Tests
of continuum theories
as models of ion channels: I. Poisson-Boltzmann theory versus Brownian
Dynamics.
G. Moy, B. Corry, S. Kuyucak and S.H.
Chung, Biophys.
J. 78 (2000) 2349-2363.
Tests
of continuum theories
as models of ion channels: II. Poisson-Nernst-Planck theory versus
Brownian Dynamics.
B. Corry, S. Kuyucak and S.H. Chung, Biophys.
J. 78 (2000) 2364-2381.
Molecular
dynamics estimates
of ion diffusion in model hydrophobic and the KcsA potassium channels.
T.W. Allen, S. Kuyucak and S.H. Chung, Biophys.
Chem. 86 (2000) 1-14.
The
potassium channel:
structure, selectivity and diffusion.
T.W. Allen, A. Bliznyuk, A.P. Rendell,
S. Kuyucak and S.H. Chung, J.
Chem. Phys. 112 (2000) 8191-8204.
A
model of calcium channels.
B. Corry, T.W. Allen, S. Kuyucak and
S.H. Chung, Biochim.
Biophys. Acta, Rapid report 1509 (2000) 1-6.
Predicting
channel function
from channel structure using Brownian Dynamics simulations.
S.H. Chung and S. Kuyucak, Clinical
& Exp. Physiology & Pharmacology 28 (2001) 89-94.
Mechanisms
of permeation and
selectivity in calcium channels.
B. Corry, T.W. Allen, S. Kuyucak and
S.H. Chung, Biophys.
J. 80 (2001) 195-214.
Models
of permeation in ion channels.
S. Kuyucak, O.A. Andersen and S.H.
Chung, Rep.
Prog. Phys. 64 (2001) 1427-1472.
Conducting-state
properties
of the KcsA potassium channel from molecular and Brownian Dynamics
simulations.
S.H. Chung, T.W. Allen and S. Kuyucak, Biophys.
J. 82 (2002) 628-645.
Permeation
models and
structure-function relationships in ion channels.
S. Kuyucak and S.H. Chung, J.
Biol. Phys. 28 (2002) 289-308.
Reservoir
boundaries in Brownian
Dynamics simulations of ion channels.
B. Corry, M. Hoyles, T.W. Allen, M.
Walker, S. Kuyucak and S.H. Chung, Biophys.
J. 82 (2002) 1975-1984.
Modeling
diverse range of potassium
channels with Brownian Dynamics.
S.H. Chung, T.W. Allen and S. Kuyucak, Biophys.
J. 83 (2002) 263-277.
Ion
channels: recent progress
and prospects.
S.H. Chung and S. Kuyucak, Eur.
Biophys. J. 31 (2002) 283-293.
Continuum
electrostatics fails
to describe ion permeation in the gramicidin A channel.
S. Edwards, B. Corry, S. Kuyucak and
S.H. Chung, Biophys.
J. 83 (2002) 1348-1360.
Recent
advances in ion channels
research.
S.H. Chung and S. Kuyucak, Biochim.
Biophys. Acta - Reviews 1565 (2002) 267-286.
Gramicidin
A channel as a test ground
for molecular dynamics force fields.
T.W. Allen, T. Bastug, S. Kuyucak and
S.H. Chung, Biophys.
J. 84 (2003) 2159-2168.
Functional
properties of 3-fold
and 4-fold channels in Ferritin deduced from electrostatic
calculations.
T. Takahashi and S. Kuyucak, Biophys.
J. 84 (2003) 2256-2263.
Role
of the dielectric constants
of membrane proteins and channel water in ion permeation.
T. Bastug and S. Kuyucak, Biophys.
J.
84
(2003) 2871-2882.
Dielectric
self energy in
Poisson-Boltzmann
and Poisson-Nernst-Planck models of ion channels.
B. Corry, S. Kuyucak and S.H. Chung, Biophys.
J. 84 (2003) 3594-3606.
Physics
of ion channels.
S. Kuyucak and T. Bastug, J.
Biol. Phys. 29 (2003) 429-446.
Memory
effects in Brownian dynamics
simulations of ion
transport.
T. Bastug and S. Kuyucak, Chem.
Phys. Lett. 401 (2005) 175-179.
Test
of molecular dynamics force fields in gramicidin A.
T.
Bastug and S. Kuyucak, Eur.
Biophys. J. 34 (2005) 377-382.
Role of protein flexibility in ion permeation: a case study in gramicidin A.
T. Bastug, A. Gray-Weale, S.M. Patra and S. Kuyucak, Biophys. J. 90 (2006) 2285-2296.
Energetics
of ion permeation,
rejection, binding and block in gramicidin A from free energy
simulations.
T. Bastug and S. Kuyucak, Biophys.
J. 90 (2006) 3941-3950.