In-Vitro Validated Methods for Encoding Digital Data in Deoxyribonucleic Acid (DNA)

Deoxyribonucleic acid (DNA) is emerging as an alternative archival memory technology. Recent advancements in DNA synthesis and sequencing have both increased the capacity and decreased the cost of storing information in de novo synthesized DNA pools. In this survey, we review methods for translating digital data to and/or from DNA molecules. An emphasis is placed on methods which have been validated by storing and retrieving real-world data via in-vitro experiments

Emerging Approaches to DNA Data Storage: Challenges and Prospects

With the total amount of worldwide data skyrocketing, the global data storage demand is predicted to grow to 1.75 × 1014GB by 2025. Traditional storage methods have difficulties keeping pace given that current storage media have a maximum density of 103GB/mm3. As such, data production will far exceed the capacity of currently available storage methods. The costs of maintaining and transferring data, as well as the limited lifespans and significant data losses associated with current technologies also demand advanced solutions for information storage. Nature offers a powerful alternative through the storage of information that defines living organisms in unique orders of four bases (A, T, C, G) located in molecules called deoxyribonucleic acid (DNA). DNA molecules as information carriers have many advantages over traditional storage media. Their high storage density, potentially low maintenance cost, ease of synthesis, and chemical modification make them an ideal alternative for information storage. To this end, rapid progress has been made over the past decade by exploiting user-defined DNA materials to encode information. In this review, we discuss the most recent advances of DNA-based data storage with a major focus on the challenges that remain in this promising field, including the current intrinsic low speed in data writing and reading and the high cost per byte stored. Alternatively, data storage relying on DNA nanostructures (as opposed to DNA sequence) as well as on other combinations of nanomaterials and biomolecules are proposed with promising technological and economic advantages. In summarizing the advances that have been made and underlining the challenges that remain, we provide a roadmap for the ongoing research in this rapidly growing field, which will enable the development of technological solutions to the global demand for superior storage methodologies

Deep Joint Source-Channel Coding for DNA Image Storage: A Novel Approach with Enhanced Error Resilience and Biological Constraint Optimization

In the current era, DeoxyriboNucleic Acid (DNA) based data storage emerges as an intriguing approach, garnering substantial academic interest and investigation. This paper introduces a novel deep joint source-channel coding (DJSCC) scheme for DNA image storage, designated as DJSCC-DNA. This paradigm distinguishes itself from conventional DNA storage techniques through three key modifications: 1) it employs advanced deep learning methodologies, employing convolutional neural networks for DNA encoding and decoding processes; 2) it seamlessly integrates DNA polymerase chain reaction (PCR) amplification into the network architecture, thereby augmenting data recovery precision; and 3) it restructures the loss function by targeting biological constraints for optimization. The performance of the proposed model is demonstrated via numerical results from specific channel testing, suggesting that it surpasses conventional deep learning methodologies in terms of peak signal-to-noise ratio (PSNR) and structural similarity index (SSIM). Additionally, the model effectively ensures positive constraints on both homopolymer run-length and GC content

An Alternative Approach to Nucleic Acid Memory

DNA is a compelling alternative to non-volatile information storage technologies due to its information density, stability, and energy efficiency. Previous studies have used artificially synthesized DNA to store data and automated next-generation sequencing to read it back. Here, we report digital Nucleic Acid Memory (dNAM) for applications that require a limited amount of data to have high information density, redundancy, and copy number. In dNAM, data is encoded by selecting combinations of single-stranded DNA with (1) or without (0) docking-site domains. When self-assembled with scaffold DNA, staple strands form DNA origami breadboards. Information encoded into the breadboards is read by monitoring the binding of fluorescent imager probes using DNA-PAINT super-resolution microscopy. To enhance data retention, a multi-layer error correction scheme that combines fountain and bi-level parity codes is used. As a prototype, fifteen origami encoded with ‘Data is in our DNA!\n’ are analyzed. Each origami encodes unique data-droplet, index, orientation, and error-correction information. The error-correction algorithms fully recover the message when individual docking sites, or entire origami, are missing. Unlike other approaches to DNA-based data storage, reading dNAM does not require sequencing. As such, it offers an additional path to explore the advantages and disadvantages of DNA as an emerging memory material

