Neue konzeptionelle Ansätze zur Modellierung und Simulation komplexer Systeme / New Conceptual Approaches to Modeling and Simulation of Complex Systems

 

Bewilligungen / Grants 2010

 

Complex Self-Organizing Networks of Interacting Machines: Principles of Design, Control, and Functional Optimization (Extension)

Bewilligung: 29.11.2010  Laufzeit:  3 Jahre

Based on the knowledge gained in the first part of the project, general organization principles will be applied to a range of interdisciplinary problems in molecular biology, industrial production, traffic and logistics. Methods from the theory of industrial production lines and operation research will be used to study collective functional dynamics of molecular machines in genetic expression and signal transduction and in the enzyme complexes.  Evolutionary optimization approaches, developed in the studies of biological systems, will be employed to design prototypes of logistic and factory production networks robust against fluctuations and local damage. Self-organized control of factory logistics and transportation traffic flows will be investigated. Broad collaborations with external partners in the US, Japan, EU and Switzerland are planned.

Fritz-Haber-Institut der
Max-Planck-Gesellschaft (FHI), Berlin
Abt. Physikalische Chemie
Prof. Dr. Alexander S. Mikhailov
Faradayweg 4-6
14195 Berlin
Tel.: 030 8413 5122
Fax: 030 8413 5106
Homepage: http://www.fhi-berlin.mpg.de/complsys/

Arizona State University, Tempe / Phoenix
Department of Mathematics
Prof. Dr. Dieter Armbruster
Postfach
USA-Tempe, AZ 85287-1804
Tel.: +1 480 965 5441
Fax: +1 480 965 8119
Homepage: http://math.la.asu.edu/~dieter/

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Evolution of Networks: Modeling the complexity and robustness of evolving biochemical networks (Extension)

Bewilligung: 29.11.2010  Laufzeit:  3 Jahre

The project tackles concepts as well as numerical and analytic methods that allow for a refined understanding of the evolution of biochemical networks. The aim is a computer simulation for adaptive and neutral evolution of complex chemical reaction networks including the catalyzing enzymes and their regulation. The corresponding mathematical methods will be refined, in particular about hypergraphs, combinatorial vector fields, and network dynamics. These numerical as well as purely mathematical studies focus on two model systems: Metabolic networks which are more general than graphmodels, and Boolean networks as abstract models of regulatory networks conveying a non-trivial dynamics on their nodes. Drawing from the expected insights into evolution of networks, a further clarification of conceptual issues is envisaged, in particular robustness of function under evolving structure.

Universität Leipzig
Institut für Informatik
Lehrstuhl für Bioinformatik
Prof. Dr. Peter Stadler

Universität Leipzig
Institut für Informatik
Lehrstuhl für Bioinformatik
Dr. Konstantin Klemm

Max-Planck-Institut für Mathematik
in den Naturwissenschaften, Leipzig
Abt. Geometrische Methoden
Prof. Dr. Jürgen Jost

Max-Planck-Institut für Mathematik
in den Naturwissenschaften, Leipzig
Priv.-Doz. Dr. Nihat Ay

Max-Planck-Institut für Mathematik
in den Naturwissenschaften, Leipzig
Research Group Complex Structures in Biology and
Cognition
Dr. Eckehard Olbrich

Ansprechpartner:
Universität Leipzig
Institut für Informatik
Lehrstuhl für Bioinformatik
Prof. Dr. Peter Stadler
Härtelstr. 16-18
04107 Leipzig
Tel.: 0341 97 16690
Fax: 0341 97 16679

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Bioinvasion and epidemic spread in complex transportation networks (Extension)

Bewilligung: 29.11.2010  Laufzeit:  3 Jahre

Human mediated bioinvasion refers to the geographical expansion of species into a new range, in which they establish, spread and persist to the detriment of the environment. The phenomenon of bioinvasion is dynamically related to the geographic spread of emergent human infectious diseases driven by mobility of the human hosts. The proposed research is designed to apply complex network theory to investigate the dynamics of bioinvasion and the geographic spread of epidemics as phenomena driven by multi-scale transportation and human mobility networks, ranging from air-transportation and traffic networks, networks of trade- and ship-routes, to migratory bird travel routes. Key to the proposed research is the investigation of both phenomena in a common and comparative context, based on computational as well as analytical methods. Based on the results the team will investigate issues of risk assessment, adaptive predictions and management strategies.

