Water is a fundamental part of life as we know it, and by that also a fundamental for biology, chemistry, and parts of physics. Understanding how water behaves and interacts is key in many fields of all these three branches of science. Numerical simulation using molecular dynamics can aid in building insight in the behavior and interactions of water. In this thesis molecular dynamics is used to simulate common rigid 3 point water models to see how well they replicate certain physical and chemical properties as functions of temperature. This is done with molecular dynamics program GROMACS which offers a complete set of tools to run simulations and analyze results. Everything has been automated to work with a python script and a file of input parameters. Most of the models follow the same trends and are valid within a limited temperature range. / Vatten är en av de fundamentala byggstenarna för liv, därmed är det även fundamentalt för biologi, kemi och delar av fysiken. Att förstå hur vatten beter sig och interagerar är en stor fråga inom dessa tre grenar av vetenskap. Med molekyldynamik går det att utföra numeriska simuleringar som kan användas som hjälpmedel för att bygga en djupare förståelse för riktigt vatten. I den här uppsatsen så har molekyldynamik använts till att simulera vanliga rigida 3 punkts parametiseringar av vatten för att se hur bra de kan replikera vissa egenskaper som funktioner av temperatur. Simuleringen är gjord med hjälp av molekyldynamik programet GROMACS som ger en fullständig uppsättning verktyg för att simulera och analysera molekylsystem. Alla simuleringar och analys är automatiserat med ett pythonprogram och en fil för parametrar. De allra flesta modeller följer liknande trender och är giltiga inom små temperaturintervall.

"The purpose of this study was to survey the cases of forty mentally retarded patients who have been presented by the Pre-parole Service to the Social Service Planning Staff of the Rosewood State Training School, Owings Mills, Maryland, from March through October 1959, in order to describe the differences--if any--on 18 selected items between the 28 retarded patients approved and the 12 disapproved for eventual return to the community. It was anticipated that such an analysis might more clearly define the term 'readiness for parole'"--Introduction. / Typescript. / "June, 1960." / "Submitted to the Graduate Council of Florida State University in partial fulfillment of the requirements for the degree of Master of Social Work." / Advisor: Merle M. Foeckler, Professor Directing Study. / Includes bibliographical references.

"The purpose of this study was to describe to a limited degree the characteristics of five patients of the Rosewood State Training School under consideration for discharge from the institution through the Community Adjustment Unit during December, 1958. It was believed that a case study of five patients would reveal some of the observable factors which may have influenced these five patients being ready for discharge. In addition, the five case illustrations descriptively present the function and procedures of one unit of the Social Services Department, Rosewood State Training School, Owings Mills, Maryland"--Introduction. / Typescript. / "June, 1959." / "Submitted to the Graduate Council of Florida State University in partial fulfillment of the requirements for the degree of Master of Social Work." / Advisor: Dorothy D. Hayes, Professor Directing Study. / Includes bibliographical references.

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Orientador: Marcos Roberto de Mattos Fontes / Resumo: Acidentes ofídicos são considerados um problema de saúde pública global, dada sua alta ocorrência de mortes, onde alguns casos resultam em sequelas irreparáveis, deixando o indivíduo desabilitado por toda a vida. Somente no Brasil, em média 20 mil mortes ao ano são registradas. Desta forma, alguns pesquisadores têm buscado estudar a estrutura-função de componentes dos venenos de serpentes peçonhentas à fim de desenvolver alternativas terapêuticas para esse problema de grande interesse médico. Um dos componentes que tem recebido atenção nas últimas décadas é a BthTX-I, uma proteína PLA2s-homóloga não catalítica, devido seu efeitos farmacológico notadamente miotóxico. Embora diversas técnicas tenham sido empregadas na compreensão do mecanismo de ação dessas proteínas, o conhecimento nessa área permanece controverso, tornando-se necessário a continuidade de estudos. O estudo estrutural e computacional de proteínas constitui uma alternativa viável para identificar as várias conformações de uma dada proteína, bem como seu comportamento dinâmico. Sendo assim, o presente trabalho buscou aplicar métodos computacionais, como simulação de MD, análise de Modos Normais (NM) e Dinâmica Molecular excitada por Modos Normais (MDeNM) à BthTX-I em pH ácido ou básico e nativa ou em complexo com o α-tocoferol – molécula tida como ativadora alostérica – na descrição do seu espaço conformacional, buscando compreender os aspectos estruturais do seu mecanismo de ação. Além disso, foram empregadas té... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Ophidian accidents constitute a global public health problem due its high mortality, with some cases leading to permanent sequels. In Brazil, around 20 thousand deaths are registered. Therefore, researchers have been studying the snake venom composition in order to develop therapeutic alternatives to this medical problem. Some components from snake venom are highlighted in the past decades, as BthTX-I, a non-catalytic PLA2s-homologous protein, due its many pharmacological effects, notably myotoxic. Although many techniques have been employed to better understand the molecular mechanism of action for these proteins, this knowledge remains controversial, emphasizing the need to progress this field. The structural and computational study of proteins is a valuable tool to access the various conformations of a given protein, as well its dynamical behavior. Thus, the present work applied computational methods as MD, Normal Modes (NM) analysis and Molecular Dynamics with excited Normal Modes (MDeNM) to BthTX-I in acidic or basic pH and unbound or bound to α-tocopherol – a molecule identified as an allosteric activator – in order to describe the conformational space of this protein and determine the structural aspects of its mechanism of action. Further, biophysical experiments as Dynamic Light Scattering (DLS) were employed in order to comprehend the oligomeric form of BthTX-I with or without α-tocopherol. MD simulations showed that dimeric form of BthTX-I is stable when in neutral/... (Complete abstract click electronic access below) / Doutor

