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“Special issue on fundamentals of plasmasurface interactions”. Bogaerts A, Neyts EC, Rousseau A, Journal of physics: D: applied physics 47, 220301 (2014). http://doi.org/10.1088/0022-3727/47/22/220301
Keywords: Editorial; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.588
Times cited: 2
DOI: 10.1088/0022-3727/47/22/220301
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“Special Issue on future directions in plasma nanoscience”. Neyts EC, Frontiers of Chemical Science and Engineering 13, 199 (2019). http://doi.org/10.1007/S11705-019-1843-Y
Keywords: Editorial; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 1.712
DOI: 10.1007/S11705-019-1843-Y
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“Special Issue on Numerical Modelling of Low-Temperature Plasmas for Various Applications –, Part I: Review and Tutorial Papers on Numerical Modelling Approaches”. Alves LL, Bogaerts A, Plasma processes and polymers 14, 1690011 (2017). http://doi.org/10.1002/ppap.201690011
Keywords: Editorial; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.846
Times cited: 3
DOI: 10.1002/ppap.201690011
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“Special issue on numerical modelling of low-temperature plasmas for various applications –, part II: Research papers on numerical modelling for various plasma applications”. Bogaerts A, Alves LL, Plasma processes and polymers 14, 1790041 (2017). http://doi.org/10.1002/ppap.201790041
Keywords: Editorial; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.846
Times cited: 2
DOI: 10.1002/ppap.201790041
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“Special Issue on “Dielectric Barrier Discharges and their Applications&rdquo, in Commemoration of the 20th Anniversary of Dr. Ulrich Kogelschatz’s Work”. Bogaerts A, Plasma Chemistry and Plasma Processing 43, 1281 (2023). http://doi.org/10.1007/s11090-023-10431-x
Abstract: n/a
Keywords: A1 Journal Article; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ;
Impact Factor: 3.6
DOI: 10.1007/s11090-023-10431-x
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“Special issue: Plasma Conversion”. Nozaki T, Bogaerts A, Tu X, Sanden R, Plasma processes and polymers 14, 1790061 (2017). http://doi.org/10.1002/ppap.201790061
Keywords: Editorial; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.846
DOI: 10.1002/ppap.201790061
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“Splitting of CO2 by vibrational excitation in non-equilibrium plasmas : a reaction kinetics model”. Kozák T, Bogaerts A, Plasma sources science and technology 23, 045004 (2014). http://doi.org/10.1088/0963-0252/23/4/045004
Abstract: We present a zero-dimensional kinetic model of CO2 splitting in non-equilibrium plasmas. The model includes a description of the CO2 vibrational kinetics (25 vibrational levels up to the dissociation limit of the molecule), taking into account state-specific VT and VV relaxation reactions and the effect of vibrational excitation on other chemical reactions. The model is applied to study the reaction kinetics of CO2 splitting in an atmospheric-pressure dielectric barrier discharge (DBD) and in a moderate-pressure microwave discharge. The model results are in qualitative agreement with published experimental works. We show that the CO2 conversion and its energy efficiency are very different in these two types of discharges, which reflects the important dissociation mechanisms involved. In the microwave discharge, excitation of the vibrational levels promotes efficient dissociation when the specific energy input is higher than a critical value (2.0 eV/molecule under the conditions examined). The calculated energy efficiency of the process has a maximum of 23%. In the DBD, vibrationally excited levels do not contribute significantly to the dissociation of CO2 and the calculated energy efficiency of the process is much lower (5%).
