Papers, Theses, and Presentations

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Here are links to our papers, theses, proposals, 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.


Computing with Random Bit Streams

title: Time-Encoded Values for Highly Efficient Stochastic Circuits
authors: M. Hassan Najafi, S. Jamali-Zavareh, David Lilja, Marc Riedel, Kia Bazargan and
Ramesh Harjani
to appear in: IEEE Transactions on VLSI, 2017
presented at: IEEE International Symposium on Circuits and Systems, 2017

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title: Polysynchronous Clocking: Exploiting the Skew Tolerance of Stochastic Circuits
authors: M. Hassan Najafi, David Lilja, Marc Riedel, and Kia Bazargan
to appear in: IEEE Transactions on Computers, 2017
presented at: IEEE/ACM Asia and South Pacific Design Automation Conference, 2016

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title: Computing Polynomials with Positive Coefficients using Stochastic Logic by Double NAND Expansion
authors: Ahmad Salehi, Yin Liu, Marc Riedel, and Keshab Parhi
presented at: ACM Great Lakes Symposium on VLSI, 2017

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title: A Reconfigurable Architecture with Sequential Logic-based Stochastic Computing
authors: M. Hassan Najafi, Peng Li, David J. Lilja, Weikang Qian and Marc Riedel
to appear in: ACM Journal on Emerging Technologies in Computing Systems, 2017

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title: A Deterministic Approach to Stochastic Computing
authors: Devon Jenson and Marc Riedel
presented at: IEEE/ACM International Conference on Computer-Aided Design, 2016

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title: Synthesis of Correlated Bit Streams for Stochastic Computing
authors: Yin Liu, Megha Parhi, Marc Riedel and Keshab Parhi
presented at: Asilomar Conference on Signals, Systems, and Computers, 2016

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title: Effect of Bit-Level Correlation in Stochastic Computing
authors: Megha Parhi, Marc Riedel, and Keshab Parhi
presented at: IEEE International Conference on Digital Signal Processing, Singapore, 2015.

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title: Computation on Stochastic Bit Streams: Digital Image Processing Case Studies
authors: Peng Li, David Lilja, Weikang Qian, Kia Bazargan and Marc Riedel
appeared in: IEEE Transactions on VLSI Sytems, Vol. 22, No. 3, pp. 449–462, 2014
appeared in: Lecture Notes in Computer Science
Power and Timing Modeling, Optimization and Simulation Workshop

G. Goos, J. Hartmanis, and J. V. Leeuwen Editors, Springer, pp. 235–244, 2012

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title: Logical Computation on Stochastic Bit Streams with Linear Finite State Machines
authors: Peng Li, David Lilja, Weikang Qian,Kia Bazargan and Marc Riedel
appeared in: IEEE Transactions on Computers, Vol. 63, No. 6., pp. 1474–1486, 2014
presented at: IEEE/ACM Asia and South Pacific Design Automation Conference,
Sydney, Australia, 2012

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title: IIR Filters Using Stochastic Arithmetic
authors: Naman Saraf, Kia Bazargan, David Lilja, and Marc Riedel
appeared in: IEEE/ACM Design, Automation, and Test in Europe, 2014

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title: Stochastic Functions Using Sequential Logic
authors: Naman Saraf, Kia Bazargan, David Lilja, and Marc Riedel
appeared in: IEEE International Conference on Computer Design, Asheville, NC, 2013

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title: An Efficient Implementation of Numerical Integration Using Logical Computation
on Stochastic Bit Streams
authors: Weikang Qian, Cheng Wang, Peng Li, David Lilja,
Kia Bazargan and Marc Riedel
appeared in: IEEE/ACM Int'l Conference on Computer-Aided Design, San Jose, CA 2012

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title: The Synthesis of Complex Arithmetic Computation on Stochastic Bit Streams Using Sequential Logic
authors: Peng Li, David Lilja, Weikang Qian, Kia Bazargan and Marc Riedel
presented at: IEEE/ACM International Conference on Computer-Aided Design, San Jose, CA 2012
presented at: IEEE/ACM International Workshop on Logic and Synthesis, Berkeley, CA 2012

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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
appeared in: Advanced Techniques in Logic Synthesis, Optimizations and Applications
Sunil Khatri and Kanupriya Gulati editors, Springer Publishing, 2011
presented at: IEEE/ACM International Conference on Computer-Aided Design, San Jose, 2009
(nominated for IEEE/ACM William J. McCalla ICCAD Best Paper Award).
presented at: IEEE/ACM International Workshop on Logic and Synthesis, Berkeley, CA, 2009

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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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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
presented at: IEEE/ACM International Workshop on Logic and Synthesis, San Diego, CA, 2007

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

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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: IEEE International Symposium on Quality Electronic Design, San Jose, CA, 2009.

