BEGIN:VCALENDAR VERSION:2.0 PRODID:-//CERN//INDICO//EN BEGIN:VEVENT SUMMARY:Dynamical Features of Complex Systems: A Molecular Simulation Stud y DTSTART;VALUE=DATE-TIME:20121017T123000Z DTEND;VALUE=DATE-TIME:20121017T130000Z DTSTAMP;VALUE=DATE-TIME:20261010T225913Z UID:indico-contribution-291-164@indico.ipb.ac.rs DESCRIPTION:Speakers: Hrachya ASTSATRYAN (Head of HPC Laboratory\, Institu te for Informatics and Automation Problems of the National Academy of Scie nces of Armenia)\nThe parallel molecular dynamics simulation of complex mi cellar system consisting of long hydrocarbon chain surfactant was carried out. The GROMACS software package\, which is designed for high-performance simulation of large complex system\, was applied. The simulations were pa ralell on Bulgarian BlueGene/P supermachine. The goal of this paper is the detail analysis of surfactant molecules in complex system. The initially random distributed surfactant molecules in aqueous solute hydration have b een simulated using GROMOS united atom force field. The computation was ca rried out on BlueGene/P supermachine using from 256 to 1024 processors. Th e estimated benchmarks show about 0.5ns per day optimized by 512 processor s. It should be noted that the further increase of processors (for instanc e\, 1024 processors) do not lead to significant increase in benchmarking v alue and therefore 512 processors were chosen for final run. The received data shows that the long hydrocarbon chain surfactant self-assemble into s mall oligomers since 50ns of simulation run\, meanwhile in our previous st udy with surfactant rich content shows that 43ns is enough for self-assemb ling of spherical micelle. It is planning to continue the simulation to se e the self-assembling process of huge complex systems.\n\nhttps://events.s aifa.rs/event/291/contributions/164/ LOCATION:National Library of Serbia URL:https://events.saifa.rs/event/291/contributions/164/ END:VEVENT BEGIN:VEVENT SUMMARY:Conformational Analysis of Kyotorphin Analogues Containing Unnatur al Amino Acids DTSTART;VALUE=DATE-TIME:20121018T134500Z DTEND;VALUE=DATE-TIME:20121018T150000Z DTSTAMP;VALUE=DATE-TIME:20261010T225913Z UID:indico-contribution-291-158@indico.ipb.ac.rs DESCRIPTION:Speakers: Nicolay Dodoff (Roumen Tsanev Institute of Molecular Biology\, Bulgarian Academy of Sciences\, 1113 Sofia\, Bulgaria)\nThe dip eptide kyotorphin (Tyr-Arg\, Kyo) plays a role in pain modulation in the m ammalian central nervous system (CNS)\, and is one of the most investigate d neuropeptides. The Tyr-Arg motif exists widely throughout the brain not only as kyotorphin\, but also as the N-terminal part of several endogenous analgesic peptides1\,2. Also\, this peptide is very rapidly degraded by a minopeptidases3. One of the successful strategies in the design of neurope ptides with enhanced stability and improved delivery to the CNS is that wi th the use of non-protein amino acids\, like canavanive (Cav)\, a structur al analogue and antimetabolite of arginine (Arg). In our previous in vivo experiments we demonstrated that Tyr-Cav exerted a strong-reversible analg esic effect\, more pronounced than that of Kyo. Bearing in mind these and the fact that norsulfoarginine (NsArg)4 is a structural analogue of argini ne and canavanine\, we synthesized a series of new peptides with expected analgesic activity\, containing NsArg residues in their molecules: NsArg-T yr\, Tyr-NsArg\, Tyr-NsArg-NH2 and Tyr-NsArg-OBzl5\,6. \nThe conformationa l features of these dipeptides are of particular interest\, both from theo retical and pharmacological point of view. Since no single-crystal X-ray d iffraction data for the compounds are available until now\, we undertook a quantum-chemical modelling of their structure. \nWe have undertaken a pro found conformational study of kyotorphin and its synthetic analogues\, con taining unnatural amino acid nor-sulfoarginine (NsArg). \nHere we present our preliminary computational results for Kyo\, NsArg-Tyr аnd Tyr-NsArg. Molecular mechanics (MM+ force field) conformational search for the two sp ecies was performed\, and the global minimum-energy conformations thus obt ained\, were further optimized at HF ab initio (3-21G** basis set) level o f theory. In the three cases (Kyo\, NsArg-Tyr\, and Tyr-NsArg) specific\, scorpion-like conformations are realized\, with hydrogen bonds involving t he guanidino-group and the phenolic hydroxyl. Numerical results are obtain ed using HPC cluster deployed at the Institute of Information and Communic ation Technologies. This cluster is part of High-Performance Computing Inf rastructure for South East Europe’s Research Communities.\n\nhttps://eve nts.saifa.rs/event/291/contributions/158/ LOCATION:National Library of Serbia URL:https://events.saifa.rs/event/291/contributions/158/ END:VEVENT BEGIN:VEVENT SUMMARY:Some aspects of the comparative study of semi-empirical combustion models on FLUENT and OpenFOAM codes DTSTART;VALUE=DATE-TIME:20121018T134500Z DTEND;VALUE=DATE-TIME:20121018T150000Z DTSTAMP;VALUE=DATE-TIME:20261010T225913Z UID:indico-contribution-291-159@indico.ipb.ac.rs DESCRIPTION:Speakers: Sreten Lekic (Faculty of Natural Sciences University of Banja Luka)\nDevelopment of an optimal medium power gas burner started under the FP6 project and was continued in HP-SEE project. CFD simulation s were initially performed using FLUENT and partly StarCD Adapco sotware\, but due to limited computing resources were limited to simulations of sma ll segments with assumptions of absolute radial symmetry. In HP-SEE projec t we used OpenFOAM for full scale model simulations using solver for combu stion with chemical reactions using density based thermodynamics package ( rhoReactingFoam). An analysis of the differences in the results obtained w as performed. The advantages of the new approach to CFD modeling of combus tion are demonstrated.\n\nhttps://events.saifa.rs/event/291/contributions/ 159/ LOCATION:National Library of Serbia URL:https://events.saifa.rs/event/291/contributions/159/ END:VEVENT BEGIN:VEVENT SUMMARY:In the search of the HDAC-1 inhibitors. The preliminary results of ligand based virtual screening. DTSTART;VALUE=DATE-TIME:20121019T120000Z DTEND;VALUE=DATE-TIME:20121019T123000Z DTSTAMP;VALUE=DATE-TIME:20261010T225913Z UID:indico-contribution-291-160@indico.ipb.ac.rs DESCRIPTION:Speakers: Cvijetić Ilija N. (Innovation Center of the Faculty of Chemistry\, University of Belgrade\, Studentski Trg 12-16\, Belgrade)\ nAcetylation and deacetylation of histone is an important mechanism to reg ulate the DNA expression. Two main classes of enzymes catalyze this regula tory mechanism: histone acetyltransferase (HAT) and histone deacetylase (H DAC). HDACs are involved in signal transduction\, cell growth and cancer [ 1]. We report the results of the preliminary ligand-based virtual screenin g in the search of the novel HDAC-1 inhibitors. By this virtual screening study\, we aimed to test the performances of the OpenEye applications inst alled on our home cluster PARADOX. As the template\, we used the ligand fr om 3MAX PDB entry [2]\, Figure 1. (HDAC-2 isozyme has the identical active site with HDAC-1). The ChemBank set of 2346 molecules was taken from the ligand.info [3]. After the filtering (exclusion of the metal containing co mpounds\, and limiting of the number of HBA (10) and HBD (5)) we obtained 1990 molecules\, which are submitted to OMEGA [4] to generate conformation al assemblies of the molecules studied. The OMEGA options were set to defa ult\, yielding ~ 142000 conformers in total. We searched the shape and the pharmacophoric similarity of the multiconformer ligand set against the te mplate molecule by ROCS program [5]. The best-ranked solution of the 100 h its by TanimotoCombo score (1.305) was Nifenazone\, that has been used as the analgesic drug and was withdrawn due to heavy side effects. The subset of ligand conformers prepared with ROCS is further submitted to EON [6]\, to search for the electrostatic similarity to the template molecule. The compound labeled as the itdac-7 in ChemBank appears as the best-ranked sol ution by the ET-combo score (1.403)\, Figure 1b. There is no literature da ta on this compound\, but ChemBank results from the high-throughput screen ing campaigns indicates itdac-7 as active toward enzymes involved in deace tylation. Our preliminary screen\, as reported in this communication\, inv olves the MMFF94s charges ascribed by default. Further work will be direct ed to assignation of the semiempirical charges for the electrostatic simil arity screen\, using the larger database of the compounds. All calculation s by OpenEye applications were performed in BJD work group on PARADOX clus ter\, Institute of Physics\, Belgrade.\nAcknowledgement: The work reported makes use of results produced by the High-Performance Computing Infrastru cture for South East Europe’s Research Communities (HP-SEE)\, a project co-funded by the European Commission (under Contract Number 261499) throug h the Seventh Framework Programme HP-SEE (http://www.hp-see.eu/).\nThe Min istry of Education and Science of Serbia support this work. Grant 172035. \nReferences: [1] Nature 389 (1997) 349\; [2] Bioorg. Med. Chem. Lett. 20 (2010) 3142\; [3] Comb. Chem. High. Throughput Screen. 7 (2004) 757\; [4] J. Chem. Inf. Model. 50 (2010) 572\, OMEGA 2.4.2\; [5] J. Med. Chem. 48 (2 005) 1489\, ROCS 3.1.1\; [6] EON 2.0.1\, OpenEye Scientific Software\, In c.\, Santa Fe\, NM\, USA\, www.eyesopen.com .\n\nhttps://events.saifa.rs/e vent/291/contributions/160/ LOCATION:National Library of Serbia URL:https://events.saifa.rs/event/291/contributions/160/ END:VEVENT BEGIN:VEVENT SUMMARY:Advanced Vulnerability Assessment Tool for Distributed Systems DTSTART;VALUE=DATE-TIME:20121017T130000Z DTEND;VALUE=DATE-TIME:20121017T133000Z DTSTAMP;VALUE=DATE-TIME:20261010T225913Z UID:indico-contribution-291-161@indico.ipb.ac.rs DESCRIPTION:Speakers: Miklos Kozlovszky (OU)\nLarge-scale high performance systems have significant amount of processing power. HP-SEE's HPC/Superco mputing infrastructure is geologically distributed\, and provide 24/7\, la rge scale\, high performance computing services primarily for various high -end research communities thus such system can be categorized as critical regional/national infrastructure. System features such as non-stop availab ility\, large scale processing power and community based usage make such i nfrastructure vulnerable against malicious attacks. In order to decrease t he menace\, we designed the Advanced Vulnerability Assessment Tool for HPC /supercomputing Systems. We propose the implementation of the tool that ar e integrated to the HP-SEE infrastructure. Our vulnerability assessment so ftware can submit jobs into the HP-SEE infrastructure and run vulnerabilit y assessment on the components of the infrastructure. The decentralized Se curity Monitor collects and stores the results from the components and mak es them available via a web interface for the local/regional administrator s. We tested our solution from reliability and from performance point of v iew as well.