Development of empirical potentials for amorphous silica

Development of empirical potentials for amorphous silica Amorphous silica (SiO2) is of great importance in geoscience and mineralogy as well as a raw material in glass industry. Its structure is characterized as a disordered continuous network of SiO4 tetrahedra. Many efforts have been undertaken to understand the microscopic properties of silica by classical molecular dynamics (MD) simulations. In this method the interatomic interactions are modeled by an effective potential that does not take explicitely into account the electronic degrees of freedom. In this work, we propose a new methodology to parameterize such a potential for silica using ab initio simulations, namely Car-Parrinello (CP) method [Phys. Rev. Lett. 55, 2471 (1985)]. The new potential proposed is compared to the BKS potential [Phys. Rev. Lett. 64, 1955 (1990)] that is considered as the benchmark potential for silica. First, CP simulations have been performed on a liquid silica sample at 3600 K. The structural features so obtained have been compared to the ones predicted by the classical BKS potential. Regarding the bond lengths the BKS tends to underestimate the Si-O bond whereas the Si-Si bond is overestimated. The inter-tetrahedral angular distribution functions are also not well described by the BKS potential. The corresponding mean value of theSiOSi angle is found to be ≃ 147◦, while the CP yields to aSiOSi angle centered around 135◦. Our aim is to fit a classical Born-Mayer/Coulomb pair potential using ab initio calculations. To this end, we use the force-matching method proposed by Ercolessi and Adams [Europhys. Lett. 26, 583 (1994)]. The CP configurations and their corresponding interatomic forces have been considered for a least square fitting procedure. The classical MD simulations with the resulting potential have lead to a structure that is very different from the CP one. Therefore, a different fitting criterion based on the CP partial pair correlation functions was applied. Using this approach the resulting potential shows a better agreement with the CP data than the BKS ones: pair correlation functions, angular distribution functions, structure factors, density of states and pressure/density were improved. At low temperature, the diffusion coefficients appear to be three times higher than those predicted by the BKS model, however showing a similar temperature dependence. Calculations have also been carried out on crystalline samples in order to check the transferability of the potential. The equilibrium geometry as well as the elastic constants of α-quartz at 0 K are well described by our new potential although the crystalline phases have not been considered for the parameterization. We have developed a new potential for silica which represents an improvement over the pair potentials class proposed so far. Furthermore, the fitting methodology that has been developed in this work can be applied to other network forming systems such as germania as well as mixtures of SiO2 with other oxides (e.g. Al2O3, K2O, Na2O).

Structure, organization and dynamics of functional supramolecular materials studied by solid-state NMR

Functional materials have great importance due to their many important applications. The characterization of supramolecular architectures which are held together by non-covalent interactions is of most importance to understand their properties. Solid-state NMR methods have recently been proven to be able to unravel such structure-property relations with the help of fast magic-angle spinning and advanced pulse sequences. The aim of the current work is to understand the structure and dynamics of functional supramolecular materials which are potentially important for fuel-cell (proton conducting membrane materials) and solar-cell or plastic-electronic applications (photo-reactive aromatic materials). In particular, hydrogen-bonding networks, local proton mobility, molecular packing arrangements, and local dynamics will be studied by the use of advanced solid-state NMR methods. The first class of materials studied in this work is proton conducting polymers which also form hydrogen-bonding network. Different materials, which are prepared for high 1H conduction by different approaches are studied: PAA-P4VP, PVPA-ABPBI, Tz5Si, and Triazole-functional systems. The materials are examples of the following major groups; - Homopolymers with specific functional groups (Triazole functional polysiloxanes). - Acid-base polymer blends approach (PAA-P4VP, PVPA-ABPBI). - Acid-base copolymer approach (Triazole-PVPA). - Acid doped polymers (Triazole functional polymer doped with H3PO4). Perylenebisimide (PBI) derivatives, a second type of important functional supramolecular materials with potent applications in plastic electronics, were also investigated by means of solid-state NMR. The preparation of conducting nanoscopic fibers based on the self-assembling functional units is an appealing aim as they may be incorporated in molecular electronic devices. In this category, perylene derivatives have attracted great attention due to their high charge carrier mobility. A detailed knowledge about their supramolecular structure and molecular dynamics is crucial for the understanding of their electronic properties. The aim is to understand the structure, dynamics and packing arrangements which lead to high electron conductivity in PBI derivatives.