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.302
Times cited: 170
DOI: 10.1088/0963-0252/23/4/045004
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“Sputter deposition of MgxAlyOz thin films in a dual-magnetron device : a multi-species Monte Carlo model”. Yusupov M, Saraiva M, Depla D, Bogaerts A, New journal of physics 14, 073043 (2012). http://doi.org/10.1088/1367-2630/14/7/073043
Abstract: A multi-species Monte Carlo (MC) model, combined with an analytical surface model, has been developed in order to investigate the general plasma processes occurring during the sputter deposition of complex oxide films in a dual-magnetron sputter deposition system. The important plasma species, such as electrons, Ar+ ions, fast Ar atoms and sputtered metal atoms (i.e. Mg and Al atoms) are described with the so-called multi-species MC model, whereas the deposition of MgxAlyOz films is treated by an analytical surface model. Targetsubstrate distances for both magnetrons in the dual-magnetron setup are varied for the purpose of growing stoichiometric complex oxide thin films. The metal atoms are sputtered from pure metallic targets, whereas the oxygen flux is only directed toward the substrate and is high enough to obtain fully oxidized thin films but low enough to avoid target poisoning. The calculations correspond to typical experimental conditions applied to grow these complex oxide films. In this paper, some calculation results are shown, such as the densities of various plasma species, their fluxes toward the targets and substrate, the deposition rates, as well as the film stoichiometry. Moreover, some results of the combined model are compared with experimental observations. Note that this is the first complete model, which can be applied for large and complicated magnetron reactor geometries, such as dual-magnetron configurations. With this model, we are able to describe all important plasma species as well as the deposition process. It can also be used to predict film stoichiometries of complex oxide films on the substrate.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.786
Times cited: 2
DOI: 10.1088/1367-2630/14/7/073043
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“Sputter-deposited Mg-Al-O thin films: linking molecular dynamics simulations to experiments”. Georgieva V, Saraiva M, Jehanathan N, Lebelev OI, Depla D, Bogaerts A, Journal of physics: D: applied physics 42, 065107 (2009). http://doi.org/10.1088/0022-3727/42/6/065107
Abstract: Using a molecular dynamics model the crystallinity of MgxAlyOz thin films with a variation in the stoichiometry of the thin film is studied at operating conditions similar to the experimental operating conditions of a dual magnetron sputter deposition system. The films are deposited on a crystalline or amorphous substrate. The Mg metal content in the film ranged from 100% (i.e. MgO film) to 0% (i.e. Al2O3 film). The radial distribution function and density of the films are calculated. The results are compared with x-ray diffraction and transmission electron microscopy analyses of experimentally deposited thin films by the dual magnetron reactive sputtering process. Both simulation and experimental results show that the structure of the MgAlO film varies from crystalline to amorphous when the Mg concentration decreases. It seems that the crystalline MgAlO films have a MgO structure with Al atoms in between.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.588
Times cited: 37
DOI: 10.1088/0022-3727/42/6/065107
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“Sputtering of Si(001) and SiC(001) by grazing ion bombardment”. Elmonov AA, Yusupov MS, Dzhurakhalov AA, Bogaerts A, , 209 (2008)
Abstract: The peculiarities of sputtering processes at 0.5-5 keV Ne grazing ion bombardment of Si(001) and SiC(001) surfaces and their possible application for the surface modification have been studied by computer simulation. Sputtering yields in the primary knock-on recoil atoms regime versus the initial energy of incident ions (E(0) = 0.5-5 keV) and angle of incidence (psi = 0-30 degrees) counted from a target surface have been calculated. Comparative studies of layer-by-layer sputtering for Si(001) and SiC(001) surfaces versus the initial energy of incident ions as well as an effective sputtering and sputtering threshold are discussed.
Keywords: P1 Proceeding; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
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“Stabilities of bimetallic nanoparticles for chirality-selective carbon nanotube growth and the effect of carbon interstitials”. Vets C, Neyts EC, The journal of physical chemistry: C : nanomaterials and interfaces 121, 15430 (2017). http://doi.org/10.1021/ACS.JPCC.7B02880
Abstract: Bimetallic nanoparticles play a crucial role in various applications. A better understanding of their properties would facilitate these applications and possibly even enable chirality-specific growth of carbon nanotubes (CNTs). We here examine the stabilities of NiFe, NiGa, and FeGa nanoparticles and the effect of carbon dissolved in NiFe nanoparticles through density functional theory (DFT) calculations and Born Oppenheimer molecular dynamics (BOMD) simulations. We establish that nanoparticles with more Fe in the core and more Ga on the surface are more stable and compare these results with well-known properties such as surface energy and atom size. Furthermore, we find that the nanoparticles become more stable with increasing carbon content, both at 0 K and at 700 K. These results provide a basis for further research into the chirality-specific growth of CNT's.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.536
Times cited: 2
DOI: 10.1021/ACS.JPCC.7B02880
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“Stability of Si epoxide defects in Si nanowires : a mixed reactive force field/DFT study”. Schoeters B, Neyts EC, Khalilov U, Pourtois G, Partoens B, Physical chemistry, chemical physics 15, 15091 (2013). http://doi.org/10.1039/c3cp51621k
Abstract: Modeling the oxidation process of silicon nanowires through reactive force field based molecular dynamics simulations suggests that the formation of Si epoxide defects occurs both at the Si/SiOx interface and at the nanowire surface, whereas for flat surfaces, this defect is experimentally observed to occur only at the interface as a result of stress. In this paper, we argue that the increasing curvature stabilizes the defect at the nanowire surface, as suggested by our density functional theory calculations. The latter can have important consequences for the opto-electronic properties of thin silicon nanowires, since the epoxide induces an electronic state within the band gap. Removing the epoxide defect by hydrogenation is expected to be possible but becomes increasingly difficult with a reduction of the diameter of the nanowires.
