Knowledge of the ultrastructural arrangement within wood fibres is important for understanding the mechanical properties of the fibres themselves, as well as for understanding and controlling the ultrastructural changes that occur during pulp processing. The object of this work was to explore the use of atomic force microscopy (AFM) in studies of the cell wall ultrastructure and to see how this structure is affected in the kraft pulp fibre line. This is done in order to eventually improve fibre properties for use in paper and other applications, such as composites. On the ultrastructural level of native spruce fibres (tracheids), it was found that cellulose fibril aggregates exist as agglomerates of individual cellulose microfibrils (with a width of 4 nm). Using AFM in combination with image processing, the average side length (assuming a square cross-section) for a cellulose fibril aggregate was found to be 15–16 nm although with a broad distribution. A concentric lamella structure (following the fibre curvature) within the secondary cell wall layer of native spruce fibres was confirmed. These concentric lamellae were formed of aligned cellulose fibril aggregates with a width of about 15 nm, i.e. of the order of a single cellulose fibril aggregate. It was further found that the cellulose fibril aggregates had a uniform size distribution across the fibre wall in the transverse direction. During the chemical processing of wood chips into kraft pulp fibres, a 25 % increase in cellulose fibril aggregate dimension was found, but no such cellulose fibril aggregate enlargement occurred during the low temperature delignification of wood into holocellulose fibres. The high temperature in the pulping process, over 100 ºC, was the most important factor for the cellulose fibril aggregate enlargement. Neither refining nor drying of kraft or holocellulose pulp changed the cellulose fibril aggregate dimensions. During kraft pulping, when lignin is removed, pores are formed in the fibre cell wall. These pores were uniformly distributed throughout the transverse direction of the wood cell wall. The lamellae consisting of both pores and matrix material (“pore and matrix lamella”) became wider and their numeral decreased after chemical pulping. In holocellulose pulp, no such changes were seen. Refining of kraft pulp increased the width of the pore and matrix lamellae in the outer parts of the fibre wall, but this was not seen in holocellulose. Upon drying of holocellulose, a small decrease in the width of the pore and matrix lamellae was seen, reflecting a probable hornification of the pulp. Refining of holocellulose pulp led to pore closure probably due to the enhanced mobility within the fibre wall. Enzymatic treatment using hemicellulases on xylan and glucomannan revealed that, during the hydrolysis of one type of hemicellulose, some of the other type was also dissolved, indicating that the two hemicelluloses were to some extent linked to each other in the structure. The enzymatic treatment also decreased the pore volume throughout the fibre wall in the transverse direction, indicating enzymatic accessibility to the entire fibre wall. The results presented in this thesis show that several changes in the fibre cell wall ultrastructure occur in the kraft pulp fibre line, although the effects of these ultrastructural changes on the fibre properties are not completely understood. / QC 20101012

