Ivan Kondov

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Preprint This is the submitted version of a paper presented at NBiS 2015. Abstract—While the HPC community is working towards the development of the first Exaflop computer (expected around 2020), after reaching the Petaflop milestone in 2008 still only few HPC applications are able to fully exploit the capabilities of Petaflop systems. In this paper we(More)
Methods for in-silico screening of large databases of molecules increasingly complement and replace experimental techniques to discover novel compounds to combat diseases. As these techniques become more complex and computationally costly we are faced with an increasing problem to provide a community of life-science researchers with a convenient way to run(More)
Molecular simulation methods have increasingly contributed to our understanding of molecular and nanoscale systems. However, the family of Monte Carlo techniques has taken a backseat to molecular dynamics based methods, which is also reflected in the number of available simulation packages. Here, we report the development of a generic, versatile simulation(More)
Particle swarm optimization is a powerful technique for computer aided prediction of proteins’ three-dimensional structure. In this work, employing an all-atom force field and the standard algorithm, as implemented in the ArFlock library in previous work, the low-energy conformations of several peptides of different sizes in vacuum starting from completely(More)
In this paper we propose an approach for preparing HPC applications for Exascale. A high-level application model capturing non-functional properties combined with an abstract machine model will enable application improvements, and will serve as input to runtime systems to handle performance and energy optimizations, and self-aware fault management. A(More)
Molecular dynamics (MD) simulations provide valuable insight into biomolecular systems at the atomic level. Notwithstanding the ever-increasing power of high performance computers current MD simulations face several challenges: the fastest atomic movements require time steps of a few femtoseconds which are small compared to biomolecular relevant timescales(More)