Research - Publications

Lorenzo D. Martino

   Ni, Q., Lin, D., Bertino, E., "Multi-domain and Privacy-aware Role Based Access Control in eHealth " , 2008. View Paper

David Ebert

   Huang J., Bue B., Pattath A., Ebert D., Thomas K., "Interactive Illustrative Rendering for Mobile Devices" , To appear in IEEE Computer Graphics and Applications, 2006.

   Qiao, W., McLennan, M., Kennell, R., Ebert, D., Klimeck, G., "Hub-Based Simulation and Graphics Hardware Accelerated Visualization for Nanotechnology Applications," IEEE Transactions on Visualization and Computer Graphics (Proc. IEEE Visualization 2006) , Vol. 12, No. 5, September/October 2006.

   Song, Y., Ye, J., Svakhine, N., Lasher-Trapp, S., Baldwin , M., Ebert, D., "An Atmospheric Visual Analysis and Exploration System," IEEE Transactions on Visualization and Computer Graphics (Proc. IEEE Visualization 2006) , Vol. 12, No. 5, September/October 2006.

   Pattath, A., Bue, B., Jang, Y., Ebert, D., Zhong, X., Ault, A., Coyle, E., "Interactive Visualization and Analysis of Network and Sensor Data on a Mobile Device", IEEE Symposium on Visual Analytics Science and Technology 2006, 2006.

   Rheingans, P., Ebert, D., Laidlaw, D., Munzner, T., van Wijk, J., "Publishing Your Visualization Research," panel statement, IEEE Visualization 2006, 2006.

   Foley, J., Card, S., Ebert, D., MacEachren, A., Ribarsky, W., "Visual Analytics Education," panel statement, IEEE Symposium on Visual Analytics Science and Technology 2006, 2006.

   Svakhine N. A., Ebert D., Tejada E., Ertl T., Gaither K., "Pre-integrated Flow Illustration for Tetrahedral Meshes," Volume Graphics 2006, 2006.

   Jang, Y., Botchen, R., Lauser, A., Ebert, D., Gaither, K., and Ertl, T., "Enhancing the Interactive Visualization of Procedurally Encoded Multifield Data by Ellipsoidal Basis Functions," Computer Graphics Forum, Vol. 25, Issue 3, (Eurographics 2006), 2006.

   Lasher-Trapp, S., Song, Y., Ebert, D., "Turbulence and Liquid Water Patterns in Simulated Small Cumulus Clouds," in 12th Conference on Cloud Physics(refereed abstract), 2006.

   Lu, A., Maciejewski, R., Ebert, D., "Volume Composition Using Eye Tracking Data," Proceedings Eurovis 2006 , 2006.

   Ebert, D., Lu, Y-H, Delp, E., Cleveland , W., Chaturvedi, A., Elmagarmid, A., Ouzzani, M., "Resource- and Task-Driven Visualization Adaptation," CHI'06 Workshop: Information Visualization and Interaction Techniques for Collaboration across Multiple Displays," (refereed short paper), 2006

   Lu, Y-H, Ebert, D., and Delp, E., "Resource-Driven Content Adaptation", Computational Imaging IV, IS&T/SPIE Symposium on Electronic Imaging 2006 (full paper with refereed abstract).

   Riley, K., Song, Y., Kraus, M., Levit, J., and Ebert, D., "Visualization of Structured Nonuniform Grids, " IEEE Computer Graphics and Applications, Vol. 26, No. 1, pp. 24-33, 2006.

   Costa Sousa, M., Ebertd, D., Stredney, D., Svakhine, N., "Illustrative Visualization for Medical Training," Proceedings of Computational Aesthetics 2005 - First Eurographics Workshop on Computational Aesthetics in Graphics, Visualization and Imaging, pp. 201-209, 2005.

   Svakhine, N., Jang, Y., Ebert, D. S., Gaither, K., "Illustration and Photography-Inspired Visualization of Flows and Volumes," IEEE Visualization 2005, pp. 687-694, 2005.

   Lu, A. and Ebert, D.S., "Example-based Volume Illustrations," IEEE Visualization 2005, pp. 655-662, 2005.

   Qiao, W., Ebert, D.S., Entezari, A., Korkusinski, M., Klimeck, G., "VolQD: Direct Volume Rendering of Multi-million Atom Quantum Dot Simulations," IEEE Visualization 2005, pp. 319-326, Best Application Paper finalist, 2005.

   Mora, B. and Ebert, D. S., "Low Complexity Maximum Intensity Projection," ACM Transactions on Graphics, Vol. 24, No. 4, pp. 1392-1416, 2005.

   Weiler, M., Botchen, R., Huang, J., Jang, Y., Stegmeier, S., Gaither, K., Ebert, D. S., Ertl, T., "Hardware-assisted Feature Analysis and Visualization of Procedurally Encoded Multifield Volumetric Data," IEEE Computer Graphics and Applications, Vol. 25, No. 5, pp. 72-81, 2005.

   Hanrahan, P., Eick, S., Ebert D., Hansen, C., Joy, K., Ward, M., Billinghurst, M., White, D., "Visual Representations and Interaction Technologies," Illuminating the Path: The Research and Development Agenda for Visual Analytics, IEEE Computer Society, 2005.

   Schpok, J., Dwyer, W., Ebert, D. S., "Modeling and Animating Gases with Simulation Features," ACM Symposium on Computer Animation (SCA 2005), pp. 97-106, 2005.

   Gaither, K., and Ebert, D., "Facilitating the Visual Analysis of Large-Scale Unsteady Computational Fluid Dynamics Simulations," Scientific Visualization: The Visual Extraction of Knowledge from Data, Springer, ISBN 3-540-26066-8, 2005.

   Ebert, D., "Improved Task-Specific Visual Representations of Data Enabling Actionable Visual Analytics," (refereed abstract) Working Together: Research & Development Partnerships in Homeland Security, 2005.

   Svakhine, N., Ebert, D.S., Stredney, D., "Illustration Motifs for Effective Medical Volume Illustration," IEEE Computer Graphics and Applications, Vol. 25 No. 3, pp. 31-39, 2005.

   Costa Sousa, M., Ebert, D. S., Stredney, D., "Computer-generated Illustrative Visualization Medical Training," (extended abstract) First Eurographics Workshop on Computational Aesthetics in Graphics, Visualization and Imaging, May 2005.

   Maciejewski, R., Choi, S., Ebert, D. S., Tan, H. Z., "Multi-Modal Perceptualization of Volumetric Data and Its Application to Molecular Docking," World Haptics Conference 2005, 2005.

   Stredney, D., Ebert, D., Svakhine, N., Bryan , J., Sessanna, D., "Emphatic, Interactive Volume Rendering to Support Variance in User Expertise," (full paper with refereed abstract) Proceedings Medicine Meets Virtual Reality 2005 (MMVR 2005), 2005.

   Kraus, M., Qiao, W., and Ebert, D. S., "Projecting Tetrahedra without Rendering Artifacts," Proceedings IEEE Visualization 2004, pp. 27-34, 2004.

   Gaither, K., Ebert, D., Geisler, W., Laidlaw, D., "In the Eye of the Beholder: The Role of Perception in Scientific Visualization," panel statement, Proceedings IEEE Visualization 2004, 2004.

   Johnson, G., Ebert, D., Hansen, C., Kirk, D., Mark, W., Pfister, H., "The Future Visualization Platform," panel statement, Proceedings IEEE Visualization 2004, 2004.

   Ebert, D., Jang, J., "Volume Encoding," Procedural Encoding of Scattered Data, Theory and Applications Course, IEEE Visualization 2004 Tuturial Notes, 2004.

   Ebert, D., "Specific Challenges in Visualization Research and Deployment," position Statement, NIH/NSF Future Visualization Challenges Panel, September 2004.

   Mora, B. and Ebert, D. S., "Instant Volumetric Understanding with Order-Independent Volume Rendering," Computer Graphics Forum (Proceedings Eurographics 2004), vol. 23, no. 3, pp. 489-497, 2004.

   Riley, K., Ebert, D. S., Kraus, M., Tessendorf, J., and Hansen, C., "Efficient Rendering of Atmospheric Phenomena," Proceedings Eurographics Symposium on Rendering 2004, pp. 375-386, 2004.

   Jang, Y., Weiler, M., Hopf, M., Huang, J., Ebert, D., Gaither, K., and Ertl, T., "Interactively Visualizing Procedurally Encoded Scalar Fields," Eurographics-IEEE TCVG Symposium on Visualization 2004, pp. 35-44, 2004.

