Staff Catalogue


Department of Physics
FST 02 - Faculty of Pure and Applied Sciences,
University Campus

Current position:

Associate Professor, Department of Physics, University of Cyprus.


Born: 22 September 1965, Athens, Greece.


Harvard University, USA. Ph.D in Theoretical Biophysics (1994). “Statistical Mechanical Studies of Proteins”;

Research supervisor: Martin Karplus (Nobel Prize in Chemistry, 2013).

University of Athens, Greece. B.S. in Physics (1987); GPA 9.41 (Graduated 1st in class).


  1. University of Cyprus, 2007-today. Associate Professor, Department of Physics.
  2. University of Cyprus, 2002-2007. Assistant Professor, Department of Physics.
  3. Ecole Polytechnique, Paris, France, January 2005 – November 2005. Visiting Professor.
  4. University of Cyprus, 2001-2002. Lecturer, Department of Physics.
  5. University of Cyprus, August 1996-2001. Lecturer, Department of Natural Sciences.
  6. University Louis Pasteur, Strasbourg, France, June 1994 – August 1996. Post-doctoral associate.
  7. Harvard University, USA, August 1988 – June 1994. Research and Teaching Assistant, Committee on Higher Degrees in Biophysics.

Other Affiliations:

  1. Graduate Program “Masters in Bioinformatics”, Department of Biology, University of Athens. In the period 2004-2006, I gave a series of lectures and computational exercises, based on the Molecular Dynamics program CHARMM.  I also supervised the Masters thesis of Dr. Spyrou (January 2006), in partial fulfillment of the requirements of the program.


  • Human Capital and Mobility:Research Fellow (1995-1996).
  • Harvard University: Research Fellow (1988-1994).
  • Harvard University: Teaching Fellow. (1991-1994).
  • Greek Science Foundation (IKY: (1983-1987). Yearly awards for highest undergraduate grade point average in the Dept. of Physics, University of Athens.
  • Papadakis Foundation. Fellowship for excellence in undergraduate studies (1985-1987).

Group Alumni:

Post-doctoral researchers:

  1. Savvas Polydoridis (9/2019-8/2020, 9/2013-9//2015). (Currently employed in Secondary Education).
  2. Phanourios Tamamis (6/2010-12/2012). (Currently employed as Assistant Professor, Dept. of Chemical Engineering, Texas A&M University)..
  3. Cosmina Dutan (10/2006-9/2009). (Currently employed at UCLAN, Cyprus).
  4. Majid Monajjemi (February-September 2003). (Currently employed as Professor, Isl. Azhad University, Tehran, Iran). 
  5. Dr. Qian (Charles) Xie (1997-2000). (Currently employed at Institute for Future Intelligence, previously at Concord Consortium).

PhD students:

  1. Elena Michael (9/2013-8/2020). “Development and Application of Efficient and Accurate Free Energy Models and Methodologies for High-Throughput Protein Design”. Elena continues as a post-doctoral associate at the Ecole Polytechnique, France.
  2. Philippos Ioannou (9/2008-1/2013) “Computational Study of Ionic Effects on the Conformational Stability and the Helix/Coil Equilibrium of Model Oligopeptides”..
  3. Phanourios Tamamis (9/2006-5/2010). “Molecular Dynamics studies of the structural, dynamical and thermodynamical properties of biomolecular complexes in explicit and implicit solvent models".
  4. Savvas Polydoridis (9/2006-5/2011). “Redesigning the specificity of Aminoacyl-tRNA Synthetases with Biomolecular Simulations”.

Masters students:

  1. Chrystalla Mytidou (2010-2012). “Study of the Structural Stability of Protein Segments from the Adenovirus Fiber and of Biomolecular Complexes Implicated in the Function of the Complement System; Insights from Molecular Dynamics simulations”.
  2. Philippos Ioannou (2006-2008). “Investigation of the air/water interface of alcohol-water mixtures by MD simulations”..
  3. Georgios Spyrou (2004-2006). “Investigation of the formation of amyloid fibers by peptidic analogues of silk-worm chorion proteins, with folding simulations”.  
  4. Savvas Polydoridis(2003-2005). “Application of Free Energy Calculations to the Thermodynamic stability of Biomolecular Complexes”. 
  5. Georgia Andreou (2002-2005) “Simulations of hydrated ions with polarized ion- and water models” (GA did her Masters studies in the Dept. of Chemistry. U. of  Cyprus; she was co-advised by Prof. E. Leontidis). 

