Undoubtedly, water is the most abundant and important molecular liquid and is likely the most necessary for life on Earth. The pursuit of understanding water's properties and behaviors has placed it in a unique scientific and even mythical position throughout human history. It is no surprise that much scientific research today centers around this molecule and its interactions with others. The interfacial region between liquid water solutions and other phases is still poorly understood, and only recently have experiments developed to where we can probe this unique environment. Water surfaces exist throughout the Earth's atmosphere and oceans but also make up many of the microscopic interfaces necessary for metabolic processes within living cells. Yet, the influence of water surfaces on the chemistry that drives life and terrestrial processes is still largely unknown, and many research efforts today are attempting to gain insight to this critically important frontier. This dissertation documents several unique computational studies aimed to further our understanding of the complex interactions within a water system and between water and simple, common solutes. Reported herein are the results of molecular dynamics (MD) simulations and computational analysis of interfacial aqueous systems of small hydrated acids, ionic aqueous salt solutions interfaced with a liquid oil, and gas molecules adsorbing onto water surfaces. The composition of the systems chosen for the studies reported in this dissertation reflect environmentally relevant interfaces and also complement recent experimental efforts by the Richmond laboratory. Classical and quantum ab initio MD techniques were used for simulation of the molecular systems and the subsequent analyses provided new information regarding molecular interactions, geometries, orientations, and surface behaviors of water and hydrated interfacial solute molecules. This dissertation includes both previously published and unpublished co-authored material.

<p>Aluminum is present throughout the environment and in many industrial processes and consumer goods. While very useful in everyday lives, it has no inherent biological functions in humans. High quantities in the human body can be toxic, resulting a range of skeletal, neurological, and hematopoietic effects. A system has been developed to analyze aluminum using the neutron activation analysis (NAA) technique in vivo. NAA was performed with a transportable neutron generator as a neutron source and a high purity germanium (HPGe) detector for spectroscopy. The neutron generator and HPGe detector were completely modelled in MCNP6. Measurements were carried out to evaluate the accuracy of the MCNP6 simulations and to determine the detection capabilities of the system for aluminum. Simulations were also conducted to determine the acceptability of radiation dose to subjects undergoing analysis. The detection limit for the system was evaluated using skeletal bone as a long-term aluminum biomarker. The detection limit was determined to be 3.41 x 10¹ μg of Al per g of dry bone for an irradiation time of six minutes. This detection level is below a point at which physiological effects have been observed in humans. A lower detection level was demonstrated to be possible with a longer irradiation time. The radiation absorbed dose was determined to be 7.30 mGy for an irradiation of six minutes. The system can therefore be utilized as a potential screening and monitoring tool for high skeletal burdens of aluminum that may lead to physiological effects.</p> <p>The simulation and calculation techniques developed herein were applied to a set of human subject data that were acquired for a purpose other than evaluating aluminum. The human subject data included both bone Al from NAA and fingernail Al from mass spectrometry measurements. No significant aluminum signals were observed when assessing the in vivo NAA spectra data. Through simulation and calculation, it was demonstrated that the NAA experimental parameters resulted in an elevated detection limit for aluminum that is above Al skeletal loads observed in healthy individuals. The elevated detection limit prevented the in vivo detection of aluminum in a healthy population, thus confirming the NAA results. </p>

Title: Self-assembly of polyelectrolytes in aqueous solutions (dissipative particle dynamics) Author: Karel Šindelka Department: Faculty of science, Charles University in Prague Supervisor: Doc. Ing. Zuzana Limpouchová, CSc. Consultant: Doc. Ing. Martin Lísal, DSc. Abstract In the thesis, the coarse-grained dissipative particle dynamics (DPD) is used for the study of self-assembly of equimolar mixtures of oppositely charged symmetric block PEs with one PE block (either strong polycation or strong polyanion) and one readily water-soluble neutral block in aqueous media. In the first part of the diploma thesis, the principles of DPD simulations are described and the correct implementation of electrostatic interactions in the DPD method is demonstrated on the example of counterion (Manning) condensation. In the second main part, the effect of the blocks solubility, incompatibility and the interplay of different forces on electrostatic assembly is investigated. The cor- responding neutral systems are also simulated for comparison. The study shows that the hydrophobicity of the PE backbone and the incompatibility of blocks sig- nificantly affects the electrsotatic co-assembly. The presence of opposite charges on different chains promotes the aggregation process and the aggregation number in- creases in comparison...

