Publications

Articles
  1. Özen, C. and Tüzün, N. S. (2008). A DFT study on the mechanism of cyclopropanation via Cu(acac)(2)-catalyzed diazo ester decomposition. Organometallics, 27(18), 4600-4610. http://dx.doi.org/10.1021/om800094k
  2. Tüzün, S., Bayata, F. and Sarac, A. S. (2008). An experimental and quantum mechanical study on electrochemical properties of N-substituted pyrroles. Journal of Molecular Structure: Theochem, 857 (1-3) , 95-104. http://dx.doi.org/10.1016/j.theochem.2008.02.007
  3. Sevinçli, H., Topsakal, M., Durgun, E., and Ciraci, S., (2008). Electronic and magnetic properties of 3d transition-metal atom adsorbed graphene and graphene nanoribbons , Physical Review B , 77 (19) ,195434. http://dx.doi.org/10.1103/PhysRevB.77.195434
  4. Topsakal, M., Aktürk, E., Sevinçli, H. and Ciraci, S. (2008). First-principles approach to monitoring the band gap and magnetic state of a graphene nanoribbon via its vacancies , Physical Review B , 78 (23), 235435. http://dx.doi.org/10.1103/PhysRevB.78.235435
  5. Topsakal, M., Sevinçli, H. and Ciraci, S. (2008). Spin confinement in the superlattices of graphene ribbons, Applied Physics Letters, 92 ,173118. http://dx.doi.org/10.1063/1.2919525
  6. Ataca, C., Cahangirov, S., Durgun, E., Jang, Y.-R. and Ciraci, S. (2008). Structural, electronic, and magnetic properties of 3d transition metal monatomic chains: First-principles calculations , Physical Review B, 77, 214413. http://dx.doi.org/10.1103/PhysRevB.77.214413
  7. Sevinçli, H., Topsakal, M. and Ciraci, S. (2008). Superlattice structures of graphene-based armchair nanoribbons, Physical Review B, 78, 245402. http://dx.doi.org/10.1103/PhysRevB.78.245402
  8. Çakır, D., Gülseren,  O., Mete,  E. and  Ellialtıoğlu, Ş. (2009). Dye adsorbates BrPDI, BrGly, and BrAsp on anatase TiO2(001) for dye-sensitized solar cell applications. Physical Review B, 80, 35431. http://dx.doi.org/10.1103/PhysRevB.80.035431
  9. Onat, B., Konuk, M., Durukanoğlu, S. and Dereli, G. (2009). Energetics and atomic relaxations of Cu nanowires: the effect of local strain and cross-sectional area, Nanotechnology, 20 (7), 75707. http://iopscience.iop.org/article/10.1088/0957-4484/20/7/075707
  10. Özen, C., S. Konuklar, F. A. and Tüzün, N. S. (2009) Mechanistic Study on [3+2] Cycloaddition and Cyclopropanation Reactions of 1,3-Dioxepine Derivatives in the Presence of Copper(I) Catalyst , Organometallics, 28 (17), 4964-4973. http://pubs.acs.org/doi/abs/10.1021/om900235a
  11. Topsakal, M., Cahangirov, S., Bekaroglu, E. and Ciraci, S. (2009). First-principles study of zinc oxide honeycomb structures. Physical Review B, 80 (23), 23519.  http://dx.doi.org/10.1103/PhysRevB.80.235119
  12. Sahin, H., Ataca, C. and Ciraci, S. (2009). Magnetization of graphane by dehydrogenation. Applied Physics Letters, 95 (22). http://dx.doi.org/10.1063/1.3268792
  13. Cahangirov, S. and Ciraci, S. (2009). Confinement of electrons in size-modulated silicon nanowires. Physical Review B, 80 (7-8), 075305. http://dx.doi.org/10.1103/PhysRevB.80.075305
  14. Cahangirov, S., Topsakal, M. and Akturk, E. (2009). Two- and One-Dimensional Honeycomb Structures of Silicon and Germanium. Physical Review Letters , 102 (23), 236804. ttp://dx.doi.org/10.1103/PhysRevLett.102.236804
  15. Cahangirov, S. and Ciraci, S. (2009). First-principles study of GaAs nanowires. Physical Review B, 79 (16), 165118. http://dx.doi.org/10.1103/PhysRevB.79.165118
  16. Topsakal, M., Akturk, E. and Ciraci, S. (2009). First-principles study of two- and one-dimensional honeycomb structures of boron nitride. Physical Review B, 79 (11), 115442. http://dx.doi.org/10.1103/PhysRevB.79.115442
  17. Akturk, E. and Ciraci, S. (2009). A First-principles study of iron-pnictide BaFe2As2. Physical Review B, 79, 184523. http://dx.doi.org/10.1103/PhysRevB.79.184523
  18. Ataca, C., Akturk, E. and  Ciraci, S. (2009). Hydrogen storage of calcium atoms adsorbed on grapheme: First-principles plane wave calculations. Physical Review B: Rapid Communications, 79, 041406(R). http://dx.doi.org/10.1103/PhysRevB.79.041406
  19. Cakir, D. and Gulseren, O. (2009). First-principles study of thin TiOx and bulklike rutile nanowires, Physical Review B, 80 (12). http://dx.doi.org/10.1103/PhysRevB.80.125424
  20. Erkol, G., Oka, M. and Takahashi, T. T. (2010). Axial Charges of Octet Baryons in Two-flavor Lattice QCD, Physics Letters B , 686 (1) , 36-40. http://dx.doi.org/10.1016/j.physletb.2010.02.016
  21. Dönmez, O. (2010). Sgr A* Karadeliğinin Etrafındaki Yığılma Diskinin Dinamik Yapısının Modellenmesi , Journal of Natural and Applied Science , 14 (1) , 4-9.
