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A number of microcantilever systems of fundamental importance are explored using theoretical and numerical methods to quantify and provide physical insights into the dynamics of experimentally accessible systems that include a variety of configurations and viscous fluids. It is first shown that the correlated dynamics of both a laterally and vertically offset cantilever pair can be accurately predicted by numerical simulations. This is verified by comparing the correlated dynamics yielded by numerical simulations with experimental measurement. It is also demonstrated that in order to obtain these accurate predictions, geometric details of the cantilever must be included in the numerical simulation to directly reflect the experimental cantilever. A microrheology technique that utilizes the fluctuation-dissipation theorem is proposed. It is shown that by including the frequency dependence of the fluid damping, improvements in accuracy of the predictions of the rheological properties of the surrounding fluid are observed over current techniques. The amplitude spectrum of a 2-D cantilever in a power-law fluid is studied. The resulting amplitude spectrum yielded a curve similar to an overdamped system. It is observed that the amplitude and noise spectrum yield the same qualitative response for a 2-D cantilever in a shear thinning, power-law fluid. The correlated dynamics of a tethered vertically offset cantilever pair is investigated. It is shown that for a range of stiffness ratios, which is the ratio of the spring constant of the tethering relative to the cantilever spring constant, the change in the correlated dynamics of a Hookean spring tethered cantilever pair can be seen in the presence of fluid coupling. The dynamics of a spring-mass tethered, vertically offset cantilever pair is qualitatively studied by simplifying the model to an array of springs and masses. The resulting study found that the correlated dynamics of the displacement of mass of the tethered object yielded newly observed features and characteristics. It is shown that the curve shape of the cross-correlation of the displacement of the mass of the tethered object is similar to that of the auto-correlation of the displacement of the mass representing a step forced cantilever. The cross-correlation of the displacement of the mass of the tethered object, however, is found to be significantly more dependent on the stiffness ratio than the auto-correlation of the displacement of the mass representing a cantilever for t > 0. At t = 0, it is observed that the mass of the tethered object yields the same finite value for the cross-correlation for all studied values of the stiffness ratio. This characteristic is a result of the symmetry of the studied spring-mass system. / Ph. D.

Next generation polymer composites that utilize the high electrical conductivity and tensile strength of carbon nanotubes are of interest. To effectively disperse carbon nanotubes into polymers, a more fundamental understanding of the polymer/nanotube interface is needed. This requires the development of new analytical methods and techniques for measuring the adhesion between a single molecule and the sidewalls of carbon nanotubes. Atomic Force Microscopy is an integral tool in the characterization of materials on the nanoscale. The objectives of this research were to: 1) characterize the binding force between single molecules and the backbone of a single walled carbon nanotube (SWNT), and 2) measure and interpret the mechanical response of carbon-based nano-objects to compressive loads using an atomic force microscope. To identify chemical moieties that bind strongly to the sidewall of the nanotubes, two experimental approaches have been explored. In the first, force volume images of SWNT paper were obtained using gold-coated AFM tips functionalized with terminally substituted alkanethiols and para-substituted arylthiols. Analysis of these images enabled quantification of the adhesive interactions between the functionalized tip and the SWNT surface. The resultant adhesive forces were shown to be dependent upon surface topography, tip shape, and the terminal group on the alkanethiol. The mechanical response of several single- and multi-walled carbon nanotubes under compressive load was examined with an AFM. When the scanner, onto which the substrate has been mounted, was extended and retracted in a cyclic fashion, cantilever deflection, oscillation amplitude and resonant frequency were simultaneously monitored. By time-correlating cantilever resonance spectra, deflection and scanner motion, precise control over the length of nanotube in contact with the substrate, analogous to fly-fishing was achieved. This multi-parameter force spectroscopy method is applicable for testing the mechanical and interfacial properties of a wide range of nanoscale objects. This research has led to a clearer understanding of the chemistry at the nanotube/polymer interface, as well as the mechanical response of nanoscale materials. A new force spectroscopic tool, multi-parameter force spectroscopy, should be extremely helpful in characterizing the mechanical response of a myriad of nanoscale objects and enable nanoscale devices to become a reality.

