D. E. Shaw Research

Selected Publications

2014

Stefano Piana, John L. Klepeis, and David E. Shaw, "Assessing the Accuracy of Physical Models Used in Protein-Folding Simulations: Quantitative Evidence from Long Molecular Dynamics Simulations," Current Opinion in Structural Biology, vol. 24, 2014, pp. 98–105. Text

2013

Daniele P. Scarpazza, Douglas J. Ierardi, Adam K. Lerer, Kenneth M. Mackenzie, Albert C. Pan, Joseph A. Bank, Edmond Chow, Ron O. Dror, J.P. Grossman, Daniel Killebrew, Mark A. Moraes, Cristian Predescu, John K. Salmon, and David E. Shaw, "Extending the Generality of Molecular Dynamics Simulations on a Special-Purpose Machine," Proceedings of the 27th IEEE International Parallel and Distributed Processing Symposium (IPDPS '13), Boston, MA: IEEE Computer Society, 2013, pp. 933–945. Text
Best Paper Award, Applications Track.

Ron O. Dror, Hillary F. Green, Celine Valant, David W. Borhani, James R. Valcourt, Albert C. Pan, Daniel H. Arlow, Meritxell Canals, J. Robert Lane, Raphaël Rahmani, Jonathan B. Baell, Patrick M. Sexton, Arthur Christopoulos, and David E. Shaw, "Structural Basis for Modulation of a G-Protein-Coupled Receptor by Allosteric Drugs," Nature, vol. 503, no. 7475, 2013, pp. 295–299. Text

Ross A. Lippert, Cristian Predescu, Douglas J. Ierardi, Kenneth M. Mackenzie, Michael P. Eastwood, Ron O. Dror, and David E. Shaw, "Accurate and Efficient Integration for Molecular Dynamics Simulations at Constant Temperature and Pressure," Journal of Chemical Physics, vol. 139, no. 16, 2013, pp. 164106:1–11. Text

Anton Arkhipov, Yibing Shan, Rahul Das, Nicholas F. Endres, Michael P. Eastwood, David E. Wemmer, John Kuriyan, and David E. Shaw, "Architecture and Membrane Interactions of the EGF Receptor," Cell, vol. 152, no. 3, 2013, pp. 557–569. Text

Nicholas F. Endres, Rahul Das, Adam W. Smith, Anton Arkhipov, Erika Kovacs, Yongjian Huang, Jeffrey G. Pelton, Yibing Shan, David E. Shaw, David E. Wemmer, Jay T. Groves, and John Kuriyan, "Conformational Coupling across the Plasma Membrane in Activation of the EGF Receptor," Cell, vol. 152, no. 3, 2013, pp. 543–556. Text

J.P. Grossman, Brian Towles, Joseph A. Bank, and David E. Shaw, "The Role of Cascade, a Cycle-Based Simulation Infrastructure, in Designing the Anton Special-Purpose Supercomputers," Proceedings of the 50th Annual Design Automation Conference (DAC '13), Austin, TX, June 2–6, 2013. Text

J.P. Grossman, Jeffrey S. Kuskin, Joseph A. Bank, Michael Theobald, Ron O. Dror, Douglas J. Ierardi, Richard H. Larson, U. Ben Schafer, Brian Towles, Cliff Young, and David E. Shaw, "Hardware Support for Fine-Grained Event-Driven Computation in Anton 2," Proceedings of the Eighteenth International Conference on Architectural Support for Programming Languages and Operating Systems (ASPLOS '13), New York: NY: ACM, 2013, pp. 549–560. Text

Stefano Piana, Kresten Lindorff-Larsen, and David E. Shaw, "Atomistic Description of the Folding of a Dimeric Protein," The Journal of Physical Chemistry B, vol. 117, no. 42, 2013, pp. 12935–12942. Text

Anton Arkhipov, Yibing Shan, Eric T. Kim, Ron O. Dror, and David E. Shaw, "Her2 Activation Mechanism Reflects Evolutionary Preservation of Asymmetric Ectodomain Dimers in the Human EGFR Family," eLife, vol. 2, 2013, pp. e00708. Text