  22. Şengün, Y. and Durukanoğlu, S. (2010). Vibrational properties of Cu nanowires. Physica A: Statistical Mechanics and its Applications, 389 (15), 2945-2950. http://dx.doi.org/10.1016/j.physa.2010.02.013
  23. Cahangirov, S., Topsakal, M. and Ciraci, S. (2010). Long-range interactions in carbon atomic chains, Physical Review B , 83 (19), 195444.  http://dx.doi.org/10.1103/PhysRevB.82.195444
  24. Yildiran, D. and Donmez, O. (2010). Numerical Treatment of Thin Accretion Disk Dynamics Around Rotating Black Holes. International Journal of Modern Physics D, 19 (13), 2111-2133. http://dx.doi.org/10.1142/S0218271810018256
  25. Sahin, H., Senger, R. T. and Ciraci, S. (2010). Spintronic properties of zigzag-edged triangular graphene flakes. Journal of Applied Physics, 108 (7-8), 074301. http://dx.doi.org/10.1063/1.3489919
  26. Dedeoglu, B., Catak, S., Houk, K. N. and Aviyente, V.  (2010). A Theoretical Study of the Mechanism of the Desymmetrization of Cyclic meso-Anhydrides by Chiral Amino Alcohols. CHEMCATCHEM, 2 (9), 1122-1129. http://dx.doi.org/10.1002/cctc.201000065
  27. Akturk, E., Ataca, C. and Ciraci, S. (2010). Effects of silicon and germanium adsorbed on graphene. Applied Physics Letters, 96 (12), 123112. http://dx.doi.org/10.1063/1.3368704
  28. Gul, S., Schoenebeck, F. and Aviyente, V. (2010) Computational Study of Factors Controlling the Boat and Chair Transition States of Ireland-Claisen Rearrangements , Journal of Organic Chemistry , 75 (6) , 2115-2118. http://pubs.acs.org/doi/abs/10.1021/jo100033d
  29. Topsakal, M., Bagci, V. M. K. and Ciraci, S. (2010). Current-voltage (I-V) characteristics of armchair graphene nanoribbons under uniaxial strain, Physical Review B, 81 (20). http://dx.doi.org/10.1103/PhysRevB.81.205437
  30. Sahin, H., Ataca C. and Ciraci, S. (2010). Electronic and magnetic properties of graphene nanoribbons,Physical Review B, 81 (20). http://dx.doi.org/10.1103/PhysRevB.81.205417
  31. Degirmenci, I., Eren, S., Aviyente V., De Sterck, B., Hemelsoet, K., Van Speybroeck, V. and Waroquier, M. (2010). Modeling the solvent effect on the tacticity in the free radical polymerization of methyl methacrylate, Macromolecules, 43 (13), 5602-5610.   http://dx.doi.org/10.1021/ma100608g
  32. Furuncuoglu, T., Ugur, I., Degirmenci, I. and Aviyente, V. (2010). Role of Chain Transfer Agents in Free Radical Polymerization Kinetics , Macromolecules , 43 (4) , 1823-1835. http://dx.doi.org/10.1021/ma902803p
  33. Bekaroglu, E., Topsakal, M. and Cahangirov, S. (2010). First-principles study of defects and adatoms in silicon carbide honeycomb structures. Physical Review B, 81(7-8), 075433. http://dx.doi.org/10.1103/PhysRevB.81.075433
  34. Topsakal, M. and Ciraci, S. (2010). Elastic and plastic deformation of graphene, silicene, and boron nitride honeycomb nanoribbons under uniaxial tension: A first-principles density-functional theory study. Physical Review B, 81, 024107. http://dx.doi.org/10.1103/PhysRevB.81.024107
  35. Yılmaz, İ., Davidson, L., Edis, F. O. and Saygın, H. (2011). Numerical simulation of Kelvin-Helmholtz instability using an implicit, non-dissipative DNS algorithm. Journal of Physics Conference Series, 318 (3),  32024.
  36. Ozen, A. S. (2011). Peripheral and Structural Effects on the Band Gap of Acceptor-Donor Type Conducting Polymers Containing Pendant Bisfulleroid Groups , Journal of Physical Chemistry C, 115 (50), 25007-25018. http://pubs.acs.org/doi/abs/10.1021/jp2063673
  37. Ozaltin, T. F. Degirmenci, I. and Aviyente, V. (2011). Controlling the tacticity in the polymerization of N-isopropylacrylamide: A computational study.  Polymer, 52 (24), 5503-5512. http://dx.doi.org/10.1016/j.polymer.2011.10.009
  38. Cakir, D. and Gulseren, O. (2011) Effect of impurities on the mechanical and electronic properties of Au, Ag, and Cu monatomic chain nanowires. Physical Review B, 84 (8), 085450. http://dx.doi.org/10.1103/PhysRevB.84.085450
  39. Ozen, C., Yurtsever, M. and Ozturk, T. (2011).  A theoretical approach to the formation mechanism of diphenyldithieno[3,2-b:2′,3 ‘-d]thiophene from 1,8-diketone, 4,5-bis(benzoylmethylthio)thiophene: a DFT study. TETRAHEDRON , 67 (34) , 6275-6280. http://dx.doi.org/10.1016/j.tet.2011.06.037
  40. Sahin, M. (2011). A stable unstructured finite volume method for parallel large-scale viscoelastic fluid flow calculations. Journal of Non-Newtonian Fluid Mechanics, 116 (14-15), 779-791. http://dx.doi.org/10.1016/j.jnnfm.2011.03.010
  41. Cirak, C., Demir, S. and Ucun, F. (2011). Experimental and theoretical study on the structure and vibrational spectra of beta-2-aminopyridinium dihydrogenphosphate. Spectrochimica Acta Part A-Molecular and Biomolecular Spectroscopy, 79(3), 529-532 .
  42. Karahan, O., Avci, D. and Aviyente, V. (2011). Structure-Reactivity Relationships of Alkyl alpha-Hydroxymethacrylate Derivatives, Journal of Polymer Science Part A-Polymer Chemistry, 49 (14), 3058-3068.
  43. Topcuoglu, H. R., Ermis, M. and Sifyan, M. (2011). Positioning and Utilizing Sensors on a 3-D Terrain Part II-Solving With a Hybrid Evolutionary Algorithm. IEEE Transactions On Systems Man and Cybernetics Part C-Applications and Reviews, 41 (4), 470-480. http://dx.doi.org/10.1109/TSMCC.2010.2055851
  44. Ataca, C. and Ciraci, S. (2011). Perpendicular growth of carbon chains on graphene from first-principles, Physical Review B, 83 (23), 235417. http://dx.doi.org/10.1103/PhysRevB.83.235417
  45. Karahan, O., Isik, M. and Cifci, G. (2011). Cyclization Tendencies in the Free Radical Polymerization of Allyl Acrylate Derivatives: A Computational Study. Journal of Polymer Science Part A-Polymer Chemistry,  49  (11), 2474-2483.