Thesis (B.A.)--Bryn Mawr College, Growth and Structure of Cities Program, 2007. / Includes bibliographical references.

Les principaux algorithmes de placement et d'interconnexion sont passes en revues. On propose ensuite une classification des représentations symboliques de circuits intégrés, et on s'intéresse aux circuits représentés à l'aide du symbolisme défini pour le MD-MOS. Une methode de placement des portes et de traces des connexions automatises est présentée pour les circuits MD-MOS organisés en cellules à une et deux lignes d'alimentation.

Thesis (M.S.)--University of Delaware, 2006. / Principal faculty advisor: James E. Pizzuto, Dept. of Geological Sciences. Includes bibliographical references.

It is well known that folded proteins in water are destabilized by the addition of urea. When a protein loses its ability to perform its biological activity due to a change in its structure, it is said to denaturate. The mechanism by which urea denatures proteins has been thoroughly studied in the past but no proposed mechanism has yet been widely accepted. The topic of this thesis is the study of the mechanism of urea-induced protein denaturation, by means of Molecular Dynamics (MD) computer simulations and Nuclear Magnetic Resonance (NMR) spectroscopy. Paper I takes a thermodynamic approach to the analysis of protein – urea solution MD simulations. It is shown that the protein – solvent interaction energies decrease significantly upon the addition of urea. This is the result of a decrease in the Lennard-Jones energies, which is the MD simulation equivalent to van der Waals interactions. This effect will favor the unfolded protein state due to its higher number of protein - solvent contacts. In Paper II, we show that a combination of NMR spin relaxation experiments and MD simulations can successfully be used to study urea in the protein solvation shell. The urea molecule was found to be dynamic, which indicates that no specific binding sites exist. In contrast to the thermodynamic approach in Paper I, in Paper III we utilize MD simulations to analyze the affect of urea on the kinetics of local processes in proteins. Urea is found to passively unfold proteins by decreasing the refolding rate of local parts of the protein that have unfolded by thermal fluctuations. Based upon the results of Paper I – III and previous studies in the field, I propose a mechanism in which urea denatures proteins mainly by an enthalpic driving force due to attractive van der Waals interactions. Urea interacts favorably with all the different parts of the protein. The greater solvent accessibility of the unfolded protein is ultimately the factor that causes unfolded protein structures to be favored in concentrated urea solutions.

This thesis consists of seven research publications concerning (i) pKa studies of nucleobases in model nucleotides to understand why RNA duplexes are more stable than DNA duplexes (Paper I), (ii) the role of Me(T)-π interactions in the relative stability of DNA-RNA heteroduplexes (Paper II), (iii) pKa measurements in nucleotides with different 2′-substituents (paper III), (iv) a conformation study of constrained sugars and a pKa study of 1-thyminyl to reveal effect of sugar constraints on the pKa of the nucleobase (paper IV), (v) NMR and MD studies of 1′, 2′-oxetane constrained thymidine incorporated Dickerson Drew dodecamer (paper V), (vi) the sequence dependent pKa perturbation of 9-guaninyl moeity in single stranded (ss) DNA and RNA (paper VI), (vii) the non identical chemical nature of internucleotidic phosphates in (ss) RNA using 31P NMR (paper VI), and an alkaline hydrolysis study of phosphodiesters in ssRNAs (paper VII). The architecture of DNA and RNA molecules is determined by (a) hydrogen bonding (b) base stacking (c) a variety of additional non-covalent interactions. In paper (I) we showed that A-U and G-C base pairings in RNA are more stable than A-T and G-C base pairings in DNA by 4.3 and 1 kJ mol-1 respectively. Me(T)-π interaction plays a dominant role in the relative stability of DNA-RNA duplexes (paper II). In paper III and IV, we have shown that 1′ , 2′- oxetane and azetidine rings have strong inductive effect on pyrimidine bases, and that the H2′-sugar proton can be the marker to understand the pseudoaromaticity of pyrimidine bases, as well as increasing constraints in sugar reducing the basicity of nucleobases. A 1′, 2′-oxetane locked thymidine (T) moiety deforms the local structure of Dickerson-Drew dodecamer, d(CGCGAATTCGCG)2- investigated by High resolution NMR and MD study, as is discussed in the paper V. In papers VI and VII, we showed sequence context dependent pKa (N1) of 9-guaninyl perturbation in (ss) DNAs and RNAs and the non identical chemical nature of inter-nucleotidic phosphate groups in single stranded RNAs.