Yibing Shan, Anton Arkhipov, Eric T. Kim, Albert C. Pan, and David E. Shaw, "Transitions to Catalytically Inactive Conformations in EGFR Kinase," Proceedings of the National Academy of Sciences of the United States of America, vol. 110, no. 18, 2013, pp. 7270–7275. Text

Rie Nygaard, Yaozhong Zou, Ron O. Dror, Thomas J. Mildorf, Daniel H. Arlow, Aashish Manglik, Albert C. Pan, Corey W. Liu, Juan Jose Fung, Michael P. Bokoch, Foon Sun Thian, Tong Sun Kobilka, David E. Shaw, Luciano Mueller, R. Scott Prosser, and Brian K. Kobilka, "The Dynamic Process of β2-Adrenergic Receptor Activation," Cell, vol. 152, no. 3, 2013, pp. 532–542. Text

Morten Ø. Jensen, Vishwanath Jogini, Michael P. Eastwood, and David E. Shaw, "Atomic-Level Simulation of Current–Voltage Relationships in Single-File Ion Channels," The Journal of General Physiology, vol. 141, no. 5, 2013, pp. 619–632. Text

Aaron G. Schmidt, Huafeng Xu, Amir R. Khana, Timothy O’Donnell, Surender Khurana, Lisa R. King, Jody Manischewitz, Hana Golding, Pirada Suphaphiphat, Andrea Carfi, Ethan C. Settembre, Philip R. Dormitzer, Thomas B. Kepler, Ruijun Zhang, M. Anthony Moody, Barton F. Haynes, Hua-Xin Liao, David E. Shaw, and Stephen C. Harrison, "Preconfiguration of the Antigen-Binding Site During Affinity Maturation of a Broadly Neutralizing Influenza Virus Antibody," Proceedings of the National Academy of Sciences of the United States of America, vol. 110, no. 1, 2013, pp. 264–269. Text

Albert C. Pan, David W. Borhani, Ron O. Dror, and David E.  Shaw, "Molecular Determinants of Drug–Receptor Binding Kinetics," Drug Discovery Today, vol. 18, no. 13–14, 2013, pp. 667–673. Text

Stefano Piana, Kresten Lindorff-Larsen, and David E. Shaw, "Atomic-Level Description of Ubiquitin Folding," Proceedings of the National Academy of Sciences of the United States of America, vol. 110, no. 15, 2013, pp. 5915–5920. Text

Michael P. Eastwood, Tarun Chitra, John M. Jumper, Kim Palmo, Albert C. Pan, and David E. Shaw, "Rotational Relaxation in ortho-Terphenyl: Using Atomistic Simulations to Bridge Theory and Experiment," The Journal of Physical Chemistry B, vol. 117, no. 42, 2013, pp. 12898–12907. Text

Tae Hun Kim, Ka Young Chung, Aashish Manglik, Alexandar L. Hansen, Ron O. Dror, Thomas J. Mildorf, David E. Shaw, Brian K. Kobilka, and R. Scott Prosser, "The Role of Ligands on the Equilibria Between Functional States of a G Protein-Coupled Receptor," Journal of the American Chemical Society, vol. 135, no. 25, 2013, pp. 9465–9474. Text

2012

Morten Ø. Jensen, Vishwanath Jogini, David W. Borhani, Abba E. Leffler, Ron O. Dror, and David E. Shaw, "Mechanism of Voltage Gating in Potassium Channels," Science, vol. 336, no. 6078, 2012, pp. 229–233. Text

Yibing Shan, Michael P. Eastwood, Xuewu Zhang, Eric T. Kim, Anton Arkhipov, Ron O. Dror, John Jumper, John Kuriyan, and David E. Shaw, "Oncogenic Mutations Counteract Intrinsic Disorder in the EGFR Kinase and Promote Receptor Dimerization," Cell, vol. 149, no. 4, 2012, pp. 860–870. Text

Stefano Piana, Kresten Lindorff-Larsen, and David E. Shaw, "Protein Folding Kinetics and Thermodynamics from Atomistic Simulation," Proceedings of the National Academy of Sciences of the United States of America, vol. 109, no. 44, 2012, pp. 17845–17850. Text

