With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and ...dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA–ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field.
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•A positive correlation of arsenic, copper and cadmium is observed in the flotation process.•Arsenic-copper alloys in FSF slag account for nearly 90 % of arsenic-bearing ...phases.•Different fates of arsenic are depended on its embeded ways.•The recombination of As-O and Cu-S affects the selectivity of copper and arsenic.
Separating copper and arsenic has always been a major problem in the copper slag flotation process, which influences copper slag utilization and the environmental safety. A comparative study of flash smelting furnace (FSF) slag and its flotation products (concentrate and tailing) reveals the factors affecting the separation of copper and arsenic in the beneficiation process from the perspective of mineralogy and morphology. The elemental fractionation in the process shows a positive correlation of As, Cu and Cd and an obvious correlation between speciation transformation of copper and arsenic was observed. The occurrence of arsenic and copper in FSF slag correlate the key phases of arsenic copper alloys, accounted for 88.91 % of total arsenic-bearing phases and 32.28% of copper-bearing phases. Closely-embeded matte and copper-arsenic alloys incerease the difficulty of the separation suggesting the finer grinding is needed for slag. Arsenic is liberated and oxidized into arsenate compounds while the recombination of As-O and Cu-S happened in the process affecting the selectivity of copper and arsenic. Arsenic fixed in silicate minerals is discharged into tailing which suggested to induce and fix arsenic into silicate minerals can facilitate arsenic removal from concentrate. FSF slag and its flotation concnetrate show risks of some of some of HMs which should be cautiously transported, disposed, and utilized.
Emerging from the origins of supramolecular chemistry and the development of selective chemical receptors that rely on lock‐and‐key binding, activity‐based sensing (ABS)—which utilizes molecular ...reactivity rather than molecular recognition for analyte detection—has rapidly grown into a distinct field to investigate the production and regulation of chemical species that mediate biological signaling and stress pathways, particularly metal ions and small molecules. Chemical reactions exploit the diverse chemical reactivity of biological species to enable the development of selective and sensitive synthetic methods to decipher their contributions within complex living environments. The broad utility of this reaction‐driven approach facilitates application to imaging platforms ranging from fluorescence, luminescence, photoacoustic, magnetic resonance, and positron emission tomography modalities. ABS methods are also being expanded to other fields, such as drug and materials discovery.
ABSolute selectivity: Stemming from supramolecular chemical receptors that rely on lock‐and‐key binding, activity‐based sensing (ABS) methods utilizing a variety of chemical reaction approaches offer the highly selective detection of small molecules and metals in biological systems. This Review discusses key design principles, reaction development, and sensing methods, and gives an outlook on this emerging field.
Neurotoxic methylmercury (MeHg) is formed by microbial methylation of inorganic divalent Hg (HgII) and constitutes severe environmental and human health risks. The methylation is enabled by hgcA and ...hgcB genes, but it is not known if the associated molecular-level processes are rate-limiting or enable accurate prediction of MeHg formation in nature. In this study, we investigated the relationships between hgc genes and MeHg across redox-stratified water columns in the brackish Baltic Sea. We showed, for the first time, that hgc transcript abundance and the concentration of dissolved HgII-sulfide species were strong predictors of both the HgII methylation rate and MeHg concentration, implying their roles as principal joint drivers of MeHg formation in these systems. Additionally, we characterized the metabolic capacities of hgc + microorganisms by reconstructing their genomes from metagenomes (i.e., hgc + MAGs), which highlighted the versatility of putative HgII methylators in the water column of the Baltic Sea. In establishing relationships between hgc transcripts and the HgII methylation rate, we advance the fundamental understanding of mechanistic principles governing MeHg formation in nature and enable refined predictions of MeHg levels in coastal seas in response to the accelerating spread of oxygen-deficient zones.
Abstract
The understanding and rational design of heterogeneous catalysts for complex reactions, such as CO
2
reduction, requires knowledge of elementary steps and chemical species prevalent on the ...catalyst surface under operating conditions. Using in situ nanoscale surface-enhanced Raman scattering, we probe the surface of a Ag nanoparticle during plasmon-excitation-driven CO
2
reduction in water. Enabled by the high spatiotemporal resolution and surface sensitivity of our method, we detect a rich array of C
1
–C
4
species formed on the photocatalytically active surface. The abundance of multi-carbon compounds, such as butanol, suggests the favorability of kinetically challenging C–C coupling on the photoexcited Ag surface. Another advance of this work is the use of isotope labeling in nanoscale probing, which allows confirmation that detected species are the intermediates and products of the catalytic reaction rather than spurious contaminants. The surface chemical knowledge made accessible by our approach will inform the modeling and engineering of catalysts.
