Abstract: Despite significant progress in single walled carbon nanotube (SWCNT) production by plasma enhanced chemical vapor deposition (PECVD), the growth mechanism in this method is not clearly understood. We employ reactive molecular dynamics simulations to investigate how plasma-based deposition allows growth at low temperature. We first investigate the SWCNT growth mechanism at low and high temperatures under conditions similar to thermal CVD and PECVD. We then show how ion bombardment during the nucleation stage increases the carbon solubility in the catalyst at low temperature. Finally, we demonstrate how moderate energy ions sputter amorphous carbon allowing for SWCNT growth at 500 K. (C) 2013 Elsevier B. V. All rights reserved.

Abstract: The atmospheric pressure dielectric barrier discharge in helium is a pulsed discharge in nature. If during the electrical current pulse a glow discharge is reached, then this pulse will last only a few microseconds in operating periods of sinusoidal voltage with lengths of about 10 to 100 µs. In this paper we demonstrate that right before a glow discharge is reached, the discharge very closely resembles the commonly assumed Townsend discharge structure, but actually contains some significant differing features and hence should not be considered as a Townsend discharge. In order to clarify this, we present calculation results of high time and space resolution of the pulse formation. The results indicate that indeed a maximum of ionization is formed at the anode, but that the level of ionization remains high and that the electric field at that time is significantly disturbed. Our results also show where this intermediate structure comes from.

Abstract: The optical behavior of a four-level system in a ring cavity driven by two coherent laser fields is studied. One laser field is treated as the incident field and the other the control field, respectively. It is found that there is optical transparency when the difference between the two frequency detunings of the incident and control fields from the corresponding atomic transition frequencies is zero. Optical bistability can be produced and controlled by increasing the magnitude of the frequency difference. The bistable hysteresis becomes larger when the frequency difference is increased. Further increase of the latter can lead to onset of multistability.

Abstract: An inductively coupled plasma, connected to a mass spectrometer interface, is computationally investigated. The effect of pressure behind the sampler, injector gas flow rate, auxiliary gas flow rate, and applied power is studied. There seems to be an optimum range of injector gas flow rate for each setup which guaranties the presence and also a proper length of the central channel in the torch. Moreover, our modeling results show that for any specific purpose, it is possible to control that either only the central gas flow passes through the sampler orifice or that it is accompanied by the auxiliary gas flow. It was also found that depending on geometry, the variation of outgoing gas flow rate is much less than the variation of the injector gas flow rate and this causes a slightly higher pressure inside the torch. The general effect of increasing the applied power is a rise in the plasma temperature, which results in a higher ionization in the coil region. However, the negative effect is reducing the length of the cool central channel which is important to transfer the sample substances to the sampler. Using a proper applied power can enhance the efficiency of the system. Indeed, by changing the gas path lines, the power can control which flow (i.e., only from injector gas or also from the auxiliary gas) goes to the sampler orifice. Finally, as also reported from experiments in literature, the pressure behind the sampler has no dramatic effect on the plasma characteristics.

Abstract: Background Patient-derived organoids are invaluable for fundamental and translational cancer research and holds great promise for personalized medicine. However, the shortage of available analysis methods, which are often single-time point, severely impede the potential and routine use of organoids for basic research, clinical practise, and pharmaceutical and industrial applications. Methods Here, we developed a high-throughput compatible and automated live-cell image analysis software that allows for kinetic monitoring of organoids, named Organoid Brightfield Identification-based Therapy Screening (OrBITS), by combining computer vision with a convolutional network machine learning approach. The OrBITS deep learning analysis approach was validated against current standard assays for kinetic imaging and automated analysis of organoids. A drug screen of standard-of-care lung and pancreatic cancer treatments was also performed with the OrBITS platform and compared to the gold standard, CellTiter-Glo 3D assay. Finally, the optimal parameters and drug response metrics were identified to improve patient stratification. Results OrBITS allowed for the detection and tracking of organoids in routine extracellular matrix domes, advanced Gri3D (R)-96 well plates, and high-throughput 384-well microplates, solely based on brightfield imaging. The obtained organoid Count, Mean Area, and Total Area had a strong correlation with the nuclear staining, Hoechst, following pairwise comparison over a broad range of sizes. By incorporating a fluorescent cell death marker, infra-well normalization for organoid death could be achieved, which was tested with a 10-point titration of cisplatin and validated against the current gold standard ATP-assay, CellTiter-Glo 3D. Using this approach with OrBITS, screening of chemotherapeutics and targeted therapies revealed further insight into the mechanistic action of the drugs, a feature not achievable with the CellTiter-Glo 3D assay. Finally, we advise the use of the growth rate-based normalised drug response metric to improve accuracy and consistency of organoid drug response quantification. Conclusion Our findings validate that OrBITS, as a scalable, automated live-cell image analysis software, would facilitate the use of patient-derived organoids for drug development and therapy screening. The developed wet-lab workflow and software also has broad application potential, from providing a launching point for further brightfield-based assay development to be used for fundamental research, to guiding clinical decisions for personalized medicine.

