TCB Publications - Search
114. Enhancing Mn(II)-binding and manganese peroxidase activity in a designed cytochrome c peroxidase through fine-tuning secondary-sphere interactions. Parisa Hosseinzadeh, Evan N. Mirts, Thomas D. Pfister, Yi-Gui Gao, Christopher Mayne, Howard Robinson, Emad Tajkhorshid, and Yi Lu. Biochemistry, 55:1494-1502, 2016.
112. Molecular basis for differential anion binding and proton coupling in the Cl-/H+ exchanger ClC-ec1. Tao Jiang, Wei Han, Merritt Maduke, and Emad Tajkhorshid. Journal of the American Chemical Society, 138:3066-3075, 2016.
111. All the O2 consumed by Thermus thermophilus cytochrome ba3 is delivered to the active site through a long, open hydrophobic tunnel with entrances within the lipid bilayer. Paween Mahinthichaichan, Robert Gennis, and Emad Tajkhorshid. Biochemistry, 55:1265-1278, 2016.
110. Revealing an outward-facing open conformational state in a CLC Cl/H exchange transporter. Chandra M Khantwal, Sherwin J Abraham, Wei Han, Tao Jiang, Tanmay S Chavan, Ricky C Cheng, Shelley M Elvington, Corey W Liu, Irimpan I Mathews, Richard A Stein, Hassane S Mchaourab, Emad Tajkhorshid, and Merritt Maduke. eLife, pp. e11189, 2016. (PMC: PMC4769167)
109. Estrogen receptor alpha somatic mutations Y537S and D538G confer breast cancer endocrine resistance by stabilizing the activating function-2 binding conformation. Sean W Fanning, Christopher G Mayne, Venkatasubramanjan Dharmarajan, Kathryn E Carlson, Teresa A Martin, Scott J Novick, Weiyi Toy, Bradley Green, Srinivas Panchamukhi, Benita S Katzenellenbogen, Emad Tajkhorshid, Patrick R Griffin, Yang Shen, Sarat Chandarlapaty, John A Katzenellenbogen, and Geoffrey L Greene. eLife, pp. e12792, 2016. (PMC: PMC4821807)
107. Redox potential tuning through differential quinone binding in the photosynthetic reaction center of Rhodobacter sphaeroides. Josh V. Vermaas, Alexander T. Taguchi, Sergel A. Dikanov, Colin A. Wraight, and Emad Tajkhorshid. Biochemistry, 54:2104-2116, 2015. (NIHMS: 25734689)
106. Conformational dynamics of the nucleotide binding domains and the power stroke of a heterodimeric ABC transporter. Smriti Mishra, Brandy Verhalen, Richard A Stein, Po-Chao Wen, Emad Tajkhorshid, and Hassane S Mchaourab. eLife, 3:e02740, 2014. (19 pages). (PMC: PMC4046567)
105. Changing the peptide specificity of a human T-cell receptor by directed evolution. Sheena N. Smith, Yuhang Wang, Javier L. Baylon, Nishant K. Singh, Brian M. Baker, Emad Tajkhorshid, and David M. Kranz. Nature Communications, 5:5223, 2014. (13 pages). (PMC: PMC4225554)
104. Membrane-induced structural rearrangement and identification of a novel membrane anchor in Talin F2F3. Mark J. Arcario and Emad Tajkhorshid. Biophysical Journal, 107:2059-2069, November 2014. (PMC: PMC4223205)
103. Conformational heterogeneity of α-synuclein in membrane. Josh V. Vermaas and Emad Tajkhorshid. Biochimica et Biophysica Acta - Biomembranes, 1838:3107-3117, 2014. (PMC: PMC4194229)
