A compact model representing the dynamics between piezoelectric voltage inputs and cantilever probe positioning, including nonlinear surface interaction forces, for atomic force microscopes (AFM) is considered. By considering a relatively large cantilever stiffness, singular perturbation methods reduce complexity in the model and allows for faster responses to Van der Waals interaction forces experienced by the cantilever's tip and measurement sample. In this study, we outline a nonlinear near-optimal feedback control approach for non-contact mode imaging designed to move the cantilever tip laterally about a desired trajectory and maintain the tip vertically about the equilibrium point of the attraction and repulsion forces. We also consider the universal instance when the tip-sample interaction force is unknown, and we construct cascaded high-gain observers to estimate these forces and multiple AFM dynamics for the purpose of output feedback control. Our proposed output feedback controller is used to accomplish the outlined control objective with only the piezotube position available for state feedback. / Master of Science / In this thesis, the idea of an atomic force microscope (AFM), specifically the applications of the non-contact mode, will be discussed. An atomic force microscope (AFM) is a tool that measures the surface height of nanometer sized samples. To improve the speed and precision of the machine under a non-contact mode objective, a controller is designed based on optimality and is applied to the system. The system contains a series of equations designed to steer the system towards a desired trajectory and minimal vibrations. Given the complexity of the system, resulting from nonlinearities, we will apply singular perturbation principles on the system's stiffness property to separate the larger problem into two smaller ones. These two problems are inserted into a near-optimal controller and a series of simulations are conducted to demonstrate performance. Alongside this, we will outline an observer to estimate the unknown dynamics of the system. These estimates are then applied to our controller to demonstrate that only the AFM's piezotube position is to be known in order to estimate and control the remaining dynamics of the system.

An atomic force microscope (AFM) has been used to conduct force measurements to better understand the role of hydrophobic forces in flotation. The force measurements were conducted between a flat mineral substrate and a hydrophobic glass sphere in aqueous solutions. It is assumed that the hydrophobic glass sphere may simulate the behavior of air bubbles during flotation. The results may provide information relevant to the bubble-particle interactions occurring during flotation. The glass sphere was hydrophobized by octadecyltrichlorosilane so that its water contact angle was 109 degrees. The mineral systems studied include covellite (CuS), sphalerite (ZnS) and hornblende (Ca₂(Mg, Fe)₅(Si₈O₂₂)(OH,F)₂). The collector used for all the mineral systems studied was potassium ethyl xanthate (KEX). For the covellite-xanthate system, a biopotentiostat was used in conjunction with the AFM to control the potential of the mineral surface during force measurements. This was necessary since the adsorption of xanthate is strongly dependent on the electrochemical potential (Eₕ) across the solid/liquid interface. The results show the presence of strong hydrophobic forces not accounted for by the DLVO (named after Derjaguin, Landau, Verwey and Overbeek) theory. Furthermore, the potential at which the strongest hydrophobic force was measured corresponds to the potential where the flotation recovery of covellite reaches a maximum, indicating a close relationship between the two. Direct force measurements were also conducted to study the mechanism of copper-activation of sphalerite. The force measurements conducted with unactivated sphalerite in 10⁻³ M KEX solutions did not show the presence of hydrophobic force while the results obtained with copper-activated sphalerite at pH 9.2 and 4.6 showed strong hydrophobic forces. However, at pH 6.8, no hydrophobic forces were observed, which explains why the flotation of sphalerite is depressed in the neutral pH regime. Direct force measurements were also conducted using hornblende in xanthate solutions to study the mechanism of inadvertent activation and flotation of rock minerals. The results show the presence of long-range hydrophobic forces when hornblende was activated by heavy metal cations such as Cu²⁺ and Ni²⁺ ions. The strong hydrophobic forces were observed at pHs above the precipitation pH of the activating cation. These results were confirmed by the XPS analysis of the activated hornblende samples. Force measurements were conducted between silanated silica surfaces to explore the relationship between hydrophobicity, advancing contact angle (CA), and the magnitude (K) of hydrophobic force. In general, K increases as Contact Angle increases and does so abruptly at Contact Angle=90°. At the same time, the acid-base component of the surface free energy decreases with increasing CA and K. At CA>90°, GammaS^AB approaches zero. Based on the results obtained in the present work a mathematical model for the origin of the hydrophobic force has been developed. It is based on the premise that hydrophobic force originates from the attraction between large dipoles on two opposing surfaces. The model has been used successfully to fit the measured hydrophobic forces using dipole moment as the only adjustable parameter. However, the hydrophobic forces measured at CA>90° cannot be fitted to the model, indicating that there may be an additional mechanism, possibly cavitation, contributing to the appearance of the long-range hydrophobic force. / Ph. D.

