Associate Professor Serdar Kuyucak

A28 - Physics Building
The University of Sydney

Telephone +61 2 9036 5306
Fax +61 2 9351 7726

Research interests

o Study of ion transport across membrane channels using Brownian and molecular dynamics (BD and MD) methods. Hierarchical studies to determine the model parameters from ab inito MD to MD and BD. o Modeling of ion channels using crystal and/or simplified structures (e.g. potassium, calcium and gramicidin channels). Permeation mechanisms in multi-ion channels. Structure-function relationships. o Solution of spectrum generating algebras (interacting boson model, vibron model) using the 1/N expansion method, and their application to problems in nuclear and molecular spectroscopy. Member of the Biophysics Research Group.

Selected grants

2010

  • Mechanism of glutamate transport from experimental and simulation studies; Kuyucak S, Ryan R, Vandenberg R; Australian Research Council (ARC)/Discovery Projects (DP).

2009

  • Molecular dynamics simulations of glutanate transporters; Kuyucak S; DVC Research/Bridging Support Grant.

2008

  • Quantum mechanical and dynamical investigation of ion channels; Kuyucak S, Bastug T; Australian Research Council (ARC)/Discovery Projects (DP).

2007

  • Inactivation of HERG potassium channels: dynamic changes in the outer pore structure; Van Den Berg J, Vandenberg J, Kuyucak S; National Health and Medical Research Council (NHMRC)/Project Grants.

2006

  • University of Sydney - Bridging Support Grant; Kuyucak S; University of Sydney/Bridging Support.

2005

  • Modeling the HERG potassium in heart; Kuyucak S; University of Sydney/Research & Development.

2004

  • Realistic models of permeation in ion channels; Kuyucak S; Australian Research Council (ARC)/Discovery Projects (DP).
  • Hierarchical modeling of protein interactions; Kuyucak S, Bastug T; Australian Research Council (ARC)/Discovery Projects (DP).
  • Exploiting temperature dependance in studies of biological processes; Kuyucak S; DVC Research/Research and Development Scheme: Research and Development (R&D).

