Applied Mathematics and Numerical Analysis Seminar  RSS

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09/10/2014, 14:30 — 15:30 — Room P3.10, Mathematics Building
Sílvia Barbeiro, CMUC, Department of Mathematics, University of Coimbra

Modeling electromagnetic wave’s propagation in human eye’s structure

In this talk we will discuss the a mathematical model that describes the electromagnetic wave’s propagation through the eye’s structures in order to create a virtual OCT scan. Our model is based on time-dependent Maxwell’s equations. We use the discontinuous Galerkin method for the integration in space and a low-storage Runge-Kutta method for the integration in time. In the model we consider anisotropic permittivity tensors which arise naturally in our application of interest. We illustrate the performance of the method with some numerical experiments.

09/09/2014, 11:30 — 12:30 — Room P3.10, Mathematics Building
Maria Specovius-Neugebauer, University of Kassel, Germany

The time periodic Stokes system in a layer: asymptotic behavior at infinity

While there are numerous papers on the time decay of solutions to the Stokes and Navier-Stokes initial boundary value in various types of domains only few results are devoted to the spatial decay. In this talk we consider the solutions to the time periodic Stokes problem in a layer where the data are also time periodic and smooth with bounded support for simplicity. The results were obtained in a joint work with Konstantin Pileckas,Vilnius.

23/07/2014, 11:00 — 13:00 — Room P3.10, Mathematics Building
Willi Jäger, Maria Neuss-Radu, University of Heidelberg, University of Erlangen-Nuremberg (resp.)

Interactions of the fluid and solid phases in complex media — coupling reactive flows, transport and mechanics, and applications to medical processes.

Modelling reactive flows, diffusion, transport and mechanical interactions in media consisting of multiple phases, e.g. of a fluid and a solid phase in a porous medium, is giving rise to many open problems for (multi-scale) analysis and simulation. In this lecture, the following processes are studied:

  • diffusion, transport, and reaction of substances in the fluid and the solid phases,
  • mechanical interactions of the fluid and solid phases,
  • change of the mechanical properties of the solid phase by chemical reactions,
  • volume changes (“growth”) of the solid phase.

These processes occur for instance in soil and in porous materials, but also in biological membranes, tissues and in bones. The model equations consist of systems of nonlinear partial differential equations, with initial-boundary conditions and transmission conditions on fixed or free boundaries, mainly in complex domains. The coupling of processes on different scales is posing challenges to the mathematical analysis as well as to computing. In order to reduce the complexity, effective macroscopic equations have to be derived, including the relevant information from the micro-scale.

In case of processes in tissues, a homogenization limit leads to an effective, mechanical system, containing a pressure gradient, which satisfies a generalized, time-dependent Darcy law, a Biot-law, where the chemical substances satisfy diffusion-transport-reaction equations and are influencing the mechanical parameters.

The interaction of the fluid and the material transported in a vessel with its flexible wall, incorporating material and changing its structure and mechanical behavior, is a process important e.g. in the vascular system (plaque-formation) or in porous media. 

The modeling and analytic aspects addressed in our talk are also highly relevant for the study of inflammatory processes. 

The lecture is based on recent results obtained in cooperation with A. Mikelic, F. Weller and Y. Yang. 

05/06/2014, 16:00 — 17:00 — Room P3.10, Mathematics Building
, Department of Mathematics, Kansas State University

Wave scattering by many small particles and creating materials with desired refraction coefficients

Many-body wave scattering problems are solved asymptotically, as the size \(a\) of the particles tends to zero and the number of the particles tends to infinity.

Acoustic, quantum-mechanical, and electromagnetic wave scattering by many small particles is studied. This theory allows one to give a recipe for creating materials with a desired refraction coefficient.

One can create material with negative refraction, that is, the group velocity in this material is directed opposite to the phase velocity. One can create material with some desired wave-focusing properties. For example, one can create a new material which scatters plane wave mostly in a fixed given solid angle.

15/05/2014, 15:00 — 16:00 — Room P3.10, Mathematics Building
, CMUC, Universidade de Coimbra

A non-Fickian reaction diffusion equation for polymeric stent embedded in the arterial wall

In recent years, mathematical modeling of cardiovascular drug delivery systems has become an effective tool to gain deeper insights in the cardiovascular diseases like atherosclerosis.. In the case of coronary biodegradable stent which is a tiny expandable biocompatible metallic mesh tube covered by biodegradable polymer, it leads to a deeper understanding of the drug release mechanisms from polymeric stent into the arterial wall. A coupled non-Fickian model of a cardiovascular drug delivery system using a biodegradable drug eluting stent is proposed in this talk. Energy estimates are used to study the qualitative behavior of the model. The numerical results are obtained using an IMEX finite element method. The influence of arterial stiffness in the sorption of drug eluted from the stent is analyzed. The results presented in this talk open new perspectives to adapt the drug delivery profile to the needs of the patient.

