Designing surface chemistries for in situ AFM investigations of biomolecular reactions with proteins at the nanoscale

In situ atomic force microscopy (AFM) characterizations and lithography can be applied to investigate the orientation, reactivity and stability of protein molecules adsorbed on nanostructures of self-assembled monolayers at near-physiological conditions. Automated nanografting was used to fabricate regular arrays of nanopatterns of ù-functionalized n-alkanethiols with designated terminal chemistries. After writing nanopatterns, protein binding occurs selectively on carboxylate-terminated nanopatterns via covalent bonds that are formed using N-ethyl-N\u27(dimethylaminoporpyl)-carbodiimide and N-hydroxysuccinimide activation. The amine groups of lysine residues of proteins bond covalently to nanopatterns of carboxylate-terminated alkanethiol self-assembled monolayers, to form a robust surface attachment for sustained contact-mode AFM imaging during biochemical reactions. Staphylococcal protein A (SpA) furnishes a generic foundation for binding immunoglobulins for nanometer scale sandwich assays. The self-assembly of á,ù-alkanedithiols onto Au(111) was investigated using AFM. When SAMs of 1,8-octanedithiol or 1,9-nonanedithiol are grown naturally from solution, different surface orientations are observed in comparison to methyl-terminated n-alkanethiols. Local views from AFM images reveal a layer of mixed orientations in which the majority of á,ù-alkanedithiol molecules adopt an orientation parallel to the surface with both thiol endgroups bound to Au(111). Results from AFM studies reveal that the chemisorption of thiol endgroups of dithiols inhibits the phase transition from a lying-down to a standing orientation during natural self-assembly. Another method for producing protein nanostructures is particle lithography. Monodisperse mesospheres can be applied to rapidly prepare millions of exquisitely uniform nanometer-sized structures of proteins on flat surfaces using conventional benchtop chemistry steps of mixing, centrifuging, evaporation and drying. The natural self-assembly of monodisperse spheres provides a high throughput and efficient route to prepare circular geometries over millimeter scale areas. The spontaneous assembly of silica or latex mesospheres into organized crystalline layers on flat substrates supplies a structural frame to direct the placement of proteins. Nanopatterns of ferritin, apoferritin, immunoglobulin G and bovine serum albumin were produced with particle lithography. The applicability of particle lithography to generate arrays of protein nanostructures on surfaces such as mica(0001), glass and Au(111) was demonstrated. The morphology and diameter of the protein nanostructures can be tailored by selecting the ratios of protein-to-particles and the diameters of spheres

Development of nanopatterns on self assembled monolayer (SAM) organic films using scanning probe microscope (SPM) nanolithography techique

Thesis (Master)--Izmir Institute of Technology, Materials Science and Engineering, Izmir, 2006Includes bibliographical references (leaves: 109-112)Text in English; Abstract: Turkish and Englishxiv, 112 leavesPatterning and fabrication of nanostructures on surfaces is a great demand for nanoscale electronic and mechanical devices. Current techniques such as electron beam lithography and photolithography provides limited resolution and they are not capable of reproducible in nanoscale. Among those, Scanning Probe Microscopy (SPM) lithography that uses a nanometer sharpened tip has demonstrated outstanding capabilities for nanometer level patterning on various surfaces. Moreover, SPM techniques offer creating nanopatterns of Self Assembled Monolayers (SAMs) with molecular precision and visualizing surfaces with the highest spatial resolution. In this work, nanoscratches on gold surfaces and oxidation patterns on titanium surface were successfully performed as example of SPM lithography. In the second stage, Octadecylamine-HCl, Octadecanetiol (ODT) and Decylmercaptan (DM) SAM organic films were fabricated on various substrates; i.e., mica, silica, titanium surface deposited on silicon, n and p type silicon, using self assembly film preparation techniques. The film thicknesses were measured with Atomic Force Microscope (AFM). Nanopatterns were fabricated on SAM films using AFM tip by exerting a local high pressure at the contact that causes the displacement of SAM molecules by a high shear force. It was observed that there was no formation of SAMs on n type Si and silica substrates whereas there were organic assemblies on the other substrates. Fabricated nanopatterns were examined and thickness measurement was done. Molecular lengths of the organics were evaluated by using of SPARTAM 02 LINUX-UNIX with the method of PM3 and the measured values were compared with the calculated ones and it was concluded that monolayers were formed on the surfaces

