expansion of the active site as hydrophobic core residues slide by each other, exchanging one hydrophobic contact for another. Such hydrophobic sliding may represent a general mechanism by which proteins undergo conformational changes. Mutation of these hydrophobic core residues would alter the packing of the hydrophobic core. Thus, these residues could facilitate drug resistance in HIV-1 protease by altering dynamic properties of HIV-1 protease preferentially affecting the relative affinity for inhibitors versus substrates. Chapter IV concentrates on a residue in the flap region, Ile54, which is significantly correlated with the development of drug resistance. A series of patient sequences containing the mutation I54A were evaluated for the most frequently occurring co-mutations. I54A was found to occur with mutations that were previously correlated with I54V mutations, including L10I, G48V, and V82A. Based on the results of this evaluation, the binding properties of five variant proteases were investigated: MDI54V, MDRI54A, I54V, I54A, and G48V. MDRI54V and MDRI54Aeach contained the mutations L10I, G48V, and V82A, and either I54V or I54A, respectively. The other variants contained only the mutation indicated. Mutations at Ile54 were able to significantly impact the thermodynamics of binding to saquinavir, amprenavir, and the recently approved darunavir. The magnitude of this impact depended on the presence or absence of other drug resistance mutations, including another mutation in the flap region, G48V. Therefore, while residues 48 and 54 are not in contact with each other, mutations at both sites had a cooperative effect that varies between inhibitors. The results demonstrate that residues outside the active site of HIV-1 protease are clearly important to enzyme function, possibly through their role in the dynamic properties of protease. Mutations outside the active site of protease that are known to cause drug resistance could alter the conformational flexibility of protease. While the role of protein dynamics in molecular recognition is still not fully understood, the results of this study indicate that altering the dynamic properties of a protein affects its ability to recognize ligands. Therefore, to design better inhibitors we will have to develop a more thorough understanding of protein dynamics.

A cada dia convive-se com novas tecnologias da informação. As novas gerações estão sendo chamadas de “nativos digitais”, ou seja, nascem envolvidas no mundo informatizado. As distâncias estão tornando-se cada vez mais curtas e o mundo cada vez mais globalizado. O uso das novas tecnologias da informação e comunicação (NTIC´s) é um desafio para a humanidade quando o foco é a educação. Este trabalho representa a tentativa de submeter as NTIC´s no ensino superior como forma de flexibilizar a aprendizagem para cursos das áreas científicotecnológicas. Cada vez mais percebe-se a evasão nos cursos de engenharia, principalmente devido às disciplinas de exatas. Esta tese apresenta o desenvolvimento de uma plataforma tecnológica para dar suporte ao ensino presencial através de um ambiente de aprendizado virtual 3D. Este ambiente, baseado em software gratuito, simula a realidade de uma sala de aula e pode ser uma nova fronteira para o aluno do século XXI. O conceito de imersão é aplicado. Além disto, integrado a este ambiente virtual 3D, tem-se acoplado um experimento remoto que permite ao acadêmico realizar as atividades práticas do módulo de elasticidade envolvendo conceitos fundamentais da conformação mecânica. Com a realização da tese um laboratório de experimentação remota foi montado, diversos recursos tecnológicos utilizados como: servidor Linux, redes de computadores integradas, internet, microservidores (MSW), interfaces eletrônicas, motor de passo, software como OpenSimulador, SLOODLE e MOODLE. Para consolidar o trabalho, uma proposta de avaliação foi aplicada correlacionando as habilidades cognitivas dos acadêmicos (questionário VARK), questionário de avaliação da satisfação do estudante (QASE) e o histórico escolar de cada acadêmico quando eles foram envolvidos nas aulas virtuais e experimentação remota. / Everyday we are living with new information of technology. The new generation are being called “digital natives”, this means that they were born embedded a high tech world. The distances each day shorter and world each day more “globalized”. The use of New Information and Communication Technology (ICT´s) is a challenge to the humanity when the goal is education. This paper represents a try to submit the ICT´s in the university studies as a way to flexible the learning to scientific and technologic areas. Once more we are living with the evasion in engineering courses, mainly because the math subjects. This thesis shows the developing of a technologic framework to support the classroom learning through 3D virtual learning environment. This environment based in a free software, simulates the reality of a classroom and can be the new frontier XXI century student. The concept of immersion is applied. Beyond this, integrated in this 3D virtual environment, we have coupled a remote experiment that allows the student perform the practical activities of elasticity module involving fundamental concepts of mechanical conformation. To the accomplishment of this thesis a remote experimentation lab was build and many technologies resources was used, such as: linux server, integrated compute network, microservers (MSW), electronic interfaces, step motors, software like opensimulator, sloodle and moodle. To consolidate the work, proposal evaluation was applied correlating the cognitive abilities of the students (VARK questionnaire), questionnaire for assessing student satisfaction and the student score when they were involved in virtual class and remote experimentation.

