Participants 2013

Deepika Sundarraman

Name  

Deepika Sundarraman

University

The College of Wooster, Wooster, Ohio, USA

Supervisor

Prof. Dr. Dieter W. Heermann

Workgroup  

Statistical Physics and Theoretical Biophysics

Project

Modelling the chromosomal polymer structure

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Knowledge from statistical and polymer physics has proved to be beneficial in the investigation of chromosomal structure. Experimental data from 2D localization light microscopy measurements have been analyzed using image processing techniques. Simulations for various cell nuclei were created from which data was also extracted. We use data from simulated cell nuclei and perform virtual microscopy to investigate the nature of polymer structure inside the nucleus. Previous research involved creating polymer models from experimental observations. These models help us understand the folding of the polymer at different stages within the nucleus. We would now like to create such polymer models through simulated nuclei for structural correlation with an experimental study of the same. The project primarily involves data analysis that pools in knowledge from computational physics, polymer physics and statistical mechanics.

Manushaqe Muco

Name  

Manushaqe Muco

University

Massachusetts Institute of Technology, Boston, Massachusetts, USA

Supervisor

Prof. Dr. Katja Mombaur

Workgroup  

Optimization in Robotics and Biomechanics

Project

Dynamic visualization of algorithms for solving the Travelling Salesman Problem (TSP) on a reactable machine

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I am working on visualizing algorithms that solve the Travelling Salesman Problem (TSP) on a reactable machine. TSP is one of the most famous problems of combinatorial optimization and consists of finding a shortest Hamiltonian cycle in a weighted graph. A reactable is a device that has a tangible user interface and was originally built as a musical instrument by a group from Spain. In the last semesters, this device was rebuilt by students of Prof. Mombaur. However, the reactable is not only a musical instrument: Its graphical interface can also be used to both input data as well as to display computational results in a visually pleasing manner. This is what I plan to do for the Travelling Salesman Problem. The project will also be extended to different algorithms for the TSP, modifications of the TSP, and visualization of algorithms for other problems.

Bogna Pawlowska

Name  

Bogna Pawlowska

University

Wroclaw University of Technology, Wroclaw, Poland

Supervisor

Prof. Dr. Dr. h.c. mult Willi Jäger

Workgroup  

Applied Analysis

Project

Damage accumulation in human cells

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There are several biological concepts of aging based on DNA damage. The accumulated damage is believed to lead to cell senescence and it plays a crucial role in mutation process and in age-related diseases such as cancer. That is why creating a good mathematical model of that process seems to be of extreme importance.
I develop an ODE model of the DNA damage accumulation. It consists of defining a suitable mathematical definition of damage, identifying the most important components of such process and exploration of parameter domains. There are variety of biological phenomena to capture, as for example: the repair response, cell metabolism and proliferation, or different types of rejuvenate effects. The challenging part is to identify the parameters that determine the real-world observations.

Abhinaba Roy

Name

Abhinaba Roy

University

Jadavpur University, Kolkata, India

Supervisor

Prof. Dr. Björn Ommer

Workgroup   

Computer Vision Group, HCI

Project

Recognition of Deformable Objects in Neurophysiological Data

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This project focuses on the recovery of synaptic connections in seizure stricken rodent brains. Also, finding correlation between the seizure stricken parts of the brain from MRI images and the synaptic connections from microscopic image is another task. It tries to find the abnormality present in the connections at different stages of recovery from the initial seizure attack. Initially they are segmented from the microscopic images and In the next stage, semantic segmentation of the seizure affected areas in the MRI is done.

Nayab Khalid

Name

Nayab Khalid

University

COMSATS Institute of Information Technology, Islamabad, Pakistan

Supervisor

Dr. Susanne Krömker

Workgroup   

Visualization and Numerical Geometry

Project

Visualization of the Domain of Convergence for Iterative Numerical Methods

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My research project is a numerical optimization problem. My task is to find a convincing visualization of the behavior of various numerical solvers for evaluation/rating of forces and weaknesses. 

The first step is to first find a set of sample points to iterate over. This involves a few substeps: First, I reduce a multi-dimensional variable to two dimensions. Then I look at all points within a two-dimensional neighborhood of the reduced point. Finally I map these points back to higher dimensional variables.  The second step is to use the Newton-Rhapson method to observe how each sample point approaches the root. I then present a graphical analysis of the iterative process, showing the path followed by these points as they approach the root, as well as the number of iterations it takes a particular point to reach the root. In many cases, the resulting figure is a fractal. 

I am writing the program in MATLAB, and the code can easily be modified for iterative methods other than the Newton-Rhapson method.