A molecular dynamics coarse-grained block copolymer (BCP) model was developed and used to studied directed self-assembly (DSA), especially in regards to applications for semiconductor manufacturing. Most of the thesis is spent investigating the effect that guiding layer properties and block copolymer properties have on line roughness and defect density in a BCP-DSA process. These two effects are perhaps the most critical in making BCP-DSA a cost efficient industrial process. It is found that guiding patterns have little effect on line roughness and in fact that the BCP heals the majority of roughness in the underlying pattern. BCP properties have a larger effect on line roughness. Segregation strength (as measured by χN, where χ is the Flory- Huggins interaction parameter and N is the degree of polymerization) resulted in a larger than expected increase in line roughness when χN was low. Polydispersity resulted in a moderate increase in line roughness. In regards to equilibrium defect density, free energy calculations showed that χ was the primary determining factor, not χN as many expected. Equilibrium defect density was found to decrease exponentially with increasing χ. Defect density is also found to scale exponentially with polydispersity. Concerning defect heal rate, which can increase the real defect rate of a process if said rate is too low, it is found that increasing χN linearly increased the barrier to defect healing, which means that the defect heal rate decreases exponentially. However, for thin films this is only true for χN > ~ 50. Below χN ~ 50, the barrier is approximately constant. These results give excellent guidance to the type of materials and processes necessary to optimize a BCP-DSA process. A simulation technique designed to more efficiently sample over energy barriers called protracted noise dynamics for polymer systems was developed and studied. It was found that a decrease in simulation time of up to 4 orders of magnitude was achieved. The effect of box size on allowable pitches for a lamellar forming BCP was derived and demonstrated. It was found that more elongated boxes yielded more possible pitches and more accurate results. A short study on the effect of multiblock copolymers on the location of the order-disorder transition was also carried out and it was found that multiblock copolymers had small effect on the ODT. The distribution of chain conformations was also calculated.

Various techniques of fabricating surface patterns of small scales have been widely studied due to the potential applications of surface patterns in a variety of areas. It is a challenge to fabricate well-ordered surface area efficiently and economically. Evaporation-induced surface patterning is a promising approach to fabricate well-ordered surface patterns over a large area at low cost. In this study, the evaporation-induced surface patterns with controllable geometrical characteristics have been constructed. The dewetting kinetics on deformable substrate is also investigated. Using simple templates to control the geometry and the evaporation behavior of a droplet of volatile solvent, various gradient surface patterns, such as concentric rings, multiple straight stripes formed with a straight copper wire, etc. have been constructed on PMMA films. The wavelength and amplitude are found to decreases with the decrease of the distance to the objects used in templates. There is also a nearly linear relation between the amplitude and wavelength. The effects of several experimental parameters on the geometrical characteristics of the surface structures are studied, i.e. dimensions of the template, film thickness (solution concentration), substrate temperature, etc. The wavelength and amplitude increase with the increase of the film thickness (solution concentration), with the increase of the dimension of the template. However with the increase of the substrate temperature, the wavelength increases, while the amplitude decrease. Hexagonal network in pre-cast PMMA film have been fabricated by a “breath figure” approach at low humidity and low substrate temperature. The dimensions of the hexagonal holes are dependent on the template size and film thickness. The kinetics of the evaporative dewetting of a liquid (toluene) film on a deformable substrate (PMMA film) with the confinement of a circular copper ring is also studied. The liquid film first dewets from the outside towards the copper ring. When a critical volume is reached, an internal contact line appears, which dewets from the center to the copper ring smoothly with a constant velocity, then switches to a “stick-slip” motion. The average velocity of the smooth motion increases with the increase of the copper ring size and film thickness.

