This research details the creation and characterization of a new biomimetic artificial inner hair cell sensor in an artificial cochlear environment. Designed to mimic the fluid flows around the inner hair cells of the human cochlea, the artificial cochlear environment produces controlled, linear sinusoidal fluid flows with frequencies between 25 and 400 Hz. The lipid bilayer-based artificial inner hair cell generates current through changes in the bilayer's capacitance. This capacitance change occurs as the sensor's artificial stereocilium transfers the force in the fluid flow to the bilayer. Frequency tuning tests are performed to characterize the artificial inner hair cell's response to a linear chirp signal from 1 to 400 Hz. The artificial inner hair cell's response peaks at a resonant frequency of approximately 83 Hz throughout most of the tests. Modelling the artificial stereocilium as a pinned free beam with a rotational spring at the pinned end yields a rotational spring stiffness of 177*10^-6 Nm/rad. Results with 0 mV potential applied across the bilayer indicate that current generation at 0 mV likely comes from other sources besides the bilayer. Increasing the voltage potential increases the broadband power output of the system, with an approximately linear relationship. A final test keeps the fluid flow frequency constant and varies the fluid velocity and applied voltage potential. Manipulation of the applied voltage potential results in a fluid velocity to RMS current relationship reminiscent of the variable sensitivity of the human cochlea. / Master of Science

The formation of lipid bilayer membranes between droplets of ionic liquid is presented as a means of forming functional bimolecular networks for use in sensor applications. Ionic liquids are salts that have a number of useful properties, such as low melting points making them liquid at room temperature and exceedingly low vapor pressure. Ionic liquids have seen recent popularity as environmentally friendly industrial solvent alternatives. Our research demonstrates that it is possible to consistently form lipid bilayers between droplets of ionic liquid solutions. Analysis shows that the ionic liquids have negligible effects on the physical stability and electrical properties of the bilayer. It is also shown that the magnitude of the conductance levels of Alamethicin peptide are altered by some ionic liquids. / Master of Science

abstract: Biological membranes are critical to cell sustainability by selectively permeating polar molecules into the intracellular space and providing protection to the interior organelles. Biomimetic membranes (model cell membranes) are often used to fundamentally study the lipid bilayer backbone structure of the biological membrane. Lipid bilayer membranes are often supported using inorganic materials in an effort to improve membrane stability and for application to novel biosensing platforms. Published literature has shown that a variety of dense inorganic materials with various surface properties have been investigated for the study of biomimetic membranes. However, literature does not adequately address the effect of porous materials or supports with varying macroscopic geometries on lipid bilayer membrane behavior. The objective of this dissertation is to present a fundamental study on the synthesis of lipid bilayer membranes supported by novel inorganic supports in an effort to expand the number of available supports for biosensing technology. There are two fundamental areas covered including: (1) synthesis of lipid bilayer membranes on porous inorganic materials and (2) synthesis and characterization of cylindrically supported lipid bilayer membranes. The lipid bilayer membrane formation behavior on various porous supports was studied via direct mass adsorption using a quartz crystal microbalance. Experimental results demonstrate significantly different membrane formation behaviors on the porous inorganic supports. A lipid bilayer membrane structure was formed only on SiO2 based surfaces (dense SiO2 and silicalite, basic conditions) and gamma-alumina (acidic conditions). Vesicle monolayer adsorption was observed on gamma-alumina (basic conditions), and yttria stabilized zirconia (YSZ) of varying roughness. Parameters such as buffer pH, surface chemistry and surface roughness were found to have a significant impact on the vesicle adsorption kinetics. Experimental and modeling work was conducted to study formation and characterization of cylindrically supported lipid bilayer membranes. A novel sensing technique (long-period fiber grating refractometry) was utilized to measure the formation mechanism of lipid bilayer membranes on an optical fiber. It was found that the membrane formation kinetics on the fiber was similar to its planar SiO2 counterpart. Fluorescence measurements verified membrane transport behavior and found that characterization artifacts affected the measured transport behavior. / Dissertation/Thesis / Ph.D. Chemical Engineering 2011

