Abstract: Xenobiotic nucleic acids (XNA) are nucleic acid analogues not present in nature that can be used for the storage of genetic information. In vivo XNA applications could be developed into novel biocontainment strategies, but are currently limited by the challenge of developing XNA processing enzymes such as polymerases, ligases and nucleases. Here, we present a structure-guided modelling-based strategy for the rational design of those enzymes essential for the development of XNA molecular biology. Docking of protein domains to unbound double-stranded nucleic acids is used to generate a first approximation of the extensive interaction of nucleic acid processing enzymes with their substrate. Molecular dynamics is used to optimise that prediction allowing, for the first time, the accurate prediction of how proteins that form toroidal complexes with nucleic acids interact with their substrate. Using the Chlorella virus DNA ligase as a proof of principle, we recapitulate the ligase's substrate specificity and successfully predict how to convert it into an XNA-templated XNA ligase.

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: CO2 conversion into value-added chemicals and fuels is considered as one of the great challenges of the 21st century. Due to the limitations of the traditional thermal approaches, several novel technologies are being developed. One promising approach in this field, which has received little attention to date, is plasma
technology. Its advantages include mild operating conditions, easy upscaling, and gas activation by energetic electrons instead of heat. This allows thermodynamically difficult reactions, such as CO2 splitting and the dry reformation of methane, to occur with reasonable energy cost. In this review, after exploring the traditional thermal approaches, we have provided a brief overview of the fierce competition between various novel approaches in a quest to find the most effective and efficient CO2 conversion technology. This is needed to critically assess whether plasma technology can be successful in an already crowded arena. The following questions need to be answered in this regard: are there key advantages to using plasma technology over other novel approaches, and if so, what is the flip side to the use of this technology? Can plasma technology be successful on its own, or can synergies be achieved by combining it with other technologies? To answer
these specific questions and to evaluate the potentials and limitations of plasma technology in general, this review presents the current state-of-the-art and a critical assessment of plasma-based CO2 conversion, as well as the future challenges for its practical implementation.

Abstract: A two-dimensional fluid model, including the full set of Maxwell equations, has been developed and applied to investigate the effect of a phase shift between two power sources on the radial uniformity of several plasma characteristics in a hydrogen capacitively coupled plasma. This study was carried out at various frequencies in the range 13.56200 MHz. When the frequency is low, at 13.56 MHz, the plasma density is characterized by an off-axis peak when both power sources are in-phase (phgr = 0), and the best radial uniformity is obtained at phgr = π. This trend can be explained because the radial nonuniformity caused by the electrostatic edge effect can be effectively suppressed by the phase-shift effect at a phase difference equal to π. When the frequency rises to 60 MHz, the plasma density profiles shift smoothly from edge-peaked over uniform to centre-peaked as the phase difference increases, due to the pronounced standing-wave effect, and the best radial uniformity is reached at phgr = 0.3π. At a frequency of 100 MHz, a similar behaviour is observed, except that the maximum of the plasma density moves again towards the radial edge at the reverse-phase case (phgr = π), because of the dominant skin effect. When the frequency is 200 MHz, the bulk plasma density increases significantly with increasing phase-shift values, and a better uniformity is obtained at phgr = 0.4π. This is because the density in the centre increases faster than at the radial edge as the phase difference rises, due to the increasing power deposition Pz in the centre and the decreasing power density Pr at the radial edge. As the phase difference increases to π, the maximum near the radial edge becomes obvious again. This is because the skin effect has a predominant influence on the plasma density under this condition, resulting in a high density at the radial edge. Moreover, the axial ion flux increases monotonically with phase difference, and exhibits similar profiles to the plasma density. The calculation results illustrate that the radial uniformity of the various plasma characteristics is strongly dependent on the applied frequency and the phase shift between both power sources, which is important to realize, for controlling the uniformity of the plasma etch and deposition processes.

Abstract: The possibility of application of nanomaterials is determined by our ability to control the properties of the materials, which are ultimately determined by their structure and hence their growth processes. We employ hybrid molecular dynamics / Monte Carlo (MD/MC) simulations to explore the growth of SWNTs and graphene on nickel as a catalyst, with the specific goal of unraveling the growth mechanisms. While the general observations are in agreement with the literature, we find a number of interesting phenomena to be operative which are crucial for the growth, and which are not accessible by MD simulations alone due to the associated time scale. Specifically, we observe metal mediated healing and restructuring processes to take place, reorganizing the carbon network during the initial nucleation step. In the case of carbon nanotube growth, this leads to the growth of tubes with a determinable chirality. In the case of graphene formation, we find that graphene is only formed at temperatures above 700 K. These results are of importance for understanding the growth mechanisms of these carbon nanomaterials on the fundamental level.

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: Non-destructive 14-MeV neutron activation analysis for silicon in steel has been applied with 56Mn as internal standard.56Mn is formed from the iron matrix via the 56Fe(n,p)56Mn reaction. Several methods of internal standardisation via56Mn are discussed. The 0.84-MeV photopeak of 56Mn is recommended if steel samples of about the same composition are to be analysed. Chemically analysed steel samples are used as silicon standards. A precision of 0.7% was obtained for an analysis plus standardisation time of 13 min. Special attention was paid to interferences produced by concentration changes of impurity elements. Several possible sources of errors were investigated.

Abstract: A parameter study is carried out for an inductively coupled plasma used for the synthesis of carbon nanotubes or carbon nanofibres (CNTs/CNFs), by means of the Hybrid Plasma Equipment Model. The influence of processing parameters including gas ratio for four different gas mixtures typically used for CNT/CNF growth (i.e. CH4/H2, CH4/NH3, C2H2/H2 and C2H2/NH3), inductively coupled plasma (ICP) power (501000 W), operating pressure (10 mTorr1 Torr), bias power (01000 W) and temperature of the substrate (01000 °C) on the plasma chemistry is investigated and the optimized conditions for CNT/CNF growth are analysed. Summarized, our calculations suggest that a lower fraction of hydrocarbon gases (CH4 or C2H2, i.e. below 20%) and hence a higher fraction of etchant gases (H2 or NH3) in the gas mixture result in more 'clean' conditions for controlled CNT/CNF growth. The same applies to a higher ICP power, a moderate ICP gas pressure above 100 mTorr (at least for single-walled carbon nanotubes), a high bias power (for aligned CNTs) and an intermediate substrate temperature.

Abstract: Multiple cancer therapies nowadays rely on oxidative stress to damage cancer cells. Here we investigated the biological and molecular effect of oxidative stress on the interaction between CD44 and hyaluronan (HA), as interrupting their binding can hinder cancer progression. Our experiments demonstrated that the oxidation of HA decreased its recognition by CD44, which was further enhanced when both CD44 and HA were oxidized. The reduction of CD44–HA binding negatively affected the proliferative state of cancer cells. Our multi-level atomistic simulations revealed that the binding free energy of HA to CD44 decreased upon oxidation. The effect of HA and CD44 oxidation on CD44–HA binding was similar, but when both HA and CD44 were oxidized, the effect was much larger, in agreement with our experiments. Hence, our experiments and computations support our hypothesis on the role of oxidation in the disturbance of CD44–HA interaction, which can lead to the inhibition of proliferative signaling pathways inside the tumor cell to induce cell death.

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