VI-SEEM Research-oriented Papers

  1. Podewitz M., Wang Y., Gkeka P., von Grafenstein S., Liedl KR., Cournia Z., “Phase Diagram of a Stratum Corneum Lipid Mixture”, J Phys Chem B. 2018 [Epub ahead of print]

  3. Chatzigoulas A., Karathanou K., Dellis D., Cournia Z., “Nano-Crystal: A web-based crystallographic tool for the construction of
    nanoparticles based on their crystal habit.”, J Chem Inf Model, 2018, [Epub ahead of print] Read the Free preprint on ChemRxiv –>

  5. Leontiadou H., Galdadas I., Athanasiou C., Cournia Z., “Insights into the mechanism of the PIK3CA E545K activating mutation using MD simulations.”, Sci Rep, 2018, 8(1):15544.

  7. G. Artopoulos, P. Charalambous, “Analysis of Spatio-Temporal Data in Virtual Historic Spaces”, in International Conference on Artificial Reality and Telexistence Eurographics Symposium on Virtual Environments, edited by Gerd Bruder, Shunsuke Yoshimoto, and Sue Cobb, 9–12. Limassol, Cyprus 2018: Eurographics Association. doi:10.2312/egve.20181308.

  9. G. Artopoulos, Ch. Gregoriou, Ch. Ioannou, “Immersive Design Practices: From Virtual to Real Space and Back. The Case of Reactivating the Paphos Gate”, in the Proceedings of the 4th Biennial of Architectural and Urban Restoration, BRAU4 host of the Itinerant Congress Hidden Cultural Heritage: Under Water, Under Ground and Within Buildings (Italy: CICOP Italia, 2018), pp. 63-72. ISBN: 978-88-909-1165-1

  11. G. Artopoulos, “Data accessibility, visualization and co-interpretation processes as the new urban commons”, in The Architectural Humanities Research Association (AHRA 2018) Smartness between discourse and practice, TU Eindhoven in Eindhoven, the Netherlands (2018) (to be published 2019

  13. G. Artopoulos, C. Miltiadis, “The visual imaginary of intangible cultural heritage: accessing the palimpsest of Nicosia through audio-enabled routes”, in Congress Visual Heritage 2018, hosted by CHNT 23 2018, Stadt Archaologie Wien, Vienna, Austria (2018) (to be published 2019)

  15. Z. M. Nikolaou, J.-Y. Chen, Y. Proestos, J. Lelieveld, R. Sander, “Accelerating simulations using REDCHEM_v0.0 for atmospheric chemistry mechanism reduction”, eISSN: 1991-9603

  17. V. Koleva-Efremova, “Testing performance and scalability of the pure MPI model versus hybrid MPI-2/OpenMP model on the heterogeneous supercomputer Avitohol”, Springer book series “Studies in Computational Intelligence”, Vol 793, pp. 93-106, DOI: 10.1007/978-3-319-97277-0_30

  19. V. Koleva-Efremova, T. Gurov, “Optimizing parallel CFD simulations for modelling a trimaran through OpenFoam”, AIP Conf. Proc. of the 10th AMITANS’18 conference, vol. 2025 110003 (2018),

  21. M. Lazarova, S.-M. Gurova, “Numerical Comparative Analysis on the Classical Vasicek Model for Determining the Zero Coupon Bond’s Price”, Conference Proceeding MATTEX 2018, vol. 1, pp.121-135, 2018, ISSN: 1314-3921.

  23. G. Artopoulos, P. Charalambous, “Virtual Environments as a Technological Interface between Built Heritage and the Sustainable Development of the City”, in International Journal of E-Planning Research (IJEPR), Vol 8,(1) 2019. ISSN: 2160-9918

  25. H. Astsatryan, H. Grigoryan, E. Gyulgyulyan, A. Hakobyan, A. Kocharyan, W. Narsisian, V. Sahakyan, Yu. Shoukourian, R. Abrahamyan, Z. Petrosyan, J. Aligon, “Weather data visualization and analytical platform”, SCPE, Vol 19, No. 2, 2018, pp. 79-86, DOI: 10.12694/scpe.v19i2.1351