  46. Cakir, D., Gulseren, O. and Mete, E. (2011). Interaction of BrPDI, BrGly, and BrAsp with the Rutile TiO2(110) Surface for Photovoltaic and Photocatalytic Applications: A First-Principles Study , Journal of Physical Chemistry C, 115 (18), 9220-9226.
  47. Topcuoglu, H. R., Ermis, M. and Sifyan, M. (2011). Positioning and Utilizing Sensors on a 3-D Terrain Part I-Theory and Modeling, IEEE Transactions On Systems Man and Cybernetics Part C-Applications and Reviews, 41 (3), 376-382 .
  48. Cahangirov, S. and Ciraci, S. (2011). Two-dimensional C/BN core/shell structures, Physical Review B, 83 (16), 165448. http://dx.doi.org/10.1103/PhysRevB.83.165448
  49. Donmez, O., Zanotti, O. and Rezzolla, L. (2011). On the development of quasi-periodic oscillations in Bondi-Hoyle accretion flows. Monthly Notices of the Royal Astronomical Society, 412 (3), 1659-1668. http://dx.doi.org/10.1111/j.1365-2966.2010.18003.x
  50. Sahin, H., Topsakal, M. and Ciraci, S. (2011). Structures of fluorinated graphene and their signatures. Physical Review B, 83 (11), 115432.  http://dx.doi.org/10.1103/PhysRevB.83.115432
  51. Agopcan, S., Celebi-Olcum, N., Ucisik, N. M., Sanyal, A. and Aviyente, V. (2011). Origins of the diastereoselectivity in hydrogen bonding directed Diels-Alder reactions of chiral dienes with achiral dienophiles: a computational study. Organic & Biomolecular Chemistry, 9 (23), 8079-8088. http://dx.doi.org/10.1039/C1OB06285A
  52. Bozkurt, D. and Sen, O.L. (2011) Precipitation in the Anatolian Peninsula: Sensitivity to increased SSTs in the surrounding seas. Climate Dynamics, 36 (3-4), 711-726. http://dx.doi.org/10.1007/s00382-009-0651-3
  53. Durak, A. T., Gökcan H. and  Konuklar, F. A. S. (2011). Theoretical studies on the inactivation mechanism of γ-aminobutyric acid aminotransferase. Organic & Biomolecular Chemistry, 9, 5162-5171.  http://dx.doi.org/10.1039/C1OB05146F
  54. Şengün, Y. and Durukanoğlu, S. (2011). Vibrational behavior of metal nanowires under tensile stress. Physics Letters B, 83, 113409. http://dx.doi.org/10.1103/PhysRevB.83.113409
  55. Ataca, C., Sahin, H., Akturk, E. and Ciraci, S. (2011). Mechanical and Electronic Properties of MoS2 Nanoribbons and Their Defects, Journal of Physical Chemistry C, 115 (10), 3934-3941. http://dx.doi.org/10.1021/jp1115146
  56. Sozuer, H. S. and Sengun H. D. (2011). Photonic Crystal Assisted 90 degrees Waveguide Bend, International Journal of Modern Physics B, 25 (16), 2167-2182. http://dx.doi.org/10.1142/S0217979211100072
  57. Ataca, C. and Ciraci, S. (2011).Functionalization of Single-Layer MoS2 Honeycomb Structures, Journal of Physical Chemistry C, 115 (27), 13303-13311. http://dx.doi.org/10.1021/jp2000442
  58. Yildirim, A., Konuklar, F. A. S., Catak, S., Speybroeck, V. V., Waroquier, M., Doğan, İ. and Aviyente V. (2012). Solvent-Catalyzed Ring-Chain-Ring Tautomerization in Axially Chiral Compounds. Chemistry A European Journal, 18 (40), 12725-12732. http://dx.doi.org/10.1002/chem.201200363
  59. Hummatov, R., Gulseren, O., Ozensoy, E., Toffoli, D. and Üstünel, H. (2012). First-Principles Investigation of NOx and SOx Adsorption on Anatase-Supported BaO and Pt Overlayers. Journal of Physical Chemistry C, 116 (10), 6191-6199. http://dx.doi.org/10.1021/jp208790a
  60. Cakir, D. and Gulseren, O. (2012). Adsorption of Pt and Bimetallic PtAu Clusters on the Partially Reduced Rutile (110) TiO2 Surface: A First-Principles Study. Journal of Physical Chemistry C, 116 (9), 5735-5746. http://dx.doi.org/10.1021/jp2109253
  61. Sutay, B., Tekin, A. and Yurtsever, M. (2012). Intermolecular interactions in nitrogen-containing aromatic systems. Theoretical Chemistry Accounts, 131 (2), 1120. http://dx.doi.org/10.​1007/​s00214-012-1120-3
  62. Sucsoran, O., Bekiroglu, S., Ozturk, T. and Ertaş, E. (2012). Synthesis and electronic properties of 4-cyanophenylvinylenedithiathiophene: An EDOT derivative. Synthetic Metals, 162 (1-2), 49-53. http://dx.doi.org/10.1016/j.synthmet.2011.11.007
  63. Ince, H. H., Dedeoglu, B. and Gul, S. (2012). Selectivity in the aggregates of the chiral organolithium N-Boc-2-lithiopiperidine with a chiral ligand: a DFT study. Molecular Physics, 110  (6), 353-359. http://dx.doi.org/10.1080/00268976.2011.647103
  64. Ozcelik, V. O. and Ciraci, S. (2012). Self-assembly mechanisms of short atomic chains on single-layer graphene and boron nitride. Physical Review B, 86 (15), 155421. http://dx.doi.org/10.1103/PhysRevB.86.155421
  65. Toffoli, D. and  Decleva, P. (2012). Density functional theory for molecular multiphoton ionization in the perturbative regime. Journal of Chemical Physics, 137 (13), 134103. http://dx.doi.org/10.1063/1.4754820
  66. Donmez, O. (2012). Relativistic simulation of flip-flop instabilities of Bondi-Hoyle accretion and quasi-periodic oscillations. Monthly Notices of the Royal Astronomical Society, 426 (2), 1533-1545. http://dx.doi.org/10.1111/j.1365-2966.2012.21616.x
  67. Caputo, R. and Tekin, A. (2012). Lithium Dihydroborate: First-Principles Structure Prediction of LiBH2. Inorganic Chemistry, 51 (18), 9757-9765. http://dx.doi.org/10.1021/ic301127q
  68. Cirak, C. and Koc, N. (2012). Molecular structure and effects of intermolecular hydrogen bonding on the vibrational spectrum of trifluorothymine, an antitumor and antiviral agent. Journal of Molecular Modeling, 18 (9), 4453-4464. http://dx.doi.org/10.​1007/​s00894-012-1449-5
  69. Panos, M., Sen, T. Z. and Ahunbay, M. G. (2012). Molecular Simulation of Fibronectin Adsorption onto Polyurethane Surfaces. Langmuir, 28 (34), 12619-12628. http://dx.doi.org/10.1021/la301546v