\n\nhttps://events.saifa.rs/event/291/contributions/161/ LOCATION:National Library of Serbia URL:https://events.saifa.rs/event/291/contributions/161/ END:VEVENT BEGIN:VEVENT SUMMARY:DNA muligene approach on HPC using RAxML software DTSTART;VALUE=DATE-TIME:20121017T103000Z DTEND;VALUE=DATE-TIME:20121017T110000Z DTSTAMP;VALUE=DATE-TIME:20261010T225913Z UID:indico-contribution-291-162@indico.ipb.ac.rs DESCRIPTION:Speakers: Luka Filipovic (University of Montenegro)\nComputati onal phylogeny is a challenging even for the most powerful supercomputers. One of significant application in this area is Randomized Axelerated Maxi mum Likelihood (RAxML) which is used for sequential and parallel Maximum L ikelihood based inference of large phylogenetic trees. \n\nWe choose 5 dif ferent genes\, two real genes (part of D-loop and Cytochrome b of differe nt European salmond fish species) both from mitochondrial genome and addit ional three designed genes in order to test reliability of constructed cen sus phylogeny tree. Two of those “fake” genes were designed with phylo geny information similar to phylogeny of real genes while the third one wa s completely different. Using of multigene option of RAxML software we tes t contribution of each gene (percentage of base pares in tested genes) in terms of gene contribution in phylogeny tree construction. We additionally test contribution of gene position in analysis in terms of final results of phylogeny reconstruction. \n\nThis paper will also cover scalability re sults of multigene tests on high-performance computers for coarse and fine grained parallelization using MPI\, Pthreads and hybrid version.\n\nhttps ://events.saifa.rs/event/291/contributions/162/ LOCATION:National Library of Serbia URL:https://events.saifa.rs/event/291/contributions/162/ END:VEVENT BEGIN:VEVENT SUMMARY:Investigations of biomolecular systems within the ISyMAB simulatio n framework DTSTART;VALUE=DATE-TIME:20121019T113000Z DTEND;VALUE=DATE-TIME:20121019T120000Z DTSTAMP;VALUE=DATE-TIME:20261010T225913Z UID:indico-contribution-291-163@indico.ipb.ac.rs DESCRIPTION:Speakers: Ionut Vasile (IFIN-HH)\nISyMAB is an integrated fram ework that provides secured access to a distributed set of molecular dynam ics tools for modeling and simulation of large bio-systems using high-perf ormance computing. It relies upon open-source software (such as NAMD\, MMT SB tool set\, VMD) and in-house developed analysis scripts\, which are mad e available through a\nuser-friendly graphical interface.\n\nISyMAB brings a significant contribution to the optimization of the creation of the fil es needed by the job management system and the simulation description file s. Also\, it minimizes the time between successive runs\, making the nodes within the HPC clusters run with maximum efficiency.\n\nThe use and the p erformances of the framework is illustrated through the molecular dynamics study of an acid-sensing ion channel in a 200x200 Angstrom lipid bilayer simulated within a 800 000 atoms system.\n\nhttps://events.saifa.rs/event/ 291/contributions/163/ LOCATION:National Library of Serbia URL:https://events.saifa.rs/event/291/contributions/163/ END:VEVENT BEGIN:VEVENT SUMMARY:EagleEye: Feature Extraction from Satellite Images Using a Hybrid Computing Architecture DTSTART;VALUE=DATE-TIME:20121018T134500Z DTEND;VALUE=DATE-TIME:20121018T150000Z DTSTAMP;VALUE=DATE-TIME:20261010T225913Z UID:indico-contribution-291-172@indico.ipb.ac.rs DESCRIPTION:Speakers: Razvan Dobre (University Politehnica of Bucharest)\n Feature extraction from satellite images has become a wide area of interes t in the last two decades with the increase in the number of commercial ea rth observation satellites. This work focuses on extracting roads and citi es from true color multi-spectral images that suffer from different qualit y problems like blurriness\, increased amount of noise or abnormal color v ariations. To assist in the feature extraction process we extract city loc ation information from almost 200 military maps. We present an approach fo r automatic and independent road detection in satellite images\, an automa tic city detection process in military maps and a semi-automatic (assisted ) method of detecting street layout inside cities in satellite images. We also evaluate the accuracy and performance of our implementation by tests that are done using a parallel infrastructure running over different types of blades inside an HPC computing cluster.\n\nhttps://events.saifa.rs/eve nt/291/contributions/172/ LOCATION:National Library of Serbia URL:https://events.saifa.rs/event/291/contributions/172/ END:VEVENT BEGIN:VEVENT SUMMARY:A new microRNA target prediction tool identifies a novel interacti on of a putative miRNA with CCND2 DTSTART;VALUE=DATE-TIME:20121017T093000Z DTEND;VALUE=DATE-TIME:20121017T100000Z DTSTAMP;VALUE=DATE-TIME:20261010T225913Z UID:indico-contribution-291-165@indico.ipb.ac.rs DESCRIPTION:Speakers: Anastasis Oulas (IMBG-HCMR)\nComputational methods f or miRNA target prediction vary in the algorithm used\; and while one can state opinions about the strengths or weaknesses of each particular algori thm\, the fact of the matter is that they fall substantially short of capt uring the full detail of physical\, temporal\, and spatial requirements of miRNA::target-mRNA interactions. Here\, we introduce a novel miRNA targe t prediction tool called Targetprofiler that utilizes a probabilistic lear ning algorithm in the form of a hidden Markov model trained on experimenta lly verified miRNA targets. Using a large scale protein down-regulation da taset we validate our method and compare its performance to existing tools . We find that Targetprofiler exhibits greater correlation between computa tional predictions and protein down-regulation and predicts experimentally verified miRNA targets more accurately than 3 other tools. Concurrently\, we use primer extension to identify the mature sequence of a novel miRNA gene recently identified within a cancer associated genomic region and use Targetprofiler to predict its potential targets. Experimental verificatio n of the ability of this small RNA molecule to regulate the expression of CCND2\, a gene with documented oncogenic activity\, confirms its functiona l role as a miRNA. These findings highlight the competitive advantage of o ur tool and its efficacy in extracting bio-logically significant results.\ n\nhttps://events.saifa.rs/event/291/contributions/165/ LOCATION:National Library of Serbia URL:https://events.saifa.rs/event/291/contributions/165/ END:VEVENT BEGIN:VEVENT SUMMARY:Parallellizing computational models of memory function for the inv estigation of sustained activity in the prefrontal cortex DTSTART;VALUE=DATE-TIME:20121017T120000Z DTEND;VALUE=DATE-TIME:20121017T123000Z DTSTAMP;VALUE=DATE-TIME:20261010T225913Z UID:indico-contribution-291-166@indico.ipb.ac.rs DESCRIPTION:Speakers: Anastasis Oulas ()\nNeurons in the prefrontal cortex display sustained activity in response to environmental or internal stimu li\, that continues until the behavioral outcome or a reward signal arrive s. Large-scale modeling studies have proposed intensive recurrence and slo w excitation mediated by NMDA receptors as the mechanisms able to support the sustained excitation in these neurons. In addition\, electrophysiologi cal studies suggest that single-cell intrinsic currents also underlie the delayed excitation of prefrontal neurons. In order to study learning and m emory processes\, we develop detailed biophysical computational models of small neural circuits of the prefrontal cortex (PFC). We use these models in order to study the role of biophysical and anatomical mechanisms in the emergence and maintenance of sustained activity. Additionally\, we dissec t the contribution of different types of interneurons in this sustained ac tivity. This computational work provides (a) some of the most realistic bi ophysical models of neurons in the brain which are publicly available and used by numerous labs worldwide and (b) generates interesting predictions which steer the interest of the neuroscience community and open up new ave nues for experimental verifications. All of our models are developed withi n the open source Neuron simulation environment and were parallelized for the HPCG Infrastructure provided by HP-SEE. Benchmarks show a significan t speedup when simulations are run on parallel environments.\n\nhttps://ev ents.saifa.rs/event/291/contributions/166/ LOCATION:National Library of Serbia URL:https://events.saifa.rs/event/291/contributions/166/ END:VEVENT BEGIN:VEVENT SUMMARY:Computational approaches for electronic properties of semiconducti ng materials and nanostructures DTSTART;VALUE=DATE-TIME:20121018T101500Z DTEND;VALUE=DATE-TIME:20121018T104500Z DTSTAMP;VALUE=DATE-TIME:20261010T225913Z UID:indico-contribution-291-167@indico.ipb.ac.rs DESCRIPTION:Speakers: Nenad Vukmirovic (Scientific Computing Laboratory\, Institute of Physics Belgrade\, University of Belgrade)\nDensity functiona l theory (DFT) provides a reliable theoretical framework for studying the electronic properties of atoms\, molecules\, bulk materials\, surfaces\, i nterfaces\, etc. However\, due to its computational effort\, the calculati ons based on DFT are typically performed only for relatively small molecul es or for crystalline materials where periodicity of the structure can be exploited. There is a wealth of highly relevant systems which are currentl y beyond the reach of standard DFT calculations\, such as\, for example\, disordered conjugated polymers\, inorganic nanocrystals\, and polycrystall ine materials. To study these systems\, one typically needs to do the calc ulation for a supercell containing thousands of atoms to get reliable info rmation about the properties of the system.\n\nThe methods that can be use d to study even such systems will be presented and computational aspects o f the applications of these methods will be discussed. \n\nCharge patching method (CPM) [1] is the method for the construction of electronic charge density of the system that avoids demanding self-consistent DFT calculatio ns. It is based on the idea that electronic charge density in the neighbor hood of an atom depends mainly on its local environment. Such an assumptio n is typically valid in semiconducting and insulating materials without an y long-range charge transfer. The contribution of each atom to electronic charge density of the system is therefore extracted from the calculation o f some small prototype system where atoms have the same environment as in the large system under study. Electronic charge density of the large syste m is then simply obtained by adding the contributions of each atom. With e lectronic charge density at hand\, one gets the single-particle Hamiltonia n by solving the Poisson equation for the Hartree potential and using the local density approximation formula for the exchange-correlation potential .