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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:20261010T224503Z
UID:indico-contribution-101-158@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:20261010T224503Z
UID:indico-contribution-101-159@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: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:20261010T224503Z
UID:indico-contribution-101-172@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: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:20261010T224503Z
UID:indico-contribution-101-176@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:GPAW optimisations
DTSTART;VALUE=DATE-TIME:20121018T134500Z
DTEND;VALUE=DATE-TIME:20121018T150000Z
DTSTAMP;VALUE=DATE-TIME:20261010T224503Z
UID:indico-contribution-101-178@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:20261010T224503Z
UID:indico-contribution-101-179@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: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:20261010T224503Z
UID:indico-contribution-101-193@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:Self-avoiding Hamiltonian Walks Counting in Parallel processing mo
 de
DTSTART;VALUE=DATE-TIME:20121018T134500Z
DTEND;VALUE=DATE-TIME:20121018T150000Z
DTSTAMP;VALUE=DATE-TIME:20261010T224503Z
UID:indico-contribution-101-196@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: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:20261010T224503Z
UID:indico-contribution-101-198@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: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:20261010T224503Z
UID:indico-contribution-101-200@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:20261010T224503Z
UID:indico-contribution-101-201@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
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