Abstract: Industrial ammonia production without CO2 emission and with low energy consumption is one of the technological grand challenges of this age. Current Haber-Bosch ammonia mass production processes work with a thermally activated iron catalyst needing high pressure. The need for large volumes of hydrogen gas and the continuous operation mode render electrification of Haber-Bosch plants difficult to achieve. Electrochemical solutions at low pressure and temperature are faced with the problematic inertness of the nitrogen molecule on electrodes. Direct reduction of N2 to ammonia is only possible with very reactive chemicals such as lithium metal, the regeneration of which is energy intensive. Here, the attractiveness of an oxidative route for N2 activation was presented. N2 conversion to NOx in a plasma reactor followed by reduction with H2 on a heterogeneous catalyst at low pressure could be an energy-efficient option for small-scale distributed ammonia production with renewable electricity and without intrinsic CO2 footprint.

Abstract: Industry needs a flexible and efficient technology to convert CO2 into useful products, which fits in the Carbon Capture and Utilization (CCU) philosophy. Plasma technology is intensively being investigated for this purpose. A promising candidate is the gliding arc plasmatron (GAP). Waste streams of CO2 are often not pure and contain N2 as important impurity. Therefore, in this paper we provide a detailed experimental and computational study of the combined CO2 and N2 conversion in a GAP. Is it possible to take advantage of the presence of N2 in the mixture and to combine CO2 conversion with N2 fixation? Our experiments and simulations reveal that N2 actively contributes to the process of CO2 conversion, through its vibrational levels. In addition, NO and NO2 are formed, with concentrations around 7000 ppm, which is slightly too low for valorization, but by improving the reactor design it must be possible to further increase their concentrations. Other NO-based molecules, in particular the strong greenhouse gas N2O, are not formed in the GAP, which is an important result. We also compare our results with those obtained in other plasma reactors to clarify the differences in underlying plasma processes, and to demonstrate the superiority of the GAP.

Abstract: Ion irradiation of carbon nanotubes very often leads to defect formation. However, we have recently shown that Ar ion irradiation in a limited energy window of 1025 eV may enhance the initial cap nucleation process, when the carbon network is in contact with the metal nanocatalyst. Here, we employ reactive molecular dynamics simulations to demonstrate that ion irradiation in a higher energy window of 1035 eV may also heal network defects after the nucleation stage through a non-metal-mediated mechanism, when the carbon network is no longer in contact with the metal nanocatalyst. The results demonstrate the possibility of beneficially utilizing ions in e.g. plasma-enhanced chemical vapour deposition of carbon nanotubes.

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: It is well established that lipid aldehydes (LAs) are able to increase the permeability of cell membranes and induce their rupture. However, it is not yet clear how LAs are distributed in phase-separated membranes (PSMs), which are responsible for the transport of selected molecules and intracellular signaling. Thus, we investigate here the distribution of LAs in a PSM by coarse-grained molecular dynamics simulations. Our results reveal that LAs derived from mono-unsaturated lipids tend to accumulate at the interface between the liquid-ordered/liquiddisordered domains, whereas those derived from poly-unsaturated lipids remain in the liquid-disordered domain. These results are important for understanding the effects caused by oxidized lipids in membrane structure, properties and organization.

Abstract: Laser ablation is used in a growing number of applications in various areas including medicine, archaeology, chemistry, environmental and materials sciences. In this work the heat transfer and phase change phenomena during nanosecond laser ablation of a copper (Cu) target in a helium (He) background gas at atmospheric pressure are presented. An enthalpy model is outlined, which accounts for heating, melting, and vaporization of the target. As far as we know, this is the first model that connects the thermodynamics and underlying kinetics of this challenging phase change problem in a selfconsistent way.

Abstract: Laser-assisted plasma spectrometry is a palette of analytical techniques (L-OES, LA-ICP-MS) capable of fast spatially-resolved elemental analysis in the micrometer range. For fast estimation of the occurrence in steel samples of non-metallic inclusions, which degrade the material's technical properties, simultaneous OES detection and sequential ICP-MS detection were compared. Histograms were obtained for the intensity distribution of the acquired signals (laser pulse statistics). The skewness coefficient of the histograms for Al (indicator of non-metallic inclusions) was found to be clearly dependent on the fraction of non-metallic inclusions in the case of scanning L-OES. For LA-ICP-MS less clear dependence was observed, which was influenced by the acquisition characteristics. In fact, less measurement throughput limited for LA-ICP-MS the counting statistics to an extent that overrides the benefit of higher detection power as compared to L-OES. (c) 2006 Elsevier B.V. All rights reserved.