\n\nTo study the electrical properties of the material\, one does not nee d to calculate all the electronic states of the Hamiltonian but only these in the region near the band gap. Overlapping fragments method (OFM) [2] w as developed to efficiently find these states. The method is in particular suited to study disordered conjugated polymers [3]. It is based on the di vison of the system into fragments and the representation of the Hamiltoni an in the basis of molecular orbitals of these fragments. It is typically sufficient to use only a few molecular orbitals of each fragment. This app roach strongly reduces the size of the Hamiltonian matrix that needs to b e diagonalized down to the size of several hundreds.\n\nFinally\, several applications of these methods in the studies of organic solar cell materia ls will be briefly presented.\n\n[1] N. Vukmirovic and L.-W. Wang\, J. Che m. Phys. 128\, 121102 (2008).\n[2] N. Vukmirovic and L.-W. Wang\, J. Chem. Phys. 134\, 094119 (2011).\n[3] N. Vukmirovic and L.-W. Wang\, J. Phys. C hem. B 115\, 1792 (2011).\n\nhttps://events.saifa.rs/event/291/contributio ns/167/ LOCATION:National Library of Serbia URL:https://events.saifa.rs/event/291/contributions/167/ END:VEVENT BEGIN:VEVENT SUMMARY:Use of High Performance Computing in (Bio)Chemistry DTSTART;VALUE=DATE-TIME:20121019T070000Z DTEND;VALUE=DATE-TIME:20121019T074500Z DTSTAMP;VALUE=DATE-TIME:20261010T225913Z UID:indico-contribution-291-168@indico.ipb.ac.rs DESCRIPTION:Speakers: Ivan O. Juranić (Department of Chemistry-IChTM\, Un iversity of Belgrade\, Njegoševa 12\, Belgrade\, Serbia)\nA short overvie w of computational modeling is presented. The major features of molecular geometry optimization are given\, and the computational demands are analyz ed. Short outlines of strategies that are in use for speeding-up of comput ation are presented\, too.\nIn the second part of presentation\, the speci fic examples\, and accompanying results of computational applications in c hemistry are given. The aim is to make a rational design of efficient drug s\, and\, on other hand\, to explain the mechanisms of complex chemical re actions. In last two centuries of Chemistry\, the models are in heart of a mazing progress made in it. Many models deal with non-observables\, and va lidity of model can be tested only by simulations. These simulations could be done on various levels of complexity\, and some illustrative examples are presented.\nA study of molecular potential energy surface (PES) is don e on QM level in order to explain the mechanism of the reaction of carbony l compounds with bromoform. A successful application of non-observable mo lecular descriptor – partial atomic charges - is presented\, too.\nThe a pplication of MM and MD simulations for the description of interaction of small molecules with proteins was successfully done on several examples. T he computationally derived molecular descriptors were used for statistical modeling of the correlation between molecular structure and biological ac tivity of compounds. These correlations give the leverage for the design of more potent drugs.\n\nhttps://events.saifa.rs/event/291/contributions/1 68/ LOCATION:National Library of Serbia URL:https://events.saifa.rs/event/291/contributions/168/ END:VEVENT BEGIN:VEVENT SUMMARY:The impact of GISELA Science Gateway (GSG) on the supported Latin America VRC's DTSTART;VALUE=DATE-TIME:20121019T074500Z DTEND;VALUE=DATE-TIME:20121019T083000Z DTSTAMP;VALUE=DATE-TIME:20261010T225913Z UID:indico-contribution-291-169@indico.ipb.ac.rs DESCRIPTION:Speakers: Jesus Cruz Guzman (Universidad Nacional Autonoma de Mexico UNAM)\nhttps://events.saifa.rs/event/291/contributions/169/ LOCATION:National Library of Serbia URL:https://events.saifa.rs/event/291/contributions/169/ END:VEVENT BEGIN:VEVENT SUMMARY:LinkSCEEM2: Development of an HPC ecoSystem in the Eastern Mediter ranean DTSTART;VALUE=DATE-TIME:20121018T070000Z DTEND;VALUE=DATE-TIME:20121018T074500Z DTSTAMP;VALUE=DATE-TIME:20261010T225913Z UID:indico-contribution-291-170@indico.ipb.ac.rs DESCRIPTION:Speakers: Jens Wiegand (CASTORC)\nhttps://events.saifa.rs/even t/291/contributions/170/ LOCATION:National Library of Serbia URL:https://events.saifa.rs/event/291/contributions/170/ END:VEVENT BEGIN:VEVENT SUMMARY:International HPC - Building bigger pyramide DTSTART;VALUE=DATE-TIME:20121017T081500Z DTEND;VALUE=DATE-TIME:20121017T090000Z DTSTAMP;VALUE=DATE-TIME:20261010T225913Z UID:indico-contribution-291-171@indico.ipb.ac.rs DESCRIPTION:Speakers: Richard Kenway ()\nhttps://events.saifa.rs/event/291 /contributions/171/ LOCATION:National Library of Serbia URL:https://events.saifa.rs/event/291/contributions/171/ END:VEVENT BEGIN:VEVENT SUMMARY:Regional eInfrastructure Development for South East Europe’s Res earch Communities DTSTART;VALUE=DATE-TIME:20121017T073000Z DTEND;VALUE=DATE-TIME:20121017T081500Z DTSTAMP;VALUE=DATE-TIME:20261010T225913Z UID:indico-contribution-291-173@indico.ipb.ac.rs DESCRIPTION:Speakers: Ioannis Liabotis (GRNET)\nhttps://events.saifa.rs/ev ent/291/contributions/173/ LOCATION:National Library of Serbia URL:https://events.saifa.rs/event/291/contributions/173/ END:VEVENT BEGIN:VEVENT SUMMARY:Design of novel nano-photonic materials DTSTART;VALUE=DATE-TIME:20121019T100000Z DTEND;VALUE=DATE-TIME:20121019T103000Z DTSTAMP;VALUE=DATE-TIME:20261010T225913Z UID:indico-contribution-291-174@indico.ipb.ac.rs DESCRIPTION:Speakers: Manthos Papadopoulos (National Hellenic Research Fou ndation)\nDesign of novel nano-photonic materials\n\n\nManthos G. Papadopo ulos*\, Aggelos Avramopoulos\n\nInstitute of Biology\, Medicinal Chemistry and Biotechnology\, National Hellenic Research Foundation\, 48 Vas. Const antinou Ave.\, Athens 116 35\, Greece\n*E-mail: mpapad@eie.gr\n\n\n We have designed or selected a series of derivatives\, which have very high linear and nonlinear optical L&(NLO) properties and which are likely to be useful for photonic applications. The compounds belong to three families : \n(a) Noble gas derivatives. These involve one or more noble gas (Ng) atoms inserted in the chemical bond A-B [1-2]. We have considered a numbe r of such derivatives\, for example HArF\, HXeC2H. It has been found that\ , in general\, the inserted noble gas atom increases remarkably the NLO p roperties. Two novel Xe derivatives have also been proposed: HXeOXeF and F XeOXeF. Their electronic ground state\, the stability and their L&NLO prop erties have been studied [2]. \n(b) Ni-dithiolene derivatives. We discuss how the diradicaloid character (DC) of Ni(SCH)4\, which is used as model d erivative\, affects the L&NLO properties. It has been found that the quasi degeneracy of the two lowest-energy singlet states\, 1 1Ag and 1 1B1u\, th e clear DC nature of the former and the very large number of low-lying sta tes increase the NLO properties. The very large effect of Ni on the proper ties of interest is demonstrated. A series of Ni-dithiolene derivatives w ith very large NLO properties are proposed [3].\n(c) Fullerenes. Using a w ide variety of quantum-chemical methods we have analyzed in detail the L&N LO properties of [60]fullerene-chromophore dyads of different electron-don or character [4]. The dyads are composed of [60]fullerene covalently linke d with 2\,1\,3-benzothiadiazole and carbazole derivatives. Substitution o f 2\,1\,3-benzothiadiazole by the triphenylamine group significantly incr eases the electronic first and second hyperpolarizabilities. \n These studies have been performed by employing a series of methods: HF\, DFT\, MP2\, MS-CASPT2\, CCSD and CCSD(T). \n\n1. A.Avramopoulos\, H. Reis\, J . Li and M. G. Papadopoulos\, J. Am. Chem. Soc.\, 126\, 6179 (2004)\; F. Holka\, A. Avramopoulos\, O. Loboda\, V. Kellöand M. G. Papadopou los\, Chem Phys. Letters\, 472\, 185 (2009)\; A. Avramopoulos\, L. Serrano-Andrés\, J. Li\, M. G. Papadopoulos\, J. Chem. Theor. Comp.\, 6\ , 3365 (2010)\; A. Avramopoulos\, Luis-Serrano-Andrés\, H. Reis\, M. G.Papadopoulos\, J. Chem. Phys.\, 127\, 214102 (2007).\n2. A. Avram opoulos\, J. Li\, N. Holzmann\, G. Frenking\, M. G. Papadopoulos\, J. Phys. Chem. A\, 115\, 10226 (2011).\n3. L. Serrano-Andrés\, A. Avramop oulos\, J. Li\, P. Labéquerie\, D. Bégué\, V. Kellö\, and M. G. Pa padopoulos\, J. Chem. Phys\,. 131\, 134312 (2009). \n4. O. Loboda\, R. Zalesny\, A. Avramopoulos\, J. M. Luis\, B. Kirtman\, N. Tagmatarch is\, H. Reis\, M. G. Papadopoulos\, J. Phys. Chem. A\, 113\, 1159 (200 9).\n\nhttps://events.saifa.rs/event/291/contributions/174/ LOCATION:National Library of Serbia URL:https://events.saifa.rs/event/291/contributions/174/ END:VEVENT BEGIN:VEVENT SUMMARY:Reflections on Paralelization of Gravity Inversion DTSTART;VALUE=DATE-TIME:20121018T104500Z DTEND;VALUE=DATE-TIME:20121018T111500Z DTSTAMP;VALUE=DATE-TIME:20261010T225913Z UID:indico-contribution-291-175@indico.ipb.ac.rs DESCRIPTION:Speakers: Neki Frasheri (Polytechnic University of Tirana\, Fa culty of Information Technology)\nIn the paper there is presented a summar y of results obtained for the parallelization of 3D gravity inversion usin g the principle of algorithm CLEAN [Hogborn 1974]\, undertaken in framewor k o f FP7 project HP-SEE. The problem is “ill posed” with the definiti on of [Hadamard 1902].