Abstract: Mannosylerythritol lipids (MELs) are a promising group of biosurfactants due to their high fermentation yield, selfassembly and biological activity. During fermentation by Pseudozyma aphidis, a mixture of MELs with different levels of acylation is formed, of which the fully deacetylated form is the most valuable. In order to reduce the environmental impact of deacetylation, an enzymatic process using natural deep eutectic solvents (NADES) has been developed. We tested the deacetylation of a purified MELs mixture with immobilized Candida antarctica lipase B enzyme and 2-ethylhexanol as co-substrate in 140 h reactions with different NADES. We identified hydrophobic NADES systems with similar yields and kinetics as in pure 2-ethylhexanol solvent. Our results indicate that deacetylation of MELs mixtures in NADES as a solvent is possible with yields comparable to pure co-substrate and that hydrophobic NADES without carboxylic acid compounds facilitate the reaction to the greatest extent.

Abstract: Cryogenic plasma etching is a promising technique for high-control wafer development with limited plasma induced damage. Cryogenic wafer temperatures effectively reduce surface damage during etching, but the fundamental mechanism is not well understood. In this study, the influences of wafer temperature, gas mixture and substrate bias on the (cryogenic) etch rates of Si with SF6/O2 inductively coupled plasmas are experimentally and computationally investigated. The etch rates are measured in situ with double-point reflectometry and a hybrid computational Monte Carlo – fluid model is applied to calculate plasma properties. This work allows the reader to obtain a better insight in the effects of wafer temperature on the etch rate and to find operating conditions for successful anisotropic (cryo)etching.

Abstract: The catalytic oxidative dehydrogenation of hydrocarbons is an industrially important process, in which selectivity is a key issue. We here investigate the conversion of methanol to formaldehyde on a vanadia surface employing long timescale simulations, reaching a time scale of seconds. In particular, we compare the thermal process to the case where an additional external electric field is applied, as would be the case in a direct plasma-catalysis setup. We find that the electric field influences the retention time of the molecules at the catalyst surface. These simulations provide an atomic scale insight in the thermal catalytic oxidative dehydrogenation process, and in how an external electric field may affect this process.

Abstract: Plasma medicine has been claimed to provide a novel route to heal wounds and regenerate skin, although very little is currently known about the elementary processes taking place. We carried out a series of ReaxFF-based reactive molecular dynamics simulations to investigate the interaction of O and OH radicals with lipids, more specifically with α-linolenic acid as a model for the free fatty acids present in the upper skin layer. Our calculations predict that the O and OH radicals most typically abstract a H atom from the fatty acids, which can lead to the formation of a conjugated double bond, but also to the incorporation of alcohol or aldehyde groups, thereby increasing the hydrophilic character of the fatty acids and changing the general lipid composition of the skin. Within the limitations of the investigated model, no formation of possibly toxic products was observed.

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: Plasma catalysis holds great promise for environmental applications, provided that the process viability can be maximized in terms of energy efficiency and product selectivity. This requires a fundamental understanding of the various processes taking place and especially the mutual interactions between plasma and catalyst. In this review, we therefore first examine the various effects of the plasma on the catalyst and of the catalyst on the plasma that have been described in the literature. Most of these studies are purely experimental. The urgently needed fundamental understanding of the mechanisms underpinning plasma catalysis, however, may also be obtained through modelling and simulation. Therefore, we also provide here an overview of the modelling efforts that have been developed already, on both the atomistic and the macroscale, and we identify the data that can be obtained with these models to illustrate how modelling and simulation may contribute to this field. Last but not least, we also identify future modelling opportunities to obtain a more complete understanding of the various underlying plasma catalytic effects, which is needed to provide a comprehensive picture of plasma catalysis.

Abstract: We calculate bubble nucleation rates in a Lennard-Jones fluid through explicit molecular dynamics simulations. Our approach-based on a recent free energy method (dubbed reweighted Jarzynski sampling), transition state theory, and a simple recrossing correction-allows us to probe a fairly wide range of rates in several superheated and cavitation regimes in a consistent manner. Rate predictions from this approach bridge disparate independent literature studies on the same model system. As such, we find that rate predictions based on classical nucleation theory, direct brute force molecular dynamics simulations, and seeding are consistent with our approach and one another. Published rates derived from forward flux sampling simulations are, however, found to be outliers. This study serves two purposes: First, we validate the reliability of common modeling techniques and extrapolation approaches on a paradigmatic problem in materials science and chemical physics. Second, we further test our highly generic recipe for rate calculations, and establish its applicability to nucleation processes.

Abstract: In this review paper, an overview is given of different modelling efforts for plasmas used for the formation and growth of nanostructured materials. This includes both the plasma chemistry, providing information on the precursors for nanostructure formation, as well as the growth processes itself. We limit ourselves to carbon (and silicon) nanostructures. Examples of the plasma modelling comprise nanoparticle formation in silane and hydrocarbon plasmas, as well as the plasma chemistry giving rise to carbon nanostructure formation, such as (ultra)nanocrystalline diamond ((U)NCD) and carbon nanotubes (CNTs). The second part of the paper deals with the simulation of the (plasma-based) growth mechanisms of the same carbon nanostructures, i.e. (U)NCD and CNTs, both by mechanistic modelling and detailed atomistic simulations.