Selected publications

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Journals

  • Heinzelmann, G., Chen, P., Kuyucak, S. (2014). Computation of standard binding free energies of polar and charged ligands to the glutamate receptor glua2. The Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces and Biophysical, 118(7), 1813-1824-1813-1824. [More Information]
  • Rashid, H., Kuyucak, S. (2014). Free energy simulations of binding of HsTx1 toxin to Kv1 potassium channels: The basis of Kv1.3/Kv1.1 selectivity. The Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces and Biophysical, 118(3), 707-716-707-716. [More Information]
  • Rashid, M., Heinzelmann, G., Huq, R., Tajhya, R., Chang, S., Chhabra, S., Pennington, M., Beeton, C., Norton, R., Kuyucak, S. (2013). A Potent and Selective Peptide Blocker of the Kv1.3 Channel: Prediction from Free-Energy Simulations and Experimental Confirmation. PLoS One, 8(11), 1-10. [More Information]
  • Rashid, M., Mahdavi, S., Kuyucak, S. (2013). Computational studies of marine toxins targeting ion channels. Marine Drugs, 11(3), 848-869. [More Information]
  • Heinzelmann, G., Bastug, T., Kuyucak, S. (2013). Mechanism and energetics of ligand release in the aspartate transporter GltPh. The Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces and Biophysical, 117(18), 5486-5496. [More Information]
  • Durmaz, E., Kuyucak, S., Sezerman, O. (2013). Modifying the catalytic preference of tributyrin in Bacillus thermocatenulatus lipase through in-silico modeling of enzyme-substrate complex. Protein Engineering Design and Selection (Print), 26(5), 325-333. [More Information]
  • Mahdavi, S., Kuyucak, S. (2013). Why the drosophila shaker K+ channel is not a good model for ligand binding to voltage-gated Kv1 channels. Biochemistry, 52(9), 1631-1640. [More Information]
  • Pennington, M., Rashid, M., Tajhya, R., Beeton, C., Kuyucak, S., Norton, R. (2012). A C-terminally amidated analogue of ShK is a potent and selective blocker of the voltage-gated potassium channel Kv1.3. FEBS Letters, 586(22), 3996-4001. [More Information]
  • Rashid, M., Kuyucak, S. (2012). Affinity and selectivity of ShK toxin for the Kv1 potassium channels from free energy simulations. The Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces and Biophysical, 116(16), 4812-4822. [More Information]
  • Chen, P., Kuyucak, S. (2012). Developing a comparative docking protocol for the prediction of peptide selectivity profiles: Investigation of potassium channel toxins. Toxins, 4(2), 110-138. [More Information]
  • Timko, J., Kuyucak, S. (2012). Investigation of polarization effects in the gramicidin A channel from ab initio molecular dynamics simulations. Journal of Chemical Physics, 137(20), 1-11. [More Information]
  • Bastug, T., Kuyucak, S. (2012). Molecular dynamics simulations of membrane proteins. Biophysical Reviews, 4(3), 271-282. [More Information]
  • Bastug, T., Heinzelmann, G., Kuyucak, S., Salim, M., Vandenberg, R., Ryan, R. (2012). Position of the Third Na+ Site in the Aspartate Transporter GltPh and the Human Glutamate Transporter, EAAT1. PLoS One, 7(3), 1-10. [More Information]
  • Timko, J., De Castro, A., Kuyucak, S. (2011). Ab initio calculation of the potential of mean force for dissociation of aqueous Ca-Cl. Journal of Chemical Physics, 134(20), 204510-1-204510-9. [More Information]
  • Chen, P., Kuyucak, S. (2011). Accurate determination of the Binding Free Energy for KcsA-Charybdotoxin Complex from the Potential of Mean Force Calculations with Restraints. Biophysical Journal, 100(10), 2466-2474. [More Information]
  • Bastug, T., Kuyucak, S. (2011). Comparative Study of the Energetics of Ion Permeation in Kv1.2 and KcsA Potassium Channels. Biophysical Journal, 100(3), 629-636. [More Information]
