Ivan Kondov

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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)
Particle swarm optimization (PSO) is a powerful technique for computer aided prediction of proteins' three-dimensional structure. In this work, employing an all-atom force field we demonstrate the efficiency of the standard PSO algorithm, as implemented in the ArFlock library, for finding the folded state of two proteins of different sizes starting from(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)
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)