La bactérie Pseudomonas aeruginosa (PA) est un pathogène responsable de 20%-30% des infections nosocomiales en milieu hospitalier. Pour les individus sains, elle ne présente pas de réel danger, mais pour les personnes atteintes par la mucoviscidose et les patients immunodéprimés, elle est la cause principale de mortalité et des infections pulmonaires. PA a développé des souches multi-résistantes aux antibiotiques et des nouvelles approches thérapeutiques plus efficaces sont donc nécessaires. Elle se fixe à la surface des cellules-hôtes par une interaction entre des protéines (lectines) présentes sur sa membrane et des sucres présents sur la membrane cellulaire. L’interaction lectine-sucre joue un rôle important dans l’adhésion de la bactérie puis dans la fabrication d’un biofilm pathogène.Une nouvelle approche thérapeutique consiste à créer des molécules synthétiques (glycomimes) de plus grande affinité que les sucres présents sur les cellules. Pour cela, plus de 150 glycomimes ont été synthétisés et examinés afin de trouver le meilleur candidat pour empêche le processus d'infection de bactéries. Certains d'entre eux ont été choisis et étudiés par la Microscopie à Force Atomique (AFM). Cette thèse est consacrée à l’étude des interactions lectine-glycomime et aussi cellule-bactérie par AFM. L’imagerie combinée avec la modélisation permet de comprendre le rôle du glycomime sur la géométrie des complexes créés et la spectroscopie permet de mesurer les forces d’interaction présentes lors de l’adhésion, au niveau moléculaire et cellulaire. Une réduction de l’adhésion bactérienne a été observée après l’introduction du glycomime, confirmant son rôle d’inhibiteur et la validité de toute la démarche. L’objectif ultime est l’identification des meilleurs glycomimes à introduire afin de développer de nouveaux médicaments. / Pseudomonas aeruginosa (PA) is a human opportunistic pathogen responsible for 20% -30% of nosocomial infections in French hospitals. For healthy people, it presents no real danger, but for people with cystic fibrosis disease and immune-compromised patients, it is the leading cause of mortality and lung infections. PA has developed antibiotic multi-resistant strains and new and more effective therapeutic approaches are needed. It binds to the surface of the host cells by an interaction between proteins (lectins) present on the membrane and sugars of the host-cell membrane. The lectin-sugar interaction plays an important role in adherence of the bacteria and in the manufacture of a pathogenic biofilm.A new therapeutic approach is to create synthetic molecules (glycoclusters) of greater affinity than the natural sugars present on the cells. To this aim, more than 150 glycoclusters have been synthetized and screened to find the best candidate to inhibit the bacteria infection process. Some of them have been selected and studied by Atomic Force Microscopy (AFM). In particular, this thesis is devoted to study the lectin-glycocluster and cell-bacteria interactions by AFM. The combination of AFM imaging with molecular dynamic simulations let understanding the role of the geometry of the glycoclusters on the complex formation, while AFM spectroscopy accesses the lectin-glycocluster interaction forces at the molecular and cellular levels. The reduction of bacterial adhesion has been observed upon the addition of the glycocluster. This confirms the anti-adhesive properties of the glycocluster and validates the procedure. The ultimate goal is the identification of the best glycoclusters in order to develop new drugs.

