Reverse Concatenation Error Correction DNA Data Storage
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Solution Overview
Problem
Existing DNA data storage technologies face challenges in effectively addressing errors introduced during synthesis and sequencing, particularly in propagating errors due to constrained encoding processes.
Innovation Solution
The implementation of reverse concatenation of error-correcting codes, which involves converting input nucleotide symbol strings to constrained representations, calculating redundancy codes, and incorporating them into result strings, allows for error correction and verification while relaxing the constraints imposed by traditional encoding methods.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Manufacturing precision
If constrained encoding is applied to DNA sequences, then manufacturing precision is improved, but error propagation increases during decoding
Solution Approach 1:
The patent segments the DNA storage system into distinct encoding and decoding components with different constraint applications. The encoder applies constrained encoding to meet manufacturing requirements, while the decoder uses a relaxed constraint model that prevents error propagation, effectively separating the conflicting requirements into different operational domains.
Solution Approach 2:
The patent inverts the traditional approach by applying constrained encoding only at the encoding stage while using relaxed constraints at the decoding stage. This reversal of constraint application timing and location resolves the contradiction by allowing precision during manufacturing while preventing error propagation during retrieval.
2Manufacturing precision
If redundancy code is calculated after constrained encoding, then manufacturing precision is maintained, but reliability decreases due to error propagation
Solution Approach 1:
The patent performs preliminary constrained encoding to establish manufacturing precision, then subsequently calculates and applies redundancy codes with relaxed constraints. This sequential approach with different constraint levels for different stages resolves the contradiction by prioritizing precision during encoding while enabling error correction during decoding.
Solution Approach 2:
The patent changes the constraint parameter from strict during encoding to relaxed during decoding. By dynamically adjusting the constraint level based on the operational stage, the system maintains manufacturing precision while preventing error propagation, resolving the contradiction between precision and reliability.
3Device complexity
If traditional concatenation of error-correcting codes is used, then device complexity is reduced, but error propagation increases
Solution Approach 1:
The patent segments the error correction process into encoding-specific constrained operations and decoding-specific relaxed operations. This segmentation allows simple traditional concatenation at the encoding stage while applying sophisticated error propagation prevention at the decoding stage, resolving the contradiction between simplicity and reliability.
Solution Approach 2:
The patent applies different quality levels of constraint processing to different parts of the system: strict constrained encoding for manufacturing precision and relaxed constraint decoding for error prevention. This local differentiation resolves the contradiction by allowing simplicity where appropriate while implementing complexity where needed for reliability.
Data Source
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AI summary
Redundancy information can be included in nucleotide symbol strings encoding underlying data. To avoid propagation of errors during the decoding process, during encoding, a constrained encoding can be performed before the redundancy information is computed. The redundancy information can be an outer encoding across multiple nucleotide symbol strings. An inner coding within nucleotide symbol strings can also be supported. Such redundancy information can be interleaved into the underlying nucleotide symbol strings to which the constrained encoding has been applied, resulting in a relaxed constraint. Insertion/deletion redundancy information can also be included in the resulting strings, and an insertion/deletion-sensitive sequence can be included to assist in recovering accurate sequences during decoding operations.