Papers, Presentations, Theses, and Patents

Here are links to our research output. 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.

Storing with Molecules

title: Automated Routing of Droplets for DNA Storage on a Digital Microfluidics Platform authors: Ajay Manicka, Andrew Stephan, Sriram Chari, Gemma Mendonsa, Peyton Okubo, John Stolzberg-Schray, Anil Reddy, and Marc Riedel to appear: Royal Society of Chemistry – Digital Discovery, 2023

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Computing with Molecules

title: Digital Circuits and Neural Networks Based on Acid-Base Chemistry Implemented by Robotic Fluid Handling authors: Ahmed Agiza, Kady Oakley, Jacob Rosenstein, Brenda Rubenstein, Eunsuk Kim, Marc Riedel, and Sherief Reda appeared in: Nature Communications, Vol. 14, No. 496, 2023

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title: Computing Mathematical Functions with Chemical Reactions via Stochastic Logic authors: Arnav Solanki, Tonglin Chen, and Marc Riedel appeared in: PLOS One, Vol. 18, No. 5, 2023

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title: Neural Network Execution Using Nicked DNA and Microfluidics authors: Arnav Solanki, Zak Griffin, Purab Ranjan Sutradhar, Amlan Ganguly, Marc Riedel to appear in: PLOS One, 2023

Paper

title: Parallel Pairwise Operations on Data Stored in DNA: Sorting, XOR, Shifting, and Searching authors: Arnav Solanki, Tonglin Chen, and Marc Riedel to appear in: Natural Computing, 2023 presented at: International Workshop on Bio-Design Automation, Cambridge, England, 2019. presented at: International Conference on DNA Computing and Molecular Programming, 2021

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title: Cascadable Stochastic Logic for DNA Storage authors: Arnav Solanki, Tonglin Chen and Marc Riedel presented at: IEEE Visual Communications and Image Processing Conference, 2021

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title: Stochastic Computation on DNA strands through Hydroxyl Nicking authors: Arnav Solanki, Tonglin Chen and Marc Riedel presented at: Foundations of Nanoscience: Self-Assembled Architectures and Devices, 2020

Abstract

Poster

title: Concentration-Based Polynomial Calculations on Nicked DNA authors: Tonglin Chen and Marc Riedel presented at: IEEE International Conference on Acoustics, Speech, and Signal Processing, 2020

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title: Computing Mathematical Functions using DNA via Fractional Coding authors: Ahmad Salehi, Xingyi Liu, Marc Riedel, and Keshab K. Parhi appeared in: Nature Scientific Reports, Vol. 8 No. 8312, 2018

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Supplement

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 Computation of Complex Markov Chains with Self-Loop State Transitions authors: Ahmad Salehi, Marc Riedel and Keshab Parhi presented at: IEEE Asilomar Conference on Signals, Systems and Computers, 2017

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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. Best Paper Award finalist.

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title: Asynchronous Discrete-Time Signal Processing with Molecular Reactions authors: Ahmad Salehi, Marc Riedel, and Keshab Parhi presented at: IEEE 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: IEEE/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: IEEE 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: IEEE/ACM Design Automation Conference, San Diego, 2007; and at Synthetic Biology 3.0, Zürich, 2007.

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Computing about Molecules

title: Biased Composition of NetMHCpan Training Datasets and Evaluation of MHC-Peptide authors: Thomas Atkins, Arnav Solanki, George Vasmatzis, James Cornette, and Marc Riedel under review in: Frontiers in Immunology

Paper

title: Evasive Spike Variants Elucidate the Preservation of T cell Immune Response to the SARS-CoV-2 Omicron Variant authors: Arnav Solanki, Marc Riedel, James Cornette, Julia Udell, and George Vasmatzis under review: IEEE/ACM Trans. on Computational Biology and Bioinformatics, 2023

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title: Hydrophobicity Identifies False Positives and False Negatives in Peptide-MHC Binding authors: Arnav Solanki, Marc Riedel, James Cornette, Julia Udell, and George Vasmatzis appeared in: Frontiers in Oncology, Vol. 12, No. 1034810, 2022 presented at: Symposium on Mathematical and Computational Oncology, 2021

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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

Paper

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

Paper

Computing with Random Bit Streams

title: A Scalable Approach to Performing Multiplication and Matrix Dot-Products in Unary authors: Yadu Kiran and Marc Riedel under review: Frontiers in Nanotechnology, 2023 presented at: IEEE/ACM Great Lakes Symposium on VLSI, 2022

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title: Performing Stochastic Computation Deterministically authors: Devon Jenson and Marc Riedel appeared in: IEEE Trans. on Very Large Scale Integration Systems, Vol. 27, No. 29, pp. 2925–2938, 2019 presented at: IEEE International Symposium of Circuits and Systems, 2020 presented at: IEEE/ACM International Conference on Computer-Aided Design, 2016

