Ioannis G. Karafyllidis

Ioannis G. Karafyllidis

Dr. Ioannis Karafyllidis received a Diploma in Electrical Engineering and a Ph.D in Electrical Engineering, both from the Department of Electrical and Computer Engineering, Aristotle University of Thessaloniki.

He is a Professor in the Department of Electrical and Computer Engineering, Democritus University of Thrace. His research emphasis is on Microelectronic and Nanoelectronic Circuits and Systems, Quantum Information Processing, Molecular Electronics and Systems Biology.

He is Fellow of the Institute of Nanotechnology (FIoN), a Founding Member of the American Academy of Nanomedicine and a Member of the Technical Chamber of Greece (TEE).

He is an Associate Editor in three international journals: “Open Systems Biology Journal”, “Current Nanosciences” and “Recent Patents in Nanotechnology.

He participated as principal investigator or work package leader in 12 national and international research projects.

He acted as evaluator for research proposals submitted after both national and international calls.

He has published more than 80 papers in refereed ISI-indexed journals.

More than 1800 journal, and conference papers cite his research work.

He acts as a referee and/or adjudicator for 37 international, ISI-indexed journals.

Research work in integrated circuit fabrication in collaboration with the Electrical Engineering and Computer Science Department, University of California at Berkeley lead to publications 7, 9, 10, 12, and 16 (see list of selected publications below in this page). Research work in nanobiotechnology in collaboration with Texas Institute for Intelligent Bio-nanomaterials and Structures for Aerospace Vehicles (TiiMS) lead to publication 41(see list of selected publications below in this page). Research work in molecular biology in collaboration with the Department of Molecular Biology and Genetics, DUTh lead to publications 39, 40 and 42 (see list of selected publications below in this page).

Dr. I. Karafyllidis has a large experience in analyzing and designing circuits for information processing and storage. Alone or with members of his team he designed a large number of such circuits and developed CAD tools for the design and simulation of information processing circuits.

In the last few years he has been active in the fields of quantum information processing, bioelectronics and analysis and modeling of biological circuits and networks. He proposed a quantum computer architecture (publications 32 and 34) and developed a quantum computer simulator based on the circuit model of quantum computation (publication 36). This simulator is used for training students in three post-graduate courses in Greek Universities and in two courses in USA Universities. He also developed a quantum game simulator (publication 38). He also modeled bacterial quorum sensing circuits and signaling in confined spaces (publication 44) and developed a quantum circuit model for signal integration in bacterial quorum sensing circuits (publication 45).

Dr. I. Karafyllidis is the only author in a large number of his publications and especially in publications 32, 34, 36, 44 and 45, where research on quantum information processing and quorum sensing circuit modeling is presented.

List of most important journal publications categorized by research field.

Microelectronic integrated circuit design and fabrication

1. I. Karafyllidis and A. Thanailakis, "Simulation of two-dimensional photoresist etching process in integrated circuit fabrication using cellular automata", Modelling and Simulation in Materials Science and Engineering, vol. 3, pp. 629-642, 1995.

2. I. Karafyllidis, I. Andreadis, P. Tzionas, Ph. Tsalides and A. Thanailakis, "A Cellular Automaton for the Determination of the Mean Velocity of Moving Objects and its VLSI Implementation", Pattern Recognition, vol 29, no. 4, pp. 689-699, 1996.

3. I. Karafyllidis and A. Thanailakis, " Simulation of the Image Reversal Submicron Process in Integrated Circuit Fabrication", Semiconductor Science and Technology, vol. 11, pp. 214-220, 1996.

4. I. Karafyllidis, "Simulation of the negative chemical amplification deep-ultraviolet process in integrated circuit fabrication", Microelectronic Engineering, vol. 34, pp. 155-170, 1997

5. I. Karafyllidis, A. Ioannidis, A. Thanailakis and Ph. Tsalides, "Geometrical shape recognition using a cellular automaton architecture and its VLSI implementation", Real-Time Imaging, vol. 3, pp. 243-254, 1997.

6. V. Mardyris, I. Karafyllidis, D. Soundris and A. Thanailakis, "Neural networks for the simulation of photoresist exposure process in integrated circuit fabrication", Modelling and Simulation in Materials Science and Engineering, vol. 5, pp. 439-450, 1997.

