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Water dynamics inside hydrophobic confinement, such as carbon nanotubes (CNTs), has garnered significant attention, focusing on water diffusion. However, a crucial aspect remains unexplored - the influence of confinement size on water ordering and intrinsic hydrogen bond dynamics. To address this gap, we conducted extensive molecular dynamics simulations to investigate local ordering and intrinsic hydrogen bond dynamics of water molecules within CNTs of various sizes (length:20 nm, diameters: 1.0 nm to 5.0 nm) over a wide range of temperatures (260K, 280K, 300K, and 320K). A striking observation emerged: in smaller CNTs, water molecules adopt an icy structure near tube walls while maintaining liquid state towards the center. Notably, water behavior within a 2.0 nm CNT stands out as an anomaly, distinct from other CNT sizes considered in this study. This anomaly was explained through the formation of water layers inside CNTs. The hydrogen bond correlation function of water within CNTs decayed more slowly than bulk water, with an increasing rate as CNT diameter increased. In smaller CNTs, water molecules hold onto their hydrogen bond longer than larger ones. Interestingly, in larger CNTs, the innermost layer's hydrogen bond lasts a shorter time compared to the other layers, and this changes with temperature., (© 2024. The Author(s).)

Amyloid-β (Aβ) and islet amyloid polypeptide (IAPP) are small peptides that have the potential to not only self-assemble but also cross-assemble and form cytotoxic amyloid aggregates. Recently, we experimentally investigated the nature of Aβ-IAPP coaggregation and its inhibition by small polyphenolic molecules. Notably, we found that epigallocatechin gallate (EGCG) had the ability to reduce heteroaggregate formation. However, the precise molecular mechanism behind the reduction of heteroaggregates remains unclear. In this study, the dimerization processes of Aβ40 and IAPP peptides with and without EGCG were characterized by the enhanced sampling technique. Our results showed that these amyloid peptides exhibited a tendency to form a stable heterodimer, which represented the first step toward coaggregation. Furthermore, we also found that the EGCG regulated the dimerization process. In the presence of EGCG, well-tempered metadynamics simulation indicated a notable shift in the bound state toward a greater center of mass (COM) distance. Additionally, the presence of EGCG led to a significant increase in the free energy barrier height (∼15 k B T ) along the COM distance, and we observed a transition state between the bound and unbound states. Our findings also unveiled that the EGCG formed a greater number of hydrogen bonds with Aβ40, effectively obstructing the dimer formation. In addition, we carried out microseconds of all-atom conventional molecular dynamics (cMD) simulations to investigate the formation of both hetero- and homo-oligomer states by these peptides. MD simulations illustrated that EGCG played a significant role in preventing oligomer formation by reducing the content of β-sheets in the peptide. Collectively, our results offered valuable insight into the mechanism of cross-amyloid aggregation between Aβ40 and IAPP and the inhibition effect of EGCG on the heteroaggregation process., Competing Interests: The authors declare no competing financial interest., (© 2024 The Authors. Published by American Chemical Society.)

