Publications

1. A. J. de Jesus and T. W. Allen. 2012. The determinants of hydrophobic mismatch response for transmembrane helices. BBA Biomembranes. In press. Online.


2. 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.


3. 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.


4. 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.


5. 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.


6. T. W. Allen and F. Separovic. 2012. Membrane protein structure and function. Biochimica et Biophysica Acta 1818:125. Online.


7. 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.


8. 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.


9. 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.


10. 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


11. I. Vorobyov B. Bekker and T. W. Allen. 2010. The electrostatics of deformable lipid membranes. Biophys. J. 98:2904-2913. Online, Movie


12. 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.


13. 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


14. 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.


15. 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.


16. 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.


17. 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.


18. 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.


19. 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


20. T. W. Allen. 2007. Modeling charged protein side chains in lipid membranes. J. Gen. Physiol. 130:237-240. Online.


21. 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.


22. 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.


23. 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.


24. 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.


25. 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.


26. 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.


27. 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.


28. 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.


29. 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.


30. 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.


31. 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.


32. T. W. Allen and S-H. Chung. 2001. Brownian Dynamics Study of an Open State Potassium Channel. Biophys. Biochim. Acta. 1515, 83-91. Online.


33. B. Corry, T. W. Allen, S. Kuyucak and S-H. Chung. 2001. A Model of Calcium Channels. Biophys. Biochim. Acta. 1059, 1-6. Online.


34. 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.


35. 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.


36. 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.


37. 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.


38. T. W. Allen, S. Kuyucak and S-H. Chung. 1999. Molecular Dynamics Study of the KcsA Potassium Channel. Biophys. J. 77, 2502-2516. Online.


39. 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.


40. 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.


41. 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.


42. 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.


43. T. W. Allen and C. J. Burden. 1997. Vector Positronium States in Three-dimensional QED. Phys. Rev. D 55, 4954-4966. Online.


44. T. W. Allen and C. J. Burden. 1996. Positronium States in Three-dimensional QED. Phys. Rev. D 53, 5842-5855. Online.

 

 

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