The Effects of Spatio-Temporal Heterogeneities on the Emergence and Spread of Dengue Virus

The dengue virus (DENV) remains a considerable global public health concern. The interactions between the virus, its mosquito vectors and the human host are complex and only partially understood. Dependencies of vector ecology on environmental attributes, such as temperature and rainfall, together with host population density, introduce strong spatiotemporal heterogeneities, resulting in irregular epidemic outbreaks and asynchronous oscillations in serotype prevalence. Human movements across different spatial scales have also been implicated as important drivers of dengue epidemiology across space and time, and further create the conditions for the geographic expansion of dengue into new habitats. Previously proposed transmission models often relied on strong, unrealistic assumptions regarding key epidemiological and ecological interactions to elucidate the effects of these spatio-temporal heterogeneities on the emergence, spread and persistence of dengue. Furthermore, the computational limitations of individual based models have hindered the development of more detailed descriptions of the influence of vector ecology, environment and human mobility on dengue epidemiology. In order to address these shortcomings, the main aim of this thesis was to rigorously quantify the effects of ecological drivers on dengue epidemiology within a robust and computational efficient framework. The individual based model presented included an explicit spatial structure, vector and human movement, spatio-temporal heterogeneity in population densities, and climate effects. The flexibility of the framework allowed robust assessment of the implications of classical modelling assumptions on the basic reproduction number, R₀, demonstrating that traditional approaches grossly inflate R₀ estimates. The model's more realistic meta-population formulation was then exploited to elucidate the effects of ecological heterogeneities on dengue incidence which showed that sufficient levels of community connectivity are required for the spread and persistence of dengue virus. By fitting the individual based model to empirical data, the influence of climate and on dengue was quantified, revealing the strong benefits that cross-sectional serological data could bring to more precisely inferring ecological drivers of arboviral epidemiology. Overall, the findings presented here demonstrate the wide epidemiological landscape which ecological drivers induce, forewarning against the strong implications of generalising interpretations from one particular setting across wider spatial contexts. These findings will prove invaluable for the assessment of vector-borne control strategies, such as mosquito elimination or vaccination deployment programs

Fluid aggregations for Markovian process algebra

Quantitative analysis by means of discrete-state stochastic processes is hindered by the well-known phenomenon of state-space explosion, whereby the size of the state space may have an exponential growth with the number of objects in the model. When the stochastic process underlies a Markovian process algebra model, this problem may be alleviated by suitable notions of behavioural equivalence that induce lumping at the underlying continuous-time Markov chain, establishing an exact relation between a potentially much smaller aggregated chain and the original one. However, in the modelling of massively distributed computer systems, even aggregated chains may be still too large for efficient numerical analysis. Recently this problem has been addressed by fluid techniques, where the Markov chain is approximated by a system of ordinary differential equations (ODEs) whose size does not depend on the number of the objects in the model. The technique has been primarily applied in the case of massively replicated sequential processes with small local state space sizes. This thesis devises two different approaches that broaden the scope of applicability of efficient fluid approximations. Fluid lumpability applies in the case where objects are composites of simple objects, and aggregates the potentially massive, naively constructed ODE system into one whose size is independent from the number of composites in the model. Similarly to quasi and near lumpability, we introduce approximate fluid lumpability that covers ODE systems which can be aggregated after a small perturbation in the parameters. The technique of spatial aggregation, instead, applies to models whose objects perform a random walk on a two-dimensional lattice. Specifically, it is shown that the underlying ODE system, whose size is proportional to the number of the regions, converges to a system of partial differential equations of constant size as the number of regions goes to infinity. This allows for an efficient analysis of large-scale mobile models in continuous space like ad hoc networks and multi-agent systems

Modelling Electrostatic Interactions and Solvation in Chromatin: from the single nucleosome towards the chromatin fibre

