This work examines the selective deposition of two different metals on the same DNA origami template for nanofabrication. DNA, with adjustable size and shape serves as a suitable template for fabricating metal junctions in the nanometer domain via bottom-up assembly. Bottom-up assembly utilizes the recognition capability of molecules like DNA to self-assemble and form structures. In this regard, DNA origami provides a useful means for forming nanostructures by folding single-stranded DNA into different two and three dimensional shapes. Selective deposition of metal on specific locations of a DNA template is essential for making DNA-templated electronic circuits.Site-specific metallization of DNA origami templates was recently demonstrated, for a single metal at molecularly designated sites. This study addresses the next important step of depositing multiple metals on the same template. Specifically, it is an experimental study to demonstrate the gold-copper metal junction on a DNA origami template, and to understand the challenges associated with junction fabrication. DNA-templated circuit fabrication depends on the ability to deposit multiple components on a DNA template. To achieve this, a section of the DNA template was seeded with Au nanoparticles and electrolessly plated with Au. This Au plated section of the template was then masked with an organic layer to protect it from additional deposition. The remaining section of the same template was subsequently seeded with Pd and plated with copper to form the desired metal junction. This work is the first of its kind to demonstrate metal junctions on a DNA origami template. Metallized origami templates were characterized with the help of SEM imaging and EDX composition data to confirm the presence of the two different metals on the same template. In addition, a chemical “mask” was also used successfully at nanometer resolution to protect previously metallized sites (gold plated) to prevent further metal deposition. The results obtained represent important progress toward the realization of DNA-templated components for nano-circuit fabrication. The work also provides the basis for the next step to make metal-semiconductor junctions on a DNA template.

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Building metal nanomaterials with tailored electrical properties is in high demand for electronic device fabrication. However, scalable and inexpensive fabrication of such metallic structures with nanometer precision remains a challenge. DNA origami is a versatile and robust self-assembly method which allows fabrication of arbitrary structures at the nanoscale. In this thesis, DNA origami templated metal nanostructure fabrication method is introduced. Continuous metal nanostructures with controlled geometry as well as the selective deposition of multi-nanomaterials (metals and semiconductors) at specific sites on origami templates play an im-portant role in the fabrication of DNA based nanoelectronics system. A mold DNA origami with quadratic cross-section was constructed and used as template for the gold nanoparticles metal growth. Each individual mold element acted as a lego-brick in this modular mold system. (1) Linear metallic nanostructures with controlled length and programmable patterns were fabricat-ed at superior yields by systematically investigating the interface of each mold element. (2) A versatile fabrication modular mold platform for metallic nanostructures with complex shapes was further developed by integrating particular molds with different diameters, additional dock-ing sites, and junctions. Caged metal nanostructures, constrained gold growth and branched structures with extensions in two dimensions were successfully realized. (3) Micrometer long, homogeneous and continuous gold nanowires were obtained with exceeding quality. Using elec-tron-beam lithography and low-temperature conductance measurements, ohmic behavior of such nanowires were observed, confirming metallic conductive property. (4) A method for the synthesis and DNA functionalization of semiconducting nanorods was established. Metal-semiconductor heterostructures were fabricated based