Dissertation (PhD)--Stellenbosch University, 2004 / ENGLISH ABSTRACT: Over the past decade peptide bola-amphiphiles have been the subject of much attention because of their role as potential models of functionalised membranes and as new generation surfactants. In the quest for new surfactants a peptidomimetic-based approach was used to design a library of novel 'hybrid' bola-amphiphilic peptide surfactants derived from sapecin B and a model symmetrical oligo-glycine bola-amphiphile. The library was divided into different series, each one purpose-built; first, to investigate hierarchal supramolecular architecture and, second, to investigate potential antimicrobial activity. The bola-amphiphiles were synthesised using Fmoc-polyamide based solid phase peptide synthesis and purified via high performance liquid chromatography. The peptide hybrids were characterised using electro spray mass spectrometry, nuclear magnetic resonance, different modes of electron microscopy, Fourier-transform infrared spectroscopy and, in some cases, further studies were done using circular dichroism and bioactivity tests. The model bola-amphiphile suberamide(GGh was synthesised using peptide fragment condensation based on solid phase peptide synthesis. The synthesis is bi-directional (N~C and C~N) and versatile, making it possible to synthesis new dicarboxylic oligopeptide bola-amphiphiles and other analogous compounds. The product, suberarnide(GG)2, was purified using its inherent ability to self-assemble in an acidic solution. Novel asymmetrical bola-amphiphiles composed of dipeptide head groups linked via an aliphatic (I)-amino acid, serving as a hydrocarbon spacer, were also synthesized. Two small libraries of bola-amphiphiles were established - the first involved variation in to-amino acid length and the other variation in the C-terminal amino acid. The bolaamphiphiles were self-assembled in either 0.1% trif1uoroacetic acid or 0.1% triethylamine. Electron microscopy revealed the formation of a variety of higher order supramolecular architectures based on ~-sheet self-assembly. FT-IR spectrometry indicated that interlayer and intralayer hydrogen bond networks, together with strong selfassociation, promoted by the hydrophobic effect and, in certain instances, electrostatic interactions, are responsible for the variety of supramolecular architectures. Variations in the higher order structures can be attributed to amino acid composition, specifically length of m-amino acid, nature of the C-terminal amino acid and the optimised solvent conditions used for the self-assembly process. A third library of novel 'hybrid' bola-amphiphilic peptide surfactants, in which a cationic tripeptide motif from antimicrobial peptides was combined in a hybrid molecule containing a oi-amino acid residue, was established. These bola-amphiphiles displayed potent antimicrobial activity against both Gram-positive and Gram-negative bacteria; the analogues were as active or more active than the leader peptides yet, remarkably, displayed little or no appreciable haemolytic activity. These organopeptide bolaamphiphiles thus demonstrated selective toxicity towards bacteria. The hydrophobicity imparted by the co-amino acid has contrasting effects on haemolysis and antimicrobial activity of the peptide analogues. The other unique feature of these peptides and their analogues is the fact they self-assembled into complex supramolecular architectures, composed primarily of ~-sheets. Their self-assembly is primarily governed by hydrophobic interactions together with inter and intralayer hydrogen bonding. Electron microscopy clearly revealed higher order structures for both peptides and analogues. The generation of higher order supramolecular architecture is dependent on optimisation of ~- sheet self-assembly whereas antimicrobial activity is dependent on the balance between net positive charge and optimum hydrophobicity of the peptide hybrids. This study has demonstrated that it is possible to design hybrid peptide surfactants capable of producing higher order supramolecular architecture and improving the antimicrobial activity whilst reducing the haemolytic effect. The study and design of these versatile 'purpose-built' bio-inspired surfactants heralds a novel approach, one that shows tremendous potential. / AFRIKAANSE OPSOMMING: Die afgelope dekade het bola-amfifiliese peptiede baie aandag geniet