Chromatin is a complex of proteins and DNA found in the nuclei of eukaryotic cells. It reinforces the DNA and its topology tunes DNA transcription and gene expression. It is formed by nucleosomes, structures composed of an octameric protein core and approximately 147 base pairs of DNA. Chromatin is an extremely complex system, the behaviour of which is ruled by both mechanical and electrostatic factors that are depend on its structure, and biomolecular interactions occurring in the cell nucleus. In this thesis, I analyse chromatin compaction from an electrostatic perspective and focus on the role of electrostatics and solvation as determinants of the topology of chromatin. I examine the effect of the histone tails and propose a methodology to connect electrostatic calculations to the structural and functional features of protein-DNA systems. This methodology can also be combined with coarse-grained representations. I study the electrostatic forces acting on the phosphate atoms of the DNA backbone. I investigate the electrostatic origins of effects such as different stages in DNA unwrapping, nucleosome destabilisation upon histone tail truncation, and the role of specific arginines and lysines undergoing Post - Translational Modifications. I find that the positioning of the histone tails can oppose the attractive pull of the histone core, locally deform the DNA, and tune DNA unwrapping. I conduct an analysis of the porosity of nucleosomes and related to the importance of solvation phenomena. I complement and support my computational findings on nucleosome electrostatic interactions experimental Zeta Potential and Dynamic Light Scattering measurements on single nucleosomes under varying ionic concentrations, providing information on the surface charge and the size of nucleosomes. I present a comprehensive study of the electrostatic interactions between nucleosome pairs sampling different translations and rotations. My analysis aims to provide a cohesive description of nucleosome electrostatic interactions in the chromatin fibre, combining information on the energetics of different relative positions of nucleosomes, especially in very tight packing situations. In addition to numerical estimates of electrostatic interaction energy of nucleosomes at different relative distances and orientations, obtained within the Poisson-Boltzmann framework, I present their approximation by analytical asymptotic expressions, where nucleosomes are approximated as monopoles and dipoles centred in dielectric spheres immersed in an electrolytic solution. I am able to identify a non-linearity region around the nucleosomes, and to exploit the fact that that in points outside that region the electrostatic potential can be described by the linearised Poisson-Boltzmann Equation

Structural Studies of Biomolecular Systems with Molecular Dynamics Simulations

In vorliegender Arbeit wurden computerbasierte Simulationen eingesetzt, um verschiedene strukturelle Eigenschaften und Dynamiken von Biomolekülen aufzuklären. Die bearbeiteten Themen resultieren aus Kooperationen innerhalb des Graduiertenkolleges 2039 Molekulare Architekturen für die fluoreszente Bildgebung von Zellen. Dabei wurden sowohl klassische Molekulardynamik (MD)-Simulationen verwendet als auch Simulationen mit Verwendung sogenannter coarse-grained-Ansätze, bei denen mehrere Atome zu größeren Einheiten zusammengefasst werden. Aus dem Gebiet der Peptid-Membran-Wechselwirkungen wurden in Zusammenarbeit mit dem Arbeitskreis Ulrich (KIT) zwei hydrophobe Peptide aus Typ I Toxin-Antitoxin-Systemen bearbeitet. Im Mittelpunkt von Kapitel 3 steht das stress-induzierte Peptid tisB (29 Aminosäuren) aus E. coli, welches die Formation von Biofilmen bewirkt und den elektrochemischen Gradienten an der Bakterienzellmembran stilllegen kann. Es wurden Studien der Assemblierung des Peptides tisB als paralleles Dimer und Tetramer in der Lipidmembran durchgeführt. Die anschließenden langen Simulationen ausgewählter Strukturen wurden mit experimentell gefundenen Ergebnissen verglichen, wobei das Hervortreten des charge zipper-Motivs als Interaktionsmotiv bestätigt werden konnte. Für das Dimer und das Tetramer konnten erstmals Strukturen für einen möglichen Protonentransfer über die Membran aufgespürt werden. Das Tetramer zeichnet sich durch seinen Aufbau aus zwei antiparallelen tisB-Dimeren aus, welches einen ständigen Wasserfaden über das entstandene polare Interface erlaubt, und erscheint als sehr vielversprechende Ausgangsstruktur für mögliche Protonentransferstudien. In Kapitel 4 sind erste strukturelle Studien zum Peptid bsrG (38 Aminosäuren) aus B. subtilis dargestellt. Es konnte gezeigt werden, dass bsrG als Monomer nicht in Lipidmembranen integriert, aber an die Oberfläche assoziiert ist. Die polaren Aminosäuren sind dabei zum Wasser hin ausgerichtet. Mittels Assemblierungsstudien des Peptides als Dimer in der Lipidmembran konnten stabile parallele und antiparallele Strukturen eluiert werden, die mit experimentellen Ergebnissen übereinstimmen und das Bindungsmotiv des hydrogen bond zipper zeigen. In Zusammenarbeit mit den Arbeitskreisen Wagenknecht, Nienhaus und Schepers (alle KIT) wurden MD-Simulationen zur Aufklärung des unterschiedlichen Verhaltens zweier Doppelstrang-RNA-Konstrukte mit FRET-Farbstoffen (arabino- und ribo-Konfiguration) bei der Effizienz des FRET-Transfers eingesetzt (Kapitel 5). MD-Simulationen konnten aufzeigen, dass dieser Unterschied in der Effizienz auf Grundlage der erhöhten Mobilität der arabino-konfigurierten Farbstoffe zu erklären ist, im Gegensatz zu den sehr stark wechselwirkenden und unbeweglichen ribo-konfigurierten Farbstoffen. Jene Mobilität ermöglicht einen effizienten Energietransfer zwischen den Farbstoffen, der zu FRET führt

