Supramolecular chemistry (chemistry beyond the molecule) is the study and synthesis of complex molecular architectures from simple subunits using non-covalent interactions. The types of non-covalent interactions that are used for the self-assembly of these complex molecular architectures include electrostatic interactions (e.g. ionic, halogen, and hydrogen bonding), π-effects, van der Waals interactions, metal coordination, and hydrophobic effects. While these interactions are often used in concert, some of the most successful and ubiquitous approaches for the design and construction of new host–guest architectures are the incorporation of hydrogen bonding motifs. A popular class of molecules capable of making strong, highly directional hydrogen bonds is barbiturates. Barbiturates have a well-known reputation as potent hypnotics, anticonvulsants, and anxiolytics but recent years have seen a renewed interest in these molecules due to their unique, symmetric acceptor-donor-acceptor hydrogen bonding motif. In addition, receptors with complementary hydrogen bonding motifs capable of binding barbiturates have also been reported, namely those based on the work of Hamilton et al. Collectively, barbiturates and their receptors have seen widespread use in a variety of applications including sensing, optoelectronics, catalysis, and the design of soft materials. The work presented in this dissertation describes the development of novel Hamilton receptors for supramolecular catalysis and barbiturate sensing, as well as the design of new synthetic barbiturates. Together this body of research aims to extend the utility of these types of host–guest systems as well as continue to develop and refine the supramolecular design principles that govern the binding interactions between barbiturates and a variety of Hamilton-type receptors. This dissertation includes both previously published/unpublished and co-authored material.

No description available.

Nanostructuring has led to materials with novel and improved materials properties driving innovation across fields as varied as transportation, computing, energy and biotechnology. However, the benefits of nanostructured material have not widely been extended into large-scale, three-dimensional applications as deterministic pattern techniques have proven too expensive for devices outside of high value products. This thesis explores how colloidal self-assembly can be used to form macroscopic functional materials with short-range order for electronic, photonic and electrochemical applications at scale. DNA-functionalized nanoparticles are versatile models for exploring colloidal self-assembly due to the highly specific, tunable and thermally reversible binding between DNA strands. Gold nanoparticles coated with DNA were used to investigate the temperature-dependent interaction potentials and the gel formation in DNA-colloidal systems. The electronic conductivity and the plasmonic response of the DNA-gold gels were studied to explore their applicability as porous electrodes and SERS substrates, respectively. Subsequently, silica nanoparticles were assembled into nanostructures that preferentially scatter blue light using both DNA and polymer-colloid interactions. Finally, rod-sphere structures made from DNA-coated gold nanoparticles and viruses were explored, demonstrating how high-aspect ratio building blocks can create composite structures with increased porosity. The gold-virus gel structures inspired the design and assembly of a silicon-carbon nanotube composite material using covalent bonds that shows promise for high energy density anodes.

Two-dimensional (2D) colloidal materials and their assembly are of scientific significance and industrial importance. The development of 2D colloidal structures is a key stepping stone towards three-dimensional (3D) structures in relation to controlled chemical composition, morphology, assembly and so on. Nowadays, uniform colloidal structures with complexity in both shape and interactions have become a popular topic in fundamental colloid science and applications. Being motivated by this, in this thesis, micro-scale colloidal rods and self-assembled dipeptides have been studied experimentally at the air-water interface. Monolayers containing these colloidal materials were created in a Langmuir trough. Surface pressure measurements, microscopic observations and many other techniques were combined for the investigation. The aim of this work is to understand the phase behaviours in complex monolayers, including the phase transitions during compression, the flipping dynamics of micro-rods, the contribution of dipole-dipole interactions between magnetic rods, and the interfacial self-assembly process of dipeptide molecules. Iron oxide micro-rods (β-FeOOH @silica) with different aspect ratios have been synthesized to create the monolayers at an air-water interface. Microscopic observations reveal a sequence of phase transitions by compressing the monolayers. It has been proved that the aspect ratio of the rods plays an important role in the phase transitions, —short rods flip into a perpendicular position relative to the interface to relieve the compressional stress, while longer rods form multilayers under compression. Magnetic rods (Fe3O4) were converted from the synthesized FeOOH rods. They can be aligned in an external field, which further induces the reorganization at the interface. To study these magnetic rods, differential dynamic microscopy (DDM) was carried out to measure the magnetic moment. Their interfacial properties were investigated in an external field applied perpendicular and parallel to the interface, respectively. A magnetic field-induced flipping process has been observed, which proves the theoretical prediction. Besides rod-like particles, naphthalene dipeptides have been successfully trapped at the interface of a low pH subphase, self-assembling into a hydrogel film. The mechanism of interfacial self-assembly has been studied. Both FTIR spectra and AFM images are used to investigate the fibrous structures of the film. The film has elastic properties and buckles under compression. Moreover, dipeptide hydrogel induced by metal ions has been used to create a wet foam system, which owns the advantages of long-term stability (more than two weeks), low cost, and easy preparation.