on the modular mold system. Semicon-ducting nanorods, as well as gold nanoparticles, were placed at defined positions on the DNA modular platform and a direct metal-semiconductor interface was achieved after the electroless metal deposition. (5) An improved and optimized metallization of DNA origami templated gold nanowires were further developed to increase the conductivity performance. Various reaction parameters were investigated and the obtained gold nanowires with a reduced number of AuNPs achieved an anisotropic growth. This developed DNA origami template mold modular platform addresses the size, pattern, and geometry controls over the metallic nanostructures. For the ap-plication prospect, the conductivity of such metallic nanostructures and controlled placement of different nanomaterials enable an important step towards the nanodevices and systems fabrica-tion based on DNA. / Der Aufbau metallischer Nanomaterialien mit angepassten elektrischen Eigenschaften ist für die Verwendung in elektronischen Bauteilen von großer Bedeutung. Dabei ist die skalierbare und günstige Herstellung metallischer Strukturen im Nanometerbereich weiterhin eine Herausforderung. Die DNA Origami Technik bietet hier eine vielseitig einsetzbare und stabile Methode zur Selbstassemblierung, welche die Herstellung beliebiger nanoskalierter Strukturen ermöglicht. In dieser Arbeit wird ein neuer Ansatz zur Herstellung metallischer Nanostrukturen mit Hilfe von DNA Origami Templaten vorgestellt. Kontinuierliche Metallnanostrukturen mit einer definierten Geometrie, sowie die selektive Anbindung verschiedener Nanomaterialien (Metalle und Halbleiter) an spezifischen Anbindungsstellen des Origamitemplates spielen eine wichtige Rolle bei der Herstellung DNA basierter nanoelektrischer Systeme. Ein DNA Origami Mold mit einem quadratischen Querschnitt wurde als Templat für die Metallisierung von Goldnanopartikeln verwendet. Das legostein-artige Design der einzelnen Origami Molds ermöglicht die Assemblierung in einem modularen System. (1) Lineare metallische Nanostrukturen mit kontrollierter Länge und programmierbarem Muster wurden mit hohen Ausbeuten assembliert, indem das Interface der einzelnen Origamistrukturen systematisch untersucht wurde. (2) Weiterhin wurde eine vielseitige, sowie modulare Plattform für metallische Nanostrukturen mit komplexen Formen entwickelt. Dabei wurden spezielle Origamistrukturen mit unterschiedlichem Durchmesser, sowie zusätzlichen Anbindungsstellen und Verzweigungen integriert. Die erfolgreiche Metallisierung linearer und verzweigter Nanostrukturen in zwei Dimensionen wurde durch ein restriktives Goldwachstum im Inneren der Origamistrukturen realisiert. (3) Homogene und kontinuierliche Goldnanodrähte mit Mikrometerlänge und außerordentlicher Qualität wurden fabriziert. Mit Hilfe von Elektronenstrahllithographie wurde die Leitfähigkeit der Strukturen im Niedrigtemperaturbereich untersucht, wobei ein ohmsches Ladungstransportverhalten der Nanodrähte nachgewiesen werden konnte, welches die metallische Leitfähigkeit der Strukturen bestätigte. (4) Eine Methode zur Synthese und DNA Funktionalisierung von Halbleiternanostäbchen wurde eingeführt. Zudem konnten Metall-Halbleiterheterostrukturen hergestellt werden, basierend auf dem entworfenen modularen Origamisystem. Halbleiternanostäbchen und Goldnanopartikel wurden an definierten Positionen der DNA Origami platziert. Durch eine anschließende Metallisierung konnte ein direktes Metall-Halbleiterinterface hergestellt werden. (5) Eine verbesserte und optimierte Metallisierung der DNA Origami basierten Goldnanodrähte zur Erhöhung der Leitfähigkeit wurde entwickelt. Dazu wurden verschiedene Reaktionsparameter optimiert, so dass ein anisotropes Wachstum mit einer reduzierten Anzahl von Goldnanopartikel ermöglicht werden konnte. Die, in dieser Arbeit entwickelte DNA Origami Plattform ermöglicht die Kontrolle über Größe, Struktur und Geometrie metallischer Nanostrukturen. Die ohmsche Leitfähigkeit dieser Nanostrukturen und die zusätzliche Assemblierung verschiedener Nanomaterialien stellen dabei einen wichtigen Schritt für eine potentielle Verwendung in elektrischen Nanogeräten dar.