  • Heinzelmann, G., Bastug, T., Kuyucak, S. (2011). Free Energy Simulations of Ligand Binding to the Aspartate Transporter GltPh. Biophysical Journal, 101(10), 2380-2388. [More Information]
  • Bucher, D., Gray-Weale, A., Kuyucak, S. (2010). Ab Initio Study of Water Polarization in the Hydration Shell of Aqueous Hydroxide: Comparison between Polarizable and Nonpolarizable Water Models. Journal of Chemical Theory and Computation, 6(9), 2888-2895.
  • Timko, J., Bucher, D., Kuyucak, S. (2010). Dissociation of NaCl in water from ab initio molecular dynamics simulations. Journal of Chemical Physics, 132(11), 114510-1-114510-8.
  • Bastug, T., Kuyucak, S. (2009). Importance of the Peptide Backbone Description in Modeling the Selectivity Filter in Potassium Channels. Biophysical Journal, 96(10), 4006-4012. [More Information]
  • Bucher, D., Kuyucak, S. (2009). Importance of water polarization for ion permeation in narrow pores. Chemical Physics Letters, 477(1-3), 207-210. [More Information]
  • Chen, P., Kuyucak, S. (2009). Mechanism and energetics of charybdotoxin unbinding from a potassium channel from molecular dynamics simulations. Biophysical Journal, 96(7), 2577-2588. [More Information]
  • Ju, P., Pages, G., Riek, R., Chen, P., Torres, A., Bansal, P., Kuyucak, S., Kuchel, P., Vandenberg, J. (2009). The Pore Domain Outer Helix Contributes to Both Activation and Inactivation of the hERG K+ Channel. Journal of Biological Chemistry, 284(2), 1000-1008. [More Information]
  • Bucher, D., Kuyucak, S. (2008). Polarization of water in the first hydration shell of K+ and Ca2+ ions. The Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces and Biophysical, 112(35), 10786-10790.
  • Bastug, T., Chen, P., Patra, S., Kuyucak, S. (2008). Potential of mean force calculations of ligand binding to ion channels from Jarzynski's equality and umbrella sampling. Journal of Chemical Physics, 128(15), 155104-1-155104-9.
  • Bastug, T., Kuyucak, S. (2008). Response to "Comment on 'Free energy simulations of single and double ion occupancy in gramicidin A' " [J. Chem. Phys. 128, 227101 (2008)]. Journal of Chemical Physics, 128(22), 227102-1-227102-2.
  • Bastug, T., Kuyucak, S. (2007). Application of Jarzynski's equality in simple versus complex systems. Chemical Physics Letters, 436(4-6), 383-387. [More Information]
  • Patra, S., Bastug, T., Kuyucak, S. (2007). Binding of organic cations to gramicidin a channel studied with AutoDock and molecular dynamics simulations. The Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces and Biophysical, 111(38), 11303-11311.
  • Wijesinghe, R., Coorey, N., Kuyucak, S. (2007). Charge state of the fast gate in chloride channels: Insights from electrostatic calculations in a schematic model. Journal of Chemical Physics, 127(19), 195102-1-195102-9.
  • Bastug, T., Kuyucak, S. (2007). Free energy simulations of single and double ion occupancy in gramicidin A. Journal of Chemical Physics, 126(10), 105103-1-105103-12.
  • Kuyucak, S. (2007). Modelling drug and toxin binding to ion channels. Drugs of the Future, 32(Supplementary 1), 33-34.
  • Kutteh, R., Vandenberg, J., Kuyucak, S. (2007). Molecular dynamics and continuum electrostatics studies of inactivation in the HERG potassium channel. The Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces and Biophysical, 111(5), 1090-1098.
  • Kuyucak, S. (2007). New therapeutic agents and drug development strategies. IDRUGS, 10(9), 618-620.
  • Bastug, T., Kuyucak, S. (2006). Energetics of ion permeation, rejection, binding, and block in gramicidin A from free energy simulations. Biophysical Journal, 90(11), 3941-3950.
  • Bastug, T., Patra, S., Kuyucak, S. (2006). Finite system and periodicity effects in free energy simulations of membrane proteins. Chemical Physics Letters, 425(38872), 320-323. [More Information]
