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Van der Paal, J.; Hong, S.-H.; Yusupov, M.; Gaur, N.; Oh, J.-S.; Short, R.D.; Szili, E.J.; Bogaerts, A. | ||||
| Title | How membrane lipids influence plasma delivery of reactive oxygen species into cells and subsequent DNA damage : an experimental and computational study | Type | A1 Journal article | ||
| Year | 2019 | Publication | Physical chemistry, chemical physics | Abbreviated Journal | Phys Chem Chem Phys |
| Volume | 21 | Issue | 35 | Pages | 19327-19341 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| 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. | ||||
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| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000486175400045 | Publication Date | 2019-08-21 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1463-9076; 1463-9084 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 4.123 | Times cited | 1 | Open Access | |
| Notes | Approved | Most recent IF: 4.123 | |||
| Call Number | UA @ admin @ c:irua:162782 | Serial | 6303 | ||
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| Author |
Verberck, B.; Okazaki, T.; Tarakina, N.V. | ||||
| Title | Ordered and disordered packing of coronene molecules in carbon nanotubes | Type | A1 Journal article | ||
| Year | 2013 | Publication | Physical chemistry, chemical physics | Abbreviated Journal | Phys Chem Chem Phys |
| Volume | 15 | Issue | 41 | Pages | 18108-18114 |
| Keywords | A1 Journal article; Condensed Matter Theory (CMT) | ||||
| Abstract | Monte Carlo simulations of coronene molecules in single-walled carbon nanotubes (SWCNTs) and dicoronylene molecules in SWCNTs are performed. Depending on the diameter D of the encapsulating SWCNT, regimes favoring the formation of ordered, one-dimensional (1D) stacks of tilted molecules (D <= 1.7 nm for coronene@SWCNT, 1.5 nm <= D <= 1.7 nm for dicoronylene@SWCNT) and regimes with disordered molecular arrangements and increased translational mobilities enabling the thermally induced polymerization of neighboring molecules resulting in the formation of graphene nanoribbons (GNRs) are observed. The results show that the diameter of the encapsulating nanotube is a crucial parameter for the controlled synthesis of either highly ordered 1D structures or GNR precursors. | ||||
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| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Cambridge | Editor | ||
| Language | Wos | 000325400600045 | Publication Date | 2013-09-05 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1463-9076;1463-9084; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 4.123 | Times cited | 9 | Open Access | |
| Notes | ; B.V. is a Postdoctoral Fellow of the Research Foundation Flanders (FWO-VI). N.V.T. acknowledges funding by the Bavarian Ministry of Sciences, Research and the Arts. ; | Approved | Most recent IF: 4.123; 2013 IF: 4.198 | ||
| Call Number | UA @ lucian @ c:irua:112212 | Serial | 2502 | ||
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| Author |
Verlackt, C.C.W.; Van Boxem, W.; Bogaerts, A. | ||||
| Title | Transport and accumulation of plasma generated species in aqueous solution | Type | A1 Journal article | ||
| Year | 2018 | Publication | Physical chemistry, chemical physics | Abbreviated Journal | Phys Chem Chem Phys |
| Volume | 20 | Issue | 10 | Pages | 6845-6859 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | The interaction between cold atmospheric pressure plasma and liquids is receiving increasing attention for various applications. In particular, the use of plasma-treated liquids (PTL) for biomedical applications is of growing importance, in particular for sterilization and cancer treatment. However, insight into the underlying mechanisms of plasma–liquid interactions is still scarce. Here, we present a 2D fluid dynamics model for the interaction between a plasma jet and liquid water. Our results indicate that the formed reactive species originate from either the gas phase (with further solvation) or are formed at the liquid interface. A clear increase in the aqueous density of H2O2, HNO2/NO2- and NO3- is observed as a function of time, while the densities of O3, HO2/O2- and ONOOH/ONOO- are found to quickly reach a maximum due to chemical reactions in solution. The trends observed in our model correlate well with experimental observations from the literature. |
