IBM Journal of Research and Development, Volume 52, 2008

Volume 52, Number 1-2, 2008

• Tilak Agerwala:
  Message from the Vice President, Systems, IBM Research Division. 2-2
  
• Fred Mintzer:
  Preface. 3-6
  
• Srivatsan Raman, Bin Qian, David Baker, Ross C. Walker:
  Advances in Rosetta protein structure prediction on massively parallel systems. 7-18
  
• Ruhong Zhou, Maria Eleftheriou, Chung-Chau Hon, Robert S. Germain, Ajay K. Royyuru, Bruce J. Berne:
  Massively parallel molecular dynamics simulations of lysozyme unfolding. 19-30
  
• Mikael Djurfeldt, Mikael Lundqvist, Christopher Johansson, Martin Rehn, Örjan Ekeberg, Anders Lansner:
  Brain-scale simulation of the neocortex on the IBM Blue Gene/L supercomputer. 31-42
  
• James Kozloski, Konstantinos Sfyrakis, Sean Hill, Felix Schürmann, Charles C. Peck, Henry Markram:
  Identifying, tabulating, and analyzing contacts between branched neuron morphologies. 43-56
  
• Steven R. Shave, Paul Taylor, Malcolm Walkinshaw, Lorna Smith, Judy Hardy, Arthur Trew:
  Ligand discovery on massively parallel systems. 57-68
  
• Yuan-Ping Pang, Timothy J. Mullins, Brent A. Swartz, Jeff S. McAllister, Brian E. Smith, Charles Archer, Roy G. Musselman, Amanda E. Peters, Brian P. Wallenfelt, Kurt W. Pinnow:
  EUDOC on the IBM Blue Gene/L system: Accelerating the transfer of drug discoveries from laboratory to patient. 69-82
  
• Henri Calandra, François Bothorel, Pascal Vezolle:
  A massively parallel implementation of the common azimuth pre-stack depth migration. 83-92
  
• Michael Commer, Gregory A. Newman, James J. Carazzone, Thomas A. Dickens, Kenneth E. Green, Leslie A. Wahrmund, Dennis E. Willen, Janet Shiu:
  Massively parallel electrical-conductivity imaging of hydrocarbons using the IBM Blue Gene/L supercomputer. 93-104
  
• Stéphane Ethier, William M. Tang, Robert Walkup, Leonid Oliker:
  Large-scale gyrokinetic particle simulation of microturbulence in magnetically confined fusion plasmas. 105-116
  
• John M. Dennis, Henry M. Tufo:
  Scaling climate simulation applications on the IBM Blue Gene/L system. 117-126
  
• Robert T. Fisher, Leo P. Kadanoff, Don Q. Lamb, Anshu Dubey, Tomasz Plewa, Alan Calder, Fausto Cattaneo, Peter Constantin, Ian T. Foster, Michael E. Papka, Snezhana I. Abarzhi, Shimon M. Asida, Paul M. Rich, Chad C. Glendenin, Katie Antypas, Daniel J. Sheeler, Lynn B. Reid, Brad Gallagher, Shawn G. Needham:
  Terascale turbulence computation using the FLASH3 application framework on the IBM Blue Gene/L system. 127-136
  
• François Gygi:
  Architecture of Qbox: A scalable first-principles molecular dynamics code. 137-144
  
• Blake G. Fitch, Aleksandr Rayshubskiy, Maria Eleftheriou, T. J. Christopher Ward, Mark Giampapa, Michael Pitman, Jed W. Pitera, William C. Swope, Robert S. Germain:
  Blue Matter: Scaling of N-body simulations to one atom per node. 145-158
  
• Eric J. Bohm, Abhinav Bhatele, Laxmikant V. Kalé, Mark E. Tuckerman, Sameer Kumar, John A. Gunnels, Glenn J. Martyna:
  Fine-grained parallelization of the Car - Parrinello ab initio molecular dynamics method on the IBM Blue Gene/L supercomputer. 159-176
  
• Sameer Kumar, Chao Huang, Gengbin Zheng, Eric J. Bohm, Abhinav Bhatele, James C. Phillips, Hao Yu, Laxmikant V. Kalé:
  Scalable molecular dynamics with NAMD on the IBM Blue Gene/L system. 177-188
  