This PhD thesis is devoted to the study of the conformational behavior of branched polymers in confined volumes. This behavior depends not only on polymer architecture and composition but also on steric confinement and on interaction of polymer segments with the confining wall. Better understanding of complex entropy-to-enthalpy interplay can elucidate the mechanism of the chromatographic separation at the microscopic level. An unambiguous size-exclusion chromatography (SEC) analysis of mixtures containing different polymer architectures is difficult because the sizes of polymer coils, which determine the separation, depend not only on molar mass but also on the polymer architecture. Modern chromatographic methods combine the SEC with the interaction chromatography (IC). They exploit the fact that polymer interactions with pore walls, which are the prerequisite for efficient IC separation, depend strongly on polymer architecture. The knowledge of the conformational behavior of linear and branched polymers in confined volumes and of their interactions with confining medium enables to find optimum conditions either for enhancing or for suppressing the role of individual factors that influence the separation. We have shown that the complex entropy-to-enthalpy interplay in polymer solutions in confined...

Present work is focused on the numerical study of evaporation of sessile liquid droplets on top of smooth solid substrates. The process of evaporation of a sessile liquid droplet has lots of different applications both in industry and research area. This process has been under study for many years, and still it is an actual problem, solution of which can give answers on some fundamental and practical questions. Instantaneous distribution of mass and heat fluxes inside and outside of an evaporating sessile droplet is studied in this research using computer simulations. The deduced dependences of instantaneous fluxes are applied for self-consistent calculations of time evolution of evaporating sessile droplets. The proposed theory of evaporating sessile droplets of liquid has been validated against available experimental data, and has shown a good agreement. Evaporation of surfactant solution droplets is studied experimentally. The theory, proposed for two stages of evaporation, fits experimental data well. An additional evaporation stage, specific for surfactant solutions, is observed and described. Mathematical modelling of this stage requires further research on surfactant adsorption and its influence on the value of receding contact angle. Numerical study of the evaporation of microdroplets is conducted in order to evaluate the significance of different evaporation mechanisms (diffusive and kinetic models of evaporation) and different physical phenomena (Kelvin s equation, latent heat of vaporization, thermal Marangoni convection, Stefan flow).

The evolution of materials at an atomistic level may have vital consequences for the properties of materials. Therefore, modelling long time scale behaviour of defects in a material is very important, particularly for those used in nuclear power plants. The materials used in nuclear power plants should have good mechanical properties to overcome the corrosive environment and high temperature. Examples of these materials are the austenitic stainless steel and the Ni-based alloys due to their high temperature properties. Molecular Dynamics (MD) and on the fly Kinetic Monte Carlo (otf-KMC) techniques have been used to model the radiation damage in austenitic stainless steel and the Ni-based alloys. This thesis represents the main findings obtained. Three potentials were implemented and used to study radiation damage in austenitic stainless steel. Structural properties such as the elastic constants for the point defects in the pure metals were first calculated. This was followed by calculating the formation energies and migration energies of vacancy and self interstitial defects in the pure metals. Different calculations were performed using each potential on the ternary alloy (Fe with 10 at.% Ni and 20 at.% Cr) and the binary alloy (Ni with 20 at.% Cr) . For example, the segregation in these alloys was investigated using Monte Carlo simulations and results obtained for both alloys at high temperature MD. Furthermore, the vacancy formation energies were calculated for both alloys using all the potentials. Radiation damage at Grain Boundaries (GBs) in fcc Ni and a Ni-Cr binary alloy has been studied using MD and otf-KMC techniques. From the results obtained, the mobility of interstitials were found to be higher than that of vacancies and tend to move quickly to the GB. Vacancies are found to migrate to the GB if they are near otherwise they tend to form clusters in the bulk. During the simulations, interesting mechanisms were observed for the point defects migration and recombinations. Large roughening at the GB was observed, especially in the alloy system and overall the total number of defects accumulated on the GB after multiple collision cascades were relatively small. The radiation in fcc Ni resulting from low energy collision cascades was also modelled using MD and otf-KMC techniques. This part of work aimed replicating the observations seen in experiment and trying to understand them. Recombinations between vacancies and interstitials were found to happen from large distances with low barriers. Most defects produced from low energy collision cascades were found to recombine or interstitials were found to form clusters. Modelling the evolution of the vacancies shows the possibility of producing Stacking Fault Tetrahedra (SFT) which were found to dissociate at 200°C.

