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Configuration, simulation and visualization of simple biochemical reaction-diffusion systems in 3D
(2004)
Background In biological systems, molecules of different species diffuse within the reaction compartments and interact with each other, ultimately giving rise to such complex structures like living cells. In order to investigate the formation of subcellular structures and patterns (e.g. signal transduction) or spatial effects in metabolic processes, it would be helpful to use simulations of such reaction-diffusion systems. Pattern formation has been extensively studied in two dimensions. However, the extension to three-dimensional reaction-diffusion systems poses some challenges to the visualization of the processes being simulated. Scope of the Thesis The aim of this thesis is the specification and development of algorithms and methods for the three-dimensional configuration, simulation and visualization of biochemical reaction-diffusion systems consisting of a small number of molecules and reactions. After an initial review of existing literature about 2D/3D reaction-diffusion systems, a 3D simulation algorithm (PDE solver), based on an existing 2D-simulation algorithm for reaction-diffusion systems written by Prof. Herbert Sauro, has to be developed. In a succeeding step, this algorithm has to be optimized for high performance. A prototypic 3D configuration tool for the initial state of the system has to be developed. This basic tool should enable the user to define and store the location of molecules, membranes and channels within the reaction space of user-defined size. A suitable data structure has to be defined for the representation of the reaction space. The main focus of this thesis is the specification and prototypic implementation of a suitable reaction space visualization component for the display of the simulation results. In particular, the possibility of 3D visualization during course of the simulation has to be investigated. During the development phase, the quality and usability of the visualizations has to be evaluated in user tests. The simulation, configuration and visualization prototypes should be compliant with the Systems Biology Workbench to ensure compatibility with software from other authors. The thesis is carried out in close cooperation with Prof. Herbert Sauro at the Keck Graduate Institute, Claremont, CA, USA. Due to this international cooperation the thesis will be written in English.
Chapter 1 contains the general background of our work. We briefly discuss important aspects of quantum chromodynamics (QCD) and introduce the concept of the chiral condensate as an order parameter for the chiral phase transition. Our focus is on the concept of universality and the arguments why the O(4) model should fall into the same universality class as the effective Lagrangian for the order parameter of (massless) two-flavor QCD. Chapter 2 pedagogically explains the CJT formalism and is concerned with the WKB method. In chapter 3 the CJT formalism is then applied to a simple Z(2) symmetric toy model featuring a one-minimum classical potential. As for all other models we are concerned with in this thesis, we study the behavior at nonzero temperature. This is done in 1+3 dimensions as well as in 1+0 dimensions. In the latter case we are able to compare the effective potential at its global minimum (which is minus the pressure) with our result from the WKB approximation. In chapter 4 this program is also carried out for the toy model with a double-well classical potential, which allows for spontaneous symmetry breaking and tunneling. Our major interest however is in the O(2) model with the fields treated as polar coordinates. This model can be regarded as the first step towards the O(4) model in four-dimensional polar coordinates. Although in principle independent, all subjects discussed in this thesis are directly related to questions arising from the investigation of this particular model. In chapter 5 we start from the generating functional in cartesian coordinates and carry out the transition to polar coordinates. Then we are concerned with the question under which circumstances it is allowed to use the same Feynman rules in polar coordinates as in cartesian coordinates. This question turns out to be non-trivial. On the basis of the common Feynman rules we apply the CJT formalism in chapter 6 to the polar O(2) model. The case of 1+0 dimensions was intended to be a toy model on the basis of which one could more easily explore the transition to polar coordinates. However, it turns out that we are faced with an additional complication in this case, the infrared divergence of thermal integrals. This problem requires special attention and motivates the explicit study of a massless field under topological constraints in chapter 8. In chapter 7 we investigate the cartesian O(2) model in 1+0 dimensions. We compare the effective potential at its global minimum calculated in the CJT formalism and via the WKB approximation. Appendix B reviews the derivation of standard thermal integrals in 1+0 and 1+3 dimensions and constitutes the basis for our CJT calculations and the discussion of infrared divergences. In chapter 9 we discuss the so-called path integral collapse and propose a solution of this problem. In chapter 10 we present our conclusions and an outlook. Since we were interested in organizing our work as pedagogical as possible within the narrow scope of a diploma thesis, we decided to make extensive use of appendices. Appendices A-H are intended for students who are not familiar with several important concepts we are concerned with. We will refer to them explicitly to establish the connection between our work and the general context in which it is settled.