weens hulle rolle as potensiële modelle van gefunksionaliseerde membrane en as 'n nuwe generasie surfaktante. In die soeke na nuwe surfaktante is 'n peptiedornimetiese benadering gevolg om 'n biblioteek van nuwe "hibried" bola-amfifiliese peptiedsurfaktante van sapesien B en 'n simmetriese oligoglisien bola-amfifil af te lei. Die biblioteek is in verskillende reekse onderverdeel. Elke reeks is doelmatig vervaardig om ondersoek in te stel na twee aspekte, nl. die rangorde van die supramolekulêre strukture en die potensiële antirnikrobiese aktiwiteit. Fmoc-poliamied gebaseerde soliedefase-peptied-sin-tese is aangewend vir die sintese van die bola-amfifile en hulle is met behulp van hoë doeltreffendheid vloeistofchromatografie gesuiwer. Die peptiedhibriede is gekarakteriseer met behulp van elekrosproei massaspektrometrie, kern-magnetiese resonansie, verskillende modusse elektronrnikroskopie, Fourier-transform infrarooispektrometrie en, in sommige gevalle is verdere studies met sirkulêre dichroïsme en bioaktiwiteitstoetsing uitgevoer. Die bola-amfifilsuberamiedtflfij--model is met behulp van peptiedfragment-konden-sasie gesintetiseer gegrond op soliedefase-peptiedsintese. Dit sintese vind in twee rigtings plaas (N~C en C~N) en is veelsydig aangesien dit die sintese van sowel nuwe dikar-boksielbola- amfifile as ander analoë verbindings moontlik maak. Die produk, suber-arnied(GG)2, is gesuiwer met behulp van die verbinding se inherente vermoë tot self-montering in suur oplossings. Nuwe assimetriese bola-amfifile, saamgestel uit dipeptiedkopgroepe, gekoppel via 'n alifatiese ro-aminosuur, wat as koolwaterstofspasieerder dien, is ook gesintetiseer. Twee klein bola-amfifilbiblioteke is saamgestel - die een het variasies in die ro-aminosuur se lengte omvat en die ander een variasies in die C-terrninale aminosuur. Selfmontering van die bola-amfifile het plaasgevind in of 0,1 % trifluorasynsuur Of 0,1 % trietielamien. Elektronrnikroskopie het die bestaan van 'n verskeidenheid hoërorde supramolekulêre strukture, gegrond op p-plaatselfmontering, aangetoon. Uit FT-IR-spektrometrie blyk dit dat inter - en intralaag waterstofbinbdingsnetwerke en sterk selfassosiasie, 19. word bevorder deur die hidrofobiese effek en, in sekere gevalle, elektrostatiese interaksies, is verantwoordelik vir die verskeidenheid supramolekulêre strukture. Variasies in die hoërorde strukture kan toegeskryf word aan aminosuursamestelling, in besonder die lengte van die ro-aminosuur, die aard van die C-terminale aminosuur en die geoptimiseerde oplosmiddelkondisies wat gebruik is vir die selfmonteringsproses. 'n Derde biblioteek nuwe "hibried" bola-amfifiliese peptiedsurfaktante, waarin 'n kationiese tripeptiedmotief uit antimikrobiale peptiede gekombineer is met 'n m-aminosuurresidu, is geskep. Sommige van hierdie bola-amfifile het 'n kragtige antimikrobiese aktiwiteit teenoor sowel Gram-positiewe as Gram-negatiewe bakterieë gertoon. Die analoë strukture was aktief, of selfs meer aktief as die voorste peptiede maar het, verbasend genoeg, nie 'n beduidende hemolitiese aktiwiteit vertoon nie. Hierdie organopeptied bola-amfifil het dus 'n selektiewe toksisiteit teenoor bakterieë vertoon. Die hidrofo-bisiteit, as gevolg van die ui-aminosuur, het 'n resiproke effek op hemolise en die antimikrobiese aktiwiteit van die peptiedanaloë. Die ander uitstaande kenmerk van die peptiede en hulle analoë is die vermoë om te selfmonteer en komplekse supramolekulêre strukture, bestaande hoofsaaklik uit ~-plate, te vorm. Hierdie selfmontering word in hoofsaak beheer deur hidrofobiese interaksies asook inter - en intralaagwaterstofbinding. Elektronmikroskopie het duidelik hoërorde strukture getoon by sowel dié peptiede as hulle analoë. Die ontwikkeling van hoërorde supramolekulêre struktuurvorms is afhanklik van die optimalisering van die ~-plaatselfmontering. Daarteenoor is die antimikro-biese aktiwiteit afhanklik van die balans tussen die netto positiewe lading en die opti-male hidrofobisiteit van die peptiedhibriede. Hierdie studie het getoon dat dit moontlik is om hibriedsurfaktante te ontwerp wat hoërorde supramolekulêre strukture te produseer en om die antimikrobiese aktiwiteit te verbeter terwyl die hemolitiese effek verminder word. Die studie en ontwerp van hier-die veeldoelige, "doelmatig-gesintetiseerde" biogeïnspireerde surfakante stel 'n unieke benadering daar, wat oor groot potensiaal beskik.

