High Code Density Research Articles

High-throughput DNA synthesis for data storage.

With the explosion of digital world, the dramatically increasing data volume is expected to reach 175 ZB (1 ZB = 1012 GB) in 2025. Storing such huge global data would consume tons of resources. Fortunately, it has been found that the deoxyribonucleic acid (DNA) molecule is the most compact and durable information storage medium in the world so far. Its high coding density and long-term preservation properties make itself one of the best data storage carriers for the future. High-throughput DNA synthesis is a key technology for "DNA data storage", which encodes binary data stream (0/1) into quaternary long DNA sequences consisting of four bases (A/G/C/T). In this review, the workflow of DNA data storage and the basic methods of artificial DNA synthesis technology are outlined first. Then, the technical characteristics of different synthesis methods and the state-of-the-art of representative commercial companies, with a primary focus on silicon chip microarray-based synthesis and novel enzymatic DNA synthesis are presented. Finally, the recent status of DNA storage and new opportunities for future development in the field of high-throughput, large-scale DNA synthesis technology are summarized.

Assembly of Reusable DNA Blocks for Data Storage Using the Principle of Movable Type Printing

Due to its high coding density and longevity, DNA is a compelling data storage alternative. However, current DNA data storage systems rely on the de novo synthesis of enormous DNA molecules, resulting in low data editability, high synthesis costs, and restrictions on further applications. Here, we demonstrate the programmable assembly of reusable DNA blocks for versatile data storage using the ancient movable type printing principle. Digital data are first encoded into nucleotide sequences in DNA hairpins, which are then synthesized and immobilized on solid beads as modular DNA blocks. Using DNA polymerase-catalyzed primer exchange reaction, data can be continuously replicated from hairpins on DNA blocks and attached to a primer in tandem to produce new information. The assembly of DNA blocks is highly programmable, producing various data by reusing a finite number of DNA blocks and reducing synthesis costs (∼1718 versus 3000 to 30,000 US$ per megabyte using conventional methods). We demonstrate the flexible assembly of texts, images, and random numbers using DNA blocks and the integration with DNA logic circuits to manipulate data synthesis. This work suggests a flexible paradigm by recombining already synthesized DNA to build cost-effective and intelligent DNA data storage systems.

High-Capacity Double-Sided Square-Mesh-Type Chipless RFID Tags

This paper presents a novel methodology for designing high-capacity frequency domain chipless RFID tags based on the backscattering principle. The tag consists of multiple square open-loop resonators loaded with a varying number of square metallic patches to form a mesh structure. Thus, in contrast to conventional designs, the overall physical size of each resonator remains fixed and does not change with respect to its operating resonant frequency. The RCS response of the proposed tag can be easily manipulated by varying the loading factor of each resonator. The tag size is further miniaturized by placing resonators on both sides of the substrate used. The tag configuration with resonators arranged in the form of a single row (4 × 1) printed on both sides of the substrate is finally chosen for maximum robustness and efficiency. The frequency shift coding (FSC) technique is used to encode more than one bit per resonator by using segments within sub-bands. The proposed tag encodes 16-bit data in a frequency band from 5.9 to 10.5 GHz and has a very high code density of 23.51 bits/cm2 and a spectral efficiency of 3.47 bits/GHz. The design methodology is novel and leads to a very efficient chipless RFID tag that can be used in a variety of high-data-capacity applications.

A Semi-Octagonal 40-Bit High Capacity Chipless RFID Tag for Future Product Identification

This paper presents a unique geometry of a chipless radio frequency identification (RFID) tag for encoding a large number of bits in a very small form factor. The tag geometry consists of semi-octagonal copper strips, sequentially laid on a single side of an ultra-thin substrate. A unique and robust encoding mechanism for the tag identification (ID) is proposed. The operating frequency spectrum of the tag ranges from 3.1 to 10.5 GHz. The tag is compact, having an overall size of 14.5 × 28 mm2. The proposed tag exhibits very high code density of 9.85 bits/cm2 and spectral efficiency of 5.4 bits/GHz. The unique geometric configuration of the proposed tag allows it to encode up to 40 bits of data as an RCS signature. This chipless RFID tag seems to be a potential candidate for a wide range of modern RFID applications.

