Abstract: Nitrite oxidizing bacteria (NOB) and nitrous oxide (N2O) hinder the development of mainstream partial nitritation/anammox. To overcome these, endogenous free ammonia (FA) and free nitrous acid (FNA), which can be produced in the sidestream, were used for return-sludge treatment for two integrated-film activated sludge reactors containing biomass in flocs and on carriers. The repeated exposure of biomass from one reactor to FA shocks had a limited impact on NOB suppression but inhibited anammox bacteria (AnAOB). In the other reactor, repeated FNA shocks to the separated flocs failed to limit the system’s nitrate production since NOB activity was still high on the biofilms attached to the unexposed carriers. In contrast, the repeated FNA treatment of flocs and carriers favored aerobic ammonium-oxidizing bacteria (AerAOB) over NOB activity with AnAOB negligibly affected. It was further revealed that return-sludge treatment with higher FNA levels led to lower N2O emissions under similar effluent nitrite concentrations. On this basis, weekly 4 h FNA shocks of 2.0 mg of HNO2-N/L were identified as an optimal and realistic treatment, which not only enabled nitrogen removal efficiencies of ∼65% at nitrogen removal rates of ∼130 mg of N/L/d (20 °C) but also yielded the lowest cost and carbon footprint.

Abstract: Defects on hollow silica spheres synthesized in a tetraethylorthosilicate-octylamine-HCl-H2O system were recorded by scanning microscope. Based on the results, influences of synthesis composition on the formation of these defects are discussed. It is evidenced that products prepared with different octylamine-to-tetraethylorthosilicate ratios may have surface depressions, cracks and non-hollow microspheres. However, by changing water and acid additions, these defects could be reduced or eliminated. Generally, samples synthesized with a large octylamine addition commonly exhibit surface depressions. A small octylamine or a large water addition benefits the formation of solid silica microspheres among the product. Acid, although is not indispensable for the formation of hollow spheres, helps to eliminate or reduce depressions on the hollow shells. It is explained that the added acid gives rise to a relative localized fast hydrolysis versus condensation, facilitating an easy mobility of hydrolyzed silica species, and consequently the shell surface is smoothened.

Abstract: The technique of imaging time-of-flight secondary ion mass spectrometry (TOF-SIMS) and dual beam depth,profiling has been used to study the composition of the surface of tabular silver halide microcrystals. Analysis of individual microcrystals with a size well below 1 mum from a given emulsion is possible. The method is successfully applied for the characterization of silver halide microcrystals with subpercent global iodide concentrations confined in surface layers with a thickness below 5 nm. The developed TOF-SIMS analytical procedure is explicitly demonstrated for the molecular imaging of adsorbed thiocyanate layers (SCN) at crystal surfaces of individual crystals and for the differentiation of iodide conversion layers synthesized with KI and with AgI micrates (nanocrystals with a size between 10 and 50 nm). It can be concluded that TOF-SIMS as a microanalytical, surface-sensitive technique has some unique properties over other analytical techniques for the study of complex structured surface layers of silver halide microcrystals. This offers valuable information to support the synthesis of future photographic emulsions.

Abstract: PECVD of a nanoscale SiO2 capping layer using low pressure SiCl4/O-2/Ar plasmas is numerically investigated. The purpose of this capping layer is to restore photoresist profiles with improved line edge roughness. A 2D plasma and Monte Carlo feature profile model are applied for this purpose. The deposited films are calculated for various operating conditions to obtain a layer with desired shape. An increase in pressure results in more isotropic deposition with a higher deposition rate, while a higher power creates a more anisotropic process. Dilution of the gas mixture with Ar does not result in an identical capping layer shape with a thickness linearly correlated to the dilution. Finally, a substrate bias seems to allow proper control of the vertical deposition rate versus sidewall deposition as desired.

Abstract: Experiments show that the etch rate of Si with SF6 inductively coupled plasma (ICP) is significantly influenced by the absolute gas flow rate in the range of 50–600 sccm, with a maximum at around 200 sccm. Therefore, we numerically investigate the effects of the gas flow rate on the bulk plasma properties and on the etch rate, to obtain more insight in the underlying reasons of this effect. A hybrid Monte Carlo—fluid model is applied to simulate an SF6 ICP. It is found that the etch rate is influenced by two simultaneous effects: (i) the residence time of the gas and (ii) the temperature profile of the plasma in the ICP volume, resulting indeed in a maximum etch rate at 200 sccm.