Abstract: The impact of the scaling of the channel length on the performances of metal-oxide-semiconductor field effect transistors, based on two-dimensional (2D) channel materials, is theoretically investigated, using density functional theory combined with the non-equilibrium Green's function method. It is found that the scaling of the channel length below 10nm leads to strong device performance degradations. Our simulations reveal that this degradation is essentially due to the tunneling current flowing between the source and the drain in these aggressively scaled devices. It is shown that this electron tunneling process is modulated by the effective mass of the 2D channel material, and sets the limit of the scaling in future transistor designs. (C) 2016 AIP Publishing LLC.

Abstract: The dielectric properties of confined water is of fundamental interest and is still controversial. For water confined in channels with height smaller than h = 8 angstrom, we found a commensurability effect and an extraordinary decrease in the out-of-plane dielectric constant down to the limit of the dielectric constant of optical water. Spatial resolved polarization density data obtained from molecular dynamics simulations are found to be antisymmetric across the channel and are used as input in a mean-field model for the dielectric constant as a function of the height of the channel for h > 15 angstrom. Our results are in excellent agreement with a recent experiment [L. Fumagalli et al., Science 360, 1339 (2018)].

Abstract: The laser ablation-induced plasma was used as a composition-con trolled source for ion implantation in Si crystals. Then, laser ablation in combination with inductively coupled plasma mass spectrometry was used for the elemental depth profiling of the implanted samples. Monte Carlo simulations permitted us to conclude that a depth resolution of tens of nm would be necessary to define the shape of the implantation profiles, as is obtained using XPS and RBS, whereas a hundred nm depth resolution is sufficient to determine the total implanted dose. The detection power of LA-ICP-MS would routinely allow rapid analytical control on the trace level implanted dose. Nevertheless, this technique is limited in terms of depth profiling resolution due to pulse mixing and signal tailing induced during the aerosol transport. Raw signal processing procedures were developed for the minimization of shapeline dispersion, deconvolution of pulse mixing and more appropriate assessment of the implanted profiles. Shapeline dispersion could be corrected for by determining the signal waning constant and implementing this information for a non-affine alibi transformation of the LA-ICP-MS signal traces. Pulse mixing deconvolution was attained with an algorithm that considered accumulated signal intensity due to pulse-on-pulse stacking, i.e., the latest pulse on top of all antecedent individual pulses' exponential tails proportionally.

Abstract: The aggregation of insoluble amyloid beta (Aβ) peptides in the brain is known to trigger the onset of neurodegenerative diseases, such as Alzheimer’s disease. In spite of the massive number of investigations, the underlying mechanisms to destabilize the Aβ aggregates are still poorly understood. Some studies indicate the importance of oxidation to destabilize the Aβ aggregates. In particular, oxidation induced by cold atmospheric plasma (CAP) has demonstrated promising results in eliminating these toxic aggregates. In this paper, we investigate the effect of oxidation on the stability of an Aβ pentamer. By means of molecular dynamics simulations and umbrella sampling, we elucidate the conformational changes of Aβ pentamer in the presence of oxidized residues, and we estimate the dissociation free energy of the terminal peptide out of the pentamer form. The calculated dissociation free energy of the terminal peptide is also found to decrease with increasing oxidation. This indicates that Aβ pentamer aggregation becomes less favorable upon oxidation. Our study contributes to a better insight in one of the potential mechanisms for inhibition of toxic Aβ peptide aggregation, which is considered to be the main culprit to Alzheimer’s disease.

