Publications

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. A Microsphere-Supported Lipid Bilayer Platform for DNA Reactions on a Fluid Surface. ACS Applied Materials & Interfaces, 2017.

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. Feedforward Chemical Neural Network: A Cellular Chemical System That Learns XOR. Artificial Life, 23, 295-317, 2017.

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. Implementing Molecular Logic Gates, Circuits, and Cascades Using DNAzymes. A. Adamatzky (ed.), Advances in Unconventional Computing Volume 2: Prototypes, Models and Algorithms, Emergence, Complexity and Computation, volume 23, chapter 1, pages 1-28. Springer International Publishing, 2017.

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. Logic Circuits Based on Molecular Spider Systems. BioSystems, 146, 10-25, 2016.

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. Modular Verification of Chemical Reaction Network Encodings via Serializability Analysis. Theoretical Computer Science, 632, 21-42, 2016.

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. Cactus Environment Machine: Shared Environment Call-by-Need. TFP, 2016.

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. Supervised Learning in Adaptive DNA Strand Displacement Networks. ACS Synthetic Biology, 5(8), 885-897, 2016.

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. Computational Capacity and Energy Consumption of Complex Resistive Switch Networks. AIMS Materials Science, 2(4), 530-545, 2015.

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. Hierarchical Composition of Memristive Networks for Real-Time Computing. NANOARCH, 2015.

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. Product reservoir computing: Time-Series Computation With Multiplicative Neurons. IJCNN, 2015.

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. A Principled Approach to HPC Event Monitoring. FTXS, 2015.

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. Exploring Transfer Function Nonlinearity in Echo State Networks. CISDA, 2015.

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. A Unified Sensor Architecture for Isothermal Detection of Double-Stranded DNA, Oligonucleotides, and Small Molecules. ChemBioChem, 16, 725-730, 2015.

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. Towards a Calculus of Echo State Networks. BICA, 2014.

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. Design of a Biochemical Circuit Motif for Learning Linear Functions. Journal of the Royal Society Interface, 11(101), 20140902, 2014.

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. Biophysically Inspired Rational Design of Structured Chimeric Substrates for DNAzyme Cascade Engineering. PLoS ONE, 9(10): e110986, 2014.

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. Natural Computing, Volume 13, Issue 4. 2014.

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. Visual Displays That Directly Interface and Provide Read Outs of Molecular States via Molecular Graphics Processing Units. Angewandte Chemie, 53(35), 9222-9225, 2014.

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. A Model for Variation- and Fault-Tolerant Digital Logic Using Self-Assembled Nanowire Architectures. NANOARCH, 2014.

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. Signal Propagation in Multi-Layer DNAzyme Cascades Using Structured Chimeric Substrates. Angewandte Chemie, 53(28), 7183-7187, 2014.

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. Exercises in Molecular Computing. Accounts of Chemical Research, 47 (6) 1845-1852, 2014.

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. Catalytic Molecular Logic Devices by DNAzyme Displacement. ChemBioChem, 15, 950-954, 2014.

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. Training an Asymmetric Signal Perceptron Through Reinforcement in an Artificial Chemistry. Journal of the Royal Society Interface, 11(93), 20131100, 2014.

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. The Effects of Multivalency and Kinetics in Nanoscale Search by Molecular Spiders. S. Cagnoni, M. Mirolli, and M. Villani (eds.), Evolution, Complexity and Artificial Life. Springer, 2014.

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. Lattice Gases With a Point Source. Journal of Statistical Mechanics: Theory and Experiment, P09003, 2014.

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. DNA Reservoir Computing: A Novel Molecular Computing Approach. DNA19, 2013.

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. Catalytic Molecular Walkers: Aspects of Product Release. ECAL, 2013.

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. First-Passage Time Properties of Molecular Spiders. Physical Review E, 88, 012724, 2013.

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. Computing Game Strategies. CiE, 2013.

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. Superdiffusive Transport by Multivalent Molecular Walkers Moving Under Load. Physical Review E, 87, 062713, 2013.

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. Cooperative Linear Cargo Transport With Molecular Spiders. Natural Computing, 12(2), 259-276, 2013.

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. Towards a Biomolecular Learning Machine. UCNC, 2012.

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. The Effects of Multivalency and Kinetics in Nanoscale Search by Molecular Spiders. WIVACE, 2012.

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. Some Experiments and Models in Molecular Computing and Robotics. E. Katz (ed.), Biomolecular Computing: From Unconventional Computing to ``Smart” Biosensors and Actuators, Chapter 8. Wiley-VCH, 2012.

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. Optimizing Cross-Reactivity With Evolutionary Search for Sensors. Journal of the American Chemical Society, 134(3), 1642-1647, 2012.

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. ISO: Numeric Representation of Nucleic Acid Form. BCB, 2011.

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. Chemistry at a Higher Level of Abstraction. Journal of Computational and Theoretical Nanoscience, 8(3), 434-440, 2011.

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. Mechanism of Diffusive Transport in Molecular Spider Models. Physical Review E, 83, 021117, 2011.

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. Shape Analysis With Reference Set Relations. VMCAI, 2010.

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. Training a Molecular Automaton to Play a Game. Nature Nanotechnology, 5, 773-777, 2010.

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. Molecules That Reason. Nature Nanotechnology, 10(4), 625-626 (News & Views), 2009.

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. Evolving the Deoxyribozyme Based Logic Gate Design Process Through Maya II Reconstruction. DNA15, 2009.

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. High-Resolution Cross Reactive Array for Alkaloids. Chemical Communications, 22, 3193-3195, 2009.

