Abstract: Duplexed aptamers (DAs) are widespread aptasensor formats that simultaneously recognize and signal the concentration of target molecules. They are composed of an aptamer and aptamer complementary element (ACE) which consists of a short oligonucleotide that partially inhibits the aptamer sequence. Although the design principles to engineer DAs are straightforward, the tailored development of DAs for a particular target is currently based on trial and error due to limited knowledge of how the ACE sequence affects the final performance of DA biosensors. Therefore, we have established a thermodynamic model describing the influence of the ACE on the performance of DAs applied in equilibrium assays and demonstrated that this relationship can be described by the binding strength between the aptamer and ACE. To validate our theoretical findings, the model was applied to the 29-mer anti-thrombin aptamer as a case study, and an experimental relation between the aptamer-ACE binding strength and performance of DAs was established. The obtained results indicated that our proposed model could accurately describe the effect of the ACE sequence on the performance of the established DAs for thrombin detection, applied for equilibrium assays. Furthermore, to characterize the binding strength between the aptamer and ACEs evaluated in this work, a set of fitting equations was derived which enables thermodynamic characterization of DNA-based interactions through thermal denaturation experiments, thereby overcoming the limitations of current predictive software and chemical denaturation experiments. Altogether, this work encourages the development, characterization, and use of DAs in the field of biosensing.

Abstract: Thermal expansion behavior of two-dimensional (2D) nitrides and graphene were studied by ab initio molecular dynamics (MD) simulations as well as quasiharmonic approximation (QHA). Anharmonicity of the acoustic phonon modes are related to the unusual negative thermal expansion (NTE) behavior of the nitrides. Our results also hint that direct ab initio MD simulations are a more elaborate method to investigate thermal expansion behavior of 2D materials than the QHA. Nevertheless, giant NTE coefficients are found for h-GaN and h-AlN within the covered temperature range 100-600 K regardless of the chosen computational method. This unusual NTE of 2D nitrides is reasoned with the out-of-plane oscillations related to the rippling behavior of the monolayers.

Abstract: Hyperbolic polaritons in ultra thin materials such as few layers of van derWaals heterostructures provide a unique control over light-matter interaction at the nanoscale and with various applications in flat optics. Natural hyperbolic surface plasmons have been observed on thin films of WTe2 in the light wavelength range of 16-23 mu m (similar or equal to 13-18 THz) [Nat. Commun. 11, 1158 (2020)]. Using time-dependent density functional theory, it is found that carbon doped monolayer phosphorene (beta-allotrope of carbon phosphide monolayer) exhibits natural hyperbolic plasmons at frequencies above similar or equal to 5 THz which is not observed in its parent materials, i.e. monolayer of black phosphorous and graphene. Furthermore, we found that by electrostatic doping the plasmonic frequency range can be extended to the mid-infrared. (C) 2021 Elsevier Ltd. All rights reserved.

Abstract: A small sample tilt away from a main zone axis orientation results in an elongation of the atomic columns in ADF STEM images. An often posed research question is therefore whether the ADF STEM image intensities of tilted nanomaterials should be quantified using a parametric imaging model consisting of elliptical rather than the currently used symmetrical peaks. To this purpose, simulated ADF STEM images corresponding to different amounts of sample tilt are studied using a parametric imaging model that consists of superimposed 2D elliptical Gaussian peaks on the one hand and symmetrical Gaussian peaks on the other hand. We investigate the quantification of structural parameters such as atomic column positions and scattering cross sections using both parametric imaging models. In this manner, we quantitatively study what can be gained from this elliptical model for quantitative ADF STEM, despite the increased parameter space and computational effort. Although a qualitative improvement can be achieved, no significant quantitative improvement in the estimated structure parameters is achieved by the elliptical model as compared to the symmetrical model. The decrease in scattering cross sections with increasing sample tilt is even identical for both types of parametric imaging models. This impedes direct comparison with zone axis image simulations. Nonetheless, we demonstrate how reliable atom-counting can still be achieved in the presence of small sample tilt.

