Abstract: Molecular dynamics simulations are carried out for describing growth of Pd and PdO nanoclusters using the ReaxFF force field. The resulting nanocluster structures are successfully compared to those of nanoclusters experimentally grown in a gas aggregation source. The PdO structure is quasi-crystalline as revealed by high resolution transmission microscope analysis for experimental PdO nanoclusters. The role of the nanocluster temperature in the molecular dynamics simulated growth is highlighted.

Abstract: Molecular dynamics (MD) simulations were performed to provide atomic scale insight in the initial interaction between hydroxyl radicals (OH) and peptide systems in solution. These OH radicals are representative reactive oxygen species produced by cold atmospheric plasmas. The use of plasma for biomedical applications is gaining increasing interest, but the fundamental mechanisms behind the plasma modifications still remain largely elusive. This study helps to gain more insight in the underlying mechanisms of plasma medicine but is also more generally applicable to peptide oxidation, of interest for other applications. Combining both reactive and nonreactive MD simulations, we are able to elucidate the reactivity of the amino acids inside the peptide systems and their effect on their structure up to 1 μs. Additionally, experiments were performed, treating the simulated peptides with a plasma jet. The computational results presented here correlate well with the obtained experimental data and highlight the importance of the chemical environment for the reactivity of the individual amino acids, so that specific amino acids are attacked in higher numbers than expected. Furthermore, the long time scale simulations suggest that a single oxidation has an effect on the 3D conformation due to an increase in hydrophilicity and intra- and intermolecular interactions.

Abstract: Modeling the oxidation process of silicon nanowires through reactive force field based molecular dynamics simulations suggests that the formation of Si epoxide defects occurs both at the Si/SiOx interface and at the nanowire surface, whereas for flat surfaces, this defect is experimentally observed to occur only at the interface as a result of stress. In this paper, we argue that the increasing curvature stabilizes the defect at the nanowire surface, as suggested by our density functional theory calculations. The latter can have important consequences for the opto-electronic properties of thin silicon nanowires, since the epoxide induces an electronic state within the band gap. Removing the epoxide defect by hydrogenation is expected to be possible but becomes increasingly difficult with a reduction of the diameter of the nanowires.

Abstract: Microwave plasmas are one of the most promising techniques for CO2 conversion into value-added chemicals and fuels since they are very energy efficient. Nevertheless, experiments show that this high energy efficiency is only reached at low pressures and significantly drops toward atmospheric pressure, which is a clear limitation for industrial applications. In this paper, we use a zerodimensional reaction kinetics model to simulate a CO2 microwave plasma in a pressure range from 50 mbar to 1 bar, in order to evaluate the reasons for this decrease in energy efficiency at atmospheric pressure. The code includes a detailed description of the vibrational kinetics of CO2, CO, and O2 as well as the energy exchanges between them because the vibrational kinetics is known to be crucial for energy efficient CO2 splitting. First, we use a self-consistent gas temperature calculation in order to assess the key performance indicators for CO2 splitting, i.e., the CO2 conversion and corresponding energy efficiency. Our results indicate that lower pressures and higher power densities lead to more vibrational excitation, which is beneficial for the conversion. We also demonstrate the key role of the gas temperature. The model predicts the highest conversion and energy efficiencies at pressures around 300 mbar, which is in agreement with experiments from the literature. We also show the beneficial aspect of fast gas cooling in the afterglow at high pressure. In a second step, we study in more detail the effects of pressure, gas temperature, and power density on the vibrational distribution function and on the dissociation and recombination mechanisms of CO2, which define the CO2 splitting efficiency. This study allows us to identify the limiting factors of CO2 conversion and to propose potential solutions to improve the process.

Abstract: Microplasmas can be used for a wide range of technological applications and to improve the understanding of fundamental physics. Scanning electron microscopy, on the other hand, provides insights into the sample morphology and chemistry of materials from the mm‐ down to the nm‐scale. Combining both would provide direct insight into plasma‐sample interactions in real‐time and at high spatial resolution. Up till now, very few attempts in this direction have been made, and significant challenges remain. This work presents a stable direct current glow discharge microplasma setup built inside a scanning electron microscope. The experimental setup is capable of real‐time in situ imaging of the sample evolution during plasma operation and it demonstrates localized sputtering and sample oxidation. Further, the experimental parameters such as varying gas mixtures, electrode polarity, and field strength are explored and experimental<italic>V</italic>–<italic>I</italic>curves under various conditions are provided. These results demonstrate the capabilities of this setup in potential investigations of plasma physics, plasma‐surface interactions, and materials science and its practical applications. The presented setup shows the potential to have several technological applications, for example, to locally modify the sample surface (e.g., local oxidation and ion implantation for nanotechnology applications) on the µm‐scale.

Abstract: Methane reforming by plasma catalysis is a complex process that is far from understood. It requires a multidisciplinary approach which ideally takes into account all effects from the plasma on the catalyst, and vice versa. In this contribution, we focus on the interactions of CHx (x = {1,2,3}) radicals that are created in the plasma with several nickel catalyst surfaces. To this end, we perform reactive molecular dynamics simulations, based on the ReaxFF potential, in a wide temperature range of 4001600 K. First, we focus on the H2 formation as a function of temperature and surface structure. We observe that substantial H2 formation is obtained at 1400 K and above, while the role of the surface structure seems limited. Indeed, in the initial stage, the type of nickel surface influences the CH bond breaking efficiency of adsorbed radicals; however, the continuous carbon diffusion into the surface gradually diminishes the surface crystallinity and therefore reduces the effect of surface structure on the H2 formation probability. Furthermore, we have also investigated to what extent the species adsorbed on the catalyst surface can participate in surface reactions more in general, for the various surface structures and as a function of temperature. These results are part of the ongoing research on the methane reforming by plasma catalysis, a highly interesting yet complex alternative to conventional reforming processes.

Abstract: Metal-catalyzed growth mechanisms of carbon nanotubes (CNTs) were studied by hybrid molecular dynamics−Monte Carlo simulations using a recently developed ReaxFF reactive force field. Using this novel approach, including relaxation effects, a CNT with definable chirality is obtained, and a step-by-step atomistic description of the nucleation process is presented. Both root and tip growth mechanisms are observed. The importance of the relaxation of the network is highlighted by the observed healing of defects.

Abstract: Melanoma remains a deadly cancer despite significant advances in immune checkpoint blockade and targeted therapies. The incidence of melanoma is also growing worldwide, which highlights the need for novel treatment options and strategic combination of therapies. Here, we investigate non-thermal plasma (NTP), an ionized gas, as a promising, therapeutic option. In a melanoma mouse model, direct treatment of tumors with NTP results in reduced tumor burden and prolonged survival. Physical characterization of NTP treatment in situ reveals the deposited NTP energy and temperature associated with therapy response, and whole transcriptome analysis of the tumor identified several modulated pathways. NTP treatment also enhances the cancer-immunity cycle, as immune cells in both the tumor and tumor-draining lymph nodes appear more stimulated to perform their anti-cancer functions. Thus, our data suggest that local NTP therapy stimulates systemic, anti-cancer immunity. We discuss, in detail, how these fundamental insights will help direct the translation of NTP technology into the clinic and inform rational combination strategies to address the challenges in melanoma therapy.

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.

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: 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: 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: 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 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: 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.