   Riley, K., Ebert, D., Hansen, C., Levit, J., "A Sytstem for Realistic Weather Rendering," Proceedings of the 84th American Meteorological Society Annual Meeting, January 2004.

   Ebert, D., "Advanced Modeling Techniques," in CRC Handbook of Computer Science and Engineering, CRC Press, 2004.

   Ebert, D., "Extending Visualization to Perceptualization: The Importance of Perception in Effective Communication of Information," in The Visualization Handbook, Academic Press, 2004.

Rudolf Eigenmann

   Zhelong Pan and Rudolf Eigenmann, Fast Automatic Procedure-Level Performance Tuning Proc. Parallel Architectures and Compilation Techniques (PACT'06), 2006.

   Troy Johnson and Rudolf Eigenman, Context-Sensitive Domain-Independent Algorithm Composition and Selection, Proceedings of the ACM SIGPLAN Conference on Programming Language Design and Implementation,, (10 pages,) 2006.

   Zhelong Pan and Rudolf Eigenmann, Fast and Effective Orchestration of Compiler Optimizations for Automatic Performance Tuning, The 4th Annual International Symposium on Code Generation and Optimization (CGO),, (12 pages,) March, 2006.

   Ayon Basumallik and Rudolf Eigenmann, Optimizing Irregular Shared-Memory Applications for Distributed-Memory Systems, Proc. of the ACM Symposium on Principles and Practice of Parallel Programming (PPOPP'06),, ACM Press, (10 pages,) 2006.

   Zhelong Pan, Xiaojuan Ren, Rudolf Eigenmann and Dongyan Xu, Executing MPI Programs on Virtual Machines in an Internet Sharing System, IEEE International Parallel & Distributed Processing Symposium (IPDPS), (10 pages,) April 2006.

   Brian Armstrong, Hansang Bae, Rudolf Eigenmann, Faisal Saied, Mohamed Sayeed and Yili Zheng, HPC Benchmarking and Performance Evaluation With Realistic Applications, Proceedings of Benchmarking Workshop 2006, Austin, Texas, January 2006.

   Hansang Bae and Rudolf Eigenmann, Interprocedural Symbolic Range Propagation for Optimizing Compilers, Proc. of the Workshop on Languages and Compilers for Parallel Computing(LCPC'05), (13 pages,) October, 2005.

   Zhelong Pan, Brian Armstrong, Hansang Bae and Rudolf Eigenmann, On the Interaction of Tiling and Automatic Parallelization, First International Workshop on OpenMP (Wompat), (12 pages), June, 2005.

   Xiaojuan Ren and Rudolf Eigenmann, iShare - Open Internet Sharing Built on Peer-to-Peer and Web, European Grid Conference,, pages 1117--1127, February, 2005.

   Ayon Basumallik and Rudolf Eigenmann, Towards Automatic Translation of OpenMP to MPI, Proc. of the International Conference on Supercomputing, ICS'05,, pages 189--198, 2005.

   Jong-Kook Kim, Howard Jay Siegel, Anthony A. Maciejewski and Rudolf Eigenmann, Dynamic mapping in Energy Constrained Heterogeneous Computing Systems, Proc. of International Parallel and Distributed Processing Symposium (IPDPS 2005),, April, 2005.

Ahmed Elmagarmid

   Thanaa M. Ghanem, Walid G. Aref, Ahmed K. Elmagarmid: Exploiting predicate-window semantics over data streams. SIGMOD Record 35(1): 3-8 (2006)

   Mohamed G. Elfeky, Walid G. Aref, Ahmed K. Elmagarmid: WARP: Time Warping for Periodicity Detection. ICDM 2005: 138-145

   Moustafa A. Hammad, Walid G. Aref, Ahmed K. Elmagarmid: Optimizing In-Order Execution of Continuous Queries over Streamed Sensor Data. SSDBM 2005: 143-146

   Mohamed H. Ali, Walid G. Aref, Raja Bose, Ahmed K. Elmagarmid, Abdelsalam Helal, Ibrahim Kamel, Mohamed F. Mokbel: NILE-PDT: A Phenomenon Detection and Tracking Framework for Data Stream Management Systems. VLDB 2005: 1295-1298

   Xiang Zhang, John M. Asara, Jiri Adamec, Mourad Ouzzani, Ahmed K. Elmagarmid: Data pre-processing in liquid chromatography-mass spectrometry-based proteomics. Bioinformatics 21(21): 4054-4059 (2005)

   Xingquan Zhu, Xindong Wu, Ahmed K. Elmagarmid, Zhe Feng, Lide Wu: Video Data Mining: Semantic Indexing and Event Detection from the Association Perspective - Appendices. IEEE Trans. Knowl. Data Eng. 17(5): (2005)

   Xingquan Zhu, Xindong Wu, Ahmed K. Elmagarmid, Zhe Feng, Lide Wu: Video Data Mining: Semantic Indexing and Event Detection from the Association Perspective. IEEE Trans. Knowl. Data Eng. 17(5): 665-677 (2005)

   Mohamed G. Elfeky, Walid G. Aref, Ahmed K. Elmagarmid: Periodicity Detection in Time Series Databases. IEEE Trans. Knowl. Data Eng. 17(7): 875-887 (2005)

   Xingquan Zhu, Ahmed K. Elmagarmid, Xiangyang Xue, Lide Wu, Ann Christine Catlin: InsightVideo: toward hierarchical video content organization for efficient browsing, summarization and retrieval. IEEE Transactions on Multimedia 7(4): 648-666 (2005)

   Mourad Ouzzani, Walid G. Aref, Elisa Bertino, Ann Christine Catlin, Christopher W. Clifton, Wing-Kai Hon, Ahmed K. Elmagarmid, Arif Ghafoor, Susanne E. Hambrusch, Sunil Prabhakar, Jeffrey Scott Vitter, Xiang Zhang: The Indiana Center for Database Systems at Purdue University. SIGMOD Record 34(2): 53-58 (2005)

   Athman Bouguettaya, Ahmed K. Elmagarmid, Mourad Ouzzani, Brahim Medjahed: Database Middleware for Distributed Ontologies in State and Federal Family & Social Services. DG.O 2004

   Chris Clifton, Murat Kantarcioglu, AnHai Doan, Gunther Schadow, Jaideep Vaidya, Ahmed K. Elmagarmid, Dan Suciu: Privacy-preserving data integration and sharing. DMKD 2004: 19-26

   Mohamed G. Elfeky, Walid G. Aref, Ahmed K. Elmagarmid: Using Convolution to Mine Obscure Periodic Patterns in One Pass. EDBT 2004: 605-620

   Yi-Cheng Tu, Sunil Prabhakar, Ahmed K. Elmagarmid, Radu Sion: QuaSAQ: An Approach to Enabling End-to-End QoS for Multimedia Databases. EDBT 2004: 694-711

   Moustafa A. Hammad, Mohamed F. Mokbel, Mohamed H. Ali, Walid G. Aref, Ann Christine Catlin, Ahmed K. Elmagarmid, M. Eltabakh, Mohamed G. Elfeky, Thanaa M. Ghanem, R. Gwadera, Ihab F. Ilyas, Mirette S. Marzouk, Xiaopeng Xiong: Nile: A Query Processing Engine for Data Streams. ICDE 2004: 851

   Ihab F. Ilyas, Rahul Shah, Walid G. Aref, Jeffrey Scott Vitter, Ahmed K. Elmagarmid: Rank-aware Query Optimization. SIGMOD Conference 2004: 203-214

   Walid G. Aref, Mohamed G. Elfeky, Ahmed K. Elmagarmid: Incremental, Online, and Merge Mining of Partial Periodic Patterns in Time-Series Databases. IEEE Trans. Knowl. Data Eng. 16(3): 332-342 (2004)

   Vassilios S. Verykios, Ahmed K. Elmagarmid, Elisa Bertino, Yücel Saygin, Elena Dasseni: Association Rule Hiding. IEEE Trans. Knowl. Data Eng. 16(4): 434-447 (2004)

   Jianping Fan, Hangzai Luo, Ahmed K. Elmagarmid: Concept-oriented indexing of video databases: toward semantic sensitive retrieval and browsing. IEEE Transactions on Image Processing 13(7): 974-992 (2004)

   Jianping Fan, Ahmed K. Elmagarmid, Xingquan Zhu, Walid G. Aref, Lide Wu: ClassView: hierarchical video shot classification, indexing, and accessing. IEEE Transactions on Multimedia 6(1): 70-86 (2004)

   Athena Vakali, Mohand-Said Hacid, Ahmed K. Elmagarmid: MPEG-7 based description schemes for multi-level video content classification. Image Vision Comput. 22(5): 367-378 (2004)

