Operations research: from computational biology to sensor network

In this dissertation we discuss the deployment of combinatorial optimization methods for modeling and solve real life problemS, with a particular emphasis to two biological problems arising from a common scenario: the reconstruction of the three-dimensional shape of a biological molecule from Nuclear Magnetic Resonance (NMR) data. The fi rst topic is the 3D assignment pathway problem (APP) for a RNA molecule. We prove that APP is NP-hard, and show a formulation of it based on edge-colored graphs. Taking into account that interactions between consecutive nuclei in the NMR spectrum are diff erent according to the type of residue along the RNA chain, each color in the graph represents a type of interaction. Thus, we can represent the sequence of interactions as the problem of fi nding a longest (hamiltonian) path whose edges follow a given order of colors (i.e., the orderly colored longest path). We introduce three alternative IP formulations of APP obtained with a max flow problem on a directed graph with packing constraints over the partitions, which have been compared among themselves. Since the last two models work on cyclic graphs, for them we proposed an algorithm based on the solution of their relaxation combined with the separation of cycle inequalities in a Branch & Cut scheme. The second topic is the discretizable distance geometry problem (DDGP), which is a formulation on discrete search space of the well-known distance geometry problem (DGP). The DGP consists in seeking the embedding in the space of a undirected graph, given a set of Euclidean distances between certain pairs of vertices. DGP has two important applications: (i) fi nding the three dimensional conformation of a molecule from a subset of interatomic distances, called Molecular Distance Geometry Problem, and (ii) the Sensor Network Localization Problem. We describe a Branch & Prune (BP) algorithm tailored for this problem, and two versions of it solving the DDGP both in protein modeling and in sensor networks localization frameworks. BP is an exact and exhaustive combinatorial algorithm that examines all the valid embeddings of a given weighted graph G=(V,E,d), under the hypothesis of existence of a given order on V. By comparing the two version of BP to well-known algorithms we are able to prove the e fficiency of BP in both contexts, provided that the order imposed on V is maintained

Modelling Precipitation of Carbides in Martensitic Steels

The purpose of this work was to model carbide precipitation in steels of a quaternary system which includes two substitutional elements. The work focuses on secondary hardening steels which are used for high-strength components, where hydrogen embrittlement is one of the major factors responsible for failure. It is believed that carbide particles can act as hydrogen trapping sites, thus reducing the risk of embrittlement. The thesis begins with a review of the physical metallurgy of secondary hardening steels and the phenomena of hydrogen embrittlement and hydrogen trapping. The basic theory for the precipitation processes, including the nucleation and diffusion-controlled growth of particles, is reviewed in Chapter 2. Significant progress has recently been made in modelling the overall kinetics of transformations which occur simultaneously. The new theory, also reviewed, adopts classical nucleation and diffusion-controlled growth concepts and takes into account the capillarity effect. In the present work, a modified model has been developed for the precipitation of needle-shaped carbides, and a new model for plate-shaped carbides. The models are then verified experimentally, using five steels designed specifically for this purpose. Using the chemical compositions of the steels and thermodynamic data, the carbide precipitation, dissolution and coarsening kinetics at 600 μC were estimated. It is found that reasonable agreement can be obtained between experiment and theory for ternary steels, when multicomponent diffusion and capillarity effects are taken into account. This applies to both needle and plate-shaped particles. The same approach was then used successfully for quaternary steels. For the specific steels studied, M2C- and M4C3-type carbides are expected to be hydrogen trapping sites which improve the hydrogen embrittlement properties. Experimental results on the hydrogen trapping capacity of the steels confirm this expectation and the relationships between the hydrogen trapping capacity and the features of M4C3 carbide particles are discussed. Finally, conclusions are drawn and suggestions are made for future work