Undergraduate students:

  1. Rafaela Vafea (2019-2020). “Misconceptions in the understanding of General Physics by Physics majors”.
  2. Kyriacos Nikolaou (2018-2019). “Molecular Dynamics Simulations of Integrin”.
  3. Michalis Kassinopoulos (2012-2013). “Molecular Dynamics Simulations of a peptide from the adenovirus fiber shaft, with the potential to self-assemble in amyloid-like nanostructures”.
  4. Zena Scotti (2010-2011). “Self-assembly of a peptide sequence from the adenovirus fiber shaft: Insights from Molecular Dynamics simulations with implicit and explicit solvent representations”.
  5. Elena Demosthenous (2010-2011). “Structural and dynamical properties of peptidic sequences”.
  6. Panagiota Pierrou (2010-2011). Computer-aided design of compstatin-based inhibitors of the autoimmune complement component protein C3”.
  7. Andreas Kalli (2007-2008). Self-assembly of a peptidic analogue from the silkmoth chorion protein. 
  8. Phanourios Tamamis (2005-2006). “Analysis of the structural and dynamical properties of compstatin in solution, by explicit watermolecular dynamics simulations”, 1st prize in the Competition for Undergraduate Students Research in Cyprus (PROFOIT), Cyprus RPF.
  9. Savvas Polydoridis (2002-2003). “The protein folding problem; theory and simulations”.
  10. Georgia Andreou (2001-2002). “Conformational stability of biomolecular systems in solution, studied by explicit and implicit solvent models”.

Research Activity

My research aims to understand the properties of biomolecular systems by means of computational methodologies (molecular dynamics simulations with atomic-detail or implicit-solvent models) and theoretical concepts, (based on statistical mechanics, continuum electrostatics). I am among the developers of the widely used biomolecular program Chemistry at Harvard Molecular Mechanics (CHARMM).

My research activity during my employment at the University of Cyprus (August 1996 – today) can be grouped in the following areas:

  1. Development of Free Energy functions for high-throughput protein design.
  2. Structure – Function and Dynamics – Function Relationships in Biomolecular Complexes. 
  3. Self-assembly properties of peptide-based nanostructures.
  4. Structural and thermodynamical properties of electrolyte solutions by simulations with biomolecular Hamiltonians with or without explicit polarisability.
  5. Proton-binding phenomena and protein dielectric relaxation. 

During the period 1997-today, I have coordinated 15 research grants from the Cyprus Research Promotion Foundation (Upgrade of Existing Infrastructure, PENEK, Cyprus-France International Cooperation, Cyprus-Greece International Cooperation), the A.G. Leventis Foundation and the University of Cyprus, with a total budget of 700,000 Euros. I have also participated in 2 Strategic Infrastructure Grants with a total budget of 2.7 million Euros.

Activity in Education

During the period 2015-today, a significant part of my efforts focuses on the deleopment of educational materials and educational practices for the teaching of Physics at Secondary and Tertiary Education. My list of activities in this domain include:

  • Co-authorship of the Physics books (ages 16-18), currently used in the Public sector of the Cyprus educational system. All books are accessible freely at
  • Training of teachers with specially organized seminars and visits in schools.
  • Offer of semester courses for the certification of Physics teachers.
  • Organization and offer of a new two-semester course at the Department of Physics for the enrichment of understanding of Physics principles and the development of Physics communcation skills.
  • Participation in the national examination committee for the hiring of Physics teachers in Secondary Education (training of examiners and preparation of exams)
  • Participation in the national examination committee for the preparation of the University entrance exam in Physics.


