A computational design of a programmable biological processor

Moškon, Miha (author), Pušnik, Žiga (author), Stanovnik, Lidija (author), Zimic, Nikolaj (author), Mraz, Miha (author)

Basic synthetic information processing structures, such as logic gates, oscillators and flip-flops, have already been implemented in living organisms. Current implementations of these structures have yet to be extended to more complex processing structures that would constitute a biological computer. We make a step forward towards the construction of a biological computer. We describe a model-based computational design of a biological processor that uses transcription and translation resources of the host cell to perform its operations. The proposed processor is composed of an instruction memory containing a biological program, a program counter that is used to address this memory, and a biological oscillator that triggers the execution of the next instruction in the memory. We additionally describe the implementation of a biological compiler that compiles a sequence of human-readable instructions into ordinary differential equation-based models, which can be used to simulate and analyse the dynamics of the processor. The proposed implementation presents the first programmable biological processor that exploits cellular resources to execute the specified instructions. We demonstrate the application of the described processor on a set of simple yet scalable biological programs. Biological descriptions of these programs can be produced manually or automatically using the provided compiler.

• Language: English
• Keywords: biological processor, master–slave D flip-flop, computational design, biological program, instruction memory, biological compiler
• Work type: Article
• Typology: 1.01 - Original Scientific Article
• Organization: FRI - Faculty of Computer and Information Science
• Publication status: Published
• Publication version: Version of Record
• Year: 2022
• Number of pages: 12 str.
• Numbering: Vol. 221, art. 104778
• PID: 20.500.12556/RUL-140526
• UDC: 004:575.112
• ISSN on article: 0303-2647
• DOI: 10.1016/j.biosystems.2022.104778
• COBISS.SI-ID: 120944131
• Publication date in RUL: 15.09.2022

Record is a part of a journal

• Title: Biosystems
• Shortened title: Biosystems
• Publisher: Elsevier
• ISSN: 0303-2647
• COBISS.SI-ID: 25103360

Licences

• License: CC BY 4.0, Creative Commons Attribution 4.0 International
• Link: http://creativecommons.org/licenses/by/4.0/
• Description: This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.

Secondary language

• Language: Slovenian
• Keywords: biološki procesor, pomnilna celica D s predpomnjenjem, računalniško načrtovanje, biološki program, naslovni pomnilnik, biološki prevajalnik