Abstract: Urine is a valuable resource for nutrient recovery. Stabilization is, however, recommended to prevent urea hydrolysis and the associated risk for ammonia volatilization, uncontrolled precipitation, and malodor. This can be achieved by alkalinization and subsequent biological conversion of urea and ammonia into nitrate (nitrification) and organics into CO2. Yet, without pH control, the extent of nitrification is limited as a result of insufficient alkalinity. This study explored the feasibility of an integrated electrochemical cell to obtain on-demand hydroxide production through water reduction at the cathode, compensating for the acidification caused by nitritation, thereby enabling full nitrification. To deal with the inherent variability of the urine influent composition and bioprocess, the electrochemical cell was steered via a controller, modulating the current based on the pH in the bioreactor. This provided a reliable and innovative alternative to base addition, enabling full nitrification while avoiding the use of chemicals, the logistics associated with base storage and dosing, and the associated increase in salinity. Moreover, the electrochemical cell could be used as an in situ extraction and concentration technology, yielding an acidic concentrated nitrate-rich stream. The make-up of the end product could be tailored by tweaking the process configuration, offering versatility for applications on Earth and in space.

Abstract: Intending to tackle road traffic noise in urban environments, noise barriers have been proven to effectively reduce environmental noise levels, leading to positive effects on noise perception by the exposed population. This work assesses the impacts of replacing an obsolete noise barrier in a site near a highway. The effects of this change were monitored via a combination of field surveys, acoustic measurements and noise maps. The results have shown that even though the barrier replacement led to a 4.1 dB reduction in the LA,eq,(15 min.), the annoyance levels of the respondents increased. Possibly, the expectations regarding the improvement of the noise barrier were not met, after a history of complaints. Additionally, existing exposure-response relationships were not successful in predicting the annoyance levels in this particular case. In this dataset, noise annoyance presented a weak link with reported health problems, while a strong correlation was found with the comfort level to perform activities outdoors. Questions regarding the COVID-19 pandemic showed that even though the respondents were spending more time at home, they were less annoyed due to road traffic noise in the period when circulation restrictions were in place.

Abstract: An efficient model-based estimation algorithm is introduced to quantify the atomic column positions and intensities from atomic-resolution (scanning) transmission electron microscopy ((S)TEM) images. This algorithm uses the least squares estimator on image segments containing individual columns fully accounting for overlap between neighboring columns, enabling the analysis of a large field of view. To provide end-users with this well-established quantification method, a user friendly program, StatSTEM, is developed which is freely available under a GNU public license. In this chapter, this efficient algorithm is applied to three different nanostructures for which the analysis of a large field of view is required.

Abstract: In this chapter, the principles of statistical parameter estimation theory for a quantitative analysis of atomic-resolution electron microscopy images are introduced. Within this framework, electron microscopy images are described by a parametric statistical model. Here, parametric models are introduced for different types of electron microscopy images: reconstructed exit waves, annular dark-field (ADF) scanning transmission electron microscopy (STEM) images, and simultaneously acquired ADF and annular bright-field (ABF) STEM images. Furthermore, the Cramér-Rao lower bound (CRLB) is introduced, i.e. a theoretical lower bound on the variance of any unbiased estimator. This CRLB is used to quantify the precision of the structure parameters of interest, such as the atomic column positions and the integrated atomic column intensities.