Modeling and simulations of some anisotropic soft-matter systems: from biaxial to chiral materials

We have modeled various soft-matter systems with molecular dynamics (MD) simulations. The first topic concerns liquid crystal (LC) biaxial nematic (Nb) phases, that can be possibly used in fast displays. We have investigated the phase organization of biaxial Gay-Berne (GB) mesogens, considering the effects of the orientation, strength and position of a molecular dipole. We have observed that for systems with a central dipole, nematic biaxial phases disappear when increasing dipole strength, while for systems characterized by an offset dipole, the Nb phase is stabilized at very low temperatures. In a second project, in view of their increasing importance as nanomaterials in LC phases, we are developing a DNA coarse-grained (CG) model, in which sugar and phosphate groups are represented with Lennard-Jones spheres, while bases with GB ellipsoids. We have obtained shape, position and orientation parameters for each bead, to best reproduce the atomistic structure of a B-DNA helix. Starting from atomistic simulations results, we have completed a first parametrization of the force field terms, accounting for bonded (bonds, angles and dihedrals) and non-bonded interactions (H-bond and stacking). We are currently validating the model, by investigating stability and melting temperature of various sequences. Finally, in a third project, we aim to explain the mechanism of enantiomeric discrimination due to the presence of a chiral helix of poly(gamma-benzyl L-glutamate) (PBLG), in solution of dimethylformamide (DMF), interacting with chiral or pro-chiral molecules (in our case heptyl butyrate, HEP), after tuning properly an atomistic force field (AMBER). We have observed that DMF and HEP molecules solvate uniformly the PBLG helix, but the pro-chiral solute is on average found closer to the helix with respect to the DMF. The solvent presents a faster isotropic diffusion, twice as HEP, also indicating a stronger interaction of the solute with the helix.

Dynamics, rheology and critical properties of colloidal fluid mixtures

Liquids under the influence of external fields exhibit a wide range of intriguing phenomena that can be markedly different from the behaviour of a quiescent system. This work considers two different systems — a glassforming Yukawa system and a colloid-polymer mixture — by Molecular Dynamics (MD) computer simulations coupled to dissipative particle dynamics. The former consists of a 50-50 binary mixture of differently-sized, like-charged colloids interacting via a screened Coulomb (Yukawa) potential. Near the glass transition the influence of an external shear field is studied. In particular, the transition from elastic response to plastic flow is of interest. At first, this model is characterised in equilibrium. Upon decreasing temperature it exhibits the typical dynamics of glassforming liquids, i.e. the structural relaxation time τα grows strongly in a rather small temperature range. This is discussed with respect to the mode-coupling theory of the glass transition (MCT). For the simulation of bulk systems under shear, Lees-Edwards boundary conditions are applied. At constant shear rates γ˙ ≫ 1/τα the relevant time scale is given by 1/γ˙ and the system shows shear thinning behaviour. In order to understand the pronounced differences between a quiescent system and a system under shear, the response to a suddenly commencing or terminating shear flow is studied. After the switch-on of the shear field the shear stress shows an overshoot, marking the transition from elastic to plastic deformation, which is connected to a super-diffusive increase of the mean squared displacement. Since the average static structure only depends on the value of the shear stress, it does not discriminate between those two regimes. The distribution of local stresses, in contrast, becomes broader as soon as the system starts flowing. After a switch-off of the shear field, these additional fluctuations are responsible for the fast decay of stresses, which occurs on a time scale 1/γ˙ . The stress decay after a switch-off in the elastic regime, on the other hand, happens on the much larger time scale of structural relaxation τα. While stresses decrease to zero after a switch-off for temperatures above the glass transition, they decay to a finite value for lower temperatures. The obtained results are important for advancing new theoretical approaches in the framework of mode-coupling theory. Furthermore, they suggest new experimental investigations on colloidal systems. The colloid-polymer mixture is studied in the context of the behaviour near the critical point of phase separation. For the MD simulations a new effective model with soft interaction potentials is introduced and its phase diagram is presented. Here, mainly the equilibrium properties of this model are characterised. While the self-diffusion constants of colloids and polymers do not change strongly when the critical point is approached, critical slowing down of interdiffusion is observed. The order parameter fluctuations can be determined through the long-wavelength limit of static structure factors. For this strongly asymmetric mixture it is shown how the relevant structure factor can be extracted by a diagonalisation of a matrix that contains the partial static structure factors. By presenting first results of this model under shear it is demonstrated that it is suitable for non-equilibrium simulations as well.