   Brahim Medjahed, Boualem Benatallah, Athman Bouguettaya, Ahmed K. Elmagarmid: Webbis: An Infrastructure For Agile Integration Of Web Services. Int. J. Cooperative Inf. Syst. 13(2): 121-158 (2004)

   Xingquan Zhu, Xindong Wu, Jianping Fan, Ahmed K. Elmagarmid, Walid G. Aref: Exploring video content structure for hierarchical summarization. Multimedia Syst. 10(2): 98-115 (2004)

   Walid G. Aref, Ann Christine Catlin, Ahmed K. Elmagarmid, Jianping Fan, Moustafa A. Hammad, Ihab F. Ilyas, Mirette S. Marzouk, Sunil Prabhakar, Yi-Cheng Tu, Xingquan Zhu: VDBMS: A testbed facility for research in video database benchmarking. Multimedia Syst. 9(6): 575-585 (2004)

   Elisa Bertino, Ahmed K. Elmagarmid, Mohand-Said Hacid: A Logical Approach to Quality of Service Specification in Video Databases. Multimedia Tools Appl. 23(2): 75-101 (2004)

   Ihab F. Ilyas, Walid G. Aref, Ahmed K. Elmagarmid: Supporting top-k join queries in relational databases. VLDB J. 13(3): 207-221 (2004)

Jeffrey J. Evans

   Jeffrey J. Evans, Cynthia S. Hood: PARSE: A Tool for Parallel Application Run Time Sensitivity Evaluation. ICPADS (1) 2006: 475-484

   Evans J., Wireless Sensor Networks in Electrical Manufacturing, Proceedings of the IEEE EMCWA conference 2005, October, 2005.

   Evans, J., Hood, C., "Network Performance Variability in NOW Clusters," Proceedings of the 5th IEEE/ACM conference on cluster computing and the Grid (CCGrid2005), May 2005.

   Evans, J., Hood, C., "Application Communication Emulation for Performance Management of NOW Clusters," Proceedings of the 9th IFIP/IEEE International Symposium on Integrated Network Management, May 2005.

   Evans, J., Hood, C., Baik S., Kroculik, J., "Network Adaptation in Clusters and Grids," Proceedings from the Conference on Advances in Internet Technologies and Applications (CAITA), July, 2004.

Arif Ghafoor

   Basit Shafiq, Arjmand Samuel, Elisa Bertino, Arif Ghafoor: Technique for Optimal Adaptation of Time-Dependent Workflows with Security Constraints. ICDE 2006: 119

   Rafae Bhatti, Elisa Bertino, Arif Ghafoor: X-FEDERATE: A Policy Engineering Framework for Federated Access Management. IEEE Trans. Software Eng. 32(5): 330-346 (2006)

   Mohamed Shehab, Elisa Bertino, Arif Ghafoor: Secure collaboration in mediator-free environments. ACM Conference on Computer and Communications Security 2005: 58-67

   Ammar Masood, Sahra Sedigh-Ali, Arif Ghafoor: Efficiently Managing Security Concerns in Component Based System Design. COMPSAC (1) 2005: 164-169

   Basit Shafiq, Elisa Bertino, Arif Ghafoor: Access control management in a distributed environment supporting dynamic collaboration. Digital Identity Management 2005: 104-112

   Mohamed Shehab, Elisa Bertino, Arif Ghafoor: SERAT: SEcure role mApping technique for decentralized secure interoperability. SACMAT 2005: 159-167

   Basit Shafiq, Ammar Masood, James Joshi, Arif Ghafoor: A Role-Based Access Control Policy Verification Framework for Real-Time Systems. WORDS 2005: 13-20

   Sahra Sedigh-Ali, Arif Ghafoor: A Graph-Based Model for Component-Based Software Development. WORDS 2005: 254-262

   Rafae Bhatti, Arif Ghafoor, Elisa Bertino, James Joshi: X-GTRBAC: an XML-based policy specification framework and architecture for enterprise-wide access control. ACM Trans. Inf. Syst. Secur. 8(2): 187-227 (2005)

   Rafae Bhatti, Basit Shafiq, Elisa Bertino, Arif Ghafoor, James Joshi: X-gtrbac admin: A decentralized administration model for enterprise-wide access control. ACM Trans. Inf. Syst. Secur. 8(4): 388-423 (2005)

   Rafae Bhatti, Elisa Bertino, Arif Ghafoor: A Trust-Based Context-Aware Access Control Model for Web-Services. Distributed and Parallel Databases 18(1): 83-105 (2005)

   Rafae Bhatti, Basit Shafiq, Mohamed Shehab, Arif Ghafoor: Distributed Access Management in Multimedia IDCs. IEEE Computer 38(9): 60-69 (2005)

   James Joshi, Elisa Bertino, Arif Ghafoor: An Analysis of Expressiveness and Design Issues for the Generalized Temporal Role-Based Access Control Model. IEEE Trans. Dependable Sec. Comput. 2(2): 157-175 (2005)

   James Joshi, Elisa Bertino, Usman Latif, Arif Ghafoor: A Generalized Temporal Role-Based Access Control Model. IEEE Trans. Knowl. Data Eng. 17(1): 4-23 (2005)

   Basit Shafiq, James Joshi, Elisa Bertino, Arif Ghafoor: Secure Interoperation in a Multidomain Environment Employing RBAC Policies. IEEE Trans. Knowl. Data Eng. 17(11): 1557-1577 (2005)

   Mourad Ouzzani, Walid G. Aref, Elisa Bertino, Ann Christine Catlin, Christopher W. Clifton, Wing-Kai Hon, Ahmed K. Elmagarmid, Arif Ghafoor, Susanne E. Hambrusch, Sunil Prabhakar, Jeffrey Scott Vitter, Xiang Zhang: The Indiana Center for Database Systems at Purdue University. SIGMOD Record 34(2): 53-58 (2005)

   Rafae Bhatti, Elisa Bertino, Arif Ghafoor: A Trust-based Context-Aware Access Control Model for Web-Services. ICWS 2004: 184-191

   Arif Ghafoor: Web-based multimedia databases: prospects and challenges. MMDB 2004: 1

   Rafae Bhatti, James Joshi, Elisa Bertino, Arif Ghafoor: X-GTRBAC admin: a decentralized administration model for enterprise wide access control. SACMAT 2004: 78-86

   Rafae Bhatti, Elisa Bertino, Arif Ghafoor, James Joshi: XML-Based Specification for Web Services Document Security. IEEE Computer 37(4): 41-49 (2004)

   James Joshi, Rafae Bhatti, Elisa Bertino, Arif Ghafoor: Access-Control Language for Multidomain Environments. IEEE Internet Computing 8(6): 40-50 (2004)

   Ashfaq A. Khokhar, Arif Ghafoor: Special Issue on Multimedia Document Management Systems. Multimedia Syst. 9(6): 533-534 (2004)

Matthew Huber

   Lyle, M., J. Barron, T. J. Bralower, M. Huber, A. Olivarez-Lyle, A. C. Ravelo, D. K. Rea, and P. A. Wilson, The Pacific Ocean and the Cenozoic Evolution of Climate, Reviews of Geophysics, submitted.

   Huber, M., and J. Trapp, A review of NEXRAD Level II: Data, distribution, and applications, J.Terrestrial Observation, submitted.

   Thomas, E., H. Brinkhuis, M. Huber, and U. Rohl, An Ocean View of the Early Cenozoic Greenhouse World, in press in Oceanography.

   Thomas, E., H. Brinkhuis, M. Huber, and U. Rohl, An Ocean View of the Early Cenozoic Greenhouse World, in press in Oceanography.

   Brinkhuis, H., S. Schouten, M. E. Collinson, A. Sluijs, J. S. Sinninghe-Damste, G. R. Dickens, M. Huber, and 15 others, Episodic fresh surface waters in the early Eocene Arctic Ocean, Nature, 441, doi:10.1038/nature04692, 606-609.

   Sluijs, A., S. Schouten, M. Pagani, N. Pedentchouk , H. Brinkhuis, J. Sinninghe Damsté, G. R. Dickens, M. Huber, and 7 others, Subtropical Arctic Ocean conditions during the Palaeocene Eocene thermal maximum, Nature, 441, doi:10.1038/nature/04668, 610-613.

   Pagani, M., N. Pedentchouk, M. Huber, and 7 others, Arctic hydrology during global warming at the Paleocene/Eocene thermal maximum, Nature, 442, doi:10.1038/nature05043, 671-675.

   Huber, M., and D. Nof, The ocean circulation in the Southern Hemisphere and its climatic impacts in the Eocene, Paleogeogr., Palaeoclim., Palaeocol., 231, 9-28, 2006.

