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| Author | Van der Paal, J.; Neyts, E.C.; Verlackt, C.C.W.; Bogaerts, A. | ||||
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Effect of lipid peroxidation on membrane permeability of cancer and normal cells subjected to oxidative stress | Type | A1 Journal article | ||
| Year | 2016 | Publication | Chemical science | Abbreviated Journal | Chem Sci |
| Volume | 7 | Issue | 7 | Pages | 489-498 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | We performed molecular dynamics simulations to investigate the effect of lipid peroxidation products on the structural and dynamic properties of the cell membrane. Our simulations predict that the lipid order in a phospholipid bilayer, as a model system for the cell membrane, decreases upon addition of lipid peroxidation products. Eventually, when all phospholipids are oxidized, pore formation can occur. This will allow reactive species, such as reactive oxygen and nitrogen species (RONS), to enter the cell and cause oxidative damage to intracellular macromolecules, such as DNA or proteins. On the other hand, upon increasing the cholesterol fraction of lipid bilayers, the cell membrane order increases, eventually reaching a certain threshold, from which cholesterol is able to protect the membrane against pore formation. This finding is crucial for cancer treatment by plasma technology, producing a large number of RONS, as well as for other cancer treatment methods that cause an increase in the concentration of extracellular RONS. Indeed, cancer cells contain less cholesterol than their healthy counterparts. Thus, they will be more vulnerable to the consequences of lipid peroxidation, eventually enabling the penetration of RONS into the interior of the cell, giving rise to oxidative stress, inducing pro-apoptotic factors. This provides, for the first time, molecular level insight why plasma can selectively treat cancer cells, while leaving their healthy counterparts undamaged, as is indeed experimentally demonstrated. | ||||
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| Language | Wos | 000366826900058 | Publication Date | 2015-10-16 | |
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| Series Volume | Series Issue | Edition | |||
| ISSN | 2041-6520 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 8.668 | Times cited | 106 | Open Access | |
| Notes | The authors acknowledge nancial support from the Fund for Scientic Research (FWO) Flanders, grant number G012413N. The calculations were performed in part using the Turing HPC infrastructure of the CalcUA core facility of the Universiteit Antwerpen, a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the Universiteit Antwerpen. | Approved | Most recent IF: 8.668 | ||
| Call Number | c:irua:131058 | Serial | 3986 | ||
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| Author | Kovács, A.; Yusupov, M.; Cornet, I.; Billen, P.; Neyts, E.C. | ||||
| Title |
Effect of natural deep eutectic solvents of non-eutectic compositions on enzyme stability | Type | A1 Journal article | ||
| Year | 2022 | Publication | Journal Of Molecular Liquids | Abbreviated Journal | J Mol Liq |
| Volume | 366 | Issue | Pages | 120180-17 | |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Biochemical Wastewater Valorization & Engineering (BioWaVE); Intelligence in PRocesses, Advanced Catalysts and Solvents (iPRACS) | ||||
| Abstract | Natural deep eutectic solvents (NADES) represent a green alternative to common organic solvents in the biochemical industry due to their benign behavior and tailorable properties, in particular as media for enzymatic reactions. However, to fully exploit their potential in enzymatic reactions, there is a need for a more fundamental understanding of how these neoteric solvents influence the course of these reac-tions. Thus, the aim of this study is to investigate the influence of NADES with various molar composi-tions on the stability and structure of enzymes, applying molecular dynamics simulations. This can help to better understand the effect of individual compounds of NADES, in addition to eutectic mixtures. More specifically, we simulate the behavior of Candida antarctica lipase B (CALB) enzyme in NADES com-posed of choline chloride with either urea, ethylene glycol or glycerol. Hereto, we monitor the NADES microstructure, the general stability of the enzyme and changes in the structure of its active sites and sur-face residues. Our simulations show that none of the studied NADES systems significantly disrupt the microstructure of the solvent or the stability of the CALB enzyme within the time scales of the simula-tions. The enzyme preserves its initial structure, size and intra-chain hydrogen bonds in all investigated compositions and, for the first time reported, also in NADES with increased hydrogen bond donating com-pound ratios. As the main novelty, our results indicate that, in addition to the composition, the molar ratio can be an additional variable to fine-tune the physicochemical properties of NADES without altering the enzyme characteristics. These findings could facilitate the development and application of task -tailored NADES media for biocatalytic processes. (c) 2022 Elsevier B.V. All rights reserved. | ||||
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| Language | Wos | 000865431800010 | Publication Date | 2022-08-25 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 0167-7322 | ISBN | Additional Links | UA library record; WoS full record | |
| Impact Factor | 6 | Times cited | Open Access | Not_Open_Access | |
| Notes | Approved | Most recent IF: 6 | |||
| Call Number | UA @ admin @ c:irua:191538 | Serial | 7265 | ||
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| Author | Bal, K.M.; Huygh, S.; Bogaerts, A.; Neyts, E.C. | ||||
| Title |
Effect of plasma-induced surface charging on catalytic processes: application to CO2activation | Type | A1 Journal article | ||
| Year | 2018 | Publication | Plasma sources science and technology | Abbreviated Journal | Plasma Sources Sci T |
| Volume | 27 | Issue | 2 | Pages | 024001 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Understanding the nature and effect of the multitude of plasma–surface interactions in plasma catalysis is a crucial requirement for further process development and improvement. A particularly intriguing and rather unique property of a plasma-catalytic setup is the ability of the plasma to modify the electronic structure, and hence chemical properties, of the catalyst through charging, i.e. the absorption of excess electrons. In this work, we develop a quantum chemical model based on density functional theory to study excess negative surface charges in a heterogeneous catalyst exposed to a plasma. This method is specifically applied to investigate plasma-catalytic CO2 activation on supported M/Al2O3 (M=Ti, Ni, Cu) single atom catalysts. We find that (1) the presence of a negative surface charge dramatically improves the reductive power of the catalyst, strongly promoting the splitting of CO2 to CO and oxygen, and (2) the relative activity of the investigated transition metals is also changed upon charging, suggesting that controlled surface charging is a powerful additional parameter to tune catalyst activity and selectivity. These results strongly point to plasma-induced surface charging of the catalyst as an important factor contributing to the plasma-catalyst synergistic effects frequently reported for plasma catalysis. | ||||
