К вопросу борьбы с обледенением стальных тросов

The understanding of biological processes, e.g. related to cardio-vascular disease and treatment, can significantly be improved by numerical simulation. In this paper, we present an approach for a multiscale simulation environment, applied for the prediction of in-stent re-stenos is. Our focus is on the coupling of distributed, heterogeneous hardware to take into account the different requirements of the coupled sub-systems concerning computing power. For such a concept, which is an extension of the standard multiscale computing approach, we want to apply the term Distributed Multiscale Computing

Fluid-structure interaction in blood flow capturing non-zero longitudinal structure displacement

We present a new model and a novel loosely coupled partitioned numerical scheme modeling fluid-structure interaction (FSI) in blood flow allowing non-zero longitudinal displacement. Arterial walls are modeled by a {linearly viscoelastic, cylindrical Koiter shell model capturing both radial and longitudinal displacement}. Fluid flow is modeled by the Navier-Stokes equations for an incompressible, viscous fluid. The two are fully coupled via kinematic and dynamic coupling conditions. Our numerical scheme is based on a new modified Lie operator splitting that decouples the fluid and structure sub-problems in a way that leads to a loosely coupled scheme which is {unconditionally} stable. This was achieved by a clever use of the kinematic coupling condition at the fluid and structure sub-problems, leading to an implicit coupling between the fluid and structure velocities. The proposed scheme is a modification of the recently introduced "kinematically coupled scheme" for which the newly proposed modified Lie splitting significantly increases the accuracy. The performance and accuracy of the scheme were studied on a couple of instructive examples including a comparison with a monolithic scheme. It was shown that the accuracy of our scheme was comparable to that of the monolithic scheme, while our scheme retains all the main advantages of partitioned schemes, such as modularity, simple implementation, and low computational costs

Exceptionally sweet - Studies on the bacterial arginine rhamnosyltransferase EarP

Bacterial protein glycosylation affects numerous cellular properties, including physiology and pathogenicity. The transfer of carbohydrates to a nitrogen atom is known as N glycosylation and almost exclusively occurs on asparagine side chains. In contrast, EarP represents a novel type of arginine-modifying glycosyltransferases. This enzyme uses TDP β-L-rhamnose as a donor substrate to activate the specialized translation elongation factor P (EF-P) in about 10 % of sequenced bacteria, including the clinically relevant species Pseudomonas aeruginosa and Neisseria meningitidis. The post-translational modification of EF-P is crucial for bacterial fitness and also constitutes a prerequisite for virulence. As the amido group of asparagine and the arginine guanidinium are chemically distinct, the activation of the latter might be based on a so far unsolved molecular mechanism. Consequently, the structural characterization of EarP and its products is of clinical and functional importance. In this regard, NMR analyses unambiguously identified the product of the glycosylation reaction as α-rhamnosyl-arginine. Thus, EarP inverts the anomeric configuration of rhamnose during the reaction. Anomer-specific mono-rhamnosyl-arginine-containing peptides were synthetized and used to raise antibodies against the modified side chain. These immunoglobulins were characterized with respect to their sensitivity and specificity towards the target epitope and used to determine enzyme kinetics of EarP. X-ray crystallography identified EarP as a member of the inverting GT-B superfamily and revealed the site for donor binding. Bioinformatic and mutant analyses elucidated the functional significance of several amino acids in orienting the nucleotide sugar and demonstrated the importance of two highly conserved aspartates for catalysis. Additionally, NMR titration experiments revealed that EarP mainly binds the N-terminal β barrel domain of its acceptor substrate EF-P. This information was utilized to generate the first synthetic target for EarP-mediated protein modification. The structurally but not sequentially related EF-P homologue from E. coli is naturally activated by lysylation of a lysine side chain. Successive mutation not only allowed modification but also activation of E. coli EF-P by the non-cognate and EarP-mediated rhamnosylation. This thesis provides new insights into the structure-function relationship of inverting arginine glycosylation. Additionally, it lays the groundwork for the application of EarP in synthetic biology and clinical research.Die Glykosylierung bakterieller Proteine beeinflusst zahlreiche zelluläre Eigenschaften wie Physiologie und Pathogenität. Die Übertragung von Kohlenhydraten auf ein Stickstoffatom wird als N-Glykosylierung bezeichnet und erfolgt fast ausschließlich an Asparagin-Seitenketten. Im Gegensatz dazu gehört EarP zu einer neuen Klasse von Arginin-modifizierenden Glykosyltransferasen. In etwa 10 % der sequenzierten Bakterien, einschließlich der klinisch relevanten Spezies Pseudomonas aeruginosa und Neisseria meningitidis, verwendet dieses Enzym TDP-β-L-rhamnose als Donorsubstrat zur Aktivierung des spezialisierten Translationselongationsfaktors P (EF-P). Die post-translationale Modifikation von EF-P ist von entscheidender Bedeutung für die bakterielle Fitness und eine Voraussetzung für Virulenz. Da die Amidogruppe von Asparagin und die Guanidinogruppe von Arginin chemisch unterschiedlich sind, erfolgt die Aktivierung der letzteren durch einen bisher unerforschten molekularen Mechanismus. Folglich ist die strukturelle Charakterisierung von EarP und seinen Katalyseprodukten sowohl von medizinischer als auch funktioneller Bedeutung. Mittels NMR wurde zunächst das Produkt der Glykosylierungsreaktion von EarP eindeutig als α-Rhamnosyl-Arginin identifiziert. Somit invertiert EarP die anomere Konfiguration von Rhamnose während der Reaktion. Anomer-spezifische mono-Rhamnosyl-Arginin enthaltende Peptide wurden synthetisiert und zur Generierung von Antikörpern verwendet. Diese Immunglobuline wurden hinsichtlich Sensitivität und Spezifität gegenüber dem Epitop charakterisiert und zur Bestimmung der Enzymkinetik von EarP verwendet. Die Kristallstrukturanalyse von EarP ermöglichte nicht nur eine Zuordnung des Enzyms zur Superfamilie der invertierenden GT-B-Glykosyltransferasen, sondern zeigte auch die Position der Donorbindestelle auf. Weitere bioinformatische und Mutagenese-basierte Studien führten zur Identifizierung von zwei für die Katalyse wichtigen Aspartaten sowie von mehreren Aminosäuren, die für die Orientierung des Nukleotidzuckers von Bedeutung sind. NMR-Titrationen ergaben, dass EarP hauptsächlich die N-terminale β-Barreldomäne des Akzeptorsubstrates EF-P bindet. Diese Information wurde verwendet, um den ersten synthetischen Akzeptor für eine EarP-vermittelte Proteinmodifikation zu generieren. Das strukturell, aber nicht sequentiell verwandte EF-P-Homolog von E. coli wird natürlicherweise durch Lysylierung einer Lysin-Seitenkette aktiviert. Infolge sukzessiver Aminsoäureaustausche wurde nicht nur die Modifikation von E. coli EF-P durch eine EarP vermittelte Rhamnosylierung erreicht, sondern auch die Aktivierung dieses Elongationsfaktors. Diese Arbeit liefert somit neue Erkenntnisse über die Struktur-Funktionsbeziehung der invertierenden Arginin-Glykosylierung. Darüber hinaus legt sie den Grundstein für die Anwendung von EarP in der Synthetischen Biologie und der klinischen Forschung

