DNA Storage Deduplication via Blockchain Smart Contracts

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Solution Overview

Problem

Current DNA storage technologies face high costs, slow access times, and lack effective encryption and deduplication methods, making them inefficient for real-time data storage and vulnerable to tampering.

Innovation Solution

Implementing a system that uses blockchain for decentralized, immutable storage of metadata and smart contracts for similarity-based deduplication, combined with locality similarity hashing (LSH) for random access and delta encoding, to reduce the number of nucleotides required for data representation and enhance data security.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Volume of moving object

If DNA storage is used to achieve high storage density, then storage capacity is improved, but storage cost remains high and access time is slow

Engineering Contradiction:

Improvestorage capacityVSAvoidstorage cost

Core Design Contradiction:

Volume of moving objectVSQuantity of substance

Solution Approach 1:

The system segments data into two parts: metadata stored on blockchain and actual DNA sequences stored in a database. This segmentation allows the expensive DNA storage to be used only for data that requires its unique properties, while metadata can be stored more economically, thereby reducing overall storage cost while maintaining high capacity for valuable data.

Inventive Principle:

Principle #1Segmentation

Solution Approach 2:

The blockchain serves as an intermediary layer between the data storage system and the DNA database. It provides decentralized, immutable storage for metadata and enables smart contract-based deduplication, reducing the amount of DNA material needed and thus lowering storage costs while maintaining access to high-density storage capacity.

Inventive Principle:

Principle #24Intermediary (Mediator)

2Speed

If traditional centralized storage is used, then access speed is fast, but single point of failure vulnerability increases and data security decreases

Engineering Contradiction:

Improveaccess speedVSAvoiddata security

Core Design Contradiction:

SpeedVSReliability

Solution Approach 1:

The system segments storage into decentralized blockchain nodes and a separate DNA database. The blockchain provides distributed, fail-safe metadata storage while the DNA database stores actual data sequences. This segmentation eliminates single point of failure vulnerability while maintaining fast access through the database layer, and the blockchain provides cryptographic security and immutability.

Inventive Principle:

Principle #1Segmentation

Solution Approach 2:

The patent replaces traditional centralized mechanical storage systems with a blockchain-based distributed system. The blockchain uses cryptographic hashing and decentralized consensus mechanisms to provide security and reliability, substituting the mechanical centralized control with a digital distributed architecture that is both secure and accessible.

Inventive Principle:

Principle #28Mechanics substitution (Replace mechanical system)

3Device complexity

If data is stored without deduplication, then simplicity is maintained, but storage cost increases due to redundant nucleotide material

Engineering Contradiction:

Improvesystem simplicityVSAvoidnucleotide material

Core Design Contradiction:

Device complexityVSQuantity of substance

Solution Approach 1:

The system performs deduplication as a preliminary action before storing data in the DNA database. Smart contracts automatically identify and eliminate redundant DNA sequences based on their metadata, reducing the quantity of nucleotide material that needs to be synthesized and stored. This preliminary deduplication action reduces material costs while the blockchain maintains simple, immutable records of the deduplicated data.

Inventive Principle:

Principle #10Preliminary action

4Device complexity

If encryption is not implemented, then data processing is simple, but data is vulnerable to malicious tampering

Engineering Contradiction:

Improveprocessing complexityVSAvoiddata tampering vulnerability

Core Design Contradiction:

Device complexityVSObject-affected harmful factors

Solution Approach 1:

The patent replaces simple data processing with blockchain-based cryptographic verification. The blockchain uses hash functions and digital signatures to provide tamper-proof storage for metadata, while the DNA sequences are stored with their own verification mechanisms. This substitution maintains processing simplicity at the application level while providing robust security through the blockchain's cryptographic layer.

Inventive Principle:

Principle #28Mechanics substitution (Replace mechanical system)

Data Source

PatentUS20220237470A1Storing digital data in DNA storage using blockchain and destination-side deduplication using smart contracts

Publication Date: 2022.07.28 EMC IP HLDG CO LLC

AI summary

Embodiments include a method of storing digital data in DNA storage by receiving the digital data from a user, deduplicating the data in a deduplication system of the user to form deduplicated data, and encoding the deduplicated data into a DNA string into a format for storage on a blockchain. A smart contract is deployed for deduplication on the destination side of nucleotide sequences comprising the DNA string, and the deduplicated nucleotide sequences are encoded into a Binary Aligned Map (BAM) format for storage as metadata on the blockchain. A process on the destination side synthesizes the deduplicated nucleotides for storage in the DNA storage, and stores the deduplicated nucleotides in the DNA storage as a next block in the blockchain only if the next block agrees with the smart contract.