  70. Cakir, D. and Gulseren, O. (2012). Ab initio study of neutral (TiO2)(n) clusters and their interactions with water and transition metal atoms. Journal of Physics: Condensed Matter, 24 (30), 305301. http://iopscience.iop.org/0953-8984/24/30/305301
  71. Velioğlu, S., Ahunbay, G. and Tantekin-Ersolmaz, S. B. (2012). Investigation of Sorption Induced Plasticization in Fluorinated Polyimide Membranes via Molecular Simulation. Journal of Membrane Science, 417-418, 217-227. http://dx.doi.org/10.1016/j.memsci.2012.06.043
  72. Dogan, B., Catak, S., Speybroeck, V. V., Waroquier, M. and Aviyente V.  (2012). Free radical polymerization of ethyl methacrylate and ethyl alpha-hydroxy methacrylate: A computational approach to the propagation kinetics.  Polymer, 53 (15), 3211-3219. http://dx.doi.org/10.1016/j.polymer.2012.05.018
  73. Ozcelik, V. O., Cahangirov, S. and Ciraci, S. (2012). Epitaxial growth mechanisms of graphene and effects of substrates. Physical Review B, 85 (23), 235456. http://dx.doi.org/10.1103/PhysRevB.85.235456
  74. Cirak, C., Sert, Y. and Ucun, F. (2012). Experimental and computational study on molecular structure and vibrational analysis of a modified biomolecule: 5-Bromo-2 ‘-deoxyuridine. Spectrochimica Acta Part A-Molecular and Biomolecular Spectroscopy, 92, 406-414. http://dx.doi.org/10.1016/j.saa.2012.02.053
  75. Ataca, C., Sahin, H. and Ciraci, S. (2012). Stable, Single-Layer MX2 Transition-Metal Oxides and Dichalcogenides in a Honeycomb-Like Structure. Journal of Physical Chemistry C, 116 (16), 8983-8999. http://dx.doi.org/10.1021/jp212558p
  76. Önol, B. (2012). Effects of coastal topography on climate: high-resolution simulation with a regional climate model. Climate Research, 52, 159-174. http://dx.doi.org/10.3354/cr01077
  77. Yildirim, E., Yurtsever, M., Yurtsever, E., Yilgor, I.  and  Yilgor, E. (2012). Multiscale Modeling of the Morphology and Properties of Segmented Silicone-Urea Copolymers. Journal of Inorganic and Organometallic Polymers and Materials, 22, 604-616. http://dx.doi.org/10.1007/s10904-011-9588-1
  78. Dönmez, O. (2012). Relativistic Simulation of Flip-Flop Instabilities of the Bondi- Hoyle Accretion and Quasi-Periodic Oscillations. MNRAS, 426, 1533-1545. http://dx.doi.org/10.1111/j.1365-2966.2012.21616.x
  79. Gökcan, H. and  Konuklar, F. A. S. (2012). Theoretical Study on HF Elimination and Aromatization Mechanisms: A Case of Pyridoxal 5′ Phosphate-Dependent Enzyme. The Journal of Organic Chemistry, 77(13) , 5533-5543. http://dx.doi.org/10.1021/jo3005815
  80. Osken, I., Sahin, O., Gundogan, A. S., Bildirir, H., Capan, A., Ertas, E., Eroglu, M. S., Wallis, J. D., Topal, K. and Ozturk, T. (2012). Selective syntheses of vinylenedithiathiophenes (VDTTs) and dithieno [2,3-b;2 ‘,3 ‘-d]thiophenes (DTTs); building blocks for pi-conjugated systems,Tetrahedron, 68 (4), 1216-1222.  http://dx.doi.org/10.1016/j.tet.2011.11.059
  81. Krenske, E. H., Agopcan, S., Ayiyente, V., Houk, K. N., Johnson, B. A. and Holmes, A. B. (2012). Causation in a Cascade: The Origins of Selectivities in Intramolecular Nitrone Cycloadditions, Journal of the  American Chemical Society, 134 (29), 12010-12015. http://dx.doi.org/10.1021/ja300002k
  82. Saleem, H., Erdogdu, Y., Subashchandrabose, S., Thanikachalam, V., Jayabharathi, J. and Babu, N. R., Structural and vibrational studies on (E)-2-(2-hydroxy benzyliden amino)-3-phenyl propionic acid using experimental and DFT methods, Journal of Molecular Structure, 1030, 157-167. http://dx.doi.org/10.1016/j.molstruc.2012.04.011
  83. Erdogan, Y. S. and Gundes,  P. B. (2013). Evaluation of the different genetic algorithm parameters and operators for the Finite Element Model Updating Problem. Computers and Concrete, 11(6), 541-569. http://dx.doi.org/10.12989/cac.2013.11.6.541
  84. Erzincanli, B. and Sahin, M. (2013). An arbitrary Lagrangian-Eulerian formulation for solving moving boundary problems with large displacements and rotations. Journal of Computational Physics,  255, 660-679. http://dx.doi.org/10.1016/j.jcp.2013.08.038
  85. Ozcelik, V. O. and Ciraci, S. (2013). Local Reconstructions of Silicene Induced by Adatoms. Journal of Physical Chemistry C, 117 (49), 26305-26315. http://dx.doi.org/10.1021/jp408647t
  86. Ozen, C., Yildirim, A., Tuzun, N. S., Haslak, P., Doğan, E., Acar, E. and Aviyente, V. (2013). Prediction of the H-1 NMR spectra of epoxy-fused cyclopentane derivatives by calculations of chemical shifts and spin-spin coupling constants. Molecular  Physics, 111 (20), 3147-3155. http://dx.doi.org/10.1080/00268976.2013.772256
  87. Gurel, H. H. and Ciraci, S. (2013). Enhanced reduction of graphene oxide by means of charging and electric fields applied to hydroxyl groups. Journal of Physics-Condensed Matter, 25 (43), 5304. http://dx.doi.org/10.1088/0953-8984/25/43/435304
  88. Yildirim, E., Erciyes, G. and Yurtsever, M. (2013). Theoretical approach to the structural, electronic, and morphological properties of poly(E>-caprolactone) grafted polypyrroles. Macromolecular Research, 21 (9), 949-957. http://dx.doi.org/10.1007/s13233-013-1111-9
  89. Gurel, H. H., Ozcelik, V. O. and Ciraci, S. (2013). Effects of charging and perpendicular electric field on the properties of silicene and germanene. Journal of Physics-Condensed Matter, 25 (30), 5007. http://dx.doi.org/10.1088/0953-8984/25/30/305007/
  90. Ozcelik, V. O., Gurel, H. H. and Ciraci, S. (2013). Self-healing of vacancy defects in single-layer graphene and silicene. Physical Review B, 88 (4), 5440. http://dx.doi.org/10.1103/PhysRevB.88.045440
