[Metalab] Please help me translate my thesis topic

[Maciej Pasternacki]

Hello,

I'm new here, so I'll introduce myself first.  I'm a software (Lisp/ 
Python) geek that has just moved to Vienna, has been a few times at  
the Lab, and at the moment finishes his Master's thesis.  My problem  
is that I'm still learning German and I'm glad when I can read a  
children book, and my university wants me to give them my thesis topic  
in foreign language if I want them to give me the diploma in that  
language.  So, I need to give them my topic in German.  Would the  
Lazylab help me with this?

My topic in English is "Hybrid parallelization of the UNRES molecular  
dynamics force field algorithm" (original Polish, if that helps  
anyone: Hybrydowa paralelizacja algorytmu pola siłowego dynamiki  
molekularnej UNRES).

UNRES (name stands for UNited RESidues) is program that tries to  
predict structure (3D shape) of a protein particle, given the  
protein's aminoacid sequence (protein structure prediction problem).   
It employs methods of molecular dynamics (MD): physical simulation of  
how the unfolded particle behaves in the solution (simulation of  
various attraction and repulsion forces in discrete time steps).  The  
force field is the central part of algorithm: it is field function  
that for every point in particle's conformational space (space defined  
by all possible shapes of the particle) assigns particle's potential  
and kinetic energy.  This makes the whole simulation an optimizational  
problem: we need to find the energy function's (force field's) global  
minimum.

The whole program is parallelized to run on large clusters, using  
message-passing paradigm (MPI standard), both coarse-grained (separate  
simulations), and fine-grained (splitting single simulation onto  
multiple cores).  My work was to add fine-grained parallelization to  
split single simulation ontu multiple cores, but using the threading  
paradigm (OpenMP standard) and compare this with message-passing fine  
grained parallelization.  Hybrid means using both message-passing (for  
coarse-grained parallelism) and threads (for fine-grained parallelism).

Within my work, I parallelize only the most time-consuming parts of  
the force field functions, hence the "force field algorithm" part of  
title.

Thanks in advance for any help,
regards, :)
Maciek.

-- 
Maciej Pasternacki -><- http://www.pasternacki.net/ -><- http://www.3ofcoins.net/