HGS MathComp Curriculum & Events

The course gives a thorough introduction to parallel programming. Topics
covered are

1.) Overview of the architecture of parallel computers
2.) Characterisation of parallel algorithms (e.g. Speedup)
3.) Shared memory programming with OpenMP and Threads
4.) Distributed memory programming with MPI
5.) Parallel programming on graphic adapters (CUDA)

The lectures are accompanied by exercises where the usage of the different
parallelization techniques are applied to solve practical problems.

Prerequisites: Programming skills in C or C++ (as e.g. acquired in the lecture
Informatik I)

Registration: Due to number of computers available the maximal number of
participants is 25. Please register by sending an E-Mail to
ingrid.hellwig@iwr.uni-heidelberg.de before Wednesday November 4.

Protein structure introduction, sequence-structure-function
relationship, sequence alignment, structure superposition,
SCOP database, protein-protein interaction, protein-protein
docking algorithm, protein binding site prediction.

Topic of this class will be the solution of large systems of linear equations arising from the finite element or finite difference discretization of partial differential equations. The focus will be on multi-level methods.

For details please visit the webpage.
Please register with an email to me (richter@uni-hd.de) if interested.

Differential equation models involving detailed chemical reaction kinetics inherently share a multi-scale character and often a huge state space dimension. Reaction dynamics on multiple time scales generally couple to physical transport such as diffusion or convection. Realistic modeling and numerical simulation are necessary for mechanistic understanding, model-based optimization and control of chemical processes and require the use of highly efficient scientific computing methods exploiting the multi-scale character of these problems. Theoretical and numerical aspects as well as applications of multiple time scale chemical kinetic models will be discussed in the lecture course.

Registration until Jan 15th (via email): dirk.lebiedz@iwr.uni-heidelberg.de

Complex processes are described by nonlinear differential equation systems. Only validated models allow realistic process simulations and the potential of process optimizations.

This course deals with concepts, methods and software for model validation, especially sensitivity analysis, parameter estimation, optimum experimental design and model discrimination.
The course consits of lectures, tutorials and practicals including an introduction to PARFIT and VPLAN. It is planned to conclude the course with a scientific workshop at the last day.

Remark: The course language is English although this abstract is in German

Diese Lehrveranstaltung behandelt die aktuelle Theorie und Praxis der gemischt-ganzzahligen Optimierung. Themen der Veranstaltung sind: Optimierungsmodelle, Grundlagen der linearen Optimierung und polyedrischen Kombinatorik, Dualität, Relaxierungen, Schnittebenengenerierung, Preprocessing, Dekompositionsverfahren, Heuristiken, Branch-and-Bound, Branch-and-Cut, Anwendungen in der Praxis. Die Veranstaltung umfasst einen Vorlesungsteil und einen integrierten Übungsteil mit praktischen Übungen am Computer. In den Übungen wird insbesondere vermittelt, Optimierungsmodelle zu formulieren, Modellgeneratoren zu benutzen und mit Hilfe von Optimierungsbibliotheken eigene Spezialalgorithmen zu entwickeln.

Die Vorlesung wendet sich an Studierende der Informatik oder Mathematik in Haupt- oder Nebenfach sowie an Lehramtsstudenten und Doktoranden. Außer mathematischem Grundwissen und Programmierkenntnissen in C oder C++ werden keine Kenntnisse vorausgesetzt.

Stochastic Processes are relevant to understand all microscopic phenomena in natural sciences, including quantum processes, molecular dynamics and motion of proteins in the cell. They are also useful to quantitatively model many macroscopic processes, such as stock price evolution and climate changes. In this course we will teach the basic tools for simulating and analyzing such processes.