Crystal phases and glassy dynamics in monodisperse hard ellipsoids

We have performed Monte Carlo and molecular dynamics simulations of suspensions of monodisperse, hard ellipsoids of revolution. Hard-particle models play a key role in statistical mechanics. They are conceptually and computationally simple, and they offer insight into systems in which particle shape is important, including atomic, molecular, colloidal, and granular systems. In the high density phase diagram of prolate hard ellipsoids we have found a new crystal, which is more stable than the stretched FCC structure proposed previously . The new phase, SM2, has a simple monoclinic unit cell containing a basis of two ellipsoids with unequal orientations. The angle of inclination is very soft for length-to-width (aspect) ratio l/w=3, while the other angles are not. A symmetric state of the unit cell exists, related to the densest-known packings of ellipsoids; it is not always the stable one. Our results remove the stretched FCC structure for aspect ratio l/w=3 from the phase diagram of hard, uni-axial ellipsoids. We provide evidence that this holds between aspect ratios 3 and 6, and possibly beyond. Finally, ellipsoids in SM2 at l/w=1.55 exhibit end-over-end flipping, warranting studies of the cross-over to where this dynamics is not possible. Secondly, we studied the dynamics of nearly spherical ellipsoids. In equilibrium, they show a first-order transition from an isotropic phase to a rotator phase, where positions are crystalline but orientations are free. When over-compressing the isotropic phase into the rotator regime, we observed super-Arrhenius slowing down of diffusion and relaxation, and signatures of the cage effect. These features of glassy dynamics are sufficiently strong that asymptotic scaling laws of the Mode-Coupling Theory of the glass transition (MCT) could be tested, and were found to apply. We found strong coupling of positional and orientational degrees of freedom, leading to a common value for the MCT glass-transition volume fraction. Flipping modes were not slowed down significantly. We demonstrated that the results are independent of simulation method, as predicted by MCT. Further, we determined that even intra-cage motion is cooperative. We confirmed the presence of dynamical heterogeneities associated with the cage effect. The transit between cages was seen to occur on short time scales, compared to the time spent in cages; but the transit was shown not to involve displacements distinguishable in character from intra-cage motion. The presence of glassy dynamics was predicted by molecular MCT (MMCT). However, as MMCT disregards crystallization, a test by simulation was required. Glassy dynamics is unusual in monodisperse systems. Crystallization typically intervenes unless polydispersity, network-forming bonds or other asymmetries are introduced. We argue that particle anisometry acts as a sufficient source of disorder to prevent crystallization. This sheds new light on the question of which ingredients are required for glass formation.

Monte-Carlo simulation of hard spherocylinders under confinement

When a liquid crystal is confined to a cavity its director field becomes subject to competing forces: on the one hand, the surface of the cavity orients the director field (``surface anchoring''), on the other hand deformations of the director field cost elastic energy. Hence the equilibrium director field is determined by a compromise between surface anchoring and elasticity. One example of a confined liquid crystal that has attracted particular interest from physicists is the nematic droplet. In this thesis a system of hard rods is considered as the simplest model for nematic liquid crystals consisting of elongated molecules. First, systems of hard spherocylinders in a spherical geometry are investigated by means of canonical Monte Carlo simulations. In contrast to previous simulation work on this problem, a continuum model is used. In particular, the effects of ordering near hard curved walls are studied for the low-density regime. With increasing density, first a uniaxial surface film forms and then a biaxial surface film, which eventually fills the entire cavity. We study how the surface order, the adsorption and the shape of the director field depend on the curvature of the wall. We find that orientational ordering at a curved wall in a cavity is stronger than at a flat wall, while adsorption is weaker. For densities above the isotropic-nematic transition, we always find bipolar configurations. As a next step, an extension of the Asakura-Oosawa-Vrij model for colloid-polymer mixtures to anisotropic colloids is considered. By means of computer simulations we study how droplets of hard, rod-like particles optimize their shape and structure under the influence of the osmotic compression caused by the presence of spherical particles that act as depletion agents. At sufficiently high osmotic pressures the rods that make up the drops spontaneously align to turn them into uniaxial nematic liquid crystalline droplets. The nematic droplets or ``tactoids'' that so form are not spherical but elongated, resulting from the competition between the anisotropic surface tension and the elastic deformation of the director field. In agreement with recent theoretical predictions we find that sufficiently small tactoids have a uniform director field, whilst large ones are characterized by a bipolar director field. From the shape and director-field transformation of the droplets we estimate the surface anchoring strength.

