Serdar Kuyucak

Serdar Kuyucak received a B.S. degree in physics from the Middle East Technical University, Ankara, in 1976, and a Ph.D. degree in theoretical physics from Yale University, New Haven, in 1982. He worked at the Universities of Tuebingen, Melbourne, and Australian National University before moving to his current position in the School of Physics, University of Sydney. His research interests are in the areas of computational biophysics and biomolecular modeling. He has done extensive work on modeling of ion channels using molecular and stochastic dynamics simulations. More recently he has been working on protein interactions/aggregation and protein-ligand binding problem.

Biography Updated on 10 January 2008

Personal Home Page

http://www.physics.usyd.edu.au/~serdar/serdar.html

Articles in Scholarly Journals [Incomplete List]

  1. Application of Jarzynski’s equality in simple versus complex systems
    Chemical Physics Letters, vol. 436, no. 4-6, pp. 383–387, 2007
  2. Free energy simulations of single and double ion occupancy in gramicidin A
    The Journal of Chemical Physics, vol. 126, no. 10, p. 105103, 2007
  3. Role of Protein Flexibility in Ion Permeation: A Case Study in Gramicidin A
    Biophysical Journal, vol. 90, no. 7, pp. 2285–2296, 2006
  4. Energetics of Ion Permeation, Rejection, Binding, and Block in Gramicidin A from Free Energy Simulations
    Biophysical Journal, vol. 90, no. 11, pp. 3941–3950, 2006
  5. Finite system and periodicity effects in free energy simulations of membrane proteins
    Chemical Physics Letters, vol. 425, no. 4-6, pp. 320–323, 2006
  6. Molecular dynamics simulations of calcium binding in gramicidin A
    Chemical Physics Letters, vol. 424, no. 1-3, pp. 82–85, 2006
  7. Molecular dynamics simulations of gramicidin A in a lipid bilayer: From structure–function relations to force fields
    Chemistry and Physics of Lipids, vol. 141, no. 1-2, pp. 197–204, 2006
  8. Temperature dependence of the transport coefficients of ions from molecular dynamics simulations
    Chemical Physics Letters, vol. 408, no. 1-3, pp. 84–88, 2005
  9. Memory effects in Brownian dynamics simulations of ion transport
    Chemical Physics Letters, vol. 401, no. 1-3, pp. 175–179, 2005
  10. Test of molecular dynamics force fields in gramicidin A
    European Biophysics Journal, vol. 34, no. 5, pp. 377–382, 2005
  11. Physics of Ion Channels
    Journal of Biological Physics, vol. 29, no. 4, pp. 429–446, 2003
  12. Recent advances in ion channel research
    Biochimica et Biophysica Acta (BBA) - Biomembranes, vol. 1565, no. 2, pp. 267–286, 2002
  13. Ion channels: recent progress and prospects
    European Biophysics Journal, vol. 31, no. 4, pp. 283–293, 2002
  14. Journal of Biological Physics, vol. 28, no. 2, pp. 289–308, 2002
  15. Reports on Progress in Physics, vol. 64, no. 11, pp. 1427–1472, 2001
  16. Proceedings of the Australian Physiological and Pharmacological Society Symposium: Ion Channels PREDICTING CHANNEL FUNCTION FROM CHANNEL STRUCTURE USING BROWNIAN DYNAMICS SIMULATIONS
    Clinical and Experimental Pharmacology and Physiology, vol. 28, no. 1-2, pp. 89–94, 2001
  17. Electromagnetic properties of low-excitation states in 191Ir and 193Ir and supersymmetry schemes
    Nuclear Physics A, vol. 669, no. 3-4, pp. 241–265, 2000
  18. Molecular dynamics estimates of ion diffusion in model hydrophobic and KcsA potassium channels
    Biophysical Chemistry, vol. 86, no. 1, pp. 1–14, 2000
  19. The potassium channel: Structure, selectivity and diffusion
    The Journal of Chemical Physics, vol. 112, no. 18, p. 8191, 2000
  20. Invalidity of continuum theories of electrolytes in nanopores