AN ABSTRACT OF THE THESIS OF LEWIS KENNEDY REED, for the Master of Science degree in PLANT BIOLOGY presented on October 30, 2009, at Southern Illinois University Carbondale TITLE: COMPETATIVE EVQUIVALENCY OF CULTIVAR AND NON-CULTIVAR DOMINANT GRASSES IN AN EXPERIMENTAL RETORATION MAJOR PROFESSORS: Dr. Sara G. Baer and Dr. David J. Gibson Multiple population sources of species for use in prairie restoration exist, including cultivars and non-cultivars of dominant native grasses. However, little is known about the competitive equivalency of different population sources of dominant C4 grasses and whether intraspecific variation in their competitive effect on the community scales to affect ecosystem assembly. In 2006, an experimental restoration was established in a former agricultural field using cultivars and non-cultivars of the dominant grasses (Andropogon gerardii, Sorghastrum nutans, and Schizachyrium scoparium) and two different species pools of non-dominant species containing equal richness and distribution of species among functional groups. I evaluated inter - and intra-specific variation in the competitive equivalency of A. gerardii, S. nutans, and S. scoparium in terms of community response to their individual and complete (all three species) removal. Removals were maintained for two growing seasons, though little maintenance was needed after the initial treatment. The competitive effect of each grass species and population source was determined by calculating a response ratio for percent cover and above ground primary productivity between removal and control plots for each dominant grass individually, forbs, non-dominant grasses, and legumes which were each analyzed using a mixed model procedure for a split-split-plot randomized block design. Effects of removals on overall community composition were assessed using non-metric multi-dimensional scaling (NMDS) and analysis of similarity (ANOSIM). In addition I monitored changes in photosynthetically active radiation (PAR) at the soil surface and inorganic soil nitrogen. Based on the 2008 data (after two years of maintaining removals), several important differences were detected between the focal species and in some cases the two sources of the same species in terms of their effects on neighbors, inorganic soil nitrogen, and PAR. Many of these differences depended on which species pool the comparison took place in. A 3-way interaction was detected between species pool, source, and removal treatment in the volunteer forb group (F3, 60 =3.28, p = 0.0268). Volunteer forbs showed a positive response to removal of cultivars of the dominant grass functional group in one species pool but not the other. A three-way interaction was detected between species pool, source, and removal treatment in terms of Bray-Curtis similarity (F3, 60 = 2.91, p = 0.0417). Within one of the species pools, similarity values of communities were higher between removals and controls in cultivar plots than in non-cultivar plots where A. gerardii was removed. While NMDS ordination showed separation of some plots by dominant grass source, within group variation was higher than among group variation and ANOSIM deemed this separation insignificant. Planted forb ANPP exhibited a significantly negative response to removal of S. nutans that was not observed in the other removal treatments (F3,41.1 = 3.09, p = 0.038) suggesting facilitation by the dominant grass on planted forbs. The aboveground net primary productivity (ANPP) of the subordinate community (i.e. all species except the dominant grasses) exhibited a 3-way interaction among species pool, dominant grass source, and species removed (F3,61 = 2.76, p=0.0499). This interaction resulted from a stronger negative response of subordinate community ANPP to cultivars of the dominant grass functional group removal than non-cultivars of this group that only occurred in one of the species pools. There was a significant main effect of species removed on %PAR at ground level (F3, 60 = 4.84, p = 0.0044). All removal treatments allowed higher penetration of PAR to ground level, with S. nutans and all dominant grass removal having the strongest effect. Inorganic N availability was lower in response to removal of A. gerardii cultivars compared to the removal of non-cultivars of this species in one species pool but not the other. Removal of cultivar S. scoparium lead to a positive response in total inorganic nitrogen while removal of non-cultivars of this species lead to a negative response in total inorganic nitrogen in this same species pool (F3, 51 = 3.61, p = 0.018). Results demonstrate that inter- and intra-specific variation among these dominant species affect some aspects of community structure and ecosystem properties, but these effects are not consistent among dominant species and among subordinate species pools. These complex interactions may have important implications for restoration and land management.