Abstract: It is generally known that antidiabetic activity is associated with an increased level of glucose uptake in adipocytes and skeletal muscle cells. However, the role of exogenous reactive oxygen and nitrogen species (RONS) in muscle development and more importantly in glucose uptake is largely unknown. We investigate the effect of RONS generated by cold atmospheric plasma (CAP) in glucose uptake. We show that the glucose uptake is significantly enhanced in differentiated L6 skeletal muscle cells after CAP treatment. We also observe a significant increase of the intracellular Ca++ and ROS level, without causing toxicity. One of the possible reasons for an elevated level of glucose uptake as well as intracellular ROS and Ca++ ions is probably the increased oxidative stress leading to glucose transport.

Abstract: By means of replica exchange molecular dynamics simulations we investigate how the length of a silk-like, alternating diblock oligopeptide influences its secondary and quaternary structure. We carry out simulations for two protein sizes consisting of three and five blocks, and study the stability of a single protein, a dimer, a trimer and a tetramer. Initial configurations of our simulations are β-roll and β-sheet structures. We find that for the triblock the secondary and quaternary structures upto and including the tetramer are unstable: the proteins melt into random coil structures and the aggregates disassemble either completely or partially. We attribute this to the competition between conformational entropy of the proteins and the formation of hydrogen bonds and hydrophobic interactions between proteins. This is confirmed by our simulations on the pentablock proteins, where we find that, as the number of monomers in the aggregate increases, individual monomers form more hydrogen bonds whereas their solvent accessible surface area decreases. For the pentablock β-sheet protein, the monomer and the dimer melt as well, although for the β-roll protein only the monomer melts. For both trimers and tetramers remain stable. Apparently, for these the entropy loss of forming β-rolls and β-sheets is compensated for in the free-energy gain due to the hydrogen-bonding and hydrophobic interactions. We also find that the middle monomers in the trimers and tetramers are conformationally much more stable than the ones on the top and the bottom. Interestingly, the latter are more stable on the tetramer than on the trimer, suggesting that as the number of monomers increases protein-protein interactions cooperatively stabilize the assembly.
According to our simulations, the β-roll and β-sheet aggregates must be approximately equally
stable.

Abstract: In this paper we employ first-principles calculations to investigate the effect of substitutional Si doping in the amorphous calcium-phosphate (a-HAP) structure on the work of adhesion, integral charge transfer, charge density difference and theoretical tensile strengths between an a-HAP coating and amorphous titanium dioxide (a-TiO2) substrate systemically. Our calculations demonstrate that substitution of a P atom by a Si atom in a-HAP (a-Si-HAP) with the creation of OH-vacancies as charge compensation results in a significant increase of the bonding strength of the coating to the substrate. The work of adhesion of the optimized Si-doped interfaces reaches a value of up to -2.52 J m(-2), which is significantly higher than for the stoichiometric a-HAP/a-TiO2. Charge density difference analysis indicates that the dominant interactions at the interface have significant covalent character, and in particular two Ti-O and three Ca-O bonds are formed for a-Si-HAP/a-TiO2 and one Ti-O and three Ca-O bonds for a-HAP/a-TiO2. From the stress-strain curve, the Young's modulus of a-Si-HAP/a-TiO2 is calculated to be about 25% higher than that of the a-HAP/a-TiO2, and the yielding stress is about 2 times greater than that of the undoped model. Our calculations therefore demonstrate that the presence of Si in the a-HAP structure strongly alters not only the bioactivity and resorption rates, but also the mechanical properties of the a-HAP/a-TiO2 interface. The results presented here provide an important theoretical insight into the nature of the chemical bonding at the a-HAP/a-TiO2 interface, and are particularly significant for the practical medical applications of HAP-based biomaterials.

Abstract: Xenobiotic nucleic acids (XNA) are nucleic acid analogues not present in nature that can be used for the storage of genetic information. In vivo XNA applications could be developed into novel biocontainment strategies, but are currently limited by the challenge of developing XNA processing enzymes such as polymerases, ligases and nucleases. Here, we present a structure-guided modelling-based strategy for the rational design of those enzymes essential for the development of XNA molecular biology. Docking of protein domains to unbound double-stranded nucleic acids is used to generate a first approximation of the extensive interaction of nucleic acid processing enzymes with their substrate. Molecular dynamics is used to optimise that prediction allowing, for the first time, the accurate prediction of how proteins that form toroidal complexes with nucleic acids interact with their substrate. Using the Chlorella virus DNA ligase as a proof of principle, we recapitulate the ligase's substrate specificity and successfully predict how to convert it into an XNA-templated XNA ligase.

