Publications

(2021). Science Forum: Building a community to engineer synthetic cells and organelles from the bottom-up. eLife, 10:e73556 (2021).

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(2021). Complexing Deoxyribozymes with RNA Aptamers for Detection of the Small Molecule Theophylline. Biosensors and Bioelectronics, 198, 113774 (2022).

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(2021). Diverse applications of DNAzymes in computing and nanotechnology. S. Müller, B. Masquida, W. Winkler (eds.), Ribozymes, Chapter 25. Wiley-VCH.

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(2021). Development and Application of Catalytic DNA in Nanoscale Robotics. E. Katz (ed.), DNA- and RNA-Based Computing Systems, Chapter 15. Wiley-VCH.

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(2020). Robust heterochiral strand displacement using leakless translators. ACS Synthetic Biology 9(7), 1907–1910.

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(2020). Reservoir Computing with Random Chemical Systems. ALife 2020.

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(2020). The effect of polyvalency on tethered molecular walkers on independent 1D tracks. Physical Review E, 101, 062101.

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(2019). Repeated Reuse of Deoxyribozyme-Based Logic Gates. Nano Letters, 19, 7655-7661.

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(2019). Microcompartments for Protection and Isolation of Nanoscale DNA Computing Elements. ACS Applied Materials & Interfaces.

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(2018). Verifiably Lazy: Verified Compilation of Call-by-Need. IFL.

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(2017). A Microsphere-Supported Lipid Bilayer Platform for DNA Reactions on a Fluid Surface. ACS Applied Materials & Interfaces, 9 (35), 30185-30195.

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

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(2017). 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.

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

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

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

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

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

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(2015). Scalable Design of Logic Circuits Using an Active Molecular Spider System. IPCAT.

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

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

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(2015). A Principled Approach to HPC Event Monitoring. FTXS.

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(2015). Exploring Transfer Function Nonlinearity in Echo State Networks. CISDA.

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

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(2014). Towards a Calculus of Echo State Networks. BICA.

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

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

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

(2014). Reservoir Computing Approach to Robust Computation Using Unreliable Nanoscale Networks. UCNC.

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

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

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

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

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

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

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(2014). 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.

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

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(2013). Modular Verification of DNA Strand Displacement Networks via Serializability Analysis. DNA19.

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(2013). DNA Reservoir Computing: A Novel Molecular Computing Approach. DNA19.

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(2013). Catalytic Molecular Walkers: Aspects of Product Release. ECAL.

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

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(2013). Computing Game Strategies. CiE.

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(2013). An example conference paper. In ICW.

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

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

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(2012). Towards a Biomolecular Learning Machine. UCNC.

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(2012). DNA18, 18th International Conference on DNA Computing and Molecular Programming.

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

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(2012). 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.

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

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(2011). ISO: Numeric Representation of Nucleic Acid Form. BCB.

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

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

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(2010). Shape Analysis With Reference Set Relations. VMCAI.

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

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

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(2009). Advancing the Deoxyribozyme-Based Logic Gate Design Process. DNA15.

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

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

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

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

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

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

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

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

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(2008). 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.

(2007). Heap Analysis in the Presence of Collection Libraries. PASTE.

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

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(2006). A Static Heap Analysis for Shape and Connectivity: Unified Memory Analysis: The Base Framework. LCPC.

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

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(2006). The DaCapo Benchmarks: Java Benchmarking Development and Analysis. OOPSLA.

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

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

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

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

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

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(2006). 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.

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

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

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

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(2005). 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.

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

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

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(2004). Building the Components for a Biomolecular Computer. DNA10.

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

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

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

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(2003). 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.

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

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

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

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

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(2000). On Models for Object Lifetime Distributions. ISMM.

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(2000). Limits and Graph Structure of Available Instruction Level Parallelism. Euro-Par.

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(1999). Age-Based Garbage Collection. OOPSLA.

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

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

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(1997). Learning to Schedule Straight-Line Code. NIPS.

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

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

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

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(1992). A Comparative Performance Evaluation of Write Barrier Implementations. OOPSLA.

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