Self-assembled nonionic alkyl glycoside surfactants are of interest for creating functional adsorption and catalytic sites at the surface of mesoporous metal oxides, but they typically impart poor long-range order when used as pore templates. Improved order and control over the functional site density may be achieved by mixing them with a cationic surfactant. To confirm this hypothesis, we investigate the lyotropic liquid crystalline (LLC) phase behavior of aqueous solutions of the functional nonionic surfactant n-dodecyl β-D-maltoside (C12G2) and cationic cetyltrimethylammonium bromide (C16TAB). A ternary phase diagram of the C16TAB-C12G2-water system is developed at 50 °C. By replacing the volume of water in the phase diagram with an equivalent volume of silica, ordered mesoporous materials are prepared by nanocasting with variable C12G2/C16TAB ratios. Metal oxide mesophases can almost always be predicted from the ternary phase diagram, except that silica prepared with high C12G2/C16TAB ratios are very weakly ordered, perhaps due to differences in hydrogen bonding or rate of assembly. Based on the ternary phase diagram of the system, a systematic approach is taken to the incorporation of titania sites via complexation to the maltoside headgroup of C12G2. Complexation to a saccharide is expected not only to guide titanium to the pore surface, but also to prevent uncontrolled hydrolysis and condensation of the (usually quite reactive) titanium precursor. Tetrahedrally coordinated titanium atoms incorporated into a silica network are believed to be the active oxidation sites required for heterogeneous silica-supported titania oxidation catalysts. To promote well-ordered materials and to allow control over titania site density, the mixed C12G2 / C16TAB system is used for pore templating. Series of Si-Ti mixed oxide thin films and bulk materials are synthesized with different amounts of titanium loading by utilizing pre-complexation between C12G2 and titanium isopropoxide. The degrees of homogeneity (indicated by tetracoordinated Ti) in these films are superior to those of films synthesized with the same loading of titanium but without C12G2 or without pre-complexation. Transition metal-carbohydrate complexation provides highly dispersed, tetrahedrally coordinated titanium atoms rather than the octahedral sites found without saccharide complexation.

<p>Limit-periodic (LP) structures exhibit a type of nonperiodic order yet to be found in a natural material. A recent result in tiling theory, however, has shown that LP order can spontaneously emerge in a two-dimensional (2D) lattice model with nearest-and next-nearest-neighbor interactions. In this dissertation, we explore the question of what types of interactions can lead to a LP state and address the issue of whether the formation of a LP structure in experiments is possible. We study emergence of LP order in three-dimensional (3D) tiling models and bring the subject into the physical realm by investigating systems with realistic Hamiltonians and low energy LP states. Finally, we present studies of the vibrational modes of a simple LP ball and spring model whose results indicate that LP materials would exhibit novel physical properties.</p><p>A 2D lattice model defined on a triangular lattice with nearest- and next-nearest-neighbor interactions based on the Taylor-Socolar (TS) monotile is known to have a LP ground state. The system reaches that state during a slow quench through an infinite sequence of phase transitions. Surprisingly, even when the strength of the next-nearest-neighbor interactions is zero, in which case there is a large degenerate class of both crystalline and LP ground states, a slow quench yields the LP state. The first study in this dissertation introduces 3D models closely related to the 2D models that exhibit LP phases. The particular 3D models were designed such that next-nearest-neighbor interactions of the TS type are implemented using only nearest-neighbor interactions. For one of the 3D models, we show that the phase transitions are first order, with equilibrium structures that can be more complex than in the 2D case. </p><p>In the second study, we investigate systems with physical Hamiltonians based on one of the 2D tiling models with the goal of stimulating attempts to create a LP structure in experiments. We explore physically realizable particle designs while being mindful of particular features that may make the assembly of a LP structure in an experimental system difficult. Through Monte Carlo (MC) simulations, we have found that one particle design in particular is a promising template for a physical particle; a 2D system of identical disks with embedded dipoles is observed to undergo the series of phase transitions which leads to the LP state. </p><p>LP structures are well ordered but nonperiodic, and hence have nontrivial vibrational modes. In the third section of this dissertation, we study a ball and spring model with a LP pattern of spring stiffnesses and identify a set of extended modes with arbitrarily low participation ratios, a situation that appears to be unique to LP systems. The balls that oscillate with large amplitude in these modes live on periodic nets with arbitrarily large lattice constants. By studying periodic approximants to the LP structure, we present numerical evidence for the existence of such modes, and we give a heuristic explanation of their structure.</p> / Dissertation