Liquid crystalline phases of anisotropic, polymer functionalized nanoparticles

Diese Arbeit beschäftigt sich mit der Polymerfunktionalisierung formanisotroperrnNanopartikel wie TiO2 Nanostäbchen oder Kohlenstoff Nanoröhren. Dies dient derrnSolubilisierung und sterischen Stabilisierung in organischen Medien, da diesernionenfrei hergestellt werden können, was eine Nutzung für nanoskopische,rnelektrische Schaltkreise ermöglicht. Die Polymere wurden mittels der RAFTrn(reversible addition-fragmentation chain transfer) Polymerisation mit engenrnMolekulargewichtsverteilungen hergestellt. Im Detail wurden Ankergruppen inrnBlockcopolymere und an der Alphaposition eingeführt, welche eine Anbindung an diernNanopartikeloberfläche ermöglichen. Die Polymere wurden durch Variation derrnverschiedenen Blocklängen für eine bestmögliche Adsorption optimiert. Die sorngewonnenen Polymer funktionalisierten Nanopartikel zeigten eine gute Löslichkeit inrnorganischen Medien und zeigten zudem eine lyotropes, flüssigkristallinesrnPhasenverhalten. Dies war aufgrund der Formanisotropie zu erwarten, zeigte jedochrnebenfalls ein unerwartetes thermotropes Verhalten, welches durch die Polymerhüllernerzeugt wurde. Die Flüssigkristalle wurden eingehend mittels polarisierterrnMikroskopie und Differential Scanning Calorimetry (DSC) untersucht. Diernflüssigkristallinen Phasen aus Nanostäbchen und –röhren wurde dann zurrnOrientierung der anisotropen Nanopartikel benutzt und es konnten makroskopischrngeordnete Proben hergestellt werden. Die Polymerhülle um die Nanopartikelrnermöglichte es ebenfalls diese in Polymerfilme einzuarbeiten und sornNanopartikelverstärkte Kunststoffe herzustellen.

Coarse-graining methods and polymer dynamics

This thesis studies molecular dynamics simulations on two levels of resolution: the detailed level of atomistic simulations, where the motion of explicit atoms in a many-particle system is considered, and the coarse-grained level, where the motion of superatoms composed of up to 10 atoms is modeled. While atomistic models are capable of describing material specific effects on small scales, the time and length scales they can cover are limited due to their computational costs. Polymer systems are typically characterized by effects on a broad range of length and time scales. Therefore it is often impossible to atomistically simulate processes, which determine macroscopic properties in polymer systems. Coarse-grained (CG) simulations extend the range of accessible time and length scales by three to four orders of magnitude. However, no standardized coarse-graining procedure has been established yet. Following the ideas of structure-based coarse-graining, a coarse-grained model for polystyrene is presented. Structure-based methods parameterize CG models to reproduce static properties of atomistic melts such as radial distribution functions between superatoms or other probability distributions for coarse-grained degrees of freedom. Two enhancements of the coarse-graining methodology are suggested. Correlations between local degrees of freedom are implicitly taken into account by additional potentials acting between neighboring superatoms in the polymer chain. This improves the reproduction of local chain conformations and allows the study of different tacticities of polystyrene. It also gives better control of the chain stiffness, which agrees perfectly with the atomistic model, and leads to a reproduction of experimental results for overall chain dimensions, such as the characteristic ratio, for all different tacticities. The second new aspect is the computationally cheap development of nonbonded CG potentials based on the sampling of pairs of oligomers in vacuum. Static properties of polymer melts are obtained as predictions of the CG model in contrast to other structure-based CG models, which are iteratively refined to reproduce reference melt structures. The dynamics of simulations at the two levels of resolution are compared. The time scales of dynamical processes in atomistic and coarse-grained simulations can be connected by a time scaling factor, which depends on several specific system properties as molecular weight, density, temperature, and other components in mixtures. In this thesis the influence of molecular weight in systems of oligomers and the situation in two-component mixtures is studied. For a system of small additives in a melt of long polymer chains the temperature dependence of the additive diffusion is predicted and compared to experiments.