   Y. Sun, E. Ess, D. Sapirstein, and M. Huber, Visualizing Oceanic and Atmospheric Flows with Streamline Splatting, in Visualization and Data Analysis, Proc. of SPIE and IS&T Electronic Imaging 2006,R. F. Erbacher, J. C. Roberts, and M. T. Katy, ed., San Jose, CA, 12-23, 2006.

   Huber, M., H. Brinkhuis, C. E. Stickley, K. Doos, A. Sluijs, J. Warnaar, G. L Williams, S. A. Schellenberg, Eocene circulation of the Southern Ocean: Was Antarctica kept warm by subtropical waters? Paleoceanography, PA4026, doi:10.1029/2004PA001014.

   Huber, M., H. Brinkhuis, C. E. Stickley, K. Doos, A. Sluijs, J. Warnaar, G. L Williams, S. A. Schellenberg, Eocene circulation of the Southern Ocean: Was Antarctica kept warm by subtropical waters? Paleoceanography, PA4026, doi:10.1029/2004PA001014.

   Sewall, J. O., M. Huber, and L. C. Sloan, A method for using a fully coupled climate system model to generate detailed surface boundary conditions for paleoclimate modeling investigations: an early Paleogene example. Glob. Planet. Change, 43, 173-182, 2004.

   Galeotti, S., Brinkhuis, H. and M. Huber, Records of post Cretaceous-Tertiary boundary millennial-scale cooling from the western Tethys: A smoking gun for the impact-winter hypothesis, Geology, 32, 529-532, 2004.

Gerhard Klimeck

Journals:

   Neerav Kharche, Marta Prada, Timothy B. Boykin, and Gerhard Klimeck
"Valley-splitting in strained Silicon quantum wells modeled with 2 degree miscuts, step disorder, and alloy disorder",
submitted to Applied Phys. Lett. (2006).

   Timothy B. Boykin, Neerav Kharche, and Gerhard Klimeck
"Scattering time and energy uncertainty",
submitted to Am. J. Phys. (2006).

   Ahmet Ali Yanik, Gerhard Klimeck, and Supriyo Datta
"Quantum Transport with Spin Dephasing: A Nonequilibrium Green's function Approach",
submitted to Phys. Rev. B (2006) also posted cond-mat/0605037 .

   Clemens Heitzinger and Gerhard Klimeck
"Simulation of the Functioning of Conventional and Silicon-nanowire DNAFETs",
submitted to IEEE Transactions on Biomedical Engineering (2006).

   Clemens Heitzinger and Gerhard Klimeck
"Numerical aspects of the three-dimensional feature-scale simulation of silicon-nanowire field-effect sensors for DNA detection", accepted in Journal of Computational Electronics (2006).

   Mathieu Luisier, Andreas Schenk, Wolfgang Fichtner, and Gerhard Klimeck,

"Transport Calculation of Semiconductor Nanowires Coupled to Quantum Well Reservoirs", accepted in Journal of Computational Electronics 2006.

   Neophytos Neophytou, Shaikh Ahmed, and Gerhard Klimeck,

"Non-Equilibrium Green's Function (NEGF) Simulation of Metallic Carbon Nanotube Transistors: Impact of Vacancy Defect ", accepted in Journal of Computational Electronics May.

   Vladimir V. Mitin, Nizami Z. Vagidov, Mathieu Luisier, and Gerhard Klimeck,

"Energy Dispersion Relations for Holes in Silicon Quantum Wells and Quantum Wires", accepted in Journal of Computational Electronics 2006.

   Timothy B. Boykin, Neerav Kharche, Gerhard Klimeck, Marek Korkusinski
"Approximate bandstructures of semiconductor alloys from tight-binding supercell calculations",
accepted in Journal of Physics: Condensed Matter (2006).

   Timothy B. Boykin, Mathieu Luisier, Andreas Schenk, Neerav Kharche, Gerhard Klimeck
"Atomistic, random-alloy calculations of the electronic structure and transmission characteristics of AlGaAs nanowires",
accepted in IEEE transactions on Nanotechnology (2006).

   Mathieu Luisier, Andreas Schenk, and Gerhard Klimeck
"Atomistic Simulation of Nanowires in the sp3d5s* Tight-Binding Formalism: from Boundary Conditions to Strain Calculations",
accepted in Phys. Rev. B (2006).

   Gianluca Fiori, Giuseppe Iannaccone, and Gerhard Klimeck
"A Three-dimensional simulation study of the performance of Carbon Nanotube Field Effect Transistors with doped reservoirs and realistic geometry",
IEEE Transactions on Electron Devices, vol 53, pg 1782, (2006).

   Marek Korkusinski, Gerhard Klimeck,
"Atomistic simulations of long-range strain and spatial asymmetry molecular states of seven quantum dots",
accepted in Journal of Physics: Conference Series (2005).

   Timothy B. Boykin, Neerav Kharche, Gerhard Klimeck,
"Allowed wavevectors under the application of incommensurate periodic boundary conditions",
European Journal of Physics, vol 27, p 5 (2006).

   V. P. Drachev, W. Cai, U. Chettiar, H.-K. Yuan, A. K. Sarychev, A. V. Kildishev, G. Klimeck, and V. M. Shalaev,
"Experimental verification of an optical negatve-index material",
Laser Phys. Lett. Vol. 3, 49-55 (2006).

   A. S. Martins, Timothy B. Boykin, Gerhard Klimeck, and Belita Koiller,
"A new conduction band tight-binding description for silicon applied to P donors in Si",
Phys. Rev. B Vol. 72 pg. 193204 (2005).

   Yong S. Joe, Arkady M. Satanin, and Gerhard Klimeck,
"Interactions of Fano resonances in the transmission for an Aharonov-Bohm ring with two embedded quantum dots in the presence of a magnetic field",
Physical Review B, Vol. 72, pg. 115310 (2005).
selected for the September 26, 2005 issue of Virtual Journal of Nanoscale Science & Technology.

   Timothy B. Boykin and Gerhard Klimeck,
"The discretized Schrödinger equation for the finite square well and its relationship to solid state physics",
European Journal of Physics, Vol. 26 pp. 865-881(2005).

   Jing Wang, Anisur Rahman, Avik Ghosh, Gerhard Klimeck and Mark Lundstrom
"On the Validity of the Parabolic Effective-Mass Approximation for the Current-Voltage Calculation of Silicon Nanowire Transistors",
IEEE Transactions on Electron Devices, 52 (7): 1589-1595 (2005).

   Yun Zheng, Cristian Rivas, Roger Lake, Khairul Alam, Timothy B. Boykin, and Gerhard Klimeck
"Electronic Properties of Silicon Nanowires",
IEEE Transactions on Electron Devices, Vol. 52 (6): 1097-1103 (2005).

   Jeremy Green, Timothy B. Boykin, Corrie D. Farmer, Michel Garcia, Charles N. Ironside, Gerhard Klimeck, Roger Lake, and Colin R. Stanley,
"Quantum cascade laser gain medium modeling using a second-nearest-neighbor sp3s* tight-binding model",
Superlattices and Microstructures, Vol. 37, pg. 410-424 (2005).

   Timothy B. Boykin, Gerhard Klimeck, Paul von Allmen, Seungwon Lee, and Fabiano Oyafuso,
"Valley-splitting in V-shaped quantum wells",
Journal of Applied Physics, Vol. 97, pg. 113702 (2005).

   "Smooth Quantum Hydrodynamic Model vs. NEMO Simulation of a Resonant Tunneling Diode",
Carl L. Gardner, Gerhard Klimeck, and Christian Ringhofer,
Journal of Computational Electronics, Vol. 3, No. 2, 95-102, 2004.

   Jing Wang, Anisur Rahman, Avik Ghosh, Gerhard Klimeck and Mark Lundstrom
"Performance Evaluation of Silicon Nanowire Transistors with Atomic-basis Dispersion Relations",
in Applied Phys. Lett. Vol. 86 (9): Art. No. 093113 (2005),
selected for the March 7, 2005 issue of Virtual Journal of Nanoscale Science & Technology .

   Timothy B. Boykin and Gerhard Klimeck
"Practical Application of Zone-Folding Concepts in Tight-Binding",
Physical Review B, V71, 115215 (2005),
Also selected for Virtual Journal of Nanoscale Science and Technology.

   Anisur Rahman, Gerhard Klimeck, Mark Lundstrom, Nizami Vagidov, and Timothy B. Boykin
"Atomistic Approach for Nano-Scale Devices at the Scaling Limit and Beyond - Valley Splitting in Si",
Japanese Journal of Applied Physics Vol. 44, No. 4B, pp. 2187-2190 (2005).