Die Herstellung funktionaler und strukturell wohldefinierter Nanostrukturen ist eine Voraussetzung, um hochentwickelte Device im Bereich der Nanoelektronik oder Nanooptik zu entwickeln. Bottom-Up-Verfahren, welche auf biomolekularen Selbstassemblierungsprozessen basieren, haben sich hierfür, aufgrund ihrer hoch parallelen Synthese, als besonders effizient erwiesen. In dieser Arbeit wurde die DNA-Origami-Technik genutzt, um eine funktionale Nanostruktur für elektronische Schaltkreise oder optische Anwendungen zu assemblieren. Planare DNA-Origami-Strukturen können als molekulare Steckbretter dienen, um funktionale Objekte mit Nanometer-Präzision anzuordnen. Diese Arbeit verwendete als solch ein Objekt ein p-konjugiertes Polymer. Im Vergleich zu anorganischen Nanoobjekten, wie metallische Nanopartikel, zeichnen sich diese Polymere durch mechanische Flexibilität und ein leichtes Gewicht aus. Aufgrund ihres p-konjugierten Rückgrates sind diese Polymere optisch und elektronisch funktional. Diese Eigenschaften können über ihre molekulare Struktur eingestellt werden. Dotiert sind diese Polymere Halbleiter oder sogar Leiter. Ihre Funktionalität wurde in diversen optoelektronischen und elektronischen Bauteilen, wie z.B. organischen Feldeffekt-Transistoren, bewiesen. Für Anwendungen auf der Nanoskala sind die Polythiophenderivate des Typ P3RT besonders interessant. Deren Synthese, die Kumada Katalysatorenübertragungspolykondensation, folgt einem kontrollierten Kettenwachstumsmechanismus. Die Polymere zeichnen sich durch eine eng verteilte, einstellbare Molmasse und definierte Endgruppen aus. Im ersten Teil dieser Arbeit wurde das Polythiophenderivat designt und synthetisiert. Eine Oligoethylenglykol-Seitenkette gewährleistet die Löslichkeit in Wasser und Kompatibilität zur DNA. Über einen ex-situ Initiator wurde eine funktionelle Endgruppe eingeführt, um das Polymer zugänglich zur DNA-Origami-Assemblierung zu machen. Mittels verschiedener Charakterisierungen wurden die definierte Struktur und gute Löslichkeit in Wasser demonstriert. Im zweiten Abschnitt dieser Arbeit wurde die elektronische Aktivierung dieses Polythiophens durch molekulares Dotieren auf der Mikroskala untersucht. Der Einfluss des Dotierungmittels 2,3,5,6-Tetrafluoro-7,7,8,8-tetracyanoquinodimethan auf die optischen, morphologischen und elektronischen Eigenschaften des Polymers als dünner Film wurde untersucht, um optimale Dotierungskonditionen zu etablieren. Die dotierten Polymerfilme zeigten eine deutlich verbesserte Leitfähigkeit im Vergleich zu unbehandelten Filmen. Im dritten Abschnitt dieser Arbeit wurde die DNA-Origami-gelenkte Anordnung des Polythiophens untersucht. Hierfür wurde das Polymer zunächst an ein modifiziertes, synthetisches Oligonukleotid igebunden. Das resultierende Blockcopolymer wurde dann ortsspezifisch an DNA- Überhänge angebunden, welche sich eng aufgereiht auf einer planare DNA-Origami-DNA-Origami-Struktur befanden. Die Polymer-DNA-Hybridstrukturen wurden mittels hochauflösender Rasterkraftmikroskopie charakterisiert. Aufgrund von p-p Stapelwechselwirkungen der Polythiophenrückgrate kam es zur Ausbildung supramolekulare Polymerdrähte. Die Abmaße dieser Drähte wurde über der Anordnung der DNA-Überhänge gesteuert. Es wurde gezeigt, dass durch schrittweises Aufbrechen der p-p-Stapelwechselwirkung die Fluoreszenz dieser Polythiophendrähte verändert werden kann. Die Fähigkeit könnte nützlich sein, um die optischen Eigenschaften dieser Drähte für photonische Leitungen einfach auf Sender und/oder Empfänger abzustimmen. Des Weiteren sind diese Wechselwirkungen nötig, um Ladungsträger durch diese Drähte zu transportieren. Mittels Leitfähigkeitsrasterkraftmikroskopie wurden erste Untersuchungen getätigt um die Fähigkeit dieser Polythiophen-DNA-Hybridstrukturen