Biological membranes are mainly composed of two layers of lipids, various kinds of proteins and organic macromolecules, forming the protective barriers that separate the inner milieu of living cells from the environment. The possibility of penetrating the membrane is of great importance for biomedical applications. Recently, a lot of attention has been given to the mechanisms and the details of the interactions between the membrane and nanoparticles, as well as to the development of effective delivery strategies. A manipulation of the hydrophobicity of nanoparticles can facilitate the translocation through the membrane. Modifying the physical/chemical properties of the membrane through oxidation can also influence the delivery of nanoparticles or macromolecules into the cell. In this work, using coarse-grained molecular dynamics simulations, the passive translocation of nanoparticles with a size of about 1 nm and with tunable degrees of hydrophobicity through lipid membranes is studied. It is shown that a window of nanoparticle translocation with a sharp maximum is located at a certain hydrophobicity in between fully hydrophilic and fully hydrophobic characters. By combining direct simulations with umbrella sampling simulations, the free energy landscapes for nanoparticles covering a wide range of hydrophobicities are obtained. The directly observed translocation rate of the nanoparticles can be mapped to the mean escape rate through the calculated free energy landscapes, and the maximum of translocation can be related with the maximally flat free energy landscape. For nanoparticles with the balanced hydrophobicity, the bilayer forms a remaining barrier of a few kBT and can be spontaneously surmounted. Further investigations are conducted to explore the cooperative effects of a larger number of nanoparticles and their impact on membrane properties such as membrane permeability for solvent, the area per lipid, and the orientation order of lipid tails. By calculating the partition of nanoparticles between water and oil phases, the microscopic parameter, i.e. the hydrophobicity of nanoparticles, can be mapped to an experimentally accessible partition coefficient. The studies reveal a generic mechanism for spherical nanoparticles to overcome biological membrane-barriers without the need of biologically activated processes. Two oxidatively modified lipids are studied on coarse-grained level using molecular dynamics simulations. The findings support the view that lipid oxidation leads to a change of the lipid conformation: lipid tails tend to bend toward the lipid head-tail interface due to the presence of hydrophilic oxidized beads. This change in conformation can further influence structural properties, elasticity and membrane permeability: an increase of the area per lipid, accompanied with decrease of the membrane thickness and order parameter of the lipid tails; a sharp drop of stretching modulus; a significant increase of the membrane permeability for water. Oxidized lipid bilayers interacting with NPs of various degrees of hydrophobicity are further studied. The critical hydrophobicity corresponding to the maximum translocation rate of NPs, shifts towards the hydrophilic region, which coincides with the same decrease in percentage of the average hydrophobicity in the core of the membrane upon oxidation. Around the critical point of NPs' hydrophobicity, a significant increase of the translocation rate of NPs through the oxidized bilayers is observed, when compared to non-oxidized bilayers. This is associated with a deterioration of the free energy barrier for NPs inside the oxidized bilayers, resulting from oxidation effects. These findings are consistent with the studies of the mean escape rate through the free energy landscapes using Kramers theory. Regarding the membrane perturbation induced by NPs of various hydrophobicity, the data obtained with oxidized lipid bilayers present the same general trend as in the case of the non-oxidized lipid bilayer. These findings provide a better