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- energy minimization (2)
- 3d imaging (1)
- Asymptotic homogenization (1)
- Berechnungskomplexität (1)
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- Electrophysiology (1)
- Eulerian-Lagrangian formulation (1)
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- On Abstract Shapes of RNA (2008)
- As any RNA sequence can be folded in many different ways, there are lots of different possible secondary structures for a given sequence. Most computational prediction methods based on free energy minimization compute a number of suboptimal foldings and we have to identify the native structures among all these possible secondary structures. For this reason, much effort has been made to develop approaches for identifying good predictions of RNA secondary structure. Using the abstract shapes approach as introduced by Giegerich et al., each class of similar secondary structures is represented by one shape and the native structures can be found among the top shape representatives. In this article, we derive some interesting results answering enumeration problems for abstract shapes and secondary structures of RNA. We start by computing symptotical representations for the number of shape representations of length n. Our main goal is to find out how much the search space can be reduced by using the concept of abstract shapes. To reach this goal, we analyze the number of secondary structures and shapes compatible with an RNA sequence of length n under the assumption that base pairing is allowed between arbitrary pairs of bases analytically and compare their exponential growths. Additionally, we analyze the number of secondary structures compatible with an RNA sequence of length n under the assumptions that base pairing is allowed only between certain pairs of bases and that the structures meet some appropriate conditions. The exponential growth factors of the resulting asymptotics are compared to the corresponding experimentally obtained value as given by Giegerich et al.

- On the Expected Free Energy of RNA Molecules (2008)
- This article focuses on the analytical analysis of the free energy in a realistic model for RNA secondary structures. In fact, the free energy in a stochastic model derived from a database of small and large subunit ribosomal RNA (SSU and LSU rRNA) data is studied. A common thermody-namic model for computing the free energy of a given RNA secondary structure, as well as stochastic context-free grammars and generating functions are used to derive the desired results. These results include asymptotics for the expected free energy and for the corresponding variance of a random RNA secondary structure. The quality of our model is judged by comparing the derived results to the used database of SSU and LSU rRNA data. At the end of this article, it is discussed how our results could be used to help on identifying good predictions of RNA secondary structure.

- A Lattice Boltzmann Method for immiscible multiphase flow simulations using the Level Set Method (2008)
- We consider the lattice Boltzmann method for immiscible multiphase flow simulations. Classical lattice Boltzmann methods for this problem, e.g. the colour gradient method or the free energy approach, can only be applied when density and viscosity ratios are small. Moreover, they use additional fields defined on the whole domain to describe the different phases and model phase separation by special interactions at each node. In contrast, our approach simulates the flow using a single field and separates the fluid phases by a free moving interface. The scheme is based on the lattice Boltzmann method and uses the level set method to compute the evolution of the interface. To couple the fluid phases, we develop new boundary conditions which realise the macroscopic jump conditions at the interface and incorporate surface tension in the lattice Boltzmann framework. Various simulations are presented to validate the numerical scheme, e.g. two-phase channel flows, the Young-Laplace law for a bubble and viscous fingering in a Hele-Shaw cell. The results show that the method is feasible over a wide range of density and viscosity differences.

- Homogenization in elasto-plasticity (2008)
- The theory of the two-scale convergence was applied to homogenization of elasto-plastic composites with a periodic structure and exponential hardening law. The theory is based on the fact that the elastic as well as the plastic part of the stress field two-scale converges to a limit, which is factorized by parts, depending only on macroscopic characteristics, represented in terms of corresponding part of the homogenised stress tensor and only on stress concentration tensor, related to the micro-geometry and elastic or plastic micro-properties of composite components. The theory was applied to metallic matrix material with Ludwik and Hocket-Sherby hardening law and pure elastic inclusions in two numerical examples. Results were compared with results of mechanical averaging based on the self-consistent methods.

- Determination of interaction between MCT1 and CAII via a mathematical and physiological approach (2008)
- The enzyme carbonic anhydrase isoform II (CAII), catalysing the hydration and dehydration of CO2, enhances transport activity of the monocarboxylate transporter isoform I (MCT1, SLC16A1) expressed in Xenopus oocytes by a mechanism that does not require CAII catalytic activity (Becker et al. (2005) J. Biol. Chem., 280). In the present study, we have investigated the mechanism of the CAII induced increase in transport activity by using electrophysiological techniques and a mathematical model of the MCT1 transport cycle. The model consists of six states arranged in cyclic fashion and features an ordered, mirror-symmetric, binding mechanism were binding and unbinding of the proton to the transport protein is considered to be the rate limiting step under physiological conditions. An explicit rate expression for the substrate °ux is derived using model reduction techniques. By treating the pools of intra- and extracellular MCT1 substrates as dynamic states, the time dependent kinetics are obtained by integration using the derived expression for the substrate °ux. The simulations were compared with experimental data obtained from MCT1-expressing oocytes injected with di®erent amounts of CAII. The model suggests that CAII increases the e®ective rate constants of the proton reactions, possibly by working as a proton antenna.