als elektronischer Draht zu evaluieren. Im Rahmen dieser Arbeit konnte kein Ladungstransport festgestellt werden. Zusammenfassend wurde eine neuartige, funktionale Polythiophen-basierende Nanostruktur mittels der DNA-Origami-Technik synthetisiert. Solche Polymer-DNA-Hybridstrukturen versprechen eine vielfältige Anwendbarkeit als optische oder elektronische Bauteile in Schaltkreisen.:Kurzfassung i Acknowledgements iii List of Figures vii List of Tables ix 1 Introduction and Objectives 1 1.1 Introduction 2 1.2 Objectives of the Doctoral Thesis 4 2 Background 5 2.1 p-Conjugated Polymers 6 2.1.1 Fundamentals of Conjugated Polymers 6 2.1.2 Polarons and Molecular p-Doping of Polythiophenes 10 2.1.3 Synthesis of Polythiophene Derivatives 14 2.2 DNA-Based Templates for Confined, Functional Nanostructures 22 2.2.1 Structure and Properties of Deoxyribonucleic Acid 23 2.2.2 Linear, DNA-Templated Confined Nanostructures 25 2.2.3 DNA Origami as Molecular Breadboard 27 2.2.4 DNA Origami-Templated, Confined Nanostructures 30 2.3 Characterization Techniques for Conjugated Polymers and Functional Nanostructures 33 2.3.1 Structural Characterization 33 2.3.2 Spectroscopic Characterization 34 2.3.3 Imaging of Nanostructures 35 2.3.4 Electrical Characterization at the Nanoscale 36 3 Experimental Section 39 3.1 Materials 40 3.2 Synthesis 42 3.2.1 NH 2 -P3(EO) 3 T 42 3.2.2 N 3 -P3(EO) 3 T 44 3.2.3 P3(EO) 3 T-b-ON 44 3.2.4 P3(EO) 3 T@Origami 46 3.3 Methods and Instrumentation 47 4 Results and Discussion 57 4.1 Synthesis and Characterization of the Polythiophene Derivative 58 4.1.1 Introduction 58 4.1.2 Molecular Design of the Customized Polythiophene Derivative 59 4.1.3 Ex-Situ Initiated Kumada Catalyst-Transfer Polycondensation 60 4.1.4 Structural Characterization 62 4.1.5 Optical Characterization66 4.1.6 Summary 69 4.2 Electronic Functionality of P3(EO)3T as 2D Bulk 70 4.2.1 Introduction 70 4.2.2 Solution-Based Doping 70 4.2.3 Charge Transfer Reaction Upon Doping 71 4.2.4 Optical and Vibrational Spectroscopy 73 4.2.5 Microstructure and Morphology 78 4.2.6 Electrical Characterization 82 4.2.7 Summary 85 4.3 DNA Origami-Templated Formation of Polythiophene Filaments 86 4.3.1 Introduction 86 4.3.2 Block Copolymer Formation 87 4.3.3 Planar DNA Origami Template 93 4.3.4 Synthesis of P3(EO)3T@pad Hybrid Structure 96 4.3.5 Tunable Fluorescence of P3(EO)3T@pad Hybrid Structures 100 4.3.6 Potential as Conducting Wire 102 4.3.7 Summary 109 5 Conclusions and Future Perspectives 111 5.1 Conclusions 112 5.2 Future Perspectives 113 Appendix 115 A Supplementary Information 115 B DNA Origami Sequences 123 Abbreviations 131 List of Symbols 133 Bibliography 135 Publications and Conference Contributions 158

Continuum manipulators which are robot limbs inspired by trunks, snakes, and tentacles, represent a promising field in robotic manipulation research. They are well known for their compliance, as they can conform to the shape of objects they interact with. Furthermore, they also benefit from improved dexterity and reduced weight compared to traditional rigid manipulators. The current state of the art continuum robots typically consists of a bulky pneumatic or tendon-driven actuation system at the base, hindering their scalability. Additionally, they tend to sag due to their own weight and are weak in the torsional direction, limiting their performance under external load. This work presents an origami-inspired cable-driven continuum manipulator module that offers low-cost, light-weight, and is inherently safe for human-robot interaction. This dissertation includes contributions in the design of the modular and torsionally strong continuum robot, the motion planning and control of the system, and finally the embedded sensing to close the loop providing robust feedback.