Nanoscale Studies of Proteins and Thin Films Using Scanning Probe Microscopy

Nanostructures of organosilanes, thin metal films, and protein nanopatterns were prepared and analyzed with atomic force microscopy (AFM). Organosilanes with designed functional groups were used to selectively pattern green fluorescent protein at the nanoscale using protocols developed with particle lithography. Mesospheres are deposited onto a substrate to produce a surface mask. Organosilanes are deposited to form a matrix film surrounding nanopores for depositing proteins. The nanopatterns were characterized using AFM, after steps of particle lithography for directly visualizing surface changes. Studies with AFM also provide a compelling tool for teaching undergraduates to introduce concepts of nanoscience. An undergraduate laboratory was developed with particle lithography to introduce the concepts of nanoscience and surface chemistry. Nanopatterns of organosilane films are prepared using protocols of particle lithography. An organic thin film is applied to the substrate using steps of either heated vapor deposition or immersion in solution. At the molecular level, two types of sample morphology can be made depending on the step for depositing organosilanes. Experience with advanced AFM instrumentation is obtained for data acquisition, digital image processing and analysis. Skills with chemical analysis are gained with bench methods of sample preparation. Concepts such as the organization of molecules on surfaces and molecular self-assembly are demonstrated with the visualization of nanopatterns prepared by students. Experiments with particle lithography can be used as a laboratory module or for undergraduate research projects, and are suitable for students with a multidisciplinary science background. The kinetics and properties of thin gold films during dewetting were studied using AFM. Thin films of gold with varying initial thickness were first deposited onto fire polished glass slides and imaged with AFM. Next, the films were annealed for two hours, and then imaged after annealing. Gold islands with varying degrees of separation were formed. Surface plasmon spectroscopy was also used to analyze the gold films. To further this study, a kinetic study was done. Two gold thin films of 10 nm each were imaged after being annealed for 15, 30, 45, 60 and 120 minutes. It was found that after the first 15 minutes of annealing, gold islands were observed

Optical direct-write nanolithography based on self-assembled resist

Holographic display is being developed for next generation mobile phones. However, manufacturing of miniature gratings for the holographic projectors cost a few thousand dollars today, not making the concept practical for commercial purposes. In this thesis, we discuss the feasibility of self-assembled nanoparticles to manufacture holographic gratings cost-effectively and at the nanoscale. Using our approach, the gratings can be manufactured at the scale of 20nm and the cost per chip is expected to cost a few dollars.^ In this thesis, a hydrophobic SAM was used to modify the surface of silicon. Direct-write UV laser lithography was used for photothermal patterning and obtain a hydrophobic-hydrophilic pattern. Experimental and numerical analysis of the patterning technique was done to investigate a possibility photothermal patterning mechanism. Lastly, the patterned substrate was functionalized with gold nanoparticle SAM to show the feasibility of producing the holographic gratings

Thermal scanning probe lithography

Thermal scanning probe lithography (tSPL) is a nanofabrication method for the chemical and physical nanopatterning of a large variety of materials and polymer resists with a lateral resolution of 10 nm and a depth resolution of 1 nm. In this Primer, we describe the working principles of tSPL and highlight the characteristics that make it a powerful tool to locally and directly modify material properties in ambient conditions. We introduce the main features of tSPL, which can pattern surfaces by locally delivering heat using nanosized thermal probes. We define the most critical patterning parameters in tSPL and describe post-patterning analysis of the obtained results. The main sources of reproducibility issues related to the probe and the sample as well as the limitations of the tSPL technique are discussed together with mitigation strategies. The applications of tSPL covered in this Primer include those in biomedicine, nanomagnetism and nanoelectronics; specifically, we cover the fabrication of chemical gradients, tissue-mimetic surfaces, spin wave devices and field-effect transistors based on two-dimensional materials. Finally, we provide an outlook on new strategies that can improve tSPL for future research and the fabrication of next-generation devices

