Multi-dimensional DNA Mapping for Storage Density
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Solution Overview
Problem
Conventional DNA storage methods do not optimize Signal-to-Noise Ratio (SNR) and Bit-Error-Rate (BER) while mapping binary data to DNA sequences, leading to suboptimal storage density and error rates due to the presence of homopolymers and inefficient signal constellation management.
Innovation Solution
A multi-dimensional fixed-length mapping between binary data bits and DNA bases is implemented, optimizing the bit/base ratio to approach theoretical limits, improving SNR and BER by eliminating homopolymers and using encoding schemes that restrict adjacent DNA base pairs, thereby enhancing storage density and error reduction.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If conventional DNA storage methods are used to map binary data to DNA sequences, then the storage system can operate with simple encoding, but the Signal-to-Noise Ratio and Bit-Error-Rate deteriorate due to homopolymer presence and inefficient signal constellation management
Solution Approach 1:
The patent transitions from conventional 1D or 2D mapping approaches to a multi-dimensional fixed-length mapping that utilizes multiple dimensions of DNA base combinations. This dimensional expansion allows the system to achieve higher bit/base ratios (approaching theoretical limits) while simultaneously improving SNR and BER performance through the structured organization of signal constellations in multiple dimensions, thereby resolving the contradiction between reliability improvement and complexity increase.
Solution Approach 2:
The patent employs parameter changes by implementing a fixed-length mapping that transforms variable-length binary data into fixed-length DNA sequences with controlled homopolymer content. By adjusting the mapping parameters to eliminate homopolymers and optimize base pair combinations, the system achieves improved SNR and BER while maintaining manageable encoding complexity through systematic parameter design.
2Quantity of substance
If homopolymers are present in DNA sequences, then the encoding is simpler, but storage density and error rates deteriorate
Solution Approach 1:
The patent extracts and removes homopolymer sequences from the DNA encoding through a systematic mapping process that generates fixed-length sequences avoiding consecutive identical bases. By taking out homopolymers entirely from the encoding scheme, the system achieves higher storage density through optimized base pair combinations while the complexity is managed through the use of established combinatorial design principles.
3Productivity
If a fixed-length multi-dimensional mapping is implemented, then the bit/base ratio approaches theoretical limits and SNR/BER improve, but the mapping and decoding processes become more complex
Solution Approach 1:
The patent applies preliminary action by pre-defining the fixed-length mapping table and signal constellation structure before data encoding. This pre-computed mapping framework enables the system to achieve high bit/base ratios approaching theoretical limits while simplifying the actual encoding process to table lookups and fixed transformations, thereby managing the complexity of multi-dimensional mapping through advance preparation of mapping structures.
Applied Scientific Principles
This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.
Function Achieved in This Case
The solution achieves improved Signal-to-Noise Ratio and Bit-Error-Rate, maximizing storage density and minimizing errors by optimizing the bit/base ratio and encoding schemes, resulting in a more efficient DNA storage system.
Implementation Method 1
the read process may be based at least in part on detecting blocked ionic current from passing the sequence through a nano-pore (e.g., certain nucleotides blocking more ionic current than other nucleotides)
Data Source
AI summary
Systems and methods for multi-dimensional mapping of binary data DNA sequences are described. In one embodiment, the method may include determining a current level of a first DNA base from a sequence of DNA bases based at least in part on a read process of the sequence, determining a current level of a second DNA base after the first DNA base and a current level of a third DNA base after the second DNA base, and decoding binary data from the sequence based at least in part on the determined current level of the first DNA base, the determined current level of the second DNA base, and/or the determined current level of the third DNA base.