Pratul Agarwal was awarded U.S. Patent No. 8,417,461 for "Identification and Modification of Dynamical Regions in Proteins for Alteration of Enzyme Catalytic Effect"
According to the patent's abstract, the patent covers "A method for analysis, control, and manipulation for improvement of the chemical reaction rate of a protein-mediated reaction is provided. Enzymes, which typically comprise protein molecules, are very efficient catalysts that enhance chemical reaction rates by many orders of magnitude. Enzymes are widely used for a number of functions in chemical, biochemical, pharmaceutical, and other purposes. The method identifies key protein vibration modes that control the chemical reaction rate of the protein-mediated reaction, providing identification of the factors that enable the enzymes to achieve the high rate of reaction enhancement. By controlling these factors, the function of enzymes may be modulated, i.e., the activity can either be increased for faster enzyme reaction or it can be decreased when a slower enzyme is desired. This method provides an inexpensive and efficient solution by utilizing computer simulations, in combination with available experimental data, to build suitable models and investigate the enzyme activity."
Jack Dongarra (Professional Achievement Award)
Jack Dongarra, CSMD Researcher, Distinguished Professor in the Department of Electrical Engineering and Computer Science at UTK and the director of the Innovative Computer Laboratory, will be the recipient of the 2013 Illinois Institute of Technology's (IIT) Professional Achievement Award in recognition of the contribution and achievements of IIT's most remarkable graduates and leaders. Dongarra received his MS degree from IIT. The awards ceremony will take place on the IIT campus in April.
Matt Reuter (2012 Howes Scholar in Computational Science)
Each year one or two recent graduates from the DOE Computational Science Graduate Fellowship program are chosen as the Howes Scholar. This award was established to honor Fredrick Anthony Howes, who managed the Applied Mathema)cal Science Program in the U.S. Department of Energy during the 1990s. Dr. Howes was highly respected and admired for his energy, dedication and personal integrity.
The awards committee felt that Matt captured the spirit of this award with his technical excellence, leadership and character.
Xiaoguang Zhang appointed as a Fellow of the American Physical Society (APS) for pioneering work in the development and application of the scattering theory and computational methods to materials studies, in particular to the study of electron transport in magnetic tunnel junctions.
Clayton Webster appointed as an editor of SIAM J. on Uncertainty Quantification as well as the SIAM J. on Numerical Analysis (SINUM).
Nagi Rao was awarded a US Patent for "Method and Systems for Bandwidth Scheduling and Path Computation for Connection-Oriented Networks."
Galen Shipman won the Director's Research & Development Award for a project titled "Accelerating Data Acquisition, Reduction, and Analysis at SNS."
Blair Sullivan won the Seed Award at the 2012 LDRD Poster Session for her poster titled "Connecting Combinational and Geometric Tree-Like Structure in Complex Networks."
Jeff Vetter was appointed as an ACM Distinguished Scientist Member.
The 2012 award for the most distinguished Scientific Paper goes to Jingsong Huang & Bobby Sumpter for 'A Universal Model for Nanoporous Carbon Supercapacitors Applicable to Diverse Pore Regimes, Carbon Materials, and Electrolytes' published in the European Journal Chemistry (impact factor 5.925).
This paper provided breakthrough advances in the theory, modeling and simulation of nanoporous carbon-based supercapacitors. This work is the first demonstrated capability for the computer design and predictive simulation of high-capacity, cyclable, and versatile nanoporous supercapacitors for efficient and safe energy storage application. The papers has been cited on over 112 instances since 2008 and the journal publishers recognized its significance with a cover graphic.
The 2012 award for the most distinguished software release goes to N. Podhorszki, Q. Liu, Hassan. Abbasi, J. Choi, R. Tchoua and S. Klasky for the Adaptable IO System (ADIOS).
ADIOS provides a simple, flexible way for scientists to describe the data in their code that may need to be written, read, or processed outside of the running simulation. ADIOS routinely use over 300M core hours/year. Results that use the ADIOS framework have be published in over 80 computer science conferences/journals.
The 2012 special award for the most distinguished contribution goes to Ralf Deiterding for the release and support of the Adaptive Mesh Refinement in Object-oriented C++ (AMORC) Software.
AMORC is in use by many researchers and Ralf has personally supported the mesh refinement community by presenting extended tutorials at the Joint Institute for Computer Science and the 2010 Summer School on Multi-Resolution Methods, Frejus (France). The material from this summer school was also published in the European Series in Applied and Industrial Mathematics Proceedings. The code has been downloaded over 500 times.
