abstract: DNA has recently emerged as an extremely promising material to organize molecules on nanoscale. The reliability of base recognition, self-assembling behavior, and attractive structural properties of DNA are of unparalleled value in systems of this size. DNA scaffolds have already been used to organize a variety of molecules including nanoparticles and proteins. New protein-DNA bio-conjugation chemistries make it possible to precisely position proteins and other biomolecules on underlying DNA scaffolds, generating multi-biomolecule pathways with the ability to modulate inter-molecular interactions and the local environment. This dissertation focuses on studying the application of using DNA nanostructure to direct the self-assembly of other biomolecular networks to translate biochemical pathways to non-cellular environments. Presented here are a series of studies toward this application. First, a novel strategy utilized DNA origami as a scaffold to arrange spherical virus capsids into one-dimensional arrays with precise nanoscale positioning. This hierarchical self-assembly allows us to position the virus particles with unprecedented control and allows the future construction of integrated multi-component systems from biological scaffolds using the power of rationally engineered DNA nanostructures. Next, discrete glucose oxidase (GOx)/ horseradish peroxidase (HRP) enzyme pairs were organized on DNA origami tiles with controlled interenzyme spacing and position. This study revealed two different distance-dependent kinetic processes associated with the assembled enzyme pairs. Finally, a tweezer-like DNA nanodevice was designed and constructed to actuate the activity of an enzyme/cofactor pair. Using this approach, several cycles of externally controlled enzyme inhibition and activation were successfully demonstrated. This principle of responsive enzyme nanodevices may be used to regulate other types of enzymes and to introduce feedback or feed-forward control loops. / Dissertation/Thesis / Ph.D. Biochemistry 2013

Submitted by Renata Lopes (renatasil82@gmail.com) on 2016-05-10T13:59:22Z No. of bitstreams: 1 magdacristinadeoliveiradias.pdf: 697670798 bytes, checksum: da1be79a7c474a14d775f3b19c02ef4a (MD5) / Approved for entry into archive by Adriana Oliveira (adriana.oliveira@ufjf.edu.br) on 2016-06-15T13:14:00Z (GMT) No. of bitstreams: 1 magdacristinadeoliveiradias.pdf: 697670798 bytes, checksum: da1be79a7c474a14d775f3b19c02ef4a (MD5) / Made available in DSpace on 2016-06-15T13:14:00Z (GMT). No. of bitstreams: 1 magdacristinadeoliveiradias.pdf: 697670798 bytes, checksum: da1be79a7c474a14d775f3b19c02ef4a (MD5) Previous issue date: 2015-08-15 / CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / O ensino da Matemática, em geral, é considerado muito difícil e desinteressante para muitos alunos, logo precisamos desenvolver atividades motivadoras que despertem o interesse dos mesmos. Desta forma, este trabalho tem por objetivo propor atividades que abordem conceitos e noções de Geometria plana e espacial, usando como recurso pedagógico o Origami. O uso das dobraduras tornam as aulas mais dinâmicas, prazerosas e contribui significativamente para a interação e participação dos alunos na formação de conceitos e conhecimentos. Além de melhorar a concentração e a autoestima dos alunos, o recurso da experimentação permite aos alunos a formulação de conjecturas e a exploração de suas características através do contato. O Origami, além de contribuir para uma aprendizagem efetiva, possibilita o desenvolvimento de habilidades importantes para a formação geral do aluno, como a interdisciplinaridade, a disciplina, o trabalho em equipe, o raciocínio, a concentração entre outras. / The teaching of mathematics in general is considered, by many students, very difficult and uninteresting. We must immediately develop motivating activities that arouse the their interest. In this way, this work aims to propose activities adchessing concepts and notions of plane and spatial geometry, using Origami as a pedagogical resource. The use of folds make the classes more dynamic, pleasurable and contributes significantly for interaction and partcipation of students in training concepts and knowledge. In addition to improving concentration and self-esteem of students, the trial feature allows students to formulate conjectures and exploitation of their characteristics througer contact. The Origami contributes for effective learning, enables the development of important skills for the general education of the student such as interdisciplinarity, teamwork, reasoning, concentration and others.

