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 catalysis is promising for various environmental, energy and chemical synthesis applications, but the underlying mechanisms are far from understood. Modeling can help to obtain a better insight in these mechanisms. Some burning questions relate to the plasma behavior inside packed bed reactors and whether plasma can penetrate into catalyst pores. In this paper, we try to provide answers to these questions, by means of both fluid modeling and particle-in-cell/Monte Carlo collision simulations. We present a short overview of recent findings obtained in our group by means of modeling, i.e., the enhanced electric field near the contact points and the streamer propagation through the packing in packed bed reactors, as well as the plasma behavior in catalyst pores, to determine the minimum pore size in which plasma streamers can penetrate.

Abstract: Physical plasmas generate unique mixes of reactive oxygen and nitrogen species (RONS or ROS). Only a bit more than a decade ago, these plasmas, operating at body temperature, started to be considered for medical therapy with considerably little mechanistic redox chemistry or biomedical research existing on that topic at that time. Today, a vast body of evidence is available on physical plasma-derived ROS, from their spatiotemporal resolution in the plasma gas phase to sophisticated chemical and biochemical analysis of these species once dissolved in liquids. Data from<italic>in silico</italic>analysis dissected potential reaction pathways of plasma-derived reactive species with biological membranes, and<italic>in vitro</italic>and<italic>in vivo</italic>experiments in cell and animal disease models identified molecular mechanisms and potential therapeutic benefits of physical plasmas. In 2013, the first medical plasma systems entered the European market as class IIa devices and have proven to be a valuable resource in dermatology, especially for supporting the healing of chronic wounds. The first results in cancer patients treated with plasma are promising, too. Due to the many potentials of this blooming new field ahead, there is a need to highlight the main concepts distilled from plasma research in chemistry and biology that serve as a mechanistic link between plasma physics (how and which plasma-derived ROS are produced) and therapy (what is the medical benefit). This inevitably puts cellular membranes in focus, as these are the natural interphase between ROS produced by plasmas and translation of their chemical reactivity into distinct biological responses.

Abstract: When confined between graphene layers, water behaves differently from the bulk and exhibits unusual properties such as fast water flow and ordering into a crystal. The hydrogen-bonded network is affected by the limited space and by the characteristics of the confining walls. The presence of an extraordinary number of hydronium and hydroxide ions in narrow channels has the following effects: (i) they affect water permeation through the channel, (ii) they may interact with functional groups on the graphene oxide surface and on the edges, and (iii) they change the thermochemistry of water, which are fundamentally important to understand, especially when confined water is subjected to an external electric field. Here we study the physical properties of water when confined between two graphene sheets and containing hydronium and hydroxide. We found that: (i) there is a disruption in the solvation structure of the ions, which is also affected by the layered structure of confined water, (ii) hydronium and hydroxide occupy specific regions inside the nanochannel, with a prevalence of hydronium (hydroxide) ions at the edges (interior), and (iii) ions recombine more slowly in confined systems than in bulk water, with the recombination process depending on the channel height and commensurability between the size of the molecules and the nanochannel height – a decay of 20% (40%) in the number of ions in 8 ps is observed for a channel height of h = 7 angstrom (bulk water). Our work reveals distinctive properties of water confined in a nanocapillary in the presence of additional hydronium and hydroxide ions.

Abstract: Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive cancers with a low response to treatment and a five-year survival rate below 5%. The ineffectiveness of treatment is partly because of an immunosuppressive tumor microenvironment, which comprises tumor-supportive pancreatic stellate cells (PSCs). Therefore, new therapeutic strategies are needed to tackle both the immunosuppressive PSC and pancreatic cancer cells (PCCs). Recently, physical cold atmospheric plasma consisting of reactive oxygen and nitrogen species has emerged as a novel treatment option for cancer. In this study, we investigated the cytotoxicity of plasma-treated phosphate-buffered saline (pPBS) using three PSC lines and four PCC lines and examined the immunogenicity of the induced cell death. We observed a decrease in the viability of PSC and PCC after pPBS treatment, with a higher efficacy in the latter. Two PCC lines expressed and released damage-associated molecular patterns characteristic of the induction of immunogenic cell death (ICD). In addition, pPBS-treated PCC were highly phagocytosed by dendritic cells (DCs), resulting in the maturation of DC. This indicates the high potential of pPBS to trigger ICD. In contrast, pPBS induced no ICD in PSC. In general, pPBS treatment of PCCs and PSCs created a more immunostimulatory secretion profile (higher TNF-α and IFN-γ, lower TGF-β) in coculture with DC. Altogether, these data show that plasma treatment via pPBS has the potential to induce ICD in PCCs and to reduce the immunosuppressive tumor microenvironment created by PSCs. Therefore, these data provide a strong experimental basis for further in vivo validation, which might potentially open the way for more successful combination strategies with immunotherapy for PDAC.

