Nanofabrication for Molecular Scale Devices

The predicted 22-nm barrier which is seemingly going to put a final stop to Moore’s law is essentially related to the resolution limit of lithography. Consequently, finding suitable methods for fabricating and patterning nanodevices is the true challenge of tomorrow’s electronics. However, the pure matter of moulding devices and interconnections is interwoven with research on new materials, as well as architectural and computational paradigms. In fact, while the performance of any fabrication process is obviously related to the characteristic of the materials used, a particular fabrication technique can put constraints on the definable geometries and interconnection patterns, thus somehow biasing the upper levels of the computing machine. Further, novel technologies will have to account for heat dissipation, a particularly tricky problem at the nanoscale, which could in fact prevent the most performing nanodevice from being practically employed in complex networks. Finally, production costs – exponentially growing in the present Moore rush – will be a key factor in evaluating the feasibility of tomorrow technologies. The possible approaches to nanofabrication are commonly classified into top-down and bottom-up. The former involves carving small features into a suitable bulk material; in the latter, small objects assemble to form more complex and articulated structures. While the present technology of silicon has a chiefly top-down approach, bottom-up approaches are typical of the nanoscale world, being directly inspired by nature where molecules are assembled into supramolecular structures, up to tissues and organs. As top-down approaches are resolution-limited, boosting bottom-up approaches seems to be a good strategy to future nanoelectronics; however, it is highly unlikely that no patterning will be required at all, since even with molecular-scale technologies there is the need of electrically contacting the single elements and this most often happens through patterned metal contacts, although all-molecular devices were also proposed. Here, we will give some insight into both top-down and bottom-up without the intention to be exhaustive, because of space limitations

Nanofabrication

We face many challenges in the 21st century, such as sustainably meeting the world's growing demand for energy and consumer goods. I believe that new developments in science and technology will help solve many of these problems. Nanofabrication is one of the keys to the development of novel materials, devices and systems. Precise control of nanomaterials, nanostructures, nanodevices and their performances is essential for future innovations in technology. The book "Nanofabrication" provides the latest research developments in nanofabrication of organic and inorganic materials, biomaterials and hybrid materials. I hope that "Nanofabrication" will contribute to creating a brighter future for the next generation

Biological Nanowires: Integration of the silver(I) base pair into DNA with nanotechnological and synthetic biological applications

Modern computing and mobile device technologies are now based on semiconductor technology with nanoscale components, i.e., nanoelectronics, and are used in an increasing variety of consumer, scientific, and space-based applications. This rise to global prevalence has been accompanied by a similarly precipitous rise in fabrication cost, toxicity, and technicality; and the vast majority of modern nanotechnology cannot be repaired in whole or in part. In combination with looming scaling limits, it is clear that there is a critical need for fabrication technologies that rely upon clean, inexpensive, and portable means; and the ideal nanoelectronics manufacturing facility would harness micro- and nanoscale fabrication and self-assembly techniques. The field of molecular electronics has promised for the past two decades to fill fundamental gaps in modern, silicon-based, micro- and nanoelectronics; yet molecular electronic devices, in turn, have suffered from problems of size, dispersion and reproducibility. In parallel, advances in DNA nanotechnology over the past several decades have allowed for the design and assembly of nanoscale architectures with single-molecule precision, and indeed have been used as a basis for heteromaterial scaffolds, mechanically-active delivery mechanisms, and network assembly. The field has, however, suffered for lack of meaningful modularity in function: few designs to date interact with their surroundings in more than a mechanical manner. As a material, DNA offers the promise of nanometer resolution, self-assembly, linear shape, and connectivity into branched architectures; while its biological origin offers information storage, enzyme-compatibility and the promise of biologically-inspired fabrication through synthetic biological means. Recent advances in DNA chemistry have isolated and characterized an orthogonal DNA base pair using standard nucleobases: by bridging the gap between mismatched cytosine nucleotides, silver(I) ions can be selectively incorporated into the DNA helix with atomic resolution. The goal of this thesis is to explore how this approach to “metallize” DNA can be combined with structural DNA nanotechnology as a step toward creating electronically-functional DNA networks. This work begins with a survey of applications for such a transformative technology, including nanoelectronic component fabrication for low-resource and space-based applications. We then investigate the assembly of linear Ag+-functionalized DNA species using biochemical and structural analyses to gain an understanding of the kinetics, yield, morphology, and behavior of this orthogonal DNA base pair. After establishing a protocol for high yield assembly in the presence of varying Ag+ functionalization, we investigate these linear DNA species using electrical means. First a method of coupling orthogonal DNA to single-walled carbon nanotubes (SWCNTs) is explored for self-assembly into nanopatterned transistor devices. Then we carry out scanning tunneling microscope (STM) break junction experiments on short polycytosine, polycationic DNA duplexes and find increased molecular conductance of at least an order of magnitude relative to the most conductive DNA analog. With an understanding of linear species from both a biochemical and nanoelectronic perspective, we investigate the assembly of nonlinear Ag+-functionalized DNA species. Using rational design principles gathered from the analysis of linear species, a de novo mathematical framework for understanding generalized DNA networks is developed. This provides the basis for a computational model built in Matlab that is able to design DNA networks and nanostructures using arbitrary base parity. In this way, DNA nanostructures are able to be designed using the dC:Ag+:dC base pair, as well as any similar nucleobase or DNA-inspired system (dT:Hg2+:dT, rA:rU, G4, XNA, LNA, PNA, etc.). With this foundation, three general classes of DNA tiles are designed with embedded nanowire elements: single crossover Holliday junction (HJ) tiles, T-junction (TJ) units, and double crossover (DX) tile pairs and structures. A library of orthogonal chemistry DNA nanotechnology is described, and future applications to nanomaterials and circuit architectures are discussed