The microtubule cytoskeleton plays a vital role in the spatial-temporal organization of subcellular cargo required to maintain homeostasis and direct cell division. Cytoplasmic dynein and kinesin are opposite-polarity, microtubule-based motors that transport a wide variety of cargo throughout eukaryotic cells. While much is known about the stepping mechanism of kinesin from decades of study, cytoplasmic dynein's size and complexity has limited our understanding of its underlying motor mechanism. Here, a minimal, artificially-dimerized dynein motor was observed with two-color, near-simultaneous, high-precision, single-molecule imaging, which reveals the stepping pattern of each motor domain as dynein moves along the microtubule. Although the stepping behavior appeared highly irregular and erratic, with large variability in step sizes, side stepping behavior, and back stepping behavior, dynein did show evidence of tension-based, coordinated stepping. Furthermore, advances in DNA nanotechnology enabled us to engineer a synthetic motor-cargo system, referred to as a chassis, to investigate how multiple cytoskeletal motors work in teams to produce the myriad of motile behaviors observed in vivo. Specifically, the mechanisms that coordinate motor ensemble behavior was examined using three-dimensional DNA origami to which varying numbers of DNA oligonucleotide-linked motors could be attached, allowing control of motor type, number, spacing, and orientation in vitro. Ensembles of 1-7 identical-polarity motors displayed minimal interference with respect to directional velocity, while ensembles of opposite-polarity motors engaged in a tug-of-war resolvable by disengaging one motor species. This experimental system allowed us to test directly the tug-of-war proposed to occur during dynein's delivery to the microtubule plus-end by the kinesin Kip2. This work led to the mechanistic understanding that Lis1/Pac1, CLIP170/Bik1, and EB1/Bim1 proteins function to enhance kinesin's processivity, allowing it to win a tug-of-war and transport dynein toward the microtubule plus-end. Overall, this work elucidated mechanisms of ensemble motor function and dynein's stepping mechanism in addition to building significant tools to further pave the way for future studies to elucidate how cytoskeletal motors function to organize cellular cargos.

The use of origami-based bellows is of interest in fields where traditional metal bellows are incapable of meeting compression, mass, or flexibility constraints. Metal bellows are often used in space applications but frequently complicate spacecraft design. Origami-based bellows capable of meeting design constraints while adequately shielding sensitive spacecraft parts may be advantageous to space mechanism design. The design and testing of a highly compressible origami bellows for harsh environments is described. Several origami patterns were evaluated and the Kresling fold pattern was designed to meet constraints and selected for use in the bellows design. Origami bellows were prototyped in five different materials and tested in fatigue, thermal cycling, ablation, and radiation. Tested bellows show good fatigue life exceeding 100,000 cycles for some materials and resilience to potential harsh environmental conditions such as thermal cycling, abrasion, and high radiation. The bellows can be designed to fit within a given inner and outer diameter and stroke length depending on the design requirements. The origami bellows shows promise for space application and as an adequate replacement for current metal bellows due to its high compressibility and low mass. The design, testing, and fabrication of an origami-based bellows for microgravity drilling is presented. The benefits of origami created an opportunity for application on NASA's Asteroid Redirect Mission (ARM) to protect sensitive parts from debris. Origami-based bellows were designed to fit spacial limitations and meet needed compression ratios. Designs have demonstrated high mass reductions, improved stroke length, greatly decreased stowed volume, improved flexibility, and reduced reaction forces in comparison with traditional metal bellows. Material and design testing demonstrated that a nylon-reinforced polyvinyl fluoride based bellows with an aramid fiber stitched seam is well suited for debris containment in space conditions. Various epoxies were able to maintain an adequate bond with polyvinyl fluoride below expected environmental temperature for bellows mounting to the ARM drill. Asymmetric compression of the bellows can occur at extreme low temperatures and is preventable by balancing stiffness within the structure.

Applying engineering principles to tessellation origami-based designs enables the control of certain design properties, such as flexibility, bending stiffness, mechanical advantage, shape conformance, and deployment motion. The ability to control these and other properties will enable augmented design capabilities in environments which currently limit the design to specific materials, including space, medicine, harsh environments, and scaled environments (such as MEMS applications). Other applications will be able to achieve more complex motions or better satisfy design and performance requirements.This research demonstrates augmented design capabilities of origami tessellations in engineering design in rigid-foldable and non-rigid-foldable applications. First, a method to determine Poisson's ratio and mechanical advantage for deployable, rigid-foldable tessellations is presented. The results enable the selection and tailoring of patterns based on deployment motion of specific patterns.Secondly, a model that predicts the deployment stability of the non-rigid-foldable triangulated cylinder is presented. This model defines the geometry needed to obtain a maximum deployed height, always return to a closed position, or remain in either the open or closed configurations. The Stability Transition Ratio is the ratio of the inner to outer diameter that marks the point between monostable and bistable behavior in a triangulated cylinder and is dependent only on the number of sides.Lastly, this work presents methods to reduce sag in adult diapers by increasing shape conformance, promoting wicking capabilities, and improving the structure through the implementation of origami tessellations. Several basic fold patterns were evaluated and the results reported. Reducing sag increases comfort and decreases leaking.