understanding of the interaction between NPs and oxidized lipid bilayers, and open a possibility to facilitate drug delivery.:1 Introduction 1 1.1 Lipid Bilayers 1 1.2 Oxidized Lipid Bilayers 2 1.3 Experimental Methodology 4 1.4 Lipid Models 5 1.5 The Lipid Bilayer Interacting with NPs 6 1.6 Thesis Overview 7 2 State of the art 9 2.1 Molecular Dynamics Simulations of Lipid Bilayers 9 2.1.1 Equations of Motion and the Integrations of Equations of Motion 10 2.1.2 Interaction Potentials 12 2.1.3 Periodic Boundary Conditions 14 2.1.4 Barostats and Thermostats 15 2.2 Umbrella Sampling Simulation 19 2.2.1 The Basics of Umbrella Sampling Method 20 2.2.2 Analyzing Umbrella Sampling Results by WHAM 23 2.2.3 The Principle of Choosing Bias Potential 24 3 Lipid Membranes interacting with Nanoparticles of Various Degrees of Hydrophobicity 25 3.1 Introduction 25 3.2 Coarse-grained Model and Simulation Setups 27 3.3 Results and Discussions 31 3.3.1 NPs-membrane Interactions 31 3.3.2 NPs Translocation 33 3.3.3 Concentration Effect of NPs 35 3.3.4 The Effect of Hydrophobicity on Kinetic Pathways 38 3.3.5 Potential of Mean Force 39 3.3.6 Hydrophobicity Scale 41 3.3.7 Solvent Permeation and Membrane Perturbation Induced by NPs 45 3.4 Summary 47 4 Coarse-grained Model of Oxidized Lipids and their Interactions with NPs of Varying Hydrophobicities 51 4.1 Introduction 51 4.2 Coarse-grained Model and Simulation Details 52 4.3 Results and Discussions 54 4.3.1 Characterizing the Oxidized Lipid Membranes 54 4.3.2 Oxidized Lipid Membranes Interacting with NPs of Various Degrees of Hydrophobicity 59 4.4 Summary 65 5 Summary and Outlook 69

Intracellular transport of membrane-bound vesicles and organelles is a process fundamental for many cellular functions including cell morphogenesis and signaling. The transport is mediated by ensembles of motor proteins, such as kinesins, walking on microtubule tracks. When transporting membrane-bound cargo inside a cell, the motors are linked to diffusive lipid bilayers either directly or via adaptor molecules. The fluidity of the lipid bilayers induces loose inter-motor coupling which is likely to impact the collective motor dynamics and may induce cooperativity. Here, we investigate the influence of loose coupling of kinesin motors on its transport characteristics. In the first part of this thesis, we used truncated kinesin-1 motors with a streptavidin-binding-peptide (SBP) tag and performed gliding motility assays on streptavidin-loaded biotinylated supported lipid bilayers (SLBs), so called ‘membrane-anchored’ gliding motility assays. We show that the membrane-anchored motors act cooperatively; the microtubule gliding velocity increases with increasing motor density. This is in contrast to the transport behavior of multiple motors rigidly bound to a substrate. There, the motility is either insensitive to the motor density or shows negative interference at higher motor density, depending on the structure of the motors. The cooperativity in transport driven by membrane-anchored motors can be explained as following: while stepping on a microtubule, membrane-anchored motors slip backwards in the viscous membrane, thus propelling the microtubule in the solution at a velocity, given by the difference of the motor stepping velocity and the slipping velocity. The motor stepping on the microtubule occurs at maximal stepping velocity because the load on the membrane-anchored motors is minute. Thus, the slipping velocity of membrane-anchored motors determines the microtubule gliding velocity. At steady state, the drag force on the microtubule in the solution is equal to the collective drag force on the membrane-anchored motors slipping in the viscous membrane. As a consequence, at low motor density, membrane-anchored motors slip back faster to balance the drag force of the microtubule in the solution. This results in a microtubule gliding velocity significantly lower than the maximal stepping velocity of the individual motors. In contrast, at high motor density, the microtubules are propelled faster with velocities equal to the maximal stepping velocity of individual motors. Because, in this case, the collective drag force on the motors even at very low slipping velocity, is large enough to balance the microtubule drag in the solution. The theoretical model developed based on this explanation is in good agreement with the experimental data of gliding velocities at different motor densities. The model gives information about the distance that the diffusing motors