Systematic functionalization of molecules for molecular self-assembly

This thesis describes the investigation of systematically varied organic molecules for use in molecular self-assembly processes. All experiments were performed using high-resolution non-contact atomic force microscopy under UHV conditions and at room temperature. Using this technique, three different approaches for influencing intermolecular and molecule-surface interaction on the insulating calcite(10.4) surface were investigated by imaging the structure formation at the molecular scale. I first demonstrated the functionalization of shape-persistent oligo(p-benzamide)s that was engineered by introducing different functional groups and investigating their effect on the structural formation on the sample surface. The molecular core was designed to provide significant electrostatic anchoring towards the surface, while at the same time maintaining the flexibility to fine-tune the resulting structure by adjusting the intermolecular cohesion energy. The success of this strategy is based on a clear separation of the molecule-substrate interaction from the molecule-molecule interaction. My results show that sufficient molecule-surface anchoring can be achieved without restricting the structural flexibility that is needed for the design of complex molecular systems. Three derivatives of terephthalic acid (TPA) were investigated in chapter 7. Here, the focus was on changing the adhesion to the calcite surface by introducing different anchor functionalities to the TPA backbone. For all observed molecules, the strong substrate templating effect results in molecular structures that are strictly oriented along the calcite main crystal directions. This templating is especially pronounced in the case of 2-ATPA where chain formation on the calcite surface is observed in contrast to the formation of molecular layers in the bulk. At the same time, the amino group of 2-ATPA proved an efficient anchor functionality, successfully stabilizing the molecular chains on the sample surface. These findings emphasizes, once again, the importance of balancing and fine-tuning molecule-molecule and molecule-surface interactions in order to achieve stable, yet structurally flexible molecular arrangements on the sample surface. In the last chapter, I showed how the intrinsic property of molecular chirality decisively influences the structure formation in molecular self-assembly. This effect is especially pronounced in the case of the chiral heptahelicene-2-carboxylic acid. Deposition of the enantiopure molecules results in the formation of homochiral islands on the sample surface which is in sharp contrast to the formation of uni-directional double rows upon deposition of the racemate onto the same surface. While it remained uncertain from these previous experiments whether the double rows are composed of hetero- or homochiral molecules, I could clearly answer that question here and demonstrate that the rows are of heterochiral origin. Chirality, thus, proves to be another important parameter to steer the intermolecular interaction on surfaces. Altogether, the results of this thesis demonstrate that, in order to successfully control the structure formation in molecular self-assembly, the correct combination of molecule and surface properties is crucial. This is of special importance when working on substrates that exhibit a strong influence on the structure formation, such as the calcite(10.4) surface. Through the systematic variation of functional groups several important parameters that influence the balance between molecule-surface and molecule-molecule interaction were identified here, and the results of this thesis can, thus, act as a guideline for the rational design of molecules for use in molecular self-assembly.

Gravitational Lensing as a Tool on Galactic and Cosmological Scales

This work considers the reconstruction of strong gravitational lenses from their observed effects on the light distribution of background sources. After reviewing the formalism of gravitational lensing and the most common and relevant lens models, new analytical results on the elliptical power law lens are presented, including new expressions for the deflection, potential, shear and magnification, which naturally lead to a fast numerical scheme for practical calculation. The main part of the thesis investigates lens reconstruction with extended sources by means of the forward reconstruction method, in which the lenses and sources are given by parametric models. The numerical realities of the problem make it necessary to find targeted optimisations for the forward method, in order to make it feasible for general applications to modern, high resolution images. The result of these optimisations is presented in the \textsc{Lensed} algorithm. Subsequently, a number of tests for general forward reconstruction methods are created to decouple the influence of sourced from lens reconstructions, in order to objectively demonstrate the constraining power of the reconstruction. The final chapters on lens reconstruction contain two sample applications of the forward method. One is the analysis of images from a strong lensing survey. Such surveys today contain $\sim 100$ strong lenses, and much larger sample sizes are expected in the future, making it necessary to quickly and reliably analyse catalogues of lenses with a fixed model. The second application deals with the opposite situation of a single observation that is to be confronted with different lens models, where the forward method allows for natural model-building. This is demonstrated using an example reconstruction of the ``Cosmic Horseshoe''. An appendix presents an independent work on the use of weak gravitational lensing to investigate theories of modified gravity which exhibit screening in the non-linear regime of structure formation.