High capacity chipless RFID tags for biomass tracking application

AbstractThe design of a low-cost, flexible, miniaturized, and a high code density chipless radio-frequency identification (RFID) tag is presented as a solution for tracking the transportation of biomass fuel pellets. The performance of the tag is presented and demonstrates the applicability of the design for different material systems, while maintaining a compact size of 5.06 cm2. The tag consists of nested concentric hexagonal elements and a central spiral resonator suitable for ID encoding. The tag presented demonstrates code density of 3.6-bits/cm2, possesses angular stability up to 60°, and high radar cross section (RCS). The tag performance was also observed for tracking 5 kg of fly-ash biomass. Additionally, as the tag mass mostly consists of FR4, PET, or Taconic TLX-0 with a minute mass of either copper, gold, or silver, the tag can be easily combusted and disposed of during biomass combustion. The novel features of this tag are the combination of hexagonal and spiral shape slots for maximum space utilization thereby achieving high RCS signatures along with high code density. All these properties of the proposed chipless RFID tag provide a pioneering pathway for a real-time biomass tracking application.

A 32-Bit Single Quadrant Angle-Controlled Chipless Tag for Radio Frequency Identification Applications.

A 32-bit chipless RFID tag operating in the 4.5–10.9 GHz band is presented in this paper. The tag has a unique multiple-arc-type shape consisting of closely packed 0.2 mm wide arcs of different radii and lengths. The specific tag geometry provides multiple resonances in frequency domain of an RCS plot. A frequency domain coding technique has also been proposed to encode the tag’s RCS signature into a 32-bit digital identification code. The tag has an overall dimension of 17.9 × 17.9 mm2, resulting in a high code density of 9.98 bits/cm2 and spectral efficiency of 5 bits/GHz. The proposed tag is built on a low loss substrate bearing a very small footprint, thereby making it extremely suitable for large-scale product identification purposes in future chipless RFID tag systems.

Broad domains of histone marks in the highly compact Paramecium macronuclear genome.

The unicellular ciliate Paramecium contains a large vegetative macronucleus with several unusual characteristics, including an extremely high coding density and high polyploidy. As macronculear chromatin is devoid of heterochromatin, our study characterizes the functional epigenomic organization necessary for gene regulation and proper Pol II activity. Histone marks (H3K4me3, H3K9ac, H3K27me3) reveal no narrow peaks but broad domains along gene bodies, whereas intergenic regions are devoid of nucleosomes. Our data implicate H3K4me3 levels inside ORFs to be the main factor associated with gene expression, and H3K27me3 appears in association with H3K4me3 in plastic genes. Silent and lowly expressed genes show low nucleosome occupancy, suggesting that gene inactivation does not involve increased nucleosome occupancy and chromatin condensation. Because of a high occupancy of Pol II along highly expressed ORFs, transcriptional elongation appears to be quite different from that of other species. This is supported by missing heptameric repeats in the C-terminal domain of Pol II and a divergent elongation system. Our data imply that unoccupied DNA is the default state, whereas gene activation requires nucleosome recruitment together with broad domains of H3K4me3. In summary, gene activation and silencing in Paramecium run counter to the current understanding of chromatin biology.

