A computational design of a programmable biological processor

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

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.

• Jezik: Angleški jezik
• Ključne besede: biological processor, master–slave D flip-flop, computational design, biological program, instruction memory, biological compiler
• Vrsta gradiva: Članek v reviji
• Tipologija: 1.01 - Izvirni znanstveni članek
• Organizacija: FRI - Fakulteta za računalništvo in informatiko
• Status publikacije: Objavljeno
• Različica publikacije: Objavljena publikacija
• Leto izida: 2022
• Št. strani: 12 str.
• Številčenje: Vol. 221, art. 104778
• PID: 20.500.12556/RUL-140526
• UDK: 004:575.112
• ISSN pri članku: 0303-2647
• DOI: 10.1016/j.biosystems.2022.104778
• COBISS.SI-ID: 120944131
• Datum objave v RUL: 15.09.2022

Gradivo je del revije

• Naslov: Biosystems
• Skrajšan naslov: Biosystems
• Založnik: Elsevier
• ISSN: 0303-2647
• COBISS.SI-ID: 25103360

Licence

• Licenca: CC BY 4.0, Creative Commons Priznanje avtorstva 4.0 Mednarodna
• Povezava: http://creativecommons.org/licenses/by/4.0/deed.sl
• Opis: To je standardna licenca Creative Commons, ki daje uporabnikom največ možnosti za nadaljnjo uporabo dela, pri čemer morajo navesti avtorja.

Sekundarni jezik

• Jezik: Slovenski jezik
• Ključne besede: biološki procesor, pomnilna celica D s predpomnjenjem, računalniško načrtovanje, biološki program, naslovni pomnilnik, biološki prevajalnik