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- Member of: ASU Electronic Theses and Dissertations
Description
Proteins and peptides fold into dynamic structures that access a broad functional landscape, however, designing artificial polypeptide systems continues to be a great chal-lenge. Conversely, deoxyribonucleic acid (DNA) engineering is now routinely used to build a wide variety of two dimensional and three dimensional (3D) nanostructures from simple hybridization based rules, and their functional diversity can be significantly ex-panded through site specific incorporation of the appropriate guest molecules. This dis-sertation describes a gentle methodology for using short (8 nucleotide) peptide nucleic acid (PNA) linkers to assemble polypeptides within a 3D DNA nanocage, as a proof of concept for constructing artificial catalytic centers. PNA-polypeptide conjugates were synthesized directly using microwave assisted solid phase synthesis or alternatively PNA linkers were conjugated to biologically expressed proteins using chemical crosslinking. The PNA-polypeptides hybridized to the preassembled DNA nanocage at room tempera-ture or 11 ⁰C and could be assembled in a stepwise fashion. Time resolved fluorescence anisotropy and gel electrophoresis were used to determine that a negatively charged az-urin protein was repelled outside of the negatively charged DNA nanocage, while a posi-tively charged cytochrome c protein was retained inside. Spectroelectrochemistry and an in-gel luminol oxidation assay demonstrated the cytochrome c protein remained active within the DNA nanocage and its redox potential decreased modestly by 10 mV due to the presence of the DNA nanocage. These results demonstrate the benign PNA assembly conditions are ideal for preserving polypeptide structure and function, and will facilitate the polypeptide-based assembly of artificial catalytic centers inside a stable DNA nanocage. A prospective application of assembling multiple cyclic γ-PNA-peptides to mimic the oxygen-evolving complex (OEC) catalytic active site from photosystem II (PSII) is described. In this way, the robust catalytic capacity of PSII could be utilized, without suffering the light-induced damage that occurs by the photoreactions within PSII via triplet state formation, which limits the efficiency of natural photosynthesis. There-fore, this strategy has the potential to revolutionize the process of designing and building robust catalysts by leveraging nature's recipes, and also providing a flexible and con-trolled artificial environment that might even improve them further towards commercial viability.
ContributorsFlory, Justin David (Author) / Fromme, Petra (Thesis advisor) / Yan, Hao (Committee member) / Buttry, Daniel (Committee member) / Ghirlanda, Giovanna (Committee member) / Arizona State University (Publisher)
Created2014
Description
Biomimicry is an approach that entails understanding the natural system and designs and mimicking them to create new non-biological systems that can solve human problems. From bio-based material development to biologically inspired designs, architects and designers excelled in highlighting the fascination of integrating the biomimetic thinking process into the modern design that provides more comfortable space in which to live. This thesis explores how historical sustainable strategies from Islamic traditional architecture incorporated natural design system that could now be appropriately applied to interior architecture. In addition, it explores the current existing problems in this field and the possibilities of biomimetic sustainable solutions for existing buildings in the hot dry climate regions of Saudi Arabia.
The author concentrates on examining Islamic traditional architecture where the past architects incorporated certain aspects of nature in their construction and through using local resources, built buildings that mitigated heat and provided protection from cold. As a result of completing this research, it was found that there are common characteristics between the traditional Islamic architecture elements and system solutions found in some natural organisms. Characteristics included, for example, evaporative cooling, stuck effect, and avoiding heat gain. However, in the natural world, there is always opportunities to further explore more about the impacts of biomimicry and natural strategies applicable to enhance interior environments of buildings.
The author concentrates on examining Islamic traditional architecture where the past architects incorporated certain aspects of nature in their construction and through using local resources, built buildings that mitigated heat and provided protection from cold. As a result of completing this research, it was found that there are common characteristics between the traditional Islamic architecture elements and system solutions found in some natural organisms. Characteristics included, for example, evaporative cooling, stuck effect, and avoiding heat gain. However, in the natural world, there is always opportunities to further explore more about the impacts of biomimicry and natural strategies applicable to enhance interior environments of buildings.
ContributorsHawsawi, Hawaa Ismail (Author) / Bernardi, Jose (Thesis advisor) / Fehler, Michelle (Committee member) / Harmon-Vaughan, Elizabeth (Committee member) / Arizona State University (Publisher)
Created2016
Description
Development of efficient and renewable electrocatalytic systems is foundational to creation of effective means to produce solar fuels. Many redox enzymes are functional electrocatalysts when immobilized on an electrode, but long-term stability of isolated proteins limits use in applications. Thus there is interest in developing bio-inspired functional catalysts or electrocatalytic systems based on living organisms. This dissertation describes efforts to create both synthetic and biological electrochemical systems for electrocatalytic hydrogen production.
