Scaling DNA data storage with nanoscale electrode wells.
Ontology highlight
ABSTRACT:
SUBMITTER: Nguyen BH
PROVIDER: S-EPMC8612674 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Deoxyribonucleic acid (DNA) has shown great promise in enabling computational applications, most notably in the fields of DNA digital data storage and DNA computing. Information is encoded as DNA strands, which will naturally bind in solution, thus enabling search and pattern-matching capabilities. Being able to control and predict the process of DNA hybridisation is crucial for the ambitious future of Hybrid Molecular-Electronic Computing. Current tools are, however, limited in terms of throughput and applicability to large-scale problems. We present the first comprehensive study of machine learning methods applied to the task of predicting DNA hybridisation. For this purpose, we introduce an in silico-generated hybridisation dataset of over 2.5 million data points, enabling the use of deep learning. Depending on hardware, we achieve a reduction in inference time ranging from one to over two orders of magnitude compared to the state-of-the-art, while retaining high fidelity. We then discuss the integration of our methods in modern, scalable workflows.
| S-EPMC8519920 | biostudies-literature
Project description:Description DNA synthesis and sequencing on a single electrode enables integrated data storage using a sliding microarray chip. DNA has been considered as a compelling candidate for digital data storage due to advantages such as high coding density, long retention time, and low energy consumption. Despite many works reported, the development of a DNA-based database of full integration, high efficiency, and practical applicability is still challenging. In this work, we report the synthesis and sequencing of DNA on a single electrode with scalability for an integrated DNA-based data storage system. The synthesis of DNA is based on phosphoramidite chemistry and electrochemical deprotection. The sequencing relies on charge redistribution originated from polymerase-catalyzed primer extension, leading to a measurable current spike. By regeneration of the electrode after sequencing, repeated sequencing can be achieved to improve the accuracy. A SlipChip device is developed to simplify the liquid introduction involved in DNA synthesis and sequencing. As the proof-of-concept experiment, text information is stored in the system and then accurately retrieved.
| S-EPMC8589306 | biostudies-literature
Project description:Davos DNA data storage challenge / Bitcoin challenge
| PRJEB41462 | ENA
Project description:The past several decades have witnessed rapid development of high-intensity, ultrashort pulse lasers, enabling deeper laboratory investigation of nonlinear optics, plasma physics, and quantum science and technology than previously possible. Naturally, with their increasing use, the risk of accidental damage to optical detection systems rises commensurately. Thus, various optical limiting mechanisms and devices have been proposed. However, restricted by the weak optical nonlinearity of natural materials, state-of-the-art optical limiters rely on bulk liquid or solid media, operating in the transmission mode. Device miniaturization becomes complicated with these designs while maintaining superior integrability and controllability. Here, we demonstrate a reflection-mode pulse limiter (sub-100 nm) using nanoscale refractory films made of Al2O3/TiN/Al2O3 metallic quantum wells (MQWs), which provide large and ultrafast Kerr-type optical nonlinearities due to the quantum size effect of the MQW. Functional multilayers consisting of these MQWs could find important applications in nanophotonics, nonlinear optics, and meta-optics.
| S-EPMC7228750 | biostudies-literature
Project description:Ruddlesden-Popper halide perovskites are 2D solution-processed quantum wells with a general formula A2A'n-1M n X3n+1, where optoelectronic properties can be tuned by varying the perovskite layer thickness (n-value), and have recently emerged as efficient semiconductors with technologically relevant stability. However, fundamental questions concerning the nature of optical resonances (excitons or free carriers) and the exciton reduced mass, and their scaling with quantum well thickness, which are critical for designing efficient optoelectronic devices, remain unresolved. Here, using optical spectroscopy and 60-Tesla magneto-absorption supported by modeling, we unambiguously demonstrate that the optical resonances arise from tightly bound excitons with both exciton reduced masses and binding energies decreasing, respectively, from 0.221?m0 to 0.186?m0 and from 470?meV to 125?meV with increasing thickness from n equals 1 to 5. Based on this study we propose a general scaling law to determine the binding energy of excitons in perovskite quantum wells of any layer thickness.
