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Documents

Object Lifetime Prediction in Java Hajime Inoue, Darko Stefanovic, and Stephanie Forrest. IEEE Transactions on Computers (in press).

Generating Object Lifetime Traces with Merlin. Matthew Hertz, Stephen M. Blackburn, J. Eliot B. Moss, Kathryn S. McKinley, and Darko Stefanovic. ACM Transactions on Programming Languages and Systems (in press).

Characterization of Transverse Channel Concentration Profiles Obtainable With a Class of Microfluidic Networks. Jennifer Sager, Maxwell Young, and Darko Stefanovic. Langmuir 22(9), 4452-4455 (2006).

Solution-Phase Molecular-Scale Computation With Deoxyribozyme-Based Logic Gates and Fluorescent Readouts. Joanne Macdonald, Darko Stefanovic, and Milan N. Stojanovic. In Fluorescent Energy Transfer Nucleic Acid Probes, V. V. Didenko (ed.), Methods in Molecular Biology Series, Humana Press, 2006.

Deoxyribozyme-Based Three-Input Logic Gates and Construction of a Molecular Full Adder. Harvey Lederman, Joanne Macdonald, Darko Stefanovic, and Milan N. Stojanovic. Biochemistry 45(4), 1194-1199 (2006).

Games, Strategies, and Boolean Formula Manipulation. Ben Andrews. Technical Report TR-CS-2005-41, Department of Computer Science, University of New Mexico, December 2005.

Rule discovery in epidemiologic surveillance data using EpiXCS: An evolutionary computation approach. John H. Holmes and Jennifer A. Sager. 10th Conference on Artificial Intelligence in Medicine, Aberdeen, Scotland, July 2005. (Springer-Verlag LNAI 3581)

Towards practical biomolecular computers using microfluidic deoxyribozyme logic gate networks. Joseph Farfel and Darko Stefanovic. 11th International Meeting on DNA Computing, London, Ontario, Canada, June 2005. (Springer-Verlag LNCS 3892)

Designing Nucleotide Sequences for Computation: A Survey of Constraints. Jennifer Sager and Darko Stefanovic. 11th International Meeting on DNA Computing, London, Ontario, Canada, June 2005. (Springer-Verlag LNCS 3892)

Computing with Nucleic Acids. Milan N. Stojanovic, Darko Stefanovic, Thomas LaBean, and Hao Yan. In Bioelectronics: From Theory to Applications. Itamar Willner and Eugenii Katz (Eds.), Wiley, 2005.

Deoxyribozyme-Based Ligase Logic Gates and Their Initial Circuits. Milan N. Stojanovic, Stanka Semova, Dmitry Kolpashchikov, Clint Morgan, and Darko Stefanovic. Journal of the American Chemical Society, 127(19), 6914-6915 (2005).

Comparison of Garbage Collectors Operating in a Large Address Space. Sergiy Kyrylkov and Darko Stefanovic. Technical Report TR-CS-2005-11, Department of Computer Science, University of New Mexico, April 2005.

Towards practical biomolecular computers using microfluidic deoxyribozyme logic gate networks. Joseph Farfel and Darko Stefanovic. Technical Report TR-CS-2005-7, Department of Computer Science, University of New Mexico, March 2005.

Designing Nucleotide Sequences for Computation: A Survey of Constraints. Jennifer Sager and Darko Stefanovic. Technical Report TR-CS-2005-6, Department of Computer Science, University of New Mexico, March 2005.

64-Bit Computing & JVM Performance. Sergiy Kyrylkov. Dr. Dobb's Journal, 30 (370), 24-27, March 2005.

Randomized Instruction Set Emulation. Elena Gabriela Barrantes, David H. Ackley, Stephanie Forrest, and Darko Stefanovic. ACM Transactions on Information and System Security, 8 (1), 3-40, February 2005.

A Study of Garbage Collection With a Large Address Space for Server Applications. Sergiy Kyrylkov and Darko Stefanovic. Technical Report TR-CS-2005-1, Department of Computer Science, University of New Mexico, February 2005.

The Triton Branch Predictor. Josh Karlin, Darko Stefanovic, and Stephanie Forrest. Technical Report TR-CS-2005-28, Department of Computer Science, University of New Mexico, October 2004.