Design of millimeter-wave chipless tag based on variable angle arc resonator

Faced with the development of miniaturization and compactness of chipless radio frequency identification (RFID) tags, and to reduce the cost of traditional chip tags, this paper proposes a miniaturized, polarization-insensitive, passive, and chipless based on a variable-angle arc resonator. Chipless tags have a high coding density of 44.44 bits/cm2 in the frequency range of 20GHz∼31GHz, and a coding capacity of 4.04 bits/cm2/GHz. The patch on the substrate determines the signature of each resonant frequency, thereby determining the number of identification data bits. To accommodate more data bits and pass barriers between resonant features, the metal patches are orthogonally polarized so that adjacent resonant features will not interfere with each other. As the mm-Waves ultra-wideband (UWB) chipless tags, it can be easily printed on various IoT applications and has great potential for low cost and identity verification. This work makes it easier to implement highly robust, inexpensive, and flexible chipless tags for IoT applications in the mm-Wave band.

A low-profile FSS-based high capacity chipless RFID tag for sensing and encoding applications

AbstractThis paper presents a polarization-independent 11-bit chipless RFID tag based on frequency-selective surface which has been designed for encoding and relative humidity (RH) sensing applications. The 10 exterior U-shaped resonators are used for item encoding whereas Kapton has been incorporated with the interior resonator for RH sensing. This radio-frequency identification (RFID) tag operates in S- and C-frequency bands. The proposed design offers enhanced fractional bandwidth up to 88% with the density of 4.46 bits/cm2. Both single- and dual-layer tags have been investigated. The simulated results are in good agreement with measured results and a comparison with existing literature is presented to show the performance. Simple geometry, high code density, large frequency signature bandwidth, high magnitude bit, high radar cross-section, and angular stability for more than 75° are the unique outcomes of the proposed design. In addition, RH sensing has been achieved by integrating the Kapton on the same RFID tag.

First finding of free-living representatives of Prokinetoplastina and their nuclear and mitochondrial genomes

Kinetoplastids are heterotrophic flagellated protists, including important parasites of humans and animals (trypanosomatids), and ecologically important free-living bacterial consumers (bodonids). Phylogenies have shown that the earliest-branching kinetoplastids are all parasites or obligate endosymbionts, whose highly-derived state makes reconstructing the ancestral state of the group challenging. We have isolated new strains of unusual free-living flagellates that molecular phylogeny shows to be most closely related to endosymbiotic and parasitic Perkinsela and Ichthyobodo species that, together with unidentified environmental sequences, form the clade at the base of kinetoplastids. These strains are therefore the first described free-living prokinetoplastids, and potentially very informative in understanding the evolution and ancestral states of morphological and molecular characteristics described in other kinetoplastids. Overall, we find that these organisms morphologically and ultrastructurally resemble some free-living bodonids and diplonemids, and possess nuclear genomes with few introns, polycistronic mRNA expression, high coding density, and derived traits shared with other kinetoplastids. Their genetic repertoires are more diverse than the best-studied free-living kinetoplastids, which is likely a reflection of their higher metabolic potential. Mitochondrial RNAs of these new species undergo the most extensive U insertion/deletion editing reported so far, and limited deaminative C-to-U and A-to-I editing, but we find no evidence for mitochondrial trans-splicing.

A Novel Kite-Shaped Chipless RFID Tag for Low-Profile Applications

In this paper a novel, compact 10-bit chipless radio frequency identification (RFID) tag with stable readable characteristics is proposed. The tag is composed of several concentric novel kite-shaped loop resonators. The desired data sequence is obtained by the insertion or removal of nested elements, offering a 1:1 data bit to resonance correspondence. Each data sequence is encoded in the spectral domain of the tag. The proposed tag shows operability at different polarizations and incident angles of the impinging electromagnetic waves. Operating within the ultra-wideband (UWB), the tag is realized on the Roger RT/duroid® 5880 substrate having physical dimensions of 13.55 × 13.55 mm2. The measurement results of the design reveal a high code density and spectral efficiency of 5.44 bits/cm2 and 2 bits/GHz, respectively. The compact and robust passive chipless RFID tag having scalable data storage potential can be deployed in numerous low-profile applications such as those of wearable and healthcare.

