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37. Coupling of calcium and substrate binding through loop alignment in the outer membrane transporter BtuB. James Gumbart, Michael C. Wiener, and Emad Tajkhorshid. Journal of Molecular Biology, 393:1129-1142, 2009.
36. Molecular mechanisms of active transport across the cellular membrane. Po-Chao Wen, Zhijian Huang, Giray Enkavi, Yi Wang, James Gumbart, and Emad Tajkhorshid. In Philip Biggin and Mark Sansom, editors, Molecular Simulations and Biomembranes: From Biophysics to Function. Royal Society of Chemistry, 2009.
35. Structural and functional analysis of SoPIP2;1 mutants add insight into plant aquaporin gating. Maria Nyblom, Anna Frick, Yi Wang, Mikael Ekvall, Karin Hallgren, Kristina Hedfalk, Richard Neutze, Emad Tajkhorshid, and Susanna Törnroth-Horsefield. Journal of Molecular Biology, 387:653-668, 2009.
34. Dimer opening of the nucleotide binding domains of ABC transporters after atp hydrolysis. P.-C. Wen and E. Tajkhorshid. Biophysical Journal, 95:5100-5110, 2008.
33. Potential cation and H+ binding sites in acid sensing ion channel-1. S. A. Shaikh and E. Tajkhorshid. Biophysical Journal, 95:5153-5164, 2008.
32. DNA attraction in mono- and divalent electrolytes. B. Luan and A. Aksimentiev. Journal of the American Chemical Society, 130:15754-15755, 2008.
31. Self-assembly route for embedding polyoxomolybdate capsules in lipid bilayer membranes. R. Carr, I. A. Weinstock, A. Sivaprasadarao, A. Müller, and A. Aksimentiev. Nano Letters, 8:3916-3921, 2008.
30. Strain softening in stretched DNA. B. Luan and A. Aksimentiev. Physical Review Letters, 101:118101, 2008.
29. Electro-osmotic screening of the DNA charge in a nanopore. B. Luan and A. Aksimentiev. Physical Review E, 78:021912, 2008.
27. Dynamics of the extracellular gate and ion-substrate coupling in the glutamate transporter. Zhijian Huang and Emad Tajkhorshid. Biophysical Journal, 95:2292-2300, 2008.
26. Electrostatic funneling of substrate in mitochondrial inner membrane carriers. Yi Wang and Emad Tajkhorshid. Proceedings of the National Academy of Sciences, USA, 105:9598-9603, 2008.
25. Resolution enhancement in solid-state NMR spectra of oriented membrane proteins by anisotropic differential linebroadening. T. Vosegaard, K. Bertelsen, J. M. Pedresen, L. Thøgersen, B. Schiøtt, E. Tajkhorshid, T Skrydstrup, and N. Chr. Nielsen. Journal of the American Chemical Society, 130:5028-5029, 2008.
24. Blood clotting reactions on nanoscale phospholipid bilayers. J. H. Morrissey, V. Pureza, R. L. Davis-Harrison, S. G. Sligar, Y. Z. Ohkubo, and E. Tajkhorshid. Trombosis Research, 122:S23-S26, 2008.
23. Indirect role of Ca2+ in the assembly of extracelluar matrix proteins. Jiankuai Diao and Emad Tajkhorshid. Biophysical Journal, 95:120-127, 2008.
22. Gas conduction of lipid bilayers and membrane channels. Y. Wang, Y. Zenmei Ohkubo, and E. Tajkhorshid. In Scott Feller, editor, Current Topics in Membranes: Computational Modeling of Membrane Bilayers, chapter 60, pp. 343-367. Elsevier, 2008.
21. Scalable molecular dynamics with NAMD on the IBM Blue Gene/L system. S. Kumar, C. Huang, G. Zheng, E. Bohm, A. Bhatele, J. C. Phillips, H. Yu, and L. V. Kale. IBM Journal of Research and Development, 2008. In press.
20. GPU computing. John D. Owens, Mike Houston, David Luebke, Simon Green, John E. Stone, and James C. Phillips. Proceedings of the IEEE, 96:879-899, 2008.
19. Detection of DNA sequences using an alternating electric field in a nanopore capacitor. G. Sigalov, J. Comer, G. Timp, and A. Aksimentiev. Nano Letters, 8:56-63, 2008.