Keywords: A1 Journal article; Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.123
Times cited: 3
DOI: 10.1039/c3cp51621k
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“Static secondary ion mass spectrometry (S-SIMS): part 1: methodology and structural interpretation”. van Vaeck L, Adriaens A, Gijbels R, Mass spectrometry reviews 18, 1 (1999)
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 9.373
Times cited: 112
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“Statistical grouping and controlling factors of dissolved trace elements in a surface water system”. Vandelannoote R, Blommaert W, Van 't dack L, Gijbels R, van Grieken R, Environmental technology letters 4, 363 (1983). http://doi.org/10.1080/09593338309384219
Abstract: Sensitive multi‐element analytical techniques were applied to determine 24 dissolved trace components in 25 different water samples from a 10 km2 zone in Brittany, France. Correspondence factor and multiple regression analyses showed that the elements considered are influenced mainly by the presence of: Fe‐Mn oxide accumulations, a local poly‐metallic sulfide mineralization, and non‐mineralized host rocks, agricultural activity and abundant organic material in local swamps. Via these numerical techniques the location of the poly‐metallic ore body can be derived from the data set.
Keywords: A3 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
Times cited: 1
DOI: 10.1080/09593338309384219
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“Strain-induced semiconductor to metal transition in the two-dimensional honeycomb structure of MoS2”. Scalise E, Houssa M, Pourtois G, Afanas'ev V, Stesmans A, Nano Research 5, 43 (2012). http://doi.org/10.1007/s12274-011-0183-0
Abstract: The electronic properties of two-dimensional honeycomb structures of molybdenum disulfide (MoS(2)) subjected to biaxial strain have been investigated using first-principles calculations based on density functional theory. On applying compressive or tensile bi-axial strain on bi-layer and mono-layer MoS(2), the electronic properties are predicted to change from semiconducting to metallic. These changes present very interesting possibilities for engineering the electronic properties of two-dimensional structures of MoS(2).
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 7.354
Times cited: 407
DOI: 10.1007/s12274-011-0183-0
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“Streamer propagation in a packed bed plasma reactor for plasma catalysis applications”. Wang W, Kim H-H, Van Laer K, Bogaerts A, Chemical engineering journal 334, 2467 (2018). http://doi.org/10.1016/j.cej.2017.11.139
Abstract: A packed bed dielectric barrier discharge (DBD) is widely used for plasma catalysis applications, but the exact plasma characteristics in between the packing beads are far from understood. Therefore, we study here these plasma characteristics by means of fluid modelling and experimental observations using ICCD imaging, for packing materials with different dielectric constants. Our study reveals that a packed bed DBD reactor in dry air at atmospheric pressure may show three types of discharges, i.e. positive restrikes, filamentary microdischarges, which can also be localized between two packing beads, and surface discharges (so-called surface ionization
waves). Restrikes between the dielectric surfaces result in the formation of filamentary microdischarges, while surface charging creates electric field components parallel to the dielectric surfaces, leading to the formation of surface discharges. A transition in discharge mode occurs from surface discharges to local filamentary discharges between the packing beads when the dielectric constant of the packing rises from 5 to 1000. This may have implications for the efficiency of plasma catalytic gas treatment, because the catalyst activation may be limited by constraining the discharge to the contact points of the beads. The production of reactive species occurs most in the positive restrikes, the surface discharges and the local microdischarges in between the beads, and is less significant in the longer filamentary microdischarges. The faster streamer propagation and discharge development with higher dielectric constant of the packing beads leads to a faster production of reactive species. This study is of great interest for plasma catalysis, where packing beads with different dielectric constants are often used as supports for the catalytic materials. It allows us to better understand how different packing materials can influence the performance of packed bed plasma reactors for environmental applications.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 6.216
Times cited: 36
DOI: 10.1016/j.cej.2017.11.139
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“Structural analysis of silver halide cubic microcrystals with epitaxial or conversion growths by STEM-EDX”. Wu S, van Daele A, Jacob W, Gijbels R, Verbeeck A, de Keyzer R, Mikrochimica acta: supplementum 12, 261 (1992)
Keywords: A3 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
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“Structural and analytical characterization of Ag(Br,I) nanocrystals by cryo-AEM techniques”. Oleshko VP, van Daele A, Gijbels RH, Jacob WA, Journal of nanostructured materials 10, 1225 (1998). http://doi.org/10.1016/S0965-9773(99)00003-3
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Times cited: 5
DOI: 10.1016/S0965-9773(99)00003-3
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“Structural and analytical characterization of composite tabular silver halide microcrystals by cryo-EFTEM/EELS and cryo-STEM/EDX techniques”. Oleshko VP, Gijbels RH, Jacob WA, van Daele AJ Antwerp, page 317 (1998).
