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 known that film structure may change dramatically with the extent of surface diffusion during the film growth process. In the present work, surface diffusion, induced thermally or activated by energetic impacts, is investigated theoretically under conditions appropriate for magnetron sputter-deposition of MgAlO thin films with varying stoichiometry. The distribution of surface diffusion energy barriers available to the system was determined for each stoichiometry, which allowed assessing in a qualitative way how much surface diffusion will take place on the time scale available between deposition events. The activation energy barriers increase with the Al concentration in the film, and therefore, the surface diffusion rates in the time frame of typical deposition rates drop, which can explain the decrease in crystallinity in the film structure and the transition to amorphous structure. The deposition process and the immediate surface diffusion enhanced by the energetic adatoms are simulated by means of a molecular dynamics model. The longer-time thermal surface diffusion and the energy landscape are studied by the temperature accelerated dynamics method, applied in an approximate way. The surface diffusion enhanced by the energetic impacts appears to be very important for the film structure in the low-temperature deposition regime.

Abstract: Journal of Physics D: Applied Physics published the first Plasma Roadmap in 2012
consisting of the individual perspectives of 16 leading experts in the various sub-fields of low temperature plasma science and technology. The 2017 Plasma Roadmap is the first update of a planned series of periodic updates of the Plasma Roadmap. The continuously growing interdisciplinary nature of the low temperature plasma field and its equally broad range of applications are making it increasingly difficult to identify major challenges that encompass all of the many sub-fields and applications. This intellectual diversity is ultimately a strength of the field. The current state of the art for the 19 sub-fields addressed in this roadmap demonstrates the enviable track record of the low temperature plasma field in the development of plasmas as an enabling technology for a vast range of technologies that underpin our modern society. At the same time, the many important scientific and technological challenges shared in this roadmap show that the path forward is not only scientifically rich but has the potential to make wide and far reaching contributions to many societal challenges.

Abstract: Lipid oxidation is associated with several inflammatory and neurodegenerative diseases, but many questions to unravel its effects on biomembranes are still open due to the complexity of the topic. For instance, recent studies indicated that phase-separated domains can have a significant effect on membrane function. It is reported that domain interfaces are “hot spots” for pore formation, but the underlying mechanisms and the effect of oxidation-induced phase separation on membranes remain elusive. Thus, to evaluate the permeability of the membrane coexisting of liquid-ordered (Lo) and liquid-disordered (Ld) domains, we performed atomistic molecular dynamics simulations. Specifically, we studied the membrane permeability of nonoxidized or oxidized homogeneous membranes (single-phase) and at the Lo/Ld domain interfaces of heterogeneous membranes, where the Ld domain is composed of either oxidized or nonoxidized lipids. Our simulation results reveal that the addition of only 1.5% of lipid aldehyde molecules at the Lo/Ld domain interfaces of heterogeneous membranes increases the membrane permeability, whereas their addition at homogeneous membranes does not have any effect. This study is of interest for a better understanding of cancer treatment methods based on oxidative stress (causing among others lipid oxidation), such as plasma medicine and photodynamic therapy.

Abstract: Low temperature plasmas (LTPs) enable to create a highly reactive environment at near ambient temperatures due to the energetic electrons with typical kinetic energies in the range of 1 to 10 eV (1 eV = 11600K), which are being used in applications ranging from plasma etching of electronic chips and additive manufacturing to plasma-assisted combustion. LTPs are at the core of many advanced technologies. Without LTPs, many of the conveniences of modern society would simply not exist. New applications of LTPs are continuously being proposed. Researchers are facing many grand challenges before these new applications can be translated to practice. In this paper, we will discuss the challenges being faced in the field of LTPs, in particular for atmospheric pressure plasmas, with a focus on health, energy and sustainability.

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: Mcl1 is a primary member of the Bcl–2 family—anti–apoptotic proteins (AAP)—that is overexpressed in several cancer pathologies. The apoptotic regulation is mediated through the binding of pro-apoptotic peptides (PAPs) (e.g., Bak and Bid) at the canonical hydrophobic binding groove (CBG) of Mcl1. Although all PAPs form amphipathic α-helices, their amino acid sequences vary to different degree. This sequence variation exhibits a central role in the binding partner selectivity towards different AAPs. Thus, constructing a novel peptide or small organic molecule with the ability to mimic the natural regulatory process of PAP is essential to inhibit various AAPs. Previously reported experimental binding free energies (BFEs) were utilized in the current investigation aimed to understand the mechanistic basis of different PAPs targeted to mMcl1. Molecular dynamics (MD) simulations used to estimate BFEs between mMcl1—PAP complexes using Molecular Mechanics-Generalized Born Solvent Accessible (MMGBSA) approach with multiple parameters. Predicted BFE values showed an excellent agreement with the experiment (R2 = 0.92). The van–der Waals (ΔGvdw) and electrostatic (ΔGele) energy terms found to be the main energy components that drive heterodimerization of mMcl1—PAP complexes. Finally, the dynamic network analysis predicted the allosteric signal transmission pathway involves more favorable energy contributing residues. In total, the results obtained from the current investigation may provide valuable insights for the synthesis of a novel peptide or small organic inhibitor targeting Mcl1.