\nThe core of our algorithm consists in cross-calcul ation of the effect of 3D array of underground nodes to each of 2D array g round surface points. The process is iterative\, updating at each iteratio n the mass density of one node with a predefined step in order to decrease of the least squares error. The volume of calculations for each iteration was calculated of the order O (N^5). The number of iterations to obtain t he same anomalous body resulted of the order O (N^3)\, leading to an order of calculations O (N^8). \nExperiments were carried out in two HPC system s – the HPCG system of IICT-BAS in Sofia\, Bulgaria\, and in the SGE sys tem of NIIFI at University of Pécs\, Hungary\, using both OpenMP and MPI. Obtained results confirmed the order of calculations of O (N^8). The abso lute user-time and wall-time was obtained. For moderate sized models with geosection 4000m*4000m*2000m using 3D arrays of 101*101*51 nodes\, using u p to 1\,000 parallel cores\, the run-time reached the level of 100\,000 se conds (27 hours). \nTests with models and field data resulted with clear m ass density contrasts between the anomalous bodies and the medium where th ey were situated\, in the same way as in real geological structures. Tests with multi-bodies geosections indicated the tendency of the algorithm to converge towards single body solutions. \nMPI tests carried out in HPCG sy stem of IICT-BAS showed a systematic time overhead when the number of para llel processes increased from 8 to 32. Hypothesizing that this was caused because of inter-process communication between computer nodes\, a predicti on of potential run-time in multi-cluster MPI grid platforms was undertake n\, taking into consideration the relative low bandwidth of campus and met ropolitan links (compared with the bandwidth of the BUS connecting cores o f a computer node). The extrapolation of data led to the hypothesis that t he increase in cores using multi-cluster grids may not result in reduction of the run-time.\n\nhttps://events.saifa.rs/event/291/contributions/175/ LOCATION:National Library of Serbia URL:https://events.saifa.rs/event/291/contributions/175/ END:VEVENT BEGIN:VEVENT SUMMARY:Using Parallel Computing to Calculate Quark-Antiquark Potential f rom Lattice QCD DTSTART;VALUE=DATE-TIME:20121018T134500Z DTEND;VALUE=DATE-TIME:20121018T150000Z DTSTAMP;VALUE=DATE-TIME:20261010T225913Z UID:indico-contribution-291-176@indico.ipb.ac.rs DESCRIPTION:Speakers: Dafina Xhako (Department of Engineering Science\, Pr ofessional Studies Faculty "Alexander Moisiu" University\, Durres\, Albani a\,)\nLattice Quantum Chromo-dynamics (LQCD) is an algorithmic formulation of QCD\, the mathematical model that describes quarks and their interacti ons. Computations in LQCD are typically very expensive and run on dedicate d supercomputers and large computer clusters for many months. In this pape r the calculations are performed in one of the clusters for supercomputing of HP-SEE (High-Performance Computing Infrastructure for South East Europ e’s Research Communities) project\, that is located in Bulgaria (BG HPC) . We use parallel computing with Fermiqcd software\, to determine the stat ic quark-antiquark potential. In LQCD the static quark-antiquark potential can be derive from the Wilson loops. The standard method use rectangular Wilson loops\, while we test 3-D Wilson loops\, using simulation with SU(3 ) gauge field configuration for different values of coupling constant and for different lattice sizes. The calculations are made for 100 configurati ons\, statistically independent\, of gauge fields of the lattice. We extra polate in continuum limit for different lattice constant to take string te nsion parameter and to compare with the experimental value.\n\nhttps://eve nts.saifa.rs/event/291/contributions/176/ LOCATION:National Library of Serbia URL:https://events.saifa.rs/event/291/contributions/176/ END:VEVENT BEGIN:VEVENT SUMMARY:An Analysis of FFTW and FFTE Performance DTSTART;VALUE=DATE-TIME:20121017T150000Z DTEND;VALUE=DATE-TIME:20121017T153000Z DTSTAMP;VALUE=DATE-TIME:20261010T225913Z UID:indico-contribution-291-177@indico.ipb.ac.rs DESCRIPTION:Speakers: Josip Jakic (Scientific Computing Laboratory\, Insti tute of Physics Belgrade)\nOne of the most frequently used algorithms in e ngineering and scientific applications is Fast Fourier Transform (FFT). It s open source implementation (Fastest Fourier Transform of the West\, FFTW ) is widely used\, mainly due to its excellent performance\, comparable to the vendor-supplied libraries. On the other hand\, even if not yet in a f ully production state\, FFTE (Fastest Fourier Transform of the East) keeps up with FFTW\, and outperforms it for very large transform sizes. Here we present results of the performance and scalability tests of FFTW and FFTE libraries. Comparison is done using different compilers and parallelizati on approaches on Curie and Jugene supercomputers.\n\nhttps://events.saifa. rs/event/291/contributions/177/ LOCATION:National Library of Serbia URL:https://events.saifa.rs/event/291/contributions/177/ END:VEVENT BEGIN:VEVENT SUMMARY:GPAW optimisations DTSTART;VALUE=DATE-TIME:20121018T134500Z DTEND;VALUE=DATE-TIME:20121018T150000Z DTSTAMP;VALUE=DATE-TIME:20261010T225913Z UID:indico-contribution-291-178@indico.ipb.ac.rs DESCRIPTION:Speakers: Petar Jovanovic (Scientific Computing Laboratory\, I nstitute of Physics Belgrade)\nGPAW software package implements efficient calculation of electronic structure of materials\, based on the density fu nctional theory and projector-augmented wave method. This C/Python code us es real-space formalism that allows flexible boundary conditions and effic ient parallelization. Here we present results of the optimization of GPAW hybrid code (OpenMP and MPI). OpenMP performance traps are identified and discussed\, as well as general performance gains and tradeoffs between pur e message passing and hybrid code.\n\nhttps://events.saifa.rs/event/291/co ntributions/178/ LOCATION:National Library of Serbia URL:https://events.saifa.rs/event/291/contributions/178/ END:VEVENT BEGIN:VEVENT SUMMARY:Quenched Hadron Spectroscopy Using FermiQCD DTSTART;VALUE=DATE-TIME:20121018T134500Z DTEND;VALUE=DATE-TIME:20121018T150000Z DTSTAMP;VALUE=DATE-TIME:20261010T225913Z UID:indico-contribution-291-179@indico.ipb.ac.rs DESCRIPTION:Speakers: Rudina Zeqirllari (University of Tirana\, Faculty of Natural Sciences\, Department of Physics)\nFermiQCD is a C++ library for fast development of parallel Lattice Quantum Field Theory computations. It has been developed following a top-down fully Object Oriented design appr oach with focus on simplicity of use. We present simulations for the hadro n spectrum with the Wilson action in quenched QCD carried out on the BG HP C cluster\, using this tool kit. Testing Fermiqcd as a tool kit for parall el lattice QCD applications and see how parallel calculations are implemen ted in this package are some aims of this work. Simulations are made with the plaquette gauge action on 8^4\, 12^4 and 16^4 lattices at three lattic e spacings\, for a total number of 300 SU(3) gauge configurations. The mas ses of pi and rho – meson\, nucleon and delta baryons are computed for t hese conditions. For a constant physical volume we study the dependence of the hadron masses on the lattice spacing. After chiral and continuum extr apolations\, the agreement of the calculated mass spectrum for this kind o f fermions with experiment is reasonable.\n\nhttps://events.saifa.rs/event /291/contributions/179/ LOCATION:National Library of Serbia URL:https://events.saifa.rs/event/291/contributions/179/ END:VEVENT BEGIN:VEVENT SUMMARY:SCL Quantum Espresso Extensions DTSTART;VALUE=DATE-TIME:20121017T133000Z DTEND;VALUE=DATE-TIME:20121017T140000Z DTSTAMP;VALUE=DATE-TIME:20261010T225913Z UID:indico-contribution-291-180@indico.ipb.ac.rs DESCRIPTION:Speakers: Dusan Stankovic (Scientific Computing Laboratory\, I nstitute of Physics Belgrade)\nQuantum Espresso (QE) software package allo ws electronic-structure calculations and materials modeling at the nanosca le\, based on density-functional theory\, plane waves\, and pseudopotentia ls. It extensively uses Fast Fourier Transform (FFT) during all computatio ns. In addition to the built in FFT libraries\, QE enables integration of newly developed FFT algorithms. Since Fastest Fourier Transform of the Eas t (FFTE) library has shown performance comparable with the widely used and vendor-supplied libraries\, the same behavior is foreseen in QE. In this paper we present FFTE-enabled and thread-enabled FFTW3 extensions of QE\, together with benchmarking and performance results.\n\nhttps://events.saif a.rs/event/291/contributions/180/ LOCATION:National Library of Serbia URL:https://events.saifa.rs/event/291/contributions/180/ END:VEVENT BEGIN:VEVENT SUMMARY:Number Theory Algorithms on GPU Cluster DTSTART;VALUE=DATE-TIME:20121017T160000Z DTEND;VALUE=DATE-TIME:20121017T163000Z DTSTAMP;VALUE=DATE-TIME:20261010T225913Z UID:indico-contribution-291-181@indico.ipb.ac.rs DESCRIPTION:Speakers: Dobromir Georgiev (Institute of Information and Comm unication Technologies\, BAS)\nMany algorithms from Number Theory and thei r implementation in software are of high practical\nimportance\, since th ey are the building primitives of many protocols for data encryption and\n authentication of Internet connections. Number theory algorithms are also the basic part of\ncryptanalytic procedures. Many of these algorithms can be parallelized in a natural way. In this\npaper we describe our efforts t o develop a software package that implements various Number Theory\nalgori thms on GPU clusters and in partial our implementations of integer factori zation\nusing NVIDIA CUDA on clusters equipped with NVIDIA GPUs. Also we r eport results of our\nexperiments regarding the performance of our implem entation.\n\nhttps://events.saifa.rs/event/291/contributions/181/ LOCATION:National Library of Serbia URL:https://events.saifa.rs/event/291/contributions/181/ END:VEVENT BEGIN:VEVENT SUMMARY:On HPC for Hyperspectral Image Processing DTSTART;VALUE=DATE-TIME:20121017T143000Z DTEND;VALUE=DATE-TIME:20121017T150000Z DTSTAMP;VALUE=DATE-TIME:20261010T225913Z UID:indico-contribution-291-182@indico.ipb.ac.rs DESCRIPTION:Speakers: Mihnea Dulea (National Institute of Physics and Nucl ear Engineering)\nHyperspectral image processing still requires nowadays c onsiderable computational and storage resources\, beyond the available one s for a single server. In particular\, clustering of images gathered from the current satellites can be done in a reasonable time only using high pe rformance computing facilities.\n\nIn this paper we discuss the latest app roaches for fuzzy clustering techniques that are adapted to work on hundre ds of processors as well as the pre-processing techniques for data splitti ng and reading. Comparisons between different techniques are based on impl ementations for BlueGene/P.\n \nThe paper exposes part of the concepts pr esented in [1] and [2]\,\nas well as experimental results.