Publications
- A. J. de Jesus and T. W. Allen. 2012.
The determinants of hydrophobic mismatch response for transmembrane helices.
BBA Biomembranes. In press.
Online.
- A. J. de Jesus and T. W. Allen. 2012.
The role of tryptophan side chains in membrane protein anchoring and hydrophobic mismatch.
BBA Biomembranes. In press.
Online.
- I. Kim and T. W. Allen. 2012. Bennett's acceptance ratio and histogram analysis methods enhanced by umbrella sampling along a reaction coordinate in configurational space.
J. Chem. Phys. 136:164103.
Online.
- L. B. Li, I. Vorobyov and T. W. Allen. 2012. The role of membrane thickness in charged protein-lipid interactions. Biochim. Biophys. Acta. 1818:135-145.
Online.
- I. Vorobyov, W.F.D. Bennet, D.P. Tieleman, T. W. Allen and S. Noskov. 2012. The role of atomic polarization in the thermodynamics of chloroform partitioning to lipid bilayers.
J. Chem. Theory Comput. 8:618–628.
Online.
- T. W. Allen and F. Separovic. 2012. Membrane protein structure and function. Biochimica et Biophysica Acta 1818:125.
Online.
- I. Kim and T. W. Allen. 2011. On the selective ion binding hypothesis for potassium channels.
Proc. Natl. Acad. Sci. USA. 108:17963-17968. Online.
- I. Vorobyov and T. W. Allen. 2011. On the role of anionic lipids in charged protein interactions with membranes. Biochim. Biophys. Acta. 1808:1673–1683.
Online.
- C. N. Nimigean and T. W. Allen. 2011. Origins of ion selectivity in potassium channels from the perspective of channel block. J. Gen. Physiol. 137:405-413.
Online.
- I. Vorobyov and T. W. Allen. 2010. Electrostatics of solvent and membrane interfaces and the role of electronic polarizability. J. Chem. Phys. 132:185101.
Online,
JCP Editor's choice 2010
- I. Vorobyov B. Bekker and T. W. Allen. 2010. The electrostatics of deformable lipid membranes. Biophys. J. 98:2904-2913.
Online,
Movie
- A. N. Thompson, I. Kim, T. D. Panosian, T. Iverson, T. W. Allen and C. M. Nimigean. 2009. Mechanism of potassium channel selectivity revealed by Na+ and Li+ binding sites inside the KcsA pore. Nature Structural and Molecular Biology. 16: 1317-1324.
Online.
- I. Vorobyov and T. W. Allen. 2009. Molecular Dynamics Computations for Proteins: a case study in membrane
ion permeation. Encyclopedia of Applied Physics. Ed. H.G.Bohr. Wiley, Weinheim.
Online
- L. B. Li, I. Vorobyov and T. W. Allen. 2008. Potential of Mean Force and pKa profile calculation for a lipid membrane-exposed Arg side chain. J. Phys. Chem. B. 112:9574-9587.
Online.
- I. Vorobyov, L. B. Li and T. W. Allen. 2008. Assessing atomistic and coarse-grained force fields for protein-lipid interactions: the formidable challenge of an ionizable side chain in a membrane. J. Phys. Chem. B. 112:9588-9602.
Online.
- M.C. Howland, A.R. Sapuri-Butti, A.P. Shreve, T. W. Allen and A.N. Parikh. 2008. Evidence for Leaflet-Dependent Redistribution of Charged Molecules in Fluid Supported Phospholipid Bilayers. Langmuir. 24, 13250-13253.
Online.
- B. Roux, O. S. Andersen and T. W. Allen.
2008. Comment on Free energy simulations of single and double ion occupancy in gramicidin A. J. Chem. Phys. 128:227101.
Online.
- L. B. Li, I. Vorobyov, A. D. MacKerell Jr., and T. W. Allen. 2008. Is arginine charged in a membrane? Biophys. J. 94:L11-L13.
Online.
- L. B. Li, I. Vorobyov, S. Dorairaj and T. W. Allen. 2008. Charged protein side chain movement in lipid bilayers explored with free energy simulation. Current Topics in Membranes. Volume 60.
Online
- T. W. Allen. 2007. Modeling charged protein side chains
in lipid membranes. J. Gen. Physiol. 130:237-240.
Online.
- S. Dorairaj and T. W. Allen. 2007. On the thermodynamic stability of a charged arginine side chain in a transmembrane helix. Proc. Natl. Acad. Sci. U.S.A. 104:4943-4948.
Online.
- T. W. Allen, O. S.
Andersen and B. Roux. 2006. Molecular dynamics - potential of mean force calculations as a tool for understanding ion permeation and selectivity in narrow channels.
Biophys. Chem. 124:251-257.
Online.
- T. W. Allen, O. S.
Andersen and B. Roux. 2006. Ion Permeation through a Narrow Channel: Using
gramicidin to ascertain all-atom molecular dynamics
potential of mean force methodology and biomolecular force fields. Biophys. J. 90:3447-3468.