• Pavlos Vranas, Matthias A. Blumrich, Dong Chen, Alan Gara, Mark Giampapa, Philip Heidelberger, Valentina Salapura, James C. Sexton, Ron Soltz, Gyan Bhanot:
  Massively parallel quantum chromodynamics. 189-198
  
• Overview of the IBM Blue Gene/P Project. 199-220
  

Volume 52, Number 3, 2008

• Tze-Chiang Chen:
  Message from the Vice President, Science and Technology, IBM Research Division. 222-222
  
• David F. Heidel, Jack Hergenrother, Kenneth P. Rodbell:
  Preface. 223-224
  
• David F. Heidel, Kenneth P. Rodbell, Ethan H. Cannon, Cyril Cabral Jr., Michael S. Gordon, Phil Oldiges, Henry H. K. Tang:
  Alpha-particle-induced upsets in advanced CMOS circuits and technology. 225-232
  
• Henry H. K. Tang:
  SEMM-2: A new generation of single-event-effect modeling tools. 233-244
  
• Henry H. K. Tang, Conal E. Murray, Giovanni Fiorenza, Kenneth P. Rodbell, Michael S. Gordon, David F. Heidel:
  New simulation methodology for effects of radiation in semiconductor chip structures. 245-254
  
• A. J. KleinOsowski, Ethan H. Cannon, Phil Oldiges, Larry Wissel:
  Circuit design and modeling for soft errors. 255-264
  
• Michael S. Gordon, Kenneth P. Rodbell, David F. Heidel, Cyril Cabral Jr., Ethan H. Cannon, Daniel D. Reinhardt:
  Single-event-upset and alpha-particle emission rate measurement techniques. 265-274
  
• Pia N. Sanda, Jeffrey W. Kellington, Prabhakar Kudva, Ronald Kalla, Ryan B. McBeth, Jerry Ackaret, Ryan Lockwood, John Schumann, Christopher R. Jones:
  Soft-error resilience of the IBM POWER6 processor. 275-284
  
• Carl A. Bender, Pia N. Sanda, Prabhakar Kudva, Ricardo Mata, Vikas Pokala, Ryan Haraden, Matthew Schallhorn:
  Soft-error resilience of the IBM POWER6 processor input/output subsystem. 285-292
  
• Jude A. Rivers, Pradip Bose, Prabhakar Kudva, John-David Wellman, Pia N. Sanda, Ethan H. Cannon, Luiz C. Alves:
  Phaser: Phased methodology for modeling the system-level effects of soft errors. 293-306
  
• Timothy J. Dell:
  System RAS implications of DRAM soft errors. 307-314
  

Volume 52, Number 4-5, 2008

• Mark E. Dean, Barry Rudolph:
  Message from the Vice President, Technical Strategy and Global Operations, IBM Research and the Vice President, System Storage, IBM Systems and Technology Group. 316-316
  
• Dilip D. Kandlur, Chandrasekhar Narayanaswami:
  Preface. 317-318
  
• Sven Oehme, Jürgen Deicke, Jens-Peter Akelbein, Ronnie Sahlberg, Andrew Tridgell, Roger L. Haskin:
  IBM Scale out File Services: Reinventing network-attached storage. 319-328
  
• Ujjwal Lanjewar, Manoj Naik, Renu Tewari:
  Glamor: An architecture for file system federation. 329-340
  
• Sandeep Gopisetty, Sandip Agarwala, Eric Butler, Divyesh Jadav, Stefan Jaquet, Madhukar R. Korupolu, Ramani Routray, Prasenjit Sarkar, Aameek Singh, Miriam Sivan-Zimet, Chung-Hao Tan, Sandeep Uttamchandani, David Merbach, Sumant Padbidri, Andreas Dieberger, Eben M. Haber, Eser Kandogan, Cheryl A. Kieliszewski, Dakshi Agrawal, Murthy V. Devarakonda, Kang-Won Lee, Kostas Magoutis, Dinesh C. Verma, Norbert G. Vogl:
  Evolution of storage management: Transforming raw data into information. 341-352
  
• Sandeep Gopisetty, Eric Butler, Stefan Jaquet, Madhukar R. Korupolu, Tapan Kumar Nayak, Ramani Routray, Mark Seaman, Aameek Singh, Chung-Hao Tan, Sandeep Uttamchandani, Akshat Verma:
  Automated planners for storage provisioning and disaster recovery. 353-366
  