can isotropically reach to bind to a microtubule, which for membrane-anchored kinesin-1 is ~0.3 µm, an order of magnitude higher as compared to rigidly bound motors, owing to the lateral mobility of motors on the membrane. In addition, the model can be used to predict the number of motors involved in transport of a microtubule based on its gliding velocity. In the second part of the thesis, we investigated the effect of loose inter-motor coupling on the transport behavior of KIF16B, a recently discovered kinesin motor with an inherent lipid-binding domain. Recent studies based on cell biological and cell extract experiments, have postulated that cargo binding of KIF16B is required to activate and dimerize the motor, making it a superprocessive motor. Here, we demonstrate that recombinant full-length KIF16B is a dimer even in the absence of cargo or additional proteins. The KIF16B dimers are active and processive, which demonstrates that the motors are not auto-inhibited in our experiments. Thus, in cells and cell extracts Kif16B may be inhibited by additional factors, which are removed upon cargo binding. Single molecule analysis of KIF16B-GFP reveals that the motors are not superprocessive but exhibit a processivity similar to kinesin-1 indicating that additional factors are most likely necessary to achieve superprocessivity. Transport on membrane-anchored KIF16B motors exhibited a similar cooperative behavior as membrane-anchored kinesin-1 where the microtubule gliding velocity increased with increasing motor density. Taken together, our results demonstrate that the loose coupling of motors via lipid bilayers provides flexibility to cytoskeletal transport systems and induces cooperativity in multi-motor transport. Moreover, our ‘membrane-anchored’ gliding motility assays can be used to study the effects of lipid diffusivity (e.g. the presence of lipid micro-domains and rafts), lipid composition, and adaptor proteins on the collective dynamics of different motors.

Most drugs undergo passive transport during absorption and distribution in the body. It is desirable to predict passive permeation of future drug candidates in order to increase the productivity of the drug discovery process. Unlike drug-receptor interactions, there is no receptor map for passive permeability because the process of transport across the lipid bilayer involves multiple mechanisms. This work intends to increase the understanding of permeation of drug-like molecules through lipid bilayers. Drug molecules in solution typically form various species due to ionization, complexation, etc. Therefore, species specific properties must be obtained to bridge the experiment and simulations. Due to the volume contrast between intra- and extravesicular compartments of liposomes, minor perturbations in ionic and binding equilibria become significant contributors to transport rates. Using tyramine as a model amine, quantitative numerical models were developed to determine intrinsic permeability coefficients. The microscopic ionization and binding constants needed for this were independently measured. The partition coefficient in 1,9-decadiene was measured for a series of compounds as a quantitative surrogate for the partitioning into the hydrocarbon region of the bilayer. These studies uncovered an apparent long-range interaction between the two polar substituents that caused deviations in the microscopic pKa values and partition coefficient of tyramine from the expected values. Additionally the partition coefficients in the preferred binding region of the bilayer were also measured by equilibrium uptake into liposomes. All-atom molecular dynamics simulations of lipid bilayers containing tyramine, 4- ethylphenol, or phenylethylamine provided free energies of transfer of these solutes from water to various locations on the transport path. The experimentally measured partition coefficients were consistent with the free energy profiles in showing the barrier in the hydrocarbon region and preferred binding region near the interface. The substituent contributions to these free energies were also quantitatively consistent between the experiments and simulations. Specific interactions between solutes and the bilayer suggest that amphiphiles are likely to show preferred binding in the head group region and that the most of hydrogen bonds involving solutes located inside the bilayer are with water molecules. Solute re-orientation inside the bilayer lowers the partitioning barrier by allowing favorable interactions.