A base evolucionaria da senescência é um problema biológico de longa data. Senescência, no sentido da deterioração progressiva de um organismo, distingue-se de envelhecimento, ou a mera passagem do tempo. Como, pelo menos em mamíferos, senescência e envelhecimento ocorrem simultaneamente, os termos são tomados erroneamente como sinônimos. A senescência parece explicada pelo desgaste do organismo, levando a um paradoxo frente aos mecanismos de seleção natural, pois, sendo a maquinaria biológica portadora de mecanismos de auto-reparo, esperáramos o aprimoramento destes, com gradual eliminação da deterioração associada ao envelhecimento. Historicamente, procurou-se resolver este paradoxo imaginando-se que a senescência conferisse uma vantagem adaptativa, mas este argumento, que requereria distinguir os indivíduos mais velhos, é circular. A partir de meados do século XX, três hipóteses prevaleceram. O acúmulo de mutações, proposto por Medawar (1951), considera que o decaimento gradual da força de seleção com a idade favorece o acúmulo de genes deletérios expressos em idades avançadas. O antagonismo pleiotrópico, proposto por Williams (1957), defende que genes ligados a características benéficas e deletérias poderiam ser, em certas condições, favoravelmente selecionados. Finalmente, a teoria da soma descartável, proposta por Kirkwood (1975), sugere que organismos são favoravelmente selecionados quando investem em Reprodução mesmo em detrimento da manutenção somática. A descrição dinâmica dos fenômenos envolvidos em cada hipótese e a contribuição relativa de cada uma é, ainda, objeto de debate. O presente trabalho visa ao desenvolvimento de modelos computacionais estocásticos que mimetizem as condição para cada uma delas. Iniciamos o desenvolvimento pela ordem histórica, testando o mecanismo proposto por Medawar, que é o objeto desta tese. A teoria do acúmulo de mutações encontrou críticos que sugerem que este mecanismo levaria os efeitos deletérios à sincronia em idades muito avançadas, tornando a senescência um fenômeno repentino e limitado a tais idades. Isto contrariaria a observação experimental, pois a senescência é um processo gradual e mesmo animais silvestres exibem fenômenos senescentes detectáveis precocemente. Para manter a modelagem compatível com o conhecimento atual sobre genética de populações, incluímos neste modelo os efeitos da seleção, da deriva genética e de diferentes taxas de mutação. Como previsto, em nossas simulações a moda das idades de manifestação dos genes deletérios se estabilizou apenas em idades muito avançadas, próximas ao término das distribuições etárias. Também como esperado, estas distribuições terminaram em idades mais precoces nos cenários de maior mortalidade extrínseca. No entanto, em todas as nossas simulações, houve distribuição mais ou menos larga das idades de manifestação em torno da moda. A distribuição alargou-se com o aumento da probabilidade de mutação, sugerindo que as idades de manifestação podem espalhar-se ao longo da vida, chegando, em alguns cenários, à manutenção de alelos com manifestação ao nascer. Isto é compatível com o modelo de alelos ineptos utilizado em genética populacional, em que diferentes variantes concorrem até atingirem um equilíbrio entre seleção, mutação e deriva genética. Considerando-se o critério demográfico para senescência, em que a mortalidade aumenta em função da idade, podemos dizer que as nossas simulações evoluíram populações senescentes. Embora nossos dados não contrariem as outras teorias da senescência, claramente mostram que a perda da força de seleção não é um mecanismo suficiente para a senescência. Especialmente com alelos de expressão tardia, as forças de deriva podem ser preponderantes e devem ser levadas em conta para explicar a evolução da senescência / The evolutionary basis of senescence is a long standing biological problem. Senescence, in the sense of progressive deterioration of an organism, is distinguished from aging, or the mere passage of time. Because, at least in mammals, aging and senescence occur simultaneously, the terms are wrongly taken as synonyms. Senescence seems explained by the wear of the organism, leading to a paradox facing the mechanisms of natural selection, because, being the biological machinery bearer of self-repair mechanisms, we would expect their improvement, with gradual elimination of the deterioration associated with aging. Historically, there were attempts to resolve this paradox by supposing that senescence confers an adaptive advantage, but this argument would require that older individuals were previously distinct from younger ones and is, therefore, circular. From mid-twentieth century, three hypotheses have prevailed. The mutation accumulation, proposed by Medawar (1951), proposes that the gradual decay of the force of selection with age favors the accumulation of deleterious genes expressed in advanced ages. The antagonistic pleiotropy, proposed by Williams (1957), argues that genes linked to benecial and deleterious traits could, under certain conditions, be favorably selected. Finally, the disposable soma theory, proposed by Kirkwood (1975), suggests that organisms are positively selected when they invest in reproduction even at the expense of somatic maintenance. The dynamic description of the phenomena involved in each mechanism and the relative contribution of each one is still debated. The present work aims to develop stochastic computer models that mimic the conditions for each. We started by historical order, testing the mechanism proposed by Medawar, which is the subject of this thesis. The theory of mutation accumulation found critics who suggest that this mechanism would cause deleterious eects to synchronize in very advanced ages, causing senescence to be a sudden phenomenon limited to these ages. This is a contradiction with the experimental observation, because senescence is a gradual process and even wild animals exhibit senescent phenomena detectable in young ages. To keep the model consistent with the current knowledge on population genetics, this model included the eects of selection, genetic drift and dierent mutation rates. As predicted, in our simulations the mode of the age of onset of deleterious genes stabilized only in very advanced ages, near the end of the age distribution. Also as expected, these distributions ended in earlier ages in scenarios of higher extrinsic mortality. However, in all our simulations, there was more or less wide distribution of ages of onset around the mode. The distribution is enlarged with increased probabilities of mutation, suggesting that the ages of onset may spread throughout life, including, in some scenarios, the maintenance of alleles with manifestation at birth. This is consistent with the innite alleles\' model used in population genetics, where dierent variants compete until achieving an equilibrium between selection, mutation and genetic drift. Considering the demographic criterion for senescence, in which mortality increases with age, we can say that our simulations evolved senescent populations. Although our data do not con ict with the other theories of senescence, they clearly show that the falling force of selection with age is not a sucient mechanism for senescence. Especially with alleles of late expression, the forces of genetic drift may be prominent and should be taken into account to explain the evolution of senescence

Computer simulations have become a great tool to assist the medical field. The present work is a study of a non-invasive patient-specific methodology to evaluate the hemodynamic importance of coronary stenosis using computer simulations. The severity of the lesion is evaluated by the Fractional Flow Reserve, calculated by the pressure gradient before and after the lesion. The geometry models are obtained from medical images of Computed Tomography Angiography exams, and the simulations considers the pulsatile flow and the blood as a non-Newtonian fluid. The governing equations of the blood flow are solved by using Finite Element Method applied to the numerical method called Incremental Pressure Correction Scheme, and with the aid of the libraries from the open-source software FEniCS. Computer simulations of three different patients are performed and the results are compared with the invasive FFR measurements. The methodology proposed shows to be feasible in the study and analysis of stenosed coronaries. / Simulações computacionais tornaram-se uma excelente ferramenta para auxiliar a área médica. O presente trabalho é um estudo de uma metodologia não invasiva para avaliar a importância hemodinâmica de artérias coronárias com estenose através do uso de simulações computacionais. A severidade da lesão da artéria é avaliada através do Fractional Flow Reserve, calculado pelo gradiente de pressão antes e depois da lesão. Os modelos geométricos computacionais foram obtidos a partir de imagens médicas de exames de Angiografia por Tomografia Computadorizada e as simulações consideram o fluxo pulsátil e as propriedades não-Newtonianas do sangue. As equações governantes do fluxo de sangue são resolvidas utilizando o Método dos Elementos Finitos aplicado ao método numérico chamado Incremental Pressure Correction Scheme, e com o uso de bibliotecas do programa em código aberto FEniCS. Foram realizados simulações de três pacientes e os resultados foram confrontados com as medidas invasivas do FFR. A metodologia proposta mostrou-se viável para o estudo e análise de coronárias com estenose.

