An integrative computational model for intestinal tissue renewal

Objectives\ud \ud The luminal surface of the gut is lined with a monolayer of epithelial cells that acts as a nutrient absorptive engine and protective barrier. To maintain its integrity and functionality, the epithelium is renewed every few days. Theoretical models are powerful tools that can be used to test hypotheses concerning the regulation of this renewal process, to investigate how its dysfunction can lead to loss of homeostasis and neoplasia, and to identify potential therapeutic interventions. Here we propose a new multiscale model for crypt dynamics that links phenomena occurring at the subcellular, cellular and tissue levels of organisation.\ud \ud Methods\ud \ud At the subcellular level, deterministic models characterise molecular networks, such as cell-cycle control and Wnt signalling. The output of these models determines the behaviour of each epithelial cell in response to intra-, inter- and extracellular cues. The modular nature of the model enables us to easily modify individual assumptions and analyse their effects on the system as a whole.\ud \ud Results\ud \ud We perform virtual microdissection and labelling-index experiments, evaluate the impact of various model extensions, obtain new insight into clonal expansion in the crypt, and compare our predictions with recent mitochondrial DNA mutation data. \ud \ud Conclusions\ud \ud We demonstrate that relaxing the assumption that stem-cell positions are fixed enables clonal expansion and niche succession to occur. We also predict that the presence of extracellular factors near the base of the crypt alone suffices to explain the observed spatial variation in nuclear beta-catenin levels along the crypt axis

Theoretical Studies of Structural and Electronic Properties of Donor-Acceptor Polymers

The development of new electronic devices requires the design of novel materials since the existing technologies are not suitable for all applications. In recent years, semiconducting polymers (SCPs) have evolved as fundamental components for the next generation of costumer electronics. They provide interesting features, especially flexibility, light weight, optical transparency and low-cost processability from solution. The research presented in this thesis was devoted to theoretical studies of donor-acceptor (DA) copolymers formed by electron-deficient 3,6-(dithiophene-2-yl)-diketopyrrolo[3,4-c]pyrrole (TDPP) and different electron-rich thiophene compounds. This novel type of SCPs has received a lot of attention due to experimental reports on very good electronic properties which yielded record values for organic field-effect transistor applications. In order to get a deeper understanding of the structural and electronic properties, the main objective of this work was to study this material type on the atomic scale by means of electronic structure methods. For this, density functional theory (DFT) methods were used as they are efficient tools to consider the complex molecular structure. This work comprises three main parts: a comparative study of the structural and the electronic properties of TDPP based DA polymers obtained by means of different theory levels, the calculation of the intermolecular charge transfer between pi-pi stacked DA polymer chains based on the Marcus transfer theory and investigations of molecular p-doping of TDPP based DA polymers. For the first, DFT using different functionals was compared to the density functional based tight binding (DFTB) method, which is computationally very efficient. Although differences in structural properties were observed, the DFTB method was found to be the best choice to study DA polymers in the crystalline phase. For the second, correlations between the molecular structure and the reorganization energy are found. Moreover, the dependency of the electronic coupling element on the spatial shape of the frontier orbitals is shown. Furthermore, a Boltzmann-type statistical approach is introduced in order to enable a qualitative comparison of different isomers and chemical structures. For the last part, the p-doping properties of small, multi-polar dopant molecules with local dipole provided by cyano groups were investigated theoretically and compared with experimental observations. The one with the strongest p-doping properties was studied in this work for the first time on a theoretical basis. Comparing these different p-dopants, rich evidence was found supporting the experimentally observed doping strength

Structural Dynamics and Allosteric Signaling in Ionotropic Glutamate Receptors

Ionotropic glutamate receptors (iGluRs) are ligand-gated ion channels that mediate excitatory neurotransmission events in the central nervous system. All distinct classes of iGluRs (AMPA, NMDA, Kainate) are composed of an N-terminal domain (NTD) and a ligand-binding domain (LBD) in their extracellular domain, a transmembrane domain (TMD) and an intracellular carboxy-terminal domain (CTD). Ligand binding to the LBD facilitates ion channel activation. The NTDs modulate channel gating allosterically in NMDA receptors (NMDARs). A similar function of the NTD in AMPA receptors (AMPARs) is still a matter of debate. Taking advantage of recently resolved structures of the NTD and the intact AMPAR, the main focus of this dissertation is a comprehensive examination of iGluR NTD structural dynamics, ligand binding and allosteric potential of AMPARs. We use a multiscale, multi-dimensional approach using coarse-grained network models and all-atom simulations for structural analyses and information theoretic approaches for examination of evolutionary correlations. Our major contribution has been the characterization of the global motions favored by iGluR NTD architecture. These intrinsic motions favor ligand binding in NMDAR NTDs and are also shared by other iGluR NTDs. We also identified structural determinants of flexibility in AMPARs and confirmed their role through in silico mutants. The overall similarity in collective dynamics among iGluRs hints at a putative allosteric capacity of non-NMDARs and has propelled the elucidation of interdomain and intersubunit coupling in the intact AMPAR. To this end, we identified “effector” and “sensor” regions in AMPARs using a perturbation-response technique. We identified potentially functional residues that enable information propagation between effector regions and proposed an efficient mechanism of allosteric communication based on a combination of tools including network models, graph theoretical methods and sequence analyses. Finally, we assessed the “druggability” of iGluR NTDs using molecular dynamics simulations in the presence of probe molecules containing fragments shared by drug-like molecules. Based on our study, we offer key insights into the ligand-binding landscape of iGluR NTD monomers and dimers, and we also identify a novel ligand-binding site in AMPAR dimers. These findings open an avenue of searching for molecules able to bind to iGluR NTDs and allosterically modulate receptor activity

Quasi-Brittle Self-Healing Materials: Numerical Modelling and Applications in Civil Engineering.

Ph.DDOCTOR OF PHILOSOPH