  • Bastug, T., Kuyucak, S. (2006). Molecular dynamics simulations of calcium binding in gramicidin A. Chemical Physics Letters, 424(1-3), 82-85. [More Information]
  • Bastug, T., Patra, S., Kuyucak, S. (2006). Molecular dynamics simulations of gramicidin A in a lipid bilayer: From structure-function relations to force fields. Chemistry and Physics of Lipids, 141(1 to 2), 197-204. [More Information]
  • Bastug, T., Gray-Weale, A., Patra, S., Kuyucak, S. (2006). Role of protein flexibility in ion permeation: A case study in gramicidin A. Biophysical Journal, 90(7), 2285-2296.
  • Bastug, T., Kuyucak, S. (2005). Memory effects in Brownian dynamics simulations of ion transport. Chemical Physics Letters, 401(1-3), 175-179. [More Information]
  • Bastug, T., Kuyucak, S. (2005). Temperature dependence of the transport coefficients of ions from molecular dynamics simulations. Chemical Physics Letters, 408(1-3), 84-88. [More Information]
  • Bastug, T., Kuyucak, S. (2005). Test of molecular dynamics force fields in gramicidin A. European Biophysics Journal, 34(5), 377-382. [More Information]
  • Corry, B., Kuyucak, S., Chung, S. (2003). Dielectric self-energy in Poisson-Boltzmann and Poisson-Nernst-Planck models of ion channels. Biophysical Journal, 84(6), 3594-3606.
  • Takahashi, T., Kuyucak, S. (2003). Functional properties of threefold and fourfold channels in ferritin deduced from electrostatic calculations. Biophysical Journal, 84(4), 2256-2263.
  • Allen, T., Bastug, T., Kuyucak, S., Chung, S. (2003). Gramicidin A channel as a test ground for molecular dynamics force fields. Biophysical Journal, 84(4), 2159-2168.
  • Kuyucak, S., Bastug, T. (2003). Physics of Ion Channels. Journal of Biological Physics, 29(4), 429-446.
  • Bastug, T., Kuyucak, S. (2003). Role of the dielectric constants of membrane proteins and channel water in ion permeation. Biophysical Journal, 84(5), 2871-2882.
  • Chung, S., Allen, T., Kuyucak, S. (2002). Conducting-state properties of the KcsA potassium channel from molecular and Brownian dynamics simulations. Biophysical Journal, 82(2), 628-645.
  • Edwards, S., Corry, B., Kuyucak, S., Chung, S. (2002). Continuum electrostatics fails to describe ion permeation in the gramicidin channel. Biophysical Journal, 83(3), 1348-1360.
  • Chung, S., Kuyucak, S. (2002). Ion channels: recent progress and prospects. European Biophysics Journal, 31, 283-293. [More Information]
  • Kuyucak, S., Honma, M. (2002). Mean field study of the quadrupole-octupole degree of freedom in the spdf boson model. Physical Review C (Nuclear Physics), 65(6), 064323-1-064323-14.
  • Chung, S., Allen, T., Kuyucak, S. (2002). Modeling diverse range of potassium channels with Brownian dynamics. Biophysical Journal, 83(1), 263-277.
  • Kuyucak, S., Chung, S. (2002). Permeation Models and Structure-Function Relationships in Ion Channels. Journal of Biological Physics, 28(2), 289-308.
  • Chung, S., Kuyucak, S. (2002). Recent advances in ion channel research. Biochimica et Biophysica Acta-Biomembranes, 1565 (2), 267-286.
  • Corry, B., Hoyles, M., Allen, T., Walker, M., Kuyucak, S., Chung, S. (2002). Reservoir boundaries in Brownian dynamics simulations of ion channels. Biophysical Journal, 82(4), 1975-1984.
  • Corry, B., Allen, T., Kuyucak, S., Chung, S. (2001). Mechanisms of permeation and selectivity in calcium channels. Biophysical Journal, 80(1), 195-214.
  • Kuyucak, S., Andersen, O., Chung, S. (2001). Models of permeation in ion channels. Reports on Progress in Physics, 64(11), 1427-1472.
  • Chung, S., Kuyucak, S. (2001). Predicting channel function from channel structure using Brownian dynamics simulations. Clinical and Experimental Pharmacology and Physiology, 28(1), 89-94.