27/03/2014, 15:00 — 16:00 — Room P3.10, Mathematics Building
, Institute of Applied Mathematics, Tartu University, Estonia

High-order methods for Volterra integral equations with weak singularities

We consider the numerical solution of some classes of linear Volterra integral equations with singularities. We apply to them a smoothing transformation so that the exact solution of the resulting equation does not contain any singularities in its derivatives up to a certain order. After that the regularized equation is solved by a piecewise polynomial collocation method on a mildly graded or uniform grid. Global convergence estimates are derived and some superconvergence results are given.

27/03/2014, 14:00 — 15:00 — Room P3.10, Mathematics Building
, Institut für Mathematik, University of Halle, Germany

Global error control with explicit peer methods

Step size control in the numerical solution of initial value problems y=f(t,y),y(t 0)=y 0 is usually based on the control of the local error. We present numerical tests showing that this may lead to high global errors, i.e. the real error is much larger than the prescribed tolerance. There is a tolerance proportionality, with more stringent tolerances also the global error is reduced. However, tolerance and achieved global error may differ by several magnitudes. A very simple idea to overcome this problem is to use two methods of different orders with same step size sequences and local error control for the lower order method. Then the difference of the numerical approximations of both methods is an estimate of the global error of the lower order method. This strategy was implemented for pairs of explicit peer methods in Matlab . Numerical tests show the reliability of this approach. The numerical costs are comparable with those of ode45, but in contrast to ode45 the required accuracy is achieved.

13/03/2014, 14:30 — 15:30 — Room P3.10, Mathematics Building
Elias Gudino, CMUC, Universidade de Coimbra

A 3D model for mechanistic control of drug release

A 3D mathematical model for sorption/desorption by a cylindrical polymeric matrix with dispersed drug is proposed. The model is based on a system of partial differential equations coupled with boundary conditions over a moving boundary. We assume that the penetrant diffuses into a swelling matrix and causes a deformation which induces a stress driven diffusion and consequently a non-Fickian mass flux. A physically sound non linear dependence between strain and penetrant concentration is considered and introduced in a Boltzmann integral with a kernel computed from a Maxwell-Wiechert model. Numerical simulations show how the mechanistic behavior can have a role in drug delivery design.

11/12/2013, 14:00 — 16:00 — Room V1.08, Civil Engineering Building, IST
Marco Leite, UCL Institute of Neurology and Instituto de Sistemas e Robótica, IST

Modelling populations of integrate and fire neurons: a Fokker-Planck approach to population density dynamics

Much of the phenomenology of interest in the field of neuroscience arises from the interaction of large populations of densely interconnected neurons (~\(10^5\) neurons per mm3 of mammal cortex, averaging \(10^4\) connections per neuron). Different levels of abstraction may be adopted when modelling such systems, and these need to be well suited with regards to the phenomena one is interested in studying. Here we aim at the study of the (sparse) synchronization of neurons observed during electrophysiologically recorded fast oscillatory behavior of networks of large populations. For that we use a ubiquitous simplified neuronal model - the conductance based leaky integrate and fire neuron. This model may be described by a one dimensional stochastic differential equation. Under mean field assumptions we may describe, using a linear Fokker-Planck equation, the behavior of a single population of uncoupled neurons with a PDE. The coupling of different populations will render this Fokker-Planck equation strongly non-linear. In this presentation I will also explore some details of such modelling approaches, namely: the non-natural boundary conditions generated by the neuronal firing mechanism and the numerical scheme used to deal with the brittleness from there ensued. I will also present results on the types of behavior, data, and statistics that such modelling approach is able to predict, e.g. neuronal (a)synchrony, neuronal input currents, firing rates, inter spike intervals, etc... This type of approach allows for a computationally tractable and scalable study of networks of populations of neurons. In the future we plan to implement parameter estimation algorithms to this family of models.

Since room P3.10 is occupied at this time, the seminar will take place at V1.08 (Civil Eng.)

26/11/2013, 15:00 — 16:00 — Room P3.10, Mathematics Building
, School of Pedagogical and Technological Education, Athens, Greece

Oscillations of Difference Equations of Several Deviating Arguments

Sufficient conditions are given for the oscillation of all solutions of a certain retarded linear difference equation and for its (dual) advanced difference equation.