102. Conformational dynamics at the inner gate of KcsA during activation. Raymond E Hulse, Joseph R Sachleben, Po-Chao Wen, Mahmoud Moradi, Emad Tajkhorshid, and Eduardo Perozo. Biochemistry, 53:2557-2559, 2014. (PMC: PMC4010282)
101. Mechanistic picture for conformational transition of a membrane transporter at atomic resolution. Mahmoud Moradi and Emad Tajkhorshid. Proceedings of the National Academy of Sciences, USA, 110:18916-18921, 2013. (PMC: PMC3839739)
100. Characterizing a histidine switch controlling pH-dependent conformational changes of the influenza virus hemagglutinin. Mohamad R. Kalani, Abdulvahab Moradi, Mahmoud Moradi, and Emad Tajkhorshid. Biophysical Journal, 105:993-1003, 2013. (PMC: PMC3752100)
99. On the origin of large flexibility of P-glycoprotein in the inward-facing state. Po-Chao Wen, Brandy Verhalen, Stephan Wilkens, Hassane S. Mchaourab, and Emad Tajkhorshid. Journal of Biological Chemistry, 288:19211-19220, 2013. (PMC: PMC3696692)
98. Movement of NH3 through the human urea transporter B: a new gas channel. R. Ryan Geyer, Raif Musa-Aziz, Giray Enkavi, Paween Mahinthichaichan, Emad Tajkhorshid, and Walter F. Boron. American Journal of Physiology - Renal Physiology, 304:F1447-F1457, 2013. (PMC: PMC3680674)
97. Subangstrom resolution x-ray structure details aquaporin-water interactions. Urszula Kosinska Eriksson, Gerhard Fischer, Rosmarie Friemann, Giray Enakvi, Emad Tajkhorshid, and Richard Neutze. Science, 340:1346-1349, 2013. (PMC: PMC4066176)
96. Characterizing the membrane-bound state of cytochrome P450 3A4: Structure, depth of insertion, and orientation. Javier L. Baylon, Ivan L. Lenov, Stephen G. Sligar, and Emad Tajkhorshid. Journal of the American Chemical Society, 135:8542-8551, 2013. (PMC: PMC3682445)
95. Driven metadynamics: Reconstructing equilibrium free energies from driven adaptive-bias simulations. Mahmoud Moradi and Emad Tajkhorshid. Journal of Physical Chemistry Letters, 4:1882-1887, 2013. (PMC: PMC3688312)
94. Transient formation of water-conducting states in membrane transporters. Jing Li, Saher A. Shaikh, Giray Enkavi, Po-Chao Wen, Zhijian Huang, and Emad Tajkhorshid. Proceedings of the National Academy of Sciences, USA, 110:7696-7701, 2013. (PMC: PMC3651479)
93. Visualizing functional motions of membrane transporters with molecular dynamics simulations. Saher A. Shaikh, Jing Li, Giray Enkavi, Po-Chao Wen, Zhijian Huang, and Emad Tajkhorshid. Biochemistry, 52:569-587, 2013. (PMC: PMC3560430)
92. Simulation studies of the mechanism of membrane transporters. Giray Enkavi, Jing Li, Paween Mahinthichaichan, Po-Chao Wen, Zhijian Huang, Saher A. Shaikh, and Emad Tajkhorshid. In Luca Monticelli and Emppu Salonen, editors, Biomolecular Simulations, volume 924 of Methods in Molecular Biology, pp. 361-405. Humana Press, 2013.