Universität Oldenburg
Institut für Chemie und Biologie des Meeres (ICBM)
Prof. Dr. Bernd Blasius
Ammerländer Heerstraße 114-118
26129 Oldenburg
Tel.: 0441 798 3997
Fax: 0441 798 340

Northwestern University, Evanston, IL
Department of Engineering Sciences
and Applied Mathematics
Prof. Dr. Dirk Brockmann
2145 Sheridan Road
USA-Evanston, IL 60208-3125

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Simulation models for interactive cell motility - coupling intracellular dynamics and cell-cell adhesion (Extension)

Bewilligung: 06.07.2010  Laufzeit:  2 Jahre

Aim of this project is the description of the coordinated motion of cell aggregates in two dimensions. For this purpose, the single cell model of the previous project is combined with an already developed cell-based description of biological tissues. Similar to the previous treatment of cell-substrate adhesion proteins, the external cell-cell adhesion kinetics has to be coupled to the cell-internal actin dynamics. As a first step, this coupling is investigated by means of a section through an isolated cell pair in thin-film approximation. Next, the full treatment of the two-dimensional equations for reaction, diffusion and transport in the cytoplasm is restricted to the cell body and lamella/cortex domains. Starting from the determined pressure variables, a general condition for the contact boundary between two Voronoi cells is derived.

Universität Bonn
Institut für Zelluläre und Molekulare Botanik
Abt. Theoretische Biologie
Prof. Dr. Wolfgang Alt
Kirschallee 1
53115 Bonn
Tel.: 0228 735577
Fax: 0228 735513
Homepage: http://www.theobio.uni-bonn.de/

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Investigation of complex human travel patterns as a basis for epidemic modeling

Bewilligung: 19.04.2010  Laufzeit:  3 Jahre

Human mobility is a key factor for the spatial spread of human infectious diseases. Despite a lot of work on projects in epidemiological modeling there are still open challenges concerning the explicit incorporation of human travel into these models. As shown in previous work, human mobility shows complex, however universal and regular patterns such as long-range displacements and recurrent bidirectional travel between a few most preferred locations. Starting point for this fellowship is a recently developed theoretical bidirectional model for human epidemics. This model will be extended and validated by a large empirical data set on human mobility acquired by mobile phone and smart card tracking. Building upon these data the ultimate goal is to realize a simulation platform providing us with guidelines for the mitigation of human epidemics. The first phase of the fellowship is spent at the Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge/USA, before returning to Germany.

Max-Planck-Institut für Dynamik
und Selbstorganisation, Göttingen
Abteilung für Nichtlineare Dynamik
Dr. Vitaly Belik
Postfach 2853
37018 Göttingen
Tel.: 0551 5176547
Fax: 0551 5176539
Homepage: www.nld.ds.mpg.de

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Tackling the reconciliation problem: A quantum mechanical/molecular mechanical (QM/MM) "learn-on-the-fly" study of the effect of aqueous solvent on peptide conformations (Fellowship "Computational Sciences")

Bewilligung:  16.06.2010  Laufzeit:  3 Jahre

Das Vorhaben wurde am 05.12.2011 von Karlsruhe nach Berlin umgesetzt.

The dilemma of reconciling the contradictory evidence regarding the conformation of long solvated peptide chains is the so-called "reconciliation problem". Clues regarding the stability of certain conformations likely lie in the electronic structure at the peptide-solvent interface. To this end, the influence of aqueous solvent on peptide conformations will be studied using a "learn-on-the-fly" quantum mechanical-molecular mechanical (QM/MM) molecular dynamics approach. The system of interest is a debated 11-residue peptide, X2A7O2 (XAO), composed of diaminobutyric acid, alanine, and ornithine. Recent spectroscopic and molecular dynamics data present conflicting evidence regarding the structure of XAO in water. Some results indicate that XAO adopts a polyproline II conformation, whereas other findings suggest that XAO explores a range of conformations. To investigate this contradiction, molecular dynamics simulations of several solvated dipeptides, including XAO, are carried out. Thereby, the first hydration shell is included in the QM region. Hybrid QM/MM energies and statistical weights will be obtained and used to calculate molecular properties of XAO (radius of gyration, 3J coupling constant, vibrational modes, two-dimensional infrared spectra) for comparison with experimental and theoretical values.