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| Language | Wos | 000424520100001 | Publication Date | 2018-02-07 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1361-6595 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 3.302 | Times cited | 19 | Open Access | OpenAccess |
| Notes | KMB is funded as PhD fellow (aspirant) of the FWO-Flanders (Research Foundation—Flanders), Grant 11V8915N. The computational resources and services used in this work were provided by the VSC (Flemish Supercomputer Center), funded by the FWO and the Flemish Government— department EWI. | Approved | Most recent IF: 3.302 | ||
| Call Number | PLASMANT @ plasmant @c:irua:149285 | Serial | 4813 | ||
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| Author | Grubova, I.Y.; Surmeneva, M.A.; Surmenev, R.A.; Neyts, E.C. | ||||
| Title |
Effect of van der Waals interactions on the adhesion strength at the interface of the hydroxyapatite-titanium biocomposite : a first-principles study | Type | A1 Journal article | ||
| Year | 2020 | Publication | RSC advances | Abbreviated Journal | |
| Volume | 10 | Issue | 62 | Pages | 37800-37805 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Hydroxyapatite (HAP) is frequently used as biocompatible coating on Ti-based implants. In this context, the HAP-Ti adhesion is of crucial importance. Here, we report ab initio calculations to investigate the influence of Si incorporation into the amorphous calcium-phosphate (a-HAP) structure on the interfacial bonding mechanism between the a-HAP coating and an amorphous titanium dioxide (a-TiO2) substrate, contrasting two different density functionals: PBE-GGA, and DFT-D3, which are capable of describing the influence of the van der Waals (vdW) interactions. In particular, we discuss the effect of dispersion on the work of adhesion (W-ad), equilibrium geometries, and charge density difference (CDD). We find that replacement of P by Si in a-HAP (a-Si-HAP) with the creation of OH vacancies as charge compensation results in a significant increase in the bond strength between the coating and substrate in the case of using the PBE-GGA functional. However, including the vdW interactions shows that these forces considerably contribute to the W-ad. We show that the difference (W-ad – W-ad(vdW)) is on average more than 1.1 J m(-2) and 0.5 J m(-2) for a-HAP/a-TiO2 and a-Si-HAP/a-TiO2, respectively. These results reveal that including vdW interactions is essential for accurately describing the chemical bonding at the a-HAP/a-TiO2 interface. | ||||
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| Language | Wos | 000583523300025 | Publication Date | 2020-10-14 | |
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| ISSN | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | ||
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| Notes | ; The authors gratefully acknowledge financial support from the Russian president's grant MK-330.2020.8 and BOF Fellowships for International Joint PhD students funded by University of Antwerp (UAntwerp, project number 32545). The work was carried out at Tomsk Polytechnic University within the framework of Tomsk Polytechnic University Competitiveness Enhancement Program grant and in part using the Turing HPC infrastructure of the CalcUA core facility of the UAntwerp, a division of the Flemish Supercomputer Centre (VSC), funded by the Hercules Foundation, the Flemish Government (department EWI) and the UAntwerp, Belgium. ; | Approved | Most recent IF: NA | ||
| Call Number | UA @ admin @ c:irua:173603 | Serial | 6499 | ||
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| Author | Grubova, I.Y.; Surmeneva, M.A.; Huygh, S.; Surmenev, R.A.; Neyts, E.C. | ||||
| Title |
Effects of silicon doping on strengthening adhesion at the interface of the hydroxyapatite-titanium biocomposite : a first-principles study | Type | A1 Journal article | ||
| Year | 2019 | Publication | Computational materials science | Abbreviated Journal | Comp Mater Sci |
| Volume | 159 | Issue | 159 | Pages | 228-234 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | In this paper we employ first-principles calculations to investigate the effect of substitutional Si doping in the amorphous calcium-phosphate (a-HAP) structure on the work of adhesion, integral charge transfer, charge density difference and theoretical tensile strengths between an a-HAP coating and amorphous titanium dioxide (a-TiO2) substrate systemically. Our calculations demonstrate that substitution of a P atom by a Si atom in a-HAP (a-Si-HAP) with the creation of OH-vacancies as charge compensation results in a significant increase of the bonding strength of the coating to the substrate. The work of adhesion of the optimized Si-doped interfaces reaches a value of up to -2.52 J m(-2), which is significantly higher than for the stoichiometric a-HAP/a-TiO2. Charge density difference analysis indicates that the dominant interactions at the interface have significant covalent character, and in particular two Ti-O and three Ca-O bonds are formed for a-Si-HAP/a-TiO2 and one Ti-O and three Ca-O bonds for a-HAP/a-TiO2. From the stress-strain curve, the Young's modulus of a-Si-HAP/a-TiO2 is calculated to be about 25% higher than that of the a-HAP/a-TiO2, and the yielding stress is about 2 times greater than that of the undoped model. Our calculations therefore demonstrate that the presence of Si in the a-HAP structure strongly alters not only the bioactivity and resorption rates, but also the mechanical properties of the a-HAP/a-TiO2 interface. The results presented here provide an important theoretical insight into the nature of the chemical bonding at the a-HAP/a-TiO2 interface, and are particularly significant for the practical medical applications of HAP-based biomaterials. | ||||
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| Language | Wos | 000457856900023 | Publication Date | 2018-12-18 | |
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| Series Volume | Series Issue | Edition | |||
| ISSN | 0927-0256 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 2.292 | Times cited | 1 | Open Access | Not_Open_Access |
| Notes | Approved | Most recent IF: 2.292 | |||
| Call Number | UA @ admin @ c:irua:157480 | Serial | 5272 | ||
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| Author | Xie, L.; Brault, P.; Coutanceau, C.; Bauchire, J.-M.; Caillard, A.; Baranton, S.; Berndt, J.; Neyts, E.C. | ||||
| Title |
Efficient amorphous platinum catalyst cluster growth on porous carbon : a combined molecular dynamics and experimental study | Type | A1 Journal article | ||
| Year | 2015 | Publication | Applied catalysis : B : environmental | Abbreviated Journal | Appl Catal B-Environ |
| Volume | 162 | Issue | 162 | Pages | 21-26 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Amorphous platinum clusters supported on porous carbon have been envisaged for high-performance fuel cell electrodes. For this application, it is crucial to control the morphology of the Pt layer and the Ptsubstrate interaction to maximize activity and stability. We thus investigate the morphology evolution during Pt cluster growth on a porous carbon substrate employing atomic scale molecular dynamics simulations. The simulations are based on the Pt-C interaction potential using parameters derived from density functional theory and are found to yield a Pt cluster morphology similar to that observed in low loaded fuel cell electrodes prepared by plasma sputtering. Moreover, the simulations show amorphous Pt cluster growth in agreement with X-ray diffraction and transmission electron microscopy experiments on high performance low Pt content (10 μgPt cm−2) loaded fuel cell electrodes and provide a fundamental insight in the cluster growth mechanism. | ||||