91. Structure and permeation mechanism of a mammalian urea transporter. Elena J Levin, Yu Cao, Giray Enkavi, Matthias Quick, Yaping Pan, Emad Tajkhorshid, and Ming Zhou. Proceedings of the National Academy of Sciences, USA, 109:11194-11199, 2012. (PMC: PMC3396522)
90. Tissue factor/factor VIIa complex: Role of the membrane surface. James H. Morrissey, Emad Tajkhorshid, Stephen G. Sligar, and Chad M. Rienstra. Thrombosis Research, 129:S8-S10, 2012. (PMC: PMC3335922)
89. Structural basis for iron piracy by pathogenic neisseria. Nicholas Noinaj, Nicole C. Easley, Muse Oke, Naoko Mizuno, James Gumbart, Evzen Boura, Ashley N. Steere, Olga Zak, Philip Aisen, Emad Tajkhorshid, Robert W. Evans, Andrew R. Gorringe, Anne B. Mason, Alasdair C. Steven, and Susan K. Buchanan. Nature, 483:53-58, 2012. (PMC: PMC3292680)
88. Molecular basis for the activation of a catalytic asparagine residue in a self-cleaving bacterial autotransporter. Travis J. Barnard, James Gumbart, Janine H. Peterson, Nicholas Noinaj, Nicole C. Easley, Nathalie Dautin, Adam J. Kuszak, Emad Tajkhorshid, Harris D. Bernstein, and Susan K. Buchanan. Journal of Molecular Biology, 415:128-142, 2012. (PMC: PMC3230255)
87. Mapping to irregular torus topologies and other techniques for petascale biomolecular simulation. James C. Phillips, Yanhua Sun, Nikhil Jain, Eric J. Bohm, and Laximant V. Kalé. In Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis, SC '14, pp. 81-91. IEEE Press, 2014. (PMC: PMC4292797)
86. Water access points and hydration pathways in CLC H+/Cl- transporters. Wei Han, Ricky C. Cheng, Merritt C. Maduke, and Emad Tajkhorshid. Proceedings of the National Academy of Sciences, USA, 111:1819-1824, 2014. (PMC: PMC3918786)
85. Adaptive multilevel splitting in molecular dynamics simulations. David Aristoff, Tony Lelièvre, Christopher G. Mayne, and Ivan Teo. ESAIM: Proceedings and Surveys, 48:215-225, 2015. (PMC: PMC4440697)
84. Unlocking the full potential of the Cray XK7 accelerator. Mark D. Klein and John E. Stone. In Cray User Group Conference. Cray, May 2014.
83. Runtime and architecture support for efficient data exchange in multi-accelerator applications. Javier Cabezas, Isaac Gelado, John E. Stone, Nacho Navarro, David B. Kirk, and Wen-mei Hwu. IEEE Transactions on Parallel and Distributed Systems, 26:1405-1418, May 2015. (PMC: PMC4500157)
82. Simulation of reaction diffusion processes over biologically relevant size and time scales using multi-GPU workstations. Michael J. Hallock, John E. Stone, Elijah Roberts, Corey Fry, and Zaida Luthey-Schulten. Parallel Computing, 40:86-99, 2014. (PMC: PMC4039640)
81. Methodologies for the analysis of instantaneous lipid diffusion in MD simulations of large membrane systems. Matthieu Chavent, Tyler Reddy, Joseph Goose, Anna Caroline E. Dahl, John E. Stone, Bruno Jobard, and Mark S.P. Sansom. Faraday Discussion, 169:455-475, 2014. (PMC: PMC4208077)
80. A microscopic view of phospholipid insertion into biological membranes. Josh V. Vermaas and Emad Tajkhorshid. Journal of Physical Chemistry B, 118:1754-1764, 2014. (PMC: PMC3933253)
79. Partitioning of amino acids into a model membrane: Capturing the interface. Taras V. Pogorelov, Josh V. Vermaas, Mark J. Arcario, and Emad Tajkhorshid. Journal of Physical Chemistry B, 118:1481-1492, 2014.
78. Lattice microbes: High-performance stochastic simulation method for the reaction-diffusion master equation. Elijah Roberts, John E. Stone, and Zaida Luthey-Schulten. Journal of Computational Chemistry, 34:245-255, 2013.
77. Optimizing fine-grained communication in a biomolecular simulation application on Cray XK6. Yanhua Sun, Gengbin Zheng, Chao Mei, Eric J. Bohm, Terry Jones, Laxmikant V. Kalé, and James C. Phillips. In Proceedings of the 2012 ACM/IEEE conference on Supercomputing, pp. 1-11, Salt Lake City, Utah, 2012. IEEE press.
76. Control of nanoscale environment to improve stability of immobilized proteins on diamond surfaces. Adarsh D. Radadia, Courtney J. Stavis, Rogan Carr, Hongjun Zeng, William P. King, John A. Carlisle, Aleksei Aksimentiev, Robert J. Hamers, and Rashid Bashir. Advanced Functional Materials, 21:1040-1050, 2011.