How to assess the quality of a genome assembly without the help of a reference sequence is an open question. Only a few techniques are currently used in the literature and each has obvious bias. An additional method, restriction enzyme associated DNA (RAD) marker alignment, is proposed here. With high enough density, this method should be able to assess the quality of de novo assemblies without the biases of current methods. With the growing ambition to sequence new genomes and the accelerating ability to do so cost effectively, methods to assess the quality of reference-free genome assemblies will become increasingly important. In addition to the existing methods of EST and conserved sequence alignment, RAD marker alignment may contribute to this effort.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / FOTO-ASSEMBLAGE consiste em nomenclatura sugestionada para definir os trabalhos que tenho produzido a partir da junção de fotografias digitais. As elaborações e fundamentações desses trabalhos representam também o cerne das pesquisas que resultaram na presente dissertação. Em princípio, o termo foto-assemblage haveria de referir-se a questões técnicas ou formais dessa prática. Contudo, ao desenvolver as pesquisas alguns procedimentos acabaram por determinar certas nuances que revelaram aspectos comuns também em seus e conteúdos. Como resultado de construções artísticas juntando fotografias desde 2009, cheguei às composições sintéticas aqui apresentadas, construídas a partir de duas fotografias. Aventei o nome foto-assemblage por observar nas imagens resultantes ressalvas que as distinguiriam de certas convenções atribuídas à ideia de fotografia. Ao mesmo tempo, as referidas imagens proporiam um possível desdobramento ao entendimento de assemblage enquanto técnica artística. Ainda que não seja uma regra, fotografias revelam imagens de momentos. Em sua relação com a compreensão humana de tempo ou espaço, fotografias quase sempre contêm instâncias mínimas. Fotografias, contudo, podem ser também compreendidas como uma contração de um percurso de tempo. Toda imagem fotográfica pode ser assimilada como resultante de determinados acontecimentos anteriores e mesmo tida como elemento gerador de conseqüências futuras. Seguindo esse entendimento, o que proponho com a foto-assemblage é que essa lide com segmentos de tempo ou de espaço contidos numa mesma imagem. Essas fotografias originárias ganhariam uma nova atribuição, sendo retiradas de seu contexto original, serviriam de balizas do percurso de tempo ou espaço suprimido e subjetivado entre elas. Poeticamente, eventos ocorridos entre as fotografias originárias estariam contidos nas imagens produzidas. O termo assemblage foi incorporado às artes a partir de 1953, por Jean Dubuffet, para descrever trabalhos que seriam algo mais do que simples colagem. A ideia de assemblage se baseia no princípio de que todo e qualquer material ou objeto colhido de nosso mundo cotidiano pode ser incorporado a uma obra de arte, criando um novo conjunto, sem que perca seu sentido original. Esse objeto é arrancado de seu uso habitual e inserido num novo contexto, tecendo laços de relação com os demais elementos, construindo narrativas num novo ambiente, o da obra. Na ideia da foto-assemblage, entretanto, é sugerido uso das imagens fotográficas originárias não como objetos que estariam em um mundo cotidiano, mas sim como imagem na concepção do que seria uma entidade mental. Adoto como que uma visão mágica onde as imagens originárias e básicas estariam numa outra dimensão, num plano bidimensional, não manipulável por nós habitantes da tridimensionalidade. Nesse ambiente imaginário ou não, as fotografias são assentadas consolidando a foto-assemblage. Quando a foto-assemblage se concretiza, se corporifica numa mídia, sendo impressa para uma contemplação, ai então, passaria a integrar nosso mundo tridimensional. O resultado poderia ser admitido como um híbrido, uma terceira coisa, a partir de duas que já não se dissociam mais no ensejo de uma compreensão estética. Ao final da dissertação, apresento experiências práticas que resultaram em quatro séries de imagens em foto-assemblage. Cada série enfatiza aspectos peculiares do que denomino paisagem expandida, representando percursos de tempo, espaço ou trajetos entre o mundo concreto e mundos do inconsciente. / PHOTO-ASSEMBLAGE consists on nomenclature to define the work that I have produced from the junction of digital photographs. The elaboration and justification of these works also represent the core of the research that resulted in this dissertation. In