Abstract: Biosensing platforms are answering the increasing demand for analytical tools for environmental monitoring of small molecules, such as per- and polyfluoroalkyl substances (PFAS). By transferring toxicological findings in bioreceptor design we can develop innovative pathways for biosensor design. Indeed, toxicological studies provide fundamental information about PFAS-biomolecule complexes that can help evaluate the applicability of the latter as bioreceptors. The toolbox of native mass spectrometry (MS) can support this evaluation, as shown by the two case studies reported in this work. The analysis of model proteins’ (i.e. albumin, haemoglobin, cytochrome c and neuroglobin) interactions with well-known PFAS, such as perfluorooctanoic acid (PFOA) and perfluorooctanesulfonic acid (PFOS), demonstrated the potential of this native MS screening approach. In the first case study, untreated albumin and delipidated albumin were compared in the presence and absence of PFOA confirming that the delipidation step increases albumin affinity for PFOA without affecting protein stability. In the second case study, the applicability of our methodology to identify potential bioreceptors for PFOS/PFOA was extended to other proteins. Structurally related haemoglobin and neuroglobin revealed a 1 : 1 complex, whereas no binding was observed for cytochrome c. These studies have value as a proof-of-concept for a general application of native MS to identify bioreceptors for toxic compounds.

Abstract: Aptamers are short, synthetic DNA or RNA molecules that are characterized by a specific 3D conformation which enables specific target recognition. Aptamers are promising tools in many application fields from sensing to therapeutics. One of the major challenges in the aptamer field is understanding the relationship between the sequence and what determines the higher-order structure and specific interactions with targets. Therefore, this PhD thesis focuses on the use of different mass spectrometry (MS) based approaches to characterize aptamers and their interactions. Several of these approaches are already widely applied to study other biomolecules, such as proteins, but are still largely unexplored for aptamers and oligonucleotides in general. A first focus was put on obtaining information on the higher-order structure and conformational stability of aptamers using a combination of MS and with ion mobility (IM) spectrometry by performing collision-induced unfolding (CIU) experiments. CIU was shown to hold great promise to analyze the conformational dynamics and gas-phase stabilities of aptamers. Next, the capabilities and limitations of native IM-MS for the analysis of noncovalent interactions of aptamers were demonstrated. The conformational behavior and interactions of cocaine-binding aptamers were studied and it was found that relative binding affinities of aptamers that only differ slightly in sequence and structure can be determined using native MS. Moreover, native IM-MS allowed the detection of small conformational changes upon binding of a target, which were found to be dependent on the binding mode of the aptamer. An adaptive binding mechanism was suggested for flexible aptamers that require more reorganization upon binding. In the final part of this thesis, the importance of thoroughly characterizing and validating aptamer-target interactions before using them in an application was emphasized. Moreover, the gathered insights were applied in our own development of a proof-of-concept aptamer-based sensor. This was shown by investigating the interactions of ampicillin aptamers which were found to not bind the target they were selected for in the first place. A multi-analytical approach combining complementary techniques was used for this purpose since no single technique is generally applicable to characterize all aptamers and their interactions and to obtain a comprehensive picture of the aptamer-target interactions. Furthermore, such multi-analytical approach was used to characterize a testosterone-binding aptamer while developing an aptamer-based electrochemiluminescent sensing strategy for this target. This shows the importance of native MS, in combination with other techniques, to thoroughly understand the aptamer-target interactions in the development of a designed application.

