Publications, Theses, and Presentations

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Here are links to our papers, theses, and presentations. When several version of a paper were published, for instance one in conference proceedings and another in a journal, these are grouped together and only the most significant version is linked. All materials are subject to copyrights.

Contents

Computing with Molecules

title: Digital Logic with Molecular Reactions
authors: Hua Jiang, Marc Riedel, Keshab Parhi
presented at: The International Conference on Computer-Aided Design, San Jose, CA, 2013.

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Paper

title: Discrete-Time Signal Processing with DNA
authors: Hua Jiang, Ahmed Salehi, Marc Riedel and Keshab Parhi
to appear in: ACS Synthetic Biology, 2013.
Supplementary Information: List of Reactions
appeared in: IEEE Design & Test of Computers, Vol. 29, No. 3, pp. 21–31, 2012.
presented at: International Conference on Computer-Aided Design, San Jose, CA, 2010.

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Slides

title: Robust Tunable In Vitro Transcriptional Oscillator Networks
authors: Vishwesh Kulkarni, Thee Chanyaswad, Marc Riedel and Jongmin Kim
presented at: Allerton Conference, Urbana-Champaign, IL, 2012.

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Paper

title: Rate-Independent Constructs for Chemical Computation
authors: Phil Senum and Marc Riedel
appeared in: PLoS ONE, Vol. 6, No. 6, 2011.
Supplementary Information

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Paper

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Slides

title: Synchronous Sequential Computation with Molecular Reactions
authors: Hua Jiang, Marc Riedel and Keshab Parhi
presented at: Design Automation Conference, San Diego, CA, 2011.

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Slides

title: Binary Counting with Chemical Reactions
authors: Aleksandra Kharam, Hua Jiang, Marc Riedel and Keshab Parhi
presented at: Pacific Symposium on Biocomputing, Hawaii, 2011.

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Slides

title: Writing and Compiling Code into Biochemistry
authors: Adam Shea, Brian Fett, Marc Riedel, and Keshab Parhi
presented at: International Conference on Computer-Aided Design , San Jose, CA, 2009; and at
Pacific Symposium on Biocomputing, Kona, Hawaii, 2010 (see blog).

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Slides

title: Stochastic Transient Analysis of Biochemical Systems
authors: Bin Cheng and Marc Riedel
presented at: Pacific Symposium on Biocomputing, Hawaii, 2009.

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Paper

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Slides

title: Module Locking in Biochemical Systems
authors: Brian Fett and Marc Riedel
presented at: International Conference on Computer-Aided Design, San Jose, CA, 2008; and at
Synthetic Biology 4.0, Hong Kong, 2008.

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Paper

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title: Synthesizing Stochasticity in Biochemical Systems
authors: Brian Fett, Shuki Bruck, and Marc Riedel
presented at: Design Automation Conference, San Diego, 2007; and at
Synthetic Biology 3.0, Zürich, 2007.

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Slides

Computing about Molecules

title: Characterizing the Memory of the GAL Regulatory Network in
Saccharomyces cerevisiae
authors: Vishwesh Kulkarni, Venkatesh Kareenhalli, Ganesh Viswananthan, and Marc Riedel
to appear in: Systems and Synthetic Biology, 2011.

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Paper

Computing with Random Bit Streams

title: Synthesizing Logical Computation on Stochastic Bit Streams
authors: Weikang Qian and Marc Riedel
submitted to: Proceedings of the IEEE, 2011.
presented at: Design Automation Conference, Anaheim, CA, 2008.
Nominated as a Research Highlight, Communications of the ACM, 2010.

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Slides

title: Transforming Probabilities with Combinational Logic
authors: Weikang Qian, Marc Riedel, Hongchao Zhou, and Jehoshua Bruck
appeared in: IEEE Trans. on Computer-Aided Design of Integrated Circuits and Systems,
Vol. 30, No. 9, pp. 1279–1292, 2011.

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Paper

title: An Architecture for Fault-Tolerant Computation with Stochastic Logic
authors: Weikang Qian, Xin Li, Marc Riedel, Kia Bazargan, and David Lilja
appeared in: IEEE Transactions on Computers, Vol. 60, No. 1, pp. 93–105, 2011.

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Paper

title: Synthesizing Combinational Logic to Generate Probabilities: Theories and Algorithms
authors: Weikang Qian, Marc Riedel, Kia Bazargan, and David Lilja
appeared in: Advanced Techniques in Logic Synthesis, Optimizations and Applications
Sunil Khatri and Kanupriya Gulati editors, Springer Publishing, 2011.