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title: Synthesis of Polynomial Functions authors: Weikang Qian and Marc Riedel appeared in: Chapter 4, Stochastic Computing: Techniques and Applications, Springer, W.J Gross and V. C. Gaudet, Editors, pp. pp. 103–120, 2019

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title: Deterministic Approaches to Bitstream Computing author: Marc Riedel appeared in: Chapter 5, Stochastic Computing: Techniques and Applications, Springer, W.J Gross and V. C. Gaudet, Editors, pp. pp. 121–136, 2019

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title: A Survey of Computation-Driven Data Encodings authors: Weikang Qian, Runsheng Wang, Yuan Wang, Marc Riedel and Ru Huang presented at: IEEE Workshop on Signal Processing Systems, 2019

Paper

title: Deterministic Methods for Stochastic Computing using Low-Discrepancy Sequences authors: M. Hassan Najafi, David Lilja, and Marc Riedel presented at: IEEE/ACM International Conference on Computer-Aided Design, 2018 presented at: IEEE/ACM International Workshop on Logic and Synthesis, 2018

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title: Low Cost Sorting Network Circuits using Unary Processing authors: M. Hassan Najafi, David Lilja, Marc Riedel, and Kia Bazargan appeared in: IEEE Trans. on Very Large Scale Integration Sytems, Vol. 26, No. 8, pp. 1471–1480, 2018 presented at: IEEE International Conference on Computer Design, 2017

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title: An Overview of Time-Based Computing with Stochastic Constructs authors: M. Hassan Najafi, S. Jamali-Zavareh, David Lilja, Marc Riedel, Kia Bazargan and Ramesh Harjani appeared in: IEEE Micro, Vol. 37, No. 6, pp. 62--71, 2017	Paper
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 appeared in: IEEE Trans. on Very Large Scale Integration Systems, Vol. 25, No. 5, pp. 1644–1657, 2017 presented at: IEEE International Symposium on Circuits and Systems, 2017	Paper

title: Unary Positional Computing authors: McKenzie van der Hagen and Marc Riedel presented at: IEEE Global Conference on Signal and Information Processing, 2017

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Poster

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: IEEE/ACM Great Lakes Symposium on VLSI, 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 appeared in: IEEE Transactions on Computers, Vol. 66, No. 10, pp. 1734–1746, 2017 Feature Paper of the Month presented at: Work-in-Progress Session, IEEE/ACM Design Automation Conference, 2016 presented at: IEEE/ACM Asia and South Pacific Design Automation Conference, 2016

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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 appeared in: ACM Journal on Emerging Technologies in Computing Systems, Vol. 13, No. 4, pp. 1–28, 2017

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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: IEEE 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 Trans. on Very Large Scale Integration Systems, Vol. 22, No. 3, pp. 449–462, 2014 presented at: Power and Timing Modeling, Optimization and Simulation Workshop, 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. 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, 2009 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: IEEE/ACM 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: IEEE/ACM Design Automation Conference, Anaheim, CA, 2008

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Computing with Emerging Technology

title: A Comparison Study of Spin Transfer Torque and Spin-Orbit Torque Based Stochastic Computing Using Computational Random Access Memory (SC-CRAM) authors: Brandon Zink, Marc Riedel, Ulya Karpuzcu and Jian-Ping Wang ro appear in: IEEE Transactions on Magnetics presented at: IEEE Magnetics Recording Conference, 2023

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title: A Stochastic Computing Scheme of Embedding_Random Bit Generation and Processing in Computational Random Access Memory (SC-CRAM) authors: Brandon Zink, Yang Lv, Masoud Zabihi, Husrev Cilasun , Sachin Sapatnekar, Ulya Karpuzcu, Marc Riedel, and Jian-Ping Wang appeared in: IEEE Journal on Exploratory Solid-State Computational Devices and Circuits, Vol. 9, No. 1, pp. p. 29–37, 2023

Paper

title: Interconnects for DNA, Quantum, In-Memory, and Optical Computing authors: Amlan Ganguly, Sergi Abadal, Ishan Thakkar, Natalie Enright Jerger, Marc Riedel, Masoud Babaie, Rajeev Balasubramonian, Abu Sebastian, Sudeep Pasricha, and Baris Taskin appeared in: IEEE_Micro, Vol. 42, No. 3, pp. 40–49, 2022

Paper

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

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title: Application of LUT Cascades to Numerical Function Generators authors: Tsutomu Sasao, Jon Butler, and Marc Riedel presented at: Workshop on Synthesis And System Integration of Mixed Information Technologies, pp. 422–429, 2004

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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 Trans. 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 presented at: IEEE/ACM Int. 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. 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: IEEE/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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Slides

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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title: Tolerating Faults in Counting Networks authors: Marc Riedel and Jehoshua Bruck appeared in: Dependable Network Computing, Springer, Dimiter Avresky, Editor, 267–277, 2000