Abstract: We present an approach to incorporate the effect of vibrational nonequilibrium in molecular dynamics (MD) simulations. A perturbed canonical ensemble, in which selected modes are excited to higher temperature while all others remain equilibrated at low temperature, is simulated by applying a specifically tailored bias potential. Our method can be readily applied to any (classical or quantum mechanical) MD setup at virtually no additional computational cost and allows the study of reactions of vibrationally excited molecules in nonequilibrium environments such as plasmas. In combination with enhanced sampling methods, the vibrational efficacy and mode selectivity of vibrationally stimulated reactions can then be quantified in terms of chemically relevant observables, such as reaction rates and apparent free energy barriers. We first validate our method for the prototypical hydrogen exchange reaction and then show how it can capture the effect of vibrational excitation on a symmetric SN2 reaction and radical addition on CO2.

Abstract: Understanding the folding and stability of membrane proteins is of great importance in protein science. Recently, osmolytes and ionic liquids (ILs) are increasingly being used as drug delivery systems in the biopharmaceutical industry. However, the stability of membrane proteins in the presence of osmolytes and ILs is not yet fully understood. Besides, the effect of oxidative stress on membrane proteins with osmolytes or ILs has not been investigated. Therefore, we studied the influence of osmolytes and ILs as co-solvents on the stability of a model membrane protein (i.e., Bacteriorhodopsin in purple membrane of Halobacterium salinarum), using UV–Vis spectroscopy and molecular dynamics (MD) simulations. The MD simulations allowed us to determine the flexibility and solvent accessible surface area (SASA) of Bacteriorhodopsin protein in the presence and/or absence of cosolvents, as well as to carry out principal component analysis (PCA) to identify the most important movements in this protein. In addition, by means of UV–Vis spectroscopy we studied the effect of oxidative stress generated by cold atmospheric plasma on the stability of Bacteriorhodopsin in the presence and/or absence of co-solvents. This study is important for a better understanding of the stability of proteins in the presence of oxidative stress.

Abstract: In recent years, cold atmospheric plasma (CAP) has been proposed as a novel method to enhance transdermal drug delivery, while avoiding tissue damage. However, the underlying mechanism for the increasing skin permeability upon CAP treatment is still undefined. We propose a mechanism in which CAP-generated reactive species induce cross-linking of skin lipids, leading to the generation of nanopores, thereby facilitating the permeation of drug molecules. Molecular dynamics simulations support this proposed mechanism. Furthermore, our results indicate that to achieve maximum enhancement of the permeability, the optimal treatment will depend on the exact lipid composition of the skin, as well as on the CAP source used.

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: The mechanisms of plasma in medicine are broadly attributed to plasma-derived reactive oxygen and nitrogen species (RONS). In order to exert any intracellular effects, these plasma-derived RONS must first traverse a major barrier in the cell membrane. The cell membrane lipid composition, and thereby the magnitude of this barrier, is highly variable between cells depending on type and state (e.g. it is widely accepted that healthy and cancerous cells have different membrane lipid compositions). In this study, we investigate how plasma-derived RONS interactions with lipid membrane components can potentially be exploited in the future for treatment of diseases. We couple phospholipid vesicle experiments, used as simple cell models, with molecular dynamics (MD) simulations of the lipid membrane to provide new insights into how the interplay between phospholipids and cholesterol may influence the response of healthy and diseased cell membranes to plasma-derived RONS. We focus on the (i) lipid tail saturation degree, (ii) lipid head group type, and (iii) membrane cholesterol fraction. Using encapsulated molecular probes, we study the influence of the above membrane components on the ingress of RONS into the vesicles, and subsequent DNA damage. Our results indicate that all of the above membrane components can enhance or suppress RONS uptake, depending on their relative concentration within the membrane. Further, we show that higher RONS uptake into the vesicles does not always correlate with increased DNA damage, which is attributed to ROS reactivity and lifetime. The MD simulations indicate the multifactorial chemical and physical processes at play, including (i) lipid oxidation, (ii) lipid packing, and (iii) lipid rafts formation. The methods and findings presented here provide a platform of knowledge that could be leveraged in the development of therapies relying on the action of plasma, in which the cell membrane and oxidative stress response in cells is targeted.