Proceedings:

   Wei Qiao, Michael McLennan, Rick Kennell, David S. Ebert, Gerhard Klimeck,

"Hub-based Simulation and Graphics Hardware Accelerated Visualization for Nanoelectronics Applications", proceedings of IEEE Visualization 2006, Baltimore , MD , October 29 - Nov 3, 2006. Accepted as one of 63 in 228 submissions.

   Eddie Howell, Clemens Heitzinger, and Gerhard Klimeck,

"Investigation of Device Parameters for Field-Effect DNA-Sensors by Three-Dimensional Simulation", in proceedings of IEEE Nanotechnology Materials and Devices Conference, October 22-25, pg 154, 2006. (about 67% acceptance rate).

   Clemens Heitzinger and Gerhard Klimeck,

"Investigation of Conventional DNAFETs for Genome-wide Detection of Polymorphisms", Proceedings of Eurosensor Conference, Goteborg , Sweden , September 21, 2006.

   Gerhard Klimeck, Timothy Boykin, Mathieu Luisier, Neerav Kharche, Andreas Schenk,

"A Study of alloyed nanowires from two perspectives: approximate dispersion diagrams and transmission coefficients", proceedings of the 28th International Conference on the Physics of Semiconductors, ICPS 2006, Vienna, Austria, July 24-28 2006.

   Shaikh Ahmed, Muhammad Usman, Clemens Heitzinger. Rajib Rahman, Andrei Schliwa, and Gerhard Klimeck,

"Symmetry Breaking and Fine Structure Splitting in Self-Assembled Zincblende Quantum Dots: Atomistic Simulations of Long-Range Strain and Piezoelectric Field", proceedings of the 28th International Conference on the Physics of Semiconductors, ICPS 2006, Vienna, Austria, July 24-28 2006.

   Muhammad Usman, Shaikh Ahmed, Marek Korkusinski, Clemens Heitzinger, and Gerhard Klimeck,

"Strain and electronic structure interactions in realistically scaled quantum dot stacks", proceedings of the 28th International Conference on the Physics of Semiconductors, ICPS 2006, Vienna, Austria, July 24-28 2006.

   Clemens Heitzinger and Gerhard Klimeck,

"Numerical aspects of the three-dimensional feature-scale simulation of silicon-nanowire field-effect sensors for DNA detection", Extended Abstract in Proceedings of 11th International Workshop on Computational Electronics (IWCE 11), Vienna, Austria, May 2006.

   Mathieu Luisier, Gerhard Klimeck, Andreas Schenk, and Wolfgang Fichtner,

"Transport Calculation of Semiconductor Nanowires Coupled to Quantum Well Reservoirs", Extended Abstract in Proceedings of 11th International Workshop on Computational Electronics (IWCE 11), Vienna , Austria , May 2006.

   Gianluca Fiori, Giuseppe Iannaccone, and Gerhard Klimeck,

"Coupled mode space vs Real space approach for the simulation of CNT-FETs", Extended Abstract in Proceedings of 11th International Workshop on Computational Electronics (IWCE 11), Vienna, Austria, May 2006.

   Neophytos Neophytou, Shaikh Ahmed, M.P. Anantram, and Gerhard Klimeck,

"Non-Equilibrium Green's Function (NEGF) Simulation of Metallic Carbon Nanotube Transistors: Impact of Vacancy Defect ", Extended Abstract in Proceedings of 11th International Workshop on Computational Electronics (IWCE 11), Vienna , Austria , May 2006.

   Vladimir V. Mitin, Nizami Z. Vagidov, Mathieu Luisier, and Gerhard Klimeck,

"Energy dispersion relations for holes in silicon quantum wells and quantum wires", Extended Abstract in Proceedings of 11th International Workshop on Computational Electronics (IWCE 11), Vienna, Austria, May 2006.

   Mark S. Lundstrom and Gerhard Klimeck,

"The NCN: Science, Simulation, and Cyber Services", 2006 IEEE Conference on Emerging Technologies - Nanoelectronics, 10-13 Jan. 2006 Page(s):496 - 500.

   Jing Wang, Anisur Rahman, Gerhard Klimeck and Mark Lundstrom,

"Bandstructure and Orientation Effects in Si and Ge Nanowire FETs", 2005 IEEE International Electron Devices Meeting, Washington , DC , December 5 - 7, 2005. (One of 27 accepted out 120 submitted Modeling and Simulation abstracts).

   Anisur Rahman, Gerhard Klimeck, and Mark Lundstrom,

"Novel channel materials for ballistic nanoscale MOSFETs bandstructure effects", 2005 IEEE International Electron Devices Meeting, Washington , DC , December 5 - 7, 2005. (One of 27 accepted out 120 submitted Modeling and Simulation abstracts).

   Gianluca Fiori, Giuseppe Iannaccone, Gerhard Klimeck,

"Performance of Carbon Nanotube Field Effect Transistors with doped source and drain extensions and arbitrary geometry", 2005 IEEE International Electron Devices Meeting, Washington , DC , December 5 - 7, 2005. (One of 27 accepted out 120 submitted Modeling and Simulation abstracts).

   Wei Qiao, David S. Ebert ,Alireza Entezari, Marek Korkusinski, Gerhard Klimeck,

"VolQD: Direct Volume Rendering of Multi-million Atom Quantum Dot Simulations", IEEE Visualization 2005, October 23-28, Minneapolis , Minnesota , USA , one of 88 accepted from 268 submissions.

   Gianluca Fiori, Giuseppe Iannaccone, Mark Lundstrom, and Gerhard Klimeck,

"Three-dimensional atomistic simulation of Carbon Nanotube FETs with realistic geometry", European Solid-State Device Research Conference, ESSDERC, Grenoble , France , 12 - 16 September 2005, . Paper, Conference site.

   Gerhard Klimeck, Marek Korkusinski, Haiying Xu, Seungwon Lee, Sebastien Goasguen, and Faisal Saied,

"Atomistic simulations of long-range strain effects in multimillion-atom quantum dot nanostructures", SISPAD 2005, International Conference on Simulation of Semiconductor Processes and Devices, Komaba Eminence, Tokyo, Japan, September 1-3, 2005. Paper, Conference Site.

   Gerhard Klimeck, Marek Korkusinski, Haiying Xu, Seungwon Lee, Sebastien Goasguen, and Faisal Saied,
"Building and Deploying Community Nanotechnology Software Tools on nanoHUB.org and Atomistic simulations of multimillion-atom quantum dot nanostructures",
Proceedings of the 5th IEEE Conference on Nanotechnology, July 11-15, pg 807, Vol 2 (2005)

   Marek Korkusinski, Gerhard Klimeck, Haiying Xu, Seungwon Lee, Sebastien Goasguen, Faisal Saied,

"Atomistic Simulations in Nanostructures Composed of Tens of Millions of Atoms:Importance of long-range Strain Effects in Quantum Dots", 2005 NSTI Nanotechnology Conference and Trade Show, Anaheim , CA , May 8-12, 2005.

   Sebastien Goasguen, Michael McLennan, Gerhard Klimeck, and Mark S. Lundstrom,

"What do Mambo, VNC, UML and Grid computing have in common?", 2005 Linux Cluster Institute Conference, Raleigh , NC , April, 2005 Proceedings.

   Marek Korkusinski, Faisal Saied, Haiying Xu, Seungwon Lee, Mohamed Sayeed, Sebastien Goasguen,and Gerhard Klimeck,

"Large Scale Simulations in Nanostructures with NEMO3-D on Linux Clusters", 2005 Linux Cluster Institute Conference, Raleigh , NC , April, 2005, Proceedings.

   Richard J. Terrile, Christoph Adami, Hrand Aghazarian, Savio N. Chau, Van T. Dang, Michael I. Ferguson, Wolfgang Fink, Terrance L. Huntsberger, Gerhard Klimeck, Mark A. Kordon, Seungwon Lee, Paul von Allmen and Joseph Xu,
"Evolutionary Computation Technologies for the Automated Design of Space Systems",
IEEE Aerospace Conference Proceedings, 5-12 March 2005 Page(s):1 - 12 .

Conferences:

   Marta Prada, Neerav Kharche, Gerhard Klimeck,

"Electronic Structure of Si/InAs Composite Channels", Accepted as oral presentation in MRS Spring conference 2007, Symposium G: Extending Moore's Law with Advanced Channel Materials . Accepted as one of 10 oral presentations in 54 submissions.