\n\n[1] D. Petcu \, D. Zaharie\, S. Panica\, A. S. Hussein\, A. Sayed\, H. El-Shishiny\, “Fuzzy Clustering of Large Satellite Images using High Performance Compu ting\,” In Proceedings of SPIE Volume 8183\, SPIE Remote Sensing Confere nce: High-Performance Computing in Remote Sensing\, http://dx.doi.org/10.1 117/12.898281\, 2011\n\n[2] A.C. Toma\, S. Panica\, D. Zaharie\, D. Petcu \, "Computational Challenges in Processing Large Hyperspectral Images"\, s ubmitted to Grid\, Cloud & High Performance Computing Science"\, RO-LCG 20 12\, October 2012\n\nhttps://events.saifa.rs/event/291/contributions/182/ LOCATION:National Library of Serbia URL:https://events.saifa.rs/event/291/contributions/182/ END:VEVENT BEGIN:VEVENT SUMMARY:Electronic Structure and Lattice Dynamics Calculations of FeSb2 an d CoSb2 DTSTART;VALUE=DATE-TIME:20121018T153000Z DTEND;VALUE=DATE-TIME:20121018T160000Z DTSTAMP;VALUE=DATE-TIME:20261010T225913Z UID:indico-contribution-291-183@indico.ipb.ac.rs DESCRIPTION:Speakers: Milos M. Radonjic (Scientific Computing Laboratory\, Institute of Physics Belgrade\, University of Belgrade)\nFirst principles calculations of the electronic structure and lattice\ndynamics of FeSb2 a nd CoSb2 are performed using the Quantum Espresso package. Calculated vibr ational modes and frequencies are used for proper assignation of the norma l modes in the corresponding Raman scattering experiments.\n\nhttps://even ts.saifa.rs/event/291/contributions/183/ LOCATION:National Library of Serbia URL:https://events.saifa.rs/event/291/contributions/183/ END:VEVENT BEGIN:VEVENT SUMMARY:Iterative Perturbative Method for a Study of Disordered Strongly C orrelated Systems DTSTART;VALUE=DATE-TIME:20121018T131500Z DTEND;VALUE=DATE-TIME:20121018T134500Z DTSTAMP;VALUE=DATE-TIME:20261010T225913Z UID:indico-contribution-291-184@indico.ipb.ac.rs DESCRIPTION:Speakers: Jaksa Vucicevic (Institute of Physics Belgrade\, Bel grade University\, Pregrevica 118\, 11080 Belgrade)\nTwenty years after th e introduction of the Dynamical Mean Field Theory as a means of solving th e Hubbard model\, the focus has moved towards computationally very intensi ve multi-site and multi-orbital calculations\, which are aimed at includin g spatial correlations\, disorder and detailed atomic structure to the oth erwise fairly simple model. However\, limited computational resources crea te a need for faster and more optimized codes and even approximative solut ions. We present here a highly optimized parallel implementation of the ap proximative second order perturbative approach especially suitable for a s tudy of strongly disordered correlated systems. On this example\, we give an overview of numerical challenges that arise in dealing with large syste ms of non-linear equations\, ill-behaved discretized functions and self-co nsistent calculations in general. In the end\, we discuss results of perfo rmance tests\, outline possible improvements and make a comparison to the exact\, but computationally very demanding Quantum Monte Carlo method.\n\n https://events.saifa.rs/event/291/contributions/184/ LOCATION:National Library of Serbia URL:https://events.saifa.rs/event/291/contributions/184/ END:VEVENT BEGIN:VEVENT SUMMARY:Quantum-Chemical Calculations for the Quantitative Estimations of the Processes in DNA DTSTART;VALUE=DATE-TIME:20121017T100000Z DTEND;VALUE=DATE-TIME:20121017T103000Z DTSTAMP;VALUE=DATE-TIME:20261010T225913Z UID:indico-contribution-291-185@indico.ipb.ac.rs DESCRIPTION:Speakers: George Mikuchadze (Programmer in Georgian Research a nd Educational Networking Association - GRENA)\nInvestigated the DNA tende ncy to denaturation using Dencity Functional(DFT) Theory method.\nPresence of the polaric solvents with small polarity index Et - such as ethanol\, in the aquatic ambient causes protons transfer between nucleobases pair\, which in turn fires DNA denaturation and mutation proceses. Using Software for analysing chemical compounds the tautomeric equilibrium indexes of th e nucleobases were calculated. The software was ported on the HPC (NCIT-Cl uster) infrastructure.\n\nhttps://events.saifa.rs/event/291/contributions/ 185/ LOCATION:National Library of Serbia URL:https://events.saifa.rs/event/291/contributions/185/ END:VEVENT BEGIN:VEVENT SUMMARY:Development of o Hybrid Statistical Physics – Quantum Mechanical Methodology for Computer Simulations of Condensed Phases and its Implemen tation on High-Performance Computing Systems DTSTART;VALUE=DATE-TIME:20121019T090000Z DTEND;VALUE=DATE-TIME:20121019T093000Z DTSTAMP;VALUE=DATE-TIME:20261010T225913Z UID:indico-contribution-291-186@indico.ipb.ac.rs DESCRIPTION:Speakers: Ljupco Pejov (Institute of Chemistry\, Faculty of Sc ience\, Skopje\, Macedonia)\nA hybrid\, complex statistical mechanics – quantum mechanical approach which enables exact computational modeling of condensed phases at finite temperatures has been developed and implemented on high-performance computing systems. The computational approach is robu st and inherently sequential. First\, the studied physico-chemical system is modeled by a statistical physics approach\, either Monte Carlo (MC) or molecular dynamics (MD). Though in the first phase it is often sufficient to carry out a classical MC or MD simulation\, in particular cases\, when it is necessary\, one can also perform a quantum molecular dynamics simula tion (e.g. ADMP\, BOMD or CPMD). Even the classical MC/MD simulations carr ied out in the first phase can be based on interaction potentials which ha ve been derived by quantum chemical calculations. Sequentially to the firs t phase of the computation\, which actually generates either a MD trajecto ry or an appropriate sample of the system’s configurational space\, the generated trajectories are analyzed employing time-series analytic methods . In the case of e.g. MC simulations\, this is done most frequently by com putation and subsequent integration of the energy autocorrelation function \, which leads to the so-called correlation step. The last quantity is the n used to choose a representative number of configurations representing th e state of the physico-chemical system at finite temperature which will be further analyzed by a quantum mechanical approach. These\, appropriately chosen configurations for the system of interest\, are further modeled by exact quantum mechanical (QM) approach. The particular approach that needs to be implemented depends on the quantity that needs to be computed. For example\, in the case of X-H stretching vibrations\, the anharmonic X-H vi brational frequency is computed in a quantum mechanical manner with respec t to both electronic and nuclear subsystem. In this case\, first a 1D cut through the vibrational potential energy surface is computed at series of suitably generated points\, and subsequently\, the vibrational Schrodinger equation is solved either by diagonalization approach or using a variant of the discrete variable representation (DVR) methodology. As the statisti cal mechanics simulations are often done implementing periodic boundary co ndition\, the exact QM calculations in the final simulation phase are ofte n done implementing some sort of embedding of the relevant part of the sys tem. All these aspects of our developed methodology are illustrated throug h a particular example – the fluoroform solvated in liquid Kr and the no ncovalently bonded complexes which are formed between fluoroform and dimet hylether in liquid Kr. A vast variety of condensed phase systems can be tr eated by the developed approach. Achieving good parallel efficiency for ca lculations of such type is far from a trivial task without the use of high -performance low-latency MPI interconnect (such as\, e.g. a supercomputer or HPC cluster).\n\nhttps://events.saifa.rs/event/291/contributions/186/ LOCATION:National Library of Serbia URL:https://events.saifa.rs/event/291/contributions/186/ END:VEVENT BEGIN:VEVENT SUMMARY:Monte Carlo methods for Electron Transport: Scalability Study usin g HP-SEE infrastructure DTSTART;VALUE=DATE-TIME:20121018T083000Z DTEND;VALUE=DATE-TIME:20121018T091500Z DTSTAMP;VALUE=DATE-TIME:20261010T225913Z UID:indico-contribution-291-187@indico.ipb.ac.rs DESCRIPTION:Speakers: Aneta Karaivanova (IICT-BAS)\nIn this work we consid er Monte Carlo methods for solving quantum-kinetic integral equations whic h describe the electron transport in semiconductors. The corresponding alg orithms are included in SET (Simulation of Electron Transport) application . Here we study the scalability of the presented algorithms using HPC reso urces in South-Eastern Europe. Numerical results for parallel efficiency a nd computational cost are also presented. In addition we discuss the coord inated use of heterogeneous HPC resources from one and same application in order to achieve a good performance.\n\nhttps://events.saifa.rs/event/291 /contributions/187/ LOCATION:National Library of Serbia URL:https://events.saifa.rs/event/291/contributions/187/ END:VEVENT BEGIN:VEVENT SUMMARY:Using Structured Adaptive Computational Grid for Solving Multidime nsional Computational Physics Tasks DTSTART;VALUE=DATE-TIME:20121018T094500Z DTEND;VALUE=DATE-TIME:20121018T101500Z DTSTAMP;VALUE=DATE-TIME:20261010T225913Z UID:indico-contribution-291-188@indico.ipb.ac.rs DESCRIPTION:Speakers: Peter Bogatencov (RENAM Association)\nIn the work de scribed the algorithm and program for solving multidimensional problems re presented by differential equations with partial derivatives adopted for u sing SEE regional HPC resources. The algorithm based on the AMR method - a daptive mesh refinement of the computational grid. Utilization of AMR meth od can significantly improve the resolution of the difference grid in area s of high interest and accelerate the processes of the multi-dimensional p roblems calculating.\nOne of the methods that allow developing optimized a pplications and speeding up the process of complicated models execution is the method based on adaptive refinement of computational mesh – AMR (Ad aptive Mesh Refinement) method. Many complex problems of continuum mechani cs are numerically solved on structured or unstructured grids. To improve the accuracy of the calculations is necessary to choose a sufficiently sma ll grid (with a small cell size). This leads to the drawback of a substant ial increase of computation time. Therefore\, for the calculations of comp lex problems it is reasonable to use AMR method. That is\, the grid refine ment is performed only in the areas of interest of the structure\, where e .g. the shock waves are generated\, or a complex geometry or other such fe atures exist. Applying AMR the computing time is greatly reducing and the execution of the application on the resulting sequence of nested\, decreas ing nets can be parallelized. We are considering solution of two- and thre e- dimensional tasks of gas dynamics that have obvious practical interest. These solutions can be applied to many nowadays problems. However\, the m aking of three-dimensional calculations for high definition grids requires large computational resources.