This work is dedicated to the study of the vector and axial vector spectral functions of the τ lepton within the framework of a U(2)L × U(2)R Linear Sigma Model with electroweak interaction. As an effective field theory the Linear Sigma Model describes hadronic degrees of freedom based on the symmetries of the Standard Model. Therefore, the following section aims at giving a very general and concise introduction to the Standard Model and the meaning of symmetries for contemporary elementary particle physics. In the next section the SU(3)C symmetry group will be discussed in short, followed by an introduction to chiral symmetry SU(2)L × SU(2)R. In the last section of this chapter the Glashow-Weinberg-Salam theory of the local group SU(2)L × U(1)Y is presented. Important concepts of the theoretical framework of the Standard Model, such as the Noether Theorem, the Gauge Principle, Spontaneous Symmetry Breaking, and the Higgs Mechanism will be introduced in the context of these three symmetry groups. In Chapter 2 it will be first shown how the symmetries of the Standard Model are realised within the global U(2)L × U(2)R Linear Sigma Model and how electroweak interactions can be introduced to the model on the basis of local SU(2)L × U(1)Y symmetry transformations of the hadronic degrees of freedom. The vertices that are relevant for the vector and axial vector decay channels in weak τ decay are extracted from the Lagrangian with electroweak interaction in Chapter 3. This is followed by a short introduction to the Källen-Lehmann Representation of spectral functions and how these can be parametrised within the framework of this model (Chapter 4). The results of the vector and axial vector spectral functions are presented in Chapter 5 and 6.
RDF is widely used in order to catalogue the chaos of data across the internet. But these descriptions must be stored, evaluated, analyzed and verified. This creates the need to search for an environment to realize these aspects and strengthen RDFs influence. InterSystems postrelational database Caché exposes many features that are similar to RDF and provide persistence with semantic part. Some models for relational databases exist but these lack features like object-oriented data-structures and multidimensional variables. The aim of this thesis is to develop an RDF model for Caché that saves RDF data in an object-oriented form. Furthermore an interface for importing RDF data will be presented and implemented.
Approximating Perpetuities
(2006)
A perpetuity is a real valued random variable which is characterised by a distributional fixed-point equation of the form X=AX+b, where (A,b) is a vector of random variables independent of X, whereas dependencies between A and b are allowed. Conditions for existence and uniqueness of solutions of such fixed-point equations are known, as is the tail behaviour for most cases. In this work, we look at the central area and develop an algorithm to approximate the distribution function and possibly density of a large class of such perpetuities. For one specific example from the probabilistic analysis of algorithms, the algorithm is implemented and explicit error bounds for this approximation are given. At last, we look at some examples, where the densities or at least some properties are known to compare the theoretical error bounds to the actual error of the approximation. The algorithm used here is based on a method which was developed for another class of fixed-point equations. While adapting to this case, a considerable improvement was found, which can be translated to the original method.
The thesis in general deals with CORBA, the Common Object Request Broker Architecture. More specifically, it takes a look at the server-side, where object adapters exist to aid the developer in implementing objects and in dealing with request processing. The new Portable Object Adapter was recently added to the CORBA 2.2 standard. My task was the implementation of the POA in MICO and the examination if (a) the POA specification is sensible and (b) in which areas it improves over the old Basic Object Adapter. After introducing distributed platforms in general and CORBA in particular, the thesis' main two chapters are a detailed abstract examination ("Design") of the POA design and their relization ("Implementation"), highlighting the potential trouble spots, persistence and collocation.
This thesis presents the implementation of the online reconstruction, calibration and monitoring of the data of the Transition Radiation Detector of ALICE. This reconstruction is performed on the High Level Trigger, the third level of the ALICE trigger system, and enables online calibration and monitoring of the incoming data. Additionally, the HLT can steer the data storage, such that only physical interesting events are saved. The online reconstruction, as well as the calibration, makes use of the existing offline algorithms. Therefore, interfaces between the HLT and these offline algorithms were implemented. For being able to reach the speed of 2000 Hz in proton-proton collisions, and 200 Hz in leadlead collisions, the algorithms had to be accelerated. Bottlenecks were tracked down using dedicated tools, and respective code was either reimplemented or it is being skipped during the online reconstruction. The quality of the output data was monitored throughout the implementation, to assure that it is not being cut too much.
The synchronization of neuronal firing activity is considered an important mechanism in cortical information processing. The tendency of multiple neurons to synchronize their joint firing activity can be investigated with the 'unitary event' analysis (Grün, 1996). This method is based on the nullhypothesis of independent Bernoulli processes and can therefore not tell whether coincidences observed between more than two processes can be considered "genuine" higher- order coincidences or whether they might be caused by coincidences of lower order that coincide by chance ("chance coincidences"). In order to distinguish between genuine and chance coincidences, a parametric model of independent interaction processes (MIIP) is presented. In the framework of this model, Maximum-Likelihood estimates are derived for the firing rates of n single processes and for the rates with which genuine higher order correlations occur. The asymptotic normality of these estimates is used to derive their asymptotic variance and in order to investigate whether higher order coincidences can be considered genuine or whether they can be explained by chance coincidences. The empirical test power of this procedure for n=2 and n=3 processes and for finite analysis windows is derived with simulations and compared to the asymptotic values. Finally, the model is extended in order to allow for the analysis of correlations that are caused by jittered coincidences.
This work connects Markov chain imbedding technique (MCIT) introduced by M.V. Koutras and J.C. Fu with distributions concerning the cycle structure of permutations. As a final result program code is given that uses MCIT to deliver proper numerical values for these. The discrete distributions of interest are the one of the cycle structure, the one of the number of cycles, the one of the rth longest and shortest cycle and finally the length of a random chosen cycle. These are analyzed for equiprobable permutations as well as for biased ones. Analytical solutions and limit distributions are also considered to put the results on a safe, theoretical base.