Prerequisites:
* Basic knowledge in Mathematics (Integral and Differential calculus, Basic Matrix Algebra, Random Numbers)
* Open to PhD, MSc and BSc students in Maths, Physics, Chemistry, Biology and Economics

Content:
- Overview: Applications in Biology, Chemistry, Physics and Economy
- Random Walks
- Stochastic Differential Equations (SDE)
- Continuous State Markov Processes: Brownian/Smoluchowski dynamics and Langevin dynamics
- From SDE to Fokker-Planck Equation
- Discrete State Markov Chains
- Numerics: Discretization of continuous random processes.
- Estimation and Statistical uncertainties
- Markov Chain Monte Carlo
- Statistical analysis of Molecular Dynamics

Registartion: by email frank.noe@fu-berlin.de

The numerical solutions of initial value problems of ordinary differential equations is a standard task for many scientists working with dynamical models. This course aims at non-mathematicians who work with such models and teaches the basic usage of software tools to solve such IVP. In order to understand the functionality and usability of such software, an overview of the theory of IVP solving is given.
Goals for students:
* being able to solve IVP problems
* getting experience in troubleshooting during usage
* integration of IVP libraries in their own research project.
The compact course will include extensive practical exercises.

Grundzüge der Erd- und Regionalgeschichte der Pfalz, drei Burgen (Hambacher Schloss, Riedtburg, Trifels) erwandern und kennenlernen, Grundzüge der Mittelalter-Archäologie und des Denkmalschutzes, entsprechende Grundtechniken (Vermessung, Aufnahme, 3D-Scanning, Ausgrabung, Sicherung und Begehbarmachung/Vermittlung) erarbeiten, archäologische Quellen und geographische Daten für historische Forschung zu verwenden lernen, Orientierung im Gelände und Lesen des Geländes anlernen.

Day 1: Fotography in Science & Research
Day 2: Documentary Photography - Theory & Practice
Day 3: Digital Postproduction

lecture & practicals

Mathematical and Computational Methods of Image Processing (lecture & practicals)

Die Grundlagen der Graphikprogrammierung wie Koordinatensysteme, Projektionen, Transformationen, Zeichenalgorithmen, Bufferkonzepte (z-Buffer, Double-Buffer), Shading, Lichtmodelle und Texturverfahren werden vorgestellt und anhand der Graphikbibliothek OpenGl in den Übungen (Computerpool im OMZ, Fr 9:00-11:00) praktisch erprobt. Dabei werden die Vor- und Nachteile der Methoden des Dircet Rendering (lokale Verfahren) den globalen Verfahren wie Raytracing und Volume Rendering gegenübergestellt.

Die Vorlesung behandelt die Modellierung, Simulation und Optimierung mit gewoehnlichen Differentialgleichungen. Themen werden voraussichtlich sein: Wiederholung Theorie und Algorithmik der nichtlinearen Optimierung, Parameterschaetzung, verallgemeinerte Gauss-Newton Verfahren, Optimale Steuerung: HJB Gleichung, Pontryagins Maximum Prinzip, direkte Methoden.
Volesung mit Übungen

lecture & practicals

Modeling and simulation of chemical reactions, detailed mechanisms, reduction of chemical reactions schemes, reactive flows, laminar and turbulent flows as well as two-phase flows will be addressed.

The lecture is intended for PhD students in their first semesters.

Professor em. Dr.-Ing. habil. Erwin Stein ist einer der wegweisenden
Vermittler zwischen Ingenieurbereich und Angewandter
Mathematik. Er hat nachhaltig die Zusammenarbeit beider Bereiche
gefördert. Seit rund 20 Jahren forscht Professor Stein
über die Erfindungen von Gottfried Wilhelm Leibniz und hat mit seinen Mitarbeitern Leibnitz-Rechenmaschinen nachgebaut und verbessert.

Gottfried Wilhelm Leibniz war als Philosoph, Mathematiker, Physiker und Techniker seiner Zeit weit voraus. Seine ganzheitliche und vernetzte Denkweise mit den Maximen nihil sine ratione und ratio et religio ist auch in unserer heutigen globalisierten Gesellschaft ein spannender Ansatz.
Im Mittelpunkt des Vortrages stehen die aufwändigen Nachbauten von Leibniz´ dezimalen und binären Rechenmaschinen. Mit seinem systematischen binären Zahlensystem, seinen übergeordneten Erkenntnissen als Philosoph und Mathematiker und der ersten Bauanleitung für eine binäre Rechenmaschine hat Leibniz Grundideen des heutigen Informationszeitalters vorweg genommen.