<p>The intricate interplay of biomolecules acting together, rather than alone, provides insight into the most basic of cellular functions, such as cell signaling, metabolism, defense, and, ultimately, the creation of life. Inherent in each of these processes is an evolutionary tendency towards increased efficiency by means of biolgocial synergy-- the ability of individual elements of a system to produce a combined effect that is different and often greater than the sum of the effects of the parts. Modern biochemists are challenged to find model systems to characterize biological synergy.</p><p>We discuss the multicomponent, enzyme complex the cellulosome as a model system of biological synergy. Native cellulosomes comprise numerous carbohydrate-active binding proteins and enzymes designed for the efficient degradation of plant cell wall matrix polysaccharides, namely cellulose. Cellulosomes are modular enzyme complexes, comparable to enzyme "legos" that may be readily constructed into multiple geometries by synthetic design. Cellulosomal enzymes provide means to measure protein efficiency with altered complex geometry through assay of enzymatic activity as a function of geometry.</p><p>Cellulosomes are known to be highly efficient at cellulose depolymerization, and current debates on the molecular origins of this efficiency suggest two related effects provide this efficiency: i) substrate targeting, which argues that the localization of the enzyme complex at the interface of insoluble cell wall polysaccharides facilitates substrate depolymerization; and ii) proximity effects, which describe the implicit benefit for co-localizing multiple enzymes with divergent substrate preferences on the activity of the whole complex.</p><p>Substrate targeting can be traced to the activity of a single protein, the cellulosomal scaffoldin cellulose binding module CBM3a that is thought to uniquely bind highly crystalline, insoluble cellulose. We introduce methods to develop a molecular understanding of the substrate preferences for CBM3a on soluble and insoluble cellulosic substrates. Using pivaloylysis of cellulose triacetate, we obtain multiple soluble cello-oligosaccharides with increasing degree of glucose polymerization (DP) from glucose (DP1) to cellodecaose (DP10) in high yield. Using calorimetry and centrifugal titrations, cello-oligosacharides were shown to not bind Clostridial cellulolyticum CMB3a. We developed AFM cantilever functionalization protocols to immobilize CBM3a and then probe the interfacial binding between CBM3a and a cellulose nanocrystal thin film using force spectroscopy. Specific binding at the interface was demonstrated in reference to a control protein that does not bind cellulose. The results indicate that i) CBM3a specifically binds nanocrystalline cellulose and ii) specific interfacial binding may be probed by force spectroscopy with the proper introduction of controls and blocking agents.</p><p>The question of enzyme proximity effects in the cellulosome must be answered by assaying the activity of cellulosomal cellulases in response to cellulosome geometry. The kinetic characterization of cellulases requires robust and reproducible assays to quantify functional cellulase content of from recombinant enzyme preparations. To facilitate the real-time routine assay of cellulase activity, we developed a custom synthesis of a fluorogenic cellulase substrate based on the cellohexaoside of Driguez and co-workers (vide infra). Two routes to synthesize a key thiophenyl glycoside building block were presented, with the more concise route providing the disaccharide in four steps from a commercial starting material. The disaccharide building blocks were coupled by chemical activation to yield the fully protected cellohexaoside over additional six steps. Future work will include the elaboration of this compound into an underivatized FRET-paired hexasaccharide and its subsequent use in cellulase activity assays.</p><p>This dissertation also covers an experimental system for the evaluation of methonium desolvation thermodynamics. Methonium (-N+Me3, Am) is an organic cation widely distributed in biological systems. The appearance of methonium in biological transmitters and receptors seems at odds with the large unfavorable desolvation free energy reported for tetramethylammonium (TMA+), a frequently utilized surrogate of methonium. We report an experimental system that facilitates incremental internalization of methonium within the molecular cavity of cucurbit[7]uril (CB[7]).