   Neerav Kharche, Marta Prada, Timothy B. Boykin, Gerhard Klimeck,

"Valley-splitting in strained Silicon quantum wells on a miscut substrate using tight-binding model", Amperican Physical Society, March Meeting 2007,

   Michael McLennan, Wei Qiao, Rick Kennell, and Gerhard Klimeck,

"Visualizing Current Flow in Quantum Wires and other Devices on nanoHUB.org", Advanced Heterostructure Workshop , Hawaii , Dec. 3 - 8, 2006.

   Gerhard Klimeck, Timothy B. Boykin, Mathieu Luisier, Neerav Kharche, Andreas Schenk, "Electronic structure and transport in random alloy AlGaAs nanowires", Advanced Heterostructure Workshop, Hawaii, Dec. 3 - 8, 2006.

   Wei Qiao, Michael McLennan, Rick Kennell, David S. Ebert, Gerhard Klimeck,

"Hub-based Simulation and Graphics Hardware Accelerated Visualization for Nanoelectronics Applications", IEEE Visualization 2006, Baltimore , MD , October 29 - Nov 3, 2006. Accepted as one of 63 in 228 submissions.

   Eddie Howell, Clemens Heitzinger, and Gerhard Klimeck,

"Investigation of Device Parameters for Field-Effect DNA-Sensors by Three-Dimensional Simulation", IEEE Nanotechnology Materials and Devices Conference, October 22-25, 2006, about 67% acceptance rate, www.ieee-nmdc.org

   K.P.C. Madhavan, Sebastien Goasguen, Gerhard Klimeck

"The impact of the nanoscale vision on the future of learning and teaching", Nanomodeling 2006 Conference, International Society for Optical Engineering, San Diego, CA.

   Clemens Heitzinger and Gerhard Klimeck,

"Investigation of Conventional DNAFETs for Genome-wide Detection of Polymorphisms", Eurosensor Conference, Goteborg , Sweden , September 21, 2006.

   Shaikh Ahmed and Gerhard Klimeck,
"Quantum Simulations of Electronic Structure and Transport Properties in Conventional and Novel Nanoscale Devices",
7th World Congress on Computational Mechanics, Minisymposium on Transport and Coupled Processes in Micro- and Nanotechnology Los Angeles , July 16-22, 2006

   Gerhard Klimeck, Timothy Boykin, Mathieu Luisier, Neerav Kharche, Andreas Schenk,

"A Study of alloyed nanowires from two perspectives: approximate dispersion diagrams and transmission coefficients", 28th International Conference on the Physics of Semiconductors, ICPS 2006, Vienna, Austria, July 24-28 2006.

   Muhammad Usman, Shaikh Ahmed, Clemens Heitzinger. Rajib Rahman, and Gerhard Klimeck,

"Symmetry Breaking and Fine Structure Splitting in Self-Assembled Zincblende Quantum Dots: Atomistic Simulations of Long-Range Strain and Piezoelectric Field", 28th International Conference on the Physics of Semiconductors, ICPS 2006, Vienna, Austria, July 24-28 2006.

   Clemens Heitzinger, Muhammad Usman, Shaikh Ahmed, Gerhard Klimeck, Marek Korkusinski,

"Strain and electronic structure interactions in realistically scaled quantum dot stacks", 28th International Conference on the Physics of Semiconductors, ICPS 2006, Vienna, Austria, July 24-28 2006.

   Gerhard Klimeck, Mathieu Luisier, Timothy B. Boykin, Neerav Kharche, and Andreas Schenk,

"A Study of alloyed nanowires from two perspectives: approximate dispersion diagrams and transmission coefficient", 28th International Conference on the Physics of Semiconductors, ICPS 2006, Vienna, Austria, July 24-28 2006.

   Clemens Heitzinger and Gerhard Klimeck,

"Simulation study of silicon-nanowire field-effect DNA-sensors", International Congress on Nanobiotechnology and Nanomedicine (NanoBio 2006), San Francisco , CA , USA , June 2006.

   Sebastien Goasguen, Jon Camden, Muhammad Usman, Steven Clark, Jaime Frey, Clemens Heitzinger, and Gerhard Klimeck,

"nanoHUB - nanoscience gateway to the TeraGrid", Teragrid 2006, Indianapolis , IN June 12-15, 2006.

   Michael McLennan, Sebastien Goasguen, Krishna Madhavan, Derrick Kearney, Joe Cychosz, Alicia Goodman, Shaikh Ahmed, Swaroop Shivarajapura, Shawn Rice, Carol Song, Steve Clark, Rick Kennel, Clemens Heitzinger, Mark Lundstrom, Gerhard Klimeck,

"The nanoHUB -- Online simulations and a community for nano-science and nano-technology", Teragrid 2006, Indianapolis , IN June 12-15, 2006.

   Srikant Srinivasan, Gerhard Klimeck, Leonid Rokhinson,

"Modeling of a strained-Silicon quantum dot embedded in strain-relaxed Silicon-Germanium", Synergy Between Experiment and Computation in Nanoscale Science, Harvard University , May 31-June 3.

   Clemens Heitzinger and Gerhard Klimeck,

"Numerical aspects of the three-dimensional feature-scale simulation of silicon-nanowire field-effect sensors for DNA detection", 11th International Workshop on Computational Electronics (IWCE 11), Vienna , Austria , May 2006.

   Mathieu Luisier, Gerhard Klimeck, Andreas Schenk, and Wolfgang Fichtner,

"Transport Calculation of Semiconductor Nanowires Coupled to Quantum Well Reservoirs", 11th International Workshop on Computational Electronics (IWCE 11), Vienna , Austria , May 2006.

   Gianluca Fiori, Giuseppe Iannaccone, and Gerhard Klimeck,

"Coupled mode space vs Real space approach for the simulation of CNT-FETs", 11th International Workshop on Computational Electronics (IWCE 11), Vienna , Austria , May 2006.

   Neophytos Neophytou, Shaikh Ahmed, M.P. Anantram, and Gerhard Klimeck,

"Non-Equilibrium Green's Function (NEGF) Simulation of Metallic Carbon Nanotube Transistors: Impact of Vacancy Defect ", 11th International Workshop on Computational Electronics (IWCE 11), Vienna , Austria , May 2006.

   Vladimir V. Mitin, Nizami Z. Vagidov, Mathieu Luisier, and Gerhard Klimeck,

"Energy dispersion relations for holes in silicon quantum wells and quantum wires", 11th International Workshop on Computational Electronics (IWCE 11), Vienna , Austria , May 2006.

   Neerav Kharche, Mathieu Luisier, Timothy B. Boykin, Gerhard Klimeck,

"Is it a Device or a Material? Atomistic Modeling of AlGaAs Nanowires", Purdue University , Electrical Engineering Graduate Student Conference, April 7, 2006

   Elizabeth A Gardner, Mark S Lunstrom, and Gerhard Klimeck,

"NCN NanoHUB: a resource for nanotechnology education", Presentation at 2006 Materials Research Society Spring Meeting, April 17-21, 2006.

   Elizabeth A Gardner, Mark S Lunstrom, and Gerhard Klimeck,

"NCN NanoHUB: a resource for nanotechnology education", Poster at American Chemical Society Meeting and Exposition, March 26 - 30, 2006, Atlanta , GA USA .

   Neophytos Neophytou, Shaikh Ahmed, Diego Kienle, Mark Lundstrom, Gerhard Klimeck,

"Building and Deploying Community Nanotechnology Software Tools on nanoHUB.org -- Non-Equilibrium Green's Function Simulations of the Impact of Atomic Defects on the Performance of Carbon Nanotube Transistors", March Meeting of the Americal Physical Society, March 13-17, 2006, Baltimore, MD.

   Gerhard Klimeck, Shaikh Ahmed, Marek Korkusiniski, Seungwon Lee, Faisal Saied,

"Atomistic Simulations of Long-Range Strain and Close-Range Electronic Structure in Self-Assembled Quantum Dot Systems", March Meeting of the Americal Physical Society, March 13-17, 2006, Baltimore , MD.

   Neerav Kharche, Clemens Heitzinger, Gerhard Klimeck, Mathieu Luisier, Timothy Boykin,

"Bandstructure Effects in Unstructured AlGaAs Nanowires", March Meeting of the Americal Physical Society, March 13-17, 2006, Baltimore , MD.

   Shaikh Ahmed, Dragica Vasileska, Gerhard Klimeck, Christian Ringhofer,

"Efficiancy of the Thermalized Quantum Potential Approach for Modeling Nanoscale Semiconductor Devices", March Meeting of the Americal Physical Society, March 13-17, 2006, Baltimore , MD.

