Asist. Gabriel NEGARA
Universitatea Alexandru Ioan Cuza, Facultatea de Informatica
Iasi
Romania
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The Protein Folding Problem. 
Algorithms for solving the Protein Folding Problem in the HP 2D model.
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ABSTRACT
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The widely-studied HP model was introduced by Dill. 
A protein is a chain of amino acid residues. 
In the HP model, each amino acid residue is classified as an 
H (hydrophobic or non-polar) or a P (hydrophilic or polar). 
An optimal conformation for a string of amino acids in this model 
is one that has the lowest energy, which is achieved when 
the maximum number of H-H contacts (i.e. pairs of H's that 
are adjacent in the folding but not in the string) are present. 
The problem of protein folding in the two-dimensional 
HP model (square lattice) is combinatorially equivalent to 
folding a string of 0's and l's so that the string forms a 
self-avoiding walk on the lattice and the number of 
adjacent pairs of l's is maximized.
          
SHORT CV
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* 1998-2002: Faculty of Computer Science - undergraduate student
* 2002: graduation thesis - 
    "Solving Optimisation Problems using <Ant Colony Optimization>"
* 2002-2003: Master in Parallel and Distributed Calculus - 
    "Classification Technics in Data Mining"
* Research Assistant, Faculty of Computer Science, Iasi : March 2003 - September 2006
* Teaching Assistant, Faculty of Computer Science, Iasi : from September 2006
* PhD student, FCS Doctoral School, from October 2005 - 
    "Optimisation Methods using Nature inspired Metaheuristics"
* Visiting Research Associate, Brown University, Providence, USA,
    September 2006 - December 2006