75. Functional interplay between acetylation and methylation of the RelA subunit of NF-kB. X.-D. Yang, E. Tajkhorshid, and L.-F. Chen. Molecular and Cellular Biology, 30:2170-2180, 2010.
74. The binding interface of cytochrome c and cytochrome c1 in the bc1 complex: rationalizing the role of key residues. O. Kokhan, C. Wraight, and E. Tajkhorshid. Biophysical Journal, 99:2647-2656, 2010.
73. The effect of calcium on the conformation of cobalamin transporter BtuB. B. Luan, M. Caffrey, and A. Aksimentiev. PROTEINS: Structure, Function, and Bioinformatics, 78:1153-1162, 2010.
72. Surface functionalization of thin-film diamond for highly stable and selective biological interfaces. C. Stavis, T. L. Clare, J. E. Butler, A. D. Radadia, R. Carr, H. Zeng, W. King, J. A. Carlisle, A. Aksimentiev, R. Bashir, and R.J. Hamers. Proceedings of the National Academy of Sciences, USA, 108:983-988, 2011.
71. Slowing the translocation of double-stranded DNA using a nanopore smaller than the double helix. U. Mirsaidov, J. Comer, V. Dimitrov, A. Aksimentiev, and G. Timp. Nanotechnology, 21:395501-10, 2010.
70. Accelerating membrane insertion of peripheral proteins with a novel membrane mimetic model. Y. Zenmei Ohkubo, Taras V. Pogorelov, Mark J. Arcario, Geoff A. Christensen, and Emad Tajkhorshid. Biophysical Journal, 102:2130-2139, 2012.
69. Nucleotide discrimination with DNA immobilized in the MspA nanopore. E. A. Manrao, I. M. Derrington, M. Pavlenok, M. Niederweis, and J. H. Gundlach. PLoS One, 6(10):e25723, 2011.
68. Nanopore analysis of individual RNA/antibiotic complexes. S. Wanunu, S. Bhattacharya, Y. Xie, Y. Tor, A. Aksimentiev, and M. Drndic. ACS Nano, 5:9345-9353, 2011.
67. Predicting the DNA sequence dependence of nanopore ion current using atomic-resolution Brownian dynamics. J. Comer and A. Aksimentiev. Journal of Physical Chemistry C, 116:3376-3393, 2012.
66. ATP hydrolysis at one of the two sites in ABC transporters initiates transport related conformational transitions. G. Gyimesi, S. Ramachandran, P. Kota, N. V. Dokholyan, B. Sarkadi, and T. Hegedus. Biochimica et Biophysica Acta, 1808:2954-2964, 2011.
65. A gate-free pathway for substrate release from the inward-facing state of the Na+-galactose transporter. Jing Li and Emad Tajkhorshid. Biochimica et Biophysica Acta - Biomembranes, 1818:263-271, 2012.
64. Membrane transporters: Molecular machines coupling cellular energy to vectorial transport across the membrane. Zhijian Huang, Saher A. Shaikh, Po-Chao Wen, Giray Enkavi, Jing Li, and Emad Tajkhorshid. In Benoit Roux, editor, Molecular Machines, chapter 9, pp. 151-182. World Scientific Publishing, Singapore, 2011.
63. Capturing spontaneous partitioning of peripheral proteins using a biphasic membrane-mimetic model. Mark J. Arcario, Y. Zenmei Ohkubo, and Emad Tajkhorshid. Journal of Physical Chemistry B, 115:7029-7037, 2011.
