A estabilidade de vesículas unilamelares gigantes (GUVs) foi monitorada através de microscopia de contraste de fase e de fluorescência, com o auxílio de gradientes de açúcares, do fluoróforo 1,3,6,8 pireno tetrasulfonato de sódio (PTS), do supressor de fluorescência cloreto de 1,1\'-dimetil-4,4\'-bipiridínio (MV) e do análogo lipídico fluorescente 2-(12-(7-nitrobenz-2-oxa-1,3-diazol-4-il) amino) dodecanoil-1-hexadecanoil-sn-glicero-3-fosfocolina (NBD-PC). Uma grande variabilidade no comportamento individual das GUVs foi obtida no que tange a: (i) manutenção do meio interno; (ii) interações da bicamada lipídica com superfícies e; (iii) estruturas lipídicas conectadas à bicamada. Os resultados experimentais podem ser explicados pelo aparecimento de poros transientes formados pelo aumento da tensão da bicamada lipídica das GUVs. Após o processo de geração de tensão na bicamada, poros são abertos para relaxação desta tensão, com concomitante efluxo da solução internalizada pela GUV, devido a pressão de Laplace. Com a diminuição do volume interno, a tensão da bicamada é relaxada e o fechamento dos poros guiado pela tensão de linha, minimizando o componente energético de curvatura dos lipídios nas bordas do poro. O modelo de poros transientes explica resultados como troca de massa entre meios interno e externo das GUVs, possibilidade da existência de fluxos unilaterais em GUVs, transitoriedade dos poros, diâmetro limite dos poros e manutenção do meio interno em GUVs após abertura e fechamento de poros. / The stability of giant unilamellar vesicles (GUVs) has been monitored by phase contrast and fluorescence microscopy, using sugar gradients, sodium 1,3,6,8 pirene tetrasulfonate (PTS) as fluorescent probe, 1,1\'-dimethyl-4,4\'-bipiridinium chloride (MV) as fluorescence quencher and 2-(12-(7-nitrobenz-2-oxa-1,3-diazol-4-il) amino) dodecanoyl-1-hexadecanoyl-sn-glicero-3-phosphocholine (NBD-PC) as fluorescent lipid analog. An accentuated variability in the individual behaviour of GUVs was observed as far as (i) stability of encapsulation; (ii) lipid bilayer-surface interactions and; (iii) lipid structures connected to GUVs are concerned. Experimental results can be explained by transient pores formation due to an increase in lipid bilayer tension. After processes of bilayer tension generation, pores are opened, while effluxes of GUVs internal solution are promoted by Laplace pressure. With the internal volume decrease, bilayer tension is relaxed and pores closure guided by line tension, minimizing the energetic component of lipid curvature in pore edges. Transient pores model explains experimental results such as mass exchange between internal and external GUVs media, GUVs effluxes, pores\' lifetime, pores diameter\'s limit and stability of GUV encapsulation after opening and closure of pores.