Abstract: Non-thermal plasma (NTP), defined as a partially ionized gas, is an emerging technology with several biomedical applications, including tissue regeneration. In particular, NTP treatment has been shown to activate endogenous biological processes to promote cell regrowth, differentiation, and proliferation in multiple cell types. However, the effects of this therapy on nervous system regeneration have not yet been established. Accordingly, the current study explored the effects of a nanosecond-pulsed dielectric barrier discharge plasma on neural regeneration. Following mechanical trauma in vitro, plasma was applied either directly to (1) astrocytes alone, (2) neurons alone, or (3) neurons or astrocytes in a non-contact co-culture. Remarkably, we identified NTP treatment intensities that accelerated both neurite regeneration and astrocyte regrowth. In astrocyte cultures alone, an exposure of 20-90 mJ accelerated astrocyte re-growth up to three days post-injury, while neurons required lower treatment intensities (<= 20 mJ) to achieve sub-lethal outgrowth. Following injury to neurons in non-contact co-culture with astrocytes, 20 mJ exposure of plasma to only neurons or astrocytes resulted in increased neurite regeneration at three days post-treatment compared to the untreated, but no enhancement was observed when both cell types were treated. At day seven, although regeneration further increased, NTP did not elicit a significant increase from the control. However, plasma exposure at higher intensities was found to be injurious, underscoring the need to optimize exposure levels. These results suggest that growth-promoting physiological responses may be elicited via properly calibrated NTP treatment to neurons and/or astrocytes. This could be exploited to accelerate neurite re-growth and modulate neuron-astrocyte interactions, thereby hastening nervous system regeneration.

Abstract: Selective conversion of bio-renewable ethanol under mild conditions especially at room temperature remains a major challenge for sustainable production of hydrogen and valuable carbon-based materials. In this study, adaptive non-thermal plasma is applied to deliver pulsed energy to rapidly and selectively reform ethanol in the absence of a catalyst. Importantly, the carbon atoms in ethanol that would otherwise be released into the environment in the form of CO or CO2 are effectively captured in the form of carbon dots (CDs). Three modes of non-thermal spark plasma discharges, i.e. single spark mode (SSM), multiple spark mode (MSM) and gliding spark mode (GSM), provide additional flexibility in ethanol reforming by controlling the processes of energy transfer and distribution, thereby affecting the flow rate, gas content, and energy consumption in H-2 production. A favourable combination of low temperature (< 40 degrees C), attractive conversion rate (gas flow rate of similar to 120 mL/min), high hydrogen yield (H-2 content > 90%), low energy consumption (similar to 0.96 kWh/m(3) H-2) and the effective generation of photoluminescent CDs (which are applicable for bioimaging or biolabelling) in the MSM indicate that the proposed strategy may offer a new carbon-negative avenue for comprehensive utilization of alcohols and mitigating the increasingly severe energy and environmental issues.

Abstract: The limitation in time and length scale is a major issue of molecular dynamics (MD) simulation. Although several methods have been developed to extend the MD time scale, their performance usually deteriorates with increasing system size. Therefore, an acceleration method which is applicable to large systems is required to bridge the gap between the MD simulations and target phenomena. In this study, an accelerated MD method for large system is developed based on the collective variable-driven hyperdynamics (CVHD) method [K.M. Bal and E.C. Neyts, 2015]. The key idea is to run CVHD in parallel with rate control and accelerate multiple possible events simultaneously. Using this novel method, carbon diffusion in bcc-iron bicrystal with grain boundary is examined as an application for practical materials. Carbon atoms reaching at the grain boundary are trapped whereas carbon atoms in the bulk region diffuse randomly, and both dynamic regimes can be simultaneously accelerated with the parallel CVHD technique.