Fakultät für Physik - Digitale Hochschulschriften der LMU - Teil 04/05

Knowledge about the kinetics of chemical reactions in cells is important for an understanding

of signaling pathways and regulation. Even though there are many kinetic measurements

of in vitro reactions in literature, methods for in vivo measurements are sparse. With help

of Temperature Oscillation Optical Lock-in (TOOL) microscopy we measure the kinetics of

DNA hybridization inside cells and detect signicant acceleration or deceleration compared to

in vitro measurements, dependent on the DNA sample. The dierences can not be explained

by molecular crowding eects. Only models that take the background interactions with genomic

DNA and RNA as well as the activity of single stranded and double stranded binding

proteins into account, can be tted to data. The results imply that the biological relevance

of kinetic rates measured in vitro has to be rejudged carefully.

The RNA world hypothesis predicts catalytic molecules based on RNA, as for example

early replicators, as precursor of modern biology. But how can a pool of appropriate RNA

molecules arise under early earth conditions? In a Gillespie-model, we observe the length distribution,

secondary structure and sequences of a pool of RNA molecules in porous rocks like

they appear near sites of volcanic activity. We assume a monomer in

ux, a length dependent

out

ux, a random, non-templated polymerisation and a degradation that is much stronger

for single stranded than for double stranded RNA. After equilibrium is reached, the pool

is populated with many hairpin-like structures due to the selection pressure for hybridized

strands that can be bricks for RNA machines.

Once sequence motifs and their complements appear in the reactor, they protect each other

and are present longer than statistically expected. This "protection by hybridization" has

the same ngerprint as a weak replication. As a consequence, the pool does not cover the

full sequence space but includes more similar sequences, which is an important condition for

chemical reactions.

Replication of genetic information by RNA molecules is considered to be a key process in the

beginning of evolution. It is so crucial that traces of this early replication are expected to be

present in key processes of modern biology. We present a replication scheme based on hairpins

derived from the sequence of tRNA that replicates the genetic information about a succession

of sequence snippets. The replication is driven by temperature oscillations as they occur

naturally inside of porous rocks in presence of temperature gradients, and independent on

external chemical energy sources. It is selective for correct information and shows exponential

growth rates with doubling times in the range of seconds to minutes and is thereby the fastest

early replicator in the literature.

The replication scheme can naturally be expanded to longer successions by using double

hairpins derived from full tRNA sequences by only few mutations. By charging double hairpins

with amino acids or peptides, the proposed replication bridges the gap from the RNA world

to modern biology by oering a rudimentary translation mechanism, that sorts amino acids

to chains according to genetic information.

Die vorliegende Dissertation befasst sich mit verschiedenen Aspekten und Techniken zur Konstruktion von String-Modellen. In diesem Kontext ist es nötig die Topologie von Calabi-Yau Mannigfaltigkeiten zu verstehen, da diese ausschlaggebend für die Nullmodenstruktur des entsprechenden Differenzialoperators und damit für das Teilchenspektrum der kompaktifizierten Niederenergietheorie ist. Für diejenigen Calabi-Yau Räume, die als Unterräume torischer Varietäten definiert werden, sind alle topologischen Größen in der Kohomololgie von Linienbündeln über der entsprechenden torischen Varietät verschlüsselt. Aus diesem Grund umfasst ein Teil dieser Dissertation die Entwicklung eines effizienten Algorithmus’ für ihre Berechnung. Nach der mathematischen Vorbereitung widmen wir uns der Herleitung und dem Beweis des auf diese Weise entstandenen mathematischen Theorems. Wir untersuchen zudem eine Verallgemeinerung auf Räume, die durch das Herausteilen einer Zn-Symmetrie konstruiert werden. Anschließend demonstrieren wir die zahlreichen Anwendungen dieser Methoden zur Konstruktion von String-Modellen. Außerdem finden wir einen Zusammenhang zwischen Kohomologiegruppen von Linienbündeln und getwisteten Sektoren von Landau-Ginzburg Modellen. Als nächstes nutzen wir die entwickelten Methoden um so genannte Zielraum Dualitäten zwischen heterotischen Modellen zu untersuchen. Diese Modelle weisen eine asymmetrische (0,2)-Weltflächensupersymmetrie auf und können über geeichte lineare Sigma-Modelle formuliert werden, in welchen sie eine Phasenstruktur ausbilden. Es lässt sich nun zeigen, dass die Phasenräume verschiedener physikalischer Modelle durch nicht-geometrische Phasen miteinander verbunden sind, was eine hochgradig nicht-triviale Dualität der entsprechenden Geometrien implizieren könnte. Unser Beitrag ist nun die Untersuchung der hierdurch verbundenen und daher potentiell dualen Modelle. Wir entwickeln ein Verfahren, welches die Konstruktion aller dualer Modelle zu einem beliebigen (0,2) Modell erlaubt und finden Evidenz dafür, dass es sich hierbei um eine echte Dualität und nicht bloß um einen Übergang verschiedener physikalischer Modelle ineinander handelt. In diesem Kontext untersuchen wir verschiedenste Szenarien, u.A. Modelle mit den Eichgruppen E6, SO(10) und SU(5), sowie mit Kompaktifizierungsräumen der Kodimension eins und zwei. In einer Untersuchung der Stringlandschaft werden dazu über 80.000 Räume auf diese Dualität untersucht.