The 2012 award for the most distinguished Scientific or Technical Contribution goes to Forrest Hoffman, Richard Mills and Jitendra (Jitu) Kumar for the ForWarn system.
ForWarn is a satellite-based monitoring and assessment tool that recognizes and tracks potential forest disturbances caused by insects, diseases, wildfires, extreme weather, or other natural or human-caused events. It is deployed operationally with the USDA Forest Service.
ForWarn is a partnership between ORNL, the USDA Forest Service, NASA's Stennis Space Center, and the U.S. Geological Survey's EROS Data Center and has been awarded the
- 2012 Southern Research Station Director's Award for Excellence in Science Delivery and the
- 2013 Federal Laboratory Consortium (FLC) for Technology Transfer Interagency Partnership Award
The ORNL ForWarn team - comprised of Forrest Hoffman (ORNL PI), Jitendra "Jitu" Kumar, and Richard Tran Mills - contributed data mining methodologies for change detection to satellite remote sensing data.
Distinguished Employee Program
Norbert Podhorszki worked with Mathieu Gontier from NUMECA International S.A to implement an efficient I/O module for the FineTM/Turbo solver for CFD applications. The new solver has been used by RAMGEN Power Systems, LLC on Jaguar, with a tenfold increase in checkpoint/restart performance, allowing this application to scale much better. The unusual characteristics of the solver is that, for load balancing reasons, each processor holds multiple and a variable number of pieces of each variable because of a non uniform balancing of the structured model over the processes. This renders all traditional I/O solutions very inefficient, especially their original host-slaves IO approach based on CGNS on a very large number of sub domains, and which becomes the bottleneck at scale. The buffering mechanism and the aggregation I/O method provided by ADIOS, combined with an easy-to-use API, helped them to separate the problem of I/O performance from the definition of I/O in the application itself and to provide efficient I/O performance on Jaguar. Additionally, the self-describing data format of ADIOS allows the application to restart from a previous checkpoint on an arbitrary number of processes. In numbers, a computation originally requiring about 2000-sec was optimized until 120-sec with a non negligible memory over consumption, against 40-sec with ADIOS without additional memory.
Cory Hauck is the Oak Ridge node leader for Ki-Net, a new research network funded by the NSF for the next five years. Research networks are a new mode of operation under the Division of Mathematical Sciences at the NSF. Their purpose is to facilitate travel and interaction between institutional members. Ki-Net is focused on kinetic theory, primarily on "emerging applications" in quantum dynamics, network dynamics, and biological sciences. It is one of only three funded projects and the only one in applied mathematics.
Cindy Sonewald is an exemplary employee that is always willing to help others and strives to deliver the utmost quality and timeliness as a group's administrative assistant. She has built a relationship with all of the groups and no one has a problem with coming to her for help. Cindy has worked above and beyond the call of duty on everything from planning meetings to handling even the most in-depth details of subcontracts so that the researchers can be left to their science. She regularly works overtime to help with proposals, budgets and purchases. And if the programming ever gets the researchers down, they can always go to Cindy for a good laugh or a brief discussion on literary classics for a short break. Cindy's contribution to the group is phenomenal and we wouldn't be the same without here.
Forrest Hoffman - When the Climate SciDAC call was announced it became obvious that instead of the large monolithic proposals that had been funded in previous calls, DOE was looking for smaller more focused proposals. This opened the door for competition from new players interested in winning support but also threatened to undermine the longstanding cooperation between ORNL and some of the other principal Labs in Climate. Thus, the landscape for negotiating the collaboration between many of the partners became much more complex and uncertain. Forrest was asked to serve as the ORNL point of contact for the definition phase which involved several meetings to negotiate the content of several SciDAC themes mostly in content areas where Forrest had no personal interest and no prospect of support for himself. When the negotiations were complete Forrest had managed to help define three subject areas in biogeochemistry, multiscale processes and ice sheets. Forrest and others at ORNL were then able to bid for and win support for work in all three defined SciDAC Climate areas. Furthermore, Forrest was able maintain the positive and collaborative atmosphere between ORNL and the other labs principally involved in climate science. This epitomizes the selfless leadership we sometimes ask of our staff; Forrest had to look to the bigger picture and not just focus narrowly on his own research interests and needs.