principle, the term photo-assemblage would refer to formal or technical issues this practice. However, research to develop some procedures ultimately determine certain nuances that reveal common aspects and also in their content. As a result of joining constructions artistic photographs since 2009, I came to the synthetic compositions presented here, constructed from two photographs. I suggested name photo-assemblage by observing the resulting images caveats that distinguish certain conventions attributed to the idea of photography. At the same time, these images would propose a possible unfolding to the understanding of assemblage as artistic technique. Although it is not a rule, photographs show images of times. In its relation to the human understanding of time and space, photographs almost always contain instances minimal. Photographs, however, can also be understood as a contraction of a course of time. Every photographic image can be assimilated as a result of certain events before and even seen as an element that generates future consequences. Following this understanding, what I propose with the photo-assemblage is that it deals with segments of time or space contained in the same picture. These photographs originating win a new award, being removed from their original context, serve as beacons of travel time or space and deleted subjectivizing between them. Poetically, events originating from the photographs would be contained in the images produced. The term assemblage to the arts was built as from 1953 by Jean Dubuffet to describe works that would be something more than simple collage. The idea of assemblage is based on the principle that any material or object drawn from our everyday world can be incorporated into a work of art, creating a new set without losing its original meaning. This object is torn from its habitual use and placed in a new context, weaving bonds of relationship with the other elements, constructing narratives in a new environment, the work. In view of photo-assemblage, however, is suggested use of photographic images as objects originating not they would be in an everyday world, but as the design image of what a mental entity. I adopt it as a magical sight where the images originate, basic, would be in another dimension, a two-dimensional plane, we can not be manipulated by the inhabitants of three-dimensionality. In this "environment" imaginary or not, pictures are settled consolidating photo-assemblage. When the photo-assemblage materializes, is embodied in media, being printed for contemplation there would then integrate our three-dimensional world. The result could be admitted as a hybrid, a third thing from two no longer dissociate more opportunity in an aesthetic understanding. In the concluding stages of dissertation, practical experiences that resulted in four sets of images in photo-assemblage. Each one emphasizing peculiar aspects of what I title "expanded landscape", reproducing images that contain paths of time, space or paths between the concrete world and unconscious worlds

abstract: Deoxyribonucleic acid (DNA) has emerged as an attractive building material for creating complex architectures at the nanometer scale that simultaneously affords versatility and modularity. Particularly, the programmability of DNA enables the assembly of basic building units into increasingly complex, arbitrary shapes or patterns. With the expanding complexity and functionality of DNA toolboxes, a quantitative understanding of DNA self-assembly in terms of thermodynamics and kinetics, will provide researchers with more subtle design guidelines that facilitate more precise spatial and temporal control. This dissertation focuses on studying the physicochemical properties of DNA tile-based self-assembly process by recapitulating representative scenarios and intermediate states with unique assembly pathways. First, DNA double-helical tiles with increasing flexibility were designed to investigate the dimerization kinetics. The higher dimerization rates of more rigid tiles result from the opposing effects of higher activation energies and higher pre-exponential factors from the Arrhenius equation, where the pre-exponential factor dominates. Next, the thermodynamics and kinetics of single tile attachment to preformed “multitile” arrays were investigated to test the fundamental assumptions of tile assembly models. The results offer experimental evidences that double crossover tile attachment is determined by the electrostatic environment and the steric hindrance at the binding site. Finally, the assembly of