High-quality factor oscillators are often used in measurements of verysmall force since they exhibit an enhanced sensitivity in the narrow frequencyband around resonance. Forces containing frequencies outside this frequencyband are often not detectable and the total force acting on the oscillatorremains unknown. In this thesis we present methods to eciently use theavailable bandwidth around resonance to reconstruct the force from partialspectral information.We apply the methods to dynamic atomic force microscopy (AFM) wherea tip at the end of a small micro-cantilever oscillates close to a sample surface.By reconstructing the force between the tip and the surface we can deducedierent properties of the surface. In contrast, in conventional AFM only oneof the many frequency components of the time-dependent tip-surface forceallowing for only qualitative conclusions about the tip-surface force.To increase the number of measurable frequency components we developed Intermodulation AFM (ImAFM). ImAFM utilizes frequency mixing ofa multifrequency drive scheme which generates many frequencies in the response to the nonlinear character of the tip-surface interaction. ImAFM,amplitude-modulated AFM and frequency-modulated AFM can be considered as special cases of narrow-band AFM, where the tip motion can bedescribed by a rapidly oscillating part and a slowly-varying envelope function. Using the concept of force quadratures, each rapid oscillation cycle canbe analyzed individually and ImAFM measurements can be interpreted as arapid measurement of the dependence of the force quadratures on the oscillation amplitude or frequency. To explore the limits of the force quadraturesdescription we introduce the force disk which is a complete description of thetip-surface force in narrow-band AFM at xed static probe height.We present a polynomial force reconstruction method for multifrequencyAFM data. The polynomial force reconstruction is a linear approximativeforce reconstruction method which is based on nding the parameters of amodel force which best approximates the tip-surface force. Another classof reconstruction methods are integral techniques which aim to invert theintegral relation between the tip-surface force and the measured spectraldata. We present an integral method, amplitude-dependence force spectroscopy (ADFS), which reconstructs the conservative tip-surface force fromthe amplitude-dependence of the force quadratures. Together with ImAFMwe use ADFS to combine high-resolution AFM imaging at high speeds withhighly accurate force measurements in each point of an image. For the measurement of dissipative forces we discuss how methods from tomography canbe used to reconstruct forces that are a function of both tip position andvelocity.The methods developed in this thesis are not limited to dynamic AFM andwe describe them in the general context of a harmonic oscillator subject to anexternal force. We hope that theses methods contribute to the transformationof AFM from a qualitative imaging modality into quantitative microscopy andwe hope that they nd application in other measurements which exploit theenhanced sensitivity of a high-quality factor oscillator. / <p>QC 20130527</p>

Physical forces in the cellular microenvironment play an important role in governing cell function. Forces transmitted through the cell cause distinct deformation of the nucleus, and possibly play a role in force-mediated gene expression. The work presented in this thesis drew upon innovative strategies employing simultaneous atomic force and laser-scanning confocal microscopy, as well as parallel optical stretching experiments, to gain unique insights into the response of eukaryotic cell nuclei to external force. Non-destructive approaches confirmed the existence of a clear anisotropy in nuclear mechanical properties, and showed that the nucleus' mechanical response to extracellular forces is differentially governed by both nuclear and cytoskeletal prestress: nuclear prestress regulates shape and anisotropic deformation, whereas cytoskeletal prestress modulates the magnitude and degree of deformation. Importantly, the anisotropic mechanical response was conserved among diverse differentiated cell types from multiple species, suggesting that nuclear mechanical anisotropy plays an important role in cell function.

Nanolithography is a rapidly evolving field that requires new combinations of techniques to improve patterning and to assist in fabricating electromechanical devices. An increasing number of applications require surfaces with defined regions of different chemical functionality. In our previous project optimum conditions for lithographic patterning were determined and potential blockers were identified to reduce force on the tip. This work is focused on identifying good chemical modifications that will allow better control of basic patterning and to investigate the minimum force of patterning required while using each chemical system. The primary aim is to gain better control of basic pattern techniques in order to create more intricate patterns such as interdigitated arrays, which can subsequently be used in sensors. An atomic force microscope (AFM) is used to pattern the prepared colloid-coated glass slides. Several compounds were used in the investigation, including sodium sulphate, potassium sulphate, magnesium sulphate, sodium fluoride, sodium chloride, sodium bromide, and sodium iodide, potassium chloride, potassium bromide, potassium iodide, potassium dihydrogen phosphate, and potassium hydrogen phosphate. In Summary, the following were found as a result of this work:  The groups of sulphates were determined to require minimum patterning forces as indicated. Sodium sulphate took a force of 49 n Potassium sulphate took a force of 45 nN Magnesium sulphate took a force of 744.4 nN  The group of sodium and potassium halides were determined the minimum patterning forces as indicated. Sodium fluoride took a force of 8.42 nN Sodium chloride and potassium chloride took a force of 20.19 and 61.9nN Sodium bromide and potassium bromide took a force of 601.4 nN and 37.2 nN, respectively Sodium iodide and potassium iodide took a force of 953.7 nN and 47.2 nN, respectively  The phosphates were determined to require the minimum patterning forces as indicated. Potassium hydrogen phosphate took a force of 25nN Potassium dihydrogen phosphate took a force of 43 nN