The preparation of the shape-persistent carbosilane-functionalized porphyrins H2TPP(4-SiRR’Me)4, Zn(II)- TPP(4-SiRR’Me)4 (R = R’ = Me, CH2CHvCH2, CH2 CH2CH2OH; R = Me, R’ = CH2 CHvCH2, CH2CH2CH2OH; TPP = tetraphenyl porphyrin), H2TPP(4-Si(C6H4-1,4-SiRR’Me)3)4, and Zn(II)-TPP(4-Si- (C6H4-1,4-SiRR’Me)3)4 (R = R’ = Me, CH2CHvCH2; R = Me, R’ = CH2CHvCH2) using the Lindsey condensation methodology is described. For a series of five samples their structures in the solid state were determined by single crystal X-ray structure analysis. The appropriate 0th and 1st generation porphyrin-based 1,4-phenylene carbosilanes form 2D and 3D supramolecular network structures, primarily controlled by either π–π interactions (between pyrrole units and neighboring phenylene rings) or directional molecular hydrogen recognition and zinc–oxygen bond formation in the appropriate hydroxyl-functionalized molecules. UV-Vis spectroscopic studies were carried out in order to analyze the effect of the dendritic branches on the optical properties of the porphyrin ring. / Dieser Beitrag ist aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.

Supracrystals are highly symmetrical ordered superstructures built up from nanoparticles via self-assembly. While the NP assembly has been intensively investigated, the formation mechanism is still not understood. To shed some light onto the formation mechanism, we are using one of the most common supracrystal morphologies, the trigonal structures, as a model system to investigate the formation process in solution. To explain the formation of the trigonal structures and determining the size of the supracrystal seeds formed in solution, we introduce the concept of substrate-affected growth. Furthermore, we show the influence of the NP concentration on the seed size and extend our investigations from Ag towards Au. 1.

In the 1970s it was discovered that organic polymers, a class of materials otherwise best know as insulating plastics, could be made electronically conductive. As an alternative to silicon semiconductors, organic polymers offer many novel features, characteristics, and opportunities, such as producing electronics at low costs using printing techniques, using organic chemistry to tune optical and electronic properties, and mechanical flexibility. The conducting organic polymers have been used in a vast array of devices, exemplified by organic transistors, light-emitting diodes, and solar cells. Due to their softness, biocompatibility, and combined electronic and ionic transport, organic electronic materials are also well suited as the active material in bioelectronic applications, a scientific and engineering area in which electronics interface with biology. The coupling of ions and electrons is especially interesting, as ions serve as signal carriers in all living organisms, thus offering a direct translation of electronic and ionic signals. To further enable complex control of ionic fluxes, organic electronic materials can be integrated with various ionic components, such as ion-conducting diodes and transistors. This thesis reports a background to the field of organic bioelectronic and ionic devices, and also presents the integration of ionic functions into organic bioelectronic devices. First, an electrophoretic drug delivery device is presented, capable of delivering ions at high spatiotemporal resolution. The device, called the organic electronic ion pump, is used to electronically control amyloid-like aggregation kinetics and morphology of peptides, and offers an interesting method for studying amyloids in vitro. Second, various ion-conducting diodes based on bipolar membranes are described. These diodes show high rectification ratio, i.e. conduct ions better for positive than for negative applied voltage. Simple ion diode based circuits, such as an AND gate and a full-wave rectifier, are also reported. The AND gate is intended as an addressable pH pixel to regulate for example amyloid aggregation, while the full-wave rectifier decouples the electrochemical capacity of an electrode from the amount of ionic charge it can generate. Third, an ion transistor, also based on bipolar membranes, is presented. This transistor can amplify and control ionic currents, and is suitable for building complex ionic logic circuits. Together, these results provide a basic toolbox of ionic components that is suitable for building more complex and/or implantable organic bioelectronic devices.

