Publications, Theses, and Presentations

From The Circuits and Biology Lab at UMN

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 1 Computing with Molecules 2 Computing about Molecules 3 Computing with Random Bit Streams 4 Computing with Nanoscale Lattices 5 Computing with Feedback 6 Algorithms and Data Structures 7 Mathematics 8 Theses 9 Funding Proposals

Computing with Molecules

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.

Paper

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.

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

Paper

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.

Paper

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.

Paper

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.

Paper

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.

Paper

Slides

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.

Paper

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.

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.

Paper

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.

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.

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.

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.

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.

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).

Paper

Slides

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.

Paper

Slides

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.

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.

Paper

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.

Paper

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.

Paper

Slides

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.

Paper

Slides

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.

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.

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.

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.

Paper

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.

Paper

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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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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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Slides

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.

Paper

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.

Paper

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.

Paper

Slides

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.

Paper

Slides

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

Paper

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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.

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.

Ph.D. Dissertation

Slides

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

Ph.D. Dissertation

Slides

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

Ph.D. Dissertation

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.

Ph.D. Dissertation

Slides

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

M.S. Thesis

Slides

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

M.S. Thesis

Slides

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.

Ph.D. Dissertation

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

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

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

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

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

Proposal

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