Die Heidelberger Graduiertenschule für Mathematische und Computergestützte Methoden
für die Wissenschaften am Interdisziplinären Zentrum für Wissenschaftliches Rechnen fördert die Zusammenarbeit der verschiedenen Disziplinen. In diesem Vortrag bietet Prof. em. Dr.-Ing. Erwin Stein faszinierende Einblicke in die Erfindungswelt von Leibniz.

Diverse modelling formalisms are applied in Computational Biology. Some describe the biological system in a continuous manner, others focus on discrete-event systems, or on a combination of continuous and discrete descriptions. Similarly, there are many simulators that support different formalisms and execution types of one and the same model.
The latter is often done to increase efficiency, sometimes at the cost of accuracy and level of detail. JAMES II has been developed to support different modelling formalisms and different simulators and their combinations. Its focus is on discrete event simulation and it is based on a plug-in concept which enables developers to integrate spatial and non-spatial modeling formalisms, simulation algorithms and supporting technologies into an existing framework. This eases method development and result evaluation in applied modelling and simulation as well as in modelling and simulation research. Based on different Gillespie variants it is shown how the plug-in concept in James II supports the implementation, evaluation, and on demand configuration of simulation algorithms.

Grundlagen der Genomstruktur von Eukaryonten, insbesondere Säugerzellen; Experimentelle Methoden, Modellierung, Validierung

Videoseminar mit Global Networks Partner IMB, ME.
Vorträge aus dem Institute for Molecular Biophysics, einem Biophysik Netzwerk der Universität Heidelberg, der University of Maine, dem Jackson Laboratory/ME und dem Maine Medical Research Center Institute/ME.
Themen: Neue Ergebnisse aus der experimentellen und theoretischen Biophysik.

Neue laseroptische Verfahren zur Überwindung der Beugungsgrenze (Abbe-Limit) und zur lichtoptischen Realisierung einer molekularen optischen Auflösung zellulärer Strukturen; Validierung von numerischen Modellen

Gegenstand des Seminars sind die Ableitung und die mathematische Analyse von
Modellgleichungen für Prozesse wie Strömung, Transport und Reaktion sowie
biomechanische-biochemische Interaktionen in Böden, technischen und biologischen
Geweben und Membranen.

ADF 2009-Software:
* Molecular and periodic DFT, new developments and applications
* Spectroscopic methods
* the graphical user interface
* recent developements in ADF 2009

Current topics in computational and applied mathematics.

Due to the revolutionary new technologies that have arisen in the field of biological data collection, an enormous amount of information on a molecular and cellular scale has become available and much has been learned about the molecular components involved in signal transduction during normal and pathological development. Such progress is producing a growing need to quantitatively understand and manipulate this data and translate it into practical applications. Researchers in computational and theoretical biology are using a variety of mathematical approaches to understand and manipulate biological processes.

This workshop is devoted to multiscale aspects of mathematical modelling and analysis of transport processes and regulatory feedbacks in cell systems. Recent results and theoretical methods from multiscale analysis and nonlinear dynamics will be discussed in the context of applications to the study of the collective properties of biological systems.

The main topics to be studied are:
Models for cell differentiation and transformation
Models of the transport processes in a complex medium

The workshop is organised within the framework of the Polish-German Graduate College (Research Training Group 710), Heidelberg Graduate School of Mathematical and Computational Methods for the Sciences and International PhD Programme (MPD).

Main Topics:

• Biotechnology


• Biomedicine


• Biophysics


• Medical Physics


• Bio/Medical Statistics

Representatives of IWR, Heidelberg University and Jioa Tong University, Shanghai, meet for the second time to hold a workshop on computational methods. This workshop will strengthen the ties between the two universities.