Abstract: The ever increasing global production and dispersion of methane requires novel chemistry to transform it into easily condensable energy carriers that can be integrated into the chemical infrastructure. In this context, single atom catalysts have attracted considerable interest due to their outstanding catalytic activity. We here use density functional theory (DFT) computations to compare the reaction and activation energies of M and MN4 embedded graphene (M = Ni and Si) on the methane-to-methanol conversion near room temperature. Thermodynamically, conversion of methane to methanol is energetically favorable at ambient conditions. Both singlet and triplet spin state of the studied systems are considered in all of the calculations. The DFT results show that the barriers are significantly lower when the complexes are in the triplet state than in the singlet state. In particular, Si-G with the preferred spin multiplicity of triplet seems to be viable catalysts for methane oxidation thanks to the corresponding lower energy barriers and higher stability of the obtained configurations. Our results provide insights into the nature of methane conversion and may serve as guidance for fabricating cost-effective graphene-based single atom catalysts.

Abstract: Monte Carlo (MC) methods have a long-standing history as partners of molecular dynamics (MD) to simulate the evolution of materials at the atomic scale. Among these techniques, the uniform-acceptance force-bias Monte Carlo (UFMC) method [ G. Dereli Mol. Simul. 8 351 (1992)] has recently attracted attention [ M. Timonova et al. Phys. Rev. B 81 144107 (2010)] thanks to its apparent capacity of being able to simulate physical processes in a reduced number of iterations compared to classical MD methods. The origin of this efficiency remains, however, unclear. In this work we derive a UFMC method starting from basic thermodynamic principles, which leads to an intuitive and unambiguous formalism. The approach includes a statistically relevant time step per Monte Carlo iteration, showing a significant speed-up compared to MD simulations. This time-stamped force-bias Monte Carlo (tfMC) formalism is tested on both simple one-dimensional and three-dimensional systems. Both test-cases give excellent results in agreement with analytical solutions and literature reports. The inclusion of a time scale, the simplicity of the method, and the enhancement of the time step compared to classical MD methods make this method very appealing for studying the dynamics of many-particle systems.

Abstract: Natural deep eutectic solvents (NADES) represent a green alternative to common organic solvents in the biochemical industry due to their benign behavior and tailorable properties, in particular as media for enzymatic reactions. However, to fully exploit their potential in enzymatic reactions, there is a need for a more fundamental understanding of how these neoteric solvents influence the course of these reac-tions. Thus, the aim of this study is to investigate the influence of NADES with various molar composi-tions on the stability and structure of enzymes, applying molecular dynamics simulations. This can help to better understand the effect of individual compounds of NADES, in addition to eutectic mixtures. More specifically, we simulate the behavior of Candida antarctica lipase B (CALB) enzyme in NADES com-posed of choline chloride with either urea, ethylene glycol or glycerol. Hereto, we monitor the NADES microstructure, the general stability of the enzyme and changes in the structure of its active sites and sur-face residues. Our simulations show that none of the studied NADES systems significantly disrupt the microstructure of the solvent or the stability of the CALB enzyme within the time scales of the simula-tions. The enzyme preserves its initial structure, size and intra-chain hydrogen bonds in all investigated compositions and, for the first time reported, also in NADES with increased hydrogen bond donating com-pound ratios. As the main novelty, our results indicate that, in addition to the composition, the molar ratio can be an additional variable to fine-tune the physicochemical properties of NADES without altering the enzyme characteristics. These findings could facilitate the development and application of task -tailored NADES media for biocatalytic processes. (c) 2022 Elsevier B.V. All rights reserved.

Abstract: Molecular dynamics simulations using improved TersoffBrenner potential parameters were performed to investigate Cl+ etching of a {2×1} reconstructed Si(100) surface. Steady-state Si etching accompanying the Cl coverage of the surface is observed. Furthermore, a steady-state chlorinated reaction layer is formed. The thickness of this reaction layer is found to increase with increasing energy. The stoichiometry of SiClx species in the reaction layer is found to be SiCl:SiCl2:SiCl3 = 1.0:0.14:0.008 at 50 eV. These results are in excellent agreement with available experimental data. While elemental Si products are created by physical sputtering, most SiClx (0<x<4) etch products are produced by chemical-enhanced physical sputtering.

Abstract: Piezoelectricity is considered to be one of the key functionalities in biomaterials to boost bone tissue regeneration, however, integrating biocompatibility, biodegradability and 3D structure with pronounced piezoresponse remains a material challenge. Herein, novel hybrid biocompatible 3D scaffolds based on biodegradable poly(3-hydroxybutyrate) (PHB) and reduced graphene oxide (rGO) flakes have been developed. Nanoscale insights revealed a more homogenous distribution and superior surface potential values of PHB fibers (33 +/- 29 mV) with increasing rGO content up to 1.0 wt% (314 +/- 31 mV). The maximum effective piezoresponse was detected at 0.7 wt% rGO content, demonstrating 2.5 and 1.7 times higher out-of-plane and in-plane values, respectively, than that for pure PHB fibers. The rGO addition led to enhanced zigzag chain formation between paired lamellae in PHB fibers. In contrast, a further increase in rGO content reduced the alpha-crystal size and prevented zigzag chain conformation. A corresponding model explaining structural and molecular changes caused by rGO addition in electrospun PHB fibers is proposed. In addition, finite element analysis revealed a negligible vertical piezoresponse compared to lateral piezoresponse in uniaxially oriented PHB fibers based on alpha-phase (P2(1)2(1)2(1) space group). Thus, the present study demonstrates promising results for the development of biodegradable hybrid 3D scaffolds with an enhanced piezoresponse for various tissue engineering applications.