Self-assembly --- by which ordered structures spontaneously emerge from disordered components --- and biological evolution --- by which Charles Darwin's "endless forms most beautiful" have emerged from the simple chemistry of prehistoric Earth --- may both be pictured as search processes on high-dimensional landscapes, defined respectively by the concepts of energy and fitness. The rich dynamics of these search processes will be studied in order to explain biologically observed features of self-assembly and evolution. This study will introduce and analyse the behaviour of a model for a paradigmatic example of self-assembly, the icosahedral virus capsid, a symmetric structure formed from interacting protein subunits. Results for the thermodynamics and kinetics of model virus assembly will be presented, and the model will be extended to include complicating effects such as different subunit types and cellular crowding. A more general formalism for analysing self-assembling systems will then be introduced and used to suggest a well-defined complexity measure of universal applicability to self-assembled structures. The biological evolution of simple self-assembling structures will be studied using genetic algorithms. The suitability of this modelling approach and its dependence on the many parameters involved will be investigated. Several active areas of enquiry in the field of evolution, including the evolution of complexity, the presence and effect of neutral networks, fluctuations in evolutionary time series and the emergence of symmetry will be investigated within this framework. Throughout this study, we will use the picture of "exploration and exploitation": different approaches to performing optimisation on an unknown landscape, essentially corresponding to a random search and a hill-climbing approach respectively . We will show that, both in self-assembly and evolution, finding an optimal combination of these two approaches gives rise to many of the observed features in this study.

Silk proteins have provided a source of unique and versatile building blocks in the fabrication of biomedical devices for addressing a range of applications. Critical to advancing this field is the ability to establish an understanding of these proteins in their native and engineered states as well as in developing scalable processing strategies, which can fully exploit or enhance the stability, structure, and functionality of the two constituent proteins, silk fibroin and sericin. The research outlined in this dissertation focuses on the evolution in architecture and capability of silks, to effectively position a functionally-diverse, renewable class of silk materials within the rapidly expanding field of smart biomaterials. Study of the process of building macroscopic silk fibers provides insight into the initial steps in the broader picture of silk assembly, yielding biomaterials with greatly improved attributes in the assembled state over those of protein precursors alone. Self-organization processes in silk proteins enable their aggregation into highly organized architectures through simple, physical association processes. In this work, a model is developed for the process of aqueous behavior and aggregation, and subsequent two-dimensional behavior of natural silk sericin, to enable formation of a range of distinct, complex architectures. This model is then translated to an engineered system of fibroin microparticles, demonstrating the role of similar phenomena in creating autonomously-organized structures, providing key insight into future “bottom up” assembly strategies. The aqueous behavior of the water-soluble silk sericin protein was then exploited to create biocomposites capable of enhanced response and biocompatibility, through a novel protein-template strategy. In this work, sericin was added to the biocompatible and biodegradable poly(amino acid), poly(aspartic acid), to improve its pH-dependent swelling response. This work demonstrated the production of a range of porous scaffolds capable providing meaningful response to environmental stimuli, with application in tissue engineering scaffolds and biosensing technologies. Finally, to expand the capabilities of silk proteins beyond process-driven parameters to directly fabricate engineered architectures, a method for silk photopatterning was explored, enabling the direct fabrication of biologically-relevant structures at the micro and nanoscales. Using a facile bioconjugation strategy, native silk proteins could be transformed into proteins with a photoactive capacity. The well-established platform of photolithography could then be incorporated into fabrication strategies to produce a range of architectures capable of addressing spatially-directed material requirements in cell culture and further applications in the use of non-toxic, renewable biological materials.