  1. Morikis D, Gorham RD Jr, Khoury GA, Bellows-Peterson ML, Floudas CA, Archontis GA, Tamamis P (2016) Compstatin Analogs, Patent Number 9512180. 
  2. Morikis D, Gorham RD Jr, Bellows-Peterson ML, Floudas CA, Archontis G, Tamamis P (2013) Molecular Dynamics in Drug Design: New Generations of Compstatin Analogs, U.S. Provisional Patent Application No. 61/585, 146. 
  3. Morikis D, Gorham RD Jr, Bellows-Peterson ML, Floudas CA, Archontis G, Tamamis P (2012) Molecular Dynamics in Drug Design: New Generations of Compstatin Analogs, U.S. Provisional Patent Application No. 61/739, 438. 
  1. S. Polydorides, Archontis G (2021). Computational optimization of the SARS-CoV-2 receptor-binding-motif affinity for hACE2. Accepted at Biophysical Journal.
  2. E. Michael, S. Polydorides, V. Prombonas, P. Skourides, G. Archontis (2021). Recognition of LD motifs by the Focal Adhesion Targeting Domains of FAK and PYK2: Insights from Molecular Dynamics Simulations. Proteins, Structure, Function and Bioinformatics, 89(1):29-52.
  3. D. Mignon, K. Druart, E. Michael, V. Opuu, S. Polydorides, F. Villa, T. Gaillard, N. Panel, G. Archontis, T. Simonson (2020). Physics-based Computational Protein Design: An Update. J. Phys. Chem. A., Feature Article, 124(51):10637-10648.
  4. E. Michael, S. Polydorides, T. Simonson, G. Archontis (2020).Hybrid MC/MD for Protein Design. J. Chem. Phys 153, 054113;  
  5. M. V. Sullivan, S. R. Dennison, G. Archontis, S. M. Reddy, J. M. Hayes, G. Archontis, (2019). Towards Rational Design of Selective Molecularly Imprinted Polymers (MIPs) for Proteins: Computational and Experimental Studies of Acrylamide-Based Polymers for Myoglobin. Journal of Physical Chemistry B, 123:5432-5443.
  6. E. Michael, S. Polydorides, T. Simonson, G. Archontis (2017). Simple models for nonpolar solvation. Parameterization and testing. Journal of Computational Chemistry, 38:2509-2519.
  7. S. Polydorides, E. Michael, D. Mignon, K. Druart, G. Archontis, T. Simonson (2016). Proteus and the design of ligand binding sites.Computational design of ligand-binding proteins, Vol 1414, Series “Methods in Molecular Biology”, pp. 77-97, Springer, New-York. doi: 10.1007/978-1-4939-3569-7_6.
  8. J. van Heemst, Diahann T.S.L. Jansen, S. Polydorides, A. K. Moustakas,M. Bax, A. L. Feitsma, D. G. Bontrop-Elferink, M. Baarse, D. van der Woude, G.-J. Wolbink, T. Rispens, F. Koning, R. R.P. de Vries, G. K. Papadopoulos, G. Archontis, T. W. Huizinga, R. E. Toes (2015).  Microbe-Vinculin cross-reactivity provides a molecular basis for the HLA-RA association. Nature Communications, doi:10.1038/ncomms7681.
  9. R. D. Gorham, D.L. Forest, G.A. Khoury, J. Smadbeck, C.N. Beecher, E.D. Healy, P. Tamamis, G. Archontis, C.K. Larive, C.A. Floudas, M.J. Radeke, L.V. Johnson, D. Morikis (2015). New Compstatin Peptides Containing N-terminal Extensions and Non-Natural Amino Acids Exhibit Potent Complement Inhibition and Improved Solubiity Characteristics.Journal of Medicinal Chemistry, 58:814-826.
  10. P. Tamamis, K. Terzaki,, M. Kassinopoulos, L. Mastrogiannis, E. Mossou, V. T. Forsyth, E. P. Mitchell, A. Mitraki, G. Archontis (2014). “Self-Assembly of an Aspartate-Rich Sequence from the Adenovirus Fiber Shaft: Insights from Molecular Dynamics Simulations and Experiments.”Journal of Physical Chemistry B, 118:1765-1774.
  11. P. Tamamis, C. A. Kieslich, G. V. Nikiforovich, T. M. Woodruff, D. Morikis, G. Archontis (2014). “Insights into the mechanism of C5aR inhibition by PMX53 via implicit solvent molecular dynamics simulations and docking.”BMC Biophysics, 7:5.