Thermodynamic concepts in adaptive resolution simulations

This thesis work is devoted to the conceptual and technical development of the Adaptive Resolution Scheme (AdResS), a molecular dynamics method that allows the simulation of a system with different levels of resolution simultaneously. The simulation domain is divided into high and low resolution zones and a transition region that links them, through which molecules can freely diffuse.rnThe first issue of this work regards the thermodynamic consistency of the method, which is tested and verified in a model liquid of tetrahedral molecules. The results allow the introduction of the concept of the Thermodynamic Force, an external field able to correct spurious density fluctuations present in the transition region in usual AdResS simulations.rnThe AdResS is also applied to a system where two different representations with the same degree of resolution are confronted. This simple test extends the method from an Adaptive Resolution Scheme to an Adaptive Representation Scheme, providing a way of coupling different force fields based on thermodynamic consistency arguments. The Thermodynamic Force is successfully applied to the example described in this work as well.rnAn alternative approach of deducing the Thermodynamic Force from pressure consistency considerations allows the interpretation of AdResS as a first step towards a molecular dynamics simulation in the Grand Canonical ensemble. Additionally, such a definition leads to a practical way of determining the Thermodynamic Force, tested in the well studied tetrahedral liquid. The effects of AdResS and this correction on the atomistic domain are analyzed by inspecting the local distribution of velocities, radial distribution functions, pressure and particle number fluctuation. Their comparison with analogous results coming from purely atomistic simulations shows good agreement, which is greatly improved under the effect of the external field.rnA further step in the development of AdResS, necessary for several applications in biophysics and material science, consists of its application to multicomponent systems. To this aim, the high-resolution representation of a model binary mixture is confronted with its coarse-grained representation systematically parametrized. The Thermodynamic Force, whose development requires a more delicate treatment, also gives satisfactory results.rnFinally, AdResS is tested in systems including two-body bonded forces, through the simulation of a model polymer allowed to adaptively change its representation. It is shown that the distribution functions that characterize the polymer structure are in practice not affected by the change of resolution.rnThe technical details of the implementation of AdResS in the ESPResSo package conclude this thesis work.

Coarse-graining and quantum-classical adaptive coupling in soft matter

Die vorliegende Arbeit untersucht den Zusammenhang zwischen Skalen in Systemen weicher Materie, der für Multiskalen-Simulationen eine wichtige Rolle spielt. Zu diesem Zweck wurde eine Methode entwickelt, die die Approximation der Separierbarkeit von Variablen für die Molekulardynamik und ähnliche Anwendungen bewertet. Der zweite und größere Teil dieser Arbeit beschäftigt sich mit der konzeptionellen und technischen Erweiterung des Adaptive Resolution Scheme'' (AdResS), einer Methode zur gleichzeitigen Simulation von Systemen mit mehreren Auflösungsebenen. Diese Methode wurde auf Systeme erweitert, in denen klassische und quantenmechanische Effekte eine Rolle spielen.rnrnDie oben genannte erste Methode benötigt nur die analytische Form der Potentiale, wie sie die meisten Molekulardynamik-Programme zur Verfügung stellen. Die Anwendung der Methode auf ein spezielles Problem gibt bei erfolgreichem Ausgang einen numerischen Hinweis auf die Gültigkeit der Variablenseparation. Bei nicht erfolgreichem Ausgang garantiert sie, dass keine Separation der Variablen möglich ist. Die Methode wird exemplarisch auf ein zweiatomiges Molekül auf einer Oberfläche und für die zweidimensionale Version des Rotational Isomer State (RIS) Modells einer Polymerkette angewandt.rnrnDer zweite Teil der Arbeit behandelt die Entwicklung eines Algorithmus zur adaptiven Simulation von Systemen, in denen Quanteneffekte berücksichtigt werden. Die Quantennatur von Atomen wird dabei in der Pfadintegral-Methode durch einen klassischen Polymerring repräsentiert. Die adaptive Pfadintegral-Methode wird zunächst für einatomige Flüssigkeiten und tetraedrische Moleküle unter normalen thermodynamischen Bedingungen getestet. Schließlich wird die Stabilität der Methode durch ihre Anwendung auf flüssigen para-Wasserstoff bei niedrigen Temperaturen geprüft.