A Comparison of Three Methods for Covering Missing Data in XCS. John H. Holmes, Jennifer A. Sager, and Warren B. Bilker. Seventh International Workshop on Learning Classifier Systems (IWLCS-2004) during the Genetic and Evolutionary Computation Conference (GECCO 2004), Seattle, Washington, June 2004. abstract

Building the components for a biomolecular computer. Clint Morgan, Darko Stefanovic, Cristopher Moore, and Milan N. Stojanovic. 10th International Meeting on DNA Computing, Milano, Italy, June 2004. (Springer-Verlag LNCS 3384, 247-257) (Technical Report TR-CS-2004-33 , Department of Computer Science, University of New Mexico.)

Design and Implementation of a 64 Bit PowerPC Port of Jikes RVM 2.0.3. Sergiy Kyrylkov, Darko Stefanovic, and Eliot Moss. 2nd Workshop on Managed Run-time Environments, Palo Alto, CA, March 2004. slides

Jikes Research Virtual Machine: Design and Implementation of a 64-bit PowerPC Port. Sergiy Kyrylkov. Technical Report TR-CS-2003-41, Department of Computer Science, University of New Mexico, December 2003.

A Tool for Monitoring and Recording Heap-Allocated Object Behavior. Qingfeng Duan. Technical Report TR-CS-2003-40, Department of Computer Science, University of New Mexico, December 2003.

Design and Implementation of SIND, a Dynamic Binary Translator. Trek Palmer. Technical Report TR-CS-2003-38, Department of Computer Science, University of New Mexico, December 2003.

A Deoxyribozyme-Based Molecular Automaton. Milan N. Stojanovic and Darko Stefanovic. Nature Biotechnology, 21, 1069-1074 (2003).

Randomized instruction set emulation to disrupt binary code injection attacks. Elena Gabriela Barrantes, David H. Ackley, Stephanie Forrest, Trek S. Palmer, Darko Stefanovic, and Dino Dai Zovi. 10th ACM Conference on Computer and Communications Security, Washington, DC, October 2003.

Implicit-OR tiling of Deoxyribozymes: Construction of Molecular Scale OR, NAND, and Four-Input Logic Gates. Milan N. Stojanovic, Dragan B. Nikic, and Darko Stefanovic. Journal of the Serbian Chemical Society, 68(4-5), 321-326 (2003).

Object Lifetime Prediction in Java. Hajime Inoue, Darko Stefanovic, and Stephanie Forrest. Technical Report TR-CS-2003-28, Department of Computer Science, University of New Mexico, May 2003.

Model Checking Reconfigurable Processor Configurations for Safety Properties. John Cochran, Deepak Kapur, and Darko Stefanovic. FPL 2003, The 13th International Conference on Field Programmable Logic and Applications, Lisbon, Portugal, September, 2003. (Springer-Verlag LNCS 2778) (Extended version available as Technical Report TR-CS-2003-18, Department of Computer Science, University of New Mexico, April 2003.)

Experiences Constructing a Lightweight SPARC Interpreter for a Dynamic Binary Translator. Trek Palmer and Darko Stefanovic. Technical Report TR-CS-2003-12, Department of Computer Science, University of New Mexico, March 2003.

Randomized instruction set emulation to disrupt binary code injection attacks. Gabriela Barrantes, David H. Ackley, Trek S. Palmer, Dino Dai Zovi, Stephanie Forrest and Darko Stefanovic. Technical Report TR-CS-2003-10, Department of Computer Science, University of New Mexico, February 2003.

Deoxyribozyme-Based Half Adder. Milan N. Stojanovic and Darko Stefanovic. Journal of the American Chemical Society, 125(22), 6673-6676 (2003).

Security Applications of Dynamic Binary Translation. Dino Dai Zovi. Technical Report TR-CS-2002-38, Department of Computer Science, University of New Mexico, December 2002.

Older-first Garbage Collection in Practice: Evaluation in a Java Virtual Machine. Darko Stefanovic, Matthew Hertz, Stephen M. Blackburn, Kathryn S. McKinley and J. Eliot B. Moss. ACM SIGPLAN Workshop on Memory System Performance, Berlin, Germany, June 2002.

Error-Free Garbage Collection Traces: How to Cheat and Not Get Caught. Matthew Hertz, Stephen M. Blackburn, J. Eliot B. Moss, Kathryn S. McKinley, and Darko Stefanovic. ACM SIGMETRICS, Marina Del Rey, California, June 2002.