Non-thermal properties of two galaxy filament candidates from JVLA observations

Large-scale structures can be considered an interesting and useful "laboratory" to better investigate the Universe; in particular the filaments connecting clusters and superclusters of galaxies can be a powerful tool for this intent, since they are not virialised systems yet. The large structures in the Universe have been studied in different bands, in particular the present work takes into consideration the emission in the radio band. In the last years both compact and diffuse radio emission have been detected, revealing to be associated to single objects and clusters of galaxies respectively. The detection of these sources is important, because the radiation process is the synchrotron emission, which in turn is linked to the presence of a magnetic field: therefore studying these radio sources can help in investigating the magnetic field which permeates different portions of space. Furthermore, radio emission in optical filaments have been detected recently, opening new chances to further improve the understanding of structure formation. Filaments can be seen as the net which links clusters and superclusters. This work was made with the aim of investigating non-thermal properties in low-density regions, looking for possible filaments associated to the diffuse emission. The analysed sources are 0917+75, which is located at a redshift z = 0.125, and the double cluster system A399-A401, positioned at z = 0.071806 and z = 0.073664 respectively. Data were taken from VLA/JVLA observations, and reduced and calibrated with the package AIPS, following the standard procedure. Isocountour and polarisation maps were yielded, allowing to derive the main physical properties. Unfortunately, because of a low quality data for A399-A401, it was not possible to see any radio halo or bridge.

Konfokalmikroskopie an stabilen und metastabilen kolloidalen Hartkugel-Fluiden : interne Struktur, Kristallnukleation und Kristallwachstum

Die vorliegende Forschungsarbeit behandelt konfokalmikroskopische Untersuchungen zur Strukturbildung in kolloidalen Suspensionen, die als experimentelles Modellsystem für harte Kugeln verwendet werden. Die lokale und globale Struktur wurde im stabilen und metastabilen Fluid bestimmt. Bereits unterhalb des Gefriervolumenbruchs wurden nah-geordnete Cluster vorgefunden, die mit zunehmendem Volumenbruch häufiger und größer werden. Das Kristallwachstum aus der metastabilen kolloidalen Schmelze konnte quantitativ analysiert werden und es zeigt sich eine Übereinstimmung mehrerer Kenngrößen mit Literaturdaten nahe dem Schmelzvolumenbruch. Die Untersuchung demonstrierte die Realisierbarkeit der quantitativen Analyse der Kristallisationskinetik mittels konfokaler Mikroskopie. Es zeigte sich ein mehrstufiges Nukleationsszenario bei dem zuerst nah-geordnete Cluster gebildet werden, die im weiteren Verlauf zu kristall-artigen Clustern transformieren. Die Beobachtungen belegen den Mechanismus der Precursornukleation in Hartkugelsystemen. Die heterogene Nukleation wurde an glatten und an hexagonal strukturierten Substraten untersucht. Anhand der Kristallisationskinetik und der direkten Messung der Benetzungswinkel konnte ein Übergang des Benetzungsverhaltens unter Variation des Substratgitterabstands nachgewiesen werden: An glatten und an kommensurabel strukturierten Substraten zeigten sich eine vollständige Bedeckung des Substrats mit der kristallinen Phase und ein sofortiges unidirektionales Wachstum. Bei inkommensurabel strukturierten Substraten wurde eine unvollständige Bedeckung des strukturierten Substrats mit der kristallinen Phase sowie ein verzögertes isotropes Wachstum bei fortwährender Kristallnukleation beobachtet.

