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New approach to DNA data storage makes system more dynamic, scalable

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Jun 12, 2020 (Nanowerk News) Researchers from North Carolina State University have developed a fundamentally new approach to DNA data storage systems, giving users the ability to read or modify data files without destroying them and making the systems easier to scale up for practical use (Nature Communications, “Dynamic and scalable DNA-based information storage”). “Most of the existing DNA data storage systems rely on polymerase chain reaction (PCR) to access stored files, which is very efficient at copying information but presents some significant challenges,” says Albert Keung, co-corresponding author of a paper on the work. “We’ve developed a system called Dynamic Operations and Reusable Information Storage, or DORIS, that doesn’t rely on PCR. That has helped us address some of the key obstacles facing practical implementation of DNA data storage technologies.” Keung is an assistant professor of chemical and biomolecular engineering at NC State. DNA data storage systems have the potential to hold orders of magnitude more information than existing systems of comparable size. However, existing technologies have struggled to address a range of concerns related to practical implementation. DNA-based information storage (Image: Kevin Lin) Current systems rely on sequences of DNA called primer-binding sequences that are added to the ends of DNA strands that store information. In short, the primer-binding sequence of DNA serves as a file name. When you want a given file, you retrieve the strands of DNA bearing that sequence. Many of the practical barriers to DNA data storage technologies revolve around the use of PCR to retrieve stored data. Systems that rely on PCR have to drastically raise and lower the temperature of the stored genetic material in order to rip the double-stranded DNA apart and reveal the primer-binding sequence. This results in all of the DNA – the primer-binding sequences and the data-storage sequences – swimming free in a kind of genetic soup. Existing technologies can then sort through the soup to find, retrieve and copy the relevant DNA using PCR. The temperature swings are problematic for developing practical technologies, and the PCR technique itself gradually consumes – or uses up – the original version of the file that is being retrieved. DORIS takes a different approach. Instead of using double-stranded DNA as a primer-binding sequence, DORIS uses an “overhang” that consists of a single-strand of DNA – like a tail that streams behind the double-stranded DNA that actually stores data. While traditional techniques required temperature fluctuations to rip open the DNA in order to find the relevant primer-binding sequences, using a single-stranded overhang means that DORIS can find the appropriate primer-binding sequences without disturbing the double-stranded DNA. “In other words, DORIS can work at room temperature, making it much more feasible to develop DNA data management technologies that are viable in real-world scenarios,” says James Tuck, co-corresponding author of the paper and a professor of electrical and computer engineering at NC State. The other benefit of not having to rip apart the DNA strands is that the DNA sequence in the overhang can be the same as a sequence found in the double-stranded region of the data file itself. That’s difficult to achieve in PCR-based systems without sacrificing information density – because the system wouldn’t be able to differentiate between primer-binding sequences and data-storage sequences. “DORIS allows us to significantly increase the information density of the system, and also makes it easier to scale up to handle really large databases,” says Kevin Lin, first author of the paper and a Ph.D. student at NC State. And once DORIS has identified the correct DNA sequence, it doesn’t rely on PCR to make copies. Instead, DORIS transcribes the DNA to RNA, which is then reverse-transcribed back into DNA which the data-storage system can read. In other words, DORIS doesn’t have to consume the original file in order to read it. The single-stranded overhangs can also be modified, allowing users to rename files, delete files or “lock” them – effectively making them invisible to other users. “We’ve developed a functional prototype of DORIS, so we know it works,” Keung says. “We’re now interested in scaling it up, speeding it up and putting it into a device that automates the process – making it user friendly.”

Source: https://feeds.nanowerk.com/~/627064464/0/nanowerk/agwb~New-approach-to-DNA-data-storage-makes-system-more-dynamic-scalable.php

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Rock ‘n’ control: Göttingen physicists use oscillations of atoms to control a phase transition

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Home > Press > Rock ‘n’ control: Göttingen physicists use oscillations of atoms to control a phase transition

Artist's impression of the phase transition of indium atoms on a silicon crystal controlled by light pulses CREDIT
Dr Murat Sivis
Artist’s impression of the phase transition of indium atoms on a silicon crystal controlled by light pulses CREDIT
Dr Murat Sivis

Abstract:
The goal of “Femtochemistry” is to film and control chemical reactions with short flashes of light. Using consecutive laser pulses, atomic bonds can be excited precisely and broken as desired. So far, this has been demonstrated for selected molecules. Researchers at the University of Göttingen and the Max Planck Institute for Biophysical Chemistry have now succeeded in transferring this principle to a solid, controlling its crystal structure on the surface. The results have been published in the journal Nature.