The first part of this dissertation describes the preparation of three different types of proton reduction catalysts. First, four bioinspired diiron complexes of the form (μ-SRS)Fe(CO)3[Fe(CO)(N-N)] for SRS = 1,2-benzenedithiolate (bdt) and 1,3-propanedithiolate (pdt) and N-N = 2,2’-bipyridine (bpy) and 2,2’-bypyrimidine (bpym), are described. Electrocatatlytic experiments show that although the byprimidinal complexes are not catalysts, the bipyridyl complexes produce hydrogen from acetic acid under reducing conditions. Second, three new mononuclear FeII carbonyl complexes of the form [Fe(CO)(bdt)(PPh2)2] in which P2 = bis-phosphine: 4,5-Bis(diphenylphosphino)- 9,9-dimethylxanthene (Xantphos), 1,2-Bis(diphenylphosphino)benzene (dppb), or cis- 1,2-Bis(diphenylphosphino)ethylene (dppv) are described. All are functional bio-inspired models of the distal Fe site of [FeFe]-hydrogenases. Of these, the Xanthphos complex is the most stable to redox reactions and active as an electrocatalyst. Third, a molybdenum catalyst based on the redox non-innocent PDI ligand framework is also shown to produce hydrogen in the presence of acid.
The second part of this dissertation describes creating functional interfaces between chemical and biological models at electrode surfaces to create electroactive systems. First, covalent tethering of the redox probe ferrocene to thiol-functionalized reduced graphene oxide is demonstrated. I demonstrate that this attachment is via the thiol functional groups. Second, I demonstrate the ability to use electricity in combination with light to drive production of hydrogen by the anaerobic, phototrophic microorganism Heliobacterium modesticaldum.
The first part of this dissertation describes the preparation of three different types of proton reduction catalysts. First, four bioinspired diiron complexes of the form (μ-SRS)Fe(CO)3[Fe(CO)(N-N)] for SRS = 1,2-benzenedithiolate (bdt) and 1,3-propanedithiolate (pdt) and N-N = 2,2’-bipyridine (bpy) and 2,2’-bypyrimidine (bpym), are described. Electrocatatlytic experiments show that although the byprimidinal complexes are not catalysts, the bipyridyl complexes produce hydrogen from acetic acid under reducing conditions. Second, three new mononuclear FeII carbonyl complexes of the form [Fe(CO)(bdt)(PPh2)2] in which P2 = bis-phosphine: 4,5-Bis(diphenylphosphino)- 9,9-dimethylxanthene (Xantphos), 1,2-Bis(diphenylphosphino)benzene (dppb), or cis- 1,2-Bis(diphenylphosphino)ethylene (dppv) are described. All are functional bio-inspired models of the distal Fe site of [FeFe]-hydrogenases. Of these, the Xanthphos complex is the most stable to redox reactions and active as an electrocatalyst. Third, a molybdenum catalyst based on the redox non-innocent PDI ligand framework is also shown to produce hydrogen in the presence of acid.
The second part of this dissertation describes creating functional interfaces between chemical and biological models at electrode surfaces to create electroactive systems. First, covalent tethering of the redox probe ferrocene to thiol-functionalized reduced graphene oxide is demonstrated. I demonstrate that this attachment is via the thiol functional groups. Second, I demonstrate the ability to use electricity in combination with light to drive production of hydrogen by the anaerobic, phototrophic microorganism Heliobacterium modesticaldum.
ContributorsLaureanti, Joseph Anthony (Author) / Jones, Anne K. (Thesis advisor) / Moore, Thomas (Committee member) / Redding, Kevin E. (Committee member) / Arizona State University (Publisher)
Created2017
Description
Good food, or food that is good for people and planet, demands a different worldview and approach than the current industrial food system. As an ecofeminist researcher who values reciprocity, justice, and a holistic approach, my research investigates varying good food perspectives by integrating scientific evidence and practical experience. Specifically, I explore the opportunities climatic change have created for innovative and solutions-oriented small-scale food systems techniques in arid regions to define, identify, regulate and communicate good food and its related practices. A significant gap exists between current small-scale good food practices and how they can fit and be valorized into a wider food system. This dissertation combines social science and arts-based methodologies with the intention of digging deeper to understand what is required to support a food system that produces good food. This dissertation is broken down into three deliverables, bound by this introduction and a conclusion: (1) a theoretical research framework for regenerative food systems, grounded in biomimicry and traditional ecological knowledge (TEK) defining and identifying good food and the systems that produce it, (2) a research paper that follows three traditional fermented foods in Arizona to contextualize their socio-cultural aspects within a regulatory framework and propose a way to make food governance more inclusive, and (3) an analytical autoethnographic exploration of the normative aspect of sustainability, and how it can be more regenerative. The narrative is an exploration through the author's past, present, and future in finding ways to instill more regenerative practices in their life in Arizona, as well as amplify the voices of others using podcasts. The dissertation aims to expand the field of food system sustainability to be more inclusive of diverse knowledge systems and arts-based methods in creating an understanding of good food in arid regions.