Light-assisted hierarchical fabrication of two-dimensional surfaces using DNA-functionalized semiconductor nanocrystal quantum dots

The development of novel strategies for self-assembly in the field of nanotechnology has witnessed remarkable progress in recent years. Here, we present a DNA-driven programmable self-assembly to fabricate the targeted nanophotonic structures. The exploitation of the programmable properties of DNA and the unique optical properties of QDs unfolds the ability to engineer complex nanostructures with laser irradiation. The main advantages of this method are the precise interaction of colloidal quantum dots (QDs)/nanoparticles (NPs) with the substrate and its reversibility in tuning the temperature of the medium. Two-dimensional (2D) hierarchical patterns of QD-ssDNA (ss-single stranded) conjugates were formed over the amine-ssDNA (NH-ssDNA complementary to the ssDNA conjugated with QDs) coated glass substrates using the laser (green laser light) radiation for3 or4 h. The localised heating effect of laser created a dark spot on the substrate where the laser was irradiated. The optical microscopy images confirmed the effect of laser irradiation on the coating behaviour of QD-ssDNA conjugates on the substrate. Further, green-emitting QD-ssDNA were coated onto the hole created by laser radiation over the red-emitting QD-ssDNA-coated substrate. The optical properties of DNA-functionalized QDs can be actively controlled on the complementary DNA-functionalized glass surface by an external optical excitation. The results of this study demonstrate the potential of light-driven self-assembly as a powerful tool for fabricating desired nanostructures of DNA-QD conjugates. This technique holds promise for various applications, including the development of advanced optical devices, nanophotonic circuits, and bioengineering systems

