Papers, Presentations, Theses, Proposals, and Patents

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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
appeared in:	Royal Society of Chemistry – Digital Discovery, Vol. 2, pp. 1436–1451, 2023

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

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

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, Vol. 18, No. 10, 2023

title:	Parallel Pairwise Operations on Data Stored in DNA: Sorting, XOR, Shifting, and Searching
authors:	Arnav Solanki, Tonglin Chen, and Marc Riedel
appeared:	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

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

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

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

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

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

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

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

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.

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.

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.

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

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.

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

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.

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.

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

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

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

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.

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.

Computing about Molecules

title:	Geographically Biased Composition of NetMHCpan Training Datasets and Evaluation of MHC-Peptide
authors:	Thomas Atkins, Arnav Solanki, George Vasmatzis, James Cornette, and Marc Riedel
appeared in:	Frontiers in Immunology, Vol. 14, 2023

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
appeared in:	IEEE/ACM Trans. on Computational Biology and Bioinformatics, pp. 1–11, March, 2024

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

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

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

Computing with Random Bit Streams

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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.

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

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

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

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

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

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

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

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

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

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

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

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.

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

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

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
appeared in:	IEEE Transactions on Magnetics, 2023
presented at:	IEEE Magnetics Recording Conference, 2023

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

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

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.

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.

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

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

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

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

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

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

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

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).

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

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

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

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

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

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

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

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

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

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

Theses

title:	Carving a Random Access DNA Registers
author:	Jake Kaslewicz
degree:	M.S., Electrical & Computer Engineering, University of Minnesota
year:	2023

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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