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Information Theory & Mathematics

title: Characterizing Polynomial Arithmetic with Stochastic Circuits authors: Patrick Holec, Weikang Qian, Marc Riedel, and Ivo Rosenberg to appear in: Journal of Multiple-Valued Logic and Soft Computing, 2023

Paper

title: A Study on Monotone Self-Dual Boolean Functions authors: Mustafa Altun and Marc Riedel appeared in: Acta Mathematicae Applicatae Sinica, Vol. 33, No. 1, pp. 43–52, 2017

Paper

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

Paper

title: Computing in the Rain A Reliable Array of Independent Nodes authors: Vasken Bohossian, Charles Fan, Paul LeMahieu, Marc Riedel, Lihao Xu, Jehoshua Bruck appeared in: IEEE Transactions on Parallel and Distributed Systems, Vol. 12, No. 2, pp. pp. 99–114, 2001 presented at: Int. Parallel and Distributed Processing Symposium, pp. 1204–1213, Cancun, Mexico, 2000

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Theses

title: Carving a Niche in the Intersection of Computer Engineering and Molecular Biology author: Arnav Solanki degree: Ph.D., Electrical Engineering, University of Minnesota year: 2023

Ph.D. Dissertation

title: DNA Storage and Computation author: Zoe Dormuth degree: M.S., Electrical Engineering, University of Minnesota year: 2019

M.S. Report

title: Digital Logic and Signal Processing Computations with Molecular Reactions author: Ahmad Salehi degree: Ph.D., Electrical Engineering, University of Minnesota year: 2017

Ph.D. Dissertation

title: Data Cycling in Networks: Thoughts and Experiments author: Vaibhav Desai degree: M.S., Electrical Engineering, University of Minnesota year: 2016

M.S. Thesis

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

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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

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Funding Proposals

title: Moving Millions of Droplets at Megahertz Speeds: DNA Computing, DNA Storage, and Synthetic Biology on an Industrial Platform for Digital Microfluidics Investigators: Marc Riedel, Kate Adamala, David Soloveichik, and Anil Reddy Agency: National Science Foundation Program: SemiSynBio-III Award: $1,000,000 Duration: 2022 – 2026

Proposal

title: The UMN/Mayo Computational Human Immuno-Peptidome (CHIP) Project Investigator: Marc Riedel Agency: Oracle Program: Oracle Research Fellowship Award: $200,000 Duration: 2022 – 2024

Proposal

title: Routing and Optimization of Digital Microfluidics for DNA Storage Investigator: Marc Riedel Agency: Seagate Technology Program: UMN enter for Micromagnetics and Information Technologies (MINT) Award: $115,000 Duration: 2021 – 2023 title: Storage and Processing with Native DNA Investigators: Olgica Milenkovic, Marc Riedel, David Soloveichik, Huimin Zhao, and Alvaro Hernandez Agency: DARPA Program: Molecular Informatics Award: $2,200,000 Duration: 2018 – 2022 Proposal 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 – 2018 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 – 2018 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 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: 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 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: 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 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 File:Sponsors.jpg

Patents

1.       "Parallel Computing using Stochastic Circuits and Deterministic Shuffling Networks" Soheil Mohajer, Zhiheng Wang,Kiarash Bazargan, Marc Riedel, David J. Lilja, and Sayed Abdolrasoul Faraji U.S. Patent No. 11,018,689 B2, 2021 2. "Low Discrepancy Deterministic Bit-Stream Processing Using Sobol Sequences" M. Hassan Najafi, David J. Lilja, Marc Riedel, Kia Bazargan, Sayed A. Faraji, and Bengzhe Li U.S. Patent No. 20,200,401,376 A1, 2021 3. "Sorting Networks using Unary Processing" M. Hassan Najafi, David J. Lilja, Marc Riedel, and Kia Bazargan U.S. Patent No. 20,200,143,234 A1, 2020 4. "Polysynchronous Stochastic Circuits" David J. Lilja, M. Hassan Najafi, Marc Riedel, and Kiarash Bazargan U.S. Patent No. 10,520,975 B2, 2019 5. "Stochastic Computation using Pulse-Width Modulated Signals" M. Hassan Najafi, S Jamali-Zavareh, D. J. Lilja, Marc Riedel, K. Bazargan, and R. Harjani U.S. Patent No. 10,740,686 B2, 2018 6. "Stochastic Computing on Deterministic Bit Streams" Devon Jenson and Marc Riedel U.S. Patent No. 10,063,255, 2018 7. "Synthesis of Cyclic Combinational Circuits" Marc Riedel and Jehoshua Bruck U.S. Patent No. 7,249,341, 2007 8. "A Reliable Array of Distributed Computing Nodes" Vincent Bohossian, Charles Fan, Paul LeMahieu, Marc Riedel, Lihao Xu, and Jehoshua Bruck U.S. Patent No. 6,128,277, 2000