Doctor of Philosophy / Department of Physics / Bret N. Flanders / Directed electrochemical nanowire assembly (DENA) is a method for fabricating nano-structured materials via electrochemical dendritic solidification. This thesis presents two new applications of nano-structured materials that are fabricated via the DENA methodology: cellular force sensors to probe adhesive sites on living cells and single-crystalline metallic dendrites as surface coating materials. Fast migrating cells like D. discoideum, leukocytes, and breast cancer cells migrate by attachment and detachment of discrete adhesive contacts, known as actin foci, to the substrate where the cell transmits traction forces. Despite their importance in migration, the physics by which actin foci bind and release substrates is poorly understood. This gap is largely due to the compositional complexity of actin foci in living cells and to a lack of technique for directly probing these sub-cellular structures. Recent theoretical work predicts these adhesive structures to depend on the density of adhesion receptors in the contact sites, the receptor-substrate potential, and cell-medium surface tension. This thesis describes the fabrication of sub-microscopic force sensors composed of poly(3,4-ethylene dioxythiophene) fibers that can interface directly with sub-cellular targets such as actin foci. The spring constants of these fibers are in the range of 0.07-430 nN m-1. These fibers were used to characterize the strength and lifetime of adhesion between the single adhesive contacts of D. discoideum cells and the fibers, finding an average force of 3.1 ± 2.7 nN and lifetime of 23.4 ± 18.5 s. This capability is significant because direct measurement of these properties will be necessary to measure the cell-medium surface tension and to characterize the receptor-substrate potential in the next (future) stage of this project. The fabrication of smart materials that are capable of the high dynamic range structural reconfiguration would lead to their use to confer hydrophobic, lipophobic, and anti-corrosive character to substrates in a regenerative manner. As a step towards this goal, we have extended the DENA method to enable repetitive growth and dissolution of metallic dendrites to substrates. The experimental parameters that control this process are the frequency and duty cycle of the alternating voltage signal that initiates the dendritic growth.

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.

This thesis makes contributions towards the development of two different small-scale sensing systems which show promise for measurements in fluid mechanics. Well-resolved turbulent Wall Shear Stress (WSS) measurements could provide a basis for realistic computational models of near-wall turbulent flow in aerodynamic design. In aerodynamics field applications, they could provide indication of flow direction and regions of separation, enabling inputs for flight control or active control of wind-turbine blades to reduce shock and fatigue loading due to separated flow regions. Traditional thermal WSS sensors consist of a single microscale hot-film, flush-mounted with the surface and maintained at constant temperature. Their potential for fast response to small fluctuations may not be realized, as heat transfer through the substrate creates heat-exchange with fluid, leading to loss of spatial and temporal resolution. The guard-heated thermal WSS sensor is a design introduced to block this loss of resolution. A numerical flow-field with a range of length and time and scales was generated to study the response of both guard-heated and conventional single-element thermal WSS sensors. A conjugate heat transfer solution including substrate heat conduction and flow convection, provides spatiotemporal data on both the actual and the “measured” WSS fluctuations calculated from the heat transfer rates experienced due to the WSS field. For a single-element sensor in air, we found that the heat transfer through the substrate was up to six times larger than direct heat transfer from the hot-film to the fluid. The resulting loss of resolution in the single-element sensor can be largely recovered by using the guard-heated design. Spectra for calculated WSS from heat transfer response show that high frequencies are considerably better resolved in guard-heated sensors than in the single element sensor. Nanoresonators are nanowires (NWs) excited into mechanical vibration at a resonance frequency, with a change in spectral width created by gas damping from the environment, or a shift in the resonance peak frequency created by added mass. They enable a wide range of applications, from sensors to study rarefied gas flow friction to the detection of early-stage cancer. The extraordinary sensitivity of nanoresonators for disease molecule detection has been demonstrated with a few NWs, but the high cost of traditional electron-beam lithography patterning, have inhibited practical applications requiring large arrays of sensors. Field-directed assembly techniques under development in our laboratory enable a large number of devices at low cost. Electro-deposition of metals in templates yields high-quality single nanowires, but undesired clumps must be removed. This calls for separation (extraction) of single nanowires. In this work, single nanowires are extracted by using the sedimentation behavior of particles. Based on numerical and experimental analyses, the optimum time and region for extracting samples with the highest fraction of single nanowires ratio was found. We show that it is possible to take samples free of large clumps of nanowires and decrease the ratio of undesired particles to single nanowires by over one order of magnitude. / Graduate