Rock ‘n’ control: Göttingen physicists use oscillations of atoms to control a phase transition


Göttingen, Germany | Posted on July 8th, 2020

The team, led by Jan Gerrit Horstmann and Professor Claus Ropers, evaporated an extremely thin layer of indium onto a silicon crystal and then cooled the crystal down to -220 degrees Celsius. While the indium atoms form conductive metal chains on the surface at room temperature, they spontaneously rearrange themselves into electrically insulating hexagons at such low temperatures. This process is known as the transition between two phases – the metallic and the insulating – and can be switched by laser pulses. In their experiments, the researchers then illuminated the cold surface with two short laser pulses and immediately afterwards observed the arrangement of the indium atoms using an electron beam. They found that the rhythm of the laser pulses has a considerable influence on how efficiently the surface can be switched to the metallic state.

This effect can be explained by oscillations of the atoms on the surface, as first author Jan Gerrit Horstmann explains: “In order to get from one state to the other, the atoms have to move in different directions and in doing so overcome a sort of hill, similar to a roller coaster ride. A single laser pulse is not enough for this, however, and the atoms merely swing back and forth. But like a rocking motion, a second pulse at the right time can give just enough energy to the system to make the transition possible.” In their experiments the physicists observed several oscillations of the atoms, which influence the conversion in very different ways.

Their findings not only contribute to the fundamental understanding of rapid structural changes, but also open up new perspectives for surface physics. “Our results show new strategies to control the conversion of light energy at the atomic scale,” says Ropers from the Faculty of Physics at the University of Göttingen, who is also a Director at the Max Planck Institute for Biophysical Chemistry. “The targeted control of the movements of atoms in solids using laser pulse sequences could also make it possible to create previously unobtainable structures with completely new physical and chemical properties.”

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The work was funded by the German Research Foundation (DFG) and the European Research Council (ERC).

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For more information, please click here

Contacts:
Melissa Sollich
49-551-392-6228

Professor Claus Ropers
University of Göttingen
Faculty of Physics, Professor of Experimental Solid State Physics and Director, Max Planck Institute for Biophysical Chemistry

Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
Tel: +49 551 39-24549
Email:
http://www.uni-goettingen.de/en/598878.html

Jan Gerrit Horstmann
Tel: +49 (0)551 3921485
Email:
http://www.uni-goettingen.de/en/598878.html

Copyright © University of Göttingen

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Original publication: J. G. Horstmann et al: Coherent control of a surface structural phase transition. Nature 2020, DoI: 10.1038/s41586-020-2440-4:

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Old X-rays, new vision: A nano-focused X-ray laser: Researchers enhance the accuracy of X-ray free-electron laser measurements closer to the diameter of typical atoms than previously possible

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Home > Press > Old X-rays, new vision: A nano-focused X-ray laser: Researchers enhance the accuracy of X-ray free-electron laser measurements closer to the diameter of typical atoms than previously possible

Schematic of the new method, based on speckles of coherent scattering. CREDIT
Osaka University
Schematic of the new method, based on speckles of coherent scattering. CREDIT
Osaka University

Abstract:
Imagine taking movies of the fastest chemical processes, or imaging atomic-scale detail of single virus particles without damaging them. Researchers from Japan have advanced the state-of-the-art in such endeavors, by enhancing the utility of a special X-ray laser for nanometer-scale measurements.