The work presented here has a multidisciplinary character, having as a common factor the characterization of self-assembled nanostructures through force spectroscopy. Exploring AFM as a tool for characterizing self-assembly and interaction forces in soft matter nanostructures, three different Bio and nonbiological systems where investigated, all of them share the common characteristic of being soft matter molecular structures at the nanoscale. The studied systems in question are: a) Polyelectrolyte – lipid nanocomposites. Single polyelectrolyte adsorption-desorption from supported lipid bilayers, b) Polyelectrolyte brushes and c) Virus-Like particles (VLPs). The scientific interest and industrial applications for each of these different nanostructures is broad, and their potential uses in the near future ranges from smart nanocontainers for drug and gene delivery, surface platforms for molecular recognition to the development of new nanodevices with ultrasensitive external stimuli responsiveness. These nano-structures are constructed following assembly of smaller subunits and belong to representative examples of soft matter in modern nanotechnology. The stability, behavior, properties and long term durability of these self-organized structures depends strongly on the environmental conditions to which they are exposed since their building mechanism is a balance between attractive noncovalent interactions and momentum transmitted collisions due Brownian motion of the solvent molecules. For example a set of long chain molecules firmly attached to one end to a surface will alter their conformation as the space between them is reduced or the environmental conditions are modified (i.e. ionic strength, pH or temperature). For a highly packed condition, this fuzzy surface known as a polyelectrolyte brush will then behave as a responsive material with tunable responsiveness. Thus the objective in the present case was to investigate the change in morphology and the mechanical response of a polyelectrolyte brush to external forces by application of AFM nanoindentations under different ionic strength conditions. The degree of penetration of the AFM tip through the brush will provide insights into the forces exerted by the brush against the tip. Compressions on the brush should aid to characterize its changes in compressibility for different salt concentrations. For the second chosen system, the interaction between two assembled interfaces was investigated at the single molecular level. A multilayered film formed by the consecutive assembly of oppositely charged polyelectrolytes and subsequently coated with a lipid membrane represents a fascinating soft composite material resembling more than a few structural components emerging in living organisms. The fluid bilayer, thus provide a biocompatible interface where additional functionalities can further be integrated (fusion peptides for instance). The smooth polymer cushion confers not only structural flexibility but also adaptability of the chosen substrate properties to be coated. This type of interface could be useful in the development of novel molecular biosensors with single molecule recognition capacities or in the fabrication of assays against pathogenic agents. The aim of this project was to study the molecular binding mechanism between the last polyelectrolyte layer and the lipid head group of the lower lipid leaflet. Understanding this adsorption mechanism between both interfaces, should likewise contribute to improve the fabrication of lipid coated polymeric nano/micro capsules with targeting properties. For example this could be critical in the field of nonviral gene therapy, where the improvement in the design of condensates of nucleic acids and other polymers with lipids (lipoplexes) are of main interest for its posterior use as delivery vectors. Finally, viral capsids were investigated. These naturally occurring assembled nanocontainers within living organisms stand for a remarkable example of nature’s morphological designs. These structures self-assemble from a small number of different proteins occurring in identical copies. The capsid as a self-assembled structure carries multiple functions: compaction of the genome, protection against external chemical threats, target recognition, structural support and finally facilitating the release of the genome into the host cell. It is highly interesting how these different functions are organized within the capsid which consists, for example, in the case of the norovirus of 180 identical copies of one single protein. Therefore, the mechanical stability and elastic properties of virus-like particles of Rubella and Norovirus were investigated by external application of loading forces with an AFM tip. The measurements were performed under conditions relevant for the virus infection mechanism. The applied compressions on these protein shells at pH values mimicking the virus life cycle will aid to learn about possible internal transitions among proteins which may be important for switching between the various functions of the capsid. The choice of two unrelated viral systems with different entry pathways into the cell and with different morphological architectures is expected to reveal crucial information about the stability and mechanical resistance to deformation of these empty membrane-coated and bare viral capsids. This last might provide clues on the stage of particle disassembly and cargo release during the final step of the infection process.

