Literature DB >> 35242267

Cytomorphic Electronic Systems: A review and perspective.

Douglas Raymond Beahm1, Yijie Deng1, Tanner G Riley2, Rahul Sarpeshkar3.   

Abstract

Boltzmann-exponential thermodynamic laws govern noisy molecular flux in chemical reactions as well as noisy subthreshold electron current flux in transistors. These common mathematical laws enable one to map and simulate arbitrary stochastic biochemical reaction networks in highly efficient cytomorphic systems built on subthreshold analog circuits. Such simulations can accurately model noisy, nonlinear, asynchronous, stiff, and non-modular feedback dynamics in interconnected networks in the physical circuits, automatically. The scaling in simulation time for stochastic networks with the number of reactions or molecules is constant in cytomorphic systems. In contrast, it grows rapidly in digital systems, which are not parallelizable. Therefore, cytomorphic systems enable large-scale supercomputing systems-biology simulations of arbitrary and highly computationally intensive biochemical reaction networks that can nevertheless be compiled to them via digitally programmable parameters and connectivity. We outline how cytomorphic systems can be utilized for rapid drug-cocktail formulation and discovery in future pandemics like COVID-19; can simulate networks important in cancer; and can help automate the design of synthetic biological circuits, e.g. a synthetic biological operational amplifier for robust and precise drug delivery. Thus, just as neuromorphic systems have enabled multiple applications in A.I., cytomorphic systems will enable multiple applications in biology and medicine.

Entities:  

Keywords:  COVID-19; analog computing; biological design automation; cytomorphic; drug discovery; supercomputer; synthetic biology; systems biology

Year:  2021        PMID: 35242267      PMCID: PMC8887891          DOI: 10.1109/mnano.2021.3113192

Source DB:  PubMed          Journal:  IEEE Nanotechnol Mag        ISSN: 1932-4510


  12 in total

Review 1.  Synthetic Biology: A Unifying View and Review Using Analog Circuits.

Authors:  Jonathan J Y Teo; Sung Sik Woo; Rahul Sarpeshkar
Journal:  IEEE Trans Biomed Circuits Syst       Date:  2015-09-11       Impact factor: 3.833

2.  A Cytomorphic Chip for Quantitative Modeling of Fundamental Bio-Molecular Circuits.

Authors: 
Journal:  IEEE Trans Biomed Circuits Syst       Date:  2015-08-18       Impact factor: 3.833

3.  Analog versus digital: extrapolating from electronics to neurobiology.

Authors:  R Sarpeshkar
Journal:  Neural Comput       Date:  1998-10-01       Impact factor: 2.026

4.  Fast and Precise Emulation of Stochastic Biochemical Reaction Networks With Amplified Thermal Noise in Silicon Chips.

Authors:  Jaewook Kim; Sung Sik Woo; Rahul Sarpeshkar
Journal:  IEEE Trans Biomed Circuits Syst       Date:  2018-04       Impact factor: 3.833

5.  A Digitally Programmable Cytomorphic Chip for Simulation of Arbitrary Biochemical Reaction Networks.

Authors:  Sung Sik Woo; Jaewook Kim; Rahul Sarpeshkar
Journal:  IEEE Trans Biomed Circuits Syst       Date:  2018-04       Impact factor: 3.833

6.  Measuring and modeling energy and power consumption in living microbial cells with a synthetic ATP reporter.

Authors:  Yijie Deng; Douglas Raymond Beahm; Steven Ionov; Rahul Sarpeshkar
Journal:  BMC Biol       Date:  2021-05-17       Impact factor: 7.431

7.  Analog synthetic biology.

Authors:  R Sarpeshkar
Journal:  Philos Trans A Math Phys Eng Sci       Date:  2014-02-24       Impact factor: 4.226

8.  Acceleration of discrete stochastic biochemical simulation using GPGPU.

Authors:  Kei Sumiyoshi; Kazuki Hirata; Noriko Hiroi; Akira Funahashi
Journal:  Front Physiol       Date:  2015-02-13       Impact factor: 4.566

Review 9.  SARS and MERS: recent insights into emerging coronaviruses.

Authors:  Emmie de Wit; Neeltje van Doremalen; Darryl Falzarano; Vincent J Munster
Journal:  Nat Rev Microbiol       Date:  2016-06-27       Impact factor: 60.633

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  1 in total

1.  Rapid modeling of experimental molecular kinetics with simple electronic circuits instead of with complex differential equations.

Authors:  Yijie Deng; Douglas Raymond Beahm; Xinping Ran; Tanner G Riley; Rahul Sarpeshkar
Journal:  Front Bioeng Biotechnol       Date:  2022-09-28
  1 in total

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