Galaxy clusters are optimal laboratories to test cosmology as well as models for physical

processes acting on smaller scales. X–ray observations of the hot gas filling their dark

matter potential well, i.e. the intra–cluster medium (ICM), still provides one of the

best ways to investigate the intrinsic properties of clusters. Methods based on X–ray

observations of the ICM are commonly used to estimate the total mass, assuming that

the gas traces the underlying potential well and satisfies spherical symmetry, and thermal

motions dominate the total pressure support. However, non–thermal motions are likely

to establish in the ICM, hence, contribute to the total pressure and have to be taken into

account in the mass estimate.

In this thesis I study the ICM thermo–dynamical structure by combining

hydrodynamical simulations and synthetic X–ray observations of galaxy clusters. The

main goal is to study their gas velocity field and the implications due to non–thermal

motions: first, by analysing directly the velocity patterns in simulated clusters and,

secondly, by reconstructing the internal ICM structure from mock X–ray spectra. To

this aim, I developed and applied an X–ray photon simulator to obtain synthetic X–ray

spectra from the gas component in hydrodynamical simulations of galaxy clusters.

The main findings of this work are as follows.

(i) Ordered, rotational patterns in the gas velocity field in cluster cores can establish

during the mass assembly process, but are found to be transient phenomena, easily

destroyed by passages of gas–rich subhaloes. This suggests that in smoothly growing

haloes the phenomenon is in general of minor effect. Nonetheless, major mergers or

highly disturbed systems can indeed develop significant ordered motions and rotation,

which contribute up to 20% to the total mass. (ii) It is indeed possible to reconstruct

the thermal structure of the ICM in clusters from X–ray spectral analysis, by recovering

the emission measure (EM) distribution of the gas as a function of temperature. This is possible with current X–ray telescopes (e.g. Suzaku) via multi–temperature fitting of X–

ray spectra. (iii) High–precision X–ray spectrometers, such as ATHENA, will allow us to

measure velocity amplitudes of ICM non–thermal motions, from the velocity broadening

of heavy–ion (e.g. iron) emission lines. In this work, these achievements are obtained by

applying the virtual X–ray simulator to generate ATHENA synthetic spectra of simulated

clusters. The non–thermal velocity of the ICM in the central region is used to further

characterise the cluster and the level of deviation from the expected self–similarity. By

excluding the clusters with the highest non–thermal velocity dispersion, the scatter of the

LX −T relation for the sample is significantly reduced, which will allow for a more precise

comparison between observations and simulations.

Galaxies have been found to divide into two families: one dominated by late-type, star forming, blue objects, which are rich in cold gas and have a low stellar mass surface density (mu*); the other is made of early-type, red and

passive galaxies with higher mu* and on average low gas content. The physical mechanisms responsible for the galaxy transition between the active and passive regime are still debated. In the high mass range, mechanisms proposed to quench the star formation (SF) through cold gas heating or depletion are not efficient enough to reproduce the correct red sequence of passive systems, when implemented in models of galaxy evolution. Input for a better understanding of

the physics of quenching mechanisms, and of their relative importance and efficiency, can come from a comparison of the cold atomic neutral hydrogen (HI) content and SF for a statistically significant sample of massive systems where

quenching is at work. However, existing surveys do not sample this high mass, gas poor regime well enough. In this work, we study the HI properties of a volume-limited sample of ~5000 nearby galaxies with stellar mass M*>10^10 Msun, selected from the state-of-the-art blind HI survey ALFALFA to have optical and ultraviolet data so that star formation and galaxy properties can be derived. As ALFALFA does not sample with sufficient sensitivity the high mass, gas poorest range, we developed a software tool to co-add its data, in order to obtain average gas properties of galaxy classes which individually may be largely undetected.

Using this technique, we study three types of quenching processes, namely the presence of a bulge component, feedback from an active galactic nucleus (AGN), and environmental mechanisms acting on the interstellar medium. Simulations of early-type galaxies with non star-forming HI disks have suggested that the presence of a bulge can stabilize the gas, thus preventing star formation, but

on average we do not observe this. We find that, once mu* and NUV-r colours are fixed, the HI gas fraction in massive bulge- and disk-dominated galaxies is the same. A similar negative result is obtained if we compare M_HI/M* of AGN hosts and control galaxies, despite simulations that invoke feedback from AGN to heat or deplete cold gas in

massive systems. The relation we observe between the cold gas content and the accretion rate in the red population actually points towards a co-evolution of SF and AGN activity, both driven by the amount of gas available. The last class of quenching mechanisms studied in this work includes environmental processes, which are known to affect the SF properties of galaxies and, at least in rich clusters, their cold gas content. For the first time, though, we study the effect of the environment on the HI content as a continuous function of local density, comparing it with global and inner specific star formation rate. The gradual increase in the suppression of SF from the inner to the outer regions that we observe, and the even stronger HI deficiency as a function of increasing local density, can be explained by a mechanism acting on the disk from the outside-in, like ram-pressure stripping of the HI. A comparison with mock catalogs from models, which include only removal of the hot gas, shows how

models underestimate environmental effects, especially on the cold gas component of galaxies.

We therefore suggest that, in order to improve our understanding of the galaxy bimodality in the local Universe, observations and models should particularly

focus on environmental mechanisms acting on the cold interstellar medium. These processes are efficient over a broader range of local densities than previously thought,

and could solve parts of the puzzle in the formation of massive and passive systems.