Improved determination of sterile neutrino dark matter spectrum

The putative recent indication of an unidentified 3.55 keV X-ray line in certain astrophysical sources is taken as a motivation for an improved theoretical computation of the cosmological abundance of 7.1 keV sterile neutrinos. If the line is interpreted as resulting from the decay of Warm Dark Matter, the mass and mixing angle of the sterile neutrino are known. Our computation then permits for a determination of the lepton asymmetry that is needed for producing the correct abundance via the Shi-Fuller mechanism, as well as for an estimate of the non-equilibrium spectrum of the sterile neutrinos. The latter plays a role in structure formation simulations. Results are presented for different flavour structures of the neutrino Yukawa couplings and for different types of pre-existing lepton asymmetries, accounting properly for the charge neutrality of the plasma and incorporating approximately hadronic contributions.

Non B-DNA structures and genomic instability associated with myotonic dystrophy type 2 (CCTG).(CAGG) repeats

There are many diseases associated with the expansion of DNA repeats in humans. Myotonic dystrophy type 2 is one of such diseases, characterized by expansions of a (CCTG)•(CAGG) repeat tract in intron 1 of zinc finger protein 9 (ZNF9) in chromosome 3q21.3. The DM2 repeat tract contains a flanking region 5' to the tract that consists of a polymorphic repetitive sequence (TG)14-25(TCTG)4-11(CCTG) n. The (CCTG)•(CAGG) repeat is typically 11-26 repeats in persons without the disease, but can expand up to 11,000 repeats in affected individuals, which is the largest expansion seen in DNA repeat diseases to date. This DNA tract remains one of the least characterized disease-associated DNA repeats, and mechanisms causing the repeat expansion in humans have yet to be elucidated. Alternative, non B-DNA structures formed by the expanded repeats are typical in DNA repeat expansion diseases. These sequences may promote instability of the repeat tracts. I determined that slipped strand structure formation occurs for (CCTG)•(CAGG) repeats at a length of 42 or more. In addition, Z-DNA structure forms in the flanking human sequence adjacent to the (CCTG)•(CAGG) repeat tract. I have also performed genetic assays in E. coli cells and results indicate that the (CCTG)•(CAGG) repeats are more similar to the highly unstable (CTG)•(CAG) repeat tracts seen in Huntington's disease and myotonic dystrophy type 1, than to those of the more stable (ATTCT)•(AGAAT) repeat tracts of spinocerebellar ataxia type 10. This instability, however, is RecA-independent in the (CCTG)•(CAGG) and (ATTCT)•(AGAAT) repeats, whereas the instability is RecA-dependent in the (CTG)•(CAG) repeats. Structural studies of the (CCTG)•(CAGG) repeat tract and the flanking sequence, as well as genetic selection assays may reveal the mechanisms responsible for the repeat instability in E. coli, and this may lead to a better understanding of the mechanisms contributing to the human disease state. ^

(Table T2) Sulfur isotopes of pore water from ODP Leg 201 sites

Fifty-seven interstitial water samples from six sites (Ocean Drilling Program Sites 1225-1229 and 1231) in the eastern equatorial Pacific Ocean and the Peru margin were analyzed for the stable sulfur isotopic composition (34S/32S) of dissolved sulfate along with major and minor ions. With the exception of Site 1231, sulfate from the interstitial fluids (d34S values as much as 89 per mil vs. the SF6-based Vienna-Canyon Diablo troilite standard) is found at depth to be enriched in 34S with respect to modern seawater sulfate (d34S = ~21 per mil), indicating that microbial sulfate reduction (MSR) took place to different extents at all investigated sites. Deeper sediments at Sites 1228 and 1229 are additionally influenced by diffusion of a sulfate-rich brine that has already undergone sulfate reduction. The intensity of MSR depends on the availability of substrate (organic matter), sedimentation conditions, and the active bacterial community structure. Formation of isotopically heavy diagenetic barite at the sulfate-methane transition zone is expected at Sites 1227 (one front), 1229 (two fronts), and probably Site 1228. At Site 1231, the constant sulfur isotopic composition of sulfate and concentrations of minor pore water ions indicate that suboxic (essentially iron and manganese oxide based) diagenesis dominates and no net MSR occurs.

Turbulence models of gravitational clustering.