2014

  • Heinzelmann, G., Chen, P., Kuyucak, S. (2014). Computation of standard binding free energies of polar and charged ligands to the glutamate receptor glua2. The Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces and Biophysical, 118(7), 1813-1824-1813-1824. [More Information]
  • Rashid, H., Kuyucak, S. (2014). Free energy simulations of binding of HsTx1 toxin to Kv1 potassium channels: The basis of Kv1.3/Kv1.1 selectivity. The Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces and Biophysical, 118(3), 707-716-707-716. [More Information]

2013

  • Rashid, M., Heinzelmann, G., Huq, R., Tajhya, R., Chang, S., Chhabra, S., Pennington, M., Beeton, C., Norton, R., Kuyucak, S. (2013). A Potent and Selective Peptide Blocker of the Kv1.3 Channel: Prediction from Free-Energy Simulations and Experimental Confirmation. PLoS One, 8(11), 1-10. [More Information]
  • Rashid, M., Mahdavi, S., Kuyucak, S. (2013). Computational studies of marine toxins targeting ion channels. Marine Drugs, 11(3), 848-869. [More Information]
  • Heinzelmann, G., Bastug, T., Kuyucak, S. (2013). Mechanism and energetics of ligand release in the aspartate transporter GltPh. The Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces and Biophysical, 117(18), 5486-5496. [More Information]
  • Durmaz, E., Kuyucak, S., Sezerman, O. (2013). Modifying the catalytic preference of tributyrin in Bacillus thermocatenulatus lipase through in-silico modeling of enzyme-substrate complex. Protein Engineering Design and Selection (Print), 26(5), 325-333. [More Information]
  • Mahdavi, S., Kuyucak, S. (2013). Why the drosophila shaker K+ channel is not a good model for ligand binding to voltage-gated Kv1 channels. Biochemistry, 52(9), 1631-1640. [More Information]

2012

  • Pennington, M., Rashid, M., Tajhya, R., Beeton, C., Kuyucak, S., Norton, R. (2012). A C-terminally amidated analogue of ShK is a potent and selective blocker of the voltage-gated potassium channel Kv1.3. FEBS Letters, 586(22), 3996-4001. [More Information]
  • Rashid, M., Kuyucak, S. (2012). Affinity and selectivity of ShK toxin for the Kv1 potassium channels from free energy simulations. The Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces and Biophysical, 116(16), 4812-4822. [More Information]
  • Chen, P., Kuyucak, S. (2012). Developing a comparative docking protocol for the prediction of peptide selectivity profiles: Investigation of potassium channel toxins. Toxins, 4(2), 110-138. [More Information]
  • Timko, J., Kuyucak, S. (2012). Investigation of polarization effects in the gramicidin A channel from ab initio molecular dynamics simulations. Journal of Chemical Physics, 137(20), 1-11. [More Information]
  • Bastug, T., Kuyucak, S. (2012). Molecular dynamics simulations of membrane proteins. Biophysical Reviews, 4(3), 271-282. [More Information]
  • Bastug, T., Heinzelmann, G., Kuyucak, S., Salim, M., Vandenberg, R., Ryan, R. (2012). Position of the Third Na+ Site in the Aspartate Transporter GltPh and the Human Glutamate Transporter, EAAT1. PLoS One, 7(3), 1-10. [More Information]

2011

  • Timko, J., De Castro, A., Kuyucak, S. (2011). Ab initio calculation of the potential of mean force for dissociation of aqueous Ca-Cl. Journal of Chemical Physics, 134(20), 204510-1-204510-9. [More Information]
  • Chen, P., Kuyucak, S. (2011). Accurate determination of the Binding Free Energy for KcsA-Charybdotoxin Complex from the Potential of Mean Force Calculations with Restraints. Biophysical Journal, 100(10), 2466-2474. [More Information]
  • Bastug, T., Kuyucak, S. (2011). Comparative Study of the Energetics of Ion Permeation in Kv1.2 and KcsA Potassium Channels. Biophysical Journal, 100(3), 629-636. [More Information]
  • Heinzelmann, G., Bastug, T., Kuyucak, S. (2011). Free Energy Simulations of Ligand Binding to the Aspartate Transporter GltPh. Biophysical Journal, 101(10), 2380-2388. [More Information]

2010

  • Bucher, D., Gray-Weale, A., Kuyucak, S. (2010). Ab Initio Study of Water Polarization in the Hydration Shell of Aqueous Hydroxide: Comparison between Polarizable and Nonpolarizable Water Models. Journal of Chemical Theory and Computation, 6(9), 2888-2895.
  • Timko, J., Bucher, D., Kuyucak, S. (2010). Dissociation of NaCl in water from ab initio molecular dynamics simulations. Journal of Chemical Physics, 132(11), 114510-1-114510-8.