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| Publisher | Place of Publication | Amsterdam | Editor | ||
| Language | Wos | 000343686900003 | Publication Date | 2014-06-26 | |
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| Series Volume | Series Issue | Edition | |||
| ISSN | 0926-3373; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 9.446 | Times cited | 20 | Open Access | |
| Notes | Approved | Most recent IF: 9.446; 2015 IF: 7.435 | |||
| Call Number | c:irua:117949 | Serial | 874 | ||
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| Author | Tinck, S.; Tillocher, T.; Dussart, R.; Neyts, E.C.; Bogaerts, A. | ||||
| Title |
Elucidating the effects of gas flow rate on an SF6inductively coupled plasma and on the silicon etch rate, by a combined experimental and theoretical investigation | Type | A1 Journal article | ||
| Year | 2016 | Publication | Journal of physics: D: applied physics | Abbreviated Journal | J Phys D Appl Phys |
| Volume | 49 | Issue | 49 | Pages | 385201 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Experiments show that the etch rate of Si with SF6 inductively coupled plasma (ICP) is significantly influenced by the absolute gas flow rate in the range of 50–600 sccm, with a maximum at around 200 sccm. Therefore, we numerically investigate the effects of the gas flow rate on the bulk plasma properties and on the etch rate, to obtain more insight in the underlying reasons of this effect. A hybrid Monte Carlo—fluid model is applied to simulate an SF6 ICP. It is found that the etch rate is influenced by two simultaneous effects: (i) the residence time of the gas and (ii) the temperature profile of the plasma in the ICP volume, resulting indeed in a maximum etch rate at 200 sccm. | ||||
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| Language | Wos | 000384095900011 | Publication Date | 2016-08-24 | |
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| ISSN | 0022-3727 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 2.588 | Times cited | 1 | Open Access | |
| Notes | We are very grateful to Mark Kushner for providing the computational model. The Fund for Scientific Research Flanders (FWO; grant no. 0880.212.840) is acknowledged for financial support of this work. The work was carried out in part using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen, a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the University of Antwerp. | Approved | Most recent IF: 2.588 | ||
| Call Number | c:irua:134867 | Serial | 4108 | ||
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| Author | Chernozem, R., V; Romanyuk, K.N.; Grubova, I.; Chernozem, P., V.; Surmeneva, M.A.; Mukhortova, Y.R.; Wilhelm, M.; Ludwig, T.; Mathur, S.; Kholkin, A.L.; Neyts, E.; Parakhonskiy, B.; Skirtach, A.G.; Surmenev, R.A. | ||||
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Enhanced piezoresponse and surface electric potential of hybrid biodegradable polyhydroxybutyrate scaffolds functionalized with reduced graphene oxide for tissue engineering | Type | A1 Journal article | ||
| Year | 2021 | Publication | Nano Energy | Abbreviated Journal | Nano Energy |
| Volume | 89 | Issue | B | Pages | 106473 |
| Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Piezoelectricity is considered to be one of the key functionalities in biomaterials to boost bone tissue regeneration, however, integrating biocompatibility, biodegradability and 3D structure with pronounced piezoresponse remains a material challenge. Herein, novel hybrid biocompatible 3D scaffolds based on biodegradable poly(3-hydroxybutyrate) (PHB) and reduced graphene oxide (rGO) flakes have been developed. Nanoscale insights revealed a more homogenous distribution and superior surface potential values of PHB fibers (33 +/- 29 mV) with increasing rGO content up to 1.0 wt% (314 +/- 31 mV). The maximum effective piezoresponse was detected at 0.7 wt% rGO content, demonstrating 2.5 and 1.7 times higher out-of-plane and in-plane values, respectively, than that for pure PHB fibers. The rGO addition led to enhanced zigzag chain formation between paired lamellae in PHB fibers. In contrast, a further increase in rGO content reduced the alpha-crystal size and prevented zigzag chain conformation. A corresponding model explaining structural and molecular changes caused by rGO addition in electrospun PHB fibers is proposed. In addition, finite element analysis revealed a negligible vertical piezoresponse compared to lateral piezoresponse in uniaxially oriented PHB fibers based on alpha-phase (P2(1)2(1)2(1) space group). Thus, the present study demonstrates promising results for the development of biodegradable hybrid 3D scaffolds with an enhanced piezoresponse for various tissue engineering applications. | ||||
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| Language | Wos | 000703592700002 | Publication Date | 2021-08-31 | |
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| Series Volume | Series Issue | Edition | |||
| ISSN | 2211-2855 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 12.343 | Times cited | Open Access | Not_Open_Access | |
| Notes | Approved | Most recent IF: 12.343 | |||
| Call Number | UA @ admin @ c:irua:182579 | Serial | 7914 | ||
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| Author | Zhang, Y.-R.; Neyts, E.C.; Bogaerts, A. | ||||
| Title |
Enhancement of plasma generation in catalyst pores with different shapes | Type | A1 Journal article | ||
| Year | 2018 | Publication | Plasma sources science and technology | Abbreviated Journal | Plasma Sources Sci T |
| Volume | 27 | Issue | 5 | Pages | 055008 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Plasma generation inside catalyst pores is of utmost importance for plasma catalysis, as the existence of plasma species inside the pores affects the active surface area of the catalyst available to the plasma species for catalytic reactions. In this paper, the electric field enhancement, and thus the plasma production inside catalyst pores with different pore shapes is studied with a two-dimensional fluid model. The results indicate that the electric field will be significantly enhanced near tip-like structures. In a conical pore with small opening, the strongest electric field appears at the opening and bottom corners of the pore, giving rise to a prominent ionization rate throughout the pore. For a cylindrical pore, the electric field is only enhanced at the bottom corners of the pore, with lower absolute value, and thus the ionization rate inside the pore is only slightly enhanced. Finally, in a conical pore with large opening, the electric field is characterized by a maximum at the bottom of the pore, yielding a similar behavior for the ionization rate. These results demonstrate that the shape of the pore has a significantly influence on the electric field enhancement, and thus modifies the plasma properties. | ||||
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| Language | Wos | 000432351700002 | Publication Date | 2018-05-15 | |
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| Series Volume | Series Issue | Edition | |||