Examples illustrating the results are also given.

See also

https://www.math.tecnico.ulisboa.pt/~plima/Chatzar.pdf

26/11/2013, 14:00 — 15:00 — Room P3.10, Mathematics Building
, University of Ioannina, Greece

Oscillations of Delay and Difference Equations

Results are presented about the oscillation of all solutions of a certain class of first order linear retarded differential equations and their discrete analogues.

See also

https://www.math.tecnico.ulisboa.pt/~plima/Stavrou.pdf

13/11/2013, 15:30 — 16:30 — Room P9, Mathematics Building
, Ulyanovsk State University, Ulyanovsk, Russia

Parameter Identification in Stochastic Dynamic Systems based on API Approach (with applications in Biology)

In this talk, we discuss the following two problems. First, we present the Auxiliary Performance Functional (API) developed by Prof. I.V. Semushin and study its role in the state and parameter estimation of linear discrete-time stochastic systems. The minimization procedure of the API with respect to parameters of the Data Model is then considered. Our approach differs from what has been done earlier in the adaptive filtering theory. We may mention that the minimization with respect to the parameters of the Adaptive Filter instead of the Data Model was considered previously. Second, we concern with robust array adaptive filters grounded in SR and UD covariance matrix factorizations used for the API gradient evaluation in identification algorithms. As a reallife example, we consider an application of the API approach to linear time-invariant statespace stochastic MIMO filter systems arising in human body temperature daily variation adaptive stochastic modeling. Simulation results and conclusions are also provided. Key words: linear stochastic system, parameter estimation, model identification, Auxiliary Performance Functional (API) approach, state sensitivity evaluation methods, stochastic modeling, homeostasis, thermoregulation.

13/11/2013, 14:30 — 15:30 — Room P9, Mathematics Building
Andrey Tsyganov, Ulyanovsk State Pedagogical University, Ulyanovsk, Russia

Parallel Algorithms for NFA State Minimization Problem

This talk will start with an introduction, where we present the Laboratory of Mathematical Modeling which was recently established in Ulyanovsk State Pedagogical University. The report will cover its hardware and software facilities and main areas of conducted research: cosmology, molecular biology, combinatorial optimization, parameter identification. Then we will switch to the main subject of the talk. We consider the state minimization problem for nondeterministic finite automata (NFA) which is known to be computationally hard (PSPACE-complete) and introduce ReFaM – a software tool for its solution. This software tool provides a number of parallel algorithms: parallel versions of exact Kameda- Weiner and Melnikov methods as well as their hybrids with popular metaheurstics (genetic algorithm, simulated annealing, etc.). All parallel algorithms are implemented using MPI and OpenMP techniques. We discuss the implementation details and provide the results of numerical experiments

04/09/2013, 16:00 — 17:00 — Room P3.10, Mathematics Building
Kazuaki Nakane, Division of Health Sciences, Osaka University, Japan

A Homology-based Algorithm for the Analysis of Structures

Observations of the microstructure of objects by means of a microscope are carried out in different technical fields. The state organization of iron with quenching-annealing and the human tissue by biopsy are typical examples. Since the results of such observations depend on the skills of the technician, objective methods are required for the quantification of structures. When the observed structures are very complex, the performance of pattern recognition and Fourier methods is not satisfactory. In this talk, I will introduce an algorithm based on the concept of homology. By applying this method, we obtain rigorous quantitative estimates of a structure. Several examples of its application will be presented.

12/07/2013, 11:30 — 12:30 — Room P3.10, Mathematics Building
Jevgenija Pavlova, CEMAT, Instituto Superior Técnico, Lisbon

Modeling the Coagulation Dynamics in Human Blood

Blood coagulation is an extremely complex biological process in which blood forms clots to prevent bleeding, following by their dissolution and the subsequent repair of the injured tissue. The process involves different interactions between the plasma, the vessel wall and platelets having a huge impact of the flowing blood on the thrombus growth regularization. The blood coagulation model we are working on consists of a system of reaction-advection-diffusion equations, describing the cascade of biochemical reactions, coupled with rheological models for the blood flow (Newtonian, shear-thinning and viscoelastic models). We introduce the effect of blood slip at the vessel wall emphasizing an extra supply of activated platelets to the clotting site. We expect that such contribution could be dominant, resulting in the acceleration of thrombin production and eventually of the whole clot progression. Such model will have the capacity to predict effects of specific perturbations in the hemostatic system that can’t be done by laboratory tests, and will assist in clinical diagnosis and therapies of blood coagulation diseases. A mathematical model and numerical results for thrombus development will be presented. The chain of biochemical reactions interacting with the platelets, resulting in a fibrin-platelets clot formation and the additional blood flow influence on thrombus development will be discussed.