2009

  • Bastug, T., Kuyucak, S. (2009). Importance of the Peptide Backbone Description in Modeling the Selectivity Filter in Potassium Channels. Biophysical Journal, 96(10), 4006-4012. [More Information]
  • Bucher, D., Kuyucak, S. (2009). Importance of water polarization for ion permeation in narrow pores. Chemical Physics Letters, 477(1-3), 207-210. [More Information]
  • Chen, P., Kuyucak, S. (2009). Mechanism and energetics of charybdotoxin unbinding from a potassium channel from molecular dynamics simulations. Biophysical Journal, 96(7), 2577-2588. [More Information]
  • Ju, P., Pages, G., Riek, R., Chen, P., Torres, A., Bansal, P., Kuyucak, S., Kuchel, P., Vandenberg, J. (2009). The Pore Domain Outer Helix Contributes to Both Activation and Inactivation of the hERG K+ Channel. Journal of Biological Chemistry, 284(2), 1000-1008. [More Information]

2008

  • Bucher, D., Kuyucak, S. (2008). Polarization of water in the first hydration shell of K+ and Ca2+ ions. The Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces and Biophysical, 112(35), 10786-10790.
  • Bastug, T., Chen, P., Patra, S., Kuyucak, S. (2008). Potential of mean force calculations of ligand binding to ion channels from Jarzynski's equality and umbrella sampling. Journal of Chemical Physics, 128(15), 155104-1-155104-9.
  • Bastug, T., Kuyucak, S. (2008). Response to "Comment on 'Free energy simulations of single and double ion occupancy in gramicidin A' " [J. Chem. Phys. 128, 227101 (2008)]. Journal of Chemical Physics, 128(22), 227102-1-227102-2.

2007

  • Bastug, T., Kuyucak, S. (2007). Application of Jarzynski's equality in simple versus complex systems. Chemical Physics Letters, 436(4-6), 383-387. [More Information]
  • Patra, S., Bastug, T., Kuyucak, S. (2007). Binding of organic cations to gramicidin a channel studied with AutoDock and molecular dynamics simulations. The Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces and Biophysical, 111(38), 11303-11311.
  • Wijesinghe, R., Coorey, N., Kuyucak, S. (2007). Charge state of the fast gate in chloride channels: Insights from electrostatic calculations in a schematic model. Journal of Chemical Physics, 127(19), 195102-1-195102-9.
  • Bastug, T., Kuyucak, S. (2007). Free energy simulations of single and double ion occupancy in gramicidin A. Journal of Chemical Physics, 126(10), 105103-1-105103-12.
  • Kuyucak, S. (2007). Modelling drug and toxin binding to ion channels. Drugs of the Future, 32(Supplementary 1), 33-34.
  • Kutteh, R., Vandenberg, J., Kuyucak, S. (2007). Molecular dynamics and continuum electrostatics studies of inactivation in the HERG potassium channel. The Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces and Biophysical, 111(5), 1090-1098.
  • Kuyucak, S. (2007). New therapeutic agents and drug development strategies. IDRUGS, 10(9), 618-620.

2006

  • Bastug, T., Kuyucak, S. (2006). Energetics of ion permeation, rejection, binding, and block in gramicidin A from free energy simulations. Biophysical Journal, 90(11), 3941-3950.
  • Bastug, T., Patra, S., Kuyucak, S. (2006). Finite system and periodicity effects in free energy simulations of membrane proteins. Chemical Physics Letters, 425(38872), 320-323. [More Information]
  • Bastug, T., Kuyucak, S. (2006). Molecular dynamics simulations of calcium binding in gramicidin A. Chemical Physics Letters, 424(1-3), 82-85. [More Information]
  • Bastug, T., Patra, S., Kuyucak, S. (2006). Molecular dynamics simulations of gramicidin A in a lipid bilayer: From structure-function relations to force fields. Chemistry and Physics of Lipids, 141(1 to 2), 197-204. [More Information]
  • Bastug, T., Gray-Weale, A., Patra, S., Kuyucak, S. (2006). Role of protein flexibility in ion permeation: A case study in gramicidin A. Biophysical Journal, 90(7), 2285-2296.