The bacterial chemotaxis system is a well-understood signaling pathway that promotes bacterial success. Chemotaxis systems comprise chemoreceptors and the CheA kinase, linked by CheW or CheV scaffold proteins. Scaffold proteins provide connections between chemoreceptors and CheA and also between chemoreceptors to create macromolecular arrays. Chemotaxis is required for host colonization by many microbes, including the stomach pathogen Helicobacter pylori . This bacterium builds chemoreceptor-CheA contacts with two distinct scaffold proteins, CheW and CheV1. H. pylori cheW or cheV1 deletion mutants both lose chemoreceptor array formation, but show differing semisolid agar chemotaxis assay behaviors: ∆ cheW mutants exhibit total migration failure, whereas ∆ cheV1::cat mutants display a 50% reduction. On investigating these varied responses, we found that both mutants initially struggle with migration. However, over time, ∆ cheV1::cat mutants develop a stable, enhanced migration capability, termed "migration-able" (Mig + ). Whole-genome sequencing analysis of four distinct ∆ cheV1::cat Mig + strains identified single-nucleotide polymorphisms (SNPs ) in hpg27_252 (hp0273 ) that were predicted to truncate the encoded protein. Computational analysis of the hpg27_252 -encoded protein revealed it encoded a hypothetical protein that was a remote homolog of the PilO Type IV filament membrane alignment complex protein. Although H. pylori lacks Type IV filaments, our analysis showed it retains an operon of genes for homologs of PilO, PilN, and PilM. Deleting hpg27_252 in the ∆ cheV1::cat or wild type strain resulted in enhanced migration in semisolid agar. Our study thus reveals that while cheV1 mutants initially have significant migration defects, they can recover the migration ability through genetic suppressors, highlighting a complex regulatory mechanism in bacterial migration., Importance: Chemotactic motility, present in over half of bacteria, depends on chemotaxis signaling systems comprising receptors, kinases, and scaffold proteins. In Helicobacter pylori , a stomach pathogen, chemotaxis is crucial for colonization, with CheV1 and CheW as key scaffold proteins. While both scaffolds are essential for building chemoreceptor complexes, their roles vary in other assays. Our research reexamines cheV1 mutants' behavior in semisolid agar, a standard chemotaxis test. Initially, cheV1 mutants exhibited defects similar to those of cheW mutants, but they evolved genetic suppressors that enhanced migration. These suppressors involve mutations in a previously uncharacterized gene, unknown in motility behavior. Our findings highlight the significant chemotaxis defects in cheV1 mutants and identify new elements influencing bacterial motility., Competing Interests: The authors declare no conflict of interest.

Hypersaline brine production from desalination plants causes huge environmental stress due to the untenable conventional discharge strategies. Particularly, brine production is expected to drastically increase in the coming few decades due to the increasing desalination capacity in attempts of forestalling water scarcity. Thereby, zero liquid discharge (ZLD) is a worth-considering solution for strategic brine management. ZLD or minimal liquid discharge (MLD) systems provide maximum water recovery with least or zero liquid waste generation and valuable salt production. In this work, a theoretical design of ZLD/MLD system is proposed for reverse osmosis (RO) brine management. Different scenarios are investigated utilizing multistage freeze desalination (FD) and its hybridization with multistage direct contact membrane distillation (DCMD), and eutectic freeze crystallization (EFC) technologies. The design is based on the experimental assessment of the indirect FD process at different feed salinities, i.e., 2 g/L to 155 g/L. FD experiments showed that ice quality is reduced at greater crystallinity levels and initial concentration. Moreover, a computational fluid dynamics (CFD) model is utilized to assess the performance of DCMD. A single DCMD module could produce 53 kg/(m 2 .h) of pure water operating with 69% thermal efficiency. Eventually, water recovery, water quality, as well as specific energy consumption (SEC) are evaluated for the whole system. Based on different configurations of the hybrid ZLD system, the proposed design can achieve water recovery between 40 and 93% with SEC range of 28-114 kWh/m 3 . Results also showed that the produced water quality exceeds drinkable water standards ( ≪ 500 mg/L). This work has provided great evidence in the practicality of ZLD/MLD systems for sustainable brine management., (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

The impact of polymer chain stiffness characterized by the bending modulus ( k θ ) on the glass transition temperature ( T g ) of pure polymer systems, as well as polymer nanocomposites (PNCs), is investigated using molecular dynamics simulations. At small k θ values, the pure polymer system and respective PNCs are in an amorphous state, whereas at large k θ values, both systems are in a semicrystalline state with a glass transition at low temperature. For the pure polymer system, T g initially increases with k θ and does not change obviously at large k θ . However, the T g of PNCs shows interesting behaviors with the increasing volume fraction of nanoparticles ( f NP ) at different k θ values. T g tends to increase with f NP at small k θ , whereas it becomes suppressed at large k θ .