Lipid bilayers form the basis of the membranes that serve as a barrier between a cell and its physiological environment. Their physical properties make them ideally suited for this role: they are extremely soft with respect to bending but essentially incompressible under lateral tension, and they are quite permeable to water but essentially impermeable to ions which allows the rapid establishment of the osmotic gradients. The function of membrane proteins, which are vital for tasks ranging from signal transduction to energy conversion, depends on their interactions with the lipid environment. Because of the complexity of natural membranes, model systems consisting of simpler lipid mixtures have become indispensable tools in the study of membrane biophysics. The objective of the work reported here is to develop a deeper understanding of the underlying physics of lipid bilayers through nanoscale measurements of the mechanical properties of mixed lipid systems including cholesterol, a key ingredient of cell membranes. Atomic force microscopy (AFM) has been used extensively to measure the topographical and elastic properties of supported lipid bilayers displaying complex phase behaviour and containing mixtures of important PC, PE lipids and cholesterol. Phase transformations have been investigated varying the membrane temperature, and the effects of cholesterol in controlling membrane fluidity, phase, and energetics have been studied. Elastic modulus measurements were correlated with phase behaviour observations. To aid in the nanoscale probing of lipid bilayers, AFM probes with a high aspect ratio and tip radii of $sim$4~nm were fabricated and characterised. These probes were used to investigate the phase boundary in binary and ternary lipid systems, leading to the discovery of a raised region at the boundary which has implications for the localisation of reconstituted proteins as well as the role of natural domains or lipid rafts. The electrical properties of the probes were examined to assess their potential application for combined structural and electrical measurements in liquid. A novel technique was developed to aid in the study of the physical properties of lipid bilayers. Membrane budding was induced above microfabricated substrates through osmotic pressure. Modification of the adhesion energy of the bilayer through biotin-avidin linking was successful in modulating budding behaviour of liquid disordered bilayers. The free energy of the system was modelled to allow quantitative information to be extracted from the data.

Les particules fines émises par l'activité humaine sont la cause de diverses pathologies pulmonaires et cardiaques. Les particules de taille inférieure à 100 nm, appelées nanoparticules, sont particulièrement nocives car une fois inhalées, elles peuvent atteindre les alvéoles pulmonaires, lieux des échanges gazeux. Dans les alvéoles, les nanoparticules entrent d'abord en contact avec le surfactant pulmonaire. Ce fluide biologique tapisse les cellules épithéliales des alvéoles sur une épaisseur de quelques centaines de nanomètres et est composé de phospholipides et de protéines, les phospholipides étant assemblés sous forme de vésicules et corps multi-lamellaires. Dans ce travail, nous avons sélectionné des nanoparticules modèles de nature différente connues pour leur toxicité cellulaire (latex, oxydes métalliques, silice). Leur interaction avec un fluide pulmonaire mimétique administré aux prématurés (Curosurf®) a été étudiée en détail par microscopie optique et électronique, et par diffusion de la lumière. Nous avons mis en évidence que cette interaction est non spécifique et d'origine électrostatique. La diversité des structures hybrides obtenues entre particules et vésicules témoigne cependant de la complexité de cette interaction. En contrôlant cette interaction, nous avons formulé des particules couvertes d’une bicouche supportée de Curosurf® qui possèdent des propriétés remarquables de stabilité et de furtivité en milieu biologique.Dans une seconde partie, nous avons étudié le rôle du surfactant pulmonaire sur l’interaction entre particules et cellules épithéliales alvéolaires (A459). A l'aide d'expériences de biologie cellulaire réalisées in vitro, nous avons observé que la présence de surfactant diminue de manière significative le nombre de particules internalisées par les cellules. Dans le même temps, nous avons constaté une augmentation importante de la viabilité cellulaire. Une conclusion majeure de notre travail concerne la mise en évidence du rôle protecteur joué par le surfactant pulmonaire dans les mécanismes d'interaction des nanoparticules avec l'épithélium alvéolaire / Particulate matter emitted by human activity are the cause of various pulmonary and cardiac diseases. After inhalation, nanoparticles (ie particles smaller than 100 nm) can reach the pulmonary alveoli, where the gas exchanges take place. In the