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Paper

title: The Synthesis of Stochastic Circuits for Nanoscale Computation
authors: Weikang Qian, John Backes, and Marc Riedel
appeared in: International Journal of Nanotechnology and Molecular Computation,
Vol. 1, No. 4, pp. 39–57, 2010.

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Paper

title: Two-Level Logic Synthesis for Probabilistic Computation
authors: Weikang Qian and Marc Riedel
presented at: International Workshop on Logic and Synthesis, Irvine, CA, 2010.

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Paper

title: The Synthesis of Combinational Logic to Generate Probabilities
authors: Weikang Qian, Marc Riedel, Kia Bazargan, and David Lilja
presented at: International Conference on Computer-Aided Design, San Jose, 2009
(nominated for IEEE/ACM William J. McCalla ICCAD Best Paper Award).

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title: A Reconfigurable Stochastic Architecture for Highly Reliable Computing
authors: Xin Li, Weikang Qian, Marc Riedel, Kia Bazargan, and David Lilja
presented at: Great Lakes Symposium on VLSI, Boston, MA, 2009.

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title: Estimation and Optimization of Reliability of Noisy Digital Circuits
authors: Satish Sivaswamy, Kia Bazargan and Marc Riedel
presented at: International Symposium on Quality Electronic Design, San Jose, CA, 2009.

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Paper

title: The Synthesis of Stochastic Logic to Perform Multivariate Polynomial Arithmetic
authors: Weikang Qian and Marc Riedel
presented at: International Workshop on Logic and Synthesis, Lake Tahoe, CA, 2008.

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Paper

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Poster

title: The Synthesis of Stochastic Circuits for Nanoscale Computation
authors: Weikang Qian, John Backes, and Marc Riedel
presented at: International Workshop on Logic and Synthesis, San Diego, CA, 2007.

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Paper

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Slides

Computing with Nanoscale Lattices

title: Logic Synthesis for Switching Lattices
authors: Mustafa Altun and Marc Riedel
appear in: IEEE Transactions on Computers, Vol. 61,No. 11, pp. 1588–1600, 2012.
presented at: Design Automation Conference, Anaheim, CA, 2010.

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title: Synthesizing Logic with Percolation in Nanoscale Lattices
authors: Mustafa Altun and Marc Riedel
appeared in: International Journal of Nanotechnology and Molecular Computation,
Vol. 3, No. 2, pp. 12–30, 2011.
presented at: Design Automation Conference, San Francisco, CA, 2009.

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Computing with Feedback

title: The Synthesis of Cyclic Dependencies with Boolean Satisfiability
authors: John Backes and Marc Riedel
to appear in: ACM Transactions on Design Automation of Electronic Systems.

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Paper

title: The Analysis and Mapping of Cyclic Circuits with Boolean Satisfiability
authors: John Backes, Brian Fett, and Marc Riedel
submitted to: Journal on Satisfiability, Boolean Modeling and Computation.

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Paper

title: Cyclic Boolean Circuits
authors: Marc Riedel and Shuki Bruck
appeared  in: Discrete Applied Mathematics, Vol. 160, No. 13–14, pp. 1877–1900, 2012.

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Paper

title: The Synthesis of Cyclic Dependencies with Craig Interpolation
authors: John Backes and Marc Riedel
presented at: The International Workshop on Logic and Synthesis, Berkeley, CA, 2009.

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Slides

title: The Analysis of Cyclic Circuits with Boolean Satisfiability
authors: John Backes, Brian Fett, and Marc Riedel
presented at: The International Conference on Computer-Aided Design, San Jose, CA, 2008.

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Slides

title: Timing Analysis of Cyclic Combinational Circuits
authors: Marc Riedel and Shuki Bruck
presented at: The International Workshop on Logic and Synthesis, Temecula, CA, 2004.

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Paper

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Slides

title: The Synthesis of Cyclic Combinational Circuits
authors: Marc Riedel and Shuki Bruck
presented at: Design Automation Conference, Anahiem, CA, 2003
(winner of DAC Best Paper Award).

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Algorithms and Data Structures

title: Using Cubes of Non-state Variables With Property Directed Reachability
authors: John Backes and Marc Riedel
presented at: Design Automation & Test in Europe, Grenoble, France, 2013.

