Periodic Reporting for period 1 - DISCO (DNA-based Infrastructure for Storage and Computation)
Periodo di rendicontazione: 2023-10-01 al 2024-09-30
Funded by the European Innovation Council PATHFINDER Challenge on DNA-based digital data storage, DISCO aims to create a new method of storing data and computing on that data, all in DNA. The work addresses the significant and growing gap between data generation and global storage capacity in a way that is scalable, environmentally sustainable and increases the integrity and is reliable over time. The project is coordinated by Prof Damien Woods who leads the TAPDANCE Research Group at Maynooth University.
Throughout evolution, Biology has found an almost-perfect molecule to pass information down through the millennia. Whether, for a simple bacterium or the largest whale, DNA achieves high information density while permitting cellular machinery rapid random access retrieval to decode everything from a single protein to the development of an entire human brain. Humanity’s rapidly growing data storage and computing needs make it tempting to exploit optimised biological molecules and processes, but biology is messy, poorly understood and much more specialised for life than it is for our needs — we propose to use DNA for storage together with a rationally designed, well-characterised and robust molecular computing architecture.
The DISCO project will address the challenge of engineering a programmable and robust DNA storage and computing platform. DISCO combines powerful molecular-algorithmic ideas from DNA computing with notions of thermodynamic stability from DNA nanostructures, to provide an expressive and robust system design. The project proposes the use of long DNA scaffold strands, upon which hundreds of smaller strands bind to store data, which can be later read, erased, rewritten and computed upon.
Throughout evolution, Biology has found an almost-perfect molecule to pass information down through the millennia. Whether, for a simple bacterium or the largest whale, DNA achieves high information density while permitting cellular machinery rapid random access retrieval to decode everything from a single protein to the development of an entire human brain. Humanity’s rapidly growing data storage and computing needs make it tempting to exploit optimised biological molecules and processes, but biology is messy, poorly understood and much more specialised for life than it is for our needs — we propose to use DNA for storage together with a rationally designed, well-characterised and robust molecular computing architecture.
The DISCO project will address the challenge of engineering a programmable and robust DNA storage and computing platform. DISCO combines powerful molecular-algorithmic ideas from DNA computing with notions of thermodynamic stability from DNA nanostructures, to provide an expressive and robust system design. The project proposes the use of long DNA scaffold strands, upon which hundreds of smaller strands bind to store data, which can be later read, erased, rewritten and computed upon.
As summarised in the First Report review:
Objective 1 - DISCO: Fundamental computing principles
• O1.1 Optimise preliminary data on 4-component DISCO (10 bits). [Objective completed. Significant activities (all are on schedule or ahead of schedule), detailed as follows:]
– Manuscript: St´erin, Eshra, Woods. A Thermodynamically Favoured Molecular Computer: Robust, Fast,
Renewable Under submission, at second stage of review (authors and title subject to change).
– Software: uploaded by partner prgm
– Patent filed: St´erin, Eshra Woods. Thermodynamically Favoured Molecular Computations
• O1.2 Develop abstract model, and kinetics model for DISCO. This objective spans months 4–27.
– As of month 12 we have an abstract model and an initial kinetic model coded up (in rust, by Research
Fellow Dr Constantine Evans and undergrad Angel Cervera Roldan at NUIM and Tristan Sterin at prgm).
• O1.3 Ten component DISCO (30 bits)
– Objective underway, on schedule. This objective spans months 4–27. As of month 12 we had begun
scale-up to 20, with partial/initial results.
Objective 2 - Scale-up of computation and storage with DISCO
• O2.1 1 kbit storage: write, read and edit on DISCO DNA RAM
– Some initial progress, ahead of schedule.
• O2.2 Custom scaffold sequences [not started, as scheduled]
• O2.3 MIMD computing on a 1 kbit to multi-kbit memory [not started, as scheduled]
• O2.4 Develop DNA sequencing-based readout [not started, as scheduled]
• O2.5 Software pipeline for lab automation of DISCO [not started, as scheduled]
Objective 3 - Two-dimensional (2D) DISCO on DNA origami
• O3.1 2D DISCO fundamentals
– Work started, ahead of schedule. S.
• O3.2 Readout for 2D DISCO [not started, as scheduled]
• O3.3 Custom scaffold for 2D DISCO [not started, as scheduled]
• O3.4 Large-scale 2D DISCO across origami and multi-origami [not started, as scheduled]
Objective 1 - DISCO: Fundamental computing principles
• O1.1 Optimise preliminary data on 4-component DISCO (10 bits). [Objective completed. Significant activities (all are on schedule or ahead of schedule), detailed as follows:]
– Manuscript: St´erin, Eshra, Woods. A Thermodynamically Favoured Molecular Computer: Robust, Fast,
Renewable Under submission, at second stage of review (authors and title subject to change).
– Software: uploaded by partner prgm
– Patent filed: St´erin, Eshra Woods. Thermodynamically Favoured Molecular Computations
• O1.2 Develop abstract model, and kinetics model for DISCO. This objective spans months 4–27.
– As of month 12 we have an abstract model and an initial kinetic model coded up (in rust, by Research
Fellow Dr Constantine Evans and undergrad Angel Cervera Roldan at NUIM and Tristan Sterin at prgm).
• O1.3 Ten component DISCO (30 bits)
– Objective underway, on schedule. This objective spans months 4–27. As of month 12 we had begun
scale-up to 20, with partial/initial results.
Objective 2 - Scale-up of computation and storage with DISCO
• O2.1 1 kbit storage: write, read and edit on DISCO DNA RAM
– Some initial progress, ahead of schedule.
• O2.2 Custom scaffold sequences [not started, as scheduled]
• O2.3 MIMD computing on a 1 kbit to multi-kbit memory [not started, as scheduled]
• O2.4 Develop DNA sequencing-based readout [not started, as scheduled]
• O2.5 Software pipeline for lab automation of DISCO [not started, as scheduled]
Objective 3 - Two-dimensional (2D) DISCO on DNA origami
• O3.1 2D DISCO fundamentals
– Work started, ahead of schedule. S.
• O3.2 Readout for 2D DISCO [not started, as scheduled]
• O3.3 Custom scaffold for 2D DISCO [not started, as scheduled]
• O3.4 Large-scale 2D DISCO across origami and multi-origami [not started, as scheduled]
1 patent has been filed in Reporting Period 1. To be updated in subsequent review periods.