Мікропроцесорний пристрій для діагностування електромагнітного привода вакуумного вимикача

The paper proposes a microprocessor device for diagnosing the electromagnetic drive of a vacuum switch. It is investigated that the reliable operation of the vacuum switch depends on the technical condition of the electromagnetic actuator. Microprocessor diagnostic devices allow controlling the quality of manufactured electromagnetic actuators at the stage of initial control of the manufacturer and in the process of their operation in production. On the basis of a mathematical model, which provides for the measurement of the "reference" curve of the magnetic characteristic after the new switch is put into operation or after its overhaul and comparison of this curve with the subsequent measured magnetic characteristics in the course of its further operation. During operation, the shape of the web-ampere characteristics of the windings of the electromagnetic drive of the vacuum switches changes. The control of deviation from the "reference" characteristic allows estimating the current state of the electromagnet and its degree of wear. The block diagram of the microprocessor device of the system of diagnostics of the electromagnetic drive of the vacuum switch is developed. The microprocessor device functions according to the developed mathematical model. The main components of the device are the AT32UC3L032 microcontroller, switching units, current sensors and voltages. The AT32UC3L032 microcontroller is the best option in terms of cost and specifications (low power consumption, high code density, and high performance). The algorithm of functioning of the diagnostic device and its hardware necessary for the construction of the diagnostic system has been developed. The operation of the device involves determining the technical condition of the drive, indicating the result of the diagnosis on the display device near the diagnostic device and transmitting through the interface of the converter the current status of the electromagnetic drive from the microcontroller to the computer operating personnel.

An Instruction Set Architecture for Machine Learning

Machine Learning (ML) are a family of models for learning from the data to improve performance on a certain task. ML techniques, especially recent renewed neural networks (deep neural networks), have proven to be efficient for a broad range of applications. ML techniques are conventionally executed on general-purpose processors (such as CPU and GPGPU), which usually are not energy efficient, since they invest excessive hardware resources to flexibly support various workloads. Consequently, application-specific hardware accelerators have been proposed recently to improve energy efficiency. However, such accelerators were designed for a small set of ML techniques sharing similar computational patterns, and they adopt complex and informative instructions (control signals) directly corresponding to high-level functional blocks of an ML technique (such as layers in neural networks) or even an ML as a whole. Although straightforward and easy to implement for a limited set of similar ML techniques, the lack of agility in the instruction set prevents such accelerator designs from supporting a variety of different ML techniques with sufficient flexibility and efficiency. In this article, we first propose a novel domain-specific Instruction Set Architecture (ISA) for NN accelerators, called Cambricon, which is a load-store architecture that integrates scalar, vector, matrix, logical, data transfer, and control instructions, based on a comprehensive analysis of existing NN techniques. We then extend the application scope of Cambricon from NN to ML techniques. We also propose an assembly language, an assembler, and runtime to support programming with Cambricon, especially targeting large-scale ML problems. Our evaluation over a total of 16 representative yet distinct ML techniques have demonstrated that Cambricon exhibits strong descriptive capacity over a broad range of ML techniques and provides higher code density than general-purpose ISAs such as x86, MIPS, and GPGPU. Compared to the latest state-of-the-art NN accelerator design DaDianNao [7] (which can only accommodate three types of NN techniques), our Cambricon-based accelerator prototype implemented in TSMC 65nm technology incurs only negligible latency/power/area overheads, with a versatile coverage of 10 different NN benchmarks and 7 other ML benchmarks. Compared to the recent prevalent ML accelerator PuDianNao, our Cambricon-based accelerator is able to support all the ML techniques as well as the 10 NNs but with only approximate 5.1% performance loss.