Die dynamische Verknüpfung zwischen Plasmamembran und dem unterliegenden Zytoskelett der Zelle ist fundamental für zelluläre Prozesse wie Zellmorphogenese, Zellmotilität und Zelladhäsion. Ezrin als Bestandteil der ERM (Ezrin, Radixin, Moesin) Proteinfamilie verbindet L-α-Phosphatidylinositol-4,5-bisphosphat (PIP2) der Plasmamembran mit filamentösem Aktin (F-Aktin) des Zytoskeletts. Die Ezrinbindung an F-Aktin wird reguliert über den Aktivierungsgrad des Proteins, welcher von der N-terminalen PIP2 Bindung und der Phosphorylierung des Threoninrests 567 abhängt. Aufgrund der Bindung an PIP2 und der Phosphorylierung wechselt Ezrin von einer inaktiven, N- und C-terminal assoziierten Konformation in einen aktivierten, geöffneten Zustand, welcher die C-terminale F-Aktinbindung ermöglicht. Ziel dieser Arbeit war es Aspekte der Verknüpfung zwischen Plasmamembran und Zytoskelett zu untersuchen. Basierend auf Bindung von Ezrin an PIP2-haltige artifizielle Lipidmembranen und der anschließenden F-Aktinbindung, wurden Bindungseigenschaften, die Organisation des F-Aktinnetzwerkes und die durch das Aktinnetzwerk beeinflusste Lipidmembranmechanik untersucht. Im ersten Abschnitt dieser Arbeit wurde der molekulare Aktivierungsprozess von Ezrin anhand der Charakterisierung von Bindungsaffinitäten und der Organisation von Ezrin an Lipidmembranen untersucht. Aufgrund einer reduzierten Proteinhöhe und FRET (FÖRSTER-Resonanzenergietransfer)-Effizienz im Fall der vollständigen Aktivierung (PIP2-Bindung und Phosphorylierung) wurde postuliert, dass Ezrin eine weniger dicht gepackte, geöffnete Konformation gebunden an Lipidmembranen ausbildet. Dies ermöglicht dem Protein C-terminal F-Aktin zu binden. Im zweiten Teil der Arbeit wurden Aktinnetzwerke an festkörperunterstützten Lipidmembranen (SLBs) immobilisiert und über Ezrin an PIP2- oder elektrostatisch an 1,2-Dioleoyl-sn-glycero-3-ethylphosphocholin (DOEPC)-haltige SLBs gebunden. Die Netzwerkorganisation wurde mit Hilfe der Fluoreszenzmikroskopie untersucht und unter Berücksichtigung der Immobilisierungsstrategie in Hinblick auf den Einfluss der Anzahl an Verknüpfungspunkten und aktinbindender Proteine (Fascin und α-Actinin) analysiert. Es konnte gezeigt werden, dass beide Immobilisierungsstrategien zu Aktinnetzwerken mit ähnlichen Eigenschaften führten, bezugnehmend auf Maschengröße und Filamentsegmentlänge. Die Aktinnetzwerkdichte konnte direkt über die Anzahl an Verknüpfungspunkten und aktinbindende Proteine (ABPs) reguliert werden, dies demonstriert die physiologische Relevanz der Ergebnisse. Es ist bekannt, dass die Aktindichte in Zellen über PIP2- und ABP-Konzentration gesteuert wird. Im dritten Teil der Arbeit wurde das etablierte Modelsystem auf poröse Substrate übertragen. Unter Kenntnis der vorangegangenen Teile der Arbeit wurde der Einfluss des F-Aktinnetzwerkes auf die Lipidmembranmechanik untersucht. Mit Hilfe der Rasterkraftmikroskopie wurden Indentationsexperimente an porenüberspannenden Lipidmembranen (PSLBs) durchführt, welche zeigten, dass ein aufliegendes F-Aktinnetzwerk die PSLBs versteift. Dies ließ sich auf die reduzierte laterale Mobilität der Lipide innerhalb der PSLBs aufgrund des Aktinnetzwerkes zurückführen, vergleichbar mit dem Picket-Fence-Modell der Plasmamembran bei welchem die Mobilität der Lipide und (Membran-)Proteine, aufgrund der Kompartimentierung der Membran durch das Aktin-Zytoskelett, eingeschränkt ist.

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

The following project presents in silico investigation of axonal damage in Diffuse Axonal Injury (DAI). When axons face a shear force, orientation of the lipids in the axonal membrane gets disrupted. Depending on the value of the force, a tensile strain causes the axons to get partially or fully deformed and in some cases a pore forms in the membrane. Using Molecular Dynamic (MD) simulation and a coarse grain model, a series of bilayers with various bilayer structure (single bilayer, parallel bilayer and cylindrical bilayer) and similar composition to biological axonal membrane were simulated. This was initially done to investigate the strain rate dependency of the bilayers, and their viscoelastic ability on returning to their original shape from their deformed forms. To achieve this, various deformation velocities were applied to the bilayers reaching 20% strain and relaxing the bilayer after. Additionally, the bilayers were deformed further until they reached a pore. It was found that the bilayers can almost recover from their deformed forms to their original length when they were deformed at 20% strain level. In conjunction, no correlation between the deformation velocity and lipid deformation was observed. Further, it was found that bilayers with different lipid percentage to axonal bilayer has different strain values for water penetration and for pore formation. The strain value for cylindrical bilayer was found very high compared to the strain values found in vitro. The strain for pore formation of parallel and single bilayer was found to be around 80% to 90% and for water penetration was found to be 70% for single bilayer and 50% for parallel bilayer. A slight difference in strain for pore formation between single and parallel bilayer was found which showed the bilayer structure can play a role in simulation results. The effect of the length in the simulations results was also observed where shorter bilayers showed lower strain for pore formation compared to longer bilayers.