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| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000429286100009 | Publication Date | 2018-02-06 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1463-9076 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 4.123 | Times cited | 35 | Open Access | OpenAccess |
| Notes | The authors thank Petr Luke`s (Institute of Plasma Physics AS CR, Czech Republic) and Yury Gorbanev (UAntwerp, group PLASMANT) for the fruitful discussions regarding the chemistry in the model and the plasma–liquid interactions. | Approved | Most recent IF: 4.123 | ||
| Call Number | PLASMANT @ plasmant @c:irua:149557 | Serial | 4908 | ||
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| Author |
Vermeyen, T.; Brence, J.; Van Echelpoel, R.; Aerts, R.; Acke, G.; Bultinck, P.; Herrebout, W. | ||||
| Title | Exploring machine learning methods for absolute configuration determination with vibrational circular dichroism | Type | A1 Journal article | ||
| Year | 2021 | Publication | Physical Chemistry Chemical Physics | Abbreviated Journal | Phys Chem Chem Phys |
| Volume | 23 | Issue | 35 | Pages | 19781-19789 |
| Keywords | A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation); Molecular Spectroscopy (MolSpec) | ||||
| Abstract | The added value of supervised Machine Learning (ML) methods to determine the Absolute Configuration (AC) of compounds from their Vibrational Circular Dichroism (VCD) spectra was explored. Among all ML methods considered, Random Forest (RF) and Feedforward Neural Network (FNN) yield the best performance for identification of the AC. At its best, FNN allows near-perfect AC determination, with accuracy of prediction up to 0.995, while RF combines good predictive accuracy (up to 0.940) with the ability to identify the spectral areas important for the identification of the AC. No loss in performance of either model is observed as long as the spectral sampling interval used does not exceed the spectral bandwidth. Increasing the sampling interval proves to be the best method to lower the dimensionality of the input data, thereby decreasing the computational cost associated with the training of the models. | ||||
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| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000691366500001 | Publication Date | 2021-08-25 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1463-9076; 1463-9084 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 4.123 | Times cited | Open Access | OpenAccess | |
| Notes | Approved | Most recent IF: 4.123 | |||
| Call Number | UA @ admin @ c:irua:180290 | Serial | 7951 | ||
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| Author |
Yagmurcukardes, M.; Horzum, S.; Torun, E.; Peeters, F.M.; Senger, R.T. | ||||
| Title | Nitrogenated, phosphorated and arsenicated monolayer holey graphenes | Type | A1 Journal article | ||
| Year | 2016 | Publication | Physical chemistry, chemical physics | Abbreviated Journal | Phys Chem Chem Phys |
| Volume | 18 | Issue | 18 | Pages | 3144-3150 |
| Keywords | A1 Journal article; Condensed Matter Theory (CMT) | ||||
| Abstract | Motivated by a recent experiment that reported the synthesis of a new 2D material nitrogenated holey graphene (C2N) [Mahmood et al., Nat. Commun., 2015, 6, 6486], the electronic, magnetic, and mechanical properties of nitrogenated (C2N), phosphorated (C2P) and arsenicated (C2As) monolayer holey graphene structures are investigated using first-principles calculations. Our total energy calculations indicate that, similar to the C2N monolayer, the formation of the other two holey structures are also energetically feasible. Calculated cohesive energies for each monolayer show a decreasing trend going from the C2N to C2As structure. Remarkably, all the holey monolayers considered are direct band gap semiconductors. Regarding the mechanical properties (in-plane stiffness and Poisson ratio), we find that C2N has the highest in-plane stiffness and the largest Poisson ratio among the three monolayers. In addition, our calculations reveal that for the C2N, C2P and C2As monolayers, creation of N and P defects changes the semiconducting behavior to a metallic ground state while the inclusion of double H impurities in all holey structures results in magnetic ground states. As an alternative to the experimentally synthesized C2N, C2P and C2As are mechanically stable and flexible semiconductors which are important for potential applications in optoelectronics. | ||||