  12. V. Parmenopoulou, A. L. Kantsadi, V. G. Tsirkone, D. S. M. Chatzileontiadou, S. Manta, S. E. Zographos. C. Molfeta,G. Archontis, L. Agius, J. M. Hayes, D. D. Leonidas, D. Komiotis (2014). “Structure based inhibitor design targeting glycogen phosphorylase b. Virtual screening, synthesis, biochemical and biological assessment of novel N-acyl-b-D-glucopyranosylamines.” Bioorganic and Medicinal Chemistry, 2014, 22:4810-4825.
  13. P. Tamamis, E. Kassotakis, G. Archontis, A. Mitraki (2014). “Combination of theoretical and experimental approaches for the design and study of fibril-forming peptides.Protein Design: Methods and Applications, Vol. 1216, Series «Methods in Molecular Biology», pp. 53-70, Springer, New-York.
  14. T. Simonson, T. Gaillard, D. Mignon, M. Schmidt am Busch, A. Lopes, N. Amara, S. Polydorides, A. Sedano, K. Druart, G. Archontis (2013).Computational Protein Design: The Proteus Software and Selected Applications.Journal of Computational Chemistry 34:2472-2484.
  15. F. Ioannou, E. Leontidis, G. Archontis (2013). Helix Formation by Alanine-based Peptides in Pure Water and Electrolyte Solutions: Insights from Molecular Dynamics Simulations. Journal of Physical Chemistry B 117:9866-9876. 
  16. R. D. Gorham, D. L. Forest, P. Tamamis, A. Lopez de Victoria, M. Kraszni, C. A. Kieslich, C. D. Banna, M. L. Bellows-Peterson, C. K. Larive, C. A. Floudas, G. Archontis, L. V. Johnson, D. Morikis (2013). Novel Compstatin Family Peptides Inhibit Complement Activation by Drusen-like Deposits in Human Retinal Pigmented Epithelial Cell Cultures. Experimental Eye Research 116:96-108.  
  17. J. Hayes, G. Archontis (2012). MM-GB(PB)SA Calculations of Protein-Ligand Binding Free Energies. Chapter 9 in Molecular Dynamics - Studies of Synthetic and Biological Mactomolecules, pp. 171-190.  Edited by Lichang Wang, Publisher Intechopen.
  18. C. A. Kieslich, P. Tamamis, R. D. Gorham Jr., A. L. De Victoria, N. U. Sausman, G. Archontis, D. Morikis (2012).Exploring Protein-Protein and Protein-Ligand Interactions in the Immune System using Molecular Dynamics and Continuum Electrostatics. Current Physical Chemistry 2:324-343.
  19. P. Tamamis, A. L. de Victoria, R. D. Gorham, M. L. Bellows-Peterson, P. Pierou, C. A. Floudas, D. Morikis, G. Archontis (2012). Molecular Dynamics in Drug Design: New Generations of Compstatin Analogs. Chemical Biology & Drug Design 79:703-718.
  20. F. Ioannou, G. Archontis and E. Leontidis (2011). Specific Interactions of Sodium Salts With Alanine Dipeptide and Tetrapeptide in Water: Insights from MD Simulations. Journal of Physical Chemistry B 115:13389-13400.
  21. P. Tamamis and G. Archontis (2011Amyloid-like self-assembly of a dodecapeptide sequence from the adenovirus fiber shaft: Perspectives from molecular dynamics simulations.Journal of Non-Crystalline Solids 357:717-722.
  22. P. Tamamis, P. Pierou, C. Mytidou, CA. Floudas, D. Morikis and G. Archontis (2011). Design of a Modified Mouse Protein with Ligand Binding Properties of its Human Analog using Molecular Dynamics Simulations: The Case of C3 Inhibition by Compstatin.Proteins: Structure, Function and Bioinformatics 79:3166-3179.
  23. S. Polydoridis, N. Amara, C. Aubard, P. Plateau, T. Simonson and G. Archontis (2011). Computational protein design with a generalized Born solvent model: application to Asparaginyl-tRNA synthetaseProteins: Structure, Function and Bioinformatics, 79:3448-3468,Special Issue in protein electrostatics.