This thesis presents work done investigating methods for constructing patterns on the nanometer scale. Various methods of nanolithography using atomic force microscopes (AFMs) are investigated. The use of AFMs beyond their imaging capabilities is demonstrated in various experiments involving nanografting and surface electrochemical modification. The use of an AFM to manipulate a monolayer of thiols deposited on a gold substrate via nanografting is shown in our work to enable chemical modification of the surface of the substrate by varying the composition of the monolayer deposited on it. This leads to the selective deposition of various polymers on the patterned areas. Conditions for enhancing the selective deposition of the self-assembled polymers are studied. Such conditions include the types of polymers used and the pH of the polyelectrolyte solutions used for polymer deposition. Another method of nanolithography is investigated which involves the electrochemical modification of a monolayer of silanes deposited on a silicon substrate. By applying a potential difference and maintaining the humidity of the ambient environment at a certain level we manage to change the chemical properties of select areas of the silane monolayer and thus manage to establish selective deposition of polymers and gold nanoparticles on the patterned areas. Parameters involved in the patterning process using surface electrochemical modification, such as humidity levels, are investigated. The techniques established are then used to construct circuit elements such as wires. / Ph. D.

Neste trabalho foram utilizadas técnicas de modelagem molecular computacional para descrever nanossuperfícies funcionalizadas com biomoléculas do sistema imunológico correlacionando resultados experimentais obtidos com o microscópio de força atômica, simulações de dinâmica molecular e dinâmica molecular direcionada. O objetivo principal proposto é avaliar as forças intermoleculares provenientes das interações antígeno-anticorpo (funcionalizados em nanossuperfícies) para aplicação no desenvolvimento de nanoimunossensores e detecção de doenças desmielinizantes, como a Neuromielite Óptica. A Neuromielite Óptica é uma doença inflamatória autoimune na qual o próprio sistema imunológico reage contra os nervos ópticos e a medula espinhal, causando lesão desmielinizante. Estudos na literatura estabeleceramo anticorpo anti-aquaporina4 como um importante biomarcador da doença. Neste contexto, um nanoimmunosensorvem sendo desenvolvido com a técnica de Microscopia de Força Atômica, o qual visa detectar o anticorpoanti-aquaporina4 no soro de portadores da doença. Tal estudo necessitou de uma nova abordagem computacional para a descrição de estruturas tridimensionais de anticorpos. Essa nova aproximação consistiu na aplicação de técnicas de computacionais de modelagem e engenharia molecular para a geração de modelos de anticorpos com base em sucessivas substituições dos resíduos componentes do sítio de interação com o antígeno. Testes realizados envolvendo modelos de anticorpos disponíveis em bancos de dados especializadosindicaram (48 ± 18) % e (65 ± 14) % de identidade das cadeias leve e pesada, respectivamente, entre os modelos gerados computacionalmente e as estruturas 3D reais de anticorpos. Por fim, para comprovar o funcionamento dos nanoimunossensores, foi desenvolvido um modelo estatístico para tratar e interpretar os dados experimentais. Este modelo foi eficiente para distinguir os pacientes soropositivos de sujeitos soronegativos para determinados biomarcadores relacionados à Neuromielite Óptica e a Esclerose Múltipla, fornecendo assim um novo e mais preciso processopara diagnóstico de doenças desmielinizantes. / Study of the biological coverage of nanosurfaces by computational modeling: application in the development of nanoimunoresensors. In this work, computational molecular modeling techniques were applied to describe nanosurfaces functionalized with immune system biomolecules, correlating data from atomic force microscope experiments, molecular dynamics, and steered molecular dynamics simulations. The main goal of this research was to evaluate intermolecular forces involved in the antigen-antibody interaction on the nanosurfaces during the development of nanoimmunosensors for demyelinating diseases detection, especially neuromyelitisoptica. The neuromyelitisoptica is an autoimmune inflammation in which components of the immune system respond against optical nerves and spinal cord, resulting in demyelinating lesions. In the literature, studies have established anti-aquaporin 4 as an important biomarker for neuromyelitisoptica. Then, a nanoimmunosensor for anti-aquaporin 4 antibodies detection in neuromyelitisoptica patients serum via Atomic Force Microscopy is in development. This study requested a computational approach for describing the tridimensional structure of antibodies. The novel approach consisted of computer molecular modeling and engineering to perform successive substitutions in residues of the antigen interaction site. Tests carried out using antibody structures available in specialized data banks demonstrated the similarity of (48 ± 18) % and (65 ± 14) % for light and heavy chains, respectively, of the computationally generated models and experimental 3D structures of antibodies. Additionally, a statistical model was developed to prove the nanoimmunosensor sensing activity, which was useful to treat and interpret the experimental data. This statistical model was efficient to distinguish seropositive patients from seronegative subjects considering specific biomarkers related to neuromyelitisoptica and multiple sclerosis, providing a novel and more precise process for demyelinating disease diagnosis.