Polyethylene glycol-stabilized lipodisks have emerged as a novel type of lipid-based nanoparticles with high potential as both drug carriers and biomimetic membranes. In this thesis we assess both of these applications, and show how the properties of the lipodisks can be further developed and optimized. Initially, we show that the antimicrobial peptides melittin, alamethicin and magainin 2, in spite of their very different physico-chemical properties and suggested modes of action on membranes, all have high affinity to lipodisks. Using melittin as a model peptide, we confirm a maintained antimicrobial effect of disk-formulated peptides. We also show that melittin dissociates slowly from the disks, resulting in extended drug release and prolonged antibacterial effect. Additionally, we present evidence that the peptide is protected against enzymatic degradation when formulated in the disks. Further, we develop a stable HPLC-MS system with immobilized lipodisks as model membranes. The stability of the system is confirmed by drug partitioning analysis using 15 different drug compounds. We also show how the lipodisk column can be supplemented with cyclooxygenase by in situ incorporation of the protein in the lipodisks. The specific binding of the protein to the disks is confirmed using QCM-D. Finally, by changing the polymer length and applying a new preparation protocol, we have optimized the lipodisks for use as drug carriers and biomimetic membranes. Previous lipodisk studies have been conducted on systems containing PEG-lipids with polymer molecular weights of 2000 or 5000 Da. Also, conventional protocols for the preparation of lipodisks typically require a PEG-lipid concentration of 15 mol% or more. Here we show that stable lipodisks can also be produced using PEG-lipids with a 1000 Da molecular weight polymer and that the use of shorter PEG-lipids dramatically improve the amount of lipodisks that can be immobilized on silica surfaces. Moreover, through the development of a method in which lipid mixtures are sonicated at low temperatures, we produce lipodisks containing as little as 2 mol% PEG-lipid. We present data verifying that these disks are superior to disks with higher PEG-lipid content in terms of their ability to incorporate externally added PEG-lipids functionalized with targeting agents.