Mechanisms of delivery and mode of action of type VI secretion system effectors

In order to manipulate their environment, bacteria evolved a diverse set of secretion systems. Three of these were found to be able to inject their substrates directly into target cells, the type VI secretion system (T6SS) being the most recently discovered of these. The T6SS shares structural and functional homology with other contractile nanomachines such as the contractile phages. It is capable of delivering its substrates into both pro- and eukaryotes in a contact dependent manner and has become a major player in the field of microbial interactions. Recently, medium and high resolution structural data of T6SS subcomplexes and in situ structures provided detailed mechanistic insights into its functioning, further supported by live cell fluorescence microscopy of the assembly dynamics. Nonetheless, the role of some of the conserved core components is not yet fully understood even less so for the associated components. Moreover, despite its implication in numerous processes, the effector repertoire remains poorly characterized. In this thesis, both the effector repertoire and the functional contribution of selected T6SS components were characterized in Acinetobacter baylyi ADP1. We developed a new scarless chromosomal mutagenesis method for A. baylyi ADP1 and fluorescently labeled structural components of the T6SS using this method. Furthermore, we constructed in frame deletions of selected T6SS components and evaluated their role by observing the T6SS dynamics, secretion capacity, target cell lysis and the ability to inhibit a competitor. The results of the fluorescence microscopy in combination with the sensitive lysis assay show that certain components, previously thought to be required for T6SS assembly, are in fact dispensable. Furthermore, we observed that most mutations which diminished the T6SS activity reduced the number of active T6SS structures but did not affect the sheath dynamics. This indicates, that these components are involved in a step preceding the contractile tail formation. Despite ongoing concerted efforts, we were so far unable to fluorescently label secreted components. We identified and characterized five cargo effectors and their corresponding immunity proteins. One of the effectors was disrupted by an insertion element and could be restored. All five effectors exhibited antibacterial activity and did not cross-react with non-cognate immunity proteins. The morphological changes of prey cells targeted by the effectors were observed by fluorescence microscopy of competition mixtures and allowed us to confirm the predicted peptidoglycan amidase activity of Tae1 and the phospholipase activity of Tle1. Although the bioinformatic predictions together with the observed morphological changes and the lysis phenotype of prey cells targeted by the remaining effectors hinted at the subcellular location of their respective targets, the targets themselves remain to be identified. Furthermore, we constructed an effector deficient strain which retained wild-type T6SS activity and elicited the retaliatory attack of Pseudomonas aeruginosa, but failed to inhibit or lyse prey cells. Transcriptome data further indicated, that the damage inflicted by the effector deficient strain does not induce a stress response in the prey. Recently the T6SS was shown to be involved in the horizontal gene transfer of naturally competent Vibrio cholerae. Since A. baylyi ADP1 is known to be naturally competent, we tested whether its T6SS also contributes to horizontal gene transfer. Not only could we demonstrate that the T6SS facilitates the acquisition of DNA from prey cells, but also that lytic effectors are superior to non-lytic effectors suggesting that a lytic effector set may increase the ability to acquire DNA from a diverse range of bacteria. These findings provide further evidence that the T6SS mediated horizontal gene transfer may be a general characteristic of naturally competent bacteria bearing a T6SS. To better understand the role of the T6SS in shaping polymicrobial communities, we employed individual based modelling of interbacterial competition mixtures, the results of which we confirmed by performing the corresponding bacterial competition. We found that the contact dependent antagonistic interactions led to a segregation of the competitors minimizing their contact surface. Once segregated, the prey cells were able to survive or even outgrow the attack of a predator so long as the growth within the domain equaled or outweighed the killing on the surface of the domain. We further demonstrated that this critical domain size, beyond which the prey would survive, depends on the growth rate ratio of the competitors and the attack rate. Recently, others showed that this segregation of the competitors promotes the evolution of public goods

Structure and surface reactions of iodine and cadmium iodide on fcc(111) metal surfaces

