Self-assembling peptides have emerged as new nanobiomaterials and received considerable attention in the areas of nanoscience and biomedical engineering. In this category are ionic-complementary peptides, which contain a repeating charge distribution and alternating hydrophobic and hydrophilic residues in the amino acid sequence, leading to the unusual combination of amphiphilicity and ionic complementarity. Although their self-assembled nanostructures have been successfully applied as scaffoldings for tissue engineering, novel materials for regenerative medicine and nanocarriers for drug and gene/siRNA delivery, aspects of the assembly process remain unclear. Since many of these applications involve peptide-modified interfaces and surfaces, a better understanding and control of the peptide assembly on a surface are very crucial for future development of peptide-based applications in nano-biotechnology. This thesis contains two major parts: (i) fundamental study of the assembly of a model ionic-complementary peptide EAK16-II on surfaces and (ii) potential applications of such a peptide in surface modification and nanofabrication. In the fundamental study, EAK16-II assembly on negatively charged mica was first investigated via in-situ Atomic Force Microscopy (AFM). It was found that EAK16-II nanofiber growth on mica is surface-assisted and follows a nucleation and growth mechanism involving two steps: (i) adsorption of nanofibers and fiber clusters (from the bulk solution) on the surface to serve as the seeds and (ii) fiber elongation from the active ends of the seeds. Such a process can be controlled by adjusting the solution pH since it modulates the adsorption of the seeds and the growth rates. Unlike what is observed on mica, EAK16-II formed well-ordered nanofiber patterns with preferential orientations at angles of 60° or 120° to each other on hydrophobic highly ordered pyrolytic graphite (HOPG) surfaces, resembling the crystallographic structure of the graphite. Nanofiber formation on HOPG is also surface-assisted and adopts a nucleation and growth mechanism that can be affected by solution pH. The pH-dependent adsorption of peptides to HOPG is attributed to the resulting changes in peptide hydrophobicity. It was also found that EAK16-II assembly can be induced by the mechanical force of a tapping AFM tip. It occurs when the tip cuts the adsorbed EAK16-II nanofibers into segments that then serve as seeds for new nanofiber growth. This finding allows one to locally grow nanofibers at specific regions of the surface. The tip cutting has been combined with the effect that solution pH has on peptide assembly to develop a new AFM lithography method to fabricate local patterned peptide nanostructures on HOPG. To study the use of EAK16-II for surface modification applications, the wettability and stability of the peptide-modified surfaces were characterized. EAK16-II-modified mica becomes slightly hydrophobic as the water contact angle increases from <10° to 20.3 ± 2.9°. However, the hydrophobicity of the HOPG surface is significantly reduced, as reflected in a contact angle change from 71.2 ± 11.1° to 39.4 ± 4.3°. The EAK16-II-modified mica surface is stable in acidic solution, while the modified HOPG surface is stable in both acidic and alkaline solutions. The peptide-modified HOPG shows potential as a biocompatible electrode for (bio)molecular sensing. The ability of EAK16-II to form nanofibers on surfaces has also promoted research on peptide-based metallic nanowire fabrication. Our approach is to provide EAK16-II with metal ion binding ability by adding a GGH motif to the C-terminus. This new peptide EAK16(II)GGH has been found to form one-dimensional nanofibers while binding to Cu2+ ions. The dimensions of the nanofibers were significantly affected by the nature of the anions (SO42-, Cl- and NO3-) in the copper salt solution. This work demonstrates the potential usage of EAK16-II for nanowire fabrication.

Self-assembling peptides have emerged as new nanobiomaterials and received considerable attention in the areas of nanoscience and biomedical engineering. In this category are ionic-complementary peptides, which contain a repeating charge distribution and alternating hydrophobic and hydrophilic residues in the amino acid sequence, leading to the unusual combination of amphiphilicity and ionic complementarity. Although their self-assembled nanostructures have been successfully applied as scaffoldings for tissue engineering, novel materials for regenerative medicine and nanocarriers for drug and gene/siRNA delivery, aspects of the assembly process remain unclear. Since many of these applications involve peptide-modified interfaces and surfaces, a better understanding and control of the peptide assembly on a surface are very crucial for future development of peptide-based applications in nano-biotechnology. This thesis contains two major parts: (i) fundamental study of the assembly of a model ionic-complementary peptide EAK16-II on surfaces and (ii) potential applications of such a peptide in surface modification and nanofabrication. In the fundamental study, EAK16-II assembly on negatively charged mica was first investigated via in-situ Atomic Force Microscopy (AFM). It was found that EAK16-II nanofiber growth on mica is surface-assisted and follows a nucleation and growth mechanism involving two steps: (i) adsorption of nanofibers and fiber clusters (from the bulk solution) on the surface to serve as the seeds and (ii) fiber elongation from the active ends of the seeds. Such a process can be controlled by adjusting the solution pH since it modulates the adsorption of the seeds and the growth rates. Unlike what is observed on mica, EAK16-II formed well-ordered nanofiber patterns with preferential orientations at angles of 60° or 120° to each other on hydrophobic highly ordered pyrolytic graphite (HOPG) surfaces, resembling the crystallographic structure of the graphite. Nanofiber formation on HOPG is also surface-assisted and adopts a nucleation and growth mechanism that can be affected by solution pH. The pH-dependent adsorption of peptides to HOPG is attributed to the resulting changes in peptide hydrophobicity. It was also found that EAK16-II assembly can be induced by the mechanical force of a tapping AFM tip. It occurs when the tip cuts the adsorbed EAK16-II nanofibers into segments that then serve as seeds for new nanofiber growth. This finding allows one to locally grow nanofibers at specific regions of the surface. The tip cutting has been combined with the effect that solution pH has on peptide assembly to develop a new AFM lithography method to fabricate local patterned peptide nanostructures on HOPG. To study the use of EAK16-II for surface modification applications, the wettability and stability of the peptide-modified surfaces were characterized. EAK16-II-modified mica becomes slightly hydrophobic as the water contact angle increases from <10° to 20.3 ± 2.9°. However, the hydrophobicity of the HOPG surface is significantly reduced, as reflected in a contact angle change from 71.2 ± 11.1° to 39.4 ± 4.3°. The EAK16-II-modified mica surface is stable in acidic solution, while the modified HOPG surface is stable in both acidic and alkaline solutions. The peptide-modified HOPG shows potential as a biocompatible electrode for (bio)molecular sensing. The ability of EAK16-II to form nanofibers on surfaces has also promoted research on peptide-based metallic nanowire fabrication. Our approach is to provide EAK16-II with metal ion binding ability by adding a GGH motif to the C-terminus. This new peptide EAK16(II)GGH has been found to form one-dimensional nanofibers while binding to Cu2+ ions. The dimensions of the nanofibers were significantly affected by the nature of the anions (SO42-, Cl- and NO3-) in the copper salt solution. This work demonstrates the potential usage of EAK16-II for nanowire fabrication.