Online.
- T. W. Allen, O. S.
Andersen and B. Roux. 2004. On the Importance of Flexibility in Studies of
Ion Permeation. J. Gen. Physiol. 124, 679-690.
Online.
- T. W. Allen, O. S. Andersen
and B. Roux. 2004. The Energetics of Ion Conduction in the Gramicidin A
Channel. Proc. Nat. Acad. Sci. 101, 117-122.
Online.
- B. Roux, T. W. Allen,
S. Berneche and W. Im. 2004. Theoretical and Computational Models of
Biological Ion Channels. Q. Rev. Biophys. 37, 15-103.
Online.
- T. W. Allen, O. S.
Andersen and B. Roux. 2003. The Structure of Gramicidin A in a Lipid
Bilayer Environment Determined using Molecular Dynamics Simulations and
Solid-State NMR Data. J. Am. Chem. Soc. 125, 9868-9877.
Online.
- T. W. Allen, T. Bastug,
S. Kuyucak and S. H. Chung. 2003. Gramicidin A Channel as a Test Ground
for Molecular Dynamics Force Fields. Biophys. J. 84, 2159-2168.
Online.
- S-H. Chung, T. W.
Allen and S. Kuyucak. 2002. Conducting State Properties of the KcsA
Potassium Channel from Molecular and Brownian Dynamics Simulations. Biophys.
J. 82, 628-645.
Online.
- S. H. Chung, T. W.
Allen and S. Kuyucak. 2002. Modeling Diverse Range of Potassium Channels
with Brownian dynamics. Biophys. J. 83, 263-277.
Online.
[Editorial: P.C. Jordan. 2002. Unclogging a Pipe: Potassium Channel Pinball. Biophys. J. 83, 2-4.
Online.
- B. Corry, M. Hoyles, T.
W. Allen, M. Walker, S. Kuyucak and S-H. Chung. 2002. Reservoir Boundaries
in Brownian Dynamics Simulations of Ion Channels. Biophys. J. 82, 1975-1982.
Online.
- T. W. Allen and S-H.
Chung. 2001. Brownian Dynamics Study of an Open State Potassium Channel. Biophys.
Biochim. Acta. 1515, 83-91.
Online.
- B. Corry, T. W. Allen,
S. Kuyucak and S-H. Chung. 2001. A Model of Calcium Channels. Biophys. Biochim.
Acta. 1059, 1-6.
Online.
- B. Corry, T. W. Allen,
S. Kuyucak and S-H. Chung. 2001. Mechanisms of Permeation and Selectivity
in Calcium Channels. Biophys. J. 80, 195-214.
Online.
- A. Bliznyuk, A. P.
Rendell, T. W. Allen and S-H. Chung. 2001. The Potassium Ion Channel:
Comparison of Linear Scaling Semiempirical and Molecular Mechanics
Representations of the Electrostatic Potential. J. Phys. Chem. B. 105, 12674-12679.
Online.
- T. W. Allen, A. Bliznyuk,
A. Rendell, S. Kuyucak and S-H. Chung. 2000. The Potassium Channel:
Structure, Selectivity and Diffusion. J. Chem. Phys. 112, 8191-8204.
Online.
- T. W. Allen, S. Kuyucak
and S-H. Chung. 2000. Molecular Dynamics Estimates of Ion Diffusion in
Model Hydrophobic and the KcsA Potassium Channel. Biophys. Chem. 86, 1-14.
Online.
- T. W. Allen, S. Kuyucak
and S-H. Chung. 1999. Molecular Dynamics Study of the KcsA Potassium
Channel. Biophys. J. 77, 2502-2516.
Online.
- T. W. Allen, S. Kuyucak
and S-H. Chung. 1999. Effect of Hydrophobic and Hydrophilic Channels on
Water and Ion Structure and Diffusion. J. Chem. Phys. 111, 7985-7999.
Online.
- T. W. Allen, S. Kuyucak
and S-H. Chung. 1999.Molecular and Brownian Dynamics Studies of the
Potassium Channel. Chem. Phys. Lett. 313, 358-365.
Online.
- S-H. Chung, T. W.
Allen, M. Hoyles and S. Kuyucak. 1999. Permeation of Ions Across the
Potassium Channel: Brownian Dynamics Studies. Biophys. J. 77, 2517-2533.
Online.
- S-H. Chung, M. Hoyles,
T. W. Allen and S. Kuyucak. 1998. Study of Ion Currents across a Model
Membrane Channel Using Brownian Dynamics. Biophys. J. 75, 793-809.
Online.
- T. W. Allen and C. J.
Burden. 1997. Vector Positronium States in Three-dimensional QED. Phys.
Rev. D 55, 4954-4966.
Online.
- T. W. Allen and C. J.
Burden. 1996. Positronium States in Three-dimensional QED. Phys. Rev. D 53, 5842-5855.
Online.
(Ask for reprints)