ContributorsAly El-Sayed, Sara (Author) / Cloutier, Scott (Thesis advisor) / Spackman, Christy (Thesis advisor) / Adamson, Joni (Committee member) / Baumeister, Dayna (Committee member) / Arizona State University (Publisher)
Created2021
Description
Biomimetics is a field where natural and biological systems are replicated in a lab. The evolved hierarchical designs of the floating leaves of the water fern Salvinia Molesta are taken as inspiration as they reveal excellent dual scale roughness capability which also presents superhydrophobic properties in the nature. The microscale eggbeater-shaped hairs are coated with microscopic granules and nanoscopic wax crystals (dual-scale roughness) and wrinkled hydrophilic patches are coated with wax crystals which are evenly distributed on the terminal of each hair. The combination of features with diverse wettability, such as wrinkled hydrophilic patches atop superhydrophobic eggbeater hairs, makes such structures unique. The hydrophilic patches bind the air-water interface to the tips of the eggbeater hairs and inhibit air bubble formation. Salvinia effect of several Salvinia species has been extensively researched. Superhydrophobicity is attracting increasing attention for various applications. Salvinia exhibit multiscale roughness because of the unique combination of smooth hydrophilic patches on elastic eggbeater structures decorated with nanoscopic wax crystals. However, how to reproduce such hierarchical structures with controllable surface roughness is challenging for current fabrication approaches, which hinders the applications of these superhydrophobic properties as well as multi-scale roughness on surfaces in engineered products.The objective of this research is to fabricate and study the superhydrophobic structures using electrically assisted Vat Photopolymerization. In this project, an electrically assisted Vat Photopolymerization 3D printing (e-VPP-3DP) process was developed to control the surface roughness of printed eggbeater structures with distribution of multi walled carbon nanotubes (MWCNTs) for multi scale roughness. Vat Photopolymerization (VPP) is a Photopolymerization technique where a Photo Curable resin is used to rapidly produce dense photopolymer parts. A fundamental understanding of e-VPP technique to create superhydrophobic structures was studied to identify the relation between geometric morphology and mechanical enhancements of these structures. The correlation between the material properties for different weight percentage mixtures of MWCNT, printing parameters and the mechanical properties like attaching forces, surface roughness and superhydrophobic nature are also identified with this study on bioinspired hierarchical structures.
ContributorsDwarampudi, Gana Sai Kiran Avinash Raj (Author) / Li, Xiangjia (Thesis advisor) / Ladani, Leila (Committee member) / Jin, Kailong (Committee member) / Arizona State University (Publisher)
Created2022
Description
Since the conception of DNA nanotechnology, the field has evolved towards the development of complex, dynamic 3D structures. The predictability of Watson-Crick base pairing makes DNA an unparalleled building block, and enables exceptional programmability in nanostructure shape and size. The work presented in this dissertation focuses on expanding two facets of the field: (1) introducing functionality through the incorporation of peptides to create DNA-peptide hybrid materials, and (2) the development of self-assembling DNA crystal lattices for scaffolding biomolecules. DNA nanostructures have long been proposed as drug delivery vehicles; however, they are not biocompatible because of their low stability in low salt environments and entrapment within the endosome. To address these issues, a functionalized peptide coating was designed to act as a counterion to a six-helix bundle, while simultaneously displaying numerous copies of an endosomal escape peptide to enable cytosolic delivery. This functionalized peptide coating creates a DNA-peptide hybrid material, but does not allow specific positioning or orientation of the peptides. The ability to control those aspects required the synthesis of DNA-peptide or DNA-peptide-DNA conjugates that can be incorporated into the nanostructure. The approach was utilized to produce a synbody where three peptides that bind transferrin with micromolar affinity, which were presented for multivalent binding to optimize affinity. Additionally, two DNA handle was attached to an enzymatically cleavable peptide to link two unique nanostructures. The second DNA handle was also used to constrain the peptide in a cyclic fashion to mimic the cell-adhesive conformations of RGD and PHSRN in fibronectin.
The original goal of DNA nanotechnology was to use a crystalline lattice made of DNA to host proteins for their structural determination using X-ray crystallography. The work presented here takes significant steps towards achieving this goal, including elucidating design rules to control cavity size within the scaffold for accommodating guest molecules of unique sizes, approaches to improve the atomic detail of the scaffold, and strategies to modulate the symmetry of each unique lattice. Finally, this work surveys methodologies towards the incorporation of several guest molecules, with promising preliminary results that constitute a significant advancement towards the ultimate goal of the field.
ContributorsMacCulloch, Tara Lynn (Author) / Stephanopoulos, Nicholas (Thesis advisor) / Borges, Chad (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2021