Abstract: Sulfur hexafluoride (SF6), as a man-made gas, is widely used in power industry, semiconductor industry and metal-processing industry. However, SF6 is a greenhouse gas and its global warming potential is 23500 times that of CO2. Besides, SF6 is very stable, with a lifetime in the atmosphere for more than one thousand years. Under natural conditions, only the ultraviolet light can make it slowly decomposed. Thus, the emission of SF6 has a great threat to the environment. In recent years, with the development of our national economy, the use of SF6 increased dramatically. And 90% of the SF6 emissions come from the power industry. In the meantime, the emission of SF6 exists a ‘hysteresis effect’, as many of the SF6-gas insulation equipment will retire in next decades, the emission of SF6 may increase sharply, and this may put great pressure on the environment. Therefore, it’s necessary to make efforts in controlling and treating the SF6 emission. Among the SF6 abatement technologies, the non-thermal plasma(NTP) represented by the dielectric barrier discharge(DBD) can effectively degrade SF6 and is suitable for large-scale industry applications. However, its energy efficiency still gets room for improvement and this kind of method has a defect that it’s hard to regulate the degradation by-products. Therefore, this paper proposed the combination of the packed bed reactor and the DBD technology to form a packed DBD discharge system for SF6 degradation, so that to further improve the energy efficiency and regulate the selectivity of by-products. By experiment and simulation research, the following innovations have been achieved: (1) Based on the packed bed DBD platform, the power parameter and gas-phase parameters of SF6 degradation were studied. It was found that the discharge process was significantly enhanced with the addition of packing particles, and the discharge energy efficiency was improved. The increase of input voltage can obviously increase the degradation rate, but reduces the energy efficiency. The increase of SF6 initial concentration and gas flow rate can improve the energy efficiency, but reduce the degradation rate. Therefore, both degradation rate and energy efficiency should be considered in deciding basic experimental conditions. (2) Active gases, such as O2, H2O and NH3, could effectively promote the degradation rate of SF6, and changed the product selectivity. In our packed bed DBD system, O2 and H2O have the optimal concentration conditions, which are 2% and 1%, respectively. The addition of O2 can promote the generation of S-O-F products, and inhibit the selectivity of SO2, while the addition of H2O had the opposite effects. In addition, the synergistic degradation of NH3 and SF6 will produce solid products, such as NH3HF, NH4HF2 and elemental S. For gaseous products, the increase of NH3 will lead to the generation of SO2 in the final degradation products and inhibit the generation of S-O-F products. (3) Different kinds of packing materials have great impacts on the degradation system in the discharge parameters, degradation rate and energy efficiency, as well as the products distribution. In the experiment, we compared the degradation results in three systems: glass beads packing, γ-Al2O3 packing and no-packing system. The packing of glass beads effectively improved the discharge voltage amplitude and discharge power, while had a limited effect on the equivalent capacitance of the dielectric. Besides, γ-Al2O3 packing had little effect on voltage amplitude, but obviously increased the equivalent capacitance of the dielectric. Furthermore, the degradation rate and energy efficiency in γ-Al2O3 system was higher than that of glass bead system. For products selectivity, γ-Al2O3 system was more desirable, where S-O-F type of product selectivity was suppressed and the SO2 selectivity increased significantly. By contrast, the glass beads system hardly affected the product selectivity. This results are presumably due to the relatively high dielectric constant of γ-Al2O3 particles and γ-Al2O3 itself may act as a reactant or a catalyst participating in the degradation reactions. (4) The size and status of the packing particles also have significant effects on the degradation process. The systems packed with 1, 2 and 4mm γ-Al2O3 particles for SF6 degradation were compared, and the 2mm system had the best performance, which may because the 2mm system had a good balance between the active contact area and the gas residence time. In addition, the packing pellets suffered from a hydration process slightly reduced the discharge parameters in the γ-Al2O3 packing system and significantly reduced the degradation rate was, which may because the H2O molecules pre-occupied the active sites on the γ-Al2O3 surface and reduced the discharge process. (5) Based on density functional theory (DFT), the degradation process of SF6 in the packed bed DBD system was studied at atomic scale. It was found that the SF6 can occur a physical adsorption at AlⅢ active sites on γ-Al2O3 surface. The activation barrier for the first degradation step of SF6 on γ-Al2O3 surface is much lower than in gas phase, which proved that the SF6 molecule is activated on the γ-Al2O3 surface. In addition, the plasma may affect the γ-Al2O3 surface to generate excess electrons or external electric fields. This two effects can change the adsorbed SF6 molecules from physical adsorption to chemisorption, together with an obvious stretching of S-F bonds, indicating that the plasma surface effects prmote the activation and decomposition of SF6 molecules. Furthermore, the stepwise degradation process of SF6 on γ-Al2O3 surface were investigated. The influence of radicals produced by plasma on the degradation process was analyzed. It was found that via Eley–Rideal (ER) reactions, high-energy radicals could effectively reduce the activation barriers and promote the surface reactions. Finally, the degradation mechanism of SF6 molecules in the packed bed plasma system was summarized, which may provide a theoretical basis for the study of harmless degradation of SF6. Keywords: SF6; Packed Bed DBD; Discharge Parameters; Products Analysis; Degradation Mechanism