| ISSN | 1361-6595 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 3.302 | Times cited | 11 | Open Access | OpenAccess |
| Notes | This work was supported by the Fund for Scientific Research Flanders (FWO) (Grant No. G.0217.14N) and the Fundamental Research Funds for the Central Universities (Grant No. DUT17LK52). | Approved | Most recent IF: 3.302 | ||
| Call Number | PLASMANT @ plasmant @c:irua:151546 | Serial | 4998 | ||
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| Author | Bal, K.M.; Bogaerts, A.; Neyts, E.C. | ||||
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Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium | Type | A1 Journal article | ||
| Year | 2020 | Publication | Journal Of Physical Chemistry Letters | Abbreviated Journal | J Phys Chem Lett |
| Volume | 11 | Issue | 2 | Pages | 401-406 |
| Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| 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. | ||||
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| Language | Wos | 000508473400008 | Publication Date | 2020-01-16 | |
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| ISSN | 1948-7185 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 5.7 | Times cited | Open Access | ||
| Notes | Universiteit Antwerpen; Fonds Wetenschappelijk Onderzoek, 12ZI420N ; Departement Economie, Wetenschap en Innovatie van de Vlaamse Overheid; K.M.B. was funded as a junior postdoctoral fellow of the FWO (Research Foundation − Flanders), Grant 12ZI420N, and through a TOP-BOF research project of the University of Antwerp. The computational resources and services used in this work were provided by the VSC (Flemish Supercomputer Center), funded by the FWO and the Flemish Government− department EWI. | Approved | Most recent IF: 5.7; 2020 IF: 9.353 | ||
| Call Number | PLASMANT @ plasmant @c:irua:165587 | Serial | 5442 | ||
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| Author | Fukuhara, S.; Bal, K.M.; Neyts, E.C.; Shibuta, Y. | ||||
| Title |
Entropic and enthalpic factors determining the thermodynamics and kinetics of carbon segregation from transition metal nanoparticles | Type | A1 Journal article | ||
| Year | 2021 | Publication | Carbon | Abbreviated Journal | Carbon |
| Volume | 171 | Issue | Pages | 806-813 | |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | The free energy surface (FES) for carbon segregation from nickel nanoparticles is obtained from advanced molecular dynamics simulations. A suitable reaction coordinate is developed that can distinguish dissolved carbon atoms from segregated dimers, chains and junctions on the nanoparticle surface. Because of the typically long segregation time scale (up to ms), metadynamics simulations along the developed reaction coordinate are used to construct FES over a wide range of temperatures and carbon concentrations. The FES revealed the relative stability of different stages in the segregation process, and free energy barriers and rates of the individual steps could then be calculated and decomposed into enthalpic and entropic contributions. As the carbon concentration in the nickel nanoparticle increases, segregated carbon becomes more stable in terms of both enthalpy and entropy. The activation free energy of the reaction also decreases with the increase of carbon concentration, which can be mainly attributed to entropic effects. These insights and the methodology developed to obtain them improve our understanding of carbon segregation process across materials science in general, and the nucleation and growth of carbon nanotube in particular. | ||||
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| Language | Wos | 000598371500084 | Publication Date | 2020-09-25 | |
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| ISSN | 0008-6223 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 6.337 | Times cited | Open Access | OpenAccess | |
| Notes | Scientific Research, 19H02415 ; JSPS, 18J22727 ; Japan Society for the Promotion of Science; JSPS; JSPS; FWO; Research Foundation; Flanders, 12ZI420N ; This work was supported by Grant-in-Aid for Scientific Research (B) (No.19H02415) and Grant-in-Aid for JSPS Research Fellow (No.18J22727) from Japan Society for the Promotion of Science (JSPS), Japan. S.F. was supported by JSPS through the Program for 812 | Approved | Most recent IF: 6.337 | ||
| Call Number | PLASMANT @ plasmant @c:irua:172452 | Serial | 6421 | ||
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| Author | Neyts, E.C.; Thijsse, B.J.; Mees, M.J.; Bal, K.M.; Pourtois, G. | ||||
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Establishing uniform acceptance in force biased Monte Carlo simulations | Type | A1 Journal article | ||
| Year | 2012 | Publication | Journal of chemical theory and computation | Abbreviated Journal | J Chem Theory Comput |
| Volume | 8 | Issue | 6 | Pages | 1865-1869 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Uniform acceptance force biased Monte Carlo (UFMC) simulations have previously been shown to be a powerful tool to simulate atomic scale processes, enabling one to follow the dynamical path during the simulation. In this contribution, we present a simple proof to demonstrate that this uniform acceptance still complies with the condition of detailed balance, on the condition that the characteristic parameter lambda = 1/2 and that the maximum allowed step size is chosen to be sufficiently small. Furthermore, the relation to Metropolis Monte Carlo (MMC) is also established, and it is shown that UFMC reduces to MMC by choosing the characteristic parameter lambda = 0 [Rao, M. et al. Mol. Phys. 1979, 37, 1773]. Finally, a simple example compares the UFMC and MMC methods. | ||||
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| Language | Wos | 000305092400002 | Publication Date | 2012-05-16 | |
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| ISSN | 1549-9618;1549-9626; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 5.245 | Times cited | 20 | Open Access | |
| Notes | Approved | Most recent IF: 5.245; 2012 IF: 5.389 | |||
| Call Number | UA @ lucian @ c:irua:99090 | Serial | 1082 | ||
| Permanent link to this record | |||||
| Author | Bal, K.M.; Neyts, E.C. | ||||
| Title |
Extending and validating bubble nucleation rate predictions in a Lennard-Jones fluid with enhanced sampling methods and transition state theory | Type | A1 Journal article | ||
| Year | 2022 | Publication | Journal Of Chemical Physics | Abbreviated Journal | J Chem Phys |
| Volume | 157 | Issue | 18 | Pages | 184113-10 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | We calculate bubble nucleation rates in a Lennard-Jones fluid through explicit molecular dynamics simulations. Our approach-based on a recent free energy method (dubbed reweighted Jarzynski sampling), transition state theory, and a simple recrossing correction-allows us to probe a fairly wide range of rates in several superheated and cavitation regimes in a consistent manner. Rate predictions from this approach bridge disparate independent literature studies on the same model system. As such, we find that rate predictions based on classical nucleation theory, direct brute force molecular dynamics simulations, and seeding are consistent with our approach and one another. Published rates derived from forward flux sampling simulations are, however, found to be outliers. This study serves two purposes: First, we validate the reliability of common modeling techniques and extrapolation approaches on a paradigmatic problem in materials science and chemical physics. Second, we further test our highly generic recipe for rate calculations, and establish its applicability to nucleation processes. | ||||