\nIn all cases\, at the beginning of solvin g the problem we define a way to highlight areas in which we need to const ruct the grid\, and then the program builds a sequence of grids and makes a decision on them. During calculations in the computational area there ar e domains with large gradients of the parameters - such as temperature\, p ressure\, density and others. These areas are contiguous with areas with a smooth behavior of the investigated functions. Therefore\, to reduce the requirements for computing resources a detailed grid with small mesh sizes can be created only in areas of high gradients. Approach to creation of s uch area - adaptive mesh refinement will significantly clarify the definit ion of the multi-dimensional flows features. The proposed AMR method is th e most suitable method of grid generation for solving three-dimensional pr oblem of the collapsing star. \nCalculations using of AMR method based on the hierarchical grid cells\, which can significantly improve the quality of the calculations in the various fields of science and engineering. Prog ram based on AMR technology uses object-oriented approach\, which is avail able in the current version of Fortran 90.\n\nhttps://events.saifa.rs/even t/291/contributions/188/ LOCATION:National Library of Serbia URL:https://events.saifa.rs/event/291/contributions/188/ END:VEVENT BEGIN:VEVENT SUMMARY:Determination of zone of flow instability in a gas flow past a sq uare particle in a narrow microchannel DTSTART;VALUE=DATE-TIME:20121018T150000Z DTEND;VALUE=DATE-TIME:20121018T153000Z DTSTAMP;VALUE=DATE-TIME:20261010T225913Z UID:indico-contribution-291-189@indico.ipb.ac.rs DESCRIPTION:Speakers: Kiril Shterev (Institute of Mechanics - BAS)\nRapidl y emerging micro-electro-mechanical devices create new potential microflui dic applications. Fluid flow regime is important for their design. For a g as flow the transition between steady and unsteady regimes occurs at small Knudsen number Kn < 0.1 (Kn = l0 / L\, where l0 is the mean free path of the gas molecules and L is the characteristic length). A continuum approac h based on the Navier-Stokes-Fourier equations is applicable for this inve stigation. On the other the microfluidic application requires the problem to be investigated starting at very low Mach numbers (M=0.1)\, close to in compressible regime. This makes pressure based methods very suitable for t his investigation. The system of Navier-Stokes-Fourier equations is calcul ated numerically using pressure based algorithm SIMPLE-TS 2D. The results are validated by comparison to data obtained by using molecular approach ( direct simulation Monte Carlo (DSMC) method).\n\nhttps://events.saifa.rs/e vent/291/contributions/189/ LOCATION:National Library of Serbia URL:https://events.saifa.rs/event/291/contributions/189/ END:VEVENT BEGIN:VEVENT SUMMARY:Numerical Simulations of the Structure and Transport Properties of the Complex Networks DTSTART;VALUE=DATE-TIME:20121018T121500Z DTEND;VALUE=DATE-TIME:20121018T124500Z DTSTAMP;VALUE=DATE-TIME:20261010T225913Z UID:indico-contribution-291-190@indico.ipb.ac.rs DESCRIPTION:Speakers: Igor Stankovic (Scientfic Computing Laboratory\, Ins titute of Physics Belgrade\, University of Belgrade)\nIn this talk we revi ew our recent numerical study of various complex networks. First\, we wil l introduce results of Monte Carlo simulations of the percolation and cond uctivity of two-dimensional random stick systems. Based on the renormalis ation group considerations\, generalized scaling function is introduced to describe the scaling behaviour of the percolation distribution moments\, i.e.\, average percolation density and percolation density variance [1]. W e show that the prefactors in the generalized scaling function depend on t he system aspect ratio. The definite parity of the prefactors in the gener alized scaling function for the first two moments is a generic feature of whole class of percolating systems. The conductivity of the random stick systems is investigated from the percolation up to ten times percolation d ensity. An analytic model is proposed describing transition from the condu ctivity determined by the structure of a percolating cluster to the conduc tivity of the dense random stick networks. The derived model for conductiv ity should be broadly applicable to the random networks of the rodlike par ticles [2].\n\nIn the second part of the talk\, we will present paths for optimization of the transport capacity of the complex networks without cha nging average connectivity or total network capacity. The focus is on effi cient routing [3]. The routing strategies are compared using two generic m odels\, i.e.\, Barabási-Albert scale-free network and scale-free network on lattice\, and academic router networks of the Netherlands and France. T he nodes without buffers are considered\, so\, if congestion occurs\, pack ets will be dropped. We propose a dynamic routing algorithm which automati cally extends path of the packet before it arrives at congested node. Simu lation results indicate that proposed routing strategy can further reduce number of dropped packets in a combination with the efficient path routing proposed by Yan et al. [4].\n\n[1] M. Zezelj\, I. Stankovic and A. Belic\ , "Finite-size Scaling in Asymmetric Systems of Percolating Sticks"\, Phys . Rev. E 85\, 021101 (2012).\n[2] M. Zezelj\, I. Stankovic\, “From perco lating to dense random stick networks: conductivity model investigation” \, submitted.\n[3] Jelena Smiljanic\, Milan Zezelj\, and Igor Stankovic\, “Study of routing strategies in the small complex networks”\, Telekom unikacije 9\, to appear.\n[4] G. Yan\, T. Zhou\, B. Hu\, Z.-Q. Fu\, and B. -H. Wang\, “Efficient Routing on Complex Networks”\, Phys. Rev. E 73\, 046108 (2006).\n\nhttps://events.saifa.rs/event/291/contributions/190/ LOCATION:National Library of Serbia URL:https://events.saifa.rs/event/291/contributions/190/ END:VEVENT BEGIN:VEVENT SUMMARY:Free-energy surfaces of 2-[(carboxymethyl)sulfanyl]-4-oxo-4-arylbu tanoic acids. Molecular dynamics study in explicit solvents. DTSTART;VALUE=DATE-TIME:20121019T110000Z DTEND;VALUE=DATE-TIME:20121019T113000Z DTSTAMP;VALUE=DATE-TIME:20261010T225913Z UID:indico-contribution-291-191@indico.ipb.ac.rs DESCRIPTION:Speakers: Branko Drakulic (Department of Chemistry-IChTM\, Uni versity of Belgrade)\nThe 2-[(carboxymethyl)sulfanyl]-4-oxo-4-arylbutanoic acids (Scheme 1) exert antiproliferative potency and significant selectiv ity toward human tumor cells in vitro in low micromolar to submicromolar c oncentrations [1]. In the congeneric set of compounds we observed the regu larity between the selectivity and the properties derived from the conform ational assemblies of compounds [2]. As the part of ongoing studies\, in t his communication we repot the free-energy surfaces of the representative congeners (some examples is given on the Figure 1)\, as obtained by molecu lar dynamics simulations\, using adaptive biasing force (ABF) procedure [3 ] to speed-up sampling of the systems. All simulations were performed invo lving simulation of explicit solvents having different polarity and hydrog en bond donor/acceptor abilities (water\, chloroform\, dimethyl-sulfoxide\ , ethanol\, n-octanol/water mixture)\, lasting from 20 to 50 ns. For compa rison\, the molecular dynamics simulations on the representative system wi thout applied biasing forces was also reported. The differences in the fre e-energy surfaces of the same\, representative\, congener in different sol vents reflect the fact that flexible molecules change conformations in a w ay to mimic surroundings (i.e. solvent in which are dissolved) [4]. Range s of property spaces [5] of compounds under the study were analyzed and co mpared. In all simulations molecules were treated in their neutral form. T he effect of using different types of atomic charges on the final results is also commented. All systems under the study were minimized during 20000 steps\, than heated to 310 K for 10000 steps. Molecular dynamics simulati on\, on 310 ± 10 K\, with applied ABF procedure was performed on the each system. CHARMm22 force field and Geisteiger charges\, or charges derived from the semiempirical calculations\, were used. Electrostatics was treate d by Particle Mesh Ewald method. The periodic boundary conditions were app lied\, and 12 Å cut-off (8 Å switching)\, with pair list distances set t o 13.5 Å. All calculations were performed by NAMD 2.8 [6] on the multimod e Linux cluster. For the preparation of the systems and analysis of the re sults VegaZZ 2.4.0 was used [7].\n\n\nAcknowledgement: The work is support ed by the European Commission under EU FP7 project HP-SEE\, http://www.hp- see.eu/. The Ministry of Education and Science of Serbia support this work . Grant 172035. \n\n\nReferences: [1] J. Med. Chem. 48 (2005) 5600\; [2] a ) The 18th European Symposium on Quantitative Structure-Activity Relations hips\, Book of Abstracts\, pp. 278-279\, Greece\, 2010\; b) The 19th Europ ean Symposium on Quantitative Structure-Activity Relationships\, Book of A bstracts\, p 147\, Austria\, 2012\; [3] J. Chem. Theory Comput. 6 (2010) 3 5\; [4] Med. Res. Rev. 17 (1997) 303\; [5] J. Med. Chem. 48 (2005) 4947\; [6] J. Compt. Chem. 26 (2005) 1781\; [7] J. Comp. Aided Mol. Des. 18 (2004 ) 167\n\nhttps://events.saifa.rs/event/291/contributions/191/ LOCATION:National Library of Serbia URL:https://events.saifa.rs/event/291/contributions/191/ END:VEVENT BEGIN:VEVENT SUMMARY:Dynamics of uninhibited and covalently inhibited cysteine protease on non-physiological pH DTSTART;VALUE=DATE-TIME:20121019T083000Z DTEND;VALUE=DATE-TIME:20121019T090000Z DTSTAMP;VALUE=DATE-TIME:20261010T225913Z UID:indico-contribution-291-192@indico.ipb.ac.rs DESCRIPTION:Speakers: Branko J. Drakulić (Department of Chemistry-IChTM\, University of Belgrade\, Njegoševa 12\, Belgrade\, Serbia)\nCysteine pro teases involved in degradation of proteins\, widespread in plants\, parasi tes and vertebrates\, are an important medicinal chemistry target implicat ed in the diseases ranging from immunological processes to cancer. Due to conserved cysteine residue in their active site\, unsaturated ketones and their analogs represent one of the major chemotypes used for inhibitors de sign [1]. In this communication the dynamics of the papain-like cysteine p rotease isolated from the fruit\, uninhibited and inhibited with covalent inhibitor E-64 (Scheme 1)\, on non-physiological pH\, were reported mergin g results and experiences from our biochemical and medicinal chemistry lab oratories.The aim of our study is to explain some experimental findings. P roteins are modeled using similar ones with the known 3D structure\, taken from Protein Data Bank [2]. After sequence alignment residues that differ entiate templates from the experimental proteins were manually changed. Af terward the eventual existence of close contacts\, bumps or similar was ca refully checked. The protonation states of the aminoacid residues and the inhibitor ionizable groups were adjusted to pH 1.5\, using empirical funct ion [3]. Systems were neutralized with explicit counterions\, than embed i n explicit water\, obtaining the sphere having ~ 100 Å radius. Systems un der simulations were minimized during 30000 steps\, than heated to 300 K d uring 10000 steps. After equilibration\, the 5 ns unconstrained and unbias ed molecular dynamics simulation\, on 300 ± 10 K\, were performed on the each system. CHARMm22 force field and Geisteiger charges were used. Electr ostatics was treated by Particle Mesh Ewald method. The periodic boundary conditions were applied\, and 12 Å cut-off (8 Å switching)\, with pair l ist distances set to 13.5 Å. Each simulation was performed in duplicate\, using different random seeds and giving comparable results. The root-mean -square deviation of the backbone atoms and the energy profiles of the sys tems under the study proved stable\, converged simulation. The movement of the loops and the (flexible) inhibitor\, as well as radius of gyration of the selected amino-acid side chains was analyzed and conclusion derived o n the influence of the covalently bound inhibitors on the dynamics of the enzyme on pH 1.5. All calculations were performed by NAMD 2.8 [4] on the m ultimode Linux cluster. For the preparation of the systems\, and analysis of the results VegaZZ 2.4.0 were used [5].