Papers, Theses, and Presentations

All materials are subject to copyrights.

Computing with Molecules

title: Digital Signal Processing with Molecular Reactions authors: Hua Jiang, Marc Riedel and Keshab Parhi to appear in: IEEE Design & Test of Computers Special Section on Bio-Design Automation in Synthetic Biology, 2012.

Paper

title: Rate-Independent Constructs for Chemical Computation authors: Phil Senum and Marc Riedel appeared in: PLoS ONE, Volume 6, Issue 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: Digital Signal Processing with Biomolecular Reactions authors: Hua Jiang, Aleksandra Kharam, Marc Riedel and Keshab Parhi presented at: International Conference on Computer-Aided Design, San Jose, CA, 2010.

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).

Paper

Slides

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

Paper

Slides

M.S. Thesis

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

M.S. Thesis

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 will appear in: IEEE Trans. on Computer-Aided Design of Integrated Circuits and Systems, 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: Digital Yet Deliberately Random: Synthesizing Logical Computation on.Stochastic Bit Streams author: Weikang Qian dissertation: Ph.D., Electrical Engineering, University of Minnesota, 2011.

PhD Dissertation

Slides

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 will appear in: IEEE Transactions on Computers, 2011.

Paper

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, Issue 2, pp. 12--30, 2011.

Paper

title: Lattice-Based Computation of Boolean Functions authors: Mustafa Altun and Marc Riedel presented at: Design Automation Conference, Anaheim, CA, 2010.

Paper

Slides

title: Nanoscale Digital Computation Through Percolation authors: Mustafa Altun, Marc Riedel, and Claudia Neuhauser presented at: Design Automation Conference, San Francisco, CA, 2009.

Paper

Slides

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

PhD Dissertation

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, 2011.

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, 2011.

Paper

title: Cyclic Boolean Circuits authors: Marc Riedel and Shuki Bruck will appear  in: Journal of Discrete Applied Mathematics, 2011.

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

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.

Paper

Slides

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

Ph.D. Dissertation

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).

Paper

Slides

Algorithms and Data Structures

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

Slides

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

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: Pending.

Proposal

title: Digital Signal Processing with Biomolecular Reactions Investigators: Keshab Parhi and Marc Riedel Agency: National Science Foundation Program: BIO Computing 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: Exploiting Percolation and Randomness in the 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