Deoxyribozyme-Based Logic Gates. Milan N. Stojanovic, Tiffany Elizabeth Mitchell, and Darko Stefanovic. Journal of the American Chemical Society, 124(14), 3555-3561 (2002).

SIND: A Framework for Binary Translation. Trek Palmer, Dino Dai Zovi, and Darko Stefanovic. Technical Report TR-CS-2001-38, Department of Computer Science, University of New Mexico, December 2001.

On Models for Object Lifetime Distributions. Darko Stefanovic, Kathryn S. McKinley, and J. Eliot B. Moss. ISMM 2000 (International Symposium on Memory Management), Minneapolis, Minnesota, October 2000.

On Availability of Bit-narrow Operations in General-purpose Applications. Darko Stefanovic and Margaret Martonosi. FPL 2000, The 10th International Conference on Field Programmable Logic and Applications, Villach, Austria, August 2000. (Springer-Verlag LNCS 1896)

Limits and Graph Structure of Available Instruction-Level Parallelism. Darko Stefanovic and Margaret Martonosi. Euro-Par 2000, European Conference on Parallel Computing, Munich, Germany, August-September 2000. (Springer-Verlag LNCS 1900)

Age-Based Garbage Collection. Darko Stefanovic, J. Eliot B. Moss, and Kathryn S. McKinley. Proceedings of the ACM Conference on Object-Oriented Programming Systems, Languages, and Applications, Denver, Colorado, November 1999.

Properties of Age-Based Automatic Memory Reclamation Algorithms. Darko Stefanovic. (PhD dissertation, University of Massachusetts, 1999) Postscript, gzipped (1.7MB) or PDF (14MB)

Learning to Schedule Straight-Line Code. J. Eliot B. Moss, Paul E. Utgoff, John Cavazos, Doina Precup, Darko Stefanovic, Carla Brodley, and David Scheeff. Neural Information Processing Systems -- Natural and Synthetic, Denver, Colorado, December 1997.

Characterisation of object behaviour in Standard ML of New Jersey. Darko Stefanovic and J. Eliot B. Moss. Proceedings of the 1994 ACM Conference on Lisp and Functional Programming, pp 43-54 (Orlando, Florida, 27-29 June 1994). LISP Pointers 7(3), July-September 1994.

Generational copying garbage collection for Standard ML: a quantitative study. Darko Stefanovic. (MS Project Report, University of Massachusetts) December 1993.

The Garbage Collection Toolkit as an Experimentation Tool. Darko Stefanovic OOPSLA '93 Workshop on Memory Management and Garbage Collection, Washington, DC, September 1993.

A Comparative Performance Evaluation of Write Barrier Implementations , Antony L. Hosking, J. Eliot B. Moss and Darko Stefanovic. Proceedings of the ACM Conference on Object-Oriented Programming Systems, Languages, and Applications, pp 92-109 (Vancouver, Canada, October 1992). ACM SIGPLAN Notices 27(10), October 1992.


Other writings

Networks and Operating Systems for Smart Spaces, E.G. Sirer, D. Stefanovic, R. Dimitrov, S. Venkatesan, S. Neema, and H. Simitci, panel presentation at DARPA/ITO Graduate Student Workshop, Arlington, Virginia, July 1998.

Rethinking age-based garbage collectors, white paper for DARPA/ITO Graduate Student Workshop, Arlington, Virginia, July 1998.

Oldest-First Garbage Collection, Technical Report UM-CS-1998-081 D. Stefanovic, J.E.B. Moss, & K.S. McKinley January, 1998. (Revised April 1998.)

The character of the instruction scheduling problem March 1997.

Adaptive Prefetching using Neural Networks John Cavazos and Darko Stefanovic. August 1996.

Object-level tracing toolkit: design, implementation, and purpose September 1995.

Language Implementor's Guide to the Garbage Collection Toolkit (draft) April 1995.

Adaptive compilation for complex uniprocessor hardware Katja Daumueller and Darko Stefanovic. December 1994.

A note on data access patterns in Standard ML of New Jersey. May 1994.

An experimental optimising compiler for Modula-X June 1994.

Implementing a small imperative language with safe dynamic allocation April 1993.


Contributions to the DIMACS implementation challenge, 1995-1996