Cheng Zhang, Yoga Srinivasan, Daniel H. Arlow, Juan Jose Fung, Daniel Palmer, Yaowu Zheng, Hillary F. Green, Anjali Pandey, Ron O. Dror, David E. Shaw, William I. Weis, Shaun R. Coughlin, and Brian K. Kobilka, "High-Resolution Crystal Structure of Human Protease-Activated Receptor 1," Nature, vol. 492, no. 7429, 2012, pp. 387–392. Text

Stefano Piana, Kresten Lindorff-Larsen, Robert M. Dirks, John K. Salmon, Ron O. Dror, and David E. Shaw, "Evaluating the Effects of Cutoffs and Treatment of Long-range Electrostatics in Protein Folding Simulations," PLoS ONE, vol. 7, no. 6, 2012, pp. e39918. Text

Cristian Predescu, Ross A. Lippert, Michael P. Eastwood, Douglas Ierardi, Huafeng Xu, Morten Ø. Jensen, Kevin J. Bowers, Justin Gullingsrud, Charles A. Rendleman, Ron O. Dror, and David E. Shaw, "Computationally Efficient Molecular Dynamics Integrators with Improved Sampling Accuracy," Molecular Physics, vol. 110, no. 9–10, 2012, pp. 967–983. Text

Kresten Lindorff-Larsen, Nikola Trbovic, Paul Maragakis, Stefano Piana, and David E. Shaw, "Structure and Dynamics of an Unfolded Protein Examined by Molecular Dynamics Simulation," Journal of the American Chemical Society, vol. 336, no. 8, 2012, pp. 3787–3791. Text

Alpan Raval, Stefano Piana, Michael P. Eastwood, Ron O. Dror, and David E. Shaw, "Refinement of Protein Structure Homology Models via Long, All-Atom Molecular Dynamics Simulations," Proteins: Structure, Function, and Bioinformatics, vol. 80, no. 8, 2012, pp. 2071–2079. Text

Kresten Lindorff-Larsen, Paul Maragakis, Stefano Piana, Michael P. Eastwood, Ron O. Dror, and David E. Shaw, "Systematic Validation of Protein Force Fields against Experimental Data," PLoS ONE, vol. 7, no. 2, 2012, pp. e32131. Text

Robert M. Dirks, Huafeng Xu, and David E. Shaw, "Improving Sampling by Exchanging Hamiltonians with Efficiently Configured Nonequilibrium Simulations," Journal of Chemical Theory and Computation, vol. 8, no. 1, 2012, pp. 162–171. Text

Ron O. Dror, Robert M. Dirks, J.P. Grossman, Huafeng Xu, and David E. Shaw, "Biomolecular Simulation: A Computational Microscope for Molecular Biology," Annual Review of Biophysics, vol. 41, 2012, pp. 429–452. Text

Andrew C. Kruse, Jianxin Hu, Albert C. Pan, Daniel H. Arlow, Daniel M. Rosenbaum, Erica Rosemond, Hillary F. Green, Tong Liu, Pil Seok Chae, Ron O. Dror, David E. Shaw, William I. Weis, Jürgen Wess, and Brian K. Kobilka, "Structure and Dynamics of the M3 Muscarinic Acetylcholine Receptor," Nature, vol. 482, no. 7386, 2012, pp. 552–556. Text

Moon Hee Yang, Seth Nickerson, Eric T. Kim, Caroline Liot, Gaelle Laurent, Robert Spang, Mark R. Philips, Yibing Shan, David E. Shaw, Dafna Bar-Sagi, Marcia C. Haigis, and Kevin M. Haigis, "Regulation of RAS Oncogenicity by Acetylation," Proceedings of the National Academy of Sciences of the United States of America, vol. 109, no. 27, 2012, pp. 10843–10848. Text

Edmond Chow, John L. Klepeis, Charles A. Rendleman, Ron O. Dror, and David E. Shaw, "New Technologies for Molecular Dynamics Simulations," in Comprehensive Biophysics, Elsevier: Amsterdam, NL, vol. 9, 2012, pp. 86–104. Text