Este trabalho procura avaliar o retorno elástico em aços avançados de alta resistência utilizados em processo de dobramento. Para isso, foram usadas chapas de aço bifásico DP 600 e DP 800, ambas revestidas. Foram empregados dois métodos de medição a fim de abordar e avaliar o retorno elástico. O primeiro método abordado foi à conformação de tiras em U e o segundo método foi à realização do ensaio Dobramento Sob Tensão, aos quais possibilitaram a coleta de dados para aplicação em cálculo de coeficiente de atrito no processo de dobramento. Em ambas as avaliações foram utilizadas duas diferentes condições de lubrificação para o processo de dobramento, visando variar a condição de atrito no processo. A primeira foi à aplicação de um lubrificante em forma de pasta, de nome comercial Clarus Desmoldax DCP 35 e a segunda foi à aplicação em forma líquida, denominado Clarus Desmoldax DCP 35X. Para analisar o retorno elástico, foram utilizadas como critério de avaliação as medições de abertura da parede da tira conformada, permitindo desta forma considerar o atrito por intermédio da variação do tipo lubrificante. As análises realizadas nos corpos de prova conformados em formato U evidenciaram um retorno elástico menor para as amostras do aço DP 600, se comparadas com as amostras do aço DP 800. Não existiu relevância na variação dos lubrificantes quanto ao retorno elástico nas amostras de um mesmo tipo de aço. As análises realizadas nos corpos de prova submetidos ao ensaio de dobramento sob tensão, também evidenciaram um retorno elástico menor para as amostras do aço DP 600 se comparadas com as amostras do aço DP 800. Comparando as amostras com base nos dados coletados e aplicados ao cálculo de coeficiente de atrito, percebeu-se que as amostras que tiveram um retorno elástico menor, também possuíam coeficientes de atrito menor, constatando assim que quanto menor o coeficiente de atrito, menor é o retorno elástico. / This piece of work seeks to evaluate the springback effect on advanced high strength steel used in the bending process. For this, biphasic steel plates DP 600 and DP 800, both coated, were used. Two methods of measurement were used to approach and asses the springback effect. The first method approached was the conformation of strips in U and the second method was the preformance of the Bending Under Tension test, which enabled the data collect for the application in calculation of the friction coefficient in the bending process. In both assessments two different lubricant conditions for the bending process were used with the aim of varying the condition of friction in the process. The first one was the application of a paste lubricant, with the brand name Clarus Desmoldax DCP 35 and the second one was the application of a liquid lubricant, called Clarus Desmoldax DCP 35X. To analyze the springback effect the measurements of the opening of the wall of the conformed strip were used, thus allowing to consider the friction through the variation of the type of lubricant. The assessments carried out in the specimens in U shape showed a smaller springback effect for the steel samples DP 600 in comparison with the DP 800 ones. There was no relevance in the range of lubricants as the springback effect in the samples of the same type of steel. The analyzes carried out in the specimens subjected to bending under pressure test also showed a smaller springback effect for the steel samples DP 600 compared with the DP 800 ones. Comparing the samples based on the data collected and applied to the calculation of the friction coefficient, it was noticed that the samples that had a smaller springback effect also had lower friction coefficients, therefore verifying that the lower the friction coefficient is, the lower the springback effect.