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| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000885260600002 | Publication Date | 2022-11-14 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 0021-9606 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 4.4 | Times cited | Open Access | OpenAccess | |
| Notes | Approved | Most recent IF: 4.4 | |||
| Call Number | UA @ admin @ c:irua:192076 | Serial | 7266 | ||
| Permanent link to this record | |||||
| Author | Tinck, S.; Neyts, E.C.; Bogaerts, A. | ||||
| Title |
Fluorinesilicon surface reactions during cryogenic and near room temperature etching | Type | A1 Journal article | ||
| Year | 2014 | Publication | The journal of physical chemistry: C : nanomaterials and interfaces | Abbreviated Journal | J Phys Chem C |
| Volume | 118 | Issue | 51 | Pages | 30315-30324 |
| Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Cyrogenic etching of silicon is envisaged to enable better control over plasma processing in the microelectronics industry, albeit little is known about the fundamental differences compared to the room temperature process. We here present molecular dynamics simulations carried out to obtain sticking probabilities, thermal desorption rates, surface diffusion speeds, and sputter yields of F, F2, Si, SiF, SiF2, SiF3, SiF4, and the corresponding ions on Si(100) and on SiF13 surfaces, both at cryogenic and near room temperature. The different surface behavior during conventional etching and cryoetching is discussed. F2 is found to be relatively reactive compared to other species like SiF03. Thermal desorption occurs at a significantly lower rate under cryogenic conditions, which results in an accumulation of physisorbed species. Moreover, ion incorporation is often observed for ions with energies of 30400 eV, which results in a relatively low net sputter yield. The obtained results suggest that the actual etching of Si, under both cryogenic and near room temperature conditions, is based on the complete conversion of the Si surface to physisorbed SiF4, followed by subsequent sputtering of these molecules, instead of direct sputtering of the SiF03 surface. | ||||
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| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Washington, D.C. | Editor | ||
| Language | Wos | 000347360200101 | Publication Date | 2014-11-25 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1932-7447;1932-7455; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 4.536 | Times cited | 11 | Open Access | |
| Notes | Approved | Most recent IF: 4.536; 2014 IF: 4.772 | |||
| Call Number | UA @ lucian @ c:irua:122957 | Serial | 1239 | ||
| Permanent link to this record | |||||
| Author | Neyts, E.C.; Bogaerts, A. | ||||
| Title |
Formation of endohedral Ni@C60 and exohedral NiC60 metallofullerene complexes by simulated ion implantation | Type | A1 Journal article | ||
| Year | 2009 | Publication | Carbon | Abbreviated Journal | Carbon |
| Volume | 47 | Issue | 4 | Pages | 1028-1033 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | The interaction of thermal and hyperthermal Ni ions with gas-phase C60 fullerene was investigated at two temperatures with classical molecular dynamics simulations using a recently developed interatomic many-body potential. The interaction between Ni and C60 is characterized in terms of the NiC60 binding sites, complex formation, and the collision and temperature induced deformation of the C60 cage structure. The simulations show how ion implantation theoretically allows the synthesis of both endohedral Ni@C60 and exohedral NiC60 metallofullerene complexes. | ||||
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| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Oxford | Editor | ||
| Language | Wos | 000264252900012 | Publication Date | 2008-12-25 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 0008-6223; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 6.337 | Times cited | 15 | Open Access | |
| Notes | Approved | Most recent IF: 6.337; 2009 IF: 4.504 | |||
| Call Number | UA @ lucian @ c:irua:76434 | Serial | 1260 | ||
| Permanent link to this record | |||||
| Author | Neyts, E.C.; van Duin, A.C.T.; Bogaerts, A. | ||||
| Title |
Formation of single layer graphene on nickel under far-from-equilibrium high flux conditions | Type | A1 Journal article | ||
| Year | 2013 | Publication | Nanoscale | Abbreviated Journal | Nanoscale |
| Volume | 5 | Issue | 16 | Pages | 7250-7255 |
| Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | We investigate the theoretical possibility of single layer graphene formation on a nickel surface at different substrate temperatures under far-from-equilibrium high precursor flux conditions, employing state-of-the-art hybrid reactive molecular dynamics/uniform acceptance force bias Monte Carlo simulations. It is predicted that under these conditions, the formation of a single layer graphene-like film may proceed through a combined depositionsegregation mechanism on a nickel substrate, rather than by pure surface segregation as is typically observed for metals with high carbon solubility. At 900 K and above, nearly continuous graphene layers are obtained. These simulations suggest that single layer graphene deposition is theoretically possible on Ni under high flux conditions. | ||||
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| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Cambridge | Editor | ||
| Language | Wos | 000322315600019 | Publication Date | 2013-04-26 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 2040-3364;2040-3372; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 7.367 | Times cited | 25 | Open Access | |
| Notes | Approved | Most recent IF: 7.367; 2013 IF: 6.739 | |||
| Call Number | UA @ lucian @ c:irua:109249 | Serial | 1264 | ||
| Permanent link to this record | |||||
| Author | Bogaerts, A.; Neyts, E.C.; Guaitella, O.; Murphy, A.B. | ||||
| Title |
Foundations of plasma catalysis for environmental applications | Type | A1 Journal article | ||
| Year | 2022 | Publication | Plasma Sources Science & Technology | Abbreviated Journal | Plasma Sources Sci T |
| Volume | Issue | Pages | |||
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Plasma catalysis is gaining increasing interest for various applications, but the underlying mechanisms are still far from understood. Hence, more fundamental research is needed to understand these mechanisms. This can be obtained by both modelling and experiments. This foundations paper describes the fundamental insights in plasma catalysis, as well as efforts to gain more insights by modelling and experiments. Furthermore, it discusses the state-of-the-art of the major plasma catalysis applications, as well as successes and challenges of technology transfer of these applications. | ||||
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| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000804396200001 | Publication Date | 2022-03-21 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 0963-0252 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 3.8 | Times cited | Open Access | OpenAccess | |