Rajintha M. Bandaranayake, Daniela Ungureanu, Yibing Shan, David E. Shaw, Olli Silvennoinen, and Stevan R. Hubbard, "Crystal Structures of the JAK2 Pseudokinase Domain and the Pathogenic Mutant V617F," Nature Structural & Molecular Biology, vol. 19, no. 8, 2012, pp. 754–759. Text

2011

Kresten Lindorff-Larsen, Stefano Piana, Ron O. Dror, and David E. Shaw, "How Fast-Folding Proteins Fold," Science, vol. 334, no. 6055, 2011, pp. 517–520. Text

John K. Salmon, Mark A. Moraes, Ron O. Dror, and David E. Shaw, "Parallel Random Numbers: As Easy as 1, 2, 3," Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC11), New York, NY: ACM, 2011. Text
Best Paper Award.

Ron O. Dror, Daniel H. Arlow, Paul Maragakis, Thomas J. Mildorf, Albert C. Pan, Huafeng Xu, David W. Borhani, and David E. Shaw, "Activation Mechanism of the β2-Adrenergic Receptor," Proceedings of the National Academy of Sciences of the United States of America, vol. 108, no. 46, 2011, pp. 18684–18689. Text

Ron O. Dror, Albert C. Pan, Daniel H. Arlow, David W. Borhani, Paul Maragakis, Yibing Shan, Huafeng Xu, and David E. Shaw, "Pathway and Mechanism of Drug Binding to G-Protein-Coupled Receptors," Proceedings of the National Academy of Sciences of the United States of America, vol. 108, no. 32, 2011, pp. 13118–13123. Text

Yibing Shan, Eric T. Kim, Michael P. Eastwood, Ron O. Dror, Markus A. Seeliger, and David E. Shaw, "How Does a Drug Molecule Find Its Target Binding Site?" Journal of the American Chemical Society, vol. 133, no. 24, 2011, pp. 9181–9183. Text

Ron O. Dror, Cliff Young, and David E. Shaw, "Anton, a Special-Purpose Molecular Simulation Machine," Encyclopedia of Parallel Computing, New York: Springer, 2011, pp. 60–71. Text

Stefano Piana, Kresten Lindorff-Larsen, and David E. Shaw, "How Robust Are Protein Folding Simulations with Respect to Force Field Parameterization?" Biophysical Journal, vol. 100, no. 9, 2011, pp. L47–L49. Text

J. Adam Butts, Ping Tak Peter Tang, Ron O. Dror, and David E. Shaw, "Radix-8 Digit-by-Rounding: Achieving High-Performance Reciprocals, Square Roots, and Reciprocal Square Roots," Proceedings of the 20th IEEE Symposium on Computer Arithmetic 2011 (ARITH20), Tübingen, Germany: IEEE Computer Society, 2011, pp. 149–158. Text

Ping Tak Peter Tang, J. Adam Butts, Ron O. Dror, and David E. Shaw, "Tight Certification Techniques for Digit-by-Rounding Algorithms with Application to a New 1/√x Design," Proceedings of the 20th IEEE Symposium on Computer Arithmetic 2011 (ARITH20), Tübingen, Germany: IEEE Computer Society, 2011, pp. 159–168. Text

Ron O. Dror,  J.P. Grossman, Kenneth M. Mackenzie, Brian Towles, Edmond Chow, John K. Salmon, Cliff Young, Joseph A. Bank, Brannon Batson, Martin M. Deneroff, Jeffrey S. Kuskin, Richard H. Larson, Mark A. Moraes, and David E. Shaw, "Overcoming Communication Latency Barriers in Massively Parallel Scientific Computation," IEEE Micro, vol. 31, no. 3, 2011, pp. 8–19. Text