  91. Toffoli, D. and Decleva, P. (2013). Multiphoton core ionization dynamics of polyatomic molecules. Journal of Physics B: Atomic, Molecular and Optical Physics,  46 (14), 5101. http://dx.doi.org/10.1088/0953-4075/46/14/145101
  92. Ozcelik, V. O. and Ciraci, S. (2013). Nanoscale Dielectric Capacitors Composed of Graphene and Boron Nitride Layers: A First-Principles Study of High Capacitance at Nanoscale. Journal of Physical Chemistry C, 117 (29), 15327-15334. http://dx.doi.org/10.1021/jp403706e
  93. Gurel, H. H. and Ciraci, S. (2013). Effects of charging and electric field on graphene functionalized with titanium , Journal of Physics-Condensed Matter, 25 (27), 5302. http://dx.doi.org/10.1088/0953-8984/25/27/275302/
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  180. Kecik, D., Durgun, E. and Ciraci, S. (2016) Optical properties of single-layer and bilayer arsenene phases, Physical Review B, 94 (20). http://dx.doi.org/10.1103/PhysRevB.94.205410
  181. Sezer, E., Osken, I., Cinar, M.E., Demirel, O., Ustamehmetoglu, B. and Ozturk, T. (2016) Synthesis and Electropolymerization of Bis(phenylthieno[3,2-b]thiophenes)- (4,4 ‘-dinonyl-2,2 ‘-bithiazole) co-monomer, ELECTROCHIMICA ACTA, 222, 1592-1603, http://dx.doi.org/10.1016/j.electacta.2016.11.145
  182. Kayik, G., Tuzun, N.S. and Durdagi, S. (2017) Investigation of PDE5/PDE6 and PDE5/PDE11 selective potent tadalafil-like PDE5 inhibitors using combination of molecular modeling approaches, molecular fingerprint-based virtual screening protocols and structure-based pharmacophore development, JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY, 32 (1), 311-330, http://dx.doi.org/10.1080/14756366.2016.1250756
  183. Onat, B., Hallioglu, L., Ipek, S. and Durgun, E. (2017) Tuning Electronic Properties of Monolayer Hexagonal Boron Phosphide with Group III-IV-V Dopants, JOURNAL OF PHYSICAL CHEMISTRY C, 121 (8), 4583-4592, http://dx.doi.org/10.1021/acs.jpcc.6b10334
  184. Gurkan, YY., Kasapbasi, E., Turkten, N and Cinar, Z. (2017). Influence of Se/N Codoping on the Structural, Optical, Electronic and Photocatalytic Properties of TiO2, Molecules, 22 (3). http://dx.doi.org/3390/molecules22030414
  185. Ustamehmetoglu, B., Osken, I., Cinar, M.E., Sezer, E., Karaca, E. and Ozturk, T. (2017). Synthesis and Characterization of Dithienothiophene, Bithiazole and Thiophene Containing Polymer, Electrochimica Acta, 227, 435-446. http://dx.doi.org/1016/j.electacta.2016.12.153
  186. Donmez, O. (2017). Investigating the instability of the torus around the black hole in the presence of the radial and angular velocity perturbations, Turkish Journal of Physics, 41 (1), 25-40. http://dx.doi.org/3906/fiz-1604-12 2017
  187. Buyruk, A., Cinar, M.E., Eroglu, M.S. and Ozturk, T. (2017). Polymerization of Thienothiophenes and Dithienothiophenes via Click-Reaction for Electronic Applications, Chemistryselect, 1 (12), 3028-3032. http://dx.doi.org/1002/slct.201600697
  188. Allushi, A., Kutahya, C., Aydogan, C., Kreutzer, J., Yilmaz, G. and Yagci, Y. (2017). Conventional Type II photoinitiators as activators for photoinduced metal-free atom transfer radical polymerization, Polymer Chemistry, 8 (12), 1972-1977. http://dx.doi.org/1039/c7py00114b
  189. Demirci, S., Avazli, N., Durgun, E. and Cahangirov, S. (2017). Structural and electronic properties of monolayer group III monochalcogenides, Physical Review B, 95 (11). http://dx.doi.org/10.1103/PhysRevB.95.115409
  190.  Turuncoglu, U.U. and Sannino, G. (2017). Validation of newly designed regional earth system model (RegESM) for Mediterranean Basin, Climate Dynamics, 48 (9), 2919-2947. http://dx.doi.org/10.1007/s00382-016-3241-1
  191.  Sahin, O., Cinar, M.E., Tekin, E., Mucur, S.P., Topal, S., Suna, G., Eroglu, M.S. and Ozturk, T. (2017). White Light Emitting Polymers Possessing Thienothiophene and Boron Units, Chemistryselect, 2 (10),2889-2894. http://dx.doi.org/10.1002/slct.2017001742
  192. Turkoglu, G., Cinar, M.E. and Ozturk, T. (2017). Organoboron copolymers containing thienothiophene and selenophenothiophene analogues: optical, electrochemical and fluoride sensing properties, RSC ADVANCES, 7 (37), 23197-23207. http://dx.doi.org/10.1039/c7ra01793f3
  193. Onen, A., Kecik, D., Durgun, E. and Ciraci, S. (2017). In-plane commensurate GaN/AlN junctions: Single-layer composite structures, single and multiple quantum wells and quantum dots, Physical Review B, 95 (15). http://dx.doi.org/10.1103/PhysRevB.95.155435
  194. Ugur, I., Cinar, S.A., Dedeoglu, B., Aviyente, V., Hawthorne, M.F., Liu, P., Liu, F., Houk, K.N. and Jimenez-Oses, G. (2017. 1,3-Dipolar Cycloaddition Reactions of Low-Valent Rhodium and Iridium Complexes with Arylnitrile N-Oxides, Journal of Organic Chemistry, 82 (10), 5096-5101, http://dx.doi.org/10.1021/acs.joc.7b00282
  195. Yildiz, G., Aydogmus, Z., Cinar, M.E., Senkal, F. and Ozturk, T. (2017). Electrochemical oxidation mechanism of eugenol on graphene modified carbon paste electrode and its analytical application to pharmaceutical analysis, TALANTA, 173, 1-8, http://dx.doi.org/10.1016/jtalanta.2017.05.056
  196. Eken, A. and Sahin, M. (2017). A parallel monolithic approach for fluid-structure interaction in a cerebral aneurysm, Computers & Fluids, 153, 61-75; http://dx.doi.org/10.1016/j.compfluid.2017.05.005
  197. Celebi, M.S., Duran, A., Oztoprak, F., Tuncel, M. and Akaydin, B. (2017). On the improvement of a scalable sparse direct solver for unsymmetrical linear equations, JOURNAL OF SUPERCOMPUTING, 73 (5), 1852-1904, http://dx.doi.org/10.1007/s11227-016-1892-73.