Elektrostatisk självorganisation av DNA origami och guldnanopartiklar

Spatially well-ordered structures of gold nanoparticles(AuNPs) and other metal nanoparticles have unique electronic, magnetic and optical properties, and hence there is ever-increasing interest towards these kinds of nanomaterials. DNA and DNA nanostructures have successfully been used to direct the higher-ordered arrangement of AuNPs, but the programmable arrangement of them into larger, well-defined structures is still challenging. The objective of this thesis is to establish a self-assembly method based on electrostatic interactions in which DNA origami nanostructures can be used to guide the higher ordered arrangement of cationic AuNPs in a controlled and programmable manner. The AuNP binding properties of different DNA origami structures was studied with UV/Vis spectroscopy and agarose gel electrophoretic mobility shift assay. DNA origami-AuNP assemblies were formed during dialysis against decreasing ionic strength, and the formed assemblies were characterized using small-angle X-ray scattering, transmission electron microscopy and cryogenic electron tomography. Electrostatic self-assembly of DNA origami 6HB nanostructures and small AuNPs (D_core = 2.5 nm, D_hydrodynamic_diameter = 8.5 nm) yielded highly ordered superlattice structures with a 3D tetragonal lattice structure, whereas other studied combinations of DNA origami structures and AuNPs resulted in amorphous aggregates. These results suggest that both shape and charge complementarity between the building blocks are needed for well-ordered structures to be formed through electrostatic self-assembly. According to the results, electrostatic self-assembly guided by DNA origami structures seems promising for construction of novel, well-ordered structures with unique properties, such as lattice geometry, designed specifically for the chosen application.Guldnanopartiklar och andra metallnanopartiklar organiserade i välordnade strukturer har unika elektroniska, magnetiska och optiska egenskaper och därför finns det ett ständigt växande intresse för dessa typer av nanomaterial. DNA och nanostrukturer av DNA har framgångsrikt använts för att framställa välordnade, förutbestämda tredimensionella guldnanopartikelstrukturer, men det finns fortfarande utmaningar att tackla. Målet med detta diplomarbete är att utveckla en metod för självorganisation baserat på elektrostatiska interaktioner i vilken DNA-origaminanostrukturer på ett programmerbart och kontrollerat sätt kan användas för att styra hurudana strukturer som byggs upp av katjoniska guldnanopartiklar. De olika DNA-origamistrukturernas förmåga att binda guldnanopartiklar studerades med UV/Vis-spektroskopi och agarosgelelektrofores. DNA-origami-guldnanopartikelsystem byggdes upp genom dialys mot stegvis minskade jonkoncentrationer och de uppkomna strukturerna karaktäriserades med lågvinkelspridning, transmissionselektronmikroskopi och kryelektrontomografi. Elektrostatisk självorganisation av DNA-origami 6HB nanostrukturer och små guldnanopartiklar (D_kärna = 2.5 nm, D_hydrodynamisk_diameter = 8.5 nm) gav välordnade tredimensionella tetragonala kristallstrukturer, medan andra undersökta kombinationer av DNA origami strukturer och guldpartiklar endast resulterade i amorfa strukturer. Detta indikerar att de enskilda byggstenarna behöver kompletterande form och laddning för att välordnade strukturer skall kunna byggas upp genom elektrostatik självorganisation. Det förefaller dock finnas goda framtidsutsikter för elektrostatisk självorganisation som en metod att framställa välordnade strukturer med egenskaper, så som typ av kristallstruktur, lämpliga just för det önskade användningsområdet

Sensing and Regulation from Nucleic Acid Devices

abstract: The highly predictable structural and thermodynamic behavior of deoxynucleic acid (DNA) and ribonucleic acid (RNA) have made them versatile tools for creating artificial nanostructures over broad range. Moreover, DNA and RNA are able to interact with biological ligand as either synthetic aptamers or natural components, conferring direct biological functions to the nucleic acid devices. The applications of nucleic acids greatly relies on the bio-reactivity and specificity when applied to highly complexed biological systems. This dissertation aims to 1) develop new strategy to identify high affinity nucleic acid aptamers against biological ligand; and 2) explore highly orthogonal RNA riboregulators in vivo for constructing multi-input gene circuits with NOT logic. With the aid of a DNA nanoscaffold, pairs of hetero-bivalent aptamers for human alpha thrombin were identified with ultra-high binding affinity in femtomolar range with displaying potent biological modulations for the enzyme activity. The newly identified bivalent aptamers enriched the aptamer tool box for future therapeutic applications in hemostasis, and also the strategy can be potentially developed for other target molecules. Secondly, by employing a three-way junction structure in the riboregulator structure through de-novo design, we identified a family of high-performance RNA-sensing translational repressors that down-regulates gene translation in response to cognate RNAs with remarkable dynamic range and orthogonality. Harnessing the 3WJ repressors as modular parts, we integrate them into biological circuits that execute universal NAND and NOR logic with up to four independent RNA inputs in Escherichia coli.Dissertation/ThesisDoctoral Dissertation Biochemistry 201