Abstract: The mechanisms of plasma in medicine are broadly attributed to plasma-derived reactive oxygen and nitrogen species (RONS). In order to exert any intracellular effects, these plasma-derived RONS must first traverse a major barrier in the cell membrane. The cell membrane lipid composition, and thereby the magnitude of this barrier, is highly variable between cells depending on type and state (e.g. it is widely accepted that healthy and cancerous cells have different membrane lipid compositions). In this study, we investigate how plasma-derived RONS interactions with lipid membrane components can potentially be exploited in the future for treatment of diseases. We couple phospholipid vesicle experiments, used as simple cell models, with molecular dynamics (MD) simulations of the lipid membrane to provide new insights into how the interplay between phospholipids and cholesterol may influence the response of healthy and diseased cell membranes to plasma-derived RONS. We focus on the (i) lipid tail saturation degree, (ii) lipid head group type, and (iii) membrane cholesterol fraction. Using encapsulated molecular probes, we study the influence of the above membrane components on the ingress of RONS into the vesicles, and subsequent DNA damage. Our results indicate that all of the above membrane components can enhance or suppress RONS uptake, depending on their relative concentration within the membrane. Further, we show that higher RONS uptake into the vesicles does not always correlate with increased DNA damage, which is attributed to ROS reactivity and lifetime. The MD simulations indicate the multifactorial chemical and physical processes at play, including (i) lipid oxidation, (ii) lipid packing, and (iii) lipid rafts formation. The methods and findings presented here provide a platform of knowledge that could be leveraged in the development of therapies relying on the action of plasma, in which the cell membrane and oxidative stress response in cells is targeted.

Abstract: Ammonia is an industrial large-volume chemical, with its main application in fertilizer production. It also attracts increasing attention as a green-energy vector. Over the past century, ammonia production has been dominated by the Haber-Bosch process, in which a mixture of nitrogen and hydrogen gas is converted to ammonia at high temperatures and pressures. Haber-Bosch processes with natural gas as the source of hydrogen are responsible for a significant share of the global CO(2)emissions. Processes involving plasma are currently being investigated as an alternative for decentralized ammonia production powered by renewable energy sources. In this work, we present the PNOCRA process (plasma nitrogen oxidation and catalytic reduction to ammonia), combining plasma-assisted nitrogen oxidation and lean NO(x)trap technology, adopted from diesel-engine exhaust gas aftertreatment technology. PNOCRA achieves an energy requirement of 4.6 MJ mol(-1)NH(3), which is more than four times less than the state-of-the-art plasma-enabled ammonia synthesis from N(2)and H(2)with reasonable yield (>1 %).

Abstract: Marine recirculating aquaculture system (MRAS) is an effective technology that provides sustainable farming of food fish globally. However, dissolved organics material (chemical oxygen demand, COD) and especially ammonia are produced from uneaten feed and metabolic wastes of fish. To purify the MRAS water, this study adopted a sequencing biofilm batch reactor (SBBR) and comparatively investigated the performances of four different carriers on ammonia and COD removal. Results indicated that the NH4+-N removal rates were 0.045 +/- 0.05, 0.065 +/- 0.008, 0.089 +/- 0.005, and 0.093 +/- 0.003 kg/(m(3)center dot d), and the COD removal rates were 0.019 +/- 0.010, 0.213 +/- 0.010, 0.255 +/- 0.015, and 0.322 +/- 0.010 kg/(m(3)center dot d) in the SBBRs packed with porous plastic, bamboo ring, maifan stone, and ceramsite carriers, respectively. Among the four carriers, ceramsite exhibited the best performance for both NH4+-N (80%) and COD (33%) removal after the SBBR reached the steady-state operation conditions. For all carriers studied, the NH4+-N removal kinetics could be well simulated by the first-order model, and the NH4+-N and COD removal rates were logarithmically correlated with the carrier's specific surface area. Due to its high ammonia removal, stable performance and easy operation, the ceramsite-packed SBBR is feasible for MRAS water treatment.