Application and Development of Charge Transfer Simulations in Biological and Organic Systems

Diese Arbeit zeigt eine theoretische Untersuchung von lichtinduzierten Ladungstransferprozessen in der Proteinfamilie der Photolyasen/Cryptochrome, als prominentes Beispiel. Während Photolyasen lichtinduzierte DNA-Schäden reparieren, sind Cryptochrome Signalmoleküle, welche die Lichtreaktion vermitteln. Beide haben eine homologe Proteinstruktur und einen Flavin-Adenin-Dinukleotid Kofaktor, der ihre biologischen Funktionen durch Ladungstransferprozesse ermöglicht. Diese weisen einen signifikanten nicht-gleichgewichts Charakter auf, welcher es für die etablierten Ladungstransfertheorien schwierig macht die richtige Kinetik vorherzusagen. Daher wird in diese Arbeit eine hybride Multi-Skalen Simulationsmethode verwendet, die klassische und Quantendynamikansätze kombiniert und nicht auf der Annahme von Gleichgewichtsprozessen basiert ist. Dieses Multi-Skalen Methode wurde angewendet, gebenchmarkt und weiterentwickelt, um die Genauigkeit der Quantenbeschreibung zu untersuchen und zu erhöhen. Dies erhöhte auch die Übertragbarkeit auf Studien zum Ladungstransfer in anderen molekularen Systemen. Darüber hinaus bietet diese Methode eine praktikable Alternative zu teuren zeitaufgelösten Spektroskopie-Verfahren, hinsichtlich der Charakterisierung von Ladungstranferprozessen in den Photolyasen und Cryptochromen. In experimentellen Studien mit PhrB, einer Photolyase von A. tumefaciens, war es nicht möglich, die Kinetik der Ladungstranferprozesse aufzulösen. Daher wurde in dieser Arbeit die Multi-Skalen Methode verwendet, um den Ladungstransfer in PhrB zu charakterisieren. Insbesondere das Vorhandensein von einem Tyrosin, anstelle von Tryptophan, im Ladungstransfer Pfad wurde untersucht. Daher wurden Molekulardynamik-Simulationen von Mutanten genutzt um eine Struktur-Funktionsbeziehung zu erstellen und ein getunnelter Ladungstransfer wurde vorgeschlagen, der die erste Aminosäure des Pfades involviert. Weitere Simulationen zeigten, dass das angrenzende Wasser einen Transfer entlang des energetisch ungünstigen Tyrosins ermöglicht, während ein Tryptophan den Rücktransfer erleichtert. PhrA, eine weitere Photolyase von A. tumefaciens, wurde untersucht, um die Ladungstranferprozesse entlang alternativer Pfade aufzuklären. Es wurden unterschiedliche Verhaltensweisen der Kinetik des Ladungstransfers beobachtet. Ein Pfad bietet einen schnellen Transfer, während der Andere eine bessere Stabilisierung der Ladung ermöglicht. Der Ladungstransfer in Photolyasen und Cryptochromen löst weitere Prozesse aus, wie zum Beispiel einen Protonentransfer zum Kofaktor oder strukturelle Umlagerungen des Reaktionszentrums. In der E. coli Photolyase kann der Kofaktor protoniert werden, jedoch ist der Protonendonator und der Mechanismus unklar. Darüber hinaus zeigten experimentelle Mutationsstudien, dass die Einbringung eines Protonendonators in die Tasche des Kofaktors die Protonierung verhindert. Daher wurden klassische und Quantendynamik Simulationen durchgeführt und ein Protonentransfermechanismus bestimmt. Simulationen einer Mutante zeigten, dass die Flexibilität und die Coulomb-Wechselwirkungen der Tasche nicht durch den Austausch von einer oder zwei Aminosäuren verändert werden kann. Somit kann eine Protonentransferfähigkeit nicht eingeführt werden, auch wenn die Mutanten scheinbar die entscheidenden strukturellen Muster aufweisen