Polymer-nanoparticle composites: from orientation phenomena to optoelectronic applications

Polymer-nanoparticle hybrids show synergistic effects, demonstrating both, the unique properties of nanosized structures and the good processability and functionalities of polymeric materials. This work shows the synthesis and application of block copolymers containing a soluble, functional block and a short anchor block, which efficiently binds to the surface of nanocrystals. We functionalized anisotropic, semiconducting nanoparticles, which can be dissolved in organic and polymeric matrices upon modification. The modified nanorods have the ability to form liquid crystalline phases, which behave similar to low molecular liquid crystals with a reversible clearing behaviour. These liquid crystalline phases could also be obtained in hole conducting matrices. For a macroscopic orientation of the nanorods, electric fields were applied and a switching (in analogy to known liquid crystals) to a homeotropic orientation was observed.rnBy introduction of dye molecules in the anchor block of a hole conducting block copolymer, all essential components of a solar cell can be combined in a single particle. Light absorption of the dye induces the injection of electrons into the particles, followed by a charging, that was monitored by a special AFM technique.rnLight emitting nanocrystals were functionalized analogously with a hole transporting polymer. The stability of the particles could be enhanced by the sterically stabilizing polymer corona and the particles showed improved properties in terms of processing. We applied these hybrid materials in light emitting devices, which showed better characteristics due to an improved hole injection and well dispersed emitting particles in the active device layer.rnThe work shows the broad spectrum of properties and applications based on the synergistic effects in hybrid and composite materials.

Ionic liquids in a multiscale study

Trotz des hohen Interesse an Ionischen Flüssigkeiten wird das zielgerichtete Design und die Anwendung Ionischer Flüssigkeiten durch fehlendes grundlegendes Verständnis erschwert. Deshalb wurde die Balance der molekularen Wechselwirkungen in Ionischen Flüssigkeiten studiert, um die Eigenschaften dieser zu verstehen und die Kraftfeldentwicklung im Rahmen des Multiskalenansatzes zu systematisieren. Es wurden reine Imidazolium-basierte Ionische Flüssigkeiten, Mischungen mit kleinen Molekülen und eine protische Ionische Flüssigkeit mit ab-initio-Methoden, hauptsächlich Car-Parrinello-Molekulardynamik, untersucht. Weiterhin wurden Eigenschaften der Flüssigphase mit denen von Ionenpaaren verglichen.rnIm Fokus standen die molekularen elektrostatischen Eigenschaften und es wurde gezeigt, dass Coulomb-Wechselwirkungen zu einzigartigen Charakteristika führten. So waren die Ionen-Nettoladungen stets reduziert, die molekularen Dipolmomentverteilungen sehr breit, elektronische Polarisation war entscheidend. Die elektrostatischen Eigenschaften waren allgemein lokal auf molekularen Größen- und Zeitskalen und hingen stark von Phasenzustand und Zusammensetzung ab. Für andere molekulare Eigenschaften, wie der Neigung zu dispersiven Kontakten oder Wasserstoffbrücken, wurde gezeigt, dass sie einen entscheidenden Einfluss auf die Feinstruktur Ionischer Flüssigkeiten hatten. Das Gleichgewicht der Wechselwirkungen zeigte sich auch in Leistungsspektren, die sich aus den ab-initio-Molekulardynamiksimulationen ergaben. Diese boten einen neuen Weg für den Vergleich zum Experiment und für einen Einblick in die schnelle Dynamik Ionischer Flüssigkeiten.