Abstract: Laurdan is one of the most used fluorescent probes for lipid membrane phase recognition. Despite its wide use for optical techniques and its versatility as a solvatochromic probe, little is known regarding its use as molecular rotor, for which clear evidence is found in the current study. Although recent computational and experimental studies suggest the existence of two stable conformations of laurdan in different membrane phases, it is difficult to experimentally probe their prevalence. By means of multiscale computational approaches, we prove now that this information can be obtained through the optical properties of the two conformers, ranging from one-photon absorption over two-photon absorption to the first hyperpolarizability. Fluorescence decay and anisotropy analyses are performed as well and stress the importance of laurdan's conformational versatility. As a molecular rotor and with reference to the distinct properties of its conformers, laurdan can be used to probe biochemical processes that change the lipid orders in cell membranes.

Abstract: Live-cell imaging with fluorescence microscopy is a powerful tool, especially in cancer research, widely-used for capturing dynamic cellular processes over time. However, light-induced toxicity (phototoxicity) can be incurred from this method, via disruption of intracellular redox balance and an overload of reactive oxygen species (ROS). This can introduce confounding effects in an experiment, especially in the context of evaluating and screening novel therapies. Here, we aimed to unravel whether phototoxicity can impact cellular homeostasis and response to non-thermal plasma (NTP), a therapeutic strategy which specifically targets the intracellular redox balance. We demonstrate that cells incorporated with a fluorescent reporter for live-cell imaging have increased sensitivity to NTP, when exposed to ambient light or fluorescence excitation, likely through altered proliferation rates and baseline intracellular ROS levels. These changes became even more pronounced the longer the cells stayed in culture. Therefore, our results have important implications for research implementing this analysis technique and are particularly important for designing experiments and evaluating redox-based therapies like NTP.

Abstract: Low-temperature growth of carbon nanotubes (CNTs) has been claimed to provide a route towards chiral-selective growth, enabling a host of applications. In this contribution, we employ reactive molecular dynamics simulations to demonstrate how plasma-based deposition allows such low-temperature growth. We first show how ion bombardment during the growth affects the carbon dissolution and precipitation process. We then continue to demonstrate how a narrow ion energy window allows CNT growth at 500 K. Finally, we also show how CNTs in contrast cannot be grown in thermal CVD at this low temperature, but only at high temperature, in agreement with experimental data. (C) 2013 Elsevier Ltd. All rights reserved.

Abstract: Low-temperature plasma has received extensive attention due to its promising application prospects in the field of air pollutants degradation and energy conversion. To fulfill the need for particular applications, constructing stable plasma sources and investigating the interaction mechanisms between plasma and substances have been hot research topics. This thesis reports the diagnosis and improvement of plasma sources, diagnosis of the active species in plasma and a modeling study of chemical kinetics processes. The main research contents are as follows: In Chapter 3, a diffuse sine AC dielectric barrier discharge (DBD) is successfully obtained by optimizing the electrode structure. It is found that using double-layer dielectric plates can limit the discharge current intensity and significantly improve the discharge uniformity. The electrical characteristics and gas temperature with different operating time show that the discharge stability is also improved by using double-layer dielectric plates. In Chapter 4, nanosecond pulses are employed to generate diffuse DBD plasmas. Three main discharge stages are distinguished by ICCD images, i.e., the streamer breakdown from the needle tip to the plate electrode, the regime transition from streamer to diffuse plasma, and the propagation of surface discharge on the plate electrode surface. The chapter reveales that in nanosecond pulsed discharges the vibrational temperature of N2 increases with the discharge duration, while the rotational temperature mainly stays constant, which means electron energy is transferred into the vibrational levels, but gas heating is not obvious during the discharge pulse. In Chapter 5, both sine AC DBD and nanosecond pulsed DBD, studied in Chapter 2 and 3, are used for formaldehyde degradation. It is found that nanosecond pulsed DBD has more homogenous characteristics, better stability, and lower plasma gas temperature. Moreover, the energy consumption of nanosecond pulsed DBD is much lower than that of AC DBD. In Chapter 6, a 0D chemical kinetics model is developed to investigate the underlying plasma chemistry of methane dry reforming in a nanosecond pulsed discharge. An overview of the dominant reaction pathways of CO2 and CH4 conversion into the major products is given. Furthermore, most of the CO2 molecules are populated into vibrational states during the pulse. Hence, the vibrational states of CO2 play an important role in its dissociation process. In general, this PhD thesis contributes to a better insight in the mechanisms of sinusoidal AC DBD and nanosecond pulsed DBD plasmas and their applications, i.e., decomposition of formaldehyde and dry reforming of methane.