  24. G. Pieridou, C. Avgousti-Menelaou, P. Tamamis, G. Archontis and S. Hayes (2011). UV Resonance Raman Study of TTR(105−115) Structural Evolution as a Function of TemperatureJ. Phys. Chem. B115:4088-4098.
  25. J. Hayes, V. T. Skamnaki, G. Archontis, C. Lamprakis, K. Sarrou, N. Bischler, A-L. Skaltsounis, S. E. Zographos, N. G. Oikonomakos (2011). Kinetics, in silicodocking, molecular dynamics, and MM-GBSA binding studies on prototype indirubins, KT5720, and staurosporine as phosphorylase kinase ATP-binding site inhibitors: The role of water molecules examinedProteins: Structure, Function and Bioinformatics 79:703-719.
  26. A. Aleksandrov, S. Polydoridis, G. Archontis and T. Simonson (2010). Predicting the Acid/Base Behavior of Proteins: A Constant-pH Monte Carlo Approach with Generalized Born Solvent.J. Phys. Chem. B. 114:10634-10648.
  27. P. Tamamis, D. Morikis, C.A. Floudas and G. Archontis (2010). SpeciesSpecificity of the Complement Inhibitor Compstatin Investigated by All-atom Molecular Dynamics simulations. Proteins; Structure, Function and Bioinformatics 78:2655-2667.
  28. P. Tamamis, E. Kasotakis, A. Mitraki and G. Archontis (2009). Amyloid-like Self-Assembly of Peptide Sequences from the Adenovirus Fiber Shaft: Insights from MD Simulations.J. Phys. Chem. B. 113:15639-15647.
  29. B. R. Brooks, C. L. Brooks III, A. D. Mackerell, L. Nilsson, R. J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch A. Caflisch, L. Caves, Q. Cui, A. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R. W. Pastor, C. B. Post, J. Z. Pu, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu, W. Yang, D. M. York, and M. Karplus(2009)CHARMM. The Biomolecular Simulation ProgramSpecial Issue, J. Comp. Chem30:1545-1615.
  30. P. Tamamis, L-A. Abramovich, M. Reiches, K. Marshall, P. Sikorski, L. Serpell, E. Gazit and G. Archontis (2009Self-Assembly of Phenylalanine Oligopeptides: Insights from Experiments and Simulations.Biophys. J96:5020.
  31. M. Benitifa, J.M. Hayes, S. Vidal, D. Gueyrard, P.G. Goekjian, J.P. Praly, G. Kizilis, C. Tiraidis, K.M. Alexacou, E.D. Chrysina, S. E. Zographos, D. D. Leonidas, G. Archontis and N.G. Oikonomakos (2009). Glucose-based spiro-isoxazolines: A new family of potent glycogen phosphorylase inhibitorsBioorganic and Medicinal Chemistry17:7368-7380.
  32. K-M. Alexacou, J.M Hayes, C. Tiraidis, S.E. Zographos, D.D. Leonidas, E.D. Chrysina, G. Archontis and N.G. Oikonomakos (2008). Crystallographic studies on N-(β-D-glucopyranosyl)-4-phenyl-1,2,3-triazoleacetamide, an inhibitor of glycogen phosphorylase:Proteins, Structure, Function and Bioinformatics 71:1307-1323.
  33. P. Tamamis, S.S. Skourtis, D. Morikis, J.D. Lambris and G. Archontis (2007). Conformational analysis of Compstatin analogues with Molecular Dynamics Simulations in Explicit WaterJ. Mol. Graph. Model26: 571.
  34. S. Polydoridis, D.D. Leonidas, N.G. Oikonomakos and G. Archontis (2007). Recognition of RNAse A by 3’-5’-Pyrophosphate-linked Dinucleotide Inhibitors: A Molecular Dynamics/Continuum Electrostatics Analysis.Biophys. J.92:1659.
  35. A. Lopes, A. Alexandrov, C. Bathelt, G. Archontis and T. Simonson (2007). Computational sidechain placement and protein mutagenesis with implicit solvent models.Proteins: Structure, Function and Bioinformatics 67:853.
  36. G. Archontis and E. Leontidis (2006). Dissecting the stabilization of iodide at the air-water interface into components: A free energy analysis.Chem. Phys. Lett420:199.
  37. G. Archontis and T. Simonson (2005). A residue-pairwise Generalized Born scheme suitable for protein design calculations.J. Phys. Chem. B 109:22667. 