The development of nanoscale patterns has a vast variety of applications going from biology to solid state devices. In this research we present a new direct patterning technique in which laser photoreduction of silver from a liquid is controlled by a scanning atomic force microscope tip. While pursuing the formation of patterns using the plasmonic field enhancement of an electromagnetic wave incident on a metallic Atomic Force Microscope (AFM) tip, our group discovered that contrary to expectations, the tip suppresses, rather than enhances, deposition on the underlying substrate, and this suppression persists in the absence of the tip. Experiments presented here exclude three potential mechanisms: purely mechanical material removal, depletion of the silver precursor, and preferential photoreduction on existing deposits. An example of a nano-scaled pattern was generated to show the possibilities of this work. These results represent a first step toward direct, negative tone, tip-based patterning of functional materials.

This work has examines the creation and use of chemical templates for nanocircuit and other nanodevice fabrication. Chemical templating can be useful in attachment, orientation and wiring of molecularly templated circuits. DNA origami provides a suitable method for creating molecularly templated circuits as DNA can be folded into complex shapes and functionalized with active circuit elements, such as semiconducting nanomaterials. Surface attachment of DNA origami structures can be accomplished by hybridization of dangling single-stranded DNA (ssDNA) on the origami structures with complementary surface-bound strands. Chemical templating provides a pathway for placing the patterned surface-bound attachment points needed for surface alignment of the molecular templates. Chemical templates can also be used to connect circuit elements on the surface by selectively metallizing the templates to form local wiring. AFM tip-directed nano-oxidation was selected as the method for patterning to create chemical templates. This project demonstrates new techniques for creating, continuous metallization of, and DNA attachment to nanochemical templates. Selective-continuous metallization of nanochemical templates is needed for wiring of circuit templates. To improve the metallization density and enable the continuous nano-scale metallization of amine-coated surfaces, the treatment of amine-coated surfaces with a plating additive prior to metallization was studied. The additive treatment resulted in a 73% increase in seed material, enabling continuous nano-scale metallization. A new method was developed to create amine nanotemplates by selective attachment of a polymer to surface oxide patterns created by nano-oxidation. The treatment of the templates with the additive enabled a five-fold reduction in feasible width for continuous metallization. Nano-oxidation was also used in the nanometer-scale patterning of a thiol-coated surface. Metallization of the background thiols but not the oxidized patterns resulted in a metal film that was a negative of the patterns. The resulting metal film may be useful for nanometer-scale pattern transfer. DNA-coated gold nanoparticles (AuNPs) were selectively attached to amine templates by an ionic interaction between the template and ssDNA attached to the particles. Only the ssDNA on the bottom of the AuNPs interacted with the template, leaving the top strands free to bind with complementary ssDNA. Attempts to attach origami structures to these particles were only marginally successful, and may have been hindered by the presence of complementary ssDNA in solution but not attached to the origami, or the by the low density of DNA-AuNPs attached to the templates. The formation of patterned binding sites by direct, covalent attachment of ssDNA to chemical templates was also explored. Initial results indicated that ssDNA was chemically bound to the templates and able to selectively bind to complementary strands; however, the observed attachment density was low and further optimization is required. Methods such as these are needed to enable nano-scale, site-specific alignment of nanomaterials.

This thesis describes application of image processing for precise distance measurement in self acting production of a tip for AFM microscopes. The main goal is to measure distances between assembly parts during fabrication process. The purpose is to acquire a data for self acting assembly line which have to substitute inaccurate and nonrecurring manual assembly process. The assembly process consists of three technological steps. In first two steps the tungsten wire is glued to the cantilever. Distance measurement is necessary in all axes for proper alignment of parts. In third step the sharp tip is etched by KOH solution. The right distance between liquid level and the cantilever must be kept. A camera with high resolution and macro objective is used to acquire an image. Camera image is then calibrated to suppress distortions and scene position with respect to camera position. Length conversion coefficient is also computed. Object recognition and distance measurement is based on standard computer vision methods, mainly: adaptive thresholding, moments, image statistics, canny edge detector, Hough transform… Proposed algorithms have been implemented in C++ using Intel OpenCV library. The final achieved distance resolution is about 10µm per pixel. Algorithm output was successfully used to assembly few test tips.