20/03/2013, 16:30 — 17:30 — Room P3.10, Mathematics Building
Mikhail Bulatov, Institute of System Dynamics and Control Theory, Irkutsk, Russia

Analytical and Numerical Methods for Integral-Algebraic Equations

In the present talk we will discuss some properties of Integral-Algebraic Equations (IAE) and their numerical solution. Concerning analytical methods, me will consider IAE with kernels of convolution type and weakly singular kernels. We will also discuss the regularization of IAE. The discussion of numerical methods will start with the case of systems of Volterra integral equations of the first kind. Then we will describe multistep methods for IAE.

13/03/2013, 16:30 — 17:30 — Room P3.10, Mathematics Building
Werner Varnhorn, Kassel University, Germany

The Navier–Stokes Equations: A never ending challenge?

More than 2500 years after the famous statement πάντα ῥεῖ by Heracleitos the investigation of the mechanical and dynamical behavior of fluid flow is more than ever of fundamental importance. Due to a large number of technical, experimental and computational innovations and related theoretical problems the investigation of fluid flow represents a challenging and exciting subject requiring a wide variety of profound mathematical methods, efficient numerical algorithms and complex experimental simulations. Fascinating from the mathematical point of view, of course, is the fact that the fundamental equations of Navier–Stokes, formulated the first time by the French engineer Navier in 1822, could not be solved in the general three–dimensional case up to now. So the famous American Clay Mathematics Institute created the Navier–Stokes Millennium Price Problem and offered one Million US–Dollar for its solution, stating: „Although the Navier–Stokes equations were written down in the 19th Century, our understanding of them remains minimal. The challenge is to make substantial progress toward a mathematical theory, which will unlock the secrets hidden in the Navier–Stokes equations“.

The lecture introduces the Navier–Stokes equations from an historical and physical point of view, touches some fundamental mathematical problems of viscous incompressible fluid flow and ends up with new regularity results.

08/02/2013, 15:00 — 16:00 — Room P1, Mathematics Building
António Baptista , ITQB

Protein conformational spaces: sampling, measuring and clustering

Proteins are large molecules composed of linear chains of connected aminoacids, being largely responsible for the processes taking place in living organisms. The conformation (spatial structural arrangment) adopted by those chains ensures the chemical and physical properties required for proper protein functioning, with a loss of the normal conformational features leading to malfunction or disease. Therefore, a detailed characterization of the distribution of conformations is determinant to understand and rationalize the behavior of proteins. This talk discusses some aspects and open issues in the study of protein conformational behavior in the field of Molecular Modelling. Although deterministic or stochastic computational methods can be used to sample protein conformations, the sampling is often partial and many alternative dissimilarity measures and classification algorithms exist. Thus, questions remain about the suitability of available measures, conformational spaces and clustering methods for properly reflecting the underlying energetics of these molecules and, ultimately, their thermodynamic and kinetic properties. Overall, the viewpoint adopted in the talk is that of a physical biochemist trying to take advantage of mathematical methods (and hoping to get helpful suggestions from the audience).

15/01/2013, 14:30 — 15:30 — Room P3, Mathematics Building, IST
, Instituto de Engenharia Mecânica-I.S.T

Fast symbolics for interpolatory quadrature rules

Quadrature rules are usually classified in terms of their degree of exactness. We show that the vector of weights of a rule, as the least-squares or minimax solution of a fundamental linear system, leads to a new parameter which we call the angle of the rule. Numerical evidence for some standard quadrature rules shows that the angle of a rule can be more interesting than its degree of exactness, providing an explanation why low degree rules can be almost performant as rules of much higher degree.

05/12/2012, 16:00 — 17:00 — Room P3.10, Mathematics Building
Nelson Marques, blueCAPE

Applications and Perspectives of Industrial CFD in Portugal

We aim to provide an accurate representation of industrial CFD activities in Portugal. For this purpose we review some work undertaken at blueCAPE. The presentation is thus comprised of three sections: basic description of physical models and numerical discretization techniques; application examples from industrial applications; hardware developments and their implications in CFD codes. The first section sets the context and the nomenclature for the examples that follow in broad technical and scientific terms. The second section puts forward some examples taken from a number of industrial problems that blueCAPE has addressed through CFD analysis. The third and final section discusses some of the implications that the widening gap between fine and coarse-grained parallelism imposed by hardware developments have on the current generation of commercial CFD codes. Questions will be taken.

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