A Flexible and Energy-Efficient Convolutional Neural Network Acceleration With Dedicated ISA and Accelerator

State-of-the-art convolutional neural networks (CNNs) usually have a large number of layers and filter weights which bring huge computation and communication overheads. A general purpose instruction set architecture (ISA) is flexible but has low code density and high power consumption. The existing CNN-specific accelerators are much more efficient but usually are inflexible or require a complex controller to handle the computation and data transfer of different CNNs. In this brief, we propose a new CNN-specific ISA which embeds the parallel computation and data reuse parameters in the instructions. An instruction generator deploys the instruction parameters according to the feature of CNNs and hardware’s computation and storage resources. In addition, a reconfigurable accelerator with 225 multipliers and 24 adder trees is realized to obtain efficient parallel computation and data transfer. Compared with x86 processors, our design has 392 times better energy efficiency and 16 times higher code density. Compared with other state-of-the-art accelerators, our solution has a higher flexibility to support all popular CNNs and a higher energy efficiency.

Pacmanvirus, a New Giant Icosahedral Virus at the Crossroads between Asfarviridae and Faustoviruses.

African swine fever virus, a double-stranded DNA virus that infects pigs, is the only known member of the Asfarviridae family. Nevertheless, during our isolation and sequencing of the complete genome of faustovirus, followed by the description of kaumoebavirus, carried out over the past 2 years, we observed the emergence of previously unknown related viruses within this group of viruses. Here we describe the isolation of pacmanvirus, a fourth member in this group, which is capable of infecting Acanthamoeba castellanii Pacmanvirus A23 has a linear compact genome of 395,405 bp, with a 33.62% G+C content. The pacmanvirus genome harbors 465 genes, with a high coding density. An analysis of reciprocal best hits shows that 31 genes are conserved between African swine fever virus, pacmanvirus, faustovirus, and kaumoebavirus. Moreover, the major capsid protein locus of pacmanvirus appears to be different from those of kaumoebavirus and faustovirus. Overall, comparative and genomic analyses reveal the emergence of a new group or cluster of viruses encompassing African swine fever virus, faustovirus, pacmanvirus, and kaumoebavirus.IMPORTANCE Pacmanvirus is a newly discovered icosahedral double-stranded DNA virus that was isolated from an environmental sample by amoeba coculture. We describe herein its structure and replicative cycle, along with genomic analysis and genomic comparisons with previously known viruses. This virus represents the third virus, after faustovirus and kaumoebavirus, that is most closely related to classical representatives of the Asfarviridae family. These results highlight the emergence of previously unknown double-stranded DNA viruses which delineate and extend the diversity of a group around the asfarvirus members.

Design of Low-Gate-Count Low-Power Microprocessors with High Code Density for Deeply Embedded Applications

Deeply embedded applications demand small area, low power, high code density, and low design complexity for high adaptability. Both a 16-bit microprocessor with a 4G byte linear memory space and a 4-bit processor are proposed and designed to achieve these goals. Hardware reuse and sharing, multicycle architecture, compact instruction set architecture, and counter-based instruction decoder are utilized to reduce gate count. As a result, gate count and power dissipation of the synthesized ASIC gate-level netlists of 16-bit and 4-bit processors are less than 14,000, 1,490, 0.5[Formula: see text]m W, and 0.06[Formula: see text]m W, respectively, at 10[Formula: see text]MHz in a 0.18[Formula: see text][Formula: see text]m digital CMOS technology. The proposed 16-bit and 32-bit processors are extendable instruction set computers whose high code density is demonstrated to reduce code bytes by 40% over a reduced instruction set computer. The pipelined EISC processor only consumes 50[Formula: see text][Formula: see text]W/MHz with 10,800 gates in a 0.18[Formula: see text][Formula: see text]m CMOS process.