Made available in DSpace on 2016-08-10T10:40:16Z (GMT). No. of bitstreams: 1 FABIO PEGORARO.pdf: 2667580 bytes, checksum: 6fc5c5ce22768636449f0666fff664c1 (MD5) Previous issue date: 2012-09-05 / This paper presents the results obtained with the application of computer simulation and theory of constraints to reduce the waiting time for urgent care at the Hospital Regional Gurupi (HRG). The simulation model focuses on the patients in a state of emergency and urgency. Patient in a state of emergency can not remain in the queue and should be treated immediately, as the patient in a state of emergency can stay up to 30 minutes in a queue. The methodology used is exploratory case study techniques supported by semi-structured interviews and questionnaires administered to managers and hospital doctors. The actual model (scenario 1) the hospital is simulated using PROMODEL® software. Two more scenarios are created following the process of continuous improvement of the theory of constraints and simulated using PROMODEL®. It is observed that through the application of computer simulation combined with the theory of constraints, the managers of the Emergency Room (ER) of HRG have adequate information to manage it in order to reduce the waiting time for urgent and emergency care. / Este trabalho apresenta os resultados obtidos com a aplicação da simulação computacionale teoria das restrições para reduzir o tempo de espera por atendimento de urgência no Hospital Regional de Gurupi (HRG). O modelo de simulação tem foco nos pacientes em estado de urgência e emergência. Paciente em estado de emergência não pode permanecer em fila de espera e deve ser atendido imediatamente, já o paciente em estado de urgência pode permanecer até 30 minutos em uma fila de espera. A metodologia usada é exploratória com estudo de caso apoiada em técnicas de entrevista semi-estruturada e questionários aplicados aos gestores e médicos do hospital. O modelo real (cenário 1) do hospital é simulado utilizando o software PROMODEL.® Mais dois cenários são criados seguindo o processo de melhoria contínua da teoria das restrições e simulados utilizando o software PROMODEL®. Observa-se que através da aplicação da simulação computacional aliada à teoria das restrições, os gestores do Pronto Socorro (PS) do HRG possuem informações adequadas para geri-lo de forma a reduzir o tempo de espera por atendimento de urgência e emergência.

Nesta tese estudamos o espectro de absorção da Merocianina de Brooker (MB) e três derivados em solventes com diferentes polaridades. O interesse no estudo desses sistemas se dá pela presença de algumas propriedades particulares das merocianinas, por exemplo, apresentam um grande deslocamento solvatocrômico devido à mudança na polaridade do meio. Nós apresentamos os resultados teóricos obtidos para o espectro de absorção das moléculas considerando diferentes estruturas para o estado fundamental: formas trans, cis, zwiteriônica (zw), protonada (MBH+) e dímero(MB2). O efeito do solvente foi considerado utilizando diferentes modelos de solvatação: (i) modelo contínuo polarizável (PCM), (ii) através de uma configuração eletrostática média do solvente (ASEC), (iii) incluindo algumas moléculas explícitas do solvente juntamente com um ambiente eletrostático gerado pelas demais moléculas do solvente. Como uma investigação adicional, apresentamos nossos resultados de medidas experimentais para o espectro de absorção da MB em vários solventes variando acidez e concentração. Vimos, através de cálculos quânticos, que as formas cis/trans apresentam a excitação eletrônica na mesma região, e que a deformação estrutural gerada pela forma zw provoca um deslocamento para o vermelho na excitação eletrônica. Os nossos resultados teóricos e experimentais mostram que a forma MBH+ apresenta um solvatocromismo pequeno, com deslocamento de 20 nm provocado pela mudança água-clorofórmio. Realizando medidas experimentais através da titulação espectroscópica nós obtivemos o pKa associado ao processo de desprotonação/protonação da MB em água e metanol. Em água obtivemos um valor de 8.7, em boa concordância com valores da literatura. Apresentamos um valor inédito do pKap da MB em metanol, 9.9. Conseguimos uma boa descrição teórica para a excitação eletrônica da MB em solventes com alta polaridade, na região