Preserving privacy in edge computing

Edge computing or fog computing enables realtime services to smart application users by storing data and services at the edge of the networks. Edge devices in the edge computing handle data storage and service provisioning. Therefore, edge computing has become a  new norm for several delay-sensitive smart applications such as automated vehicles, ambient-assisted living, emergency response services, precision agriculture, and smart electricity grids. Despite having great potential, privacy threats are the main barriers to the success of edge computing. Attackers can leak private or sensitive information of data owners and modify service-related data for hampering service provisioning in edge computing-based smart applications. This research takes privacy issues of heterogeneous smart application data into account that are stored in edge data centers. From there, this study focuses on the development of privacy-preserving models for user-generated smart application data in edge computing and edge service-related data, such as Quality-of-Service (QoS) data, for ensuring unbiased service provisioning. We begin with developing privacy-preserving techniques for user data generated by smart applications using steganography that is one of the data hiding techniques. In steganography, user sensitive information is hidden within nonsensitive information of data before outsourcing smart application data, and stego data are produced for storing in the edge data center. A steganography approach must be reversible or lossless to be useful in privacy-preserving techniques. In this research, we focus on numerical (sensor data) and textual (DNA sequence and text) data steganography. Existing steganography approaches for numerical data are irreversible. Hence, we introduce a lossless or reversible numerical data steganography approach using Error Correcting Codes (ECC). Modern lossless steganography approaches for text data steganography are mainly application-specific and lacks imperceptibility, and DNA steganography requires reference DNA sequence for the reconstruction of the original DNA sequence. Therefore, we present the first blind and lossless DNA sequence steganography approach based on the nucleotide substitution method in this study. In addition, a text steganography method is proposed that using invisible character and compression based encoding for ensuring reversibility and higher imperceptibility.  Different experiments are conducted to demonstrate the justification of our proposed methods in these studies. The searching capability of the stored stego data is challenged in the edge data center without disclosing sensitive information. We present a privacy-preserving search framework for stego data on the edge data center that includes two methods. In the first method, we present a keyword-based privacy-preserving search method that allows a user to send a search query as a hash string. However, this method does not support the range query. Therefore, we develop a range search method on stego data using an order-preserving encryption (OPE) scheme. In both cases, the search service provider retrieves corresponding stego data without revealing any sensitive information. Several experiments are conducted for evaluating the performance of the framework. Finally, we present a privacy-preserving service computation framework using Fully Homomorphic Encryption (FHE) based cryptosystem for ensuring the service provider's privacy during service selection and composition. Our contributions are two folds. First, we introduce a privacy-preserving service selection model based on encrypted Quality-of-Service (QoS) values of edge services for ensuring privacy. QoS values are encrypted using FHE. A distributed computation model for service selection using MapReduce is designed for improving efficiency. Second, we develop a composition model for edge services based on the functional relationship among edge services for optimizing the service selection process. Various experiments are performed in both centralized and distributed computing environments to evaluate the performance of the proposed framework using a synthetic QoS dataset

A Study on DNA Memory Encoding Architecture

The amount of raw generated data is growing at an exponential rate due to the greatly increasing number of sensors in electronic systems. While the majority of this data is never used, it is often kept for cases such as failure analysis. As such, archival memory storage, where data can be stored at an extremely high density at the cost of read latency, is becoming more popular than ever for long term storage. In biological organisms, Deoxyribonucleic Acid (DNA) is used as a method of storing information in terms of simple building blocks, as to allow for larger and more complicated struc- tures in a density much higher than can currently be realized on modern memory devices. Given the ability for organisms to store this information in a set of four bases for an extremely long amounts of time with limited degradation, DNA presents itself as a possible way to store data in a manner similar to binary data. This work investigates the use of DNA strands as a storage regime, where system-level data is translated into an efficient encoding to minimize base pair errors both at a local level and at the chain level. An encoding method using a Bose-Chaudhuri-Hocquenghem (BCH) pre-coded Raptor scheme is implemented in conjunction with an 8 to 6 bi- nary to base translation, yielding an informational density of 1.18 bits/base pair. A Field-Programmable Gate Array (FPGA) is then used in conjunction with a soft-core processor to verify address and key translation abilities, providing strong support that a strand-pool DNA model is reasonable for archival storage