Abstract: Low-temperature plasmas are gaining a lot of interest for environmental and energy applications. A large research field in these applications is the conversion of CO2 into chemicals and fuels. Since CO2 is a very stable molecule, a key performance indicator for the research on plasma-based CO2 conversion is the energy efficiency. Until now, the energy efficiency in atmospheric plasma reactors is quite low, and therefore we employ here a novel type of plasma reactor, the gliding arc plasmatron (GAP). This paper provides a detailed experimental and computational study of the CO2 conversion, as well as the energy cost and efficiency in a GAP. A comparison with thermal conversion, other plasma types and other novel CO2 conversion technologies is made to find out whether this novel plasma reactor can provide a significant contribution to the much-needed efficient conversion of CO2. From these comparisons it becomes evident that our results are less than a factor of two away from being cost competitive and already outperform several other new technologies. Furthermore, we indicate how the performance of the GAP can still be improved by further exploiting its non-equilibrium character. Hence, it is clear that the GAP is very promising for CO2 conversion.

Abstract: Magnetron sputtering is a widely used physical vapor deposition technique for deposition and formation of nanocatalyst thin films and clusters. Nevertheless, so far only few studies investigated this formation process at the fundamental level. We here review atomic scale molecular dynamics simulations aimed at elucidating the nanocatalyst growth process through magnetron sputtering. We first introduce the basic magnetron sputtering background and machinery of molecular dynamics simulations, and then describe the studies conducted in this field so far. We also present a perspective view on how the field may be developed further.

Abstract: Many current anti-cancer therapies rely on increasing the intracellular reactive oxygen and nitrogen species (RONS) contents with the aim to induce irreparable damage, which subsequently results in tumor cell death. A novel tool in cancer therapy is the use of cold atmospheric plasma (CAP), which has been found to be very effective in the treatment of many different cancer cell types in vitro as well as in vivo, mainly through the vast generation of RONS. One of the key determinants of the cell's fate will be the interaction of RONS, generated by CAP, with important proteins, i.e. redox-regulatory proteins. One such protein is cytoglobin (CYGB), a recently discovered globin proposed to be involved in the protection of the cell against oxidative stress. In this study, the effect of plasma-produced RONS on CYGB was investigated through the treatment of CYGB with CAP for different treatment times. Spectroscopic analysis of CYGB showed that although chemical modifications occur, its secondary structure remains intact. Mass spectrometry experiments identified these modifications as oxidations of mainly sulfur-containing and aromatic amino acids. With longer treatment time, the treatment was also found to induce nitration of the heme. Furthermore, the two surface-exposed cysteine residues of CYGB were oxidized upon treatment, leading to the formation of intermolecular disulfide bridges, and potentially also intramolecular disulfide bridges. In addition, molecular dynamics and docking simulations confirmed, and further show, that the formation of an intramolecular disulfide bond, due to oxidative conditions, affects the CYGB 3D structure, thereby opening the access to the heme group, through gate functioning of His117. Altogether, the results obtained in this study (1) show that plasma-produced RONS can extensively oxidize proteins and (2) that the oxidation status of two redox-active cysteines lead to different conformations of CYGB.

Abstract: Mcl1 is an important anti-apoptotic member of the Bcl2 family proteins that are upregulated in several cancer malignancies. The canonical binding groove (CBG) located at the surface of Mcl1 exhibits a critical role in binding partners selectively via the BH3-domain of pro-apoptotic Bcl2 family members that trigger the downregulation of Mcl1 function. There are several crystal structures of point-mutated pro-apoptotic Bim peptides in complex with Mcl1. However, the mechanistic effects of such point-mutations towards peptide binding and complex stability still remain unexplored. Here, the effects of the reported point mutations in Bim peptides and their binding mechanisms to Mcl1 were computationally evaluated using atomistic-level steered molecular dynamics (SMD) simulations. A range of external-forces and constant-velocities were applied to the Bim peptides to uncover the mechanistic basis of peptide dissociation from the CBG of Mcl1. Although the peptides showed similarities in their dissociation pathways, the peak rupture forces varied significantly. According to simulations results, the disruption of the conserved polar contacts at the complex interface causes a sequential release of the peptides from the CBG of Mcl1. Overall, the results obtained from the current study may provide valuable insights for the development of novel anti-cancer peptide-inhibitors that can downregulate Mcl1’s function.