This research focuses on the nanoscopic investigation of the three-dimensional surface morphology of the neural growth cones from the snail Helisoma trivolvis, and InN and InGaN semiconductor material systems using Atomic Force Microscopy (AFM). In the analysis of the growth cones, the results obtained from AFM experiments have been used to construct a 3D architecture model for filopodia. The filopodia from B5 and B19 neurons have exhibited different tapering mechanisms. The volumetric analysis has been used to estimate free Ca2+ concentration in the filopodium. The Phase Contrast Microscopy (PCM) images of the growth cones have been corrected to thickness provided by AFM in order to analyze the spatial refractive index variations in the growth cone. AFM experiments have been carried out on InN and InGaN epilayers. Ternary InGaN alloys are promising for device applications tunable from ultraviolet (Eg[GaN]=3.4 eV) to near-infrared (Eg [InN]=0.7 eV). The real-time optical characteristics and ex-situ material properties of InGaN epilayers have been analyzed and compared to the surface morphological properties in order to investigate the relation between the growth conditions and overall physical properties. The effects of composition, group V/III molar ratio and temperature on the InGaN material characteristics have been studied and the growth of high quality indium-rich InGaN epilayers are demonstrated.

This research delineates the design of a nanolithographic process for nanometer scale surface patterning. The process involves the combination of serial atomic force microscope (AFM) based nanolithography with the parallel patterning capabilities of soft lithography. The union of these two techniques provides for a unique approach to nanoscale patterning that establishes a research knowledge base and tools for future research and prototyping.To successfully design this process a number of separate research investigations were undertaken. A custom 3-axis AFM with feedback control on three positioning axes of nanometer precision was designed in order to execute nanolithographic research. This AFM system integrates a computer aided design/computer aided manufacturing (CAD/CAM) environment to allow for the direct synthesis of nanostructures and patterns using a virtual design interface. This AFM instrument was leveraged primarily to study anodization nanolithography (ANL), a nanoscale patterning technique used to generate local surface oxide layers on metals and semiconductors. Defining research focused on the automated generation of complex oxide nanoscale patterns as directed by CAD/CAM design as well as the implementation of tip-sample current feedback control during ANL to increase oxide uniformity. Concurrently, research was conducted concerning soft lithography, primarily in microcontact printing (µCP), and pertinent experimental and analytic techniques and procedures were investigated.Due to the masking abilities of the resulting oxide patterns from ANL, the results of AFM based patterning experiments are coupled with micromachining techniques to create higher aspect ratio structures at the nanoscale. These relief structures are used as master pattern molds for polymeric stamp formation to reproduce the original in a parallel fashion using µCP stamp formation and patterning. This new method of master fabrication provides for a useful alternative to conventional techniques for soft lithographic stamp formation and patterning. / Dissertation

<p>The goal of this work is to develop novel molecular systems, functionalization techniques, and data collection routines with which to study the binding of immobilized cognate binding partners. Our ultimate goal is the routine evaluation of thermodynamic parameters for immobilized systems through interpretation of the variation of the binary probability of binding as a function of soluble ligand concentration. The development of both data collection routines that minimize non-specific binding and functionalization techniques that produce stable ordered molecular systems on surfaces are of paramount importance towards achievement of this goal. Methodologies developed here will be applied to investigating the thermodynamics of multivalent systems.</p><p>In the first part of this work, the effect of contact force on molecular recognition force microscopy experiments was investigated. Increased contact forces (>250 pN) resulted in increased probabilities of binding and decreased blocking efficiencies for the cognate ligand-receptor pair lactose-G3. Increased contact force applied to two control systems with no known affinity, mannose-G3 and lactose-KDPG aldolase resulted in non-specific ruptures that were indistinguishable from those of specific lactose-G3 interactions. Thus, it is essential to design data collections routines that minimize contact forces to ensure that ruptures originate from specific, blockable interactions.</p><p>In the second part of this work we report the first example of the preparation of stable self assembled monolayers through hydrosilylation of a protected aminoalkene onto hydrogen-terminated silicon nitride AFM probes and subsequent conjugation with biomolecules for force microscopy studies. Our technique can be used as a general attachment technique for other molecular systems.</p><p>In the third part of this work we develop novel molecular systems for tethering oriented vancomycin and its cognate binding partner L-Lys-D-Ala-D-Ala to surfaces and AFM tips. Unbinding experiments demonstrated that traditional methods for forming low surface density amine layers (silanization with APTMS and etherification with ethanolamine) provided molecular constructs which displayed probabilities of binding that were too low and showed overall variability too high to use for probabilistic evaluation of thermodynamics parameters. Instability and heat-induced polymerization of APTMS layers on tips and surfaces also prohibited their utility. Formation of Alkyl SAMs on silicon provides a more reliable, stable molecular system anchored by Si-C bonds that facilitates attachment of vancomycin and is capable of withstanding prolonged exposure to heated organic and aqueous environments. It follows that covalent immobilization of KDADA to silicon nitride AFM tips via Si-C bonds using hydrosilylation chemistry will be similarly advantageous. These methods offer great promise for probabilistic evaluation of thermodynamic parameters characterizing immobilized binding partners and will permit unambiguous determination of the role of multivalency in ligand binding, using an experimental configuration in which intermolecular binding and aggregation are precluded.</p> / Dissertation