62. Nanoscale studies of protein-membrane interactions in blood clotting. James H. Morrissey, Emad Tajkhorshid, and Chad M. Rienstra. Journal of Thrombosis and Haemostasis, 9 (Suppl. 1):167-167, 2011. (PMC: PMC3151027)
61. Atomic view of calcium-induced clustering of phosphatidylserine in mixed lipid bilayers. John M. Boettcher, Rebecca L. Davis-Harrison, Mary C. Clay, Andrew J. Nieuwkoop, Y. Zenmei Ohkubo, Emad Tajkhorshid, James H. Morrissey, and Chad M. Rienstra. Biochemistry, 50:2264-2273, 2011. (PMC: 3069658)
60. Molecular determinants of phospholipid synergy in blood clotting. Narjes Tavoosi, Rebecca L. Davis-Harrison, Taras V. Pogorelov, Y. Zenmei Ohkubo, Mark J. Arcario, Mary C. Clay, Chad M. Rienstra, Emad Tajkhorshid, and James H. Morrissey. Journal of Biological Chemistry, 286:23247-23253, 2011. (PMC: 3123091)
59. Enabling and scaling biomolecular simulations of 100 million atoms on petascale machines with a multicore-optimized message-driven runtime. Chao Mei, Yanhua Sun, Gengbin Zheng, Eric J. Bohm, Laxmikant V. Kalé, James C. Phillips, and Chris Harrison. In Proceedings of the 2011 ACM/IEEE conference on Supercomputing, pp. 61:1-61:11, Seattle, WA, November 2011.
58. Fast analysis of molecular dynamics trajectories with graphics processing units-radial distribution function histogramming. Benjamin G. Levine, John E. Stone, and Axel Kohlmeyer. Journal of Computational Physics, 230:3556-3569, 2011. (PMC: PMC3085256)
57. Quantifying the impact of GPUs on performance and energy efficiency in HPC clusters. Jeremy Enos, Craig Steffen, Joshi Fullop, Michael Showerman, Guochun Shi, Kenneth Esler, Volodymyr Kindratenko, John E. Stone, and James C. Phillips. In International Conference on Green Computing, pp. 317-324, 2010.
56. An asymmetric distributed shared memory model for heterogeneous parallel system. Isaac Gelado, John E. Stone, Javier Cabezas, Sanjay Patel, Nacho Navarro, and Wen-mei W. Hwu. In ASPLOS '10: Proceedings of the 15th International Conference on Architectural Support for Programming Languages and Operating Systems, pp. 347-358, 2010.
55. Probing biomolecular machines with graphics processors. James C. Phillips and John E. Stone. Communications of the ACM, 52:34-41, 2009.
54. GPU clusters for high performance computing. Volodymyr Kindratenko, Jeremy Enos, Guochun Shi, Michael Showerman, Galen Arnold, John E. Stone, James Phillips, and Wen-mei Hwu. In Cluster Computing and Workshops, 2009. CLUSTER '09. IEEE International Conference on, pp. 1-8, 2009.
53. Visualization of cyclic and multi-branched molecules with VMD. Simon Cross, Michelle M. Kuttell, John E. Stone, and James E. Gain. Journal of Molecular Graphics and Modelling, 28:131-139, 2009. (NIHMS: 215013)
52. Modeling and dynamics of the inward-facing state of a Na+/Cl- dependent neurotransmitter transporter homologue. Saher Afshan Shaikh and Emad Tajkhorshid. PLoS Computational Biology, 6:e1000905, 2010. (PMC: PMC2928745)
51. Protein membrane interactions: blood clotting on nanoscale bilayer. J. H. Morrissey, V. Pureza, R. L. Davis-Harrison, S. G. Sligar, C. M. Rienstra, A. Z. Kijac, Y. Z. Ohkubo, and E. Tajkhorshid. Journal of Thrombosis and Haemostasis, 7:169-172, 2009.
50. Tyrosine phosphorylation by Src within the cavity of the adenine nucleotide translocase 1 regulates ADP/ATP exchange in mitochondria. Jianhua Feng, Eliana Lucchinetti, Giray Enkavi, Yi Wang, Peter Gehrig, Bernd Roschitzki, Marcus C. Schaub, Emad Tajkhorshid, Kathrin Zaugg, and Michael Zaugg. American Journal of Physiology, 298:C740-748, 2010. (PMC: 2838572)
49. Structural basis of substrate selectivity in the glycerol-3-phosphate:phosphate antiporter GlpT. Christopher J. Law, Giray Enkavi, Da-Neng Wang, and Emad Tajkhorshid. Biophysical Journal, 97:1346-1353, 2009.
