Thesis (Ph.D.)--University of Delaware, 2008. / Principal faculty advisors: Eric W. Kaler, College of Engineering; and Abraham M. Lenhoff, Dept. of Chemical Engineering. Includes bibliographical references.

Thesis (Ph. D.)--University of Hong Kong, 2009. / Includes bibliographical references (p. 181-216) Also available in print.

Thesis (Ph. D.)--University of Washington, 2000. / Vita. Includes bibliographical references (leaves 96-111).

Thesis (Ph.D.)--University of California, San Francisco, 2004. / Includes bibliographical references. Also available online.

Thesis (Ph. D.)--Washington State University, December 2006. / Includes bibliographical references.

Thesis (Ph.D.)--University of Delaware, 2007. / Principal faculty advisor: Anne Skaja Robinson, Dept. of Chemical Engineering. Includes bibliographical references.

The introduction of creases into thin sheets has a dramatic effect on their global mechanical properties. This can be observed by manipulating a crumpled piece of paper which has been unfolded; it no longer deforms in the same way as the original sheet. Creases have typically been modelled as singular hinge lines, often accompanied by a torsional spring to provide some opening resistance; however, the appropriate stiffness of these springs is unclear. In reality, creases have a discrete geometry based on the method they were formed. This dissertation investigates the flexural behaviour of a creased thin metallic strip and the influence of the crease geometry. When a strip is bent perpendicular to the crease, putting the crease region in tension and the strip edges in compression, initially torsional deformations occur which ultimately coalesce into a central localised flattened region. An analytical model of this flexural behaviour is developed, which idealises the crease as an initially circular segment. Predictions show the bending resistance increases as the crease decreases in size. The model predictions are compared to finite element analysis and experimental results showing excellent agreement. When a strip is bent in the opposite direction, with the crease region in compression and the strip edges in tension, a bistable snap-through occurs. The deformed shape is characterised by a sharp vertex on the crease line. An analytical model is developed by generalising a Gauss mapping approach, and used to predict the deformed shape. These predictions match experimental results well. This dissertation provides an understanding of the mechanics of creased thin strips, where the crease is given a discrete geometry, and explores the nature of localisation. It also provides the foundation to explore the mechanics of thin sheets featuring a network of creases. This offers the opportunity to improve the efficiency of thin shell structures by using creasing to optimise the mechanics, leading to reduced material use, more sustainable construction, and fuel savings from lighter vehicles.

Made available in DSpace on 2014-06-11T19:25:31Z (GMT). No. of bitstreams: 0 Previous issue date: 2006-02-21Bitstream added on 2014-06-13T20:53:30Z : No. of bitstreams: 1 beig_fb_me_rcla.pdf: 924598 bytes, checksum: 14e39e31f1f38a8a350df76ebbf91a48 (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Estudamos o enovelamento de proteínas através da termodinâmica de uma cadeia heteropolimérica. Para isso, adaptamos um método de Monte Carlo introduzido por Wang e Landau para o estudo de transições de fase em sistemas magnéticos para estudarmos a mecânica estatística dessa cadeia. Trata-se de um método que se vale do passeio randômico no espaço de energias para determinação da densidade de estados acessíveis à cadeia e com ela determinar grandezas termodinâmicas do sistema em estudo. Para obtermos essa densidade de estados, adotamos modelos de rede para gerarmos todas as conformações geométricas possíveis de uma cadeia de 27 monômeros em uma rede cúbica. Estudamos várias seqüências de monômeros adotando os modelos de rede mais relevantes utilizados para a investigação do enovelamento de proteínas tais como o modelo HP e modelos mais elaborados que utilizam as interações de Miyazawa-Jernigan entre monômeros. Calculamos diversas grandezas termodinâmicas essenciais para a compreensão do enovelamento de proteínas e com isso mostramos a eficiência do método Wang-Landau. / We studied the protein folding through investigating the thermodynamics of a hetero-polymeric chain. For this purpose, a Monte Carlo method introduced by Wang and Landau to study the phase transitions in magnetic systems, was adapted to investigate the statistical mechanics of this chain. The method is based on the random walk in the energy space to determine the density of states of the chain and important thermodynamics quantities. For this purpose, we adopted the lattice model and generate all geometric conformations of a 27-monomer chain in a cubic lattice. We studied several sequences of monomers adopting the most relevant lattice models, such as the HP model and more elaborated models considering the Miyazawa-Jernigan interactions. We computed several thermodynamics quantities to help us to understand the protein folding and show the efficiency of the Wang-Landau method.

