Papers, Presentations, Theses, Proposals, and Patents

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 under review: PLOS One, 2023

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title: Parallel Pairwise Operations on Data Stored in DNA: Sorting, XOR, Shifting, and Searching authors: Arnav Solanki, Tonglin Chen, and Marc Riedel under review 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 Int. Conference on Visual Communications and Image Processing, 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

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Poster

title: Concentration-Based-Polynomial-Calculations-on-Nicked-DNA authors: Tonglin Chen and Marc Riedel presented at: IEEE Int. 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 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 Int. 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: 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 Int'l 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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Slides

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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Slides

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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