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: Mesoporous carbon, which can be replicated from mesoporous silica and whose surface is hydrophobic, can be an ideal catalyst for the esterification of fatty acids. Here we report an easy and low cost way to prepare sulfonic acid group-functionalized mesoporous carbon. A sample of calcined mesoporous silica SBA-15 was added to an aqueous sucrose solution followed by drying and calcination at different temperatures. In contrast to existing procedures, the obtained hybrid Si/C material was then first sulfonated in H2SO4, before the final removal of the silica template in order to stabilize the porous structure towards the liquid phase sulfonation treatment. Thus the silicacarbon composites, instead of the mesoporous carbon, were successfully sulfonated to introduce SO3H groups, while keeping the ordered mesoporous structure intact. The influence of carbonization temperature was investigated, suggesting an optimum temperature of 873 K. The SO3H group-functionalized mesoporous carbon, denoted as CMK-3-873-SO3H, was characterized by means of XRD, N2 physisorption, SEM, FT-IR, elemental analysis and TEM. It followed that a uniform mesoporous carbon was obtained with an average pore size of 3.89 nm, a specific surface of 807 m2/g and a SO3H group loading of 0.39 meq/g of dry material. Compared with other solid acid catalysts, the resulting material shows enhanced activity in the acid-catalyzed esterification of oleic acid with methanol, and can be used repeatedly. The increased catalytic performance is attributed to the hydrophobic surface and larger pore size of the new catalyst. It can effectively accommodate long chain fatty acids and reject formed water, making the active sites easily accessible.

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: Microwave (MW) plasmas represent a promising solution for efficient CO2 dissociation. MW discharges are also very versatile and can be sustained at various pressure and gas flow regimes. To identify the most favorable conditions for the further scale-up of the CO2 decomposition reaction, a MW plasma reactor operating in pure CO2 in a wide pressure range (200 mbar–1 bar) is studied. Three different gas flow configurations are explored: a direct, reverse and a vortex regime. The CO2 conversion and energy efficiency drop almost linearly with increasing pressure, regardless of the gas flow regime. The results obtained in the direct flow configuration underline the importance of post-discharge cooling, as the exhaust of the MW plasma reactor in this regime expanded into the vacuum chamber without additional quenching. As a result, this system yields exhaust temperatures of up to 1000 K, which explains the lowest conversion (∼3.5% at 200 mbar and 2% at 1 bar). A post-discharge cooling step is introduced for the reverse gas inlet regime and allows the highest conversion to be achieved (∼38% at 200 mbar and 6.2% at 1 bar, with energy efficiencies of 23% and 3.7%). Finally, a tangential gas inlet is utilized in the vortex configuration to generate a swirl flow pattern. This results in the generation of a stable discharge in a broader range of CO2 flows (15–30 SLM) and the highest energy efficiencies obtained in this study (∼25% at 300 mbar and ∼13% at 1 bar, at conversions of 21% and 12%). The experimental results are complemented with computational fluid dynamics simulations and with the analysis of the latest literature to identify the further research directions.

Abstract: Modeling results are presented to gain a better insight in the properties of a SiH4/O2/Ar inductively coupled plasma (ICP) and how it interacts with a silicon substrate (wafer), as applied in the microelectronics industry for the fabrication of electronic devices. The SiH4/O2/Ar ICP is used for the filling of microtrenches with isolating material (SiO2), as applied in shallow trench isolation (STI). In this article, a detailed reaction set that describes the plasma chemistry of SiH4/O2/Ar discharges as well as surface processes, such as sputtering, oxidation, and deposition, is presented. Results are presented on the plasma properties during the plasma enhanced chemical vapor deposition process (PECVD) for different gas ratios, as well as on the shape of the filled trenches and the surface compositions of the deposited layers. For the operating conditions under study it is found that the most important species accounting for deposition are SiH2, SiH3O, SiH3 and SiH2O, while SiH+2, SiH+3, O+2 and Ar+ are the dominant species for sputtering of the surface. By diluting the precursor gas (SiH4) in the mixture, the deposition rate versus sputtering rate can be controlled for a desired trench filling process. From the calculation results it is clear that a high deposition rate will result in undesired void formation during the trench filling, while a small deposition rate will result in undesired trench bottom and mask damage by sputtering. By varying the SiH4/O2 ratio, the chemical composition of the deposited layer will be influenced. However, even at the highest SiH4/O2 ratio investigated (i.e., 3.2:1; low oxygen content), the bulk deposited layer consists mainly of SiO2, suggesting that low-volatile silane species deposit first and subsequently become oxidized instead of being oxidized first in the plasma before deposition. Finally, it was found that the top surface of the deposited layer contained less oxygen due to preferential sputtering of O atoms, making the top layer more Si-rich. However, this effect is negligible at a SiH4/O2 ratio of 2:1 or lower.

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: Molecular dynamics simulations are essential for a better understanding of dissociative chemisorption on metal surfaces, which is often the rate-controlling step in heterogeneous and plasma catalysis. The workhorse quasi-classical trajectory approach ubiquitous in molecular dynamics is able to accurately predict reactivity only for high translational and low vibrational energies. In contrast, catalytically relevant conditions generally involve low translational and elevated vibrational energies. Existing quantum dynamics approaches are intractable or approximate as a result of the large number of degrees of freedom present in molecule−metal surface reactions. Here, we extend a ring polymer molecular dynamics approach to fully include, for the first time, the degrees of freedom of a moving metal surface. With this approach, experimental sticking probabilities for the dissociative chemisorption of methane on Pt(111) are reproduced for a large range of translational and vibrational energies by including nuclear quantum effects and employing full-dimensional simulations.

Abstract: Molecular dynamics simulations using the Brenner potential have been performed to investigate reaction mechanisms of various hydrocarbon radicals with low kinetic energies on amorphous hydrogenated carbon (a-C:H) surfaces and to simulate thin a-C:H film growth. Experimental data from an expanding thermal plasma setup were used as input for the simulations. The hydrocarbon reaction mechanisms were studied both during growth of the films and on a set of surface sites specific for a-C:H surfaces. Thin film growth was studied using experimentally detected growth species. It is found that the reaction mechanisms and sticking coefficients are dependent on the specific surface sites, and the structural properties of the growth radicals. Furthermore, it is found that thin a-C:H films can be densified using an additional H-flux towards the substrate.