Simulations of amphiphilic peptides at the air-water interface

Amphiphile Peptide, Pro-Glu-(Phe-Glu)n-Pro, Pro-Asp-(Phe-Asp)n-Pro, und Phe-Glu-(Phe-Glu)n-Phe, können so aus n alternierenden Sequenzen von hydrophoben und hydrophilen Aminosäuren konstruiert werden, dass sie sich in Monolagen an der Luft-Wasser Grenzfläche anordnen. In biologischen Systemen können Strukturen an der organisch-wässrigen Grenzfläche als Matrix für die Kristallisation von Hydroxyapatit dienen, ein Vorgang der für die Behandlung von Osteoporose verwendet werden kann. In der vorliegenden Arbeit wurden Computersimulationenrneingesetzt, um die Strukturen und die zugrunde liegenden Wechselwirkungen welche die Aggregation der Peptide auf mikroskopischer Ebene steuern, zu untersuchen. Atomistische Molekulardynamik-Simulationen von einzelnen Peptidsträngen zeigen, dass sie sich leicht an der Luft-Wasser Grenzfläche anordnen und die Fähigkeit haben, sich in β-Schleifen zu falten, selbst für relativ kurze Peptidlängen (n = 2). Seltene Ereignisse wie diese (i.e. Konformationsänderungen) erfordern den Einsatz fortgeschrittener Sampling-Techniken. Hier wurde “Replica Exchange” Molekulardynamik verwendet um den Einfluss der Peptidsequenzen zu untersuchen. Die Simulationsergebnisse zeigten, dass Peptide mit kürzeren azidischen Seitenketten (Asp vs. Glu) gestrecktere Konformationen aufwiesen als die mit längeren Seitenketten, die in der Lage waren die Prolin-Termini zu erreichen. Darüber hinaus zeigte sich, dass die Prolin-Termini (Pro vs. Phe) notwendig sind, um eine 2D-Ordnung innerhalb derrnAggregate zu erhalten. Das Peptid Pro-Asp-(Phe-Asp)n-Pro, das beide dieser Eigenschaften enthält, zeigt das geordnetste Verhalten, eine geringe Verdrehung der Hauptkette, und ist in der Lage die gebildeten Aggregate durch Wasserstoffbrücken zwischen den sauren Seitenketten zu stabilisieren. Somit ist dieses Peptid am besten zur Aggregation geeignet. Dies wurde auch durch die Beurteilung der Stabilität von experimentnah-aufgesetzten Peptidaggregaten, sowie der Neigung einzelner Peptide zur Selbstorganisation von anfänglich ungeordneten Konfigurationen unterstützt. Da atomistische Simulationen nur auf kleine Systemgrößen und relativ kurze Zeitskalen begrenzt sind, wird ein vergröbertes Modell entwickelt damit die Selbstorganisation auf einem größeren Maßstab studiert werden kann. Da die Selbstorganisation an der Grenzfläche vonrnInteresse ist, wurden existierenden Vergröberungsmethoden erweitert, um nicht-gebundene Potentiale für inhomogene Systeme zu bestimmen. Die entwickelte Methode ist analog zur iterativen Boltzmann Inversion, bildet aber das Update für das Interaktionspotential basierend auf der radialen Verteilungsfunktion in einer Slab-Geometrie und den Breiten des Slabs und der Grenzfläche. Somit kann ein Kompromiss zwischen der lokalen Flüssigketsstruktur und den thermodynamischen Eigenschaften der Grenzfläche erreicht werden. Die neue Methode wurde für einen Wasser- und einen Methanol-Slab im Vakuum demonstriert, sowie für ein einzelnes Benzolmolekül an der Vakuum-Wasser Grenzfläche, eine Anwendung die von besonderer Bedeutung in der Biologie ist, in der oft das thermodynamische/Grenzflächenpolymerisations-Verhalten zusätzlich der strukturellen Eigenschaften des Systems erhalten werden müssen. Daraufrnbasierend wurde ein vergröbertes Modell über einen Fragment-Ansatz parametrisiert und die Affinität des Peptids zur Vakuum-Wasser Grenzfläche getestet. Obwohl die einzelnen Fragmente sowohl die Struktur als auch die Wahrscheinlichkeitsverteilungen an der Grenzfläche reproduzierten, diffundierte das Peptid als Ganzes von der Grenzfläche weg. Jedoch führte eine Reparametrisierung der nicht-gebundenen Wechselwirkungen für eines der Fragmente der Hauptkette in einem Trimer dazu, dass das Peptid an der Grenzfläche blieb. Dies deutet darauf hin, dass die Kettenkonnektivität eine wichtige Rolle im Verhalten des Petpids an der Grenzfläche spielt.

Liquid crystalline elastomers as stimuli-responsive microactuators

Liquid crystalline elastomers (LCEs) are known to perform a reversible change of shape upon the phase transition from the semi-ordered liquid crystalline state to the chaotic isotropic state. This unique behavior of these “artificial muscles” arises from the self-organizing properties of liquid crystals (mesogens) in combination with the entropy-elasticity of the slightly crosslinked elastomer network. In this work, micrometer-sized LCE actuators are fabricated in a microfluidic setup. The microtubular shear flow provides for a uniform orientation of the mesogens during the crosslinking, a perquisite for obtaining actuating LCE samples. The scope of this work was to design different actuator geometries and to broaden the applicability of the microfluidic device for different types of liquid crystalline mesogens, ranging from side-chain to main-chain systems, as well as monomer and polymer precursors. For example, the thiol-ene “click” mechanism was used for the polymerization and crosslinking of main-chain LCE actuators. The main focus was, however, placed on acrylate monomers and polymers with LC side chains. A LC polymer precursor, comprising mesogenic and crosslinkable side-chains was synthesized. Used in combination with an LC monomer, the polymeric crosslinker promoted a stable LC phase, which allowed the mixture to be isothermally handled in the microfluidic reactor. If processed without the additional LC components, the polymer precursor yielded actuating fibers. A suitable co-flowing continuous phase facilitates the formation of a liquid jet and lowers the tendency for drop formation. By modification of the microfluidic device, it was further possible to prepare core-shell particles, comprised of an LCE shell and filled with an isotropic liquid. In analogy to the heart, a hollow muscle, the elastomer shell expels the inner liquid core upon its contraction. The feasibility of the core-shell particles as micropumps was demonstrated. In general, the synthesized LCE microactuators may be utilized as active components in micromechanical and lab-on-chip systems.