Observation of chiral phonons Zhu, Hanyu; Yi, Jun; Li, Ming-Yang ...
Science (American Association for the Advancement of Science),
02/2018, Letnik:
359, Številka:
6375
Journal Article
Recenzirano
Odprti dostop
Chirality reveals symmetry breaking of the fundamental interaction of elementary particles. In condensed matter, for example, the chirality of electrons governs many unconventional transport ...phenomena such as the quantum Hall effect. Here we show that phonons can exhibit intrinsic chirality in monolayer tungsten diselenide. The broken inversion symmetry of the lattice lifts the degeneracy of clockwise and counterclockwise phonon modes at the corners of the Brillouin zone. We identified the phonons by the intervalley transfer of holes through hole-phonon interactions during the indirect infrared absorption, and we confirmed their chirality by the infrared circular dichroism arising from pseudoangular momentum conservation. The chiral phonons are important for electron-phonon coupling in solids, phonon-driven topological states, and energy-efficient information processing.
High levels of ultrafine particles (UFPs; diameter of less than 50 nm) are frequently produced from new particle formation under urban conditions, with profound implications on human health, weather, ...and climate. However, the fundamental mechanisms of new particle formation remain elusive, and few experimental studies have realistically replicated the relevant atmospheric conditions. Previous experimental studies simulated oxidation of one compound or a mixture of a few compounds, and extrapolation of the laboratory results to chemically complex air was uncertain. Here, we show striking formation of UFPs in urban air from combining ambient and chamber measurements. By capturing the ambient conditions (i.e., temperature, relative humidity, sunlight, and the types and abundances of chemical species), we elucidate the roles of existing particles, photochemistry, and synergy of multipollutants in new particle formation. Aerosol nucleation in urban air is limited by existing particles but negligibly by nitrogen oxides. Photooxidation of vehicular exhaust yields abundant precursors, and organics, rather than sulfuric acid or base species, dominate formation of UFPs under urban conditions. Recognition of this source of UFPs is essential to assessing their impacts and developing mitigation policies. Our results imply that reduction of primary particles or removal of existing particles without simultaneously limiting organics from automobile emissions is ineffective and can even exacerbate this problem.
To explore a novel strategy for the remediation of soils polluted with Cu and Cd, three strains of plant-growth-promoting rhizobacteria (PGPRs) isolated from contaminated mines and two grass species ...(perennial ryegrass and tall fescue) were selected in this study. The performance of PGPR strains in metal adsorption, maintaining promotion traits under stress, and ameliorating phytostabilization potential was evaluated. Cd2+ exerted a stronger deleterious effect on microbial growth than Cu2+, but the opposite occurred for grass seedlings. Adsorption experiment showed that the growing PGPR strains were able to immobilize maximum 79.49% Cu and 81.35% Cd owing to biosorption or bioaccumulation. The strains exhibited the ability to secrete indole-3-acetic acid (IAA) and dissolve phosphorus in the absence and presence of metals, and IAA production was even enhanced in the presence of low Cu2+ (5 mg L−1). However, the siderophore-producing ability of the isolates was strongly suppressed under Cu and Cd exposure. Ryegrass was further selected for pot experiments owing to its higher germination rate and tolerance under Cu and Cd stress than fescue. Pot-experiment results revealed that PGPR addition significantly increased the shoot and root biomasses of ryegrass by 11.49%–44.50% and 43.53%–90.29% in soil co-contaminated with 800 mg Cu kg−1 and 30 mg Cd kg−1, respectively. Metal uptake and translocation in inoculated ryegrass significantly decreased owing to the reduced diethylenetriamine pentaacetic acid-extractable metal content and increased residual metal-fraction percentage mediated by PGPR. Interestingly, stress mitigation was observed in these inoculated plants; in particular, their malondialdehyde content and superoxide dismutase activity were even significantly lower than those of ryegrass under normal conditions. Therefore, PGPR could be a promising option to enhance the phytostabilization efficiency of Cu and Cd in heavily polluted soils.
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•Metal toxicity on the isolates and grass seedlings depends on the type and concentration of metals.•The metal removal rate was positively correlated with bacterial cell numbers in the medium.•IAA production of the isolates was significantly enhanced at a low Cu2+ level (5 mg L−1).•PGPR inoculation improved ryegrass growth and oxidative stress management.•Metal immobilization was enhanced and less metal was transferred to the above-ground parts.
The three PGPR strains could adsorb metal, maintain promoting traits under stress, and enhance the phytostabilization efficiency of ryegrass grown in Cu- and Cd-polluted soils.
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