The objective of this thesis is to develop and demonstrate techniques for self-deployment of origami-based mechanical systems achieved through internal strain-energy storage and release, with special application to medical implant devices. The potential of compliant mechanisms and related origami-based mechanical systems to store strain-energy make them ideal candidates forapplications requiring an actuation or deployment process, such as space system arrays and minimally invasive surgical devices. The objective of this thesis is achieved by first categorizing differentdeployment methods in origami-based, deployable mechanisms and then further exploring the use of strain energy to facilitate actuation in deployable mechanisms. With this understanding inplace, there are opportunities using strain energy to develop new approaches to deploy particular mechanical systems. These origami-based mechanisms have the ability to improve devices in themedical field. This work contributes to the knowledge base of self actuating deployable structures in origami-based mechanical systems by developing design concepts and models for strain energystorage and release. By developing the foundational characteristics for self-actuation, the work will be demonstrated thorough applications in medical implant devices.

This work develops models and tools to help designers address the challenges associated with designing origami-based and developable mechanisms. These models utilize strain energy, kinematics, compliant mechanisms, and graphical techniques to make the design of origami-based and developable mechanisms approachable and intuitive. Origami-based design tools are expanded through two methods. First presented is a generalized approach for identifying single-output mechanical advantage for a multiple-input compliant mechanism, such as many origami-based mechanisms. The model is used to predict the force-deflection behavior of an origami-based mechanism (Oriceps) and is verified with experimental data from magnetic actuation of the mechanism. Second is a folding technique for thick-origami, called the regional-sandwiching of compliant sheets (ReCS), which creates flat-foldable, rigid-foldable, and self-deploying thick origami-based mechanisms. The technique is used to create mountain/valley assignments for each fold about a vertex, constraining motion to a single branch of folding. Strain energy in deflected flexible members is used to enable self-deployment. Three physical models, a simple single-fold mechanism, a degree-four vertex mechanism, and a full tessellation, are presented to demonstrate the ReCS technique. Developable mechanism design is further enabled through an exploration of their feasible design space. Terminology is introduced to define the motion of developable mechanisms while interior and exterior to a developable surface. The limits of this motion are identified using defined conditions. It is shown that the more difficult of these conditions may be treated as a non-factor during the design of cylindrical developable mechanisms given certain assumptions. These limits are then applied to create a resource for designing bistable developable mechanisms (BDMs) that reach their second stable positions while exterior or interior to a cylindrical surface. A novel graphical method for identifying stable positions of linkages using a single dominant torsional spring, called the Principle of Reflection, is introduced and implemented. The results are compared with a numerical simulation of 30,000+ mechanisms to identify possible incongruencies. Two tables summarize the results as the guide for designing extramobile and intramobile BDMs. In fulfilling the research objectives, this dissertation contributes to the scientific community of origami-based and developable mechanism design approaches. As a result of this work, practitioners will be better able to approach and design complex origami-based and developable mechanisms.

This work presents the bottom-up fabrication of DNA origami-assembled metal nanowires and metal-semiconductor junctions, and their electrical characterization. Integration of metal and semiconductor nanomaterials into prescribed sites on self-assembled DNA origami has facilitated the fabrication of electronic nanomaterials, whereas use of conventional tools in their characterization combines bottom-up and top-down technologies. To expand the contemporary DNA-based nanofabrication into nanoelectronics, I performed site-specific metallization of DNA origami to create arbitrarily arranged gold nanostructures. I reported improved yields and conductivity measurements for Au nanowires created on DNA origami tile substrates. I measured the conductivity of C-shaped Au nanowires created on DNA tiles (∼130 nm long, 10 nm diameter, and 40 nm spacing between measurement points) with a four-point measurement technique which revealed the resistivity of the gold nanowires was as low as 4.24 × 10-5 Ω m. Next, I fabricated DNA origami-templated metal-semiconductor junctions and performed electrical characterization. Au and Te nanorods were attached to DNA origami in an alternating fashion. Electroless gold plating was used to create nanoscale metal--semiconductor interfaces by filling the gaps between Au and Te nanorods. Two-point electrical characterization indicated that the Au--Te--Au junctions were electrically connected, with non-linear current--voltage curves. Finally, I formed metal-semiconductor nanowires on DNA origami by annealing polymer-encased nanorods. Polymer-coated Au and Te nanorods pre-attached to ribbon-shaped DNA origami were annealed at 170°C for 2 min. Gold migration occurred onto Te nanorods during annealing and established electrically continuous interfaces to give Au/Te nanowires. Electrical characterization of these Au/Te/Au assemblies revealed both nonlinear current-voltage curves and linear plots that are explained. The creation of electronic nanomaterials such as metal nanowires and metal-semiconductor junctions on DNA origami with multiple techniques advances DNA nanofabrication as a promising path toward future bottom-up fabrication of nanoelectronics.