This study investigates the effect of neutron irradiation on zinc oxide (ZnO) crystal bulk substrates that have been ion-implanted with gadolinium (Gd) and iron (Fe) in different concentrations in the Zn-polar (0001) face of the crystal to produce Gd:ZnO and Fe:ZnO crystal bulk samples. The neutron beams of the 241 Am-Be flux were moderated to be 7 × 10 4 n/s cm 2 by a 4.5 cm-thick wax. The implanted face was left to face the neutron beams on top of the wax for 90 h. The results show that the nuclear reaction between thermal neutrons and the implanted material produced a large amount of heat, which significantly enhanced the photoluminescence spectra of the crystal bulk surface after the surface damage caused by ion implantation. This study provides insights into the benefits of having a doped material in the ZnO crystal after irradiation and highlights the potential of neutron irradiation as a method for enhancing the properties of implanted crystal bulk substrates., Competing Interests: The authors declare no competing financial interest., (© 2023 The Authors. Published by American Chemical Society.)

Erbium-doped silica films were synthesized using a two-step sol-gel methodology that involved acid and base catalysts, with erbium concentration ranging from 0.2% to 6% and annealing temperatures varying from 500 °C to 900 °C. The photoluminescence spectra showed that the samples exhibiting efficient emission were annealed at 800 °C and 900 °C and doped with 3% and 6% erbium. The X-ray diffraction analysis revealed that the internal structure of the films was influenced by the different annealing temperatures and the doping concentrations. Samples with dominant 4f transitions were modelled. The results suggest that the proposed method is a promising approach for the synthesis of erbium-doped silica films with potential applications in optical devices.

Pentagonal two-dimensional ternary sheets are an emerging class of materials because of their novel characteristic and wide range of applications. In this work, we use first-principles density functional theory (DFT) calculations to identify a new pentagonal SiPN, p -SiPN, which is geometrically, thermodynamically, dynamically, and mechanically stable, and has promising experimental potential. The new p -SiPN shows an indirect bandgap semiconducting behavior that is highly tunable with applied equ-biaxial strain. It is mechanically isotropic, along the x-y in-plane direction, and is a soft material possessing high elasticity and ultimate strain. In addition, its exceptional anisotropic optical response with strong UV light absorbance, and small reflectivity and electron energy loss make it a potential material for optoelectronics and nanomechanics.

Postulated in 1992 and synthesized in 2004 above 2000 K and 110 GPa, the singly-bonded nitrogen cubic gauche crystal (cg-PN) is still considered to be the ultimate high energy density material (HEDM). The search however has continued for a method to synthesize cg-PN at more ambient conditions or find HEDMs which can be synthesized at lower pressure and temperature. Here, using ab initio evolutionary crystal prediction techniques, a simpler nitrogen-based molecular crystal consisting of N[Formula: see text] and N[Formula: see text] molecules is revealed to be a more favorable polynitrogen at lower pressures. The energetic gain of  534 meV/atom over cg-PN and  138 meV/atom over the N[Formula: see text] molecular crystal at zero pressure makes the N[Formula: see text]-N[Formula: see text] system more appealing. Dynamical and mechanical stabilities are investigated at 5 and 0 GPa, and vibrational frequencies are assessed for its Raman and IR spectra. The prospects of an experimental synthesis of the N[Formula: see text]-N[Formula: see text] polymeric system compared to cg-PN is higher because the C[Formula: see text] symmetry of N[Formula: see text] within this crystal would be easier to target from the readily available N[Formula: see text] azides and the observed N[Formula: see text] and N[Formula: see text] radicals., (© 2022. The Author(s).)