double crossover tiles within a rhombic DNA origami frame was employed as the model system to investigate the competition between unseeded, facet and seeded nucleation. The results revealed that preference of nucleation types can be tuned by controlling the rate-limiting nucleation step. The works presented in this dissertation will be helpful for refining the DNA tile assembly model for future designs and simulations. Moreover, The works presented here could also be helpful in understanding how individual molecules interact and more complex cooperative bindings in chemistry and biology. The future direction will focus on the characterization of tile assembly at single molecule level and the development of error-free tile assembly systems. / Dissertation/Thesis / Doctoral Dissertation Chemistry 2016

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / FOTO-ASSEMBLAGE consiste em nomenclatura sugestionada para definir os trabalhos que tenho produzido a partir da junção de fotografias digitais. As elaborações e fundamentações desses trabalhos representam também o cerne das pesquisas que resultaram na presente dissertação. Em princípio, o termo foto-assemblage haveria de referir-se a questões técnicas ou formais dessa prática. Contudo, ao desenvolver as pesquisas alguns procedimentos acabaram por determinar certas nuances que revelaram aspectos comuns também em seus e conteúdos. Como resultado de construções artísticas juntando fotografias desde 2009, cheguei às composições sintéticas aqui apresentadas, construídas a partir de duas fotografias. Aventei o nome foto-assemblage por observar nas imagens resultantes ressalvas que as distinguiriam de certas convenções atribuídas à ideia de fotografia. Ao mesmo tempo, as referidas imagens proporiam um possível desdobramento ao entendimento de assemblage enquanto técnica artística. Ainda que não seja uma regra, fotografias revelam imagens de momentos. Em sua relação com a compreensão humana de tempo ou espaço, fotografias quase sempre contêm instâncias mínimas. Fotografias, contudo, podem ser também compreendidas como uma contração de um percurso de tempo. Toda imagem fotográfica pode ser assimilada como resultante de determinados acontecimentos anteriores e mesmo tida como elemento gerador de conseqüências futuras. Seguindo esse entendimento, o que proponho com a foto-assemblage é que essa lide com segmentos de tempo ou de espaço contidos numa mesma imagem. Essas fotografias originárias ganhariam uma nova atribuição, sendo retiradas de seu contexto original, serviriam de balizas do percurso de tempo ou espaço suprimido e subjetivado entre elas. Poeticamente, eventos ocorridos entre as fotografias originárias estariam contidos nas imagens produzidas. O termo assemblage foi incorporado às artes a partir de 1953, por Jean Dubuffet, para descrever trabalhos que seriam algo mais do que simples colagem. A ideia de assemblage se baseia no princípio de que todo e qualquer material ou objeto colhido de nosso mundo cotidiano pode ser incorporado a uma obra de arte, criando um novo conjunto, sem que perca seu sentido original. Esse objeto é arrancado de seu uso habitual e inserido num novo contexto, tecendo laços de relação com os demais elementos, construindo narrativas num novo ambiente, o da obra. Na ideia da foto-assemblage, entretanto, é sugerido uso das imagens fotográficas originárias não como objetos que estariam em um mundo cotidiano, mas sim como imagem na concepção do que seria uma entidade mental. Adoto como que uma visão mágica onde as imagens originárias e básicas estariam numa outra dimensão, num plano bidimensional, não manipulável por nós habitantes da tridimensionalidade. Nesse ambiente imaginário ou não, as fotografias são assentadas consolidando a foto-assemblage. Quando a foto-assemblage se concretiza, se corporifica numa mídia, sendo impressa para uma contemplação, ai então, passaria a integrar nosso mundo tridimensional. O resultado poderia ser admitido como um híbrido, uma terceira coisa, a partir de duas que já não se dissociam mais no ensejo de uma compreensão estética. Ao final da dissertação, apresento experiências práticas que resultaram em quatro séries de imagens em foto-assemblage. Cada série enfatiza aspectos peculiares do que denomino paisagem expandida, representando percursos de tempo, espaço ou trajetos entre o mundo concreto e mundos do inconsciente. / PHOTO-ASSEMBLAGE consists on nomenclature to define the work that I have produced from the junction of digital photographs. The elaboration and justification of these works also represent the core of the research