|
| |
| |
| 153. Modulation of molecular flux using a graphene nanopore capacitor.
Manish Shankla and Aleksei Aksimentiev.
Journal of Physical Chemistry B, 121:3724-3733, 2016.
|
| |
| |
| |
| |
| |
| |
| |
| |
| |
| 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.
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| 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.
|