  38. G. Archontis, E. Leontidis and G. Andreou (2005). Attraction of Iodide Ions by the Free Water Surface Revealed by Simulations with a Polarizable Force Field, Based on Drude Oscillators.J. Phys. Chem. B109:17957. 
  39. G. Archontis, K. Α. Watson, Q. Xie, G. Andreou, E. Chrysina, S.E. Zographos, N.G. Oikonomakos, L.N. Johnson and M. Karplus (2005). Molecular Recognition and Relative Binding of Glucopyranose Spirohydantoin Analogues to Glycogen Phosphorylase: A Free Energy Perturbation StudyProteins: Structure, Function and Bioinformatics61:984. 
  40. Κ.Α. Watson, D. Chrysina, K.E. Tsitsanou, S.E. Zographos, D.D. Leonidas, G.W.J. Fleet, G. Archontis, and N.G. Oikonomakos,(2005Kinetic and crystallographic studies of glucopyranose spirohydantoin and glucopyranosylamine analogues inhibitors of glycogen phosphorylase. Proteins: Structure, Function and Bioinformatics61:966.
  41. G. Archontis and T. Simonson (2005). Proton binding to proteins: A self-consistent dielectric continuum analysis.Biophys. J.88:3888.
  42. N. G. Oikonomakos, S.E. Zographos, V.T. Skamnaki, and G. Archontis (2002The 1.76 A resolution crystal structure of glycogen phosphorylase b, complexed with glucose and CP320626, a potential antidiabetic drug.Bioorg. Med. Chem10: 313.
  43. T. Simonson, G. Archontis and M. Karplus (2002). Protein-ligand recognition: Free-energy simulations come of age.Acc. Chem. Res35, 430.
  44. G. Archontis and T. Simonson (2001Dielectric relaxation in an enzyme active site.J. Am. Chem. Soc123, 11047. 
  45. G. Archontis, T. Simonson and M. Karplus (2001Binding free energies and free energy components from MD and PB calculations. Application to aminoacid recognition by Aspartyl-tRNA synthetase.J. Mol. Biol306:307.
  46. S. Skourtis, G. Archontis and Q. Xie (2001Electron transfer through fluctuating bridges: On the validity of the superexchange mechanism and time-dependent tunneling matrix elements.Journal of Chemical Physics115:9444-9462.
  47. Q. Xie, G. Archontis and S. Skourtis (1999Protein electron transfer: A numerical study of tunneling through fluctuating bridges. Chemical Physics Letters312(2­4):237­246 .
  48. T. Simonson, G. Archontis and M. Karplus (1999A Poisson­Boltzmann study of charge insertion in an enzyme active site: the effect of dielectric relaxation.Journal of Physical Chemistry 103:6142­6156.
  49. G. Archontis, T. Simonson, D. Moras and M. Karplus (1998). Specific amino acid recognition by Aspartyl­tRNA synthetase, studied by free energy simulations. Journal of Molecular Biology275:823­846.
  50. T. Simonson, G. Archontis and M. Karplus (1997Continuum treatment of long­range interactions in free energy calculations. Application to protein­ligand binding.Journal of Physical Chemistry B 101:8349­8362.
  51. G. Archontis and M. Karplus (1996). Cumulant expansion of the free energy: application to free energy derivatives and component analysis. Journal of Chemical Physics105: 11246­11260.
  52. T. Lazaridis, G. Archontis and M. Karplus (1995The enthalpic contribution to protein stability: Insights from atom­based calculations and statistical mechanics.Advances in Protein Chemistry 47:231-296.
  53. G. Z. Archontis and E.I. Shakhnovich (1994Phase transitions in heteropolymers with ``secondary structure''. Physical Review E49;3109­3123.
  54. S. Boresch, G. Archontis and M. Karplus (1994Free energy simulations: The meaning of the individual contributions from a component analysis. Proteins: Structure, Function and Genetics20:25­33.