Development of models and methods to simulate peptide-assisted nucleation and growth of calcium-minerals

In den vergangenen Jahren wurden einige bislang unbekannte Phänomene experimentell beobachtet, wie etwa die Existenz unterschiedlicher Prä-Nukleations-Strukturen. Diese haben zu einem neuen Verständnis von Prozessen, die auf molekularer Ebene während der Nukleation und dem Wachstum von Kristallen auftreten, beigetragen. Die Auswirkungen solcher Prä-Nukleations-Strukturen auf den Prozess der Biomineralisation sind noch nicht hinreichend verstanden. Die Mechanismen, mittels derer biomolekulare Modifikatoren, wie Peptide, mit Prä-Nukleations-Strukturen interagieren und somit den Nukleationsprozess von Mineralen beeinflussen könnten, sind vielfältig. Molekulare Simulationen sind zur Analyse der Formation von Prä-Nukleations-Strukturen in Anwesenheit von Modifikatoren gut geeignet. Die vorliegende Arbeit beschreibt einen Ansatz zur Analyse der Interaktion von Peptiden mit den in Lösung befindlichen Bestandteilen der entstehenden Kristalle mit Hilfe von Molekular-Dynamik Simulationen.rnUm informative Simulationen zu ermöglichen, wurde in einem ersten Schritt die Qualität bestehender Kraftfelder im Hinblick auf die Beschreibung von mit Calciumionen interagierenden Oligoglutamaten in wässrigen Lösungen untersucht. Es zeigte sich, dass große Unstimmigkeiten zwischen etablierten Kraftfeldern bestehen, und dass keines der untersuchten Kraftfelder eine realistische Beschreibung der Ionen-Paarung dieser komplexen Ionen widerspiegelte. Daher wurde eine Strategie zur Optimierung bestehender biomolekularer Kraftfelder in dieser Hinsicht entwickelt. Relativ geringe Veränderungen der auf die Ionen–Peptid van-der-Waals-Wechselwirkungen bezogenen Parameter reichten aus, um ein verlässliches Modell für das untersuchte System zu erzielen. rnDas umfassende Sampling des Phasenraumes der Systeme stellt aufgrund der zahlreichen Freiheitsgrade und der starken Interaktionen zwischen Calciumionen und Glutamat in Lösung eine besondere Herausforderung dar. Daher wurde die Methode der Biasing Potential Replica Exchange Molekular-Dynamik Simulationen im Hinblick auf das Sampling von Oligoglutamaten justiert und es erfolgte die Simulation von Peptiden verschiedener Kettenlängen in Anwesenheit von Calciumionen. Mit Hilfe der Sketch-Map Analyse konnten im Rahmen der Simulationen zahlreiche stabile Ionen-Peptid-Komplexe identifiziert werden, welche die Formation von Prä-Nukleations-Strukturen beeinflussen könnten. Abhängig von der Kettenlänge des Peptids weisen diese Komplexe charakteristische Abstände zwischen den Calciumionen auf. Diese ähneln einigen Abständen zwischen den Calciumionen in jenen Phasen von Calcium-Oxalat Kristallen, die in Anwesenheit von Oligoglutamaten gewachsen sind. Die Analogie der Abstände zwischen Calciumionen in gelösten Ionen-Peptid-Komplexen und in Calcium-Oxalat Kristallen könnte auf die Bedeutung von Ionen-Peptid-Komplexen im Prozess der Nukleation und des Wachstums von Biomineralen hindeuten und stellt einen möglichen Erklärungsansatz für die Fähigkeit von Oligoglutamaten zur Beeinflussung der Phase des sich formierenden Kristalls dar, die experimentell beobachtet wurde.