Qing Gary Liu has been performing research in High-performance I/O and has been developing the ADaptable I/O System (ADIOS) software. ADIOS is going to reach its 5th release since 2008 and Gary has continuously improved it. His aggregation strategy to write data out has proved to be the fastest technique at scale at OLCF, therefore all applications that turned to use ADIOS due to their I/O problems, ended up exclusively using his method for running on 100k cores and up. S3D, a combustion simulation code from Sandia has been using ADIOS since before the first release, and has been a driving application for ADIOS. Gary has been the main contact for I/O related work with the authors at Sandia and has been improving their I/O. Gary is an extremely dedicated asset to the Scientific Data Group, who makes sure that ADIOS is high-quality software and is always ready to help applications pushing the limits of I/O on our petascale systems.
In the last month Gary worked nonstop to lead the ADIOS effort to get our next major release, which included I/O staging and new and enhanced reading. He has also worked to assist the S3D team, lead by Jackie Chen, to have high performance I/O.
Eirik Endeve is the CSMD distinguished employee for July. He just published his second major paper in The Astrophysical Journal. Both papers were superb and comprehensive studies of the stationary accretion shock instability in core collapse supernovae and the turbulence it induces, the latter of which has important ramifications for the supernova explosion mechanism and for all future three-dimensional supernova models.
Jennifer Williams and Lora Wolfe were instrumental in organizing the Discovery 2020 Workshop in Santa Fe, New Mexico that focused on quantum computing, modeling and simulation, and programming languages, which will provide analytics and advanced computing in the 2015/2020 time frame. The workshop was hosted by ORNL, Los Alamos National Laboratory, and the Department of Defense. Jennifer and Lora organized the location; meeting logistics; materials needed for the workshop; interacted with the sponsor on attendee requirements; work with the speakers on presentation materials, travel, and honorariums; and all social activities for the workshop. In advance of the workshop, they set up participants FOBs so they could log onto the ORNL system where OpenSHMEM was loaded and made sure that NCCS had everything set up on the computer. In Santa Fe, they made sure all of the participants were taken care of throughout the workshop and that all special dietary needs were handled. They also made sure that all of the networking, AV, seating, and WebEx was taken care of onsite during the entire workshop. They shipped manuals back to participants’ sites so they did not have to carry them in their luggage, and made all of the CD's of the workshop. Once they returned from travel, Jennifer completed all of the close-out of the workshop, which entails consolidating the surveys from the participants and providing feedback to the sponsor and the hosting of WebEx for remote participants. The work they did was so excellent, that the DoD organizers have already given high praise to Jennifer and Lora for the fantastic job that they did and especially for being available to help no matter what was needed.
George Ostrouchov is receiving this award for leading the development of R infrastructure that puts ORNL on the world map as the place to go for big data analytics in R. He designed the architecture and leads the development of a series of R packages that provide a very high-level programming interface for distributed data analytics, literally "programming with big data" (pbd). The packages, branded with a "pbd" prefix, tightly couple distributed linear algebra libraries with R and engage the R community to develop more analytics for big data. This enables R to be a scalable analytics platform on OLCF resources. George also organized a recent R programming workshop at OLCF and brought an R mirror site to NICS.
The Scientific Data Group (SDG) is proud to have George lead analytics in its portfolio that includes the best talent for scientific data research from I/O through middleware to analytics and visualization. George also leads data analytics in the Remote Data Analysis and Visualization (RDAV) center at NICS.
Ross Bartlett served as release manager for the Limited Beta Release of the Virtual Environment for Reactor Applications (VERA) through the Radiation Safety Information Computational Center (RSICC). VERA is the simulation environment being developed for the Consortium for Advanced Simulation of Light-Water Reactors (CASL), the DOE Innovation Hub for Modeling & Simulation for Nuclear Energy. Although limited to current CASL partners, this is the first "official" release of VERA components, and is a precursor to wide deployment for use by industry, academia, and research institutions.
Clayton Webster joined the Computational Engineering & Energy Sciences group in CSMD in May of 2011 to develop the growing area of uncertainty quantification. FY12 proved to be an extremely productive year, in which Clayton produced 15 papers, a similar number of invited conference presentations, and organized or co-organized 6 symposia at international conferences (such as SIAM and SAMSI). In addition, he led or participated in 16 proposals, serving as Principal Investigator on six. Five of these have been funded, with 1 expected and 5 awaiting decisions.
This award particularly recognizes Clayton’s active involvement in development of industrial partnerships, including GE Global Research, Caterpillar, United Technologies, Pratt & Whitney, and most recently Proctor & Gamble. The Caterpillar and P&G interactions have recently borne fruit, resulting in additional funding for the growing UQ activities at ORNL.