  198. Karatas, D., Tekin, A. and Celik, M.S. (2017). Density Functional Theory Computation of Organic Compound Penetration into Sepiolite Tunnels, CLAYS AND CLAY MINERALS, 65 (1), 1-13, http://dx.doi.org/10.1346/CCMN.2016.064043
  199. Salmas, R.E., Unlu, A., Bektas, M., Yurtsever, M., Mestanoglu, M. and Durdagi, S. (2017). Virtual screening of small molecules databases for discovery of novel PARP-1 inhibitors: combination of in silico and in vitro studies, JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 35 (9), 1899-1915; http://dx.doi.org/10.1080/07391102.2016.1199328
  200. Turkoglu, G., Cinar, M.E. and Ozturk, T. (2017). Synthesis and Photophysical and Anion-Sensing Properties of Triarylborane-Substituted Cross-Conjugated and Conjugated Thienothiophenes, EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, (31), 4552-4561. http://dx.doi.org/10.1002/ejoc.201700679
  201. Gunay, S.D. (2017). Thermal recovery mechanisms of UO2 lattices by defect annihilation, JOURNAL OF ALLOYS AND COMPOUNDS, 724, 841-850. http://dx.doi.org/10.1016/j.jallcom.2017.07.100
  202. Cinar, S.A., Ziylan-Yavas, A., Catak, S., Ince, N.H. and Aviyente, V. (2017). Hydroxyl radical-mediated degradation of diclofenac revisited: a computational approach to assessment of reaction mechanisms and by-products, ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH, 24 (22),18458-18469. http://dx.doi.org/10.1007/s11356-017-9482-7
  203. Tedik Basaran, S., Gokceli, S., Karabulut Kurt, G., Ozdemir E. and Yaraneri, E. (2017). Error Performance Analysis of Random Network Coded Cooperation Systems, IEEE Transactions on Wireless Communications, 16 (8), 5325-5337. http://dx.doi.org/10.1109/TWC.2017.2708702
  204. Kreutzer, J. and Yagci, Y. (2017). One-component, double-chromophoric thioxanthone photoinitiators for free radical polymerization, JOURNAL OF POLYMER SCIENCE PART A-POLYMER CHEMISTRY, 55 (20), 3475-3482, http://dx.doi.org/10.1002/pola.287293.
  205. Kutahya, C., Allushi, A., Isci, R., Kreutzer, J., Ozturk, T., Yilmaz, G. and Yagci, Y. (2017) Photoinduced Metal-Free Atom Transfer Radical Polymerization Using Highly Conjugated Thienothiophene Derivatives, MACROMOLECULES, 50 (17), 6903-6910. http://dx.doi.org/10.1021/acs.macromol.7b01335
  206. Karatas, D., Tekin, A., Bahadori, F. and Celik, M.S. (2017) Interaction of curcumin in a drug delivery system including a composite with poly(lactic-co-glycolic acid) and montmorillonite: a density functional theory and molecular dynamics study, JOURNAL OF MATERIALS CHEMISTRY B, 5 (40), http://dx.doi.org/8070-8082; 10.1039/c7tb01964e
  207. Maciel, Y., Gungor, A.G. and Simens, M. (2017) Structural differences between small and large momentum-defect turbulent boundary layers, INTERNATIONAL JOURNAL OF HEAT AND FLUID FLOW, 67, 95-110. http://dx.doi.org/10.1016/j.ijheatfluidflow.2017.07.011
  208. Manukyan, A. and Tekin, A. (2017) The intermolecular dimer potential for guanine, JOURNAL OF CHEMICAL PHYSICS, 147 (15). http://dx.doi.org/10.1063/1.4998792
  209. Gurbuz, E,. Cahangirov, S., Durgun, E. and Ciraci, S. (2017) Single layers and multilayers of GaN and AlN in square-octagon structure: Stability, electronic properties, and functionalization, PHYSICAL REVIEW B, 96 (20).  http://dx.doi.org/10.1103/PhysRevB.96.205427
  210. Khanifaev, J., Pekoz, R., Konuk, M. and Durgun, E. (2017) The interaction of halogen atoms and molecules with borophene, Physical Chemistry Chemical Physics, 19 (42), pp. 28963-28969. http://dx.doi.org/10.1039/c7cp05793h
  211. Guventurk, C. and Sahin, M. (2017) An arbitrary Lagrangian-Eulerian framework with exact mass conservation for the numerical simulation of 2D rising bubble problem, International Journal for Numerical Methods in Engineering, 112 (13), pp. 2110-2134. http://dx.doi.org/10.1002/nme.5598
  212. Onen, A., Kecik, D., Durgun, E. and Ciraci, S. (2017) Lateral and Vertical Heterostructures of h-GaN/h-AIN: Electron Confinement, Band Lineup, and Quantum Structures, Journal of Physical Chemistry C, 121 (48), 27098-27110. http://dx.doi.org/10.1021/acs.jpcc.7608344
  213.  Kayik, G., Tuzun, N.S. and Durdagi, S. (2017) Structural investigation of vesnarinone at the pore domains of open and open-inactivated states of hERG1 K+ channel, Journal of Molecular Graphics & Modelling, 77, 399-412, http://dx.doi.org/10.1016/j.jmgm.2017.08.017
  214. Yildirim, E., Yurtsever, M., Eriman, B. and Uyanik, N. (2018) Experimental and MD simulation study on the physical and mechanical properties of organically modified montmorillonite clay and compatibilized linear low density polyethylene nanocomposites, Journal of Applied Polymer Science, 135 (6) http://dx.doi.org/10.1002/app.45817