  27. H. Astsatryan, W. Narsisian, E. Gyulgyulyan, A. Poghosyan, Y. Mamasakhlisov, “An integrated web-based interactive data platform for molecular dynamics simulations”, SCPE, Vol 19, No. 2, 2018, pp. 131-138, DOI: 10.12694/scpe.v19i2.1337

  29. A.H. Poghosyan, A.A. Shahinyan, J. Koetz, Catanionic AOT/BDAC micelles on gold {111} surfaces, Colloid and Polymer Science, pp. 1-6, 2018, DOI: 10.1007/s00396-018-4348-1

  31. E. Atanassov, T. Gurov, M. Durchova, S. Ivanovska, A. Karaivanova, “Study of Scalability and Energy Efficiency of QMC Algorithmd on Hybrid HPC Systems”, Proceedings of Int. Conf. “Numerical methods for Scientific Computations and Advanced Applications” (NMSCAA’18), pp. 6-9, 2018

  33. M. Bigovic, L. Filipovic, Z. Zacevic, B. Krstajic, “Modeling and Molecular Dynamics Simulations Study of Enol-Carbonates and Their Derivatives”, SCPE, Vol 19, No. 2, 2018, pp. 139-148, DOI: 10.12694/scpe.v19i2.1353

  35. P. Charalambous, G. Artopoulos (CASTORP), „Enabling virtual collaboration in Digital Cultural Heritage in the SEEM region”, SCPE, Vol 19, No. 2, 2018, pp. 161-174, DOI: 10.12694/scpe.v19i2.1348

  37. T. Davitashvili, N. Kutaladze, R. Kvatadze, G. Mikuchadze, “Effect of dust aerosols in forming the regional climate of Georgia”, SCPE, Vol 19, No. 2, 2018, pp. 87-96, DOI: 10.12694/scpe.v19i2.1398

  39. M. Elfarargy, Amr Rizq, “VrMuF: The Virtual museum framework”, SCPE, Vol 19, No. 2, 2018, pp. 175-180, DOI: 10.12694/scpe.v19i2.1349

  41. N. Frasheri, E. Atanassov, „An Analysis for Parallel Wind Simulation Speedup using OpenFOAM“, SCPE, Vol 19, No. 2, 2018, pp. 97-105, DOI: 10.12694/scpe.v19i2.1342

  43. G. Gadzhev, I. Georgieva, K. Ganev, V. Ivanov, N. Miloshev, H. Chervenkov, D. Syrakov, “Climate appications in a virtual research environment platform”, SCPE, Vol 19, No. 2, 2018, pp. 107-118, DOI: 10.12694/scpe.v19i2.1347

  45. G. Gadzhev, V. Ivanov, K. Ganev, H. Chervenkov, “TVRegCM Numerical Simulations – Prelinary Results, Lecture Notes in Computer Science (including subseries Lecture Notes in Artifical Intelligence and Lecture Notes in Bioinformatics)”, Vol. 10655 LNCS, 2018, pp. 266-274, DOI: 10.1007/978-3-319-73441-5_28

  47. I. Georgieva, G. Gadzhev, K. Ganev, N. Miloshev, Computer Simulations of Atmospheric Composition in Urban Areas. Some Results for the City of Sofia, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intellingence and Lecture Notes in Bioinformatics), 2018, Vol. 10665, LNCS, pp. 474-482, DOI: 10.1007/978-3-319-73441-5_52

  49. Georgiou, G. K., Christoudias, T., Proestos, Y., Kushta, J., Hadjinicolaou, P., and Lelieveld, J.: Air quality modelling in the summer over the eastern Mediterranean using WRF-Chem: chemistry and aerosol mechanism intercomparison, Atmos. Chem. Phys., 18, 2018, 1555-1571, DOI: 10.5194/acp-18-1555-2018

  51. V. Koleva-Efremova, T. Gurov, Optimizing parallel CFD simulations for modeling a trimaran through OpenFoam, AIP Conference Proceedings 2025, 110003, 2018, DOI: 10.1063/1.5064946

  53. B. Koteska, V. Manevska, A. Mishev, L. Pejov, “Dynamic versus static approach to theoretical anharmonic vibrational spectroscopy of molecular species relevant to atmospheric chemistry”, SCPE, Vol 19, No. 2, 2018, pp. 119-130, DOI: 10.12694/scpe.v19i2.1352