48. Identification of the third Na+ site and the sequence of extracellular binding events in the glutamate transporter. Zhijian Huang and Emad Tajkhorshid. Biophysical Journal, 99:1416-1425, 2010. (PMC: PMC2931724)
47. OpenCL: A parallel programming standard for heterogeneous computing systems. John E. Stone, David Gohara, and Guochun Shi. Computing in Science and Engineering, 12:66-73, 2010. (PMC: 2964860)
46. Capturing functional motions of membrane channels and transporters with molecular dynamics simulation. Saher A. Shaikh, Po-Chao Wen, Giray Enkavi, Zhijian Huang, and Emad Tajkhorshid. Journal of Computational and Theoretical Nanosciences, 7:2481-2500, 2010.
45. Exploring transmembrane diffusion pathways with molecular dynamics. Yi Wang, Saher A. Shaikh, and Emad Tajkhorshid. Physiology, 25:142-154, 2010.
44. Ion-releasing state of a secondary membrane transporter. Jing Li and Emad Tajkhorshid. Biophysical Journal, 97:L29-L31, 2009.
43. Nitric oxide conduction by the brain aquaporin AQP4. Yi Wang and Emad Tajkhorshid. PROTEINS: Structure, Function, and Bioinformatics, 78:661-670, 2010.
42. Dynamical view of membrane binding and complex formation of human factor VIIa and tissue factor. Y. Zenmei Ohkubo, James H. Morrissey, and Emad Tajkhorshid. Journal of Thrombosis and Haemostasis, 8:1044-1053, 2010. (PMC: PMC2890040)
41. Interplay of mechanical and binding properties of Fibronectin type I. Jiankuai Diao, Andrew J. Maniotis, Robert Folberg, and Emad Tajkhorshid. Theoretica Chimica Acta, 125:397-405, 2010.
40. Protein-phospholipid interactions in blood clotting. James H. Morrissey, Rebecca L. Davis-Harrison, Narjes Tavoosi, Ke Ke, Vincent Pureza, John M. Boettcher, Mary C. Clay, Chad M. Rienstra, Y. Zenmei Ohkubo, Taras V. Pogorelov, and Emad Tajkhorshid. Thrombosis Research, 125(Suppl. 1):S23-S25, 2010.
39. Long time-scale simulations of in vivo diffusion using GPU hardware. Elijah Roberts, John E. Stone, Leonardo Sepulveda, Wen-mei W. Hwu, and Zaida Luthey-Schulten. In Proceedings of the IEEE International Parallel & Distributed Processing Symposium, pp. 1-8, 2009.
38. Simulation of spontaneous substrate binding revealing the binding pathway and mechanism and initial conformational response of GlpT. Giray Enkavi and Emad Tajkhorshid. Biochemistry, 49:1105-1114, 2010. (PMC: 2829668)
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. (PMC: 2775145)
36. Molecular mechanisms of active transport across the cellular membrane, chapter 10, pp. 248-286. Po-Chao Wen, Zhijian Huang, Giray Enkavi, Yi Wang, James Gumbart, and Emad Tajkhorshid. Royal Society of Chemistry, 2010.
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. (PMC: 2586561)
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. (PMC: 2586576)
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. (PMC: 2517027)
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. (PMC: 2474497)
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. Thrombosis 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. (PMC: 2426659)
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, volume 60, chapter 12, 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, 52:177-188, 2008.
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. (PMC: 2588427)
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. (PMC: 2275135)
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 α-hemolysin with grid-steered molecular dynamics. David B. Wells, Volha Abramkina, and Aleksei Aksimentiev. Journal of Chemical Physics, 127:125101, 2007.
15. Structure refinement of the OpcA adhesin using molecular dynamics. Binquan Luan, Martin Caffrey, and Aleksei Aksimentiev. Biophysical Journal, 93:3058-3069, 2007. (PMC: 2025660)
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