TCB Publications - Search
143. Large-conductance transmembrane porin made from DNA origami. Kerstin Göpfrich, Chen-Yu Li, Maria Ricci, Satya Prathyusha Bhamidimarri, Jejoong Yoo, Bertalan Gyenes, Alexander Ohmann, Mathias Winterhalter, Aleksei Aksimentiev, and Ulrich F. Keyser. ACS Nano, 10:8207-8214, 2016.
142. Ion channels made from a single membrane-spanning DNA duplex. Kerstin Göpfrich, Chen-Yu Li, Iwona Mames, Satya Prathyusha Bhamidimarri, Maria Ricci, Jejoong Yoo, Adam Mames, Alexander Ohmann, Mathias Winterhalter, Eugen Stulz, Aleksei Aksimentiev, and Ulrich F. Keyser. Nano Letters, 16:4665-4669, 2016. (PMC: PMC4948918)
141. Mechanical properties of a complete microtubule revealed through molecular dynamics simulation. David B. Wells and Aleksei Aksimentiev. Biophysical Journal, 99:629-637, 2010. (PMC: PMC2905083)
140. Microscopic perspective on the adsorption isotherm of a heterogeneous surface. Rogan Carr, Jeffrey Comer, Mark D. Ginsberg, and Aleksei Aksimentiev. Journal of Physical Chemistry Letters, 2:1804-1807, 2011. (PMC: PMC3353733)
139. Noise contributions in an inducible genetic switch: a whole-cell simulation study. Elijah Roberts, Andrew Magis, Julio O Ortiz, Wolfgang Baumeister, and Zaida Luthey-Schulten. PLoS Computational Biology, 7:e1002010, 2011. (PMC: PMC3053318)
137. Heterogeneity in protein expression induces metabolic variability in a modeled Escherichia coli population. Piyush Labhsetwar, John Andrew Cole, Elijah Roberts, Nathan D Price, and Zaida A Luthey-Schulten. Proceedings of the National Academy of Sciences, USA, 110:14006-14011, 2013. (PMC: PMC3752265)
136. Towards a whole-cell model of ribosome biogenesis: Kinetic modeling of SSU assembly. Tyler M Earnest, Jonathan Lai, Ke Chen, Michael J Hallock, James R Williamson, and Zaida Luthey-Schulten. Biophysical Journal, 109:1117-1135, 2015. (DNA P41). (PMC: PMC4576174)
135. Spatially-resolved metabolic cooperativity within dense bacterial colonies. John A Cole, Lars Kohler, Jamila Hedhli, and Zaida Luthey-Schulten. BMC Systems Biology, 9:15, 2015. (PMC: PMC4376365)
134. Computational characterization of structural dynamics underlying function in active membrane transporters. Jing Li, Po-Chao Wen, Mahmoud Moradi, and Emad Tajkhorshid. Current Opinion in Structural Biology, 31:96-105, 2015. (PMC: PMC4476910)
132. End-to-end attraction of duplex DNA. Christopher Maffeo, Binquan Luan, and Aleksei Aksimentiev. Nucleic Acids Research, 40:3812-3821, 2012. (PMC: PMC3351176)
131. Improved parametrization of Li+, Na+, K+, and Mg2+. J. Yoo and A. Aksimentiev. Journal of Physical Chemistry Letters, 3:45-50, 2012.
130. A coarse-grained model of unstructured single-stranded DNA derived from atomistic simulation and single-molecule experiment. Christopher Maffeo, Thuy T. M. Ngo, Taekjip Ha, and Aleksei Aksimentiev. Journal of Chemical Theory and Computation, 10:2891-2896, 2014. (PMC: PMC4132850)
129. DNA-DNA interactions in tight supercoils are described by a small effective charge density. Christopher Maffeo, Robert Schöpflin, Hergen Brutzer, René Stehr, Aleksei Aksimentiev, Gero Wedemann, and Ralf Seidel. Physical Review Letters, 105:158101, 2010. (PMC: PMC3170404)
128. Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation. Jejoong Yoo, Hajin Kim, Aleksei Aksimentiev, and Taekjip Ha. Nature Communications, 7:11045, 2016. (PMC: PMC4804163)
127. The structure and intermolecular forces of DNA condensates. Jejoong Yoo and Aleksei Aksimentiev. Nucleic Acids Research, 44:2036-2046, 2016. (PMC: PMC4797306)
126. Improved parameterization of amine-carboxylate and amine-phosphate interactions for molecular dynamics simulations using the CHARMM and AMBER force fields. Jejoong Yoo and Aleksei Aksimentiev. Journal of Chemical Theory and Computation, 12:430-443, 2016.
125. Molecular architecture of the retroviral capsid. Juan R Perilla and Angela M Gronenborn. Trends in Biochemical Sciences, 2016. (PMC: PMC4879823)
124. Towards a computational model of a methane producing archaeum. Joseph R Peterson, Piyush Labhsetwar, Jeremy R Ellermeier, Petra R A Kohler, Ankur Jain, Taekjip Ha, William W Metcalf, and Zaida Luthey-Schulten. Archaea, 2014, 2014. (18 pages). (PMC: PMC3960522)
122. In situ structure and dynamics of DNA origami determined through molecular dynamics simulations. Jejoong Yoo and Aleksei Aksimentiev. Proceedings of the National Academy of Sciences, USA, 110:20099-20104, 2013. (PMC: PMC3864285)
121. Ionic conductivity, structural deformation, and programmable anisotropy of DNA origami in electric field. Chen-Yu Li, Elisa A. Hemmig, Jinglin Kong, Jejoong Yoo, Silvia Hernández-Ainsa, Ulrich F. Keyser, and Aleksei Aksimentiev. ACS Nano, 9:1420-1433, 2015. PMID: 25623807. (PMC: PMC4469488)
120. Molecular dynamics of membrane-spanning DNA channels: Conductance mechanism, electro-osmotic transport and mechanical gating. Jejoong Yoo and Aleksei Aksimentiev. Journal of Physical Chemistry Letters, 6:4680-4687, 2015. (NIHMS: PMID26551518)
119. Computational recipe for efficient description of large-scale conformational changes in biomolecular systems. Mahmoud Moradi and Emad Tajkhorshid. Journal of Chemical Theory and Computation, 10:2866-2880, 2014. (PMC: PMC4089915)
118. Atomic-level characterization of transport cycle thermodynamics in the glycerol-3-phosphate:phosphate transporter. Mahmoud Moradi, Giray Enkavi, and Emad Tajkhorshid. Nature Communications, 6:8393, 2015. (PMC: PMC4598623)
117. Incorporation of charged residues in the CYP2J2 FG loop disrupts CYP2J2-lipid bilayer interactions. Daniel R McDougle, Javier L Baylon, Daryl D Meling, Amogh Kambalyal, Yelena V Grinkova, Jared Hammernik, Emad Tajkhorshid, and Aditi Das. Biochimica et Biophysica Acta - Biomembranes, 1848:2460-2470, 2015. (PMC: PMC4559526)
116. Mechanism of drug-drug interactions mediated by human cytochrome P450 CYP3A4 monomer. Ilia G. Denisov, Yelena V. Grinkova, Javier L. Baylon, Emad Tajkhorshid, and Stephen G. Sligar. Biochemistry, 54:2227-2239, 2015. (PMC: PMC4757451)
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 Enkavi, 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)
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