| Notes | H2020 Marie Skłodowska-Curie Actions, 823745 ; H2020 European Research Council, 810182 ; We acknowldege financial support from the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation programme (Grant Agreement No. 810182 – SCOPE ERC Synergy project) and the European Union’s Horizon 2020 Research and Innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 813393 (PIONEER). | Approved | Most recent IF: 3.8 | ||
| Call Number | PLASMANT @ plasmant @c:irua:188539 | Serial | 7070 | ||
| Permanent link to this record | |||||
| Author | Bal, K.M.; Fukuhara, S.; Shibuta, Y.; Neyts, E.C. | ||||
| Title |
Free energy barriers from biased molecular dynamics simulations | Type | A1 Journal article | ||
| Year | 2020 | Publication | Journal Of Chemical Physics | Abbreviated Journal | J Chem Phys |
| Volume | 153 | Issue | 11 | Pages | 114118 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Atomistic simulation methods for the quantification of free energies are in wide use. These methods operate by sampling the probability density of a system along a small set of suitable collective variables (CVs), which is, in turn, expressed in the form of a free energy surface (FES). This definition of the FES can capture the relative stability of metastable states but not that of the transition state because the barrier height is not invariant to the choice of CVs. Free energy barriers therefore cannot be consistently computed from the FES. Here, we present a simple approach to calculate the gauge correction necessary to eliminate this inconsistency. Using our procedure, the standard FES as well as its gauge-corrected counterpart can be obtained by reweighing the same simulated trajectory at little additional cost. We apply the method to a number of systems—a particle solvated in a Lennard-Jones fluid, a Diels–Alder reaction, and crystallization of liquid sodium—to demonstrate its ability to produce consistent free energy barriers that correctly capture the kinetics of chemical or physical transformations, and discuss the additional demands it puts on the chosen CVs. Because the FES can be converged at relatively short (sub-ns) time scales, a free energy-based description of reaction kinetics is a particularly attractive option to study chemical processes at more expensive quantum mechanical levels of theory. | ||||
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| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000574665600004 | Publication Date | 2020-09-21 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 0021-9606 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 4.4 | Times cited | Open Access | ||
| Notes | Japan Society for the Promotion of Science, 19H02415 18J22727 ; Fonds Wetenschappelijk Onderzoek, 12ZI420N ; This work was supported, in part, by a Grant-in-Aid for Scientific Research (B) (Grant No. 19H02415) and Grant-in-Aid for a JSPS Research Fellow (Grant No. 18J22727) from the Japan Society for the Promotion of Science (JSPS), Japan. K.M.B. was funded as a junior postdoctoral fellow of the FWO (Research Foundation – Flanders), Grant No. 12ZI420N. S.F. was supported by JSPS through the Program for Leading Graduate Schools (MERIT). The computational resources and services used in this work were provided by the HPC core facility CalcUA of the Universiteit Antwerpen, and VSC (Flemish Supercomputer Center), funded by the FWO and the Flemish Government. The authors are grateful to Pablo Piaggi for making the pair entropy CV code publicly available. | Approved | Most recent IF: 4.4; 2020 IF: 2.965 | ||
| Call Number | PLASMANT @ plasmant @c:irua:172456 | Serial | 6420 | ||
| Permanent link to this record | |||||
| Author | Bogaerts, A.; Neyts, E.; Gijbels, R.; van der Mullen, J. | ||||
| Title |
Gas discharge plasmas and their applications | Type | A1 Journal article | ||
| Year | 2002 | Publication | Spectrochimica acta: part B : atomic spectroscopy | Abbreviated Journal | Spectrochim Acta B |
| Volume | 57 | Issue | Pages | 609-658 | |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | |||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Oxford | Editor | ||
| Language | Wos | 000175779700001 | Publication Date | 2002-10-15 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 0584-8547; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 3.241 | Times cited | 462 | Open Access | |
| Notes | Approved | Most recent IF: 3.241; 2002 IF: 2.695 | |||
| Call Number | UA @ lucian @ c:irua:40181 | Serial | 1317 | ||
| Permanent link to this record | |||||
| Author | Mortet, V.; Zhang, L.; Eckert, M.; D'Haen, J.; Soltani, A.; Moreau, M.; Troadec, D.; Neyts, E.; De Jaeger, J.C.; Verbeeck, J.; Bogaerts, A.; Van Tendeloo, G.; Haenen, K.; Wagner, P. | ||||
| Title |
Grain size tuning of nanocrystalline chemical vapor deposited diamond by continuous electrical bias growth : experimental and theoretical study | Type | A1 Journal article | ||
| Year | 2012 | Publication | Physica status solidi : A : applications and materials science | Abbreviated Journal | Phys Status Solidi A |
| Volume | 209 | Issue | 9 | Pages | 1675-1682 |
| Keywords | A1 Journal article; Electron microscopy for materials research (EMAT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | In this work, a detailed structural and spectroscopic study of nanocrystalline diamond (NCD) thin films grown by a continuous bias assisted CVD growth technique is reported. This technique allows the tuning of grain size and phase purity in the deposited material. The crystalline properties of the films are characterized by SEM, TEM, EELS, and Raman spectroscopy. A clear improvement of the crystalline structure of the nanograined diamond film is observed for low negative bias voltages, while high bias voltages lead to thin films consisting of diamond grains of only ∼10 nm nanometer in size, showing remarkable similarities with so-called ultrananocrystalline diamond. These layers arecharacterized by an increasing amount of sp2-bonded carbon content of the matrix in which the diamond grains are embedded. Classical molecular dynamics simulations support the observed experimental data, giving insight in the underlying mechanism for the observed increase in deposition rate with bias voltage. Furthermore, a high atomic concentration of hydrogen has been determined in these films. Finally, Raman scattering analyses confirm that the Raman line observed at ∼1150 cm−1 cannot be attributed to trans-poly-acetylene, which continues to be reported in literature, reassigning it to a deformation mode of CHx bonds in NCD. | ||||
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| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000308942100009 | Publication Date | 2012-09-04 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1862-6300; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 1.775 | Times cited | 31 | Open Access | |
| Notes | M.E. and E.N. acknowledge financial support from, respectively, the Institute for Promotion of Innovation through Science and Technology in Flanders (IWT), and the Research Foundation-Flanders (FWO). J.V. gratefully acknowledges financial support from the GOA project “XANES meets ELNES” of the research fund of the University of Antwerp. Calculation support was provided by the University of Antwerp through the core facility CALCUA. G.V.T. acknowledges the ERC grant COUNTATOMS. The work was also financially supported by the joint UAUHasseltMethusalem “NANO” network, the Research Programs G.0068.07 and G.0555.10N of the Research Foundation-Flanders (FWO), the IAP-P6/42 project “Quantum Effects in Clusters and Nanowires”, and by the EU FP7 through the Integrated Infrastructure Initiative “ESMI” (No. 262348), the Marie Curie ITN “MATCON” (PITN-GA-2009-238201), and the Collaborative Project “DINAMO” (No. 245122). | Approved | Most recent IF: 1.775; 2012 IF: 1.469 | ||