The hypothesis behind this research is that Atomic Force Microscopy (AFM) can be used to capture changes in the surface interaction force caused by sorption of ions, and thereby can be employed as a tool to study sorption at the nano-scale. The Derjaguin??dau??wey??rbeek (DLVO) theory was used to explain surface interactions and probe DLVO and other interparticle forces. In the first part of the work, sorption of copper ions onto a silica particle resulted in charge reversal detected by AFM. Transient measurements of the interaction force between the silica particle and a flat glass surface can be related to the kinetics of copper ion sorption. In the second part, the force-volume AFM mode was used to detect heterogeneously charged regions on quartz silica surfaces resulting from copper ion sorption. Conditions of copper ion concentration and pH were varied to confirm the sorption mechanism. The surprising result of this study was the observation of growing islands during sorption indicating a heterogeneous behavior of the surface. In the third part, AFM was used to measure interaction forces between a gold sample and the silicon nitride tip of the AFM in aqueous electrolyte solutions under various values of applied electrostatic potential. Along with the applied potential, pH conditions were also varied. Experimental results were compared to theoretical calculations using the non-linear Poisson-Boltzmann equation. This work showed a relationship between the surface potential and the externally applied potential. Finally, the total interaction force between a standard silicon nitride AFM tip and a gold-coated plate in the presence of cationic surfactant, cetyltrimethylammonium bromide (CTAB), was measured under various conditions of applied potential. The interaction force-distance profile between the surface and the tip can be related to the structure of surfactant molecules sorbed onto the surface, which is influenced by the magnitude of the applied potential. The results presented in this work are of importance in natural and engineered systems involving colloidal particles and charged species with implications in separations as well as naturally occurring facilitated transport.

The invention of the atomic force microscope (AFM) revolutionized the scientific world by providing researchers with the ability to make topographical maps of both conducting and non-conducting surfaces with nanometer resolution. As an alternative to optical AFM methods, thermal cantilevers have been investigated as a method to measure topography. This study reports the fabrication and testing of heated AFM cantilevers. This study transfers a fabrication process first developed at Stanford University to the Georgia Institute of Technology micro-fabrication facility and fabricates six different heated AFM cantilever designs. Selective impurity doping of a silicon cantilever allows it to become electrically conductive with a resistive element near the cantilever free end. Voltage applied across the cantilever legs induces current flow through the cantilever that generates heat in the resistive element. A deep understanding of the operational behavior and limits of the AFM cantilever is required to use the cantilever as an experimental tool. Characterization experiments determined the cantilever electrical resistance and temperature response. Experiments were conducted that electrically test heated AFM cantilevers at various system input voltages. Electrical and thermal responses of these cantilevers were compared against a theoretical model. The model utilizes heat transfer fundamentals and links the thermal response to the cantilever temperature-dependent electrical characteristics. Results of this study show that the fabricated heated AFM cantilevers have a tip with a radius of curvature as small as 20nm. Cantilever temperatures can exceed 700㠩n short pulses and, because the resistive heating element is also a temperature sensor, calibration of the cantilever temperature response is possible to within 1㮍