Abstract: Excitons are promising candidates for generating superfluidity and Bose-Einstein condensation (BEC) in solid-state devices, but an enabling material platform with in-built band structure advantages and scaling compatibility with industrial semiconductor technology is lacking. Here we predict that spatially indirect excitons in a lattice-matched strained Si/Ge bilayer embedded into a germanium-rich SiGe crystal would lead to observable mass-imbalanced electron-hole superfluidity and BEC. Holes would be confined in a compressively strained Ge quantum well and electrons in a lattice-matched tensile strained Si quantum well. We envision a device architecture that does not require an insulating barrier at the Si/Ge interface, since this interface offers a type II band alignment. Thus the electrons and holes can be kept very close but strictly separate, strengthening the electron-hole pairing attraction while preventing fast electron-hole recombination. The band alignment also allows a one-step procedure for making independent contacts to the electron and hole layers, overcoming a significant obstacle to device fabrication. We predict superfluidity at experimentally accessible temperatures of a few Kelvin and carrier densities up to similar to 6 x 10(10) cm(-2), while the large imbalance of the electron and hole effective masses can lead to exotic superfluid phases.

Abstract: The low-pressure hollow cathode discharge made of a hollow circular tube and an anode is a type of simple structure discharge system. In particular, under the arc discharge mode, hollow cathodes have high plasma density and energy density with a wide range of adaptability of pressure and current. Low-pressure hollow cathode arc (HCA) discharges have been widely used as plasma sources in various fields such as manufacturing, vacuum welding, and aerospace since the 1960s. Despite the early experimental and applied researches on low-pressure HCA discharges, the basic theoretical study was relatively lagged much behind, resulting in many unanswered questions, such as the optimal discharge operating parameters, the power deposition inside the cathode, the causes of plasma instability, and how to effectively reduce cathode erosion and so on. Due to the special discharge structure of the hollow cathode, it is difficult to make an accurate experimental diagnosis, so a reasonable numerical simulation is an effective study method. However, up to now, there is still a lack of complete and effective numerical models which can evaluate various physical fields in the low-pressure hollow cathode discharges. To address the above problems and difficulties, a comprehensive and self-consistent 2D multi-physical coupling numerical model based on a commercial program of finite element method, the COMSOL Multiphysics, was provided in this paper. The model involves plasma transport, arc flow and heat transfer, and cathode thermal equilibrium, and can consider the effect of an applied magnetic field. The processes of secondary electron emission, thermal-field electron emission, ions and backflow high-energy electrons bombardment, and thermal radiation from the cathode surface are considered in the cathode thermal equilibrium process. Based on the above background, this paper works from the following aspects： In Chapter 1, the basic concepts of low-pressure HCA discharge including the hollow cathode effect, the basic characteristics, and operation modes were introduced firstly; Secondly, the application fields, development history, and overseas and domestic research status of hollow cathode discharge were reviewed; finally, the problems were presented and the research background was explained, and the research purpose of this paper was clarified. In Chapter 2, a complete and self-consistent numerical model of low-pressure hollow cathode discharge was proposed based on the fundamental theory and assumptions, and the set of control equations and boundary conditions in the model were elaborated. In addition, the electron energy distribution function, the collision processes, the solving tools of this model, and calculation schemes were introduced in detail. Finally, a validation example was given to test the rationality and applicability of the numerical model. In Chapter 3, the fundamental plasma properties of low-pressure hollow cathode arcs were investigated. Firstly, the ion Joule heating effect was studied. The results showed that the temperature distributions of the arc and cathode are only able to approach the experimental measurements after considering the ion Joule heating, which shows that the Joule heating of ions is crucial for the heating of the arc plasma. Secondly, by comparing the radial distribution of electron and ion density inside the cathode, the structure of the cathode sheath could be simulated well using this model. Finally, it was shown that the thermal radiation from the cathode surface is an important cooling mechanism of the cathode and only under higher surface emissivity can balance the larger heat flow given by the plasma to the cathode, and the temperature distribution of the cathode shows a non-monotonic increasing trend and is consistent with the profile of experimental measurement so that the so-called active zone is formed. In Chapter 4, the power deposition in the low-pressure HCA was studied in simulation. Two main aspects were considered: the power deposition into particles (both electrons and heavy particles) and the power deposition onto the cathode. It was found that the deposited power into particles increases with the rise of discharge current, but there is no effect on the total power deposition onto the cathode. In high-density plasmas, Coulomb collisions between electrons and ions also become very important, especially since a portion of the deposition energy on heavy particles comes mainly from the energy transfer from electrons to ions. It was also found that regardless of external parameters, half of the power deposition onto the cathode always comes from the particle contribution, while the other half is the net contribution of heat transfer and cathode radiation. The HCA model also allows the simulation of multiple discharge modes for low-pressure HCA discharges over a wide range of gas flow rates. It was also shown that the discharge operating conditions and the external magnetic field can change the distribution of the particle flow on the cathode wall. In Chapter 5, the ion sputtering erosion process on the cathode was simulated by coupling the HCA numerical model with the moving grid technique. The results showed that the ion sputtering erosion on the cathode depends on the ion flux and the plasma potential near the cathode wall and that their distribution and magnitude jointly determine the erosion morphology of the cathode. It was also found that the location of the most severe erosion on the cathode is located in the region of the densest ion flux on the cathode wall, rather than in the longitudinal correspondence with the central region of the internal positive column (IPC). The external magnetic fields can mitigate the cathode erosion and reduce the erosion depth, but stronger magnetic fields lead to a concentration of current density at the cathode tip, which can enhance erosion slightly at the cathode outlet end. Finally, the conclusions and innovation highlights were summarized, and prospects for future work were discussed.