Freie Universität Berlin
Institut für Chemie und Biochemie
Dr. Nadia Elghobashi-Meinhardt
Fabeckstraße 36 a
14195 Berlin

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International Workshop on Recent Achievements on the Study of Extreme Events

27.09.2010 - 29.09.2010 in Potsdam

Potsdam-Institut für
Klimafolgenforschung e. V.
Abt. IV: Transdisziplinäre Konzepte und Methoden
Dr. Norbert Marwan

Potsdam-Institut für
Klimafolgenforschung e. V.
Abt. IV:
Transdisziplinäre Konzepte und Methoden
Prof. Dr. Jürgen Kurths

Max-Planck-Institut für Physik
komplexer Systeme, Dresden
AG Nichtlineare Dynamik und Zeitreihenanalyse
Prof. Dr. Holger Kantz

Ansprechpartner:
Potsdam-Institut für
Klimafolgenforschung e. V.
Abt. IV: Transdisziplinäre Konzepte und Methoden
Dr. Norbert Marwan
Postfach 601203
14412 Potsdam
Tel.: 0331 2882466
Fax: 0331 2882640
Homepage: www.pik-potsdam.de/~marwan

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Dissecting the complex structure of the phenome through machine learning

Bewilligung: 17.03.2010  Laufzeit:  2 Jahre  6 Monate

Understanding phenotypic variation, and in particular identifying the causal genetic or environmental regulators, is a major aim in biological investigations. The goal of this fellowship is to develop machine learning techniques to model the structure of the underlying complex system based on modern, high-dimensional phenotype datasets. First, the temporal structure of phenotypes that are recorded over time is addressed. By statistical modelling the smoothness of time series is exploited for identifying change points. Second, the structure of images, arising when digital pictures are used as phenotypic variables, is considered. Using machine learning techniques interpretable image features that can be used as quantitative traits, are extracted complementing classical measurements. Finally, the network structure of the phenome is addressed. Different phenotype variables influence each other, resulting in a chain of effects that needs to be modelled to reveal the true causal relationships. The developed algorithms are aimed at and will be tested to understand phenotypic variation in Arabidopsis thaliana in direct collaboration with plant biologists at the Max Planck Institute for Developmental Biology.

Max-Planck-Institut für biologische
Kybernetik, Tübingen
Abt. Empirische Inferenz
Oliver Stegle, Ph.D.
Spemannstraße 38
72076 Tübingen
Tel.: 07071 601582
Homepage: http://www.kyb.mpg.de/de/~stegle

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Parametric System Modeling and Simulation for Strategic Building Design

Bewilligung: 17.03.2010  Laufzeit:  3 Jahre

Das Vorhaben wurde am 21.11.2011 von Weimar nach München umgesetzt.

The central objective of this fellowship consists of an extension of the current geometry-limited parametric modeling technique in building design to an integrative systems approach. This integrative systems model includes other discipline's information, analysis, and simulation methods and represents their interdependencies aiming at improvements in ecological, economic as well as reuse aspects. The result is a novel paradigm of Parametric Systems Modeling (PSM) that incorporates the disciplines and processes in one dynamic building model. PSM enables the designer to explore the design space. The resulting overview allows strategic design decisions that lead to economically and environmentally well-performing solutions. Therefore, PSM provides an important basis for performance-driven building design. As method, the PSM project uses the Systems Modeling Language in combination with the Industry Foundation Classes and implements an experimental modeling environment. The fellowship includes research stays at the Department of Architecture, Swiss Federal Institute of Technology Zurich (ETH).

Technische Universität München
Lehrstuhl für energieeffizientes und nachhaltiges
Planen und Bauen
Dr.-Ing. Philipp Geyer
Arcisstraße 21
80333 München
Tel.: 089 28923946
Fax: 089 28923991
Homepage: www.enpb.bv.tum.de

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Developing an Urban Simulation System for a Major West African City

Bewilligung: 17.03.2010  Laufzeit:  3 Jahre

Rapid growth of urban areas in the developing world are resulting in the need to develop quantitative models for describing land use and transportation dynamics. This fellowship proposes to improve upon an existing urban simulation system of Accra, Ghana, and introduce an integrated transport model for the Ghanaian capital city. Unified operational models that favour a microscopic approach, such as the simulation platforms UrbanSim and MATSim, have gained significant interest in both the land use and transport communities. Still, in their current forms, these models require further development within the context of a major West African city. The goal of this project is to address the modeling and computational issues of integrating modern mobility simulations with the latest micro-simulation land use models. On the modelling side, the main challenges are: to synthetically generate household, person and jobs tables for the Greater Accra population; to develop residential mobility and job choice rates within the discrete choice modeling frameworks; and the development of a comprehensive transportation model.

Technische Universität Berlin
Institut für Land- und Seeverkehr
Verkehrssystemplanung und Verkehrselematik
Sekr. SG 12
Tyler Frazier
Salzufer 17 - 19
10587 Berlin
Tel.: 030 31423308
Homepage: http://www.vsp.tu-berlin.de/projects/

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Schriftgröße