Large-scale structure formation can be modeled as a nonlinear process that transfers energy from the largest scales to successively smaller scales until it is dissipated, in analogy with Kolmogorov’s cascade model of incompressible turbulence. However, cosmic turbulence is very compressible, and vorticity plays a secondary role in it. The simplest model of cosmic turbulence is the adhesion model, which can be studied perturbatively or adapting to it Kolmogorov’s non-perturbative approach to incompressible turbulence. This approach leads to observationally testable predictions, e.g., to the power-law exponent of the matter density two-point correlation function.

Chromophore-assisted light inactivation and self-organization of microtubules and motors

Chromophore-assisted light inactivation (CALI) offers the only method capable of modulating specific protein activities in localized regions and at particular times. Here, we generalize CALI so that it can be applied to a wider range of tasks. Specifically, we show that CALI can work with a genetically inserted epitope tag; we investigate the effectiveness of alternative dyes, especially fluorescein, comparing them with the standard CALI dye, malachite green; and we study the relative efficiencies of pulsed and continuous-wave illumination. We then use fluorescein-labeled hemagglutinin antibody fragments, together with relatively low-power continuous-wave illumination to examine the effectiveness of CALI targeted to kinesin. We show that CALI can destroy kinesin activity in at least two ways: it can either result in the apparent loss of motor activity, or it can cause irreversible attachment of the kinesin enzyme to its microtubule substrate. Finally, we apply this implementation of CALI to an in vitro system of motor proteins and microtubules that is capable of self-organized aster formation. In this system, CALI can effectively perturb local structure formation by blocking or reducing the degree of aster formation in chosen regions of the sample, without influencing structure formation elsewhere.

An optimal Mg2+ concentration for kinetic folding of the Tetrahymena ribozyme

Divalent metal ions, such as Mg2+, are generally required for tertiary structure formation in RNA. Although the role of Mg2+ binding in RNA-folding equilibria has been studied extensively, little is known about the role of Mg2+ in RNA-folding kinetics. In this paper, we explore the effect of Mg2+ on the rate-limiting step in the kinetic folding pathway of the Tetrahymena ribozyme. Analysis of these data reveals the presence of a Mg2+-stabilized kinetic trap that slows folding at higher Mg2+ concentrations. Thus, the Tetrahymena ribozyme folds with an optimal rate at 2 mM Mg2+, just above the concentration required for stable structure formation. These results suggest that thermodynamic and kinetic folding of RNA are cooptimized at a Mg2+ concentration that is sufficient to stabilize the folded form but low enough to avoid kinetic traps and misfolding.

Exploring the folding free energy surface of a three-helix bundle protein

The multidimensional free energy surface for a small fast folding helical protein is explored based on first-principle calculations. The model represents the 46-residue segment from fragment B of staphylococcal protein A. The relationship between collapse and tertiary structure formation, and the order of collapse and secondary structure formation, are investigated. We find that the initial collapse process gives rise to a transition state with about 30% of the native tertiary structure and 50–70% of the native helix content. We also observe two distinct distributions of native helix in this collapsed state (Rg ≈ 12 Å), one with about 20% of the native helical hydrogen bonds, the other with near 70%. The former corresponds to a local minimum. The barrier from this metastable state to the native state is about 2 kBT. In the latter case, folding is essentially a downhill process involving topological assembly. In addition, the order of formation of secondary structure among the three helices is examined. We observe cooperative formation of the secondary structure in helix I and helix II. Secondary structure in helix III starts to form following the formation of certain secondary structure in both helix I and helix II. Comparisons of our results with those from theory and experiment are made.