Rotavirus is responsible for the death of many children annually, and current vaccines have lower efficiency in developing countries. A reverse translated consensus gene sequence of the rotavirus VP6 cloned into a pET-28a(+) plasmid was used to transform BL21 and KRX Escherichia coli cells. Optimal expression of soluble protein was induced in KRX cells by adding 0.05% L-rhamnose and 0.0001 M IPTG, with an incubation temperature of 25ºC for 6 h. VP6 was purified by combining anion exchange chromatography followed by affinity chromatography. Far-UV circular dichroism and intrinsic fluorescence were used as probes to assess the native structure of VP6 and structural in the presence of a denaturant, high sodium chloride concentrations and varying temperatures. The 0.2 M sodium chloride had an impact on the VP6’s tertiary structure and also influenced the proteins conformational changes as detected during thermal unfolding to 90ºC. Although treatment with 3 M urea showed tertiary structural changes no secondary structural loss occurred due to the presence of a denaturant. / Life Sciences / M. Sc. (Life Sciences)

xv, 177 p. : ill. (some col.) A print copy of this thesis is available through the UO Libraries. Search the library catalog for the location and call number. / When two or more fluorescent chromophores are closely spaced in a macromolecular complex, dipolar coupling leads to delocalization of the excited states, forming excitons. The relative transition frequencies and magnitudes are sensitive to conformation, which can then be studied with optical spectroscopy. Non-invasive fluorescence spectroscopy techniques are useful tools for the study of dilute concentrations of such naturally fluorescent or fluorescently labeled biological systems. This dissertation presents two phase-selective fluorescence spectroscopy techniques for the study of dynamical processes in bio-molecular systems across a wide range of timescales. Polarization-modulated Fourier imaging correlation spectroscopy (PM-FICS) is a novel phase-selective fluorescence spectroscopy for simultaneous study of translational and conformational dynamics. We utilize modulated polarization and intensity gratings with phase-sensitive signal collection to monitor the collective fluctuations of an ensemble of fluorescent molecules. The translational and conformational dynamics can be separated and analyzed separately to generate 2D spectral densities and joint probability distributions. We present results of PM-FICS experiments on DsRed, a fluorescent protein complex. Detailed information on thermally driven dipole-coupled optical switching pathways is found, for which we propose a conformation transition mechanism. 2D phase-modulation electronic coherence spectroscopy is a third-order nonlinear spectroscopy that uses collinear pulse geometry and acousto-optic phase modulation to isolate rephasing and nonrephasing contributions to the collected fluorescence signal. We generate 2D spectra, from which we are able to determine relative dipole orientations, and therefore structural conformation, in addition to detailed coupling information. We present results of experiments on magnesium tetraphenylporphyrin dimers in lipid vesicle bilayers. The 2D spectra show clearly resolved diagonal and off-diagonal features, evidence of exciton behavior. The amplitudes of the distinct spectral features change on a femtosecond timescale, revealing information on time-dependent energy transfer dynamics. This dissertation includes co-authored and previously published material. / Committee in charge: Hailin Wang, Chairperson, Physics; Andrew Marcus, Advisor, Chemistry; Stephen Gregory, Member, Physics; Michael Raymer, Member, Physics; Marina Guenza, Outside Member, Chemistry

A cada dia convive-se com novas tecnologias da informação. As novas gerações estão sendo chamadas de “nativos digitais”, ou seja, nascem envolvidas no mundo informatizado. As distâncias estão tornando-se cada vez mais curtas e o mundo cada vez mais globalizado. O uso das novas tecnologias da informação e comunicação (NTIC´s) é um desafio para a humanidade quando o foco é a educação. Este trabalho representa a tentativa de submeter as NTIC´s no ensino superior como forma de flexibilizar a aprendizagem para cursos das áreas científicotecnológicas. Cada vez mais percebe-se a evasão nos cursos de engenharia, principalmente devido às disciplinas de exatas. Esta tese apresenta o desenvolvimento de uma plataforma tecnológica para dar suporte ao ensino presencial através de um ambiente de aprendizado virtual 3D. Este ambiente, baseado em software gratuito, simula a realidade de uma sala de aula e pode ser uma nova fronteira para o aluno do século XXI. O conceito de imersão é aplicado. Além disto, integrado a este ambiente virtual 3D, tem-se