Plasmonic Nanostructures for Biosensing Applications

The aim of this work is the study, the design and the nanofabrication of innovative plasmonic nanostructured materials to develop label-free optical biosensors. Noble metalbased nanostructures have gained interest in the last years due to their extraordinary optical properties, which allow to develop optical biosensors able to detect very low concentrations of specific biomolecules, called analyte, down to the picomolar range. Such biosensors rely on the Surface Plasmon Resonance (SPR) excitation which occurs under specific conditions that depend both on the morphology of the nanostructure and on the adjacent dielectric medium. Therefore, the binding of the biomolecules to metal surfaces is revealed as a change in the SPR condition. Four kinds of nanostructures are investigated in this work: ordered and disordered nanohole array (o-NHA, d-NHA), nanoprism array (NPA) and nanodisk array (NDA). The o-NHA and d-NHA consist of a thin metallic film (50 - 100 nm) patterned with, respectively, a hexagonal and a disordered array of circular holes. The NPA consists of a honeycomb lattice of triangle shaped nanoprisms with edges of about 100 - 200 nm and height of 40 - 80 nm. Finally, the NDA consists of a disordered array of non-interacting disks with 100 - 300 nm diameter and 40 - 80 nm height. The first two support the Extended-SPR whereas the last two, due to their three-dimensional confinement, present Localized-SPR property. Two colloidal techniques are employed for the scalable and cost-effective synthesis of wide areas of nanostructures that allow a fine control of the morphology: NanoSphere Lithography (NSL) and Sparse Colloidal Lithography (SCL). Ordered arrays were nanofabricated by NSL (i.e., NPA and o-NHA) whereas disordered nanostructures were synthesized by the SCL (i.e., NDA and d-NHA). Firstly, the nanostructures are simulated by Finite Element Method (FEM) computations and their performances in revealing small variations of the dielectric medium at the interface is evaluated as a function of their geometrical parameters. Simulated local sensitivities range from 3.1 nm/RIU of the o-NHA up to 13.6 nm/RIU of the NPA. Afterwards, the sensing performances are evaluated experimentally with nanofabricated samples and comparable but slightly smaller sensitivities are obtained. Secondly, a proof-of-concept protocol for the detection assay, that relies on the binding of streptavidin protein to the biotinylated gold surfaces, is exploited to test the nanostructures as biosensors. A 4.4 nM limit of detection is reached with the best performing biosensor (NPA) and picomolar ones are expected for NPA and NDA with a suitable improvement of the functionalization protocol. Finally, complementary single stranded RNA molecules were used, respectively, as bioreceptor and analyte. Revealing short sequences of non-coding RNA, called microRNA, is fundamental for the medical research since these oligonucleotides act as biomarkers for specific diseases, like tumors. Signals of about 13 nm are obtained from the binding of bioreceptor to the nanostructure and from the hybridization of the analyte oligonucleotide at saturation concentrations (∼ 1 μM), indicating that for the moment the developed protocol is quite effective down to the 100 nM range. Of course, for reading the nm or even sub-nM range further optimizations are needed

Investigations of Structure / Property Interrelationships of Organic Thin Films Using Scanning Probe Microscopy and Nanolithography

Studies of the surface assembly and molecular organization of organic thin films were studied using scanning probe microscopy (SPM) and scanning probe lithography (SPL). Systems of organic thin films such as n-alkanethiols and pyridyl functionalized porphyrins were characterized at the molecular level, and measurements of the conductive properties of polythiophenes containing in-chain cobaltabisdicarbollides were accomplished. Understanding the self-organization and mechanisms of self-assembly of organic molecules provides fundamental insight for structure/property interrelationships. Investigations of the surface assembly of 5,10-diphenyl-15,20-di-pyridin-4-yl-porphyrin (DPP) on Au(111) were done using SPL methods of nanoshaving and nanografting. Automated computer designs were developed for nanofabrication to provide local characterizations of the thickness of DPP films and nanostructures. Nanolithography was accomplished using DPP films as either matrix self-assembled monolayers (SAMs) or as molecules for nanofabrication. Results presented in this dissertation demonstrate that DPP forms compact layers on Au(111), which can be used for inscribing nanopatterns of n-alkanethiols. Arrays of DPP nanopatterns with precise geometries and alignment were fabricated within n-alkanethiols by nanografting, demonstrating nanoscale lithography with pyridyl porphyrins can be accomplished to produce an upright surface orientation on Au(111) mediated by nitrogen-gold chemisorption. Beyond research investigations, the applicability of atomic force microscopy (AFM) and advancements with automated SPL were applied for teaching undergraduate chemistry laboratories to introduce the fundamentals of surface chemistry and molecular manipulation. New classroom activities were developed for the Chemistry 3493 Physical Chemistry laboratory to give students “hands-on” training with AFM. Undergraduates were trained to prepare nanopatterns of n-alkanethiols using software to control the position, force and speed of the AFM tip for nanolithography experiments. The sensitivity and nanoscale resolution of current sensing AFM was applied for studies of the conductive properties of electropolymerized thin films of polythiophenes with cobaltabisdicarbollide moieties. Images acquired with AFM furnished views of the morphology of different polymers prepared on gold surfaces. Surface maps of the conductivity of electropolymerized films were acquired with AFM current images. These studies provide new insight of the effects of the bound cobaltabisdicarbollide moiety and coordinated metal centers for the electronic properties of the resulting conducting materials

Self-Assembly of Electric Circuits

Self-Assembly of Electric Circuit