  55. B. Koteska, M. Simonoska, M. Glavas Dodov, J. Tonic Ribarska, L. Pejov, „Semiempirical Atom-centered Density Matrix Propagation Approach to Temperature-dependent Vibrational Spectroscopy of Irinotecan”, SCPE, Vol 19, No. 2, 2018, pp.149-159, DOI: 10.12694/scpe.v19i2.1344

  57. Bojana Koteska, Framework for Developing Scientific Applications, PhD Thesis. Extended abstract available at the VI-SEEM Repository

  59. Nikolaou, Z. M., Chen, J.-Y., Proestos, Y., Lelieveld, J., and Sander, R.: Accelerating simulations using REDCHEM_v0.0 for atmospheric chemistry mechanism reduction, Geosci. Model Dev., 11, 2018, 3391-3407, DOI: 10.5194/gmd-11-3391-2018

  61. A.H. Poghosyan, A.A. Shahinyan, J. Koetz, Self-assembled monolayer formation of distorted cylindrical AOT Micelles on Gold Surfaces, Colloids and Surfaces A: Physicochemical and Engineering Aspects, 6 March, 2018, DOI: 10.1016/j.colsurfa.2018.02.067

  63. Savić, Marijana Arapović, Mihajlo Savić, Adriana Arbutina, Mirjana Umićević Davidović, and Vladan Mirjanić. “A SYSTEM FOR MEASUREMENTS OF 3D SCANNED ORTHODONTIC STUDY MODELS.” CONTEMPORARY MATERIALS 2, no. 8 (2018): pp. 172-179.

  65. Ioanna Tremi, Dimitrios Anagnostopoulos, Ellas Spyratou, Paraskevi Gkeka, Alexandros G. Georgakilas, Chryssostomos Chatgilialoglu, Zoe Cournia, Effect of 5-trans isomer of arachidonic acid on model liposomal membranes studied by a combined simulation and experimental approach, Journal of Membrane Biology, 2018, pp. 1-15, DOI: 10.1007/s00232-018-0029-8

  67. M. Alvanos, T. Christoudias, GPU-accelerated atmospheric chemical kinetics in the ECHAM/MESSy (EMAC) Earth system model (version 2.52), Geosci. Model Dev., 10, 3679-3693, 2017, DOI: 10.5194/gmd-10-3679-2017

  69. M. Alvanos, T. Christoudias, MEDINA: MECCA Development in Accelerators – KPP Fortran to CUDA source-to-source Pre-processor. Journal of Open Research Software. 5(1), p.13, 2017, DOI: 10.5334/jors.158

  71. C. Athanasiou, S. Vasilakaki, D. Dellis, Z. Cournia, Using physics-based pose predictions and free energy perturbation calculations to predict binding poses and relative binding affinities for FXR ligands in the D3R Grand Challenge 2, J Comput Aided Mol Des (2017): 1-24

  73. Ulrike Bornheimer, Ivana Vasić, Walter Hofstetter, Phase transitions of the coherently coupled two-component Bose gas in a square optical lattice, Phys. Rev. A 96, 063623, 2017, DOI: 10.1103/PhysRevA.96.063623

  75. Z. Cournia, B. Allen, W. Sherman, Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations, J Chem Inf Model 2017, 57(12):2911-2937

  77. A. Golubev, P. Bogatencov, N. Iliuha, “DICOM Network” services – DICOM data exchange solution integrated in the regional VI-SEEM infrastructure.In: IEEE EUROCON 2017 – 17th International Conference on Smart Technologies, 6-8 July 2017, Ohrid, Macedonia, 2017. pp. 558 – 563. DOI: 10.1109/EUROCON.2017.8011174

  79. A. Golubev, P. Bogatenvov, G. Secrieru, Study Big Data storage, transmission and processing in DICOM format for medical information systems, 9th International Conference on Microelectronics and Computer Science, Chisinau, Republic of Moldova, October 19-21, 2017 (in Russian)

  81. N. Ivanova, A. Ivanova, “Testing the limits of model membrane simulations-bilayer composition and pressure scaling”, J Comput Chem. (2018), 39(8), pp. 387-396, DOI: 10.1002/jcc.25117

  83. Veljko Janković, Nenad Vukmirović, Identification of Ultrafast Photophysical Pathways in Photoexcited Organic Heterojunctions, The Journal of Physical Chemistry C 2017 121 (36), 19602-19618, DOI: 10.1021/acs.jpcc.7b05582