</p><p>Using a combination of experimental and computational studies we show that the transfer of methonium from bulk water to the CB[7] cavity is accompanied by a remarkably small desolvation enthalpy of just 0.5±0.3 kcal*mol-1, a value significantly less endothermic than those values suggested from gas-phase model studies (+49.3 kcal*mol-1). More surprisingly, the incremental withdrawal of methonium surface from water produces a non- monotonic response in desolvation enthalpy. A partially desolvated state exists, in which a portion of the methonium group remains exposed to solvent. This structure incurs an increased enthalpic penalty of ~3 kcal*mol-1 compared to other solvation states. We attribute this observation to the pre- encapsulation de-wetting of the methonium surface. Together, our results offer a rationale for the wide biological distribution of methonium and suggest limitations to computational estimates of binding affinities based on simple parameterization of solvent-accessible surface area.</p> / Dissertation

Estudos têm demonstrado o potencial da terapia fotodinâmica antimicrobiana (aPDT) na inativação de diferentes células microbianas. No geral, são três as fases de crescimento dos microrganismos: fase lag, exponencial e estacionária. Os objetivos deste estudo foram avaliar a susceptibilidade de células de Candida albicans em diferentes fases de crescimento, submetidas à aPDT, associando azul de metileno (50 &mu;M) e luz de emissão vermelha (&lambda;= 660 nm) e investigar alterações morfológicas, mecânicas e bioquímicas, antes e depois da aPDT, por microscopia eletrônica de varredura, de força atômica e por espectroscopia no infravermelho por transformada de Fourier. Os resultados obtidos sugerem que, em parâmetros letais, células em fase estacionária de crescimento (48 h) são menos susceptíveis à aPDT, quando comparadas àquelas em fases lag (6 h) e ex-ponencial (24 h) de crescimento. Entretanto, em parâmetros subletais, células de 6 h e 48 h mostraram a mesma susceptibilidade à aPDT. Em sequência, os experimentos foram realizados em parâmetros considerados subletais para células crescidas por 6 e 48 h. A avaliação morfológica mostrou menor quantidade de matriz extracelular em células de 6 h comparada àquelas de 48 h. A espectroscopia de força atômica mostrou que células em fase lag perderam a rigidez após a aPDT, enquanto que células em fase estacionária mostraram comportamento in-verso. Ainda, células de 48 h diminuíram sua adesividade após a aPDT, enquanto que células de 6 h e 24 h tornaram-se mais adesivas. Os resultados bioquímicos revelaram que as diferenças mais significativas entre as células fúngicas de 6 h e 48 h ocorreram na região de DNA e carboidratos. A aPDT promoveu mais alterações bioquímicas na região de DNA e carboidratos em células de 6 h e em lipídios e ácidos graxos em células de 48 h. Nossos resultados indicam que a fase de crescimento celular desempenha papel importante no sítio de ação da aPDT em células de C. albicans. / Studies have demonstrated the potential of antimicrobial photodynamic therapy (aPDT) on the inactivation of different microbial cells. Overall, there are three phases of cell growth: lag phase, exponential phase and stationary phase. The objectives of this study were to evaluate the susceptibility of Candida albicans in different growth stages submitted to aPDT, with methylene blue (50&mu;M) and red light (&lambda; = 660 nm) and to investigate morphological, mechanical and biochemical changes before and after aPDT, by scanning electron microscopy, atomic force microscopy and by Fourier transform infrared spectroscopy. The results suggested that with lethal parameters, cells in stationary phase (48 h) are less susceptible to aPDT, compared to those in lag phase (6 h) and exponential phase (24 h). However, in sub-lethal parameters 6 h and 48 h cells showed the same susceptibility to aPDT. The following results were obtained in sub-lethal parameters. The morphological evaluation showed lower amount of extra-cellular matrix at 6 h compared to cells growth for 48 h. The atomic force spectroscopy showed that cells in lag phase lost cell wall rigidity after aPDT, while cells in stationary phase showed a reverse behavior. Furthermore, 48 h cells presented a decrease in their adhesiveness after aPDT, whereas cells growth for 6 h and 24 h become more adhesive. The biochemical evaluation showed that the most significant differences among the fungal cells growth for 6 h and 48 h in DNA and carbohydrates. The aPDT caused more expressive alterations on DNA and carbohydrates in cells growth for 6 h, while cells growth for 48 h presented significant alterations on lipids and fatty acids. Our results indicate that cell growth phase play an important role on the target sites affected by aPDT in C. albicans cells.