Photocatalytic Nanolithography of Self-Assembled Monolayers and Proteins

Self-assembled monolayers of alkylthiolates on gold and alkylsilanes on silicon dioxide have been patterned photocatalytically on sub-100 nm length-scales using both apertured near-field and apertureless methods. Apertured lithography was carried out by means of an argon ion laser (364 nm) coupled to cantilever-type near-field probes with a thin film of titania deposited over the aperture. Apertureless lithography was carried out with a helium–cadmium laser (325 nm) to excite titanium-coated, contact-mode atomic force microscope (AFM) probes. This latter approach is readily implementable on any commercial AFM system. Photodegradation occurred in both cases through the localized photocatalytic degradation of the monolayer. For alkanethiols, degradation of one thiol exposed the bare substrate, enabling refunctionalization of the bare gold by a second, contrasting thiol. For alkylsilanes, degradation of the adsorbate molecule provided a facile means for protein patterning. Lines were written in a protein-resistant film formed by the adsorption of oligo(ethylene glycol)-functionalized trichlorosilanes on glass, leading to the formation of sub-100 nm adhesive, aldehyde-functionalized regions. These were derivatized with aminobutylnitrilotriacetic acid, and complexed with Ni2+, enabling the binding of histidine-labeled green fluorescent protein, which yielded bright fluorescence from 70-nm-wide lines that could be imaged clearly in a confocal microscope

Nanopatterns of Zinc Phthalocyanines, Gold Nanoparticles, and Porphyrins Prepared Using Particle Lithography: Characterization of Patterning Steps with Scanning Probe Microscopy

The growth and self-assembly of molecules on surfaces can be directly visualized at the molecular level using studies which combine nanoscale lithography and high-resolution imaging. Nanopatterning provides a unique and practical approach for direct views of surface changes after the key chemical steps of nanopatterning, providing landmarks and baselines for measuring growth in vertical and lateral dimensions. Controlling the arrangement of materials on surfaces at the nanoscale can be achieved using particle lithography. Arrays of well-defined nanostructures can be prepared with reproducible geometries and arrangement. Results for the preparation of nanopatterns produced with particle lithography are presented using high resolution images acquired with scanning probe microscopy (SPM). Samples were prepared using steps for depositing nanoparticles, porphyrins, and phthalocyanines on patterned surfaces to generate multicomponent nanopatterns. Studies of surface chemistry at the molecular level have practical applications for emerging technologies with photovoltaic and photoelectronic devices. Atomic force microscopy (AFM) was used to characterize samples to gain insight on the changes in surface chemistry after patterning organosilanes, organothiols and nanoparticles. For studies of surface chemistry at the nanoscale, AFM has unique capabilities for molecular visualization and ultrasensitive measurements of surface properties. The history of SPM, instrument set-up, and results for particle lithography with porphyrins, zinc phthalocyanines and gold nanoparticles are described in this dissertation. Protocols for patterning porphyrin nanostructures on Au(111) were developed based on steps with immersion combined with particle lithography. Porphyrins with a central metal ion, 5,10,15,20-tetraphenyl-21H,23H-porphine (TPP) and free-base 5,10,15,20-tetraphenyl-21H,23H-porphine nickel(II) (TPN) were studied. Samples of zinc phthalocyanines were prepared using particle lithography with surfaces that were patterned with organosilanes. The dimensions and spacing can be selectively tuned by using selected sizes of latex ad silica spheres as a surface mask. The metallated phthalocyanines bound selectively to the spatially confined sites of nanopatterns, and did not bind to areas of the organosilane resist. Bare gold nanoparticles and organosilane coated nanoparticles were synthesized for characterizations with AFM. At the nanoscale, variations in the sizes of patterns provide a surface test platform for evaluating size dependent physical properties

Laser assisted nano-optics processing in optical data storage

Ph.DDOCTOR OF PHILOSOPH

Synthesis and systematic optical investigation of selective area droplet epitaxy of InAs/InP quantum dots assisted by block copolymer lithography

We report on the systematic investigation of the optical properties of a selectively grown quantum dot gain material assisted by block-copolymer lithography for potential applications in active optical devices operating in the wavelength range around 1.55 um and above. We investigated a new type of diblock copolymer PS-b-PDMS (polystyrene-block-polydimethylsiloxane) for the fabrication of silicon oxycarbide hard mask for selective area epitaxy of InAs/InP quantum dots. An array of InAs/InP quantum dots was selectively grown via droplet epitaxy. Our detailed investigation of the quantum dot carrier dynamics in the 10-300 K temperature range indicates the presence of a density of states located within the InP bandgap in the vicinity of quantum dots. Those defects have a substantial impact on the optical properties of quantum dots.Comment: 11 pages, 5 figures, 1 tabl