  85. Kirill Plekhanov, Ivana Vasić, Alexandru Petrescu, Rajbir Nirwan, Guillaume Roux, Walter Hofstetter, Karyn Le Hur, Emergent Chiral Spin State in the Mott Phase of a Bosonic Kane-Mele-Hubbard Model, Phys. Rev. Lett. 120, 157201, 2018, DOI: 10.1103/PhysRevLett.120.157201

  87. Vladimir Veljić, Antun Balaž, Axel Pelster, Time-of-flight expansion of trapped dipolar Fermi gases: From the collisionless to the hydrodynamic regime, Phys. Rev. A 95, 053635, 2017, DOI: 10.1103/PhysRevA.95.053635

  89. D. Vudragović, P. Jovanović, A. Balaž, VI-SEEM Virtual Research Environment, The 10th RO-LCG Conference Book of Abstracts, pp. 22 – 23, ISBN: 978-973-0-25620-8, Sinaia, Romania, 26-28 Oct 2017

  91. Miljan Bigovic, Zarko Zecevic, Luka Filipovic, Bozo Krstajic: “Verification of the three-dimensional structure of synthesized molecule by molecular dynamic simulations”, EUROCON 2017: 944-948, 2016, Submitted paper

  93. H. Chervenkov, V. Ivanov, G. Gadzhev, K. Ganev – Sensitivity Study of Different RegCM4.4 Model Set-Ups – Recent Results from the TVRegCM Experiment, CIT, Volume 17, No 5 Special Issue, pp. 17-26, 2017, DOI: 10.1515/cait-2017-0051

  95. N. Frasheri, E. Atanassov – Scalability Issues for Wind Simulation Using OpenFOAM, CIT, Volume 17, No 5 Special Issue, pp.27-36, 2017, DOI: 10.1515/cait-2017-0052

  97. A. Geissler, I. Vasic and W. Hofstetter: “Condensation Versus Long-range Interaction: Competing Quantum Phases in Bosonic Optical Lattice Systems at Near-resonant Rydberg Dressing”, Phys. Rev. A 95 (2017) 063608

  99. I. Georgieva, G. Gadzhev, K. Ganev, D. Melas, T. Wang – High Performance Computing Simulations of the Atmospheric Composition in Bulgaria and the City of Sofia, CIT, Volume 17, No 5 Special Issue, pp. 37-48, 2017, DOI: 10.1515/cait-2017-0053

  101. V. Jankovic and N. Vukmirovic: “Identification of Ultrafast Photophysical Pathways in Photoexcited Organic Heterojunctions”, J. Phys. Chem. C 121 (2017) 19602

  103. I. Loncarevic, Lj. Budinski-Petkovic, D. Dujak, A. Karac, Z. M. Jaksic and S. B. Vrhovac: “The Study of Percolation with the Presence of Extended Impurities”, J. Stat. Mech.-Theory Exp. 2017 (2017) 093202

  105. B. Koteska and A. Mishev and M. G. Dodov and M. S. Crcarevska and J. T. Ribarska and V. P. Jovanovska and M. Stojanovska and L. Pejov: Modeling the solid-state vibrational spectroscopic properties of morphine-based formulations with hybrid meta density functional theory, IEEE EUROCON 2017 -17th International Conference on Smart Technologies, pp 938-943, Submitted paper

  107. B. Koteska and A. Mishev and L. Pejov: Computational approach towards vibrational spectroscopic detection of molecular species relevant to atmospheric chemistry and climate science: The formic acid rotamers, IEEE EUROCON 2017 -17th International Conference on Smart Technologies, pp 926-931, Submitted paper

  109. Ratko Pilipović and Vladimir Risojević, “Evaluation of Convnets for Large-Scale Scene Classification From High-Resolution Remote Sensing Images”, Proc. 17th IEEE International Conference on Smart Technologies IEEE EUROCON 2017, Ohrid, Macedonia, pp.955-960, July 2017

  111. A. Poghosyan, H. Astsatryan, W. Narsisian, Y. Mamasakhlisov – On the Performance and Energy Consumption of Molecular Dynamics Applications for Heterogeneous CPU-GPU Platforms Based on Gromacs, CIT, Volume 17, No 5 Special Issue, pp. 68-80, 2017, DOI: 10.1515/cait-2017-0056

  113. E. Atanassov, T. Gurov, A. Karaivanova, S. Ivanovska, M. Durchova and D. Dimitrov, On the Parallelization Approaches for Intel MIC Architecture, Citation: AIP Conf. Proc. 1773, 070001 (2016)

  115. Cantoro, G., Papadopoulos, N., (2016). “GRID computing for archaeology: AutoGR-SIFT and 3DINV applications for non-invasive landscape studies“. 4th Conference on the Archaeological Work of Crete, Rethymno, Crete, 24-27 November 2016.