Daniel M. Rosenbaum, Cheng Zhang, Joseph A. Lyons, Ralph Holl, David Aragao, Daniel H. Arlow, Søren G. F. Rasmussen, Hee-Jung Choi, Brian T. DeVree, Roger K. Sunahara, Pil Seok Chae, Samuel H. Gellman, Ron O. Dror, David E. Shaw, William I. Weis, Martin Caffrey, Peter Gmeiner, and Brian K. Kobilka, "Structure and Function of an Irreversible Agonist-β2 Adrenoceptor Complex," Nature, vol. 469, no. 7329, 2011, pp. 236–240. Text

Stefano Piana, Krishnarjun Sarkar, Kresten Lindorff-Larsen, Minghao Guo, Martin Gruebele, and David E. Shaw, "Computational Design and Experimental Testing of the Fastest-Folding β-Sheet Protein," Journal of Molecular Biology, vol. 405, no. 1, 2011, pp. 43–48. Text

Ron O. Dror, Albert C. Pan, Daniel H. Arlow, and David E. Shaw, "Probing the Conformational Dynamics of GPCRs with Molecular Dynamics Simulation," in G Protein–Coupled Receptors: From Structure to Function, RSC: Cambridge, UK, 2011, pp. 384–400. Text

2010

David E. Shaw, Paul Maragakis, Kresten Lindorff-Larsen, Stefano Piana, Ron O. Dror, Michael P. Eastwood, Joseph A. Bank, John M. Jumper, John K. Salmon, Yibing Shan, and Willy Wriggers, "Atomic-Level Characterization of the Structural Dynamics of Proteins," Science, vol. 330, no. 6002, 2010, pp. 341–346. Text

Morten Ø. Jensen, David W. Borhani, Kresten Lindorff-Larsen, Paul Maragakis, Vishwanath Jogini, Michael P. Eastwood, Ron O. Dror, and David E. Shaw, "Principles of Conduction and Hydrophobic Gating in K+ Channels," Proceedings of the National Academy of Sciences of the United States of America, vol. 107, no. 13, 2010, pp. 5833–5838. Text

Ron O. Dror, J.P. Grossman, Kenneth M. Mackenzie, Brian Towles, Edmond Chow, John K. Salmon, Cliff Young, Joseph A. Bank, Brannon Batson, Martin M. Deneroff, Jeffrey S. Kuskin, Richard H. Larson, Mark A. Moraes, and David E. Shaw, "Exploiting 162-Nanosecond End-to-End Communication Latency on Anton," Proceedings of the Conference for High Performance Computing, Networking, Storage and Analysis (SC10), New York, NY: IEEE, 2010. Text
Best Paper Award Finalist.

Ron O. Dror, Morten Ø. Jensen, David W. Borhani, and David E. Shaw, "Exploring Atomic Resolution Physiology on a Femtosecond to Millisecond Timescale Using Molecular Dynamics Simulations," The Journal of General Physiology, vol. 135, no. 6, 2010, pp. 555–562. Text

Michael P. Eastwood, Kate A. Stafford, Ross A. Lippert, Morten Ø. Jensen, Paul Maragakis, Cristian Predescu, Ron O. Dror, and David E. Shaw, "Equipartition and the Calculation of Temperature in Biomolecular Simulations," Journal of Chemical Theory and Computation, vol. 6, no. 7, 2010, pp. 2045–2058. Text

Kresten Lindorff-Larsen, Stefano Piana, Kim Palmo, Paul Maragakis, John L. Klepeis, Ron O. Dror, and David E. Shaw, "Improved Side-Chain Torsion Potentials for the Amber ff99SB Protein Force Field," Proteins: Structure, Function, and Bioinformatics, vol. 78, no. 8, 2010, pp. 1950–1958. Text

Tiankai Tu, Charles A. Rendleman, Patrick J. Miller, Federico Sacerdoti, Ron O. Dror, and David E. Shaw, "Accelerating Parallel Analysis of Scientific Simulation Data via Zazen," Proceedings of the 8th USENIX Conference on File and Storage Technologies (FAST '10), Berkeley, CA: USENIX Association, 2010. Text

Kevin J. Bowers, Ross A. Lippert, Ron O. Dror, and David E. Shaw, "Improved Twiddle Access for Fast Fourier Transforms," IEEE Transactions on Signal Processing, vol. 58, no. 3, 2010, pp. 1122–1130. Text