18. Stretching and unzipping nucleic acid hairpins using a synthetic nanopore. Q. Zhao, J. Comer, S. Yemenicioglu, A. Aksimentiev, and G. Timp. Nucleic Acids Research, 36:1532-1541, 2008.
17. In meso crystal structure and computer simulations suggest an alternative proteoglycan binding site in the OpcA outer membrane adhesin. V. Cherezov, W. Liu, J. Derrick, B. Luan, A. Aksimentiev, V. Katruc, and M. Caffrey. PROTEINS: Structure, Function, and Bioinformatics, 71:24-34, 2008.
16. Exploring transmembrane transport through alpha-hemolysin with grid-steered molecular dynamics. David Wells, Volha Abramkina, and Aleksei Aksimentiev. Journal of Chemical Physics, 127:125101-125110, 2007.
15. Structure refinement of the OpcA adhesin using molecular dynamics. Binquan Luan, Martin Caffrey, and Aleksei Aksimentiev. Biophysical Journal, 93:3058-3069, 2007.
14. Substrate binding and formation of an occluded state in the leucine transporter. L. Celik, B. Schiott, and E. Tajkhorshid. Biophysical Journal, 94:1600-1612, 2008.
13. Distinct structural and adhesive roles of Ca2+ in membrane binding of blood coagulation factors. Y. Zenmei Ohkubo and Emad Tajkhorshid. Structure, 16:72-81, 2008.
12. Molecular mechanisms of conduction and selectivity in aquaporin water channels. Yi Wang and Emad Tajkhorshid. Journal of Nutrition, 137:1509S-1515S, 2007.
11. Detecting SNPs using a synthetic nanopore. Q. Zhao, G. Sigalov, V. Dimitrov, B. Dorvel, U. Mirsaidov, S. Sligar, A. Aksimentiev, and G. Timp. Nano Letters, 7:1680-1685, 2007.
10. Mechanics of force propagation in TonB-dependent outer membrane transport. James Gumbart, Michael C. Wiener, and Emad Tajkhorshid. Biophysical Journal, 93:496-504, 2007.
9. Electrical signatures of single-stranded DNA with single base mutations in a nanopore capacitor. Maria E. Gracheva, Aleksei Aksimentiev, and Jean-Pierre Leburton. Nanotechnology, 17:3160-3165, 2006.
8. Structural mechanism of plant aquaporin gating. S. Törnroth-Horsefield, Y. Wang, K. Hedfalk, U. Johanson, M. Karlsson, E. Tajkhorshid, R. Neutze, and P. Kjellbom. Nature, 439:688-694, 2006.
7. Towards theoretical analysis of long-range proton transfer kinetics in biomolecular pumps. P. H. Koenig, N. Ghosh, M. Hoffmann, M. Elstner, E. Tajkhorshid, Th. Frauenheim, and Q. Cui. Journal of Physical Chemistry A, 110:548-563, 2006.
6. Receptive field and feature map formation in the primary visual cortex via hebbian learning with inhibitory feedback. Ted Hesselroth and Klaus Schulten. arXiv:q-bio.NC/0505011v1, 2005.
5. The dynamics of image processing by feature maps in the primary visual cortex. Ted Hesselroth and Klaus Schulten. arXiv:q-bio.NC/0505010v1, 2005.
4. Classical force field parameters for the heme prosthetic group of cytochrome c. F. Autenrieth, E. Tajkhorshid, J. Baudry, and Z. Luthey-Schulten. Journal of Computational Chemistry, 25:1613-1622, 2004.
3. Molecular basis of proton blockage in aquaporins. N. Chakrabarti, E. Tajkhorshid, B. Roux, and R. Pomes. Structure, 12:65-74, 2004.
2. Developing an energy landscape for the novel function of a (b/a)8 barrel: Ammonia conduction through HisF. Rommie Amaro, Emad Tajkhorshid, and Zaida Luthey-Schulten. Proceedings of the National Academy of Sciences, USA, 100:7599-7604, 2003.
1. NAMD: Biomolecular simulation on thousands of processors. James Phillips, Gengbin Zheng, Sameer Kumar, and Laxmikant Kale. In Proceedings of the IEEE/ACM SC2002 Conference, Technical Paper 277. IEEE Press, 2002.

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