  117. E. Atanassov, A.Karaivanova, T. Gurov, “Services And Infrastructure For Virtual Research Environments – For Use By Science And Business”, International Scientific Journal Industry 4.0, Issue 2, 2016, pp. 110-113, Published by Sci Tech Union of Mechanical Engineering, ISSN: 2543-8582

  119. T. Christoudias, M. Alvanos, Accelerated chemical kinetics in the EMAC chemistry-climate model, In Proceedings of HPCS 2016

  121. T. Davitashvili, N. Kutaladze, R. Kvatadze, G. Mikuchadze, Z. Modebadze, I. Samkharadze, Precipitations Prediction by Different Physics of WRF Model, International Journal of Environmental Science Volume 1, 2016  pp 294-299

  123. A. Golubev, P. Bogatencov, G. Secrieru. Updating DICOM Network Architecture for its Integration at International Level. Networking in Education and Research, 15th RoEduNet IEEE International Conference, Bucharest, Romania, 7-9 September 2016, pp. 161-166. ISSN 2068-1038

  125. Bojana Koteska, Anastas Mishev, Ljupco Pejov, Maja Simonoska Crcarevska, Jasmina Tonic Ribarska, and Marija Glavas Dodov. “Computational Vibrational Spectroscopy of Hydrophilic Drug Irinotecan”, SIMUL 2016 Conference, Rome, Italy, August 21-25, 2016, pp. 11-16, ISBN 978-1-61208-501-2

  127. Thomas Mertz, Ivana Vasić, Michael J. Hartmann, Walter Hofstetter, Photonic currents in driven and dissipative resonator lattices, Phys. Rev. A 94, 013809, 2016, DOI: 10.1103/PhysRevA.94.013809

  129. Anastas Mishev. “Bridging the computer and life sciences: the case of VI-SEEM”. Macedonian pharmaceutical bulletin, short communications from the Sixth Congress of Pharmacyin Macedonia with International participation, 62 (suppl) 27 – 29 (2016) ISSN 1409 – 8695 UDC: 004.7

  131. S. Nikolova, D. Toneva, I. Georgiev, Y. Yordanov, N. Lazarov, “Two cases of large bregmatic bone along with a persistent metopic suture from necropoles on the northern Black Sea coast of Bulgaria”, Anthropological Scieence, vol. 124 (2) (2016), pp. 145-153

  133. A.H. Poghosyan, L.H. Arsenyan, A.A. Shahinyan, J. Koetz, Polyethyleneimine Loaded Inverse SDS Micelle in Pentanol/Toluene Media, Colloids and Surfaces A: Physicochemical  and Engineering Aspects. 506 (2016), 402-408

  135. Vladimir Risojević, “Analysis of Learned Features for Remote Sensing Image Classification”, Proc. 13th Symposium on Neural Network Applications in Electrical Engineering NEUREL 2016, Belgrade, Serbia, pp. 151-156, November 2016.

  137. S. Stoykov, E. Atanassov, and S. Margenov, Efficient sparse matrix-matrix multiplication for computing periodic responses by shooting method on Intel Xeon Phi, Citation: AIP Conference Proceedings 1773, 110012 (2016)

  139. Hrachya Astsatryan, Zaruhi Petrosyan, Rita Abrahamyan, Anna Shahnazaryan, Vladimir Sahakyan, Yuri Shoukourian, Hamlet Melkonyan, Vassiliki Kotroni, WRF-ARW Model for the Prediction of High Temperatures in South and South East Regions of Armenia, 11th IEEE eScience Conference, Munich, Germany, 31 August – 04 September, 2015, pp. 207-113, DOI 10.1109/eScience.2015.82.