Resumo: A difusão desempenha um papel importante na cinética de eno-velamento de proteínas. Nessa tese, desenvolvemos métodos analíticos e computacionais para o estudo do coeficiente de difusão dependente da posi-ção e do tempo. Para estes estudos, utilizou-se sobretudo o modelo baseado na estrutura (modelo G¯o) via simulação computacional da representação em carbonos alfa. Investigou-se o efeito da difusão no enovelamento da proteína cold-shock (TmCSP). Encontrou-se que o efeito temporal da difusão leva a cinéticas não-exponenciais e a estatística não-poissônica da distribuição de tempos de enovelamento. Com relação a dependência com a posição, o coeficiente de difusão revelou ter um comportamento não-monotônico que foi compreendido pela análise dos valores- e da entropia residual no estado nativo. Para uma versão frustrada do modelo, encontrou-se que um baixo nível de frustração energética aumenta a difusão no estado nativo e torna o estado de transição mais homogêneo. Esses resultados corroboram com experimentos recentes de fluorescência de uma única molécula. Esse trabalho também propõe um método para a determinação da superfície de energia de enovelamento de proteína. A partir da caracterização da superfície de energia, definimos a quantidade (LD - Landscape Descriptor) que mostrou uma forte correlação entre a cinética e a termodinâmica de uma dezena de proteínas globulares, tornando-se um método útil para classificar proteínas / Abstract: Diffusion plays an important role in protein folding kinetics. In this thesis we developed analytical and computational methods in order to study the diffusion coefficient dependent on position and time. For these studies we used mainly the structure-based model (G¯o model) via computer simulation of the alpha-carbon representation. We investigated the effect of diffusion in the folding of the cold-shock protein (TmCSP). We found that the time dependence on diffusion leads to non-exponential kinetics and non-Poisson statistics of folding time distribution. With respect to the position dependence, the diffusion coefficient reveled a non-monotonic behavior that was understood by analyzing the -values and the residual entropy in the native state. For a frustrated version of the model, we found that a low level of frustration energy stabilizes and increases the diffusion in the native state and the transition state becomes more homogeneous. These results are supported by recent single-molecule fluorescence experiments. This work also proposes a method to determine the protein folding energy landscape. With the energy landscape characterized, we defined the quantity (LD - Landscape Descriptor) which showed a strong correlation between kinetics and thermodynamics of a dozen globular proteins making it a useful method to classify proteins / Orientador: Vitor Barbanti Pereira Leite / Coorientador: Jorge Chahine / Banca: Antônio Francisco Pereira de Araújo / Banca: Nelson Augusto Alves / Banca: Luis Paulo Barbour Scott / Banca: José Roberto Ruggiero / Doutor

RNA molecules interact by forming inter-molecular base pairs that compete with the intra-molecular base pairs of their secondary structures. Here we investigate the patterns of neutral mutations in RNAs whose function is the interaction with other RNAs, i.e., the co-folding with one or more other RNA molecules. We find that (1) the degree of neutrality is much smaller in interacting RNAs compared to RNAs that just have to coform to a single externally prescribed target structure, and (2) strengthening this contraint to the conservation of the co-folded structure with two or more partners essentially eliminates neutrality. It follows that RNAs whose function depends on the formation of a specific interaction complex with a target RNA molecule will evolve much more slowly than RNAs with a function depending only on their own structure.