\n\nAcknowledgement: The work is supported by the European Commission under EU FP7 project HP-SEE\, http:/ /www.hp-see.eu/. The Ministry of Education and Science of Serbia support this work. Grants 172035 and 172049.\n\nReferences: [1] Mini-Rev. Med. Che m. 7 (2007) 1040\; [2] J. Mol. Biol. 112 (1977) 535\; [3] Proteins 73 (200 8) 765\; [4] J. Compt. Chem. 26 (2005) 1781\; [5] J. Comp. Aided Mol. Des. 18 (2004) 167\n\nhttps://events.saifa.rs/event/291/contributions/192/ LOCATION:National Library of Serbia URL:https://events.saifa.rs/event/291/contributions/192/ END:VEVENT BEGIN:VEVENT SUMMARY:Generalization of the parallel HPC implementation for solving diff erential equations DTSTART;VALUE=DATE-TIME:20121018T134500Z DTEND;VALUE=DATE-TIME:20121018T150000Z DTSTAMP;VALUE=DATE-TIME:20261010T225913Z UID:indico-contribution-291-193@indico.ipb.ac.rs DESCRIPTION:Speakers: Dragan Jakimovski (Institute of Physics\, Faculty of Natural Sciences and Mathematics\, Skopje\, Macedonia)\nWe report our res ults\, obtained so far\, in developing a novel\, general two step genetic algorithm for finding an analytical solution of systems of ordinary differ ential equations\, ant its generalization for solving more complex systems of ordinary and partial differential equations. We tested extended soluti on for solving several complex systems of different type of differential e quations and achieve excellent results for small number of generations. Du e to the computationally intensive calculations the code is implemented an d tested in HPC environment with promising results in view of performance and scaling. A possibility for application in more complex research-level models is noted and evaluated.\n\nhttps://events.saifa.rs/event/291/contri butions/193/ LOCATION:National Library of Serbia URL:https://events.saifa.rs/event/291/contributions/193/ END:VEVENT BEGIN:VEVENT SUMMARY:Performance and scalability evaluation of short fragment sequence alignment applications DTSTART;VALUE=DATE-TIME:20121017T153000Z DTEND;VALUE=DATE-TIME:20121017T160000Z DTSTAMP;VALUE=DATE-TIME:20261010T225913Z UID:indico-contribution-291-194@indico.ipb.ac.rs DESCRIPTION:Speakers: Gergely Windisch (Obuda University - Hungary)\nMappi ng short fragments to open access eukaryotic genomes at a very large scale presents a data processing challenge to the scientific world. The large v olume of data processing requires an immense amount of computing power for the tools to provide feasible response time\, which is essential for the researchers. The main tool used for such an application is BLAST which is the one we use in our portlets developed at Obuda University. There are wa ys for the scientists to use the BLAST algorithm either executing it local ly or using a web based BLAST tool. Usually the scope of usability of thes e solutions is limited because of the lack of computing power available. T he portlets developed at Obuda University are served by a web server but c omputation takes place in a massively parallel supercomputing environment. The type of the algorithm and the data it has to process make it an ideal candidate for a highly parallel execution on the HPSEE infrastructure. Th e portlets are available to the scientist community on the Bioinformatics eScience Gateway hosted at OU and powered by gUSE/WS-PGRADE technology\, w hile the backend is being served by the Hungarian HPSEE Infrastructure by NIIF. \nLately most of our work has been focused on evaluating the perform ance and scalability of our applications by profiling\, analyzing the resu lts of the tests and improving the performance of both the portlets and th e server-side massively parallel algorithm by environment optimization usi ng the data collected during the testing phase. \nIn this paper we will de scribe the two portlets (Deep Aligner and Disease Gene Mapper)\, discuss t he issues and challenges during the development and the performance analys is and present our results on the performance and scalability of the appli cations.\n\nhttps://events.saifa.rs/event/291/contributions/194/ LOCATION:National Library of Serbia URL:https://events.saifa.rs/event/291/contributions/194/ END:VEVENT BEGIN:VEVENT SUMMARY:Efficient Parallel Simulations of Large-Ring Cyclodextrins on HPC cluster DTSTART;VALUE=DATE-TIME:20121019T103000Z DTEND;VALUE=DATE-TIME:20121019T110000Z DTSTAMP;VALUE=DATE-TIME:20261010T225913Z UID:indico-contribution-291-195@indico.ipb.ac.rs DESCRIPTION:Speakers: Emanouil Atanassov (Institute of Information and Com munication Technologies\, Bulgarian Academy of Sciences)\nA new class of c ompounds\, the large-ring cyclodextrins (LR-CDs)\, attracted attention in recent years\, and advances were marked in the study of their physicochemi cal properties in spite of existing difficulties in their synthesis\, isol ation and purification. Practical applications were also reported of this new class of compounds. Understanding the mechanism of their action requir es knowledge of the macroring conformational dynamics. In view of the diff iculties with the experimental examination of the conformations of LR-CDs\ , computational modeling and simulation methods provide useful tool to gai n information about their conformational dynamics\, the energetics\, and t he complex-forming ability.\nUsing molecular dynamics simulations as a con formational search protocol\, post-processing of the simulation trajectori es is carried out by: (i) the MM/GBSA (Generalized Born/Surface Area (LCPO )) methodology in order to estimate energy data\, and (ii) principal compo nent analysis (PCA)\, also called quasiharmonic analysis or essential dyna mics method. With the methodology used we can monitor the concerted motion s of the atoms of the molecule in a few dimensions\, making it easier to v isualize and investigate these motions. After examining the conformational interconversions in some lower-size LR-CDs (CDn\, n=10\, 11\, …\, 30)\, 1-3 our efforts are focused now on treating problems with much higher dime nsionality\, e.g. CD100\, as well as on inclusion complexes of LR-CDs. Due to the access to more powerful computational resources and parallelized s oftware it became practically feasible to execute molecular dynamics confo rmational searches with longer duration for large cyclodextrins examined b y us earlier with very short simulations\, 5.0 ns (CDn\, n=40\, 55\, 70\, 85\, 100\; Giant cyclodextrins).4\nSuch studies require enormous computati onal resources and it is of crucial importance to make the proper choice o f optimal hardware\, as well as software configurations in order to execut e the computations efficiently. We present in this report results produced at the HPC cluster at IICT-BAS with Infiniband interconnection\, which is part of the HP-SEE infrastructure. All tests are in support for optimal e xecution of the specifically parallelized module PMEMD of AMBER v.11 with 64 cores on eight nodes. \n___________________\n1 M. Gotsev\, P. Ivanov\, J. Phys. Chem. B\, 2009\, 113\, 5752-5759.\n2 P. Ivanov\, J. Phys. Chem. B\, 2010\, 114\, 2650-2659. \n3 P. Ivanov\, In: Current Physical Chemist ry: Biomolecular Simulations and Applications\, Vol. 2\, 2012\, in press.\ n4 P. Ivanov\, C. Jaime\, J. Phys. Chem. B\, 2004\, 108\, 6261-6274.\n\nht tps://events.saifa.rs/event/291/contributions/195/ LOCATION:National Library of Serbia URL:https://events.saifa.rs/event/291/contributions/195/ END:VEVENT BEGIN:VEVENT SUMMARY:Self-avoiding Hamiltonian Walks Counting in Parallel processing mo de DTSTART;VALUE=DATE-TIME:20121018T134500Z DTEND;VALUE=DATE-TIME:20121018T150000Z DTSTAMP;VALUE=DATE-TIME:20261010T225913Z UID:indico-contribution-291-196@indico.ipb.ac.rs DESCRIPTION:Speakers: Sreten Lekic (Faculty of Natural Sciences University of Banja Luka)\nWe have developed a program for counting self-avoiding Ha miltonian walks to run on multiple processors in a parallel mode. We study Hamiltonian walks (HWs) on the family of two-dimensional modified Sierpin ski gasket fractals\, as a simple model for compact polymers in nonhomogen eous media in two dimensions. We apply an exact recursive method which all ows for explicit enumeration of extremely long Hamiltonian walks of differ ent types: closed and open\, with end-points anywhere in the lattice\, or with one or both ends fixed at the corner sites. The leading term n is characterized by the value of the connectivity constant 1\, which depen ds on fractal type\, but not on the type of HW.\n\nhttps://events.saifa.rs /event/291/contributions/196/ LOCATION:National Library of Serbia URL:https://events.saifa.rs/event/291/contributions/196/ END:VEVENT BEGIN:VEVENT SUMMARY:Emergence of resonant waves in cigar-shaped Bose-Einstein condensa tes DTSTART;VALUE=DATE-TIME:20121018T124500Z DTEND;VALUE=DATE-TIME:20121018T131500Z DTSTAMP;VALUE=DATE-TIME:20261010T225913Z UID:indico-contribution-291-197@indico.ipb.ac.rs DESCRIPTION:Speakers: Alexandru Nicolin (Horia Hulubei National Institute for Physics and Nuclear Engineering)\nMotivated by the continuous interest shown to the nonlinear dynamics of quantum gases we present in this talk the emergence of resonant waves in cigar-shaped Bose-Einstein condensates using which has been reported in Ref. [1].