Cambricon

Neural Networks (NN) are a family of models for a broad range of emerging machine learning and pattern recondition applications. NN techniques are conventionally executed on general-purpose processors (such as CPU and GPGPU), which are usually not energy-efficient since they invest excessive hardware resources to flexibly support various workloads. Consequently, application-specific hardware accelerators for neural networks have been proposed recently to improve the energy-efficiency. However, such accelerators were designed for a small set of NN techniques sharing similar computational patterns, and they adopt complex and informative instructions (control signals) directly corresponding to high-level functional blocks of an NN (such as layers), or even an NN as a whole. Although straightforward and easy-to-implement for a limited set of similar NN techniques, the lack of agility in the instruction set prevents such accelerator designs from supporting a variety of different NN techniques with sufficient flexibility and efficiency. In this paper, we propose a novel domain-specific Instruction Set Architecture (ISA) for NN accelerators, called Cambricon, which is a load-store architecture that integrates scalar, vector, matrix, logical, data transfer, and control instructions, based on a comprehensive analysis of existing NN techniques. Our evaluation over a total of ten representative yet distinct NN techniques have demonstrated that Cambricon exhibits strong descriptive capacity over a broad range of NN techniques, and provides higher code density than general-purpose ISAs such as ×86, MIPS, and GPGPU. Compared to the latest state-of-the-art NN accelerator design DaDianNao [5] (which can only accommodate 3 types of NN techniques), our Cambricon-based accelerator prototype implemented in TSMC 65nm technology incurs only negligible latency/power/area overheads, with a versatile coverage of 10 different NN benchmarks.

낮은 복잡도의 Deeply Embedded 중앙처리장치 및 시스템온칩 구현

Abstract This paper proposes a low-complexity central processing unit (CPU) that is suitable for deeply embeddedsystems, including Internet of things (IoT) applications. The core features a 16-bit instruction set architecture (ISA) that leads to high code density, as well as a multicycle architecture with a counter-based control unit and adder sharing that lead to a small hardware area. A co-processor, instruction cache, AMBA bus, internal SRAM, externalmemory, on-chip debugger (OCD), and peripheral I/Os are placed around the core to make a system-on-a-chip (SoC) platform. This platform is based on a modified Harvard architecture to facilitate memory access by reducing the number of access clock cycles. The SoC platform and CPU were simulated and verified at the C and the assembly levels, and FPGA prototyping with integrated logic analysis was carried out. The CPU was synthesized at the ASICfront-end gate netlist level using a 0.18μm digital CMOS technology with 1.8V supply, resulting in a gate count ofmerely 7700 at a 50MHz clock speed. The SoC platform was embedded in an FPGA on a miniature board and appliedto deeply embedded IoT applications.

Complete Genome Sequence and Comparative Genomics of a Novel Myxobacterium Myxococcus hansupus.

Myxobacteria, a group of Gram-negative aerobes, belong to the class δ-proteobacteria and order Myxococcales. Unlike anaerobic δ-proteobacteria, they exhibit several unusual physiogenomic properties like gliding motility, desiccation-resistant myxospores and large genomes with high coding density. Here we report a 9.5 Mbp complete genome of Myxococcus hansupus that encodes 7,753 proteins. Phylogenomic and genome-genome distance based analysis suggest that Myxococcus hansupus is a novel member of the genus Myxococcus. Comparative genome analysis with other members of the genus Myxococcus was performed to explore their genome diversity. The variation in number of unique proteins observed across different species is suggestive of diversity at the genus level while the overrepresentation of several Pfam families indicates the extent and mode of genome expansion as compared to non-Myxococcales δ-proteobacteria.

3.56-bits/cm Compact Inkjet Printed and Application Specific Chipless RFID Tag

In this letter, a 28.5-bit chipless RFID tag, based on paper substrate and realized using inkjet printing technique is presented. Operating within ultrawideband, the tag occupies a compact size of 2 ×4 cm 2 . Focusing on applications requiring time and date identification, a novel encoding technique is presented that allows efficient frequency band allocation based on the number of required instances of time and date variables. A figure of merit (FOM) relating coding capacity and tag dimensions coined as code density is also introduced. A systematic design process followed by simulations and verified through measurements reveal a high code density of 3.56 bits/cm 2 for the presented chipless tag.