- An analysis of one regularization approach for solution of pure Neumann problem (2008)
- In this paper, the analysis of one approach for the regularization of pure Neumann problems for second order elliptical equations, e.g., Poisson’s equation and linear elasticity equations, is presented. The main topic under consideration is the behavior of the condition number of the regularized problem. A general framework for the analysis is presented. This allows to determine a form of regularization term which leads to the “natural” asymptotic of the condition number of the regularized problem with respect to mesh parameter. Some numerical results, which support theoretical analysis are presented as well. The main motivation for the presented research is to develop theoretical background for an efficient and robust implementation of the solver for pure Neumann problems for the linear elasticity equations. Such solvers usually are needed in a number of domain decomposition methods, e.g. FETI. Developed approaches are planed to be used in software, developing in ITWM, e.g. KneeMech simulation software.

- The ordered gradual covering location problem on a network (2008)
- In this paper we develop a network location model that combines the characteristics of ordered median and gradual cover models resulting in the Ordered Gradual Covering Location Problem (OGCLP). The Gradual Cover Location Problem (GCLP) was specifically designed to extend the basic cover objective to capture sensitivity with respect to absolute travel distance. Ordered Median Location problems are a generalization of most of the classical locations problems like p-median or p-center problems. They can be modeled by using so-called ordered median functions. These functions multiply a weight to the cost of fulfilling the demand of a customer which depends on the position of that cost relative to the costs of fulfilling the demand of the other customers. We derive Finite Dominating Sets (FDS) for the one facility case of the OGCLP. Moreover, we present efficient algorithms for determining the FDS and also discuss the conditional case where a certain number of facilities are already assumed to exist and one new facility is to be added. For the multi-facility case we are able to identify a finite set of potential facility locations a priori, which essentially converts the network location model into its discrete counterpart. For the multi-facility discrete OGCLP we discuss several Integer Programming formulations and give computational results.

- Multi-period public transport design: A novel model and solution approaches (2008)
- In this paper, we are going to propose the first mathematical model for Multi- Period Hub Location Problems (MPHLP). We apply this mixed integer program- ming model on public transport planning and call it Multi-Period Hub Location Problem for Public Transport (MPHLPPT). In fact, HLPPT model proposed earlier by the authors is extended to include more facts and features of the real-life application. In order to solve instances of this problem where existing standard solvers fail, a solution approach based on a greedy neighborhood search is developed. The computational results substantiate the efficiency of our solution approach to solve instances of MPHLPPT.

- Network design decisions in supply chain planning (2008)
- Structuring global supply chain networks is a complex decision-making process. The typical inputs to such a process consist of a set of customer zones to serve, a set of products to be manufactured and distributed, demand projections for the different customer zones, and information about future conditions, costs (e.g. for production and transportation) and resources (e.g. capacities, available raw materials). Given the above inputs, companies have to decide where to locate new service facilities (e.g. plants, warehouses), how to allocate procurement and production activities to the variousmanufacturing facilities, and how to manage the transportation of products through the supply chain network in order to satisfy customer demands. We propose a mathematical modelling framework capturing many practical aspects of network design problems simultaneously. For problems of reasonable size we report on computational experience with standard mathematical programming software. The discussion is extended with other decisions required by many real-life applications in strategic supply chain planning. In particular, the multi-period nature of some decisions is addressed by a more comprehensivemodel, which is solved by a specially tailored heuristic approach. The numerical results suggest that the solution procedure can identify high quality solutions within reasonable computational time.

- Anisotropy analysis of pressed point processes (2008)
- This paper introduces methods for the detection of anisotropies which are caused by compression of regular three-dimensional point patterns. Isotropy tests based on directional summary statistics and estimators for the compression factor are developed. These allow not only for the detection of anisotropies but also for the estimation of their strength. Using simulated data the power of the methods and the dependence of the power on the intensity, the degree of regularity, and the compression strength are studied. The motivation of this paper is the investigation of anisotropies in the structure of polar ice. Therefore, our methods are applied to the point patterns of centres of air pores extracted from tomographic images of ice cores. This way the presence of anisotropies in the ice caused by the compression of the ice sheet as well as an increase of their strength with increasing depth are shown.