  215. Aral, G., Islam, M.M. and van Duin, A.C.T. (2018) Role of surface oxidation on the size dependent mechanical properties of nickel nanowires: a ReaxFF molecular dynamics study, Physical Chemistry Chemical Physics, 20 (1), 284-298 http://dx.doi.org/10.1039/c7cp06906e
  216. Kaya, K., Kreutzer, J and Yagci, Y. (2018) Diphenylphenacyl sulfonium salt as dual photoinitiator for free radical and cationic polymerizations, Journal of Polymer Science Part A-Polymer Chemistry, 56 (4), 451-457. http://dx.doi.org/10.1002/pola.28918
  217. Simens, M.P. and Gungor, A.G. (2018) Influence of the transition of a laminar separation bubble on the downstream evolution of strong adverse pressure gradient turbulent boundary layers, Europen Journal of Mechanics B-Fluids, 67, 70-78. http://dx.doi.org/10.1016/j.euromechflu.2017.08.004
  218. Celebioglu, A., Aytac, Z., Kilic, M.E., Durgun, E., Uyar, T. (2018) Encapsulation of camphor in cyclodextrin inclusion complex nanofibers via polymer-free electrospinning: enhanced water solubility, high temperature stability, and slow release of camphor, Journal of Materials Science, 53 (7), 5436-5449. http://dx.doi.org/10.1007/s10853-017-1918-4
  219. Mobaraki, A., Kandemir, A., Yapicioglu, H., Gülseren, O., Sevik, C. (2018). Validation of inter-atomic potential for WS 2 and WSe 2 crystals through assessment of thermal transport properties, Computational Materials Science, 144, 92-98. https://doi.org/10.1016/j.commatsci.2017.12.005
  220. Timucin, E., Sezerman, O.U. (2018) Thermostability of the PYL-PP2C Heterodimer Is Dependent on Magnesium: In Silico Insights into the Link between Heat Stress Response and Magnesium Deficiency in Plants, Journal of Chemical Information and Modeling, 58 (3), 661-672. http://dx.doi.org/10.1021/acs.jcim.7b00655
  221. Turkoglu, G. (2018). Triarylborane functionalized selenophenothiophene analogues: Syntheses, photophysical and electrochemical properties, Organic Communications, 11 (1), 12-22. http://dx.doi.org/10.25135/acg.oc.34.17.12.061
  222. Kecik, D., Onen, A., Konuk, M., Gurbuz, E., Ersan, F., Cahangirov, S., Akturk, E., Durgun, E. Ciraci, S. (2018). Fundamentals, progress, and future directions of nitride-based semiconductors and their composites in two-dimensional limit: A first-principles perspective to recent synthesis, Applied Physics Reviews, 5 (1). http://dx.doi.org/10.1063/1.4990377
  223. Pekoz, R., Konuk, M., Kilic, M.E., Durgun, E. (2018). Two-Dimensional Fluorinated Boron Sheets: Mechanical, Electronic, and Thermal Properties, ACS OMEGA, 3 (2), 1815-1822. http://dx.doi.org/10.1021/acsomega.7b01730
  224. Sarikurt, S., Cakir, D., Keceli, M., Sevik, C. (2018). The influence of surface functionalization on thermal transport and thermoelectric properties of MXene monolayers, NANOSCALE, 10 (18), 8859-8868. http://dx.doi.org/10.1039/c7nr09144c
  225. Kocabas, T., Cakir, D., Gulseren, O., Ay, F., Perkgoz, N.K., Sevik, C. (2018). A distinct correlation between the vibrational and thermal transport properties of group VA monolayer crystals, NANOSCALE, 10 (16), 7803-7812. http://dx.doi.org/10.1039/c7nr09349g
  226. Kocabas, T., Ozden, A., Demiroglu, I., Cakir, D., Sevik, C. (2018). Determination of Dynamically Stable Electrenes toward Ultrafast Charging Battery Applications, JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 9 (15), 4267-4274. http://dx.doi.org/10.1021/acs.jpclett.8b01468
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Proceedings
  1. F. A. Konuklar. ICTAC-12, Varna-Bulgaristan. Mechanism of a Copper (I) Catalyzed Cycloaddition Reaction. 2008
  2. C. Özen, N. Ş. Tüzün, F. A. Konuklar. Chemical Physics 8, Istanbul 2008. A DFT Study on the Mechanism of Cyclopropanation via Cu(acac)2 Catalyzed Diazo Decomposition Reaction. 2008
  3. C. Özen, F. A. Konuklar ve N. Tüzün. ICTAC-12, 67, Varna, Bulgaristan, 2008. Reaction Mechanism of the Dioxepine with Dimethyl Diazomalonate via Copper-Carbene Species. 2008
  4. H. Topcuoglu, M. Ermis, M. Sifyan. The 9th International Conference on Intellegent Systems Design and Applications (ISDA’09), Pisa, Italy. Hybrid evolutionary algorithms for sensor placement on a 3D terrain. 2009
  5. S. Güryel, F.A. Konuklar, M. Yurtsever, T. Öztürk. DFT09, 31- Agustos-4 Eylül 2009, Lyon, Fransa.. A DT Study on the reaction mechanisms of some TTF derivatives obtained by coupling reactions. 2009
  6. O. Dönmez. 20-05-2009, Ahi Evran Üniversites, Kırşehir, Davetli Konuşma. Genel Rölativistik Hidrodinamik (GRH) Denklemlerinin Sayısal Yöntemler Kullanılarak Çözümlenmesi ve Dönen Kara Delikler Etrafında Oluşan Yığılma (Akresyon) Disklerinin Modellenmesi. 2009