alveoli, the nanoparticles first encounter the pulmonary surfactant which is the fluid that lines the epithelial cells. Of a few hundreds of nanometers in thickness, the pulmonary fluid is composed of phospholipids and proteins, the phospholipids being assembled in multilamellar vesicles. In this work, we considered model nanoparticles of different nature (latex, metal oxides, silica). Their interaction with a mimetic pulmonary fluid administered to premature infants (Curosurf®) was studied by light scattering and by optical and electron microscopy. We have shown that the interaction is non-specific and mainly of electrostatic origin. The wide variety of hybrid structures found in this work attests however of the complexity of the phospholipid/particle interaction. In addition, we succeeded in formulating particles covered with a Curosurf® supported bilayer. These particles exhibit remarkable stability and stealthiness in biological environment. In a second part, we studied the role of the pulmonary surfactant on the interactions between nanoparticles and alveolar epithelial cells (A459). With cellular biology assays, we observed that the number of internalized particles decreases dramatically in presence of surfactant. At the same time, we found a significant increase in the A459 cell viability. Our study shows the importance of the pulmonary surfactant in protecting the alveolar epithelium in case of nanoparticle exposure

Seven transmembrane (7-TM) G protein coupled receptors (GPCR) constitute the largest family of integral membrane proteins in eukaryotes with more than 1000 members and encoding more than 2% of the human genome. These proteins play a key role in the transmission and transduction of cellular signals responding to hormones, neurotransmitters, light and other agonists, regulating basic biological processes. Their natural abundance together with their localization in the cell membrane makes them suitable targets for therapeutic intervention. Consequently, GPCR are proteins with enormous pharmacologic interest, representing the targets of about 50% of the currently marketed drugs. The current limitations in the experimental techniques necessary for microscopic studies of the membrane as well as membrane proteins emerged the use of computational methods and specifically molecular dynamics simulations. The lead motif of this thesis is the study of GPCR by means of this technique, with the ultimate goal of developing a methodology that can be generalized to the study of most 7-TM as well as other membrane proteins. Since the bovine rhodopsin was the only protein of the GPCR family with a known threedimensional structure at an atomic level until very recently, most of the effort is centered in the study of this receptor as a model of GPCR.The scope of this thesis is twofold. On the one hand it addresses the study of the simulation conditions, including the procedure as well as the sampling box to get optimal results, and on the other, the biological implications of the structural and dynamical behavior observed in the simulations. Specifically, regarding the methodological aspects of the work, the bovine rhodopsin has been studied using different treatments of long-range electrostatic interactions and sampling conditions, as well as the effect of sampling the protein embedded in different one-component lipid bilayers. The binding of ions to lipid bilayers in the absence of the protein has also been investigated. Regarding the biological consequences of the analysis of the MD trajectories, it has been carefully addressed the binding site of retinal and its implications in the process of isomerization after photon uptake, the alteration a group of residues constituting the so-called electrostatic lock between helices TM3 and TM6 in rhodopsin putatively used as common activation mechanism of GPCR, and the structural effects caused by the dimerization based on a recent semi-empirical model. Finally, the specific binding of ions to bacteriorhodopsin has also been studied. The main conclusion of this thesis is provide support to molecular dynamics as technique capable to provide structural and dynamical informational about membranes and membrane proteins, not currently accessible from experimental methods). Moreover, the use of an explicit lipidic environment is crucial for the study the membrane protein dynamics as well as for the protein-protein and lipidprotein interactions.

Molecular dynamics simulations were used to study the permeation of four different solutesthrough different cholesterol containing lipid bilayers. In all bilayers the limiting permeationbarrier shifted towards the hydrophobic core, as the cholesterol concentration was increased.Cholesterols reducing effect on the permeation rate was observed, but under certainconditions results indicating an increased permeation rate with increasing cholesterolconcentration were also obtained.