Keywords: H3 Book chapter; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
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“Structural and vibrational properties of amorphous GeO2 from first-principles”. Scalise E, Houssa M, Pourtois G, Afanas'ev VV, Stesmans A, Applied physics letters 98, 202110 (2011). http://doi.org/10.1063/1.3593036
Abstract: The structural and vibrational properties of amorphous germanium oxide (a-GeO<sub>2</sub>) are investigated using first-principles calculations based on density functional theory. We first generate an a-GeO<sub>2</sub> structure by first-principles molecular dynamics and analyze its structural properties. The vibrational spectra is then calculated within a density-functional approach. Both static and dynamic properties are in good agreement with experimental data. We next generate defects in our structure (oxygen vacancies with several density and charge states) and consider the most stable atomic configurations, focusing on the vibrational features of threefold coordinated O and divalent Ge centers.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 3.411
Times cited: 226
DOI: 10.1063/1.3593036
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“Structural characterization of organic molecules by laser mass spectrometry”. van Vaeck L, van Roy W, Gijbels R, Adams F Wiley, New York, page 177 (1993).
Keywords: H3 Book chapter; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
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“Structural characterization of SnS crystals formed by chemical vapour deposition”. Mehta AN, Zhang H, Dabral A, Richard O, Favia P, Bender H, Delabie A, Caymax M, Houssa M, Pourtois G, Vandervorst W, Journal of microscopy
T2 –, 20th International Conference on Microscopy of Semiconducting Materials, (MSM), APR 09-13, 2017, Univ Oxford, Univ Oxford, Oxford, ENGLAND 268, 276 (2017). http://doi.org/10.1111/JMI.12652
Abstract: <script type='text/javascript'>document.write(unpmarked('The crystal and defect structure of SnS crystals grown using chemical vapour deposition for application in electronic devices are investigated. The structural analysis shows the presence of two distinct crystal morphologies, that is thin flakes with lateral sizes up to 50 m and nanometer scale thickness, and much thicker but smaller crystallites. Both show similar Raman response associated with SnS. The structural analysis with transmission electron microscopy shows that the flakes are single crystals of -SnS with [010] normal to the substrate. Parallel with the surface of the flakes, lamellae with varying thickness of a new SnS phase are observed. High-resolution transmission electron microscopy (TEM), scanning transmission electron microscopy (STEM), first-principles simulations (DFT) and nanobeam diffraction (NBD) techniques are employed to characterise this phase in detail. DFT results suggest that the phase is a strain stabilised \u0027 one grown epitaxially on the -SnS crystals. TEM analysis shows that the crystallites are also -SnS with generally the [010] direction orthogonal to the substrate. Contrary to the flakes the crystallites consist of two to four grains which are tilted up to 15 degrees relative to the substrate. The various grain boundary structures and twin relations are discussed. Under high-dose electron irradiation, the SnS structure is reduced and -Sn formed. It is shown that this damage only occurs for SnS in direct contact with SiO2. Lay description SnS is a p-type semiconductor, which has attracted significant interest for electronic devices due to its unique properties, low-toxicity and abundance of Sn in nature. Although in the past it has been most extensively studied as the absorber material in solar cells, it has recently garnered interest for application as a p-type two-dimensional semiconductor in nanoelectronic devices due to its anisotropic layered structure similar to the better known phosphorene. Tin sulphide can take the form of several phases and the electronic properties of the material depend strongly on its crystal structure. It is therefore crucial to study the crystal structure of the material in order to predict the electronic properties and gain insight into the growth mechanism. In this work, SnS crystals deposited using a chemical vapour deposition technique are investigated extensively for their crystal and defect structure using transmission electron microscopy (TEM) and related techniques. We find the presence of two distinct crystal morphologies, that is thin flakes with lateral sizes up to 50 m and nm scale thickness, and much thicker but smaller crystallites. The flakes are single crystals of -SnS and contain lamellae with varying thickness of a different phase which appear to be -SnS at first glance. High-resolution scanning transmission electron microscopy is used to characterise these lamellae where the annular bright field (ABF) mode better reveals the position of the sulphur columns. The