Parallel algorithm for large scale electronic structure calculations

SIGLEAvailable from British Library Document Supply Centre- DSC:DX84152 / BLDSC - British Library Document Supply CentreGBUnited Kingdo

IST Austria Thesis

Bacteria and their pathogens – phages – are the most abundant living entities on Earth. Throughout their coevolution, bacteria have evolved multiple immune systems to overcome the ubiquitous threat from the phages. Although the molecu- lar details of these immune systems’ functions are relatively well understood, their epidemiological consequences for the phage-bacterial communities have been largely neglected. In this thesis we employed both experimental and theoretical methods to explore whether herd and social immunity may arise in bacterial popu- lations. Using our experimental system consisting of Escherichia coli strains with a CRISPR based immunity to the T7 phage we show that herd immunity arises in phage-bacterial communities and that it is accentuated when the populations are spatially structured. By fitting a mathematical model, we inferred expressions for the herd immunity threshold and the velocity of spread of a phage epidemic in partially resistant bacterial populations, which both depend on the bacterial growth rate, phage burst size and phage latent period. We also investigated the poten- tial for social immunity in Streptococcus thermophilus and its phage 2972 using a bioinformatic analysis of potentially coding short open reading frames with a signalling signature, encoded within the CRISPR associated genes. Subsequently, we tested one identified potentially signalling peptide and found that its addition to a phage-challenged culture increases probability of survival of bacteria two fold, although the results were only marginally significant. Together, these results demonstrate that the ubiquitous arms races between bacteria and phages have further consequences at the level of the population

Topological interactions in ring polymers

Ring polymers offer a richness of behaviours that are of broad interest and have deep consequences in many fields of Science. In this Thesis I investigate some general and universal properties, i.e. independent of the chemical nature of the polymers, emerging from systems made of a collection of rings. These will be studied by using methods of equilibrium and non-equilibrium Statistical Mechanics together with Molecular Dynamics and Monte Carlo simulations of coarse-grained models for the systems under investigation. Within these frameworks, important questions regarding the macroscopic behaviour of ring-shaped polymers have yet to find a satisfactory answer. The work presented in this Thesis finds its principal motivations in problems arising in Material Science, the so called \melt" of rings, and in Biology, such as the organisation of mitochondrial DNA in some organisms and the mechanisms governing the electrophoretic separation of DNA samples in gels. There are several theoretical challenges in these fields which represent state-of-the-art scientific research and whose partial answers are provided in the work presented in this Thesis. One of the major achievements of the work presented is the general understanding of the role played by topological properties, i.e. those invariant under smooth deformations of the polymer contour, on the macroscopic behaviour of the investigated systems. Finally, the conclusions drawn from the presented work can have important scientific consequences as they may ultimately lead to a more complete understanding of complicated issues in Biology and to the design of next-generation soft materials

Avian cryptochrome 4 binds superoxide

This is the final version. Available on open access from Elsevier via the DOI in this recordData availability: The data that support the findings of this study are available from the authors upon reasonable request.Flavin-binding cryptochromes are blue-light sensitive photoreceptors that have been implicated with magnetoreception in some species. The photocycle involves an intra-protein photo-reduction of the flavin cofactor, generating a magnetosensitive radical pair, and its subsequent re-oxidation. Superoxide (O2•−) is generated in the re-oxidation with molecular oxygen. The resulting O2•−-containing radical pairs have also been hypothesised to underpin various magnetosensitive traits, but due to fast spin relaxation when tumbling in solution would require immobilisation. We here describe our insights in the binding of superoxide to cryptochrome 4 from C. livia based on extensive all-atom molecular dynamics studies and density-functional theory calculations. The positively charged “crypt” region that leads to the flavin binding pocket transiently binds O2•− at 5 flexible binding sites centred on arginine residues. Typical binding times amounted to tens of nanoseconds, but exceptional binding events extended to several hundreds of nanoseconds and slowed the rotational diffusion, thereby realising rotational correlation times as large as 1 ns. The binding sites are particularly efficient in scavenging superoxide escaping from a putative generation site close to the flavin-cofactor, possibly implying a functional relevance. We discuss our findings in view of a potential magnetosensitivity of biological flavin semiquinone/superoxide radical pairs.UK Defence Science and Technology LaboratoryLeverhulme TrustEngineering and Physical Sciences Research Council (EPSRC