2009

David E. Shaw, Ron O. Dror, John K. Salmon, J.P. Grossman, Kenneth M. Mackenzie, Joseph A. Bank, Cliff Young, Martin M. Deneroff, Brannon Batson, Kevin J. Bowers, Edmond Chow, Michael P. Eastwood, Douglas J. Ierardi, John L. Klepeis, Jeffrey S. Kuskin, Richard H. Larson, Kresten Lindorff-Larsen, Paul Maragakis, Mark A. Moraes, Stefano Piana, Yibing Shan, and Brian Towles, "Millisecond-Scale Molecular Dynamics Simulations on Anton," Proceedings of the Conference on High Performance Computing, Networking, Storage and Analysis (SC09), New York, NY: ACM, 2009. Text
Gordon Bell Prize; Best Paper Award.

Ron O. Dror, Daniel H. Arlow, David W. Borhani, Morten Ø. Jensen, Stefano Piana, and David E. Shaw, "Identification of Two Distinct Inactive Conformations of the β2-Adrenergic Receptor Reconciles Structural and Biochemical Observations," Proceedings of the National Academy of Sciences of the United States of America, vol. 106, no. 12, 2009, pp. 4689–4694. Text

Yibing Shan, Markus A. Seeliger, Michael P. Eastwood, Filipp Frank, Huafeng Xu, Morten Ø. Jensen, Ron O. Dror, John Kuriyan, and David E. Shaw, "A Conserved Protonation-Dependent Switch Controls Drug Binding in the Abl Kinase," Proceedings of the National Academy of Sciences of the United States of America, vol. 106, no. 1, 2009, pp. 139–144. Text

Daniel K. Shenfeld, Huafeng Xu, Michael P. Eastwood, Ron O. Dror, and David E. Shaw, "Minimizing Thermodynamic Length to Select Intermediate States for Free-Energy Calculations and Replica-Exchange Simulations," Physical Review E, vol. 80, no. 4, 2009, pp. 046705-1–046705-4. Text

Markus A. Seeliger, Pratistha Ranjitkar, Corynn Kasap, Yibing Shan, David E. Shaw, Neil P. Shah, John Kuriyan, and Dustin J. Maly, "Equally Potent Inhibition of c-Src and Abl by Compounds that Recognize Inactive Kinase Conformations," Cancer Research, vol. 69, no. 6, 2009, pp. 2384–2392. Text

Cliff Young, Joseph A. Bank, Ron O. Dror, J.P. Grossman, John K. Salmon, and David E. Shaw, "A 32×32×32, Spatially Distributed 3D FFT in Four Microseconds on Anton," Proceedings of the Conference on High Performance Computing, Networking, Storage and Analysis (SC09), New York, NY: ACM, 2009. Text

C. Richard Ho, Michael Theobald, Brannon Batson, J.P. Grossman, Stanley C. Wang, Joseph Gagliardo, Martin M. Deneroff, Ron O. Dror, and David E. Shaw, "Post-Silicon Debug Using Formal Verification Waypoints," Proceedings of the Design and Verification Conference and Exhibition (DVCon '09), San Jose, California, February 24–26, 2009. Text

John L. Klepeis, Kresten Lindorff-Larsen, Ron O. Dror, and David E. Shaw, "Long-Timescale Molecular Dynamics Simulations of Protein Structure and Function," Current Opinion in Structural Biology, vol. 19, 2009, pp. 1–18. Text

Willy Wriggers, Kate A. Stafford, Yibing Shan, Stefano Piana, Paul Maragakis, Kresten Lindorff-Larsen, Patrick J. Miller, Justin Gullingsrud, Charles A. Rendleman, Michael P. Eastwood, Ron O. Dror, and David E. Shaw, "Automated Event Detection and Activity Monitoring in Long Molecular Dynamics Simulations," Journal of Chemical Theory and Computation, vol. 5, no. 10, 2009, pp. 2595–2605. Text