Structural studies using the synchrotron based Normal Incidence X-Ray Standing Wave (NIXSW) technique of the copper(III)- √3x√3))R30 grad.-Iodine and copper(111)- √3x√3)R30grad.-1/2(CdI2) surfaces are presented. For the copperiodine system, the iodine was shown to adsorb in a mixture of fcc and hcp hollow sites at a distance of 2.16 ± 0.05A from the copper surface, in a (√3x√3))R30 grad. mesh. The hollow site ratio observed was 50 ± 3 % in fcc sites and 50 ± 3 % in hcp sites. For the copper-cadmium iodide system, the iodine was again shown to adsorb in a mixture of the three fold hollows, at a slightly smaller distance of 2.10 ± 0.05A from the copper surface, again in a (√3x√3)R30 grad. mesh. The ratio of occupation of the hollow sites was determined to be 37 ± 3 % in fcc sites and 63 ± 3 % in hcp sites. The copper(111)-( √3x√3)R30 grad.-Iodine surface produced by annealing the copper(111)- 1/2(CdI2) surface, was shown to have a different ratio again, at 80± 3 % in fcc sites and 20 ± 3 % in hcp sites. Possible explanations for the changing ratios are discussed including sample temperature during surface preparation, step density of the crystal, co-adsorption of adsorbate or contamination and surface coverage. The cadmium in the copper-1/2(CdI2) surface was shown to be adsorbed randomly in a mixture of the three fold hollow sites, at 2.25 ± 0.05A from the copper surface. The ratio was found to be 48 ± 3 % in fcc sites and 52 ± 3 % in hcp sites. Both studies were found to be affected by the presence of non-dipole effects in the angular distribution of the core level photoelectrons used to collect some of the data. This caused incorrect values for the standing wave structural parameters to be determined, A novel experiment was performed using two analyser geometries which enabled the importance of including the non-dipole terms in the standing wave equations to be confinned. An updated version of the standing wave equations is presented which allows quantification of and correction for the non-dipole terms. The surface reactions of iodine and cadmium iodide on an aluminium(111) surface at room temperature are shown to result in etching of the surface and the production of aluminium iodide (A1I3). For both systems, iodine forms a close-packed chemisorbed layer that has a (..J7x-..J7)R19.1° symmetry, with an iodine coverage of 3/7 of a monolayer. For the cadmium iodide surface, the cadmium is proposed as being located randomly above the chemisorbed iodine layer. With the sample liquid nitrogen cooled to low temperatures, iodine produced physisorbed multilayers, and cadmium iodide adsorbs intact, but with no ordered growth. A novel technique, Line Of Sight Sticking Probability (LOSSP), which allows the measurement of sticking and reaction probabilities is presented and applied to the I/Al system. The initial sticking probability for iodine at 300 K was determined as 0.8 ± 0.1. Under steady state etching conditions at 300 K the overall reaction probability for I2 to form AlI3, was, Rss = 0.36 ± 0.07. The surface consisted of a majority of chemisorbed iodine, with a minority of coadsorbed AlI3, with a total iodine coverage of ~ 0.6 ML. The sticking probability of I2, to solid iodine at 103 K was measured as Sphys = 0.98 ± 0.02, while the sticking probability on the halogenated surface at 300 K was measured as ~ys > 0.8 ± 0.1 Variable temperature measurements gave an activation energy for the desorption of All, of approximately 57 kJmol-1

Investigation of Relativistic Effects in Electronic Decay Processes in Small and Large Noble Gas Clusters by Ab Initio and New Simulation Approaches

The Interatomic/ Intermolecular Coulombic Decay (ICD) as well as the Electron Transfer Mediated Decay (ETMD) are electronic decay processes, which occur in a multidude of systems ranging from noble gas dimers to biological systems. If heavy atoms are involved in these processes, relativistic effects cannot be neglected. However, their influence has so far not been investigated thoroughly. In this thesis, the influence of the spin-orbit coupling as well as scalar-relativistic effects on openings and closings of decay channels as well as on the corresponding decay widths are studied. For this purpose, asymptotic expressions for the decay widths of both ICD and ETMD are derived. They allow for analytic studies of basic properties and estimations of the decay widths based on properties of the constituting atoms or molecules of the total system. A more precise description of the decay widths required the transfer of the non-relativistically known FanoADC-Stieltjes method to the relativistic regime and its implementation into the relativistic quantum chemical program package Dirac. Using this method, small noble gas systems are investigated. Experimentally, these decay processes are usually studied in noble gas clusters consisting of 100 – 2000 atoms. These clusters are too large to be treated with ab initio methods. In order to allow for a comparison of theoretical and experimental results, the influence of the cluster environment on the secondary electron spectra are investigated. These findings are used for the development of a method for the decay width estimation of clusters based on the asymptotic expressions or calculated decay widths for a multitude of geometries. This method was implemented as the program HARDRoC and is used for the investigation of the two competing processes ICD and ETMD in ArXe clusters. Additionally, it is the foundation of a new structure determination method of heteronuclear noble gas clusters, which is exemplarily explained for NeAr clusters