T. W. Allen, T. Bastug, S. Kuyucak and S. H. Chung. Gramicidin A channel as a test ground for molecular dynamics force fields. Biophysical Journal 84, 2159-2168, 2003. PDF: (Full article, PDF, 237KB)
B. Corry, S. Kuyucak and S. H. Chung. Dielectric self-energy in Poisson-Boltzmann and Poisson-Nernst-Planck models of ion channels. Biophysical Journal 84, 3594-3606, 2003. Biophysical Journal:Online version(Full article, PDF, 243KB)
M. O'Mara, P. H. Barry and S. H. Chung. A model of the glycine receptor deduced from Brownian dynamics studies. Proceedings of the National Academy of Sciences USA 100, 4310-4315, 2003. (Full article, PDF, 260KB)
V. Krishnamurthy and S. H. Chung. Adaptive learning algorithms for Nernst potential and current-voltage curves in nerve cell membrane ion channels. IEEE Transaction on NanoBioscience 2 (No. 4), 266-278, 2004. (Full article, PDF, 490KB)
B. Corry, M. O'Mara and S. H. Chung. Conduction mechanisms of chloride ions in ClC-type channels. Biophysical Journal 86, 846-860, 2004. (Full article, PDF, 502KB)
B. Corry, M. O'Mara and S. H. Chung. Permeation dynamics of chloride ions in the ClC- 0 and ClC-1 channels. Chemical Physics Letters 386, 233-238, 2004. (Full article, PDF, 341KB)
S. H. Chung and D. P. Tieleman. Computational and theoretical approaches to unraveling the permeation dynamics in biological nanotubes. In: M. Rieth and W. Schommers (eds.). Computational Nanotechnology. American Scientific Publishers, CA. Vol 6. Chapter 12, pp. 567-637. (Full article, PDF, 2372KB)
T. Vora, B. Corry and S. H. Chung. A model of sodium channels. Biochimica et Biophysica Acta - Biomembranes 1668, 106-116, 2004. (Full article, PDF, 408KB)
B. Corry and S. H. Chung. Influence of protein flexibility on the electrostatic energy landscape in gramicidin A. European Biophysics Journal 34, 208-216, 2005. (Full article, PDF, 355KB)
V. Krishnamurthy and S. H. Chung. Brownian dynamics simulation for modelling ion permeation across bionanotubes. IEEE Transactions on NanoBioscience 4, 102-111, 2005. (Full article, PDF, 436KB)
V. Krishnamurthy and S. H. Chung. Ion channels - estimation and control at macroscopic and nano scales. Australian Journal of Electrical and Electronic Engineering 2, 59-68, 2005. (Full article, PDF, 138KB)
B. Corry, T. Vora and S. H. Chung. Electrostatic basis of valence selectivity in cationic channels. Biochimica et Biophysica Acta - Biomembranes 1711, 72-86, 2005. (Full article, PDF, 414KB)
V. Krishnamurthy, S. H. Chung and G. Dumont. Editors. Ion Channels: Bionanotubes. Special Issue of IEEE Transactions on Nanobioscience 4,1-132. IEEE Press, March 2005.
M. L. O'Mara, B. Cromer, M. W. Parker and S. H. Chung. Homology model of the GABAA receptor examined using Brownian dynamics. Biophysical Journal 88, 3286-3299, 2005. (Full article, PDF, 425KB)
Bisset, B. Corry and S. H. Chung. The fast gating mechanism in ClC-0 channels. Biophysical Journal 89, 179-186, 2005. (Full article, PDF, 191KB)
B. Corry and S. H. Chung. Mechanisms of valence selectivity in biological ion channels. Cellular & Molecular Life Sciences 63, 301-315, 2006. (Full article, PDF, 509KB)
V. Krishnamurthy and S. H. Chung. Adaptive Brownian dynamics simulation for estimating potential of mean force in ion channel permeation. IEEE Transactions on Nanobioscience 5, 126-138, 2006. (Full article, PDF, 455KB)
S. H. Chung, O. S. Andersen and V. Krishnamurthy. Editors. Handbook of Ion Channels: Dynamics, Structure, and Applications. Springer Verlag, New York.
