Direct observation of 3D atomic packing in monatomic amorphous materials

Liquids and solids are two fundamental states of matter. However, due to the lack of direct experimental determination, our understanding of the 3D atomic structure of liquids and amorphous solids remained speculative. Here we advance atomic electron tomography to determine for the first time the 3D atomic positions in monatomic amorphous materials, including a Ta thin film and two Pd nanoparticles. We observe that pentagonal bipyramids are the most abundant atomic motifs in these amorphous materials. Instead of forming icosahedra, the majority of pentagonal bipyramids arrange into networks that extend to medium-range scale. Molecular dynamic simulations further reveal that pentagonal bipyramid networks are prevalent in monatomic amorphous liquids, which rapidly grow in size and form icosahedra during the quench from the liquid state to glass state. The experimental method and results are expected to advance the study of the amorphous-crystalline phase transition and glass transition at the single-atom level

Gemmini: Enabling Systematic Deep-Learning Architecture Evaluation via Full-Stack Integration

DNN accelerators are often developed and evaluated in isolation without considering the cross-stack, system-level effects in real-world environments. This makes it difficult to appreciate the impact of System-on-Chip (SoC) resource contention, OS overheads, and programming-stack inefficiencies on overall performance/energy-efficiency. To address this challenge, we present Gemmini, an open-source*, full-stack DNN accelerator generator. Gemmini generates a wide design-space of efficient ASIC accelerators from a flexible architectural template, together with flexible programming stacks and full SoCs with shared resources that capture system-level effects. Gemmini-generated accelerators have also been fabricated, delivering up to three orders-of-magnitude speedups over high-performance CPUs on various DNN benchmarks. * https://github.com/ucb-bar/gemminiComment: To appear at the 58th IEEE/ACM Design Automation Conference (DAC), December 2021, San Francisco, CA, US

Ethical framework on risk governance of synthetic biology

Synthetic biology is an emerging multidisciplinary field that aims to design and construct new biological systems not found in nature. Whereas synthetic biology may yield tremendous benefits, it may also pose substantial risks to human health and the environment that must be addressed. In this paper, we examined the environmental risks associated with synthetic biology, including changes to or depletion of the environment, competition with native species, horizontal gene transfer, pathogenicity or toxicity, bioterrorism, and laboratory biosecurity. We highlight three approaches for assessing environmental risks in synthetic biology: solution-focused risk assessment, Bayesian networks, and network of networks for sustainable capacity building. An ethical governance framework is proposed to facilitate innovation while minimising risks. This framework emphasises the precautionary principle and balancing stakeholder interests prior to project development and commercialisation. Overall, we underscore the importance and urgency of assessing and managing the environmental risks of synthetic biology to ensure its safe and ethical development and application

Label-Free Photoelectrochemical Immunosensor for Neutrophil Gelatinase-Associated Lipocalin Based on the Use of Nanobodies

Acute renal failure (ARF) represents a very important and potentially devastating disorder in clinical nephrology. Neutrophil gelatinase-associated lipocalin (NGAL) is an early biomarker for ARF in a wide range of different disease processes, which is frequently detected in clinical diagnosis. Herein, we present a label-free and sensitive photoelectrochemical (PEC) immunosensor for NGAL by utilizing a biotinylated anti-NGAL Nanobody (Nb) orientedly immobilized to streptavidin-coated cobalt 2,9,16,23-tetraaminophthalocyanine (CoPc)-sensitized TiO₂ electrode. The Nb was biotinylated at the C-terminus, which is situated at the opposite site of the antigen binding region. Using highly oriented Nb as receptor molecules, a label-free PEC immunosensor for NGAL was developed by monitoring the changes in the photocurrent signals of the electrode resulting from immunoreaction. Immobilization of Nb to streptavidin-coated CoPc-sensitized TiO₂ electrode surface provides high binding capacity to NGAL; thus, it can lead to a high sensitivity. The limit of detection (LOD) of the proposed immunosensor has been significantly lowered to 0.6 pg mL^–1. This proposed immunosensor reveals high specificity to detect NGAL, with acceptable intra-assay precision and excellent stability. In addition, the present work provides a new approach to design Nb-based PEC immunosensor and increases versatility of Nbs

Three-dimensional atomic packing in amorphous solids with liquid-like structure.

Liquids and solids are two fundamental states of matter. However, our understanding of their three-dimensional atomic structure is mostly based on physical models. Here we use atomic electron tomography to experimentally determine the three-dimensional atomic positions of monatomic amorphous solids, namely a Ta thin film and two Pd nanoparticles. We observe that pentagonal bipyramids are the most abundant atomic motifs in these amorphous materials. Instead of forming icosahedra, the majority of pentagonal bipyramids arrange into pentagonal bipyramid networks with medium-range order. Molecular dynamics simulations further reveal that pentagonal bipyramid networks are prevalent in monatomic metallic liquids, which rapidly grow in size and form more icosahedra during the quench from the liquid to the glass state. These results expand our understanding of the atomic structures of amorphous solids and will encourage future studies on amorphous-crystalline phase and glass transitions in non-crystalline materials with three-dimensional atomic resolution