Homeobox gene Prx3 expression in rodent brain and extraneural tissues

Different cDNA clones encoding a rat homeobox gene and the mouse homologue OG-12 were cloned from adult rat brain and mouse embryo mRNA, respectively. The predicted amino acid sequences of the proteins belong to the paired-related subfamily of homeodomain proteins (Prx homeodomains). Hence, the gene was named Prx3 and the mouse and rat genes are indicated as mPrx3 and rPrx3, respectively. In the mouse as well as in the rat, the predicted Prx3 proteins share the homeodomain but have three different N termini, a 12-aa residue variation in the C terminus, and contain a 14-aa residue motif common to a subset of homeodomain proteins, termed the “aristaless domain.” Genetic mapping of Prx3 in the mouse placed this gene on chromosome 3. In situ hybridization on whole mount 12.5-day-old mouse embryos and sections of rat embryos at 14.5 and 16.5 days postcoitum revealed marked neural expression in discrete regions in the lateral and medial geniculate complex, superior and inferior colliculus, the superficial gray layer of the superior colliculus, pontine reticular formation, and inferior olive. In rat and mouse embryos, nonneuronal structures around the oral cavity and in hip and shoulder regions also expressed the Prx3 gene. In the adult rat brain, Prx3 gene expression was restricted to thalamic, tectal, and brainstem structures that include relay nuclei of the visual and auditory systems as well as other ascending systems conveying somatosensory information. Prx3 may have a role in specifying neural systems involved in processing somatosensory information, as well as in face and body structure formation.

The thermodynamic origin of the stability of a thermophilic ribozyme

Understanding the mechanism of thermodynamic stability of an RNA structure has significant implications for the function and design of RNA. We investigated the equilibrium folding of a thermophilic ribozyme and its mesophilic homologue by using hydroxyl radical protection, small-angle x-ray scattering, and circular dichroism. Both RNAs require Mg2+ to fold to their native structures that are very similar. The stability is measured as a function of Mg2+ and urea concentrations at different temperatures. The enhanced stability of the thermophilic ribozyme primarily is derived from a tremendous increase in the amount of structure formed in the ultimate folding transition. This increase in structure formation and cooperativity arises because the penultimate and the ultimate folding transitions in the mesophilic ribozyme become linked into a single transition in the folding of the thermophilic ribozyme. Therefore, the starting point, or reference state, for the transition to the native, functional thermophilic ribozyme is significantly less structured. The shift in the reference state, and the resulting increase in folding cooperativity, is likely due to the stabilization of selected native interactions that only form in the ultimate transition. This mechanism of using a less structured intermediate and increased cooperativity to achieve higher functional stability for tertiary RNAs is fundamentally different from that commonly proposed to explain the increased stability of thermophilic proteins.

Cosmic microwave background theory

A long-standing goal of theorists has been to constrain cosmological parameters that define the structure formation theory from cosmic microwave background (CMB) anisotropy experiments and large-scale structure (LSS) observations. The status and future promise of this enterprise is described. Current band-powers in ℓ-space are consistent with a ΔT flat in frequency and broadly follow inflation-based expectations. That the levels are ∼(10−5)2 provides strong support for the gravitational instability theory, while the Far Infrared Absolute Spectrophotometer (FIRAS) constraints on energy injection rule out cosmic explosions as a dominant source of LSS. Band-powers at ℓ ≳ 100 suggest that the universe could not have re-ionized too early. To get the LSS of Cosmic Background Explorer (COBE)-normalized fluctuations right provides encouraging support that the initial fluctuation spectrum was not far off the scale invariant form that inflation models prefer: e.g., for tilted Λ cold dark matter sequences of fixed 13-Gyr age (with the Hubble constant H0 marginalized), ns = 1.17 ± 0.3 for Differential Microwave Radiometer (DMR) only; 1.15 ± 0.08 for DMR plus the SK95 experiment; 1.00 ± 0.04 for DMR plus all smaller angle experiments; 1.00 ± 0.05 when LSS constraints are included as well. The CMB alone currently gives weak constraints on Λ and moderate constraints on Ωtot, but theoretical forecasts of future long duration balloon and satellite experiments are shown which predict percent-level accuracy among a large fraction of the 10+ parameters characterizing the cosmic structure formation theory, at least if it is an inflation variant.

The universe at z > 5: When and how did the “dark age” end?

This paper considers how the first subgalactic structures produced the UV radiation that ionized the intergalactic medium before z = 5 and the “feedback” effects of the UV radiation on structure formation. The first “pregalaxies” may eventually be detectable by their direct UV emission, with characteristic spectral features at Lyman α; high-z supernovae may also be detectable. Other probes of the intergalactic medium beyond z = 5, and of the epochs of reheating and reionization, are discussed, along with possible links between the diffusion of pregalactic metals and the origin of magnetic fields.