|
| 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, Salt Lake City, Utah, 2012. IEEE press.
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| 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.
A. 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.
(NIHMS: 290918) |
| 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, 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.
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| 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.
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| 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(8):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.
2010.
In press.
(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.
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, chapter 10, pp. 248-286.
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, 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.
(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 alpha-hemolysin with
grid-steered molecular dynamics.
David Wells, Volha Abramkina, and Aleksei Aksimentiev.
Journal of Chemical Physics, 127:125101-125101-10, 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) |
| 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.
(PMC: 2242742) |
| 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.
(PMC: 2565804) |
| |
| 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.
(PMC: 2728601) |
| 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.
|
| |
| 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
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