Patterned silver (Ag) columnar nanorods were prepared by the glancing angle physical vapor deposition method. The Ag columnar nanorods were grown on a Si (100) substrate patterned with posts in a square “lattice” of length 1 μm. An electron beam source was used as the evaporation method, creating the deposition flux which was oriented 85˚ from the substrate normal. A Dimension Icon with NanoScope V controller atomic force microscope was used to measure the spring constant in 10 nm increments along the long axis of five 670 nm long Ag nanorod specimens. The simple beam bending model was used to analyze the data. Unexpected behavior of the spring constant data was observed which prevented a conclusive physically realistic value of the Young’s modulus to be calculated.

Candidate active pharmaceutical ingredients (APIs) are routinely tested to determine such parameters as physical stability, chemical stability, and bioavailability. Preformulation analysis of APIs does not currently attemept to determine whether they will perform to an acceptable level once they have been formulated. In practice, the APIs are subjected to extensive in vitro testing of their performance in a formulation, combined with optimisation of the formulation. This formulation testing is both time-consuming and expensive. In the field of pulmonary drug delivery from dry powder inhalers (DPIs), the API has to be aerosolized effectively in order to penetrate the lunfs and reach its deposition target. In a conventional ternary DPI fromulation, the API is combined with carrier lactose and fine lactose particles. The inter-particle forces between these three components and the bulk properties of the formulation determine the structure of the formulation and the aerolization performance of the API. In this study, physicochemical properties of salbutamol base and several of its salts were investigated both quantitatively and qualitatively. The in vitro deposition characteristics of the formulated APIs were also determined. The relationship between these parameters and the deposition was analysed to establish if a rapid preformulation screening technique could be applied to the APIs with respect to predicting the deposition performance of the formulated API. A clear relationship between the deposition of the unformulated API and the formulated API was observed that could be exploited as a screening technique.

"Bacteria during the course of their life undergo a lot of developments on their surface. The changes that occur inside a cell result in the production of a variety of biopolymers on the cell surface. These polysaccharides have been found to play a major role in deciding the adhesive or repulsive nature of a bacterial cell. Based on the application the adhesive nature of a cell sometimes needs to be manipulated such that bacteria are required to have higher adhesions for bioremediation applications and in the case of bioreactors bacteria must not stick to walls to avoid fouling. In order to control adhesions of a cell to a variety of substrates, knowledge of the polysaccharides present on its surface is needed. Therefore the goal of the present study is to detect the sugars present on the surface of Pseudomonas putida KT2442 using Atomic force microscopy and to relate properties of the polysaccharides to bacterial adhesion. Previous experiments suggested that cellulose and other sugars were produced by Pseudomonas putida KT2442. Thus the cells were grown to late exponential phase and treated with cellulase to degrade any cellulose, if present, on the surface of the cells. Control experiments were done on untreated cells and cells that were not treated with cellulase but were centrifuged, since centrifugation is a part of the cellulase treatment and may also affect the bacterial surface. An appropriate (Steric) fitting model for the atomic force microscope (AFM) approach curves was applied to calculate the height and density of the polymer brush layer present on the cell surface. There was a decrease in the density of the polymer brush and increase in the height of the brush upon treatment with cellulase. Centrifugation alone did not affect the approach curves. From looking at the retraction curves it verified the results got from the approach curves and indicated stretching out of the polymer brush to greater distances after the treatment with cellulase. Another batch of cells was treated with dextranase to check for the presence of dextran on the cell surface. Dextranase treated cells behaved identical to the control cells, suggesting that dextran is not one of the polysaccharides present on the bacterial surface. No change was observed in retraction curves data for dextranase treated and untreated cells."