Compliant mechanisms are useful for improving existing machines and creating new ones that were not previously possible. They also help us to think of new methods and technologies needed to both improve existing systems as well as manufacture systems that have not been done before. The purpose of this thesis is to show novel implementations of compliant mechanisms into folding systems, and to show new methods for fabricating such mechanisms with nontraditional materials and on difficult scales. Folding systems are shown in furniture applications with chairs, stools, and childcare furniture applications as results of research into how such structures could be created with compliant mechanisms to be deployed from a flat state. Compliant mechanisms are also shown to be folded by a laser into simple mechanisms and into a potentially more complex parabolic reflector. Small-scale flexible (or compliant) mechanisms are valuable in replacing rigid components while retaining comparable motion and behavior. However, fabricating such mechanisms on this scale (from 0.01 to 10 cm thick) proves difficult, especially with thin sheet metals. The manufacturing method of laser forming, which uses a laser to cut and bend metal into desired shapes, could facilitate this fabrication. However, specific methods for designing mechanisms formed by lasers need to be developed. This work presents laser forming as a means for creating compliant mechanisms on this scale with thin sheet metal. The unique challenges for designing mechanisms to be laser-formed are explored, and new adaptations of existing designs are fabricated and discussed. The design of basic "building blocks" and features are developed for several mechanisms: a parallel-guided mechanism, a cross-axis flexural pivot, a LET joint array, a split-tube flexure, and a bi-stable switch. These mechanisms are shown to perform repeatable behavior and motion comparable to existing non-laser-formed versions. The further possibilities for fabricating compliant mechanisms with laser forming are explored, as advanced applications can benefit from using lasers to create compliant mechanisms from thin sheet metal. One such possible system is a parabolic reflector, which is useful for making solar collectors and antennas. Such shapes have been developed in various patterns and typically manufactured out of rigid components. Applications for these systems could benefit from paraboloids that can fold up and be deployed into a final shape. This work presents a conceptual method for designing a flat-foldable paraboloid and a means for its fabrication using laser forming.

No description available.

A thin film is a material that is many orders of magnitude thinner than it is long or wide. They are commonly found in many forms and have been adapted to a wide variety of uses. The art of origami uses thin films(sheets of paper) and precise folding to create complex, three-dimensional shapes out of flat, quasi two-dimensional sheets, and has emerged as a unique way to solve problems in engineering and science. As technology and devices are scaled to smaller sizes new understanding of origami methods are required to work at these small scales. The interactions between thin films and liquids, substrates that films exist on, and other thin films is the focus of this dissertation. Capillary interactions are used to manipulate and fold thin films that are too thin to be actuated with hands or everyday tools. The relation between the macroscopic and the microscopic interactions at the point where the capillary liquid and the film meet is explored. We show how films can be manipulated by capillary drops and how exactly the force is applied to the film. The adhesive interactions of the film were studied as a method of precisely placing folds for elastic film origami. The capillary peel of a film from a substrate drove folds to desired locations. Adhesion of a film to itself was used to lock these bends in place in lieu of the permanent creases commonly used in plastic systems such as paper. The combination of these two methods enabled the creation of stable, multi-step origami systems from reusable elastic films. This research culminates in the discussion of fundamentally new origami-like designs that rely only on adhesion of the film to itself, which we call kuttsukugami (sticky+paper from Japanese). This new form allows for the creation of shapes that are nearly impossible to create with traditional origami methods such as loops, tubes, and cones. Advances made in capillary and adhesive thin film studies allow for kuttsukugami shapes to be scaled down to microscopic sizes for a huge array of applications including drug delivery, thin electronics, encapsulation, and more.

No description available.

Indiana University-Purdue University Indianapolis (IUPUI) / Thin walled tubular structures are widely used in the automotive industry because of its weight to energy absorption advantage. A lot of research has been done in different cross sectional shapes and different tapered designs, with design for manufacturability in mind, to achieve high specific energy absorption. In this study a novel type of tubular structure is proposed, in which predesigned origami initiators are introduced into conventional square tubes. The crease pattern is designed to achieve extensional collapse mode which results in decreasing the initial buckling forces and at the same time acts as a fold initiator, helping to achieve a extensional collapse mode. The influence of various design parameters of the origami pattern on the mechanical properties (crushing force and deceleration) are extensively investigated using finite element modelling. Thus, showing a predictable and stable collapse behavior. This pattern can be stamped out of a thin sheet of material. The results showed that a properly designed origami pattern can consistently trigger a extensional collapse mode which can significantly lower the peak values of crushing forces and deceleration without compromising on the mean values. Also, a comparison has been made with the behavior of proposed origami pattern for extensional mode verses origami pattern with diamond fold.