Old X-rays, new vision: A nano-focused X-ray laser: Researchers enhance the accuracy of X-ray free-electron laser measurements closer to the diameter of typical atoms than previously possible


Osaka, Japan | Posted on July 8th, 2020

In a study recently published in Journal of Synchrotron Radiation, researchers from Osaka University, in collaboration with RIKEN and Japan Synchrotron Radiation Research Institute (JASRI), have reduced the beam diameter in an X-ray free-electron laser to 6 nanometers in width. This considerably improves the utility of these lasers for imaging structures closer to the atomic level than possible in prior work.

To “see” extremely small and otherwise invisible objects, and observe ultrafast chemical processes, researchers commonly use synchrotron X-ray facilities. X-ray free-electron lasers are an alternative that can–in principle–image atomic-scale detail of, for example, a virus particle, on the timescale of an electron transition, without damaging the particle. To do this, you need an incredibly bright X-ray laser that focuses extremely fast laser pulses on the nanometer scale.

“Using multilayer focusing mirrors, we narrowed the width of our laser beam down to a diameter of 6 nanometers,” says lead author of the study Takato Inoue. “This is not quite the diameter of a typical atom, but we’re making good progress.”

Until now, it has been difficult to focus X-ray free-electron lasers to such small diameters. That’s because of challenges in fabricating the required mirrors, and confirming the focused size of the lasers. The researcher team addressed the focusing problem by analyzing the shape of the laser’s interference patterns, known as speckle profiles.

“We generated speckle profiles by coherent X-ray scattering of randomly distributed metal nanoparticles,” explains Satoshi Matsuyama, senior author. “This enabled experimental measurements of the laser beam profile, which were in good agreement with theoretical calculations.”

Because the laser beam diameter can be so precisely measured, further advancements are now feasible. For example, by using atoms for the scattering analysis, X-ray free-electron laser measurements can be improved to a 1-nanometer focus.

The researchers anticipate that extremely high-intensity lasers, over a million trillion times brighter than the Sun, will now be useful for imaging ultrafast molecular processes–at atomic-scale detail–that are beyond the capabilities of the most advanced synchrotrons. With such technology, protein molecules and other small important biological entities can be imaged without damaging them under the strategy of “diffraction before destruction,” by using a single laser pulse.

####

About Osaka University
Osaka University was founded in 1931 as one of the seven imperial universities of Japan and is now one of Japan’s leading comprehensive universities with a broad disciplinary spectrum. This strength is coupled with a singular drive for innovation that extends throughout the scientific process, from fundamental research to the creation of applied technology with positive economic impacts. Its commitment to innovation has been recognized in Japan and around the world, being named Japan’s most innovative university in 2015 (Reuters 2015 Top 100) and one of the most innovative institutions in the world in 2017 (Innovative Universities and the Nature Index Innovation 2017). Now, Osaka University is leveraging its role as a Designated National University Corporation selected by the Ministry of Education, Culture, Sports, Science and Technology to contribute to innovation for human welfare, sustainable development of society, and social transformation.

Website: https://resou.osaka-u.ac.jp/en/top

For more information, please click here

Contacts:
Saori Obayashi
81-661-055-886

@osaka_univ_e

Copyright © Osaka University

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The article, “Generation of an X-ray nanobeam of a free-electron laser using reflective optics with speckle interferometry,” was published in Journal of Synchrotron Radiation at DOI::

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Nano Technology

Beyond von Neumann

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Data-centric computation and the scalability limits of current computing systems call for the developments of alternative to von Neumann architecture.

Digital computing has deeply permeated the fabric of the modern society. Its transformative power endowed by the remarkable technological evolution and commercial success begs no question of legitimacy. Notwithstanding, the underlying concept of the computer hardware design that has remained fundamentally unchanged since the days of von Neumann is in need of serious reform. In the current architecture where data moves between the physically separated processor and memory, latency is unavoidable. With no improvement in data transfer rates, the high-speed processor spends more time idle, waiting for data to be fetched from memory. To mitigate this issue within the von Neumann framework a number of solutions including caching, multi-threading, new types of random access memory and near-memory computing, with a processor mingled with memory on a single chip, have been proposed and implemented with varying degrees of success. Although the current architecture is unlikely to be abandoned in the foreseeable future, the growing trend of computational heterogeneity and a gradual shift towards learning computing with a data-centric approach typical of machine learning and deep learning calls for more specialized non-von Neumann platforms. One notable example is the architectures loosely modelled on the human brain structure, which infer a collocation of memory and processing units. In this scenario, the redundancy associated with data traffic could be entirely eliminated provided that computational tasks and data storage are both performed in place in the memory itself. This energy efficient solution, known as in-memory computing, could reduce the computational complexity and mitigate the issue of memory thrashing. Moreover, this approach is in keeping with the requirements of learning-based computing and has been actively explored for applications related to artificial intelligence.