2005

  • Bastug, T., Kuyucak, S. (2005). Memory effects in Brownian dynamics simulations of ion transport. Chemical Physics Letters, 401(1-3), 175-179. [More Information]
  • Bastug, T., Kuyucak, S. (2005). Temperature dependence of the transport coefficients of ions from molecular dynamics simulations. Chemical Physics Letters, 408(1-3), 84-88. [More Information]
  • Bastug, T., Kuyucak, S. (2005). Test of molecular dynamics force fields in gramicidin A. European Biophysics Journal, 34(5), 377-382. [More Information]

2003

  • Corry, B., Kuyucak, S., Chung, S. (2003). Dielectric self-energy in Poisson-Boltzmann and Poisson-Nernst-Planck models of ion channels. Biophysical Journal, 84(6), 3594-3606.
  • Takahashi, T., Kuyucak, S. (2003). Functional properties of threefold and fourfold channels in ferritin deduced from electrostatic calculations. Biophysical Journal, 84(4), 2256-2263.
  • Allen, T., Bastug, T., Kuyucak, S., Chung, S. (2003). Gramicidin A channel as a test ground for molecular dynamics force fields. Biophysical Journal, 84(4), 2159-2168.
  • Kuyucak, S., Bastug, T. (2003). Physics of Ion Channels. Journal of Biological Physics, 29(4), 429-446.
  • Bastug, T., Kuyucak, S. (2003). Role of the dielectric constants of membrane proteins and channel water in ion permeation. Biophysical Journal, 84(5), 2871-2882.

2002

  • Chung, S., Allen, T., Kuyucak, S. (2002). Conducting-state properties of the KcsA potassium channel from molecular and Brownian dynamics simulations. Biophysical Journal, 82(2), 628-645.
  • Edwards, S., Corry, B., Kuyucak, S., Chung, S. (2002). Continuum electrostatics fails to describe ion permeation in the gramicidin channel. Biophysical Journal, 83(3), 1348-1360.
  • Chung, S., Kuyucak, S. (2002). Ion channels: recent progress and prospects. European Biophysics Journal, 31, 283-293. [More Information]
  • Kuyucak, S., Honma, M. (2002). Mean field study of the quadrupole-octupole degree of freedom in the spdf boson model. Physical Review C (Nuclear Physics), 65(6), 064323-1-064323-14.
  • Chung, S., Allen, T., Kuyucak, S. (2002). Modeling diverse range of potassium channels with Brownian dynamics. Biophysical Journal, 83(1), 263-277.
  • Kuyucak, S., Chung, S. (2002). Permeation Models and Structure-Function Relationships in Ion Channels. Journal of Biological Physics, 28(2), 289-308.
  • Chung, S., Kuyucak, S. (2002). Recent advances in ion channel research. Biochimica et Biophysica Acta-Biomembranes, 1565 (2), 267-286.
  • Corry, B., Hoyles, M., Allen, T., Walker, M., Kuyucak, S., Chung, S. (2002). Reservoir boundaries in Brownian dynamics simulations of ion channels. Biophysical Journal, 82(4), 1975-1984.

2001

  • Corry, B., Allen, T., Kuyucak, S., Chung, S. (2001). Mechanisms of permeation and selectivity in calcium channels. Biophysical Journal, 80(1), 195-214.
  • Kuyucak, S., Andersen, O., Chung, S. (2001). Models of permeation in ion channels. Reports on Progress in Physics, 64(11), 1427-1472.
  • Chung, S., Kuyucak, S. (2001). Predicting channel function from channel structure using Brownian dynamics simulations. Clinical and Experimental Pharmacology and Physiology, 28(1), 89-94.

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