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Poster

title: Resolution Proofs as a Data Structure For Logic Synthesis
authors: John Backes and Marc Riedel
presented at: The International Workshop on Logic Synthesis, La Jolla, CA, 2011.

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Slides

title: Reduction of Interpolants For Logic Synthesis
authors: John Backes and Marc Riedel
presented at: The International Conference on Computer-Aided Design, San Jose, CA, 2010.

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Mathematics

title: Synthesizing Cubes to Satisfy a Given Intersection Pattern
authors: Weikang Qian, Marc Riedel, and Ivo Rosenberg
submitted to: Journal of Discrete Applied Mathematics, 2011.

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Paper

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Slides

title: Networks of Passive Oscillators
authors: Vishwesh V. Kulkarni, Marc Riedel, and Guy-Bart Stan
presented at: Allerton Conference, Urbana-Champaign, Illinois, 2011.

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title: Uniform Approximation and Bernstein Polynomials with Coefficients in the Unit Interval
authors: Weikang Qian, Marc Riedel, and Ivo Rosenberg
appeared in: European Journal of Combinatorics, Vol. 32, No. 3, pp. 448–463, 2011.

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Paper




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Theses

title: Algorithms and Data Structures For Logic Synthesis And Verification
Using Boolean Satisfiability

(received the University of Minnesota Doctoral Dissertation Fellowship)
author: John Backes
degree: Ph.D., Electrical and Computer Engineering, University of Minnesota
year: 2013.

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Ph.D. Dissertation

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Slides

title: Digital Logic and Signal Processing Computations with Molecular Reactions
author: Hua Jiang
degree: Ph.D., Electrical Engineering, University of Minnesota
year: 2012.

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Ph.D. Dissertation

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Slides

title: Logic Synthesis for Networks of Four-Terminal Switches
author: Mustafa Altun
degree: Ph.D., Electrical Engineering, University of Minnesota
year: 2012.

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Ph.D. Dissertation

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Slides

title: Digital Yet Deliberately Random:
Synthesizing Logical Computation on.Stochastic Bit Streams

(received the University of Minnesota Doctoral Dissertation Fellowship)
author: Weikang Qian
degree: Ph.D., Electrical Engineering, University of Minnesota
year: 2011.

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Ph.D. Dissertation

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Slides

title: Synthesizing Stochasticity in Biochemical Systems
author: Brian Fett
degree: M.S., Biomedical Informatics and Computational Biology,
University of Minnesota
year: 2010.

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M.S. Thesis

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title: Stochastic Transient Analysis of Biochemical Systems
author: Bin Cheng
degree: M.S., Electrical Engineering, University of Minnesota
year: 2010.

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M.S. Thesis

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title: Cyclic Combinational Circuits
author: Marc Riedel
degree: Ph.D., Electrical Engineering, Caltech, 2004
(winner of Charles H. Wilts Prize for the Best Ph.D. Dissertation in EE at Caltech)
year: 2004.

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Ph.D. Dissertation

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Slides




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Funding Proposals

title: Digital Yet Deliberately Random:
Synthesizing Logical Computation on Stochastic Bit Streams
Investigators: Marc Riedel, Kia Bazargan, Ramesh Harjani, and David Lilja.
Agency: National Science Foundation
Program: Software and Hardware Foundations
Award: $300,000
Duration: 2012 – 2014

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Proposal

title: Digital Signal Processing with Biomolecular Reactions
Investigators: Keshab Parhi and Marc Riedel
Agency: National Science Foundation
Program: Computing and Communications Foundations
Amount: $400,000
Duration: 2011 – 2014

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Proposal

title: Computing with Things Small, Wet, and Random – Design Automation for Digital Computation with Nanoscale Technologies and Biological Processes
Investigator: Marc Riedel
Agency: National Science Foundation
Program: NSF CAREER Award
Amount: $500,000
Duration: 2009 – 2014

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Proposal

title: Synthesizing Signal Processing Functions with Biochemical Reactions
Investigators: Keshab Parhi and Marc Riedel
Agency: National Science Foundation
Program: Computing and Communications Foundations.
Amount: $200,000
Duration: 2009 – 2011

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Proposal

title: Concurrent Logical and Physical Design of Digital Nanoscale Circuits
Investigator: Marc Riedel
Agency: SRC Focus Center Research Program (FCRP)
Program: Functional Engineered Nano-Architectonics (FENA)
Amount: $325,000
Duration: 2006 – 2009

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Proposal




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