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| Publisher | Place of Publication | Cambridge | Editor | ||
| Language | Wos | 000369506000095 | Publication Date | 2015-12-22 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1463-9076 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 4.123 | Times cited | 36 | Open Access | |
| Notes | ; This work was supported by the Flemish Science Foundation (FWO-Vl) and the Methusalem foundation of the Flemish government. Computational resources were provided by TUBITAK ULAKBIM, High Performance and Grid Computing Center (TR-Grid e-Infrastructure). ; | Approved | Most recent IF: 4.123 | ||
| Call Number | UA @ lucian @ c:irua:132313 | Serial | 4214 | ||
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| Author |
Yorulmaz, U.; Šabani, D.; Yagmurcukardes, M.; Sevik, C.; Milošević, M.V. | ||||
| Title | High-throughput analysis of tetragonal transition metal Xenes | Type | A1 Journal article | ||
| Year | 2022 | Publication | Physical chemistry, chemical physics | Abbreviated Journal | Phys Chem Chem Phys |
| Volume | 24 | Issue | 48 | Pages | 29406-29412 |
| Keywords | A1 Journal article; Condensed Matter Theory (CMT) | ||||
| Abstract | We report a high-throughput first-principles characterization of the structural, mechanical, electronic, and vibrational properties of tetragonal single-layer transition metal Xenes (t-TMXs). Our calculations revealed 22 dynamically, mechanically and chemically stable structures among the 96 possible free-standing layers present in the t-TMX family. As a fingerprint for their structural identification, we identified four characteristic Raman active phonon modes, namely three in-plane and one out-of-plane optical branches, with various intensities and frequencies depending on the material in question. Spin-polarized electronic calculations demonstrated that anti-ferromagnetic (AFM) metals, ferromagnetic (FM) metals, AFM semiconductors, and non-magnetic semiconductor materials exist within this family, evidencing the potential of t-TMXs for further use in multifunctional heterostructures. | ||||
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| Language | Wos | 000892446100001 | Publication Date | 2022-11-30 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1463-9076; 1463-9084 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 3.3 | Times cited | 1 | Open Access | Not_Open_Access |
| Notes | Approved | Most recent IF: 3.3 | |||
| Call Number | UA @ admin @ c:irua:192762 | Serial | 7310 | ||
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| Author |
Zeng, Y.I.; Menghini, M.; Li, D.Y.; Lin, S.S.; Ye, Z.Z.; Hadermann, J.; Moorkens, T.; Seo, J.W.; Locquet, J.-P.; van Haesendonck, C. | ||||
| Title | Unexpected optical response of single ZnO nanowires probed using controllable electrical contacts | Type | A1 Journal article | ||
| Year | 2011 | Publication | Physical chemistry, chemical physics | Abbreviated Journal | Phys Chem Chem Phys |
| Volume | 13 | Issue | 15 | Pages | 6931-6935 |
| Keywords | A1 Journal article; Electron microscopy for materials research (EMAT) | ||||
| Abstract | Relying on combined electron-beam lithography and lift-off methods Au/Ti bilayer electrical contacts were attached to individual ZnO nanowires (NWs) that were grown by a vapor phase deposition method. Reliable Schottky-type as well as ohmic contacts were obtained depending on whether or not an ion milling process was used. The response of the ZnO NWs to ultraviolet light was found to be sensitive to the type of contacts. The intrinsic electronic properties of the ZnO NWs were studied in a field-effect transistor configuration. The transfer characteristics, including gate threshold voltage, hysteresis and operational mode, were demonstrated to unexpectedly respond to visible light. The origin of this effect could be accounted for by the presence of point defects in the ZnO NWs. | ||||
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| Publisher | Place of Publication | Cambridge | Editor | ||
| Language | Wos | 000288951000019 | Publication Date | 2011-03-14 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1463-9076;1463-9084; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 4.123 | Times cited | 7 | Open Access | |
| Notes | Approved | Most recent IF: 4.123; 2011 IF: 3.573 | |||
| Call Number | UA @ lucian @ c:irua:89378 | Serial | 3807 | ||
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