  7. O Dönmez, L. Rezzolla, O. Zanotti. Alternative Solutions in Astrophysics & World Year of Astronomy, 6-11 September 2009. Modeling the Disk Dynamics Around the Rotating Black Hole – Interpreting the Origin of the Black Hole QPOs. 2009
  8. N. Ş. Tüzün, E. Boz, C. Özen. DFT09, Paris, Fransa, 2009. A DFT Study on the Mechanism of Ruthenium Catalyzed Azide-Alkyne Cycloaddition Reaction. 2009
  9. E. Aribas, S. Piskin, M.S. Celebi. V European Conference on Computational Fluid Dynamics ECCOMAS CFD 2010 J. C. F. Pereira and A. Sequeira (Eds) Lisbon, Portugal. SIMULATION OF BLOOD FLOW IN HUMAN AORTA INCLUDING THIRTEEN MAIN ARTERIES. 2010
  10. H. Turkeri, S. Piskin, M. S. Celebi. V European Conference on Computational Fluid Dynamics ECCOMAS CFD 2010 J. C. F. Pereira and A. Sequeira (Eds) Lisbon, Portugal. NON-NEWTONIAN BLOOD FLOW SIMULATION IN A REALISTIC ARTERY DOMAIN. 2010
  11. S.l Piskin, E. Aribas, M. S. Celebi. V European Conference on Computational Fluid Dynamics ECCOMAS CFD 2010 J. C. F. Pereira and A. Sequeira (Eds) Lisbon, Portugal. A 3D HUMAN CAROTID ARTERY SIMULATION USING REALISTIC GEOMETRY AND EXPERIMENTAL INPUT DATA. 2010
  12. A.S. Özen. The 6th Nanoscience and Nanotechnology Conference (NanoTR6), 15-18 Haziran, 2010, İzmir, Türkiye.. Computational Insigth into the Acceptor-Donor Type of Conducting Polymers Containing Pendant Fullerene Groups. 2010
  13. A.S. Özen. Kimyasal Fizik IX, 14-16 Ekim 2010, İzmir, Türkiye. Effect of the Solvent in the Acceptor-Donor Type of Conducting Polymers. 2010
  14. O. Dönmez, O. Zanotti, L. Rezzolla. 25th Texas Symposium on Relativistic Astrophysics, Heidelberg Germany, 6-10 December 2010. Numerical Simulations of QPOs in Bondi-Hoyle type accretion: the case of SgrA*. 2010
  15. D. Yıldıran, O. Dönmez. 27. Ulusal Fizik Kongresi, 14-17 Eylül 2010, İstanbul. Dönen Karadelikler etrafındaki şok konilerinin modellenmesi. 2010
  16. O. Dönmez, O. Zanotti, L. Rezzolla. XVII. Ulusal Astronomi Kongresi, 31 Ağustos- 4 Eylül 2010, Adana. Bondi-Hoyle Tipi Küte Birikimi Durumunda Dönen Karadelikler Etrafındaki QPO’ların Modellenmesi ve Sqr A* Karadeliği için Elde Edilen Gözlem Sonuçların ile Karşılaştırılması. 2010
  17. O. Dönmez, O. Zanotti, L. Rezzolla. COST ACTION MP0905 – BLACK HOLES IN A VIOLENT UNIVERSE, 3RD WORKING GROUPS MEETING . The flip-flop instability of the shock cone around the rotating black hole: the case of Sgr A*. 2011
  18. O. Dönmez. COST ACTION MP0905 – BLACK HOLES IN A VIOLENT UNIVERSE, 4RD WORKING GROUPS MEETING . Extracting QPOs from the disk dynamics around the Sgr A*: Numerical simulation of Bondi-Hoyle accretion . 2011
  19. B. Efe, S. Menteş, Y. Ünal, E. Tan, E. Unal, T. Ozdemir, B. Barutcu, B. Onal, S. Topcu. International Conference on Renewable Energy Research and Applications, November 11-12, Nagasaki, Japan (Submitted).. 72hr forecast of wind power in manisa turkey by using the wrf model coupled to windsim. 2012
  20. A. Duran, M.S. Celebi, M. Tuncel and B. Akaydın. PRACE-2IP white paper, Libraries, WP 43. Design and implementation of new hybrid algorithm and solver on CPU for large sparse linear systems. 2012
  21. M.S. Celebi, A. Duran, M. Tuncel and B. Akaydın. PRACE-2IP white paper, Libraries, WP 44. Scalable and improved SuperLU on GPU for heterogeneous systems. 2012
  22. O. Dönmez. The Biggest Accelerators in space and on earth . Instabilities of Accreated Torus Around the Black Holes . 2013
  23. F. Koyuncu, O. Dönmez. 29th International Physics Congress . Accretion disk dynamics around the Sgr A* black hole . 2013
  24. M.P. Simens, A. G. Güngör. ASME Turbo Expo 2013 GT2013 . THE EFFECT OF SURFACE ROUGHNESS ON LAMINAR SEPARATED BOUNDARY LAYERS . 2013
  25. S. Karaca, M.P. Simens, A.G. Güngör. 7. ANKARA INTERNATIONAL AEROSPACE CONFERENCE . DIRECT NUMERICAL SIMULATION OF COMBINED EFFECTS OF WAKE AND DISCRETE SURFACE ROUGHNESS ON SEPARATED BOUNDARY LAYERS . 2013
  26. A. Duran, M.S. Celebi, B. Akaydin, M. Tuncel and F. Oztoprak. PRACE-1IP Extension white paper, Evaluations on Intel MIC, WP 135. Analysis of SuperLU Solvers on the Intel MIC Architecture,. 2013
  27. A. Duran, M.S. Celebi, M. Tuncel and F. Oztoprak. PRACE-2IP white paper, Scalable Algorithms, WP 82. Structural Analysis of Large Sparse Matrices for Scalable Direct Solvers. 2013
  28. M.S. Celebi, A. Duran, M. Tuncel, B. Akaydin and F. Oztoprak. PRACE-2IP white paper, Libraries, WP 83. Performance Analysis of BLAS Libraries in SuperLU_DIST for SuperLU_MCDT (Multi Core Distributed) Development. 2013