2008

Morten Ø. Jensen, Ron O. Dror, Huafeng Xu, David W. Borhani, Isaiah T. Arkin, Michael P. Eastwood, and David E. Shaw, "Dynamic Control of Slow Water Transport by Aquaporin 0: Implications for Hydration and Junction Stability in the Eye Lens," Proceedings of the National Academy of Sciences of the United States of America, vol. 105, no. 38, 2008, pp. 14430–14435. Text

Paul Maragakis, Kresten Lindorff-Larsen, Michael P. Eastwood, Ron O. Dror, John L. Klepeis, Isaiah T. Arkin, Morten Ø. Jensen, Huafeng Xu, Nikola Trbovic, Richard A. Friesner, Arthur G. Palmer III, and David E. Shaw, "Microsecond Molecular Dynamics Simulation Shows Effect of Slow Loop Dynamics on Backbone Amide Order Parameters of Proteins," Journal of Physical Chemistry B, vol. 112, no. 19, 2008, pp. 6155–6158. Text

David E. Shaw, Martin M. Deneroff, Ron O. Dror, Jeffrey S. Kuskin, Richard H. Larson, John K. Salmon, Cliff Young, Brannon Batson, Kevin J. Bowers, Jack C. Chao, Michael P. Eastwood, Joseph Gagliardo, J.P. Grossman, C. Richard Ho, Douglas J. Ierardi, István Kolossváry, John L. Klepeis, Timothy Layman, Christine McLeavey, Mark A. Moraes, Rolf Mueller, Edward C. Priest, Yibing Shan, Jochen Spengler, Michael Theobald, Brian Towles, and Stanley C. Wang, "Anton, A Special-Purpose Machine for Molecular Dynamics Simulation," Communications of the ACM, vol. 51, no. 7, 2008, pp. 91–97. Text

Tiankai Tu, Charles A. Rendleman, David W. Borhani, Ron O. Dror, Justin Gullingsrud, Morten Ø. Jensen, John L. Klepeis, Paul Maragakis, Patrick Miller, Kate A. Stafford, and David E. Shaw, "A Scalable Parallel Framework for Analyzing Terascale Molecular Dynamics Simulation Trajectories," Proceedings of the ACM/IEEE Conference on Supercomputing (SC08), New York, NY: IEEE, 2008. Text
Best Paper Award Finalist.

Jeffrey S. Kuskin, Cliff Young, J.P. Grossman, Brannon Batson, Martin M. Deneroff, Ron O. Dror, and David E. Shaw, "Incorporating Flexibility in Anton, a Specialized Machine for Molecular Dynamics Simulation," Proceedings of the 14th Annual International Symposium on High-Performance Computer Architecture (HPCA '08), New York, NY: IEEE, 2008. Text

Richard H. Larson, John K. Salmon, Ron O. Dror, Martin M. Deneroff, Cliff Young, J.P. Grossman, Yibing Shan, John L. Klepeis, and David E. Shaw, "High-Throughput Pairwise Point Interactions in Anton, a Specialized Machine for Molecular Dynamics Simulation," Proceedings of the 14th Annual International Symposium on High-Performance Computer Architecture (HPCA '08), New York, NY: IEEE, 2008. Text

J.P. Grossman, John K. Salmon, C. Richard Ho, Douglas J. Ierardi, Brian Towles, Brannon Batson, Jochen Spengler, Stanley C. Wang, Rolf Mueller, Michael Theobald, Cliff Young, Joseph Gagliardo, Martin M. Deneroff, Ron O. Dror, and David E. Shaw, "Hierarchical Simulation-Based Verification of Anton, a Special-Purpose Parallel Machine," Proceedings of the 26th IEEE International Conference on Computer Design (ICCD '08), New York, NY: IEEE, 2008. Text

C. Richard Ho, Michael Theobald, Martin M. Deneroff, Ron O. Dror, Joseph Gagliardo, and David E. Shaw, "Early Formal Verification of Conditional Coverage Points to Identify Intrinsically Hard-to-Verify Logic," Proceedings of the 45th Annual Design Automation Conference (DAC '08), Anaheim, California, June 9–13, 2008. Text