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

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Poster

title: The Synthesis of Robust Polynomial Arithmetic with Stochastic Logic
authors: Weikang Qian and Marc Riedel
presented at: ACM Design Automation Conference, Anaheim, CA, 2008

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Computing with Molecules

title: Chemical Reaction Networks for Computing Polynomials
authors: Ahmad Salehi, Keshab Parhi and Marc Riedel
appeared as: ACS Synthetic Biology,Vol. 6, No. 1, pp. 76–83, 2017
presented at: IEEE Globecom Symposium, 2016

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title: Molecular Sensing and Computing Systems
authors: Ahmad Salehi, Marc Riedel, Keshab Parhi
appeared as: IEEE Trans. on Molecular, Biological, and Multi-Scale Communications,
Vol. 1, No. 3, 2015

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title: Markov Chain Computations using Molecular Reactions
authors: Ahmad Salehi, Marc Riedel, Keshab Parhi
presented at: IEEE International Conference on Digital Signal Processing, 2015.

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title: Asynchronous Discrete-Time Signal Processing with Molecular Reactions
authors: Ahmad Salehi, Marc Riedel, and Keshab Parhi
presented at: Asilomar Conference on Signals, Systems, and Computers, 2014.

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

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title: Discrete-Time Signal Processing with DNA
authors: Hua Jiang, Ahmad Salehi, Marc Riedel and Keshab Parhi
appeared in: ACS Synthetic Biology, Vol. 2 no. 5, pp. 245–254, 2013.
Supplementary Information: List of Reactions
appeared in: IEEE Design & Test of Computers, Vol. 29, No. 3, pp. 21–31, 2012.
presented at: IEEE/ACM International Conference on Computer-Aided Design,
San Jose, CA, 2010.
presented at: IEEE Workshop on Signal Processing Systems, San Francisco, 2010

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

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title: Asynchronous Computation with Molecular Reactions
authors: Hua Jiang, Marc Riedel and Keshab Parhi
presented at: Asilomar Conference on Signals, Systems, and Computers, Pacific Grove, CA, 2011.

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

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

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

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Computing about Molecules

title: Gene Regulatory Network Modeling Using Literature Curated and High Throughput Data
authors: Vishwesh Kulkarni, Reza Arastoo, Anupama Bhat,
Kalyansundaram Subramanian, Mayuresh Kothare, Marc Riedel and Marc Riedel
appeared in: Systems and Synthetic Biology, Vol. 6, No. 3–4, pp. 69--77, 2012

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title: Characterizing the Memory of the GAL Regulatory Network in
Saccharomyces cerevisiae
authors: Vishwesh Kulkarni, Venkatesh Kareenhalli, Ganesh Viswananthan, and Marc Riedel
appeared in: Systems and Synthetic Biology, Vol. 5, No. 3–4, pp. 97--104, 2011

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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: ACM 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: ACM Design Automation Conference, San Francisco, CA, 2009.

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Computing with Feedback

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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title: The Synthesis of Cyclic Dependencies with Boolean Satisfiability
authors: John Backes and Marc Riedel
appeared in: ACM Transactions on Design Automation of Electronic Systems
Vol. 17, No. 4, pp. 1–24, 2012

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title: The Analysis and Mapping of Cyclic Circuits with Boolean Satisfiability
authors: John Backes, Brian Fett, and Marc Riedel
appeared as: Technical Report, UMN
presented at: IEEE/ACM Int'l Conference on Computer-Aided Design, San Jose, CA, 2008

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

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

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title: Cyclic Combinational Circuits: Analysis for Synthesis
authors: Marc Riedel and Shuki Bruck
presented at: IEEE/ACM Int'l Workshop on Logic and Synthesis, Orange County, CA, 2003

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title: The Synthesis of Cyclic Combinational Circuits
authors: Marc Riedel and Shuki Bruck
presented at: ACM 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: IEEE/ACM 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: IEEE/ACM International Workshop on Logic Synthesis, La Jolla, CA, 2011

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

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Mathematics

title: Synthesizing Cubes to Satisfy a Given Intersection Pattern
authors: Weikang Qian, Marc Riedel, and Ivo Rosenberg
appeared in: Journal of Discrete Applied Mathematics, Vol. 193, pp. 11–38, 2015
presented at: IEEE/ACM International Workshop on Logic and Synthesis, Irvine, CA, 2010

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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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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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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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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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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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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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Funding Proposals

title: Back to the Future with Printed, Flexible Electronics:
Design in a Post-CMOS Era when Transistor Counts Matter Again
Investigators: Kia Bazargan, Daniel Frisbie, Ramesh Harjani, David Lilja and Marc Riedel.
Agency: National Science Foundation
Program: Software and Hardware Foundations
Award: $800,000
Duration: 2014 – 2017

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Proposal

title: Advanced Signal Processing with DNA
Investigators: Keshab Parhi and Marc Riedel
Agency: National Science Foundation
Program: Computing and Communications Foundations.
Amount: $300,000
Duration: 2014 – 2017

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Proposal

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: Synthesizing Signal Processing Functions with Biochemical Reactions
Investigators: Yiannis Kaznessis, Claudia Dannert Schmidt and Marc Riedel
Agency: University of Minnesota
Program: Digital Technology Center Seed Grant.
Amount: $100,000
Duration: 2011 – 2012

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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: Tackling the Stochastic Simulation of Biochemical_Networks with Real Computing Power
Investigators: Marc Riedel and Tim Mullins (IBM)
Agency: University of Minnesota
Program: Biomedical Informatics and Computational Biology Traineeships
Amount: $78,000
Duration: 2007 – 2009

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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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