   Gerhard Klimeck, Marek Korkusinski, Haiying Xu, Seungwon Lee, Sebastien Goasguen, and Faisal Saied,

"Atomistic simulations of long-range strain and spatial asymmetry effects in single and coupled quantum dots", Joint International Conference on New Phenomena in Mesoscopic Systems and Surfaces and Interfaces of Mesoscopic Devices (NPMS-7/SIMD-5), Kapalua, Hawaii, Nov. 27-Dec2, 2005

   Jing Wang, Anisur Rahman, Gerhard Klimeck and Mark Lundstrom,

"Bandstructure and Orientation Effects in Si and Ge Nanowire FETs", 2005 IEEE International Electron Devices Meeting, Washington , DC , December 5 - 7, 2005. (One of 27 accepted out 120 submitted Modeling and Simulation abstracts).

   Anisur Rahman, Gerhard Klimeck, and Mark Lundstrom,

"Novel channel materials for ballistic nanoscale MOSFETs bandstructure effects", 2005 IEEE International Electron Devices Meeting, Washington , DC , December 5 - 7, 2005. (One of 27 accepted out 120 submitted Modeling and Simulation abstracts).

   Gianluca Fiori, Giuseppe Iannaccone, Gerhard Klimeck,

"Performance of Carbon Nanotube Field Effect Transistors with doped source and drain extensions and arbitrary geometry", 2005 IEEE International Electron Devices Meeting, Washington , DC , December 5 - 7, 2005. (One of 27 accepted out 120 submitted Modeling and Simulation abstracts).

   Wei Qiao, David S. Ebert ,Alireza Entezari, Marek Korkusinski, Gerhard Klimeck,

"VolQD: Direct Volume Rendering of Multi-million Atom Quantum Dot Simulations", IEEE Visualization 2005, October 23-28, Minneapolis , Minnesota , USA , one of 88 accepted from 268 submissions.

   Jing Wang, Neophytous Neophytou, Avik Ghosh, Gerhard Klimeck, and Mark Lundstrom,

"Full Band Simulation of Silicon Nanowire Transistors", SRC TECHCON, September, 2005.

   Gianluca Fiori, Giuseppe Iannaccone, Mark Lundstrom, and Gerhard Klimeck,

"Three-dimensional atomistic simulation of Carbon Nanotube FETs with realistic geometry", European Solid-State Device Research Conference, ESSDERC, Grenoble , France , 12 - 16 September 2005, .

   Neerav Kharche, Gerhard Klimeck, Marek Korkusinski, Haiying Xu, Seungwon Lee, Sebastien Goasguen, Faisal Saied,

"Atomistic Simulation of Multimillion-Atom Nanostructures using the Nanoelectronic Modeling Tool NEMO-3D", Poster Session on Computational Science and Engineering Research, joint CRI/RCAC HPC Training Workshop, Purdue University, September 7-8, 2005.

   Sebastien Goasguen, Gerhard Klimeck, Suma Adabala, Rick Kennell, Renato Figueiredo, Alain Roy, Steve Clark, Wendy Lin, Jose Fortes, Dongyan Xu, Jaime Frey, Paul Ruth,

"The Cyberinfrastructure supporting the nanoHUB", Poster Session on Computational Science and Engineering Research, joint CRI/RCAC HPC Training Workshop, Purdue University, September 7-8, 2005.

   Gerhard Klimeck,

"Parallel Applications in Nanoelectronics", joint CRI/RCAC HPC Training Workshop, Purdue University , September 7-8, 2005.

   Gerhard Klimeck, Marek Korkusinski, Haiying Xu, Seungwon Lee, Sebastien Goasguen, and Faisal Saied, "Atomistic simulations of long-range strain effects in multimillion-atom quantum dot nanostructures", IEEE SISPAD 2005, International Conference on Simulation of Semiconductor Processes and Devices, Komaba Eminence, Tokyo, Japan, September 1-3, 2005.

   Sebastien Goasguen, Krishna Madhavan, Michael McLennan, Mark S. Lundstrom and Gerhard Klimeck,

"The nanoHUB: A Science Gateway for nanotechnology", Global Grid Forum 14, Science Gateways workshop, June 28, 2005.

   Marek Korkusinski, G. Klimeck, H. Xu, S. Lee, S. Goasguen , F. Saied,

"Atomistic simulations in nanostructures composed of tens of millions of atoms", 2005 NSTI Nanotechnology Conference and Trade Show, Anaheim , CA , May 8-12, 2005.

   Sebastien Goasguen, Michael McLennan, Gerhard Klimeck, and Mark S. Lundstrom,

"What do Mambo, VNC, UML and Grid computing have in common?", 2005 Linux Cluster Institute Conference, Raleigh , NC , April, 2005

   Marek Korkusinski, Faisal Saied, Haiying Xu, Seungwon Lee, Mohamed Sayeed, Sebastien Goasguen,and Gerhard Klimeck,

"Large Scale Simulations in Nanostructures with NEMO3-D on Linux Clusters", 2005 Linux Cluster Institute Conference, Raleigh , NC , April, 2005

   Olga L. Lazarenkova, S. Lee, P. von Allmen, F. Oyafuso, G. Klimeck, M. Korkusinski, R. Timm, H. Eisele, M. Dahne,

"Effect of anharmonicity of the inter-atomic potential on the built-in strain in epitaxial quantum dot structures", APS March Meeting, Los Angeles , CA , March 21-25, 2005.

   Fabiano Oyafuso, Paul von Allmen, Seungwon Lee, Gerhard Klimeck,

"Modeling transport through Si nanowires using a nonequilibrium Green function approach", APS March Meeting, Los Angeles , CA , March 21-25, 2005.

   Marek Korkusinski, G. Klimeck, H. Xu, S. Lee, S. Goasguen , F. Saied,

"Atomistic simulations in nanostructures composed of tens of millions of atoms", APS March Meeting, Los Angeles , CA , March 21-25, 2005.

   A. M. Satanin, Y. S. Joe, and G. Klimeck,

"Fano quadrupole in a nanoscale ring", APS March Meeting, Los Angeles , CA , March 21-25, 2005.

   Timothy B. Boykin, Gerhard Klimeck, S. N. Coppersmith, Mark Friesen, Paul von Allmen, Seungwon Lee, and Fabiano Oyafuso,

"Valley splitting in low-density quantum-confined heterostructures: Superposition, not Spin!", APS March Meeting, Los Angeles , CA , March 21-25, 2005.

Daisuke Kihara

   Stan Luban & Daisuke Kihara, Comparative genomics of small RNAs in bacterial genomes, Omics, 11(1), in press.(2007).

   Troy Hawkins & Daisuke Kihara, Function prediction of uncharacterized proteins, J. Bioinformatics and Computational Biology, Accepted. (2007).

   Jianjun Hu, Yifeng David Yang & Daisuke Kihara, EMD: an ensemble algorithm for discovering regulatory motifs in DNA sequences, BMC Bioinformatics, 7:342. (2006).

   Daisuke Kihara, Troy Hawkins, Stan Luban Bin Li, Karthik Ramani, & Manish Agrawal, Protein function prediction in Proteomics Era" , Proceedings of the International Symposium on Frontiers of Computational Science 2005, Springer-Verlag, in press. (2006).

   Yen Hock Tan, He Huang & Daisuke Kihara, Statistical potential-based amino acid similarity matrices for aligning distantly related protein sequences, Proteins: Structure Funct, Bioinformatics, 64: 587-600. (2006).

   Troy Hawkins, Stan Luban & Daisuke Kihara, Enhanced automated function prediction using distantly related sequences and contextual association by PFP." , Protein Sci, 15:1550-1556 (2006).

   Daisuke Kihara, Yifeng D. Yang & Troy Hawkins, "Bioinformatics resources for cancer research with an emphasis on gene function and structure prediction tools." , Cancer Informatics, 2:25-35. (2006).

   Jianjun Hu, Bin Li & Daisuke Kihara, "Limitations and potentials of current motif discovery algorithms." , Nucleic Acid Res. 33: 4899-4913. (2005).

   Daisuke Kihara., "On the effect of long-range interactions on the secondary structure formation of proteins." , Protein Science. 14: 1955-1963. (2005).

   Daisuke Kihara., "Biomolecular Structure Databases." , Genome Function Research Handbook, Chapter 2. pp. 73-81. Yodosha Publishers, Tokyo , Japan . (2004).