7. P.I. Hagouel, I. Karafyllidis and A.R. Neureuther, "Developer temperature effect on negative deep ultraviolet resists : characterization, modeling and simulation", Journal of Vacuum Science & Technology B (Microelectronics and Nanometer Structures), vol. 15, pp. 2616-2620, 1997.

8. I. Karafyllidis, I. Andreadis, Ph. Tsalides, and A. Thanailakis " Non-linear hybrid cellular automata as pseudorandom pattern generators for VLSI systems.", VLSI Design, vol. 7, pp. 177-189, 1998.

9. P.I. Hagouel, I. Karafyllidis, and A.R. Neureuther, "Dependence of develpoped negative resisit profiles on exposure energy dose: experiment, modeling and simulation", Microelectronic Engineering, vol. 41/42, pp. 351-354, 1998.

10. I. Karafyllidis, P. I. Hagouel, and A. R. Neureuther, "Negative resist profiles in 248 nm photolithography: experiment, modeling and simulation” Semiconductor Science and Technology, vol. 13, pp. 603-610, 1998.

11. I. Karafyllidis, N. Georgoulas, P.I. Hagouel, and A. Thanailakis, "Simulation of deposition-topography granular distortion for TCAD” Modelling and Simulation in Materials Science and Engineering, vol. 6, pp. 199-210, 1998.

12. I. Karafyllidis, P. I. Hagouel and A. R. Neureuther, “Negative resist profiles of close-spaced parallel and isolated lines: experiment, modelling and simulation”, Microelectronic Engineering, vol. 45, pp 71-84, 1999.

13. I. Karafyllidis, “A three-dimensional photoresist etching simulator for TCAD”, Modelling and Simulation in Materials Science and Engineering, vol. 7, pp. 157-168, 1999.

14. G. Ch. Sirakoulis, I. Karafyllidis, V. Mardiris, and A. Thanailakis, “Study of lithography profiles developed on non-planar Si surfaces”, Nanotechnology, vol. 10, pp. 421-427, 1999.

15. I. Karafyllidis, “Design of a dedicated parallel processor for the simulation of the photolithography process using a genetic algorithm”, Engineering Applications of Artificial Intelligence, vol. 12, pp. 411-427, 1999.

16. I. Karafyllidis, P.I. Hagouel, A. Thanailakis, and A. R. Neureuther, “An efficient photoresist development simulator based on cellular automata with experimental verification”, IEEE Transactions on Semiconductor Manufacturing, vol. 13 (no. 1), pp. 61-75, 2000.

17. I. Karafyllidis, “Design of a dedicated parallel processor for the prediction of forest fire spreading”, Engineering Applications of Artificial Intelligence, vol. 17, pp. 19-36, 2004.

Nanoelectronic circuits and systems

18. I. Karafyllidis, “Determination of lowest energy state in single-electron circuits”, ΙΕΕ Electronics Letters, vol. 34, pp. 2401-2403, 1998.

19. I. Karafyllidis, “A simulator for single-electron tunnel devices and circuits based on simulated annealing”, Superlattices and Microstructures, vol. 25, pp. 567-572, 1999.

20. I. Karafyllidis, “Single-electron OR gate”, IEE Electronics Letters, vol. 36 (no.5), pp. 407-408, 2000.

21. M.M. Dasigenis, I. Karafyllidis and A. Thanailakis, “A Single-electron XOR gate”, Microelectronics Journal, vol. 32, pp. 117-119, 2001

22. I. Tsimperidis, I. Karafyllidis, and A. Thanailakis, “A single-electron three-input AND gate”, Microelectronics Journal, vol. 33, pp. 191-195, 2002

23. G. T. Zardalidis and I. Karafyllidis, “A single-electron half-adder”, Microelectronics Journal, vol. 33, pp. 265-269, 2002.

24. I. Karafyllidis, “Design and simulation of a single-electron random-access memory array”, IEEE Transactions on Circuits and Systems I, vol. 49, pp. 1370-1375, 2002.

25. M. E. Kiziroglou and I. Karafyllidis, “Design and simulation of a nanoelectronic single-electron analog to digital converter”, Microelectronics Journal, vol. 34, pp. 785-789, 2003.