Steady State Convergence Acceleration of the Generalized Lattice Boltzmann Equation with Forcing Term through Preconditioning

Several applications exist in which lattice Boltzmann methods (LBM) are used to compute stationary states of fluid motions, particularly those driven or modulated by external forces. Standard LBM, being explicit time-marching in nature, requires a long time to attain steady state convergence, particularly at low Mach numbers due to the disparity in characteristic speeds of propagation of different quantities. In this paper, we present a preconditioned generalized lattice Boltzmann equation (GLBE) with forcing term to accelerate steady state convergence to flows driven by external forces. The use of multiple relaxation times in the GLBE allows enhancement of the numerical stability. Particular focus is given in preconditioning external forces, which can be spatially and temporally dependent. In particular, correct forms of moment-projections of source/forcing terms are derived such that they recover preconditioned Navier-Stokes equations with non-uniform external forces. As an illustration, we solve an extended system with a preconditioned lattice kinetic equation for magnetic induction field at low magnetic Prandtl numbers, which imposes Lorentz forces on the flow of conducting fluids. Computational studies, particularly in three-dimensions, for canonical problems show that the number of time steps needed to reach steady state is reduced by orders of magnitude with preconditioning. In addition, the preconditioning approach resulted in significantly improved stability characteristics when compared with the corresponding single relaxation time formulation.Comment: 47 pages, 21 figures, for publication in Journal of Computational Physic

Three-Dimensional Multi-Relaxation Time (MRT) Lattice-Boltzmann Models for Multiphase Flow

In this paper, three-dimensional (3D) multi-relaxation time (MRT) lattice-Boltzmann (LB) models for multiphase flow are presented. In contrast to the Bhatnagar-Gross-Krook (BGK) model, a widely employed kinetic model, in MRT models the rates of relaxation processes owing to collisions of particle populations may be independently adjusted. As a result, the MRT models offer a significant improvement in numerical stability of the LB method for simulating fluids with lower viscosities. We show through the Chapman-Enskog multiscale analysis that the continuum limit behavior of 3D MRT LB models corresponds to that of the macroscopic dynamical equations for multiphase flow. We extend the 3D MRT LB models developed to represent multiphase flow with reduced compressibility effects. The multiphase models are evaluated by verifying the Laplace-Young relation for static drops and the frequency of oscillations of drops. The results show satisfactory agreement with available data and significant gains in numerical stability.Comment: Accepted for publication in the Journal of Computational Physic

A Parallel Coupled Lattice Boltzmann-Volume of Fluid Framework for Modeling Porous Media Evolution

In this paper, we present a framework for the modeling and simulation of a subset of physical/chemical processes occurring on different spatial and temporal scales in porous materials. In order to improve our understanding of such processes on multiple spatio-temporal scales, small-scale simulations of transport and reaction are of vital importance. Due to the geometric complexity of the pore space and the need to consider a representative elementary volume, such simulations require substantial numerical resolutions, leading to potentially huge computation times. An efficient parallelization of such numerical methods is thus vital to obtain results in acceptable wall-clock time. The goal of this paper was to improve available approaches based on lattice Boltzmann methods (LBMs) to reliably and accurately predict the combined effects of mass transport and reaction in porous media. To this end, we relied on the factorized central moment LBM as a second-order accurate approach for modeling transport. In order to include morphological changes due to the dissolution of the solid phase, the volume of fluid method with the piece-wise linear interface construction algorithm was employed. These developments are being integrated into the LBM research code VirtualFluids. After the validation of the analytic test cases, we present an application of diffusion-controlled dissolution for a pore space obtained from computer tomography (CT) scans