The profound simplicity and versatility of the molecule at the heart of all earth- bound life forms, DNA, continues to inspire new frontiers of scientific inquiry. Central to many of these, including the de novo design of novel DNA nanostructures and the use of DNA to probe the principles of biological self-assembly and the operation of cellular nanomachines, is the interaction of DNA with forces, both internal and external. This thesis comprises a survey of three key ways coarse-grained simulations using the oxDNA model can contribute to efforts to characterize these interactions. First, a non-equilibrium data analysis framework based on the Jarzynski equality from statistical physics is validated for use with oxDNA through the reconstruction of free energy landscapes for canonical DNA hairpin systems. We provide a framework for assessing errors in the method and apply it to study a system for which conventional equilibrium simulations would be impractical: DNA origami 'handles' proposed for use in force spectroscopy experiments. Next, we simulate the forcible unravelling of three DNA origami structures, the largest systems yet studied with simulated force spectroscopy. We combine these results with experimental AFM data to probe the mechanical response of origami in unprecedented detail, highlighting the effect of nanostructure design on unfolding behaviour. Lastly, we examine the validity of using widely-employed polymer elastic models to predict internal entropic forces in ssDNA. We develop a framework for measuring internal forces in the oxDNA coarse-grained model and apply it to analyze the pico-Newton range forces exerted by a recently proposed DNA origami force clamp, ultimately concluding that conventional means of estimating internal ssDNA forces are often inaccurate and should be supplemented with coarse-grained simulations. In addition to providing new insights about the DNA systems we present, our results highlight the significant fruits of complementing experimental studies with coarse-grained simulations.

Abstract This thesis describes the design, fabrication and operation of a microfluidic device for the screening of biomolecule mixture surface mediated effects. The characterisation of a surface immobilisation strategy that will allow the robust attachment of candidate biomolecules on a substrate for use in cell culture applications. This is carried out in the form of a modified and optimised layer-by-layer surface immobilisation strategy and its subsequent thorough and robust characterisation. This was achieved by compiling and critically analysing large amounts of quartz crystal microbalance with dissipation (QCM-D) data and the model utilised to provide meaningful, physical data as an output. QCM-D data was combined with surface plasmon resonance (SPR) data to validate the assumptions used within the QCM-D model package. Further evidence demonstrating the presence of the multilayer, as described by QCM-D and SPR, is achieved using x-ray photoelectron spectroscopy (XPS). These results show that the multilayer surface is robustly attached to the substrate and consists of a large amount of water whilst being able to immobilise mixtures of four proteins. A custom protocol for fabricating these two layer devices was devised and is presented. Scale limitations have been overcome to provide mixing capabilities for large extracellular matrix molecules to be immobilised on the previously described, microfluidically generated surface immobilisation strategy. The optimisation and characterisation of the mixing within this microfluidic device, affected by the incorporated staggered herring bone mixer is also shown. Using dynamic force spectroscopy (DFS) along with a custom designed force curve data processing and analysis package, the spatial localisation of a mixture of four immobilised biomolecules was determined. The aim of this study was to compare the spatial localization of a mixture of four biomolecules created by; standard cell culture protocols (adsorbed from bulk onto tissue culture polystyrene) and a surface created via microfluidic deposition on top of a previously described surface immobilisation strategy. The design and robust application of this custom analysis package allows the definition of a “Barricade of Specificity” such that interactions between an antibody functionalised AFM tip and a surface composed of a mixture of proteins, to be categorised as either a “true” specific interaction, or a non-specific interaction. The application of this Barricade of Specificity thus allows the spatial localisation of four immobilized biomolecules to be determined with a large degree of accuracy as a result of the large rage of non-specific interactions surveyed and the strict definition of a valid rupture force. The final chapter details the application of the microfluidic platform to enable high throughput screening of the effects of extracellular matrix (ECM) molecules, singly and in combination, with regards to the effect on the expression of cell surface markers on umbilical cord blood (UCB) derived CD34+ cells. Careful selection of candidate ECM molecules, cytokine and oxygen concentration has resulted in little difference in the effect on UCB derived CD34+ cells differentiation state after seven days in culture. The major effect has been the maturation towards lymphocyte and leukocyte precursors. However, of the four ECM molecules tested individually, in binary and in quaternary combinations, osteopontin (Opn) and laminin (Ln) demonstrated differences compared to other surfaces tested. In order to further assess the effect of these protein surfaces on the cell surface marker expression of UCB derived CD34+ cells, further tests are warranted for increased periods of time to enable greater discrimination in marker expression and thus increase our understanding of the fundamental biology of this rare and clinically useful cell source.