| S-EPMC5993799 | biostudies-other
Project description:Synthetic DNA is becoming an attractive substrate for digital data storage due to its density, durability, and relevance in biological research. A major challenge in making DNA data storage a reality is that reading DNA back into data using sequencing by synthesis remains a laborious, slow and expensive process. Here, we demonstrate successful decoding of 1.67 megabytes of information stored in short fragments of synthetic DNA using a portable nanopore sequencing platform. We design and validate an assembly strategy for DNA storage that drastically increases the throughput of nanopore sequencing. Importantly, this assembly strategy is generalizable to any application that requires nanopore sequencing of small DNA amplicons.
| S-EPMC6610119 | biostudies-literature
Project description:DNA has recently emerged as an attractive medium for archival data storage. Recent work has demonstrated proof-of-principle prototype systems; however, very uneven (biased) sequencing coverage has been reported, which indicates inefficiencies in the storage process. Deviations from the average coverage in the sequence copy distribution can either cause wasteful provisioning in sequencing or excessive number of missing sequences. Here, we use millions of unique sequences from a DNA-based digital data archival system to study the oligonucleotide copy unevenness problem and show that the two paramount sources of bias are the synthesis and amplification (PCR) processes. Based on these findings, we develop a statistical model for each molecular process as well as the overall process. We further use our model to explore the trade-offs between synthesis bias, storage physical density, logical redundancy, and sequencing redundancy, providing insights for engineering efficient, robust DNA data storage systems.
| S-EPMC7324401 | biostudies-literature
Project description:Renewable forms of electricity generation like solar and wind require low-cost energy storage solutions to meet climate change deployment goals. Here, we explore the use of depleted hydraulically fractured ("fracked") oil and gas wells to store electrical energy in the form of compressed natural gas to be released to spin an expander/generator when electrical demand is high. Our reservoir model indicates that the same dual-porosity geological environment of fracked wells used to liberate hydrocarbons is also suitable for storing and releasing gas in a diurnal or seasonal cycle. Round-trip storage efficiency is calculated to be 40%-70% depending on the natural reservoir temperature. Levelized cost of storage is estimated to be $70-270/MWh, on par with pumped hydro storage. This study indicates that repurposed "fracked" wells could provide a much-needed low-cost seasonal energy storage solution at the TWh scale.
| S-EPMC8640470 | biostudies-literature
Project description:DNA-based data storage is an emerging nonvolatile memory technology of potentially unprecedented density, durability, and replication efficiency. The basic system implementation steps include synthesizing DNA strings that contain user information and subsequently retrieving them via high-throughput sequencing technologies. Existing architectures enable reading and writing but do not offer random-access and error-free data recovery from low-cost, portable devices, which is crucial for making the storage technology competitive with classical recorders. Here we show for the first time that a portable, random-access platform may be implemented in practice using nanopore sequencers. The novelty of our approach is to design an integrated processing pipeline that encodes data to avoid costly synthesis and sequencing errors, enables random access through addressing, and leverages efficient portable sequencing via new iterative alignment and deletion error-correcting codes. Our work represents the only known random access DNA-based data storage system that uses error-prone nanopore sequencers, while still producing error-free readouts with the highest reported information rate/density. As such, it represents a crucial step towards practical employment of DNA molecules as storage media.
| S-EPMC5503945 | biostudies-literature
Project description:Biopolymers are an attractive alternative to store and circulate information. DNA, for example, combines remarkable longevity with high data storage densities and has been demonstrated as a means for preserving digital information. Inspired by the dynamic, biological regulation of (epi)genetic information, we herein present how binary data can undergo controlled changes when encoded in synthetic DNA strands. By exploiting differential kinetics of hydrolytic deamination reactions of cytosine and its naturally occurring derivatives, we demonstrate how multiple layers of information can be stored in a single DNA template. Moreover, we show that controlled redox reactions allow for interconversion of these DNA-encoded layers of information. Overall, such interlacing of multiple messages on synthetic DNA libraries showcases the potential of chemical reactions to manipulate digital information on (bio)polymers.
| S-EPMC5113786 | biostudies-literature