sulphur columns in the lamellae are found to be shifted relative to the -SnS structure which indicates the formation of a new phase which is a distorted version of the phase which we tentatively refer to as \u0027-SnS. Simulations based on density functional theory (DFT) are used to model the interface and a similar shift of sulphur columns in the -SnS layer is observed which takes place as a result of strong interaction at the interface between the two phases resulting in strain transfer. Nanobeam electron diffraction (NBD) is used to map the lattice mismatch in the thickness of the flakes which reveals good in-plane matching and some expansion out-of-plane in the lamellae. Contrary to the flakes the crystallites are made solely of -SnS and consist of two to four grains which are tilted up to 15 degrees relative to the substrate. The various grain boundary structures and twin relations are discussed. At high electron doses, SnS is reduced to -Sn, however the damage occurs only for SnS in direct contact with SiO2.'));
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 1.692
Times cited: 2
DOI: 10.1111/JMI.12652
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“Structural modification of NADPH oxidase activator (Noxa 1) by oxidative stress: An experimental and computational study”. Attri P, Park J-H, De Backer J, Kim M, Yun J-H, Heo Y, Dewilde S, Shiratani M, Choi EH, Lee W, Bogaerts A, International Journal Of Biological Macromolecules 163, 2405 (2020). http://doi.org/10.1016/j.ijbiomac.2020.09.120
Abstract: NADPH oxidases 1 (NOX1) derived reactive oxygen species (ROS) play an important role in the progression of cancer through signaling pathways. Therefore, in this paper, we demonstrate the effect of cold atmospheric plasma (CAP) on the structural changes of Noxa1 SH3 protein, one of the regulatory subunits of NOX1. For this purpose, firstly we purified the Noxa1 SH3 protein and analyzed the structure using X-ray crystallography, and subsequently, we treated the protein with two types of CAP reactors such as pulsed dielectric barrier discharge (DBD) and Soft Jet for different time intervals. The structural deformation of Noxa1 SH3 protein was analyzed by various experimental methods (circular dichroism, fluorescence, and NMR spectroscopy) and by MD simulations. Additionally, we demonstrate the effect of CAP (DBD and Soft Jet) on the viability and expression of NOX1 in A375 cancer cells. Our results are useful to understand the structural modification/oxidation occur in protein due to reactive oxygen and nitrogen (RONS) species generated by CAP.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 8.2
DOI: 10.1016/j.ijbiomac.2020.09.120
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“Structural modification of P-glycoprotein induced by OH radicals: Insights from atomistic simulations”. Khosravian N, Kamaraj B, Neyts EC, Bogaerts A, Scientific reports 6, 19466 (2016). http://doi.org/10.1038/srep19466
Abstract: This study reports on the possible effects of OH radical impact on the transmembrane domain 6 of P-glycoprotein, TM6, which plays a crucial role in drug binding in human cells. For the first time, we employ molecular dynamics (MD) simulations based on the self-consistent charge density functional tight binding (SCC-DFTB) method to elucidate the potential sites of fragmentation and mutation in this domain upon impact of OH radicals, and to obtain fundamental information about the underlying reaction mechanisms. Furthermore, we apply non-reactive MD simulations to investigate the long-term effect of this mutation, with possible implications for drug binding. Our simulations indicate that the interaction of OH radicals with TM6 might lead to the breaking of C-C and C-N peptide bonds, which eventually cause fragmentation of TM6. Moreover, according to our simulations, the OH radicals can yield mutation in the aromatic ring of phenylalanine in TM6, which in turn affects its structure. As TM6 plays an important role in the binding of a range of cytotoxic drugs with P-glycoprotein, any changes in its structure are likely to affect the response of the tumor cell in chemotherapy. This is crucial for cancer therapies based on reactive oxygen species, such as plasma treatment.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 4.259
Times cited: 7
DOI: 10.1038/srep19466
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“Structural modification of the skin barrier by OH radicals : a reactive molecular dynamics study for plasma medicine”. Van der Paal J, Verlackt CC, Yusupov M, Neyts EC, Bogaerts A, Journal of physics: D: applied physics 48, 155202 (2015). http://doi.org/10.1088/0022-3727/48/15/155202