| Call Number | UA @ lucian @ c:irua:101516UA @ admin @ c:irua:101516 | Serial | 1364 | ||
| Permanent link to this record | |||||
| Author | Van der Paal, J.; Verheyen, C.; Neyts, E.C.; Bogaerts, A. | ||||
| Title |
Hampering Effect of Cholesterol on the Permeation of Reactive Oxygen Species through Phospholipids Bilayer: Possible Explanation for Plasma Cancer Selectivity | Type | A1 Journal article | ||
| Year | 2017 | Publication | Scientific reports | Abbreviated Journal | Sci Rep-Uk |
| Volume | 7 | Issue | 7 | Pages | 39526 |
| Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | In recent years, the ability of cold atmospheric pressure plasmas (CAPS) to selectively induce cell death in cancer cells has been widely established. This selectivity has been assigned to the reactive oxygen and nitrogen species (RONS) created in CAPs. To provide new insights in the search for an explanation for the observed selectivity, we calculate the transfer free energy of multiple ROS across membranes containing a varying amount of cholesterol. The cholesterol fraction is investigated as a selectivity parameter because membranes of cancer cells are known to contain lower fractions of cholesterol compared to healthy cells. We find that cholesterol has a significant effect on the permeation of reactive species across a membrane. Indeed, depending on the specific reactive species, an increasing cholesterol fraction can lead to (i) an increase of the transfer free energy barrier height and width, (ii) the formation of a local free energy minimum in the center of the membrane and (iii) the creation of extra free energy barriers due to the bulky sterol rings. In the context of plasma oncology, these observations suggest that the increased ingress of RONS in cancer cells can be explained by the decreased cholesterol fraction of their cell membrane. |
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| Language | Wos | 000391306900001 | Publication Date | 2017-01-06 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 2045-2322 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 4.259 | Times cited | 27 | Open Access | OpenAccess |
| Notes | The authors acknowledge financial support from the Fund for Scientific Research (FWO) Flanders, grant number 11U5416N. The calculations were performed in part using the Turing HPC infrastructure of the CalcUA core facility of the Universiteit Antwerpen, a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the Universiteit Antwerpen. | Approved | Most recent IF: 4.259 | ||
| Call Number | PLASMANT @ plasmant @ c:irua:139512 | Serial | 4340 | ||
| Permanent link to this record | |||||
| Author | Huygh, S.; Bogaerts, A.; Bal, K.M.; Neyts, E.C. | ||||
| Title |
High Coke Resistance of a TiO2Anatase (001) Catalyst Surface during Dry Reforming of Methane | Type | A1 Journal Article | ||
| Year | 2018 | Publication | Journal Of Physical Chemistry C | Abbreviated Journal | J Phys Chem C |
| Volume | 122 | Issue | 17 | Pages | 9389-9396 |
| Keywords | A1 Journal Article; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ; | ||||
| Abstract | The resistance of a TiO2 anatase (001) surface to coke formation was studied in the context of dry reforming of methane using density functional theory (DFT) calculations. As carbon atoms act as precursors for coke formation, the resistance to coke formation can be measured by the carbon coverage of the surface. This is related to the stability of different CHx (x = 0−3) species and their rate of hydrogenation and dehydrogenation on the TiO2 surface. Therefore, we studied the reaction mechanisms and their corresponding rates as a function of the temperature for the dehydrogenation of the species on the surface. We found that the stabilities of C and CH are significantly lower than those of CH3 and CH2. The hydrogenation rates of the different species are significantly higher than the dehydrogenation rates in a temperature range of 300−1000 K. Furthermore, we found that dehydrogenation of CH3, CH2, and CH will only occur at appreciable rates starting from 600, 900, and 900 K, respectively. On the basis of these results, it is clear that the anatase (001) surface has a high coke resistance, and it is thus not likely that the surface will become poisoned by coke during dry reforming of methane. As the rate limiting step in dry reforming is the dissociative adsorption of CH4, we studied an alternative approach to thermal catalysis. We found that the temperature threshold for dry reforming is at least 700 K. This threshold temperature may be lowered by the use of plasma-catalysis, where the appreciable rates of adsorption of plasma-generated CHx radicals result in bypassing the rate limiting step of the reaction. | ||||
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| Language | Wos | 000431723700014 | Publication Date | 2018-05-03 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1932-7447 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 4.536 | Times cited | 1 | Open Access | OpenAccess |
| Notes | Federaal Wetenschapsbeleid, IAP/7 ; Fonds Wetenschappelijk Onderzoek, G.0217.14N ; Onderzoeksfonds, Universiteit Antwerpen, 32249 ; | Approved | Most recent IF: 4.536 | ||
| Call Number | PLASMANT @ plasmant @c:irua:151529c:irua:152816 | Serial | 5000 | ||
| Permanent link to this record | |||||
| Author | Khosravian, N.; Bogaerts, A.; Huygh, S.; Yusupov, M.; Neyts, E.C. | ||||
| Title |
How do plasma-generated OH radicals react with biofilm components? Insights from atomic scale simulations | Type | A1 Journal article | ||
| Year | 2015 | Publication | Biointerphases | Abbreviated Journal | Biointerphases |
| Volume | 10 | Issue | 10 | Pages | 029501 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | The application of nonthermal atmospheric pressure plasma is emerging as an alternative and efficient technique for the inactivation of bacterial biofilms. In this study, reactive molecular dynamics simulations were used to examine the reaction mechanisms of hydroxyl radicals, as key reactive oxygen plasma species in biological systems, with several organic molecules (i.e., alkane, alcohol, carboxylic acid, and amine), as prototypical components of biomolecules in the biofilm. Our results demonstrate that organic molecules containing hydroxyl and carboxyl groups may act as trapping agents for the OH radicals. Moreover, the impact of OH radicals on N-acetyl-glucosamine, as constituent component of staphylococcus epidermidis biofilms, was investigated. The results show how impacts of OH radicals lead to hydrogen abstraction and subsequent molecular damage. This study thus provides new data on the reaction mechanisms of plasma species, and particularly the OH radicals, with fundamental components of bacterial biofilms. | ||||
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| Language | Wos | 000357195600019 | Publication Date | 2014-12-17 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1934-8630;1559-4106; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 2.603 | Times cited | 10 | Open Access | |
| Notes | Approved | Most recent IF: 2.603; 2015 IF: 3.374 | |||