    Chemical Physics Letters, vol. 320, no. 1-2, pp. 35–41, 2000
  21. A model of calcium channels
    Biochimica et Biophysica Acta (BBA) - Biomembranes, vol. 1509, no. 1-2, pp. 1–6, 2000
  22. Molecular and Brownian dynamics study of ion selectivity and conductivity in the potassium channel
    Chemical Physics Letters, vol. 313, no. 1-2, pp. 358–365, 1999
  23. Shape-phase transitions in the vibron model and bent molecules
    Chemical Physics Letters, vol. 301, no. 5-6, pp. 435–440, 1999
  24. The effect of hydrophobic and hydrophilic channel walls on the structure and diffusion of water and ions
    The Journal of Chemical Physics, vol. 111, no. 17, p. 7985, 1999
  25. Journal of Physics G: Nuclear and Particle Physics, vol. 23, no. 10, pp. 1367–1375, 1999
  26. Comment on “Mean-field approach to the algebraic treatment of molecules: Bent molecules”
    Physical Review A, vol. 60, no. 6, pp. 5147–5148, 1999
  27. Tests and applications of self-consistent cranking in the interacting boson model
    Physical Review C, vol. 59, no. 6, pp. 3146–3152, 1999
  28. Excitation of nuclear anharmonic vibrations in heavy-ion fusion reactions
    Physical Review C, vol. 57, no. 3, pp. 1349–1360, 1998
  29. Computer simulation of ion conductance in membrane channels
    Physical Review E, vol. 58, no. 3, pp. 3654–3661, 1998
  30. 1/N expansion in the vibron model: Diatomic molecules
    Physical Review A, vol. 57, no. 5, pp. 3381–3402, 1998
  31. Solutions of Poisson's equation in channel-like geometries
    Computer Physics Communications, vol. 115, no. 1, pp. 45–68, 1998
  32. Role of Anharmonicities of Nuclear Vibrations in Fusion Reactions at Sub-barrier Energies
    Physical Review Letters, vol. 79, no. 16, pp. 2943–2946, 1997
  33. Journal of Physics G: Nuclear and Particle Physics, vol. 23, no. 10, pp. 1159–1166, 1997
  34. Shape transitions in proton-neutron systems
    Physics Letters B, vol. 393, no. 3-4, pp. 261–266, 1997
  35. Description of deformed nuclei in the sdg boson model
    Nuclear Physics A, vol. 604, no. 3, pp. 305–340, 1996
  36. Description of superdeformed nuclei in the interacting boson model
    Physical Review C, vol. 53, no. 5, pp. 2194–2200, 1996
  37. Relations between fusion cross sections and average angular momenta
    Physical Review C, vol. 54, no. 4, pp. 1853–1862, 1996
  38. High-spin states in boson models with applications to actinide nuclei
    Physics Letters B, vol. 354, no. 3-4, pp. 189–195, 1995
  39. 1/N expansion formalism for high-spin states
    Physics Letters B, vol. 349, no. 3, pp. 253–260, 1995
  40. Consistent description of magnetic dipole properties in transitional nuclei
    Physics Letters B, vol. 348, no. 3-4, pp. 315–319, 1995
  41. Effects of nuclear structure on average angular momentum in subbarrier fusion
    Physics Letters B, vol. 335, no. 3-4, pp. 295–299, 1994
  42. Temperature dependence of conductivity in electrolyte solutions and ionic channels of biological membranes
    Biophysical Chemistry, vol. 52, no. 1, pp. 15–24, 1994
  43. Comment on ‘‘Spectroscopy of samarium isotopes in the sdg interacting boson model’’
    Physical Review C, vol. 47, no. 4, pp. 1815–1818, 1993
  44. Critical test of multi-j supersymmetries from magnetic moment measurements
    Physical Review C, vol. 48, no. 1, pp. R13–R16, 1993
  45. Shapes and phase transitions in generalized boson models
    Physics Letters B, vol. 255, no. 3, pp. 305–310, 1991
  46. Dynamic shape transitions in the interacting boson model
    Physics Letters B, vol. 263, no. 2, pp. 146–152, 1991
  47. ?-unstable nuclei in the sdg boson model
    Physics Letters B, vol. 263, no. 3-4, pp. 347–352, 1991