As discussed in a Review in this issue by Abu Sebastian and co-workers, memory devices are essential building blocks of key computational primitives for in-memory computing. Similar to conventional memory, there is no universal solution for computational memory in that both charge-based and resistance-based memory technologies can be employed. For example, SRAM and DRAM are perfectly capable of performing in-memory logic operations while Flash memory is fit for matrix–vector multiplication operations. Another potent technology is phase-change memories (PCM) that have been successfully used to demonstrate the coexistence of storage and computation in a non-von Neumann architecture based on nanoscale PCM devices harnessing the crystallization dynamics1. Memristor-based memory devices often referred to as resistive random access memory (RRAM) relying on the formation of conducting filaments for switching between low and high resistance states are particularly attractive for in-memory computing owing to their non-volatile storage capability with a continuum of conductance states. In the context of the application-specific approach to computation, memory-based computational primitives can be used in a variety of tasks ranging from high-precision scientific computing to largely imprecise stochastic computing and everything in-between including deep learning in artificial neural networks (ANNs).

The original attempt to design ANNs in complementary metal–oxide–semiconductor (CMOS) technology has proved unsustainable with respect to energy consumption prompting the need for alternative non-von Neumann solutions for neuromorphic computing. Although, rethinking the hardware design at the device and system levels is a valid tactic, exploring the potential of emerging nanomaterials could enable the much needed departure from the conventional approaches to neuromorphic hardware. Neuromorphic nanoelectronic materials ranging from zero-dimensional, one-dimensional (1D) and two-dimensional (2D) nanomaterials to van der Waals heterostructures and mixed-dimensional heterojunctions have been actively explored for implementation in electronic and optoelectronic synapses. In a second Review in this Focus issue, Vinod Sangwan and Mark Hersam provide a detailed overview of the most prominent examples of nanomaterials for neuromorphic architectures including quantum dots that have been successfully employed in electro-photo-sensitive memristors, RRAM and quantum memristors based on Josephson junctions; 1D nanomaterials, particularly carbon nanotubes enabling the realization of synaptic transistors for unsupervised learning in spiking neural networks (SNNs) and group IV and III–V semiconducting nanowires exhibiting non-volatile memory characteristics. 2D materials, that have been widely covered by Nature Nanotechnology as potentially promising candidates for nanoelectronics, can also achieve neuromorphic functionality, particularly in view of improved device scaling and integration with planar wafer technology. For example, in one demonstration monolayer transition metal dichalcogenides (TMDCs) have been made into ultrathin vertical memristors where switching is likely to occur due to point defects2. Similar to 1D materials, synaptic transistors can be realized using ionic motion in layered TMDCs and black phosphorus, while phase transition in some TMDs have been harnessed to fabricate vertical RRAM. Moreover, the propensity of 2D materials for scalable processing and their ability to form van der Waals heterostructures can be explored for large-area, flexible and printable neuromorphic circuits.

To get a more complete overview of applications of 2D materials in nanoelectronics beyond neuromorphic computing we refer interested readers to another Review in this Focus issue by Chunsen Liu and colleagues, where the authors analyse the possibility of integrating 2D materials with the existing Si CMOS technology, in-memory computing platforms and matrix computing for ANNs and SNNs applications. By virtue of their atomic thickness 2D materials represent the ultimate limit for downscaling, the milestone that is hardly achievable in the context of the continued MOSFET shrinking.

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Beyond von Neumann. Nat. Nanotechnol. 15, 507 (2020). https://doi.org/10.1038/s41565-020-0738-x

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