• Kostas Magoutis, Murthy V. Devarakonda, Nikolai Joukov, Norbert G. Vogl:
  Galapagos: Model-driven discovery of end-to-end application - storage relationships in distributed systems. 367-378
  
• Paul L. Bradshaw, Karen Brannon, Thomas Clark, Kirby G. Dahman, Sangeeta Doraiswamy, Linda Duyanovich, Bruce Light Hillsberg, Wayne Hineman, Michael Kaczmarski, Bernhard J. Klingenberg, Xiaonan Ma, Robert M. Rees:
  Archive storage system design for long-term storage of massive amounts of data. 379-388
  
• Simona Rabinovici-Cohen, Michael Factor, Dalit Naor, Leeat Ramati, Petra Reshef, Shahar Ronen, Julian Satran, David L. Giaretta:
  Preservation DataStores: New storage paradigm for preservation environments. 389-400
  
• David Nagle, Michael Factor, Sami Iren, Dalit Naor, Erik Riedel, Ohad Rodeh, Julian Satran:
  The ANSI T10 object-based storage standard and current implementations. 401-412
  
• James L. Hafner, Veera Deenadhayalan, Wendy Belluomini, Krishnakumar Rao:
  Undetected disk errors in RAID arrays. 413-426
  
• David D. Chambliss, Prashant Pandey, Tarun Thakur, Aki Fleshler, Thomas Clark, James A. Ruddy, Kevin D. Gougherty, Matt Kalos, Lyle Merithew, John G. Thompson, Harry M. Yudenfriend:
  An architecture for storage-hosted application extensions. 427-438
  
• Richard F. Freitas, Winfried W. Wilcke:
  Storage-class memory: The next storage system technology. 439-448
  
• Geoffrey W. Burr, Bülent N. Kurdi, J. Campbell Scott, Chung Hon Lam, Kailash Gopalakrishnan, Rohit S. Shenoy:
  Overview of candidate device technologies for storage-class memory. 449-464
  
• Simone Raoux, Geoffrey W. Burr, Matthew J. Breitwisch, Charles T. Rettner, Yi-Chou Chen, Robert M. Shelby, Martin Salinga, Daniel Krebs, Shih-Hung Chen, Hsiang-Lan Lung, Chung Hon Lam:
  Phase-change random access memory: A scalable technology. 465-480
  
• Siegfried F. Karg, G. Ingmar Meijer, J. Georg Bednorz, Charles T. Rettner, Alejandro G. Schrott, Eric A. Joseph, Chung Hon Lam, Markus Janousch, Urs Staub, Fabio LaMattina, Santos F. Alvarado, Daniel Widmer, Richard Stutz, Ute Drechsler, Daniele Caimi:
  Transition-metal-oxide-based resistance-change memories. 481-492
  
• Aggeliki Pantazi, Abu Sebastian, Theodore Antonakopoulos, Peter Bächtold, Anthony R. Bonaccio, Jose Bonan, Giovanni Cherubini, Michel Despont, Richard A. DiPietro, Ute Drechsler, Urs Dürig, Bernd Gotsmann, Walter Häberle, Christoph Hagleitner, James L. Hedrick, Daniel Jubin, Armin Knoll, Mark A. Lantz, John Pentarakis, Haralampos Pozidis, Russell C. Pratt, Hugo E. Rothuizen, Richard Stutz, Maria Varsamou, Dorothea Wiesmann, Evangelos Eleftheriou:
  Probe-based ultrahigh-density storage technology. 493-512
  
• Armando J. Argumedo, David Berman, Robert G. Biskeborn, Giovanni Cherubini, Roy D. Cideciyan, Evangelos Eleftheriou, Walter Häberle, Diana J. Hellman, Robert A. Hutchins, Wayne Imaino, Jens Jelitto, Kevin Judd, Pierre-Olivier Jubert, Mark A. Lantz, Gary M. McClelland, Thomas Mittelholzer, Chandrasekhar Narayanaswami, Sedat Ölçer, Paul J. Seger:
  Scaling tape-recording areal densities to 100 Gb/in2. 513-528
  
• Stefan K. Lai:
  Flash memories: Successes and challenges. 529-535