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. Molecular Automata. R. A. Meyers (ed.), Encyclopedia of Complexity and System Science, Springer, 2009.

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. Sharing Analysis of Arrays, Collections, and Recursive Structures. PASTE, 2008.

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. DNA Computers for Work and Play. Scientific American, 299 (5), 84-91, 2008.

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. Wake Up and Smell the Coffee: Evaluation Methodology for the 21st Century. Communications of the ACM (Research Highlights), 51 (8), 83-89, 2008.

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. Identification of Heap-Carried Data Dependence via Explicit Store Heap Models. LCPC, 2008.

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. Efficient Context-Sensitive Shape Analysis With Graph Based Heap Models. CC, 2008.

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. Nanocomputing. O. Shoseyov and I. Levy (eds.), NanoBioTechnology: BioInspired Devices and Materials of the Future, Humana Press, 2008.

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. Emerging Models of Computation Directions in Molecular Computing. M. Wirsing, J.-P. Banâtre, M. Hölzl, and A. Rauschmayer (eds.), Software-Intensive Systems and New Computing Paradigms, Springer, 2008.

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. Heap Analysis in the Presence of Collection Libraries. PASTE, 2007.

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. A Rational Approach to Minimal High-Resolution Cross-Reactive Arrays. Journal of the American Chemical Society, 128(47), 15278-15282, 2006.

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. Static Heap Analysis for Automatic Parallelization. LCPC, 2006.

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. Medium Scale Integration of Molecular Logic Gates in an Automaton. Nano Letters, 6(11), 2598-2603, 2006.

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. The DaCapo Benchmarks: Java Benchmarking Development and Analysis. 2006.

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. Behavior of Polycatalytic Assemblies in a Substrate Displaying Matrix. Journal of the American Chemical Society, 128(39), 12693-12699, 2006.

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. On the Prediction of Java Object Lifetimes. IEEE Transactions on Computers, 55(7), 880-892, 2006.

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. Generating Object Lifetime Traces With Merlin. ACM Transactions on Programming Languages and Systems, 28(3), 476-516, 2006.

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. Characterization of Transverse Channel Concentration Profiles Obtainable With a Class of Microfluidic Networks. Langmuir, 22(9), 4452-4455, 2006.

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. Deoxyribozyme-Based Three-Input Logic Gates and Construction of a Molecular Full Adder. Biochemistry, 45(4), 1194-1199, 2006.

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. Solution Phase Molecular Scale Computation With Deoxyribozyme Based Logic Gates and Fluorescent Readouts. V. V. Didenko (ed.), Fluorescent Energy Transfer Nucleic Acid Probes, Humana Press, 2006.

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. Deoxyribozyme-Based Ligase Logic Gates and Their Initial Circuits. Journal of the American Chemical Society, 127(19), 6914-6915, 2005.

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

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. Randomized Instruction Set Emulation. ACM Transactions on Information and System Security, 8(1), 3-40, 2005.

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

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. Computing With Nucleic Acids. I. Willner and E. Katz (eds.), Bioelectronics: From Theory to Applications, Wiley-VCH, 2005.

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. The Triton Branch Predictor. Technical Report TR-CS-2004-28, Department of Computer Science, University of New Mexico, 2004.

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. Building the Components for a Biomolecular Computer. DNA10, 2004.

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. Randomized Instruction Set Emulation to Disrupt Binary Code Injection Attacks. CCS, 2003.

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. Model Checking Reconfigurable Processor Configurations for Safety Properties. FPL, 2003.

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. A Deoxyribozyme-Based Molecular Automaton. Nature Biotechnology, 21, 1069-1074, 2003.

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. Deoxyribozyme-Based Half Adder. Journal of the American Chemical Society, 125(22), 6673-6676, 2003.

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. Implicit-OR tiling of Deoxyribozymes: Construction of Molecular Scale OR, NAND, and Four-Input Logic Gates. Journal of the Serbian Chemical Society, 68(4-5), 321-326, 2003.

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. Older-First Garbage Collection in Practice: Evaluation in a Java Virtual Machine. MSP, 2002.

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. Error-Free Garbage Collection Traces: How to Cheat and Not Get Caught. SIGMETRICS, 2002.

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. Deoxyribozyme-Based Logic Gates. Journal of the American Chemical Society, 124(14), 3555-3561, 2002.

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. SIND: A Framework for Binary Translation. Technical Report TR-CS-2001-38, Department of Computer Science, University of New Mexico, 2001.

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. On Models for Object Lifetime Distributions. ISMM, 2000.

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. Age-Based Garbage Collection. OOPSLA, 1999.

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. Properties of Age Based Automatic Memory Reclamation Algorithms. PhD dissertation, University of Massachusetts, 1999.

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. Oldest-First Garbage Collection. Technical Report UM-CS-1998-081, Department of Computer Science, University of Massachusetts, 1998.

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. Learning to Schedule Straight-Line Code. NIPS, 1997.

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. The Character of the Instruction Scheduling Problem. Report, Department of Computer Science, University of Massachusetts, 1997.

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. Generational Copying Garbage Collection for Standard ML: A Quantitative Study. MS project report, University of Massachusetts, 1993.

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. The Garbage Collection Toolkit as an Experimentation Tool. Object-Oriented Programming Systems, Languages, and Applications (OOPSLA), Workshop on Memory Management and Garbage Collection, 1993.

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. A Comparative Performance Evaluation of Write Barrier Implementations. OOPSLA, 1992.

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