Abstract: We performed a detailed investigation of the oxidation of the technologically relevant GaAs(001)-beta 2(2x4) surface via density functional calculations. The purpose is to gain insights on the atomistic mechanisms and local bondings that underlie the degradation of the surface properties once exposed to oxygen. The study comprises the adsorption of single O atoms, through the sampling of several adsorption sites, and the subsequent formation of the O adsorbate at increasing coverage by taking into account multiple-atom adsorption. Based on the evaluation of the energetics and the structural properties of the atomistic models generated, the results here reported delineate a consistent picture of the initial stage of the surface oxidation: (i) at low coverage, in the limit of single O insertions, oxygen is incorporated on the surface forming a twofold-bridging Ga-O-As bond; (ii) at increasing coverage, as multiple O atoms are involved, this is accompanied by the formation of a threefold-coordinated bond (with two Ga and one As atoms); (iii) the latter has important implications regarding the electronic properties of the adsorbate since this O bonding may result in the formation of As dangling bonds. Moreover, a clear trend of increased energy gain for the incorporation of neighboring O atoms compared to single O insertions indicates that the formation of oxide clusters is favored over a regime of uniform oxidation. Our findings provide a detailed description of the O bonding and stress the importance of modeling the adsorption of multiple O atoms for an accurate description of the surface oxidation.

Abstract: Background
During normal pregnancy, placental oxidative stress (OS) is present during all three trimesters and is necessary to obtain normal cell function. However, if OS reaches a certain level, pregnancy complications might arise. In preeclampsia (PE), a dangerous pregnancy specific hypertensive disorder, OS induced in the ischemic placenta causes a systemic inflammatory response and activates maternal endothelial cells. In this study, we aimed to quantify superoxide concentrations (as a measure of systemic OS) using electron paramagnetic resonance (EPR) and correlate them to markers of systemic inflammation, iron status and vascular function.
Methods
Fifty-nine women with a healthy pregnancy (HP), 10 non-pregnant controls (NP) and 28 PE patients (32±3.3weeks) were included. During HP, blood samples for superoxide, neutrophil to lymphocyte ratio (NLR), mean platelet volume (MPV) and iron status were taken at 10, 25 and 39 weeks. Vascular measurements for arterial stiffness (carotid-femoral pulse wave velocity (CF-PWV), augmentation index (AIx), augmentation Pressure (AP)) and microvascular endothelial function (reactive hyperemia index (RHI)) were performed at 35 weeks. In PE, all measurements were performed at diagnosis. CMH (1-hydroxy-3-methoxycarbonyl-2,2,5,5-tetramethylpyrrolidine) was used as spin probe for EPR, since the formed CM radical
corresponds to the amount of superoxide.
Results
Superoxide concentration remains stable during pregnancy (p = 0.92), but is significantly higher compared to the NP controls (p<0.0001). At 25 weeks, there is a significant positive correlation between superoxide and ferritin concentration. (p = 0.04) In PE, superoxide, systemic inflammation and iron status are much higher compared to HP (all p<0.001). During HP, superoxide concentrations correlate significantly with arterial stiffness (all p<0.04), while in PE superoxide is significantly correlated to microvascular endothelial function (p = 0.03).
Conclusions
During HP there is an increased but stable oxidative environment, which is correlated to ferritin concentration. If superoxide levels increase, there is an augmentation in arterial stiffness. In PE pregnancies, systemic inflammation and superoxide concentrations are higher and result in a deterioration of endothelial function. Together, these findings support the hypothesis that vascular function is directly linked to the amount of OS and that measurement of OS in combination with vascular function tests might be used in the prediction of PE.