Computational Chemistry and Biophysics
Born in Perth, Australia;
Ph.D. awarded 1998, Theoretical Physics, The Australian National University, with Conrad Burden;
Postdoctoral Fellow, 1997-2001, Chemistry, The Australian National University, with Shin-Ho Chung;
Postdoctoral Fellow, 2001-2004, Physiology and Biophysics, Weill Medical College of Cornell University, with Olaf Andersen and Benoit Roux;
Assistant Professor, 2004, Chemistry, University of California, Davis.

Research Interests
Membrane protein structure and function; ion channel permeation and gating; ionic solvation; protein-lipid interactions; protein function modulation by membrane modifiers and drugs; free energy calculation and configurational sampling methods.

The Allen group focuses on the development of computational techniques to study important biophysical and physical chemistry problems. In particular, many phenomena in the cell membrane have not yet been characterized at the microscopic level. Their aim is to complement experiment by determining the microscopic driving forces of protein function in cell membranes. Dynamics simulations and advanced free energy methods are used to study explicit lipid bilayers with proteins ranging from simple model transmembrane segments to complex multi-segment proteins. The Allen group is particularly interested in the function of ion channels which allow selective permeation of charged molecules across the membrane and are associated with many neurological and cardiovascular disorders. In the process they are helping to understand many biological processes, such as the actions of antibiotic peptides, toxins, viral peptides, hormone receptors and biomembrane nano-devices. It is important that we use computer simulation to uncover the atomic-level mechanisms and thermodynamics governing protein function. Furthermore, the ability to measure the effects of membrane composition and chemical and pharmacological agents on membrane protein activity represents a significant advance in computational biophysics and will guide future drug development.

Major funding and support:

National Science Foundation. NSF Career Award.
Pittsburgh Supercomputing Center MRAC Award

• L. B. Li, I. Vorobyov, A. D. MacKerell Jr., and T. W. Allen. 2007.  Is arginine charged in a membrane? Biophys. J.  In press.
• T. W. Allen. 2007. Modeling charged protein side chains in lipid membranes. J. Gen. Physiol. 130:237-240.
• L. Li, I. Vorobyov, S. Dorairaj and T. W. Allen. 2007. Charged protein side chain movement in lipid bilayers explored with free energy simulation. Current Topics in Membranes. In press.
• 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.
• 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.
• 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.
• 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
• 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.
• B. Roux, T. W. Allen, S. Bernèche and W. Im. 2004. "Theoretical and Computational Models of Biological Ion Channels". Q. Rev. Biophys. 37, 15-103.
• 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.
• 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.
• 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.
• S. H. Chung, T. W. Allen and S. Kuyucak. 2002. "Modeling Diverse Range of Potassium Channels with Brownian dynamics." Biophys. J. 83, 263-277. [Editorial: P.C. Jordan. 2002. "Unclogging a Pipe: Potassium Channel Pinball." Biophys. J. 83, 2-4.]
• 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.
• T. W. Allen and S-H. Chung. 2001. "Brownian Dynamics Study of an Open State Potassium Channel." Biophys. Biochim. Acta. 1515, 83-91.
• B. Corry, T. W. Allen, S. Kuyucak and S-H. Chung. 2001. "A Model of Calcium Channels." Biophys. Biochim. Acta. 1059, 1-6.
• 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.
• 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.
• 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.
• 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.
• T. W. Allen, S. Kuyucak and S-H. Chung. 1999. "Molecular Dynamics Study of the KcsA Potassium Channel". Biophys. J. 77, 2502-2516.
• 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.
• 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.
• 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.
• 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.
• T. W. Allen and C. J. Burden. 1997. "Vector Positronium States in Three-dimensional QED". Phys. Rev. D 55, 4954-4966.
• T. W. Allen and C. J. Burden. 1996. "Positronium States in Three-dimensional QED". Phys. Rev. D 53, 5842-5855.