Biological nanomaterials are defined as materials with sizes within the nanoscale range of 1 - 100 nm. The fundamental functionalities and biocompatibility of these materials can be tailored for biotechnology applications. In 1983, Ned Seeman successfully developed the first customized DNA nanostructures, Holliday junctions. Since then, the field has continued to expand rapidly and various 2D and 3D nanostructures has been designed. Although the high predictability of DNA base-pairing is essential for the design of complex DNA nanostructures, it greatly limits its functional versatility; therefore, proteins are conjugated with DNA nanostructures to compensate for that. DNA origami-protein hybrid nanostructures were introduced in 2012. However, the structural units based on DNA origami-protein hybrid nanostructures are still limited, and the majority are constructed by covalent or sequence-specific non-covalent interactions. Here we utilize the inherent, non-sequence-specific interaction between DNA and histones to present sequence-independent self-assembled DNA origami-protein hybrid nanostructures. We demonstrated using various molecular biology and imaging techniques that ssDNAs and histone proteins self-assemble into structurally well-defined complexes. We successfully assembled DNA origami–histone hybrid nanostructures using two different shapes of DNA origami: rectangular (PF-3), and rectangular with central aperture (PF-2) nanostructures. We observed precise localization of nucleosome-like histone-ssDNA nanostructures at the edge (PF-3) or the center (PF-2) of the DNA origami. In addition, we demonstrated that this DNA origami-histone interaction results in the assembly of larger DNA origami complexes, including a head-to-head type dimer and a cross-shape complex. Our results suggest the successful self-assembly of the DNA origami–histone hybrid nanostructures provide a principal structural unit for constructing higher-order nanostructures. Given the reversible nature of the geometry-based noncovalent interaction between the DNA origami and the nucleosome-like histone-ssDNA nanostructures, the self-assembly/disassembly of DNA-histones hybrid nanostructures may open new opportunities to construct stimuli-responsive DNA-protein hybrid nanostructures.

Indiana University-Purdue University Indianapolis (IUPUI) / Thin-walled structures find wide applications in the automotive industry as energy absorption devices. A great deal of research has been conducted to design thin-walled structures, where the main objective is to reduce peak crushing forces and increase energy absorption capacity. With the advancement of computers and mathematics, it has been possible to develop 2D patterns which when folded turn into complex 3D structures. This technology can be used to develop patterns for getting structures with desired properties. In this study, square origami tubes with folding pattern (Yoshimura pattern) is designed and studied extensively using numerical analysis. An accurate Finite Element Model (FEM) is developed to conduct the numerical analysis. A parametric study was conducted to study the influence of geometric parameters on the mechanical properties like peak crushing force, mean crushing force, load uniformity and maximum intrusion, when subjected to dynamic loading. The results from this analysis are studied and various conclusions are drawn. It is found that, when the tube is folded with the pattern having specific dimensions, the performance is enhanced significantly, with predictable and stable collapse. It is also found that the stiffness of the module varies with geometrical parameters. With a proper study it is possible to develop origami structures with functionally graded stiffness, the performance of which can be tuned as per requirement, hence, showing promising capabilities as an energy absorption device where progressive collapse from near to end impact end is desired.