Résumé : Nous étudions dans cette thèse plusieurs propriétés du gaz d’électrons bidimensionnel (GE2D) dans le graphène et la bicouche de graphène (BG). Nous commençons par étudier la nature des excitations à une particule du GE2D dans le graphène près des facteurs de remplissage entiers dans les niveaux de Landau N [pas égal à] 0. Nous utilisons une approche de type Hartree-Fock (HF) pour comparer l’énergie de l’excitation d’une paire électron-trou à celle d’une paire skyrmion (SK)-antiskyrmion (ASK). Dans le graphène, les excitations SK et ASK sont des excitations chargées avec une texture de spin et/ou de pseudospin de vallée qui est quantifiée topologiquement. Nos calculs montrent que les paires SK-ASK sont les excitations chargées de plus basse énergie jusqu’au niveau de Landau |N| = 3. Notre approche permet en plus de calculer le domaine de couplage Zeeman pour lequel les paires SK-ASK sont les excitations de plus basse énergie et de déterminer comment l’énergie de ces paires est modifiée par les corrections d’écrantage. Le diagramme de phase du GE2D dans la bicouche de graphène a fait l’objet d’intenses recherches théoriques et expérimentales [8, 13, 15, 16], mais jusqu’à maintenant, seuls les états uniformes ont été considérés. Nous adaptons notre approche HF à l’étude des états non uniformes pour montrer que le GE2D dans la BG à remplissage ν = −1 dans le niveau de Landau N = 0 subit une série de transitions de phase lorsqu’un champ électrique perpendiculaire à la BG est appliqué. Nous étudions tout particulièrement les phases comportant une texture de pseudospin orbital soit un cristal de skyrmions et une phase spirale. Nous calculons les modes collectifs de ces phases ainsi que leur absorption électromagnétique. Nous poursuivons ensuite avec une étude des phases cristallines autour de certains remplissages entiers dans la BG. Le GE2D dans la bicouche de graphène a principalement été étudié dans le niveau de Landau N = 0. Comme dernier problème, nous étudions le diagramme de phase lorsqu’un nombre entier de niveaux de Landau est occupé dans les niveaux supérieurs |N| > 0. Alors que l’état fondamental du GE2D dans le graphène pour ces mêmes niveaux est un ferroaimant de Hall quantique (FHQ) avec une symétrie SU(2) pour le spin (en l’absence de couplage Zeeman) et le pseudospin de vallée, le GE2D dans la BG a plutôt un comportement FHQ de type Ising avec une symétrie Z[indice inférieur 2] à champ électrique nul. Cette différence de comportement a une grande influence sur la nature des transitions de phase possibles ainsi que sur celle des excitations topologiques. // Abstract : In this thesis, we study several properties of the two-dimensional electron gas (2DEG) in graphene and bilayer graphene. We first study the nature of the single-particle excitations in graphene near integer filling factors in Landau levels (LLs) N [not equal to] 0. We use a Hartree-Fock approach to compare the energy of an electron-hole excitation pair with that of a Skyrmion-antiskyrmion pair. In graphene, Skyrmions are charged excitations with a topological quantized spin and/or valley pseudo-spin texture. We give the range of Zeeman coupling for which Skyrmion-antiskyrmion has the lowest energy up to LL N = 3. Then we discuss how screening corrections modifies these results. The phase diagram of the 2DEG in bilayer graphene had been studied previously by a number of authors [8, 13, 15, 16] but only uniform states had been considered. Extending the Hartree-Fock approach to non-uniform states, we show that at filling factor ν = −1 in LL N = 0, the 2DEG goes through a series of phase transitions as the bias from an external electric field between two layers is increased. We study a crystal phase with orbital SK textures and a spiral state with the orbital pseudospin rotating in space. We compute the collective mode of these phases and their signatures in electromagnetic absorption experiments. We finally extend the Hartree-Fock approach to study the crystal states with valley or orbital textures near integer filling factors. The research on the 2DEG in bilayer graphene has been focussed almost exclusively in LL N = 0. As our last problem, we study the phase diagram at quarter and half fillings of the quartet of states in LLs |N| > 0. While the ground state of the 2DEG in graphene in |N| > 0 is a valley and spin quantum Hall ferromagnet with SU(2) symmetry in the absence of Zeeman coupling, the ground state in bilayer graphene is an Ising quantum Hall ferromagnet with a Z[subscript 2] valley symmetry at zero bias. We note that this change has important consequences on the nature of the transport properties and the single-particle excitations at integer fillings.

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.

In the first part of this work, we describe a theory of the ground states and charge gaps in the fractional quantum Hall states of graphene. The theory relies on knowledge of these properties for filling fractions smaller than one. Then, by the application of two mapping rules, one is able to obtain these properties for fractional quantum Hall states at arbitrary fillings, by conceiving the quantum Hall ferromagnets as vacua on which correlated electrons or correlated holes are added. The predicted charge gaps and phase transitions between different fractional quantum Hall states are in good agreement with recent experiments. In the second part, we investigate the low energy theory for the neutral Landau level of bilayer graphene. We closely analyze the way different terms in the Hamiltonian transform under the action of particle-hole conjugation symmetries, and identify several terms that are relevant in explaining the lack of such symmetry in experiments. Combining an accurate parametrization of the electronic structure of bilayer graphene with a systematic account of the impact of screening we are able to explain the absence of particle-hole symmetry reported in recent experiments. We also study the energetics of fractional quantum Hall states with coherence between n=0 and n=1 cyclotron quantum numbers, and obtain a general formula to map the two-point correlation function from their well-known counterparts made from only n=0 quantum numbers. Bilayer graphene has the potential for realizing these states which have no analogue in other two-dimensional electron systems such as Gallium Arsenide. We apply this formula to describe the properties of the n=0/n=1 coherent Laughlin state which displays nematic correlations. / text

Understanding the mechanisms by which proteins act on membrane surfaces is fundamental if we are to exploit their capabilities or halt the progression of the diseases they are associated with. Arguably, the best way to study these interactions is by using techniques that can obtain molecular-scale information, in real time and under physiologically relevant conditions. Studying supported lipid bilayer systems with high spatial resolution tools, such as atomic force microscopy (AFM), and high temporal resolution techniques, such as polarized total internal reflection fluorescence microscopy (pTIRFM), allows us to meet these requirements [1]. The goal of this project is to use methods that are currently available and further their applications and capabilities to provide insight into the mechanisms by which amyloidogenic and antimicrobial peptides act on membranes.