Publications

  1. 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. In press.
  2. 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
    3. PDF, Supplementary Material
  3. 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
    4. PDF, Supplementary Material
  4. I. Vorobyov and T. W. Allen. 2008. Molecular Dynamics Computations for Proteins: a case study in membrane ion permeation. Encyclopedia of Applied Biophysics. In press.
  5. 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.
  6. B. Roux, O. S. Andersen and T. W. Allen. On the Significance of 1D Free Energy Profiles in Ion Channel Simulations. 2008. ("Comment on .Free energy simulations of single and double ion occupancy in gramicidin A.") J. Chem. Phys. 128:227101
    7. PDF
  7. 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.
    8. PDF, Supplementary Material
  8. 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.
  9. T. W. Allen. 2007. Modeling charged protein side chains in lipid membranes. J. Gen. Physiol. 130:237-240.
    10. PDF,
  10. 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.
    11. PDF, Supporting Information
  11. 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. 124:251-267
    12. PDF
  12. 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.
    13. PDF
  13. 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. PDF
  14. 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. PDF; Supporting Text PDF
  15. 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. PDF
  16. 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. PDF
  17. 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. PDF
  18. 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. PDF
  19. S. H. Chung, T. W. Allen and S. Kuyucak. 2002. Modeling Diverse Range of Potassium Channels with Brownian dynamics. Biophys. J. 83, 263-277. PDF [Editorial: P.C. Jordan. 2002. Unclogging a Pipe: Potassium Channel Pinball. Biophys. J. 83, 2-4. PDF]
  20. 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. PDF
  21. T. W. Allen and S-H. Chung. 2001. Brownian Dynamics Study of an Open State Potassium Channel. Biophys. Biochim. Acta. 1515, 83-91. PDF
  22. B. Corry, T. W. Allen, S. Kuyucak and S-H. Chung. 2001. A Model of Calcium Channels. Biophys. Biochim. Acta. 1059, 1-6. PDF
  23. 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. PDF
  24. 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. PDF
  25. 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. PDF
  26. 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. PDF
  27. T. W. Allen, S. Kuyucak and S-H. Chung. 1999. Molecular Dynamics Study of the KcsA Potassium Channel. Biophys. J. 77, 2502-2516. PDF
  28. 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. PDF
  29. 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. PDF
  30. 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. PDF
  31. 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. PDF
  32. T. W. Allen and C. J. Burden. 1997. Vector Positronium States in Three-dimensional QED. Phys. Rev. D 55, 4954-4966. PDF
  33. T. W. Allen and C. J. Burden. 1996. Positronium States in Three-dimensional QED. Phys. Rev. D 53, 5842-5855. PDF

 

 

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