J.P. Grossman, Cliff Young, Joseph A. Bank, Kenneth Mackenzie, Douglas J. Ierardi, John K. Salmon, Ron O. Dror, and David E. Shaw, "Simulation and Embedded Software Development for Anton, a Parallel Machine with Heterogeneous Multicore ASICs," Proceedings of the 6th IEEE/ACM/IFIP International Conference on Hardware/Software Codesign and System Synthesis (CODES/ISSS '08), New York, NY: ACM, 2008. Text

2007

Isaiah T. Arkin, Huafeng Xu, Morten Ø. Jensen, Eyal Arbely, Estelle R. Bennett, Kevin J. Bowers, Edmond Chow, Ron O. Dror, Michael P. Eastwood, Ravenna Flitman-Tene, Brent A. Gregersen, John L. Klepeis, István Kolossváry, Yibing Shan, and David E. Shaw, "Mechanism of Na+/H+ Antiporting," Science, vol. 317, no. 5839, 2007, pp. 799–803. Text

David E. Shaw, Martin M. Deneroff, Ron O. Dror, Jeffrey S. Kuskin, Richard H. Larson, John K. Salmon, Cliff Young, Brannon Batson, Kevin J. Bowers, Jack C. Chao, Michael P. Eastwood, Joseph Gagliardo, J.P. Grossman, C. Richard Ho, Douglas J. Ierardi, István Kolossváry, John L. Klepeis, Timothy Layman, Christine McLeavey, Mark A. Moraes, Rolf Mueller, Edward C. Priest, Yibing Shan, Jochen Spengler, Michael Theobald, Brian Towles, and Stanley C. Wang, "Anton: A Special-Purpose Machine for Molecular Dynamics Simulation," Proceedings of the 34th Annual International Symposium on Computer Architecture (ISCA '07), New York, NY: ACM, 2007. Text

Ross A. Lippert, Kevin J. Bowers, Ron O. Dror, Michael P. Eastwood, Brent A. Gregersen, John L. Klepeis, István Kolossváry, and David E. Shaw, "A Common, Avoidable Source of Error in Molecular Dynamics Integrators," Journal of Chemical Physics, vol. 126, no. 4, 2007, pp. 046101:1–2. Text

Kevin J. Bowers, Ron O. Dror, and David E. Shaw, "Zonal Methods for the Parallel Execution of Range-Limited N-Body Simulations," Journal of Computational Physics, vol. 221, no. 1, 2007, pp. 303–329. Text

2006

Kevin J. Bowers, Ron O. Dror, and David E. Shaw, "The Midpoint Method for Parallelization of Particle Simulations," Journal of Chemical Physics, vol. 124, no. 18, 2006, pp. 184109:1–11. Text

Kevin J. Bowers, Edmond Chow, Huafeng Xu, Ron O. Dror, Michael P. Eastwood, Brent A. Gregersen, John L. Klepeis, István Kolossváry, Mark A. Moraes, Federico D. Sacerdoti, John K. Salmon, Yibing Shan, and David E. Shaw, "Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters," Proceedings of the ACM/IEEE Conference on Supercomputing (SC06), New York, NY: IEEE, 2006.  Text
Best Paper Award.

2005

David E. Shaw, "A Fast, Scalable Method for the Parallel Evaluation of Distance-Limited Pairwise Particle Interactions," Journal of Computational Chemistry, vol. 26, no. 13, 2005, pp. 1318–1328. Text

Yibing Shan, John L. Klepeis, Michael P. Eastwood, Ron O. Dror and David E. Shaw, "Gaussian Split Ewald: A Fast Ewald Mesh Method for Molecular Simulation," Journal of Chemical Physics, vol. 122, no. 5, 2005, pp. 054101:1–13. Text


Technical Reports

Edmond Chow, Charles A. Rendleman, Kevin J. Bowers, Ron O. Dror, Douglas H. Hughes, Justin Gullingsrud, Federico D. Sacerdoti, and David E. Shaw, "Desmond Performance on a Cluster of Multicore Processors," D. E. Shaw Research Technical Report DESRES/TR--2008-01, July 2008. Text