that resulted in this dissertation. In principle, the term photo-assemblage would refer to formal or technical issues this practice. However, research to develop some procedures ultimately determine certain nuances that reveal common aspects and also in their content. As a result of joining constructions artistic photographs since 2009, I came to the synthetic compositions presented here, constructed from two photographs. I suggested name photo-assemblage by observing the resulting images caveats that distinguish certain conventions attributed to the idea of photography. At the same time, these images would propose a possible unfolding to the understanding of assemblage as artistic technique. Although it is not a rule, photographs show images of times. In its relation to the human understanding of time and space, photographs almost always contain instances minimal. Photographs, however, can also be understood as a contraction of a course of time. Every photographic image can be assimilated as a result of certain events before and even seen as an element that generates future consequences. Following this understanding, what I propose with the photo-assemblage is that it deals with segments of time or space contained in the same picture. These photographs originating win a new award, being removed from their original context, serve as beacons of travel time or space and deleted subjectivizing between them. Poetically, events originating from the photographs would be contained in the images produced. The term assemblage to the arts was built as from 1953 by Jean Dubuffet to describe works that would be something more than simple collage. The idea of assemblage is based on the principle that any material or object drawn from our everyday world can be incorporated into a work of art, creating a new set without losing its original meaning. This object is torn from its habitual use and placed in a new context, weaving bonds of relationship with the other elements, constructing narratives in a new environment, the work. In view of photo-assemblage, however, is suggested use of photographic images as objects originating not they would be in an everyday world, but as the design image of what a mental entity. I adopt it as a magical sight where the images originate, basic, would be in another dimension, a two-dimensional plane, we can not be manipulated by the inhabitants of three-dimensionality. In this "environment" imaginary or not, pictures are settled consolidating photo-assemblage. When the photo-assemblage materializes, is embodied in media, being printed for contemplation there would then integrate our three-dimensional world. The result could be admitted as a hybrid, a third thing from two no longer dissociate more opportunity in an aesthetic understanding. In the concluding stages of dissertation, practical experiences that resulted in four sets of images in photo-assemblage. Each one emphasizing peculiar aspects of what I title "expanded landscape", reproducing images that contain paths of time, space or paths between the concrete world and unconscious worlds

abstract: As the genetic information storage vehicle, deoxyribonucleic acid (DNA) molecules are essential to all known living organisms and many viruses. It is amazing that such a large amount of information about how life develops can be stored in these tiny molecules. Countless scientists, especially some biologists, are trying to decipher the genetic information stored in these captivating molecules. Meanwhile, another group of researchers, nanotechnologists in particular, have discovered that the unique and concise structural features of DNA together with its information coding ability can be utilized for nano-construction efforts. This idea culminated in the birth of the field of DNA nanotechnology which is the main topic of this dissertation. The ability of rationally designed DNA strands to self-assemble into arbitrary nanostructures without external direction is the basis of this field. A series of novel design principles for DNA nanotechnology are presented here, from topological DNA nanostructures to complex and curved DNA nanostructures, from pure DNA nanostructures to hybrid RNA/DNA nanostructures. As one of the most important and pioneering fields in controlling the assembly of materials (both DNA and other materials) at the nanoscale, DNA nanotechnology is developing at a dramatic speed and as more and more construction approaches are invented, exciting advances will emerge in ways that we may or may not predict. / Dissertation/Thesis / Ph.D. Chemistry 2012