[pt] Nesta tese, apresentamos um procedimento utilizado para a calibração do fotodetector e dos cantileveres utilizados em nosso AFM para a medida de força lateral. Desenvolvemos um código em Matlab para o controle do microscópio que permitiu a realização do estudo da influência da força normal na fricção. Também foi desenvolvido um segundo código em Matlab para a medida automatizada da adesão. Apresentamos e discutimos a influência da energia livre superficial na fricção e adesão de várias superfícies. Neste trabalho um estudo da influência da condensação capilar na forca lateral foi estudado para superfícies hidrofílicas, e hidrofóbicas. Encontramos que as nano asperezas podem realizar contatos singulares descritos pelo modelo de Hertz ou múltiplos contatos de acordo com o modelo de Greenwood. O tipo de contato entre as nano asperezas pode ser controlado através da hidrofobicidade e da umidade relativa no ambiente de medida. É verificado que os meniscos formados entre ponta e superfície influenciam a força lateral, através do aumento da força normal e também através da energia gasta pela ponta para arrastar ou deformar o capilar durante seu deslocamento sobre a superfície. O efeito da cinética de condensação capilar da água sobre a fricção foi também estudado. É mostrado que a molhabilidade é determinante para a definição dos mecanismos da dissipação de energia entre as nanoasperezas. Apresentamos também a influência da hidrofobicidade superficial no coeficiente de atrito. A correlação observada entre o ângulo de contato e o coeficiente de atrito reforça a importância da cinética da condensação capilar nos processos de fricção que ocorre na escala de nanômetros. / [en] In this work, the procedures developed to the calibration of the AFM photodetector and cantilevers for lateral force measurements in our AFM is presented. A Matlab code that controls the microscope allows the study of the influence of the normal force on the lateral one. A second Matlab code was developed in order to study the adhesion forces in an automated way. We present and discuss the influence of the surface free energy on the friction and adhesion forces. In this work, the lateral forces were measured at hydrophilic and hydrophobic surfaces. It was observed that the nano asperities may form single asperity contacts described by the Hertz model as well as multi-asperity type of contacts described by the Greenwood model. The nanoasperity contact may be controlled by the wettability and ambient relative humidity. It is seen that the capillar formed between the tip and the surface influences the tip-surface normal force and the friction forces due to the dissipation of energy caused by the drag or brake of the capillar meniscous. The effect of capillary condensation kinetics was studied as well. It is shown that the surface wettability is determinant to the energy dissipation mechanism in nanoscale. The influence of the surface wettability on the friction coefficient is presented. The observed correlation between the friction coefficient and contact angle enhances the influence of the surface wettability and its kinetics in the friction forces at nanoscale.

Surface characteristics such as topography and critical dimensions serve as important indicators of product quality and manufacturing process performance especially at the micrometer and the nanometer scales. This paper first reviews different technologies used for obtaining high precision 3-D images of surfaces, along with some selected applications. Atomic force microscopy (AFM) is one of such methods. These images are commonly distorted by convolution effects, which become more prominent when the sample surface contains high aspect ratio features. In addition, data artifacts can result from poor dynamic response of the instrument used. In order to achieve reliable data at high throughput, dynamic interactions between the instrument's components need to be well understood and controlled, and novel image deconvolution schemes need to be developed. Our work aims at mitigating these distortions and achieving reliable data to recover metrology soundness. A summary of our findings will be presented. / Singapore-MIT Alliance (SMA)

In this paper, the problem of dual actuation in the atomic force microscope (AFM) is analyzed. The use of two actuators to balance the trade-off between bandwidth, range, and precision has been recently extended to nano-positioning systems. Despite existing demands, this concept undergoes fundamental limitations towards its extension to AFMs. This is attributed to the non-conventional requirement imposed on the control signal response, as it used to create the image of the characterized surface. / Singapore-MIT Alliance (SMA)