acoplado um experimento remoto que permite ao acadêmico realizar as atividades práticas do módulo de elasticidade envolvendo conceitos fundamentais da conformação mecânica. Com a realização da tese um laboratório de experimentação remota foi montado, diversos recursos tecnológicos utilizados como: servidor Linux, redes de computadores integradas, internet, microservidores (MSW), interfaces eletrônicas, motor de passo, software como OpenSimulador, SLOODLE e MOODLE. Para consolidar o trabalho, uma proposta de avaliação foi aplicada correlacionando as habilidades cognitivas dos acadêmicos (questionário VARK), questionário de avaliação da satisfação do estudante (QASE) e o histórico escolar de cada acadêmico quando eles foram envolvidos nas aulas virtuais e experimentação remota. / Everyday we are living with new information of technology. The new generation are being called “digital natives”, this means that they were born embedded a high tech world. The distances each day shorter and world each day more “globalized”. The use of New Information and Communication Technology (ICT´s) is a challenge to the humanity when the goal is education. This paper represents a try to submit the ICT´s in the university studies as a way to flexible the learning to scientific and technologic areas. Once more we are living with the evasion in engineering courses, mainly because the math subjects. This thesis shows the developing of a technologic framework to support the classroom learning through 3D virtual learning environment. This environment based in a free software, simulates the reality of a classroom and can be the new frontier XXI century student. The concept of immersion is applied. Beyond this, integrated in this 3D virtual environment, we have coupled a remote experiment that allows the student perform the practical activities of elasticity module involving fundamental concepts of mechanical conformation. To the accomplishment of this thesis a remote experimentation lab was build and many technologies resources was used, such as: linux server, integrated compute network, microservers (MSW), electronic interfaces, step motors, software like opensimulator, sloodle and moodle. To consolidate the work, proposal evaluation was applied correlating the cognitive abilities of the students (VARK questionnaire), questionnaire for assessing student satisfaction and the student score when they were involved in virtual class and remote experimentation.

Les structures cristallographiques de macromolécules comme les protéines, obtenues par la biologie structurale sont des modèles statiques. Or, c'est la flexibilité et la dynamique de ces macromolécules qui sont généralement responsables de leurs fonctions. La simulation permet d'explorer cette flexibilité lors de différents phénomènes qui ont lieu dans ces systèmes : une réaction chimique, des interactions avec une petite molécule… Simuler de tels phénomènes est un défi car la dynamique moléculaire classique ne permet pas de les observer. Des algorithmes permettent d'accélérer l'échantillonnage des dynamiques pour lever cette limitation et de calculer les barrières d'activation pour de tels phénomènes. Simultanément, le choix du niveau de calcul est crucial car il faut concilier la taille importante des systèmes, la nature des interactions et les phénomènes électroniques impliqués. Dans ce travail, différentes méthodes, dont principalement la métadynamique soit au niveau classique ou quantique, ou encore en combinant les deux niveaux quantique/classique, seront utilisées pour modéliser quatre processus complexes : des changements de conformations d'une protéine, des interactions entre métalloprotéine et inhibiteur, des réactions en solution et dans une enzyme. / Crystallographic structures of macromolecules, such as proteins, obtained by structural biology are static models. However, flexibility and dynamics of macromolecules are generally responsible for their functions. Modeling allows us to explore this flexibility in different phenomena that take place in these systems: a chemical reaction, interaction with a small molecule... Modeling such phenomena is a challenge because they cannot be observed by classical molecular dynamics. Algorithms can accelerate sampling of dynamics to simulate these events and calculate their activation barriers. Simultaneously, the choice of the level of calculation is crucial because it must merge with the size of the systems, the nature of interactions and the electronic phenomena involved.In this thesis, some methods, mainly metadynamics at classical level, quantum or the hybrid quantum/classical level, will be used to model four complex processes: conformational changes of proteins, metalloprotein/inhibitor interactions, reactivity in solution and enzymatic reactivity.