entre 430-500 nm, utilizando o método quântico TD-DFT com funcionais B3LYP e CAM-B3LYP e conjunto de funções base 6-311+G**, porém a excitação em solventes de baixa polaridade, que ocorre na região entre 550-650 nm, não é corretamente descrita considerando a MB nos solventes. Nós vimos, através de estudos experimentais, que a sonda MB pode agregar em solventes de baixa polaridade. Os cáculos teóricos para dímeros em solução mostraram a existência de uma excitação eletrônica de baixa intensidade nesta região. Adicionalmente, os espectros experimentais em solventes de baixa polaridade mostraram 2 bandas, onde a segunda se assemelha com a banda observada para a forma MBH+. Para explicar essas 2 bandas experimentais para a MB, apresentamos uma proposta teórica onde ocorre uma transferência de prótons (H+) entre os monômeros do dímero formado, gerando uma estrutura desprotonada (MBH-) e uma protonada (MBH+). Cálculos teóricos para a forma MBH- mostram que essa forma apresenta uma excitação eletrônica de intensidade moderada na região entre 550-650 nm. Com essa hipótese nós conseguimos descrever, através de cálculos teóricos, o solvatocromismo anômalo observado experimentalmente para o espectro eletrônico de absorção da MB nas duas regiões de polaridade dos solventes: alta polaridade, sendo descrita pela forma MB, e baixa polaridade, descrita pela forma MBH-. / In this thesis we studied the absorption spectrum of merocyanine Brooker (MB) and three derivatives in solvents with different polarities.The interest in this system is given by the presence of some particular properties of this molecule, for example, it presents a large solvatochromic shift due to the change in the polarity of the medium. We present the results for the absorption spectrum of the molecules considering different structures to the ground state: forms trans, cis, zwitterionic (zw), protonated MBH+ and dimer (MB2). The solvent effect was treaty by different ways: (i) continuous model using the PCM polarizable, (ii) by an average electrostatic configuration of solvent, ASEC, (iii) including some explicit solvent molecules with an electrostatic environment generated by other solvent molecules. As an additional investigation, we present results of experimental measurements in the thesis. We have seen, through quantum calculations, that the forms cis/trans have the electronic excitation in the same region and the structural deformation generated in the zw form causes a red shift. Our theoretical and experimental results show that the MBH+ form has a small solvatochromism, with displacement of 20 nm caused by water-chloroform change. Performing spectroscopic titration we got the pKa associated with the process of deprotonation/protonation of MB in water and methanol. In water we obtained a value of 8.7, in good agreement with the values reported in the literature. We present a unpublished pKap for the MB in methanol, 9.9. We got a good theoretical description for electronic excitation of MB in solvents with high polarity, in the region between 430-500 nm, using a method quantum TD-DFT B3LYP and CAM-B3LYP functional whit basic functions set 6-311+G** but the excitation in low polarity solvents, which occurs in the region between 550-650 nm, is not properly described considering the MB form in the solvents. We have seen, through experimental studies that the MB probe can aggregate in low polarity solvents. Theoretical calculations for dimer in solution showed the existence of a low intensity electron excitation in this region. Additionally, the experimental spectra in low polarity solvents showed 2 bands, where in the second band is similar to the observed to MBH+ form. To explain these two experimental bands for MB, we present a theoretical proposal where there is a proton transfer (H+) between the monomers of the dimer, generating a deprotonated structure (MBH-) and a protonated (MBH+). Theoretical calculations for the MBH- show that this form presents an electronic excitation of moderate intensity in the region between 550-650 nm. With this assumption we can describe, through theoretical calculations, the anomalous solvatochromism for the electronic absorption spectrum of MB in the two polarity regions of solvents: high polarity is described by the MB form, and low polarity, described by the MBH- form.