Abstract: Colloidal Cu–Ag nanocrystals measuring less than 10 nm across are promising candidates for integration in hybrid CO2 reduction reaction (CO2RR) interfaces, especially in the context of tandem catalysis and selective multicarbon (C2–C3) product formation. In this work, we vary the synthetic-ligand/copper molar ratio from 0.1 to 1.0 and the silver/copper atomic ratio from 0 to 0.7 and study the variations in the nanocrystals’ size distribution, morphology and reactivity at rates of ≥100 mA cm–2 in a gas-fed recycle electrolyzer operating under neutral to mildly basic conditions (0.1–1.0 M KHCO3). High-resolution electron microscopy and spectroscopy are used in order to characterize the morphology of sub-10 nm Cu–Ag nanodimers and core–shells and to elucidate trends in Ag coverage and surface composition. It is shown that Cu–Ag nanocrystals can be densely dispersed onto a carbon black support without the need for immediate ligand removal or binder addition, which considerably facilitates their application. Although CO2RR product distribution remains an intricate function of time, (kinetic) overpotential and processing conditions, we nevertheless conclude that the ratio of oxygenates to hydrocarbons (which depends primarily on the initial dispersion of the nanocrystals and their composition) rises 3-fold at moderate Ag atom % relative to Cu NCs-based electrodes. Finally, the merits of this particular Cu–Ag/C system and the recycling reactor employed are utilized to obtain maximum C2–C3 partial current densities of 92–140 mA cm–2 at −1.15 VRHE and liquid product concentrations in excess of 0.05 wt % in 1 M KHCO3 after short electrolysis periods.