[Formula: see text] is the first successfully synthesized salt that has a polymeric nitrogen moeity ([Formula: see text]). Although 12 other [Formula: see text] salts followed, with [Formula: see text] and [Formula: see text] being the most stable, the crystal structure of [Formula: see text] remains unknown. Currently, it is impossible to experimentally determine the structures of [Formula: see text] due to its marginal stability and explosive nature. Here, following an ab initio evolutionary prediction and using only the stoichiometry of [Formula: see text] as a starting point, we were able to reveal the crystal structure of this high energy density material (HEDM). The [Formula: see text] symmetry of the [Formula: see text] cation, as suggested from earlier investigations, is confirmed to be the symmetry adopted by this polymeric nitrogen within the crystal. This result gave full confidence in the validity of this crystal prediction approach. While stability of the [Formula: see text] within the crystal is found to be driven by electronic considerations, the marginal stability of this HEDM is found to be related to a partial softening of its phonon modes.

Although it is appreciated that bacterial chemotaxis systems rely on coupling, also called scaffold, proteins to both connect input receptors with output kinases and build interkinase connections that allow signal amplification, it is not yet clear why many systems use more than one coupling protein. We examined the distinct functions for multiple coupling proteins in the bacterial chemotaxis system of Helicobacter pylori , which requires two nonredundant coupling proteins for chemotaxis: CheW and CheV1, a hybrid of a CheW and a phosphorylatable receiver domain. We report that CheV1 and CheW have largely redundant abilities to interact with chemoreceptors and the CheA kinase, and both similarly activated CheA's kinase activity. We discovered, however, that they are not redundant for formation of the higher order chemoreceptor arrays that are known to form via CheA-CheW interactions. In support of this possibility, we found that CheW and CheV1 interact with each other and with CheA independent of the chemoreceptors. Therefore, it seems that some microbes have modified array formation to require CheW and CheV1. Our data suggest that multiple coupling proteins may be used to provide flexibility in the chemoreceptor array formation.

Many bacterial genomes are highly variable but nonetheless are typically published as a single assembled genome. Experiments tracking bacterial genome evolution have not looked at the variation present at a given point in time. Here, we analyzed the mouse-passaged Helicobacter pylori strain SS1 and its parent PMSS1 to assess intra- and intergenomic variability. Using high sequence coverage depth and experimental validation, we detected extensive genome plasticity within these H. pylori isolates, including movement of the transposable element IS 607 , large and small inversions, multiple single nucleotide polymorphisms, and variation in cagA copy number. The cagA gene was found as 1 to 4 tandem copies located off the cag island in both SS1 and PMSS1; this copy number variation correlated with protein expression. To gain insight into the changes that occurred during mouse adaptation, we also compared SS1 and PMSS1 and observed 46 differences that were distinct from the within-genome variation. The most substantial was an insertion in cagY , which encodes a protein required for a type IV secretion system function. We detected modifications in genes coding for two proteins known to affect mouse colonization, the HpaA neuraminyllactose-binding protein and the FutB α-1,3 lipopolysaccharide (LPS) fucosyltransferase, as well as genes predicted to modulate diverse properties. In sum, our work suggests that data from consensus genome assemblies from single colonies may be misleading by failing to represent the variability present. Furthermore, we show that high-depth genomic sequencing data of a population can be analyzed to gain insight into the normal variation within bacterial strains. IMPORTANCE Although it is well known that many bacterial genomes are highly variable, it is nonetheless traditional to refer to, analyze, and publish "the genome" of a bacterial strain. Variability is usually reduced ("only sequence from a single colony"), ignored ("just publish the consensus"), or placed in the "too-hard" basket ("analysis of raw read data is more robust"). Now that whole-genome sequences are regularly used to assess virulence and track outbreaks, a better understanding of the baseline genomic variation present within single strains is needed. Here, we describe the variability seen in typical working stocks and colonies of pathogen Helicobacter pylori model strains SS1 and PMSS1 as revealed by use of high-coverage mate pair next-generation sequencing (NGS) and confirmed by traditional laboratory techniques. This work demonstrates that reliance on a consensus assembly as "the genome" of a bacterial strain may be misleading., (Copyright © 2017 Draper et al.)