   Jeffrey Skolnick, Daisuke Kihara and Yang Zhang., " Development and large scale benchmark testing of the PROSPECTOR 3.0 threading algorithm." , Proteins: Structure, Funct. Bioinformatics 56:502-518. (2004)

   Daisuke Kihara and Jeffrey Skolnick., " Microbial genomes have over 72% structure assignment by the threading algorithm PROSPECTOR_Q." , Proteins: Structure, Funct. Bioinformatics 55: 464-473 (2004)

Sangtae Kim

   Sangtae Kim: Cyberinfrastructure: Enabling the Chemical Sciences. Journal of Chemical Information and Modeling 46(3): 938 (2006)

   Noritaka Osawa, Sangtae Kim: Poster3D: a system for three-dimensional authoring and presentation in immersive virtual environments. Multimedia Syst. 11(3): 216-225 (2006)

   Freeman, P.A., Crawford, D.L., Kim, S. and Munoz, J.L. (2005) "Cyberinfrastructure for science and engineering: promises and challenges," Proc. of the IEEE 93, 682-691.

   Noritaka Osawa, Sangtae Kim: A Three-dimensional Authoring/Presentation System for Immersive Virtual Environments: Poster3D. IV 2004: 785-791

   Ehud Yariv and Howard Brenner and Sangtae Kim: "Curvature-Induced Dispersion in Electro-Osmotic Serpentine Flows" SIAM Journal on Applied Mathematics, 64(4), pp. 1099-1124, 2004.

Mourad Ouzzani

   H. Elmeleegy, Mourad Ouzzani and A.K. Elmagarmid, "Usage-based Schema Matching, 24th International Conference on Data Engineering (ICDE), Cancun, Mexico, April 2008. View Paper

   M. Y. Eltabakh, M. Ouzzani, and W. G. Aref. bdbms - A Database Management System for Biological Data. Third Biennial Conference on Innovative Data Systems Research (CIDR 2007). Asilomar , CA , January 7-10 2007

   Hicham G. Elmongui, Mourad Ouzzani, Walid G. Aref: Challenges in spatiotemporal stream query optimization. MobiDE 2006: 27-34

   Mohamed Y. Eltabakh, Walid G. Aref, Mourad Ouzzani, Mohamed H. Ali: Discovering Consensus Patterns in Biological Databases. VDMB 2006: 170-184

   Massimo Mecella, Mourad Ouzzani, Federica Paci, Elisa Bertino: Access control enforcement for conversation-based web services. WWW 2006: 257-266

   D. Ebert, Lu, Y-H, Delp, E., Cleveland , W., Chaturvedi, A., Elmagarmid, A., Ouzzani, M., Resource- and Task-Driven Visualization Adaptation, CHI'06 Workshop: Information Visualization and Interaction Techniques for Collaboration across Multiple Displays," (refereed short paper), Montreal , Canada , April 2006.

   Xiang Zhang, John M. Asara, Jiri Adamec, Mourad Ouzzani, Ahmed K. Elmagarmid: Data pre-processing in liquid chromatography-mass spectrometry-based proteomics. Bioinformatics 21(21): 4054-4059 (2005)

   Mourad Ouzzani, Walid G. Aref, Elisa Bertino, Ann Christine Catlin, Christopher W. Clifton, Wing-Kai Hon, Ahmed K. Elmagarmid, Arif Ghafoor, Susanne E. Hambrusch, Sunil Prabhakar, Jeffrey Scott Vitter, Xiang Zhang: The Indiana Center for Database Systems at Purdue University. SIGMOD Record 34(2): 53-58 (2005)

   Athman Bouguettaya, Ahmed K. Elmagarmid, Mourad Ouzzani, Brahim Medjahed: Database Middleware for Distributed Ontologies in State and Federal Family & Social Services. DG.O 2004

   Athman Bouguettaya, Brahim Medjahed, Abdelmounaam Rezgui, Mourad Ouzzani, Xumin Liu, Qi Yu: WebDG - A Platform for E-Government Web Services. ER (Workshops) 2004: 553-565

   Mourad Ouzzani, Athman Bouguettaya: Query Processing and Optimization on the Web. Distributed and Parallel Databases 15(3): 187-218 (2004)

   Mourad Ouzzani, Athman Bouguettaya: Efficient Access to Web Services. IEEE Internet Computing 8(2): 34-44 (2004)

Faisal Saied

   Dennis C. Smolarski, Ramesh Balakrishnan, Eduardo F. D'Azevedo, John W. Fettig, Bronson Messer, Anthony Mezzacappa, Faisal Saied, Paul E. Saylor, and F. Douglas Swesty, "On the Performance of SPAI and ADI-like Preconditioners for Core Collapse Supernova Simulations in One Spatial Dimension." Computer Physics Communications, 175, pp. 330--338, 2006.

   Lin Sun, Chinh Le, Faisal Saied, and Jayathi Y. Murthy, A Highly Scalable Simulation Model for Atomistic Calculation of Thermal Properties of Silicon, PDPTA'06 / RTCOMP'06: June 26-29, 2006

   Brian Armstrong, Hansang Bae, Rudolf Eigenmann, Faisal Saied, Mohamed Sayeed and Yili Zheng, HPC Benchmarking and Performance Evaluation With Realistic Applications, Proceedings of Benchmarking Workshop 2006, Austin, Texas, January 2006.

   M. Korkusinski, G. Klimeck, H. Xu, S. Lee, S. Goasguen and F. Saied, Atomistic Simulations in Nanostructures Composed of Tens of Millions of Atoms: Importance of long-range Strain Effects in Quantum Dots. Nanotech 2005 Vol. 2

   Shaikh S. Ahmed, Marek Korkusinski, Faisal Saied, Haiying Xu, Seungwon Lee, Mohamed Sayeed, Sebastien Goasguen and Gerhard Klimeck, "Large Scale Simulation in Nanostructures with NEMO3-D on Linux Clusters", The 6th LCI International Conference on Linux Clusters: The HPC Revolution 2005, April 26-28, 2005, Chapel Hill , North Carolina , USA .

   S. Kilic, F. Saied and A. Sameh, Efficient iterative solvers for structural dynamics problems, Computers and Structures, vol. 82, pp. 2363--2375, 2004.

Mohamed Sayeed

   M. Mahinthakumar, Sayeed, M., J. Blondin, P. Worley, A. Mezzacappa, and R. Hix, (2004). Performance Evaluation and Modeling of a Parallel Astrophysics Application, Proceedings of High Performance Computing Symposium, Society for Computer Simulation International, Arlington, VA, April 2004.

   M Korkusinski, F Saied, Haiying Xu , Seungwon Lee , Sayeed, M., S Goasguen , and G. Klimeck, Large Scale Simulations in Nanostructures with NEMO3-D on Linux Clusters, The 5th LCI International Conference on Clusters: The HPC Revolution 2004.

   Mahinthakumar,G., and Sayeed, M. (2005) Hybrid genetic algorithm - local search approaches for solving groundwater source identification inverse problems, ASCE J. of Water Resources Planning and Management, 131(1), p 45-57, January/February 2005.

   Sayeed, M. and Mahinthakumar .G (2005) An Efficient Parallel Implementation of Hybrid Optimization Approaches for Solving Groundwater Inverse Problems, ASCE Journal of Computing in Civil Engineering, Vol.19, No. 4, pp. 329-340, October 2005.

   Mahinthakumar. G and Sayeed, M (2006) Reconstructing Groundwater Source Release Histories Using Hybrid Optimization Approaches, Environmental Forensics, 7:1-10, 2006.

   Mahinthakumar .G, Sayeed, M. and Nicholas T. Karonis (2006) Grid enabled solution of groundwater inverse problems on the Teragrid network, Proceedings of High performance computing 2006, Society for Computer Simulation International, Huntsville, AL.

   Brian Armstrong, Hansang Bae, Rudolf Eigenmann, Faisal Saied, Mohamed Sayeed, and Yili Zheng (2006) HPC Benchmarking and Performance Evaluation With Realistic Applications, SPEC Conference 2006.

Submitted

   Brian Armstrong, Hansang Bae, Rudolf Eigenmann, Faisal Saied, Mohamed Sayeed, and Yili Zheng (2006) Measuring HPC Performance With Real Applications, Submitted to Computing in Science and Engineering magazine.

   Sayeed, M, Mahinthakumar .G, and Nicholas T. Karonis (2006) Grid enabled solution of groundwater inverse problems on the Teragrid network, Submitted to Special issue on High performance computing, Simulation:Transactions of the Society for Modeling and Simulation International.

   B. Kochunas, Sayeed. M, J. W. Thomas, T. J. Downar (2007) Fine grain parallelization of modular ray tracing in 2D method of characteristics, Extended summary submitted to M&C+SNA2007 Conference (Mathematics & Computation/Supercomputing in Nuclear Applications).