26. G. T. Zardalidis and I. Karafyllidis, “Design and simulation of a single-electron full-adder”, IEE Proceedings on Circuits, Devices and Systems, vol. 150, pp. 173-177, 2003.

27. G. T. Zardalidis and I. Karafyllidis, “Design and simulation of a nanoelectronic single-electron universal Fredkin gate”, IEEE Transactions on Circuits and Systems I, vol. 51 (12), pp. 2395-2403, 2004.

28. G. T. Zardalidis and I. Karafyllidis, “SECS: A new single-electron circuit simulator”, IEEE Transactions on Circuits and Systems I, vol. 55 (9), pp. 2774-2784, 2008.

29. V. A.Mardiris and I. Karafyllidis, “Universal cellular automaton cell using quantum cellular automata”, IET Electronics Letters, vol. 45, pp. 607-609, 2009.

30. V. A. Mardiris and I. G. Karafyllidis, “Design and simulation of modular quantum-dot cellular automata multiplexers for memory accessing”, Journal of Circuits, Systems and Computers, vol. 19, pp. 349-365, 2010.

31. V.A. Mardiris and I. G. Karafyllidis, "Design and simulation of modular 2n to 1 quantum-dot cellular automata (QCA) multiplexers," International Journal of Circuit Theory and Applications, vol. 38, pp. 771-785, 2010.

Quantum information processing

32. I. Karafyllidis, “Cellular quantum computer architecture”, Physics Letters A, vol 320, pp. 35-38, 2003.

33. I. Karafyllidis, “Visualization of the quantum Fourier transform using a quantum computer simulator”, Quantum Information Processing, vol. 2, pp. 271-288, 2003.

34. I. Karafyllidis, “Definition and evolution of quantum cellular automata with two qubits per cell”, Physical Review A, vol. 70, pp. 044301-1 - 044301-4, 2004.

35. I. Karafyllidis, “Simulation of entanglement generation and variation in quantum computation”, Journal of Computational Physics, vol. 200, pp. 383-397, 2004.

36. I. Karafyllidis, “Quantum Computer Simulator based on the Circuit Model of Quantum Computation”, IEEE Transactions on Circuits and Systems I, vol. 52, pp. 1590-1596, 2005.

37. P. Vlachos and I. Karafyllidis, “Simulation of quantum key expansion using quantum cellular automata”, Computer Physics Communications, vol. 180, pp. 252-255, 2009.

38. P. Vlachos and I. Karafyllidis, “Quantum game simulator using the circuit model of quantum computation” Computer Physics Communications, vol. 180, pp. 1990-1998, 2009.

Systems biology – Molecular Electronics

39. G. Ch. Sirakoulis, I. Karafyllidis, Ch. Mizas, V. Mardiris, A. Thanailakis and Ph. Tsalides, “A cellular automaton model for the study of DNA sequence evolution”, Computers in Biology and Medicine, vol. 33, pp. 439-453, 2003.

40. G. Ch. Sirakoulis, I. Karafyllidis, R. Sandaltzopoulos, Ph. Tsalides and A. Thanailakis, “An algorithm for the study of DNA sequence evolution based on the genetic code”, BioSystems, vol. 77, pp. 11-23, 2004.

41. I. Karafyllidis and D. C. Lagoudas, “Microtubules as mechanical force sensors”, BioSystems, vol. 88, pp. 137-146, 2007.

42. Ch. Mizas, G. Ch. Sirakoulis, V. Mardiris, I. Karafyllidis, N. Glykos and R. Sandaltzopoulos, “Reconstruction of DNA sequences using genetic algorithms and cellular automata: Towards mutation prediction?”, BioSystems, vol. 92, pp. 61-68, 2008.

43. I. Karafyllidis, “Quantum mechanical model for information transfer from DNA to Protein”, BioSystems, vol. 93, pp. 191-198, 2008.

44. I. G. Karafyllidis, “Regulating the quorum sensing signaling circuit to control bacterial virulence: in silico analysis”, IET Systems Biology, vol. 5, pp. 103-109, 2011.

45. I. G. Karafyllidis, “Quantum Gate Circuit Model of Signal Integration in Bacterial Quorum Sensing”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 9, pp. 571-579, 2012.