Abstract: While plasma treatment of skin diseases and wound healing has been proven highly effective, the underlying mechanisms, and more generally the effect of plasma radicals on skin tissue, are not yet completely understood. In this paper, we perform ReaxFF-based reactive molecular dynamics simulations to investigate the interaction of plasma generated OH radicals with a model system composed of free fatty acids, ceramides, and cholesterol molecules. This model system is an approximation of the upper layer of the skin (stratum corneum). All interaction mechanisms observed in our simulations are initiated by H-abstraction from one of the ceramides. This reaction, in turn, often starts a cascade of other reactions, which eventually lead to the formation of aldehydes, the dissociation of ceramides or the elimination of formaldehyde, and thus eventually to the degradation of the skin barrier function.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.588
Times cited: 20
DOI: 10.1088/0022-3727/48/15/155202
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“Structure and function of p53-DNA complexes with inactivation and rescue mutations : a molecular dynamics simulation study”. Kamaraj B, Bogaerts A, PLoS ONE 10, e0134638 (2015). http://doi.org/10.1371/journal.pone.0134638
Abstract: The tumor suppressor protein p53 can lose its function upon DNA-contact mutations (R273C and R273H) in the core DNA-binding domain. The activity can be restored by second-site suppressor or rescue mutations (R273CT284R, R273HT284R, and R273HS240R). In this paper, we elucidate the structural and functional consequence of p53 proteins upon DNA-contact mutations and rescue mutations and the underlying mechanisms at the atomic level by means of molecular dynamics simulations. Furthermore, we also apply the docking approach to investigate the binding phenomena between the p53 protein and DNA upon DNA-contact mutations and rescue mutations. This study clearly illustrates that, due to DNA-contact mutants, the p53 structure loses its stability and becomes more rigid than the native protein. This structural loss might affect the p53-DNA interaction and leads to inhibition of the cancer suppression. Rescue mutants (R273CT284R, R273HT284R and R273HS240R) can restore the functional activity of the p53 protein upon DNA-contact mutations and show a good interaction between the p53 protein and a DNA molecule, which may lead to reactivate the cancer suppression function. Understanding the effects of p53 cancer and rescue mutations at the molecular level will be helpful for designing drugs for p53 associated cancer diseases. These drugs should be designed so that they can help to inhibit the abnormal function of the p53 protein and to reactivate the p53 function (cell apoptosis) to treat human cancer.
Keywords: A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.806
DOI: 10.1371/journal.pone.0134638
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Martin JML, Franç,ois JP, Gijbels R, Almlö,f J (1991) Structure and infrared spectroscopy of the C11 molecule. University of Minnesota, Minneapolis, Minn
Keywords: MA3 Book as author; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
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“Structure and infrared spectroscopy of the C11 molecule”. Martin JML, François JP, Gijbels R, Almlöf J, Chemical physics letters 187, 367 (1991). http://doi.org/10.1016/0009-2614(91)80267-2
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 1.897
Times cited: 42
DOI: 10.1016/0009-2614(91)80267-2
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“Structure of multispecies charged particles in a quadratic trap”. Liu YH, Chen ZY, Yu MY, Wang L, Bogaerts A, Physical review : E : statistical physics, plasmas, fluids, and related interdisciplinary topics 73, 047402 (2006). http://doi.org/10.1103/PhysRevE.73.047402
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.366
Times cited: 25
DOI: 10.1103/PhysRevE.73.047402
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“Structures and spectroscopic properties of sulfur-nitrogen-pnictogen chains : R2P-N=S=N-PR2 and R2P-N=S=N-AsR2”. Bal KM, Cautereels J, Blockhuys F, Journal of molecular structure 1132, 102 (2017). http://doi.org/10.1016/J.MOLSTRUC.2016.08.008
Abstract: The conformational and configurational preferences of Me2PNSNPMe2 (3) and Me2PNSNAsMe2 (4) have been identified using quantum chemical calculations at the DFT/B3LYP/6-311+G* level of theory. An approach in which energetic, structural (geometries and bond orders), electronic (analysis of the electron density) and spectroscopic properties are combined leads to the conclusion that these sulfur-nitrogen-pnictogen chains share many of the properties of their chalcogen-nitrogen analogues but that the through-space intramolecular interactions favouring the Z,Z configuration are even weaker than in these latter compounds. The results of this analysis also lead to an unambiguous assignment of the variable-temperature 31P and 15N NMR spectra of these compounds and their structures both in solution and in the solid state.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 1.753
DOI: 10.1016/J.MOLSTRUC.2016.08.008
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