\n\nWe introduce the analytic tr eatment of the dynamics of a trapped\, quasi-one-dimensional Bose-Einstei n condensate subject to resonant and nonresonant periodic modulation of th e transverse confinement. The dynamics of the condensate is described vari ationally through a set of coupled ordinary differential equations\, and t he period of the excited waves is determined analytically using a Mathieu- type analysis. For a modulation frequency equal to that of the radial conf inement we show that the predicted period of the resonant wave is in agree ment with the existing experimental results. Finally\, we present a detail ed comparison between the resonant waves and the Faraday waves that emerge outside of resonance.\n\n[1] A.I. Nicolin\, Phys. Rev. E 84\, 056202 (201 1).\n\nhttps://events.saifa.rs/event/291/contributions/197/ LOCATION:National Library of Serbia URL:https://events.saifa.rs/event/291/contributions/197/ END:VEVENT BEGIN:VEVENT SUMMARY:Formation of Faraday and Resonant Waves in Driven High-Density Bos e-Einstein Condensates DTSTART;VALUE=DATE-TIME:20121018T134500Z DTEND;VALUE=DATE-TIME:20121018T150000Z DTSTAMP;VALUE=DATE-TIME:20261010T225913Z UID:indico-contribution-291-198@indico.ipb.ac.rs DESCRIPTION:Speakers: Mihaela Carina Raportaru (Horia Hulubei National Ins titute for Physics and Nuclear Engineering)\nExtended parametric resonance s are one of the recurrent themes in the dynamics of quantum gases. Follow ing some inceptive theoretical works Faraday waves have been observed in p arametrically driven 87Rb BECs and 4He cells subject to vertical vibration s. These experimental observations have catalyzed the research activities and many theoretical investigations followed shortly. Among them we mentio n the emergence of density waves in dipolar and binary condensates\, the t ransition to miscibility observed in non-miscible condensates and the supp ression of Faraday waves in condensates loaded into optical lattices. \n\ nIn this work we present the variational method introduced in Ref. [1] to describe the dynamics of cigar-shaped Bose-Einstein condensates of high de nsity subject to periodic modulations of the radial component of the confi ning potential. The key ingredient of the variational treatment is the q-G aussian radial envelope which describes the Thomas-Fermi regime of the con densate. A longitudinal density wave is grafted to the ansatz to account f or Faraday and resonant waves. Using the variational equations\, we invest igate the dynamics of a realistic condensate for frequencies close to the radial frequency of the trap and show the emergence of the Faraday waves e xcited outside of resonance and that of the resonant wave that appears str aight on resonance.\n\n[1] M. C. Raportaru\, Romanian Reports in Physics 6 4\, 105\, 2012.\n\nhttps://events.saifa.rs/event/291/contributions/198/ LOCATION:National Library of Serbia URL:https://events.saifa.rs/event/291/contributions/198/ END:VEVENT BEGIN:VEVENT SUMMARY:Numerical Study of Ultracold Quantum Gases: Formation of Faraday P atterns\, Geometric Resonances\, and Fragmentation DTSTART;VALUE=DATE-TIME:20121018T074500Z DTEND;VALUE=DATE-TIME:20121018T083000Z DTSTAMP;VALUE=DATE-TIME:20261010T225913Z UID:indico-contribution-291-199@indico.ipb.ac.rs DESCRIPTION:Speakers: Antun Balaz (Institute of Physics Belgrade)\nIn this talk we will present our recent results of the study of ultracold quantum gases\, obtained using the NUQG high-performance computing application de veloped in the framework of HP-SEE project. First\, by extensive numerical simulations of the underlying Gross-Pitaevskii equation [1]\, we will sho w how parametric excitation of Bose-Einstein condensed systems can lead to formation of Faraday patterns [2]. For two-component systems we will show that the excited Faraday waves far from resonances are of similar periods \, emerge simultaneously\, and do not impact the dynamics of the bulk of t he condensate. We will also show that for a modulation frequency close to twice that of the radial trapping\, the emergent surface waves fade out in favor of a forceful collective mode that turns the two condensate compone nts miscible. Second\, we will investigate effects of the geometry of the trap to the behavior of Bose-Einstein condensates [3\,4]. By changing the anisotropy of the confining potential\, we numerically observe strong nonl inear effects: shifts in the frequencies and mode coupling of collective m odes [5]\, as well as geometric resonances. Finally\, motivated by recent experimental results on the dynamics of a cigar-shaped Bose-Einstein conde nsate subject to periodic modulation of the scattering length\, we investi gate the dynamics of the condensate and show that for resonant drives of l arge amplitude the condensate reaches a fragmented state. The fragmented s tate is a mixture of a quadrupole collective oscillation mode on top of wh ich a longitudinal resonant density wave is grafted.\n\n[1] D. Vudragovic ́\, I. Vidanović\, A. Balaž\, P. Muruganandam\, and S. K. Adhikari\, Comp. Phys. Commun. 183\, 2021 (2012).\n[2] A. Balaž and A. I. Nicolin\, Phys. Rev. A 85\, 023613 (2012).\n[3] I. Vidanović\, H. Al-Jibbouri\, A . Balaž\, and A. Pelster\, Phys. Scr. T149\, 014003 (2012).\n[4] H. Al-J ibbouri\, I. Vidanović\, A. Balaž\, and A. Pelster\, arXiv:1208.0991 ( 2012).\n[5] I. Vidanović\, A. Balaž\, H. Al-Jibbouri\, and A. Pelster\ , Phys. Rev. A 84\, 013618 (2011).\n\nhttps://events.saifa.rs/event/291/co ntributions/199/ LOCATION:National Library of Serbia URL:https://events.saifa.rs/event/291/contributions/199/ END:VEVENT BEGIN:VEVENT SUMMARY:Evolution of an gravitotional bound n-body system with DLA (Diffus ion Limited Aggregation) initial mass distribution using GPU parralel com puting DTSTART;VALUE=DATE-TIME:20121018T134500Z DTEND;VALUE=DATE-TIME:20121018T150000Z DTSTAMP;VALUE=DATE-TIME:20261010T225913Z UID:indico-contribution-291-200@indico.ipb.ac.rs DESCRIPTION:Speakers: Bogdan Alexandru Dumitru (Institute of Space Science )\, Ciprian Mitu (Institute of Space Science)\nIn this paper we present a collection of algorithms to generate power law mass distribution as initi al conditions for gravitational N-body simulations. This type of algorithm s are highly parallizable and can analyze large data customary on clusters . The input data will be high resolution images in the most used format in astrophysics\, FITS and diffusion limited aggregation generated clusters. The application will algorithm running on GPU (with CUDA and OpenCL)\, fo r the generation of initial mass distribution and fort the evolution of th e n-body sysytem. Data analysis and plotting is done in ROOT Framework. \n General scientific image on the formation and evolution of the gala xies is that they formed by gravitational collapse of matter. The study of the mass distribution of spiral galaxies will shade new light on the form ation and evolution of galaxies. The application will provide new data of spiral arms and their morphology. \n The method is name all-pairs that is a brute-force technique that evaluates all pair-wire interactions among the n bodies. The all-pairs method is combined with a faster method based on a far-field approximation of longer-range forces\, which is valid only between parts of the system that are well separated. Fast N-body alg orithms of this form include the Barnes-Hut method (BH) (Barnes and Hut 19 86)\, the fast multipole method (FMM) (Greengard 1987)\, and the particle- mesh methods (Hockney and Eastwood 1981\, Darden et al. 1993). \n The b enchmarks was done on an server with 4 GPU (Nvidia Tesla) with 480 cores e ach.\n The tests was been maid on 480\, 960\, 1440\, 1920 cores on CUDA and OpenCL and the difference was 5-10% in CUDA favor.\n\nhttps://events. saifa.rs/event/291/contributions/200/ LOCATION:National Library of Serbia URL:https://events.saifa.rs/event/291/contributions/200/ END:VEVENT BEGIN:VEVENT SUMMARY:Data analisys in high energy phisics using CUDA and OpenCL DTSTART;VALUE=DATE-TIME:20121018T134500Z DTEND;VALUE=DATE-TIME:20121018T150000Z DTSTAMP;VALUE=DATE-TIME:20261010T225913Z UID:indico-contribution-291-201@indico.ipb.ac.rs DESCRIPTION:Speakers: Bogdan Alexandru Dumitru (Institute of Space Science )\, Ciprian Mitu (Institute of Space Science)\nWe developed an aplication that allows both the analysis of data and also the real-time visualisation on the same time. This is possible with the help of the GPU. To use the p ower of GPU is need of an specific framework (we use CUDA and OpenCL).\n The aplication use data generated by UrQMD (Ultra relativistic Quantum M olecular Dynamics) to run a variety of algorithms and 3D visualization. Ho w it works:\n As a front-end to the user\, the application uses Qt libr aries to create the GUI (graphical user interface library) and user intera ction. The input data\, obtained from a SQLite3 database file\, is fetched and loaded on the graphic device. After this\, the data is processed on G PU using CUDA (Compute Unified Device Architecture) or OpenCL (Open Comput ing Language)\, depends on the GPU use. The processed data is output in a OpenGL(Open Graphics Library) viewport and in ROOT's graphs or histograms. Using widgets\, one can select/filter events\, frames or particles that a re going to be processed. Also\, render all frames in an event continually \, such that one sees the evolution of particles as a fluid animation. Jus t like movie player\, with buttons to play/pause or go forward\, backward. \n When one wants fast analysis and real-time animation\, one choos es parallel processing. Having this in mind\, we put move all processing o n the best and cheapest parallel unit one can afford: GPU parallel process ing. The framework developed by NVIDIA named CUDA and the framework develo ped by Khronos Group named OpenCL allows one to harness the power of the GPU device using parallel processing. The programming execution model on G PU in CUDA is SIMT (Single Instruction Multiple Thread) and in OpenCL is S IMD(Simple Instruction Multiple Data). This means\, only one function (run ning\nin multiple threads or instances) can run on the GPU at one time pro cessing the data. In CUDA and OpenCL terminology\, this function is named a kernel.\n After querying database for the interested data\, and lo ading it in GPU\, depending on the one's action\, a CUDA or OpenCL kernel (depends on the GPU used) is launched accordingly. The kernel\nabove\, tak es in particles information (x\,y\,z\,px\,py\,pz\,E\,...) and outputs the computed values of: transverse momentum\, direct and elliptic flow paramet ers\, pseudo-rapidity and OpenGL's necessary data to render the particles. The representation of the processed data can be seen in OpenGL viewport ( particles as spheres) and parameters in ROOTs graphs and histograms.\n\nht tps://events.saifa.rs/event/291/contributions/201/ LOCATION:National Library of Serbia URL:https://events.saifa.rs/event/291/contributions/201/ END:VEVENT END:VCALENDAR