S. H. Chung and V. Krishnamurthy. Brownian dynamics: a powerful tool for studying ion permeation in bio-nanotubes. In: Handbook of Ion Channels: Dynamics, Structure, and Applications. S. H. Chung, O. S. Andersen and V. Krishnamurthy (eds.), Springer Verlag, New York. Chapter 15. Chapter 15 (PDF, 1180KB)
V. Krishnamurthy and S. H. Chung. Signal processing based on hidden Markov models for extracting small channel currents. In: Handbook of Ion Channels: Dynamics, Structure, and Applications. S. H. Chung, O. S. Andersen and V. Krishnamurthy (eds.), Springer Verlag, New York. Chapter 19. Chapter 19 (PDF, 2643KB)
T. Vora, B. Corry and S. H. Chung. Brownian dynamics investigation into the conductance state of the MscS channel crystal structure. Biochimica et Biophysica Acta - Biomembranes 1758, 730-737, 2006. (Full article, PDF, 303KB)
V. Krishnamurthy, M. Hoyles, R. Saab and S. H. Chung. Permeation in gramicidin ion channels by directly estimating the potential of mean force using Brownian dynamics. Journal of Computational and Theoretical Nanoscience 3, 702-711, 2006. (Full article, PDF, 138KB)
V. Krishnamurthy and S. H. Chung. Large-scale dynamical models and estimation for permeation in biological membrane ion channels. Proceedings of the IEEE 95 (5), 853-880, 2007. (Full article, PDF, 985KB)
V. Krishnamurthy, T. Vora and S. H. Chung. Adaptive Brownian dynamics for shape estimation of sodium ion channels. Journal of Nanoscience and Nanotechnology 7, 1-9, 2007. (Full article, PDF, 327KB)
S. H. Chung and B. Corry. Conduction properties of KcsA measured using Brownian dynamics with flexible carbonyl groups in the selectivity filter. Biophysical Journal 93, 44-53, 2007. (Full article, PDF, 708KB)
S. H. Chung. Bionanotubes: the ultimate units of the physiology of life. Australian Physics 44, 16-17, 2007. (Full article, PDF, 3437KB)
Jin Aun Ng, Taira Vora, Vikram Krishnamurthy and Shin-Ho Chung. Estimating the dielectric constant of the channel protein and pore. European Biophysics Journal 37, 213-222, 2008. (Full article, PDF, 393KB)
Matthew Holyles, Vikram Krishnamurthy, May Siksik, and Shin-Ho Chung. Brownian dynamics theory for predicting internal and external blockages of tetraethylammonium in the KcsA potassium channel. Biophysical Journal 94, 366-378, 2008. (Full article, PDF, 538KB)
Taira Vora, David Bisset and Shin-Ho Chung. Conduction of Na+ and K+ through the NaK Channel: Molecular and Brownian Dynamics Studies. Biophysical Journal 95, 1600-1611, 2008. (Full article, PDF, 930KB)
Dan Gordon, Vikram Krishnamurthy and Shin-Ho Chung. A Generalised Langevin Algorithm for Studying Permeation Across Biological Ion Channels. Molecular Physics 106 (No. 11), 1353-1361, 2008. (Full article, PDF, 226KB)
David Bisset and Shin-Ho Chung. Efficacy of External Tetraethylammonium Block of the KcsA Potassium Channel: Molecular and Brownian Dynamics Studies. Biochimica et Biophysica Act - Biomembrane 1778, 2273-2282, 2008. (Full article, PDF, 503KB)
Taira Vora, Ben Corry and Shin-Ho Chung. Brownian dynamics study of flux ratios in sodium channels. European Biophysical Journal 38, 45-52, 2008. (Full article, PDF, 310KB)
Tamsyn A. Hilder, Daniel Gordon, and Shin-Ho Chung. Salt rejection and water transport through boron nitride nanotubes. Small 5, 2183-2190, 2009. (Full article, PDF, 519KB) DOI: 10.1002/smll.200900349
Tamsyn A. Hilder, Daniel Gordon, and Shin-Ho Chung. Boron nitride nanotubes selectively permeable to cations or anions. Small 5, 2870-2875, 2009. (Full article, PDF, 373KB) DOI: 10.1002/smll.200901229
Dan Gordon, Vikram Krishnamuthy and Shin-Ho Chung. Generalized Langevin models of molecular dynamics simulations, with applications to ion channels. Journal of Chemical Physics 131, 134102-1 - 134102-11, 2009. (Full article, PDF, 563KB)
Dan Gordon, Matthew Hoyles and Shin-Ho Chung. An algorithm for rigid-body Brownian dynamics. Physical Review E 80, 066703-1 - 066703-12, 2009. (Full article, PDf, 436KB)
Tamsyn A. Hilder, Rui Yang, V. Ganesh, Dan Gordon, Andrey Bliznyuk, Alistair P. Rendell and Shin-Ho Chung. Validity of current force fields for simulations on boron nitride nanotubes. Micro & Nano Letters 5, 150 - 156, 2010. (Full article, PDF, 241KB)
Tamsyn A. Hilder, Dan Gordon and Shin-Ho Chung. Synthetic chloride-selective carbon nanotubes examined using molecular and stochastic dynamics. Biophysical Journal 99, 1734 - 1742, 2010. (Full article, PDF, 2001KB).