| Call Number | c:irua:121371 | Serial | 1492 | ||
| Permanent link to this record | |||||
| Author | Huygh, S.; Bogaerts, A.; Neyts, E.C. | ||||
| Title |
How Oxygen Vacancies Activate CO2 Dissociation on TiO2 Anatase (001) | Type | A1 Journal article | ||
| Year | 2016 | Publication | The journal of physical chemistry: C : nanomaterials and interfaces | Abbreviated Journal | J Phys Chem C |
| Volume | 120 | Issue | 120 | Pages | 21659-21669 |
| Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | The adsorption, dissociation, and diffusion of CO2 on the anatase (001) surface was studied using DFT by means of the generalized gradient approximation using the Perdew−Burcke−Ernzerhof (PBE)-functional and applying corrections for long-range dispersion interactions. Different stable adsorption configurations were identified for the fully oxidized surface. The most stable adsorption configuration is the monodentated carbonate-like structure. Small energy barriers were identified for the conversion of a physisorbed to a chemisorbed configuration. CO2 dissociation is found to be unfeasible on the stoichiometric surface. The introduction of oxygen vacancy defects gives rise to new highly stable adsorption configurations with a stronger activation of the C−O bonds. This leads to the possibility of exothermic dissociation of CO2 with barriers up to 22.2 kcal/mol, corresponding to chemical lifetimes of less than 4 s at 300 K. These reactions cause a CO molecule to be formed, which will easily desorb, and the reduced surface to become oxidized. It is clear that oxygen vacancy defects play a key role in the catalytic activity of an anatase (001) surface. Oxygen vacancies play an important role in the dissociation of CO2 on the anatase (001) surface, and will play a significant role in complex problems, such as the catalytic conversion of CO2 to value-added chemicals. |
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| Language | Wos | 000384626800055 | Publication Date | 2016-09-02 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1932-7447 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 4.536 | Times cited | 49 | Open Access | |
| Notes | Stijn Huygh is funded as an aspirant of the Research Foundation Flanders (FWO, project number 11C0115N). This work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UAntwerpen), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI), and the UAntwerpen. | Approved | Most recent IF: 4.536 | ||
| Call Number | PLASMANT @ plasmant @ c:irua:136164 | Serial | 4291 | ||
| Permanent link to this record | |||||
| Author | Khalilov, U.; Bogaerts, A.; Xu, B.; Kato, T.; Kaneko, T.; Neyts, E.C. | ||||
| Title |
How the alignment of adsorbed ortho H pairs determines the onset of selective carbon nanotube etching | Type | A1 Journal article | ||
| Year | 2017 | Publication | Nanoscale | Abbreviated Journal | Nanoscale |
| Volume | 9 | Issue | 9 | Pages | 1653-1661 |
| Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Unlocking the enormous technological potential of carbon nanotubes strongly depends on our ability to specifically produce metallic or semiconducting tubes. While selective etching of both has already been demonstrated, the underlying reasons, however, remain elusive as yet. We here present computational and experimental evidence on the operative mechanisms at the atomic scale. We demonstrate that during the adsorption of H atoms and their coalescence, the adsorbed ortho hydrogen pairs on single-walled carbon nanotubes induce higher shear stresses than axial stresses, leading to the elongation of HC–CH bonds as a function of their alignment with the tube chirality vector, which we denote as the γ-angle. As a result, the C–C cleavage occurs more rapidly in nanotubes containing ortho H-pairs with a small γ-angle. This phenomenon can explain the selective etching of small-diameter semiconductor nanotubes with a similar curvature. Both theoretical and experimental results strongly indicate the important role of the γ-angle in the selective etching mechanisms of carbon nanotubes, in addition to the nanotube curvature and metallicity effects and lead us to clearly understand the onset of selective synthesis/removal of CNT-based materials. | ||||
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| Language | Wos | 000395422800036 | Publication Date | 2016-12-19 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 2040-3364 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 7.367 | Times cited | 6 | Open Access | OpenAccess |
| Notes | U. K. gratefully acknowledges financial support from the Fund of Scientific Research Flanders (FWO), Belgium (Grant No. 12M1315N). This work was also supported in part by Grant-in- Aid for Young Scientists A (Grant No. 25706028), Grant-in-Aid for Scientific Research on Innovative Areas (Grant No. 26107502) from JSPS KAKENHI. This work was carried out in part using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. The authors also thank Prof. A. C. T. van Duin for sharing the ReaxFF code and J. Razzokov for his assistance to perform the DFT calculations. | Approved | Most recent IF: 7.367 | ||
| Call Number | PLASMANT @ plasmant @ c:irua:140091 | Serial | 4417 | ||
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| Author | Khalilov, U.; Pourtois, G.; van Duin, A.C.T.; Neyts, E.C. | ||||
| Title |
Hyperthermal oxidation of Si(100)2x1 surfaces : effect of growth temperature | Type | A1 Journal article | ||
| Year | 2012 | Publication | The journal of physical chemistry: C : nanomaterials and interfaces | Abbreviated Journal | J Phys Chem C |
| Volume | 116 | Issue | 15 | Pages | 8649-8656 |
| Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Using reactive molecular dynamics simulations based on the ReaxFF potential, we studied the growth mechanism of ultrathin silica (SiO2) layers during hyperthermal oxidation as a function of temperature in the range 100-1300 K. Oxidation of Si(100){2 x 1} surfaces by both atomic and molecular oxygen was investigated for hyperthermal impact energies in the range of 1 to 5 eV. Two different growth mechanisms are found, corresponding to a low temperature oxidation and a high temperature one. The transition temperature between these mechanisms is estimated to be about 700 K. Also, the initial step of the Si oxidation process is analyzed in detail. Where possible, we validated our results with experimental and ab initio data, and good agreement was obtained. This study is important for the fabrication of silica-based devices in the micro- and nanoelectronics industry and, more specifically, for the fabrication of metal oxide semiconductor devices. | ||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Washington, D.C. | Editor | ||
| Language | Wos | 000302924900035 | Publication Date | 2012-03-26 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1932-7447;1932-7455; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 4.536 | Times cited | 32 | Open Access | |
| Notes | Approved | Most recent IF: 4.536; 2012 IF: 4.814 | |||
| Call Number | UA @ lucian @ c:irua:98259 | Serial | 1542 | ||
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| Author | Neyts, E.C.; Khalilov, U.; Pourtois, G.; van Duin, A.C.T. | ||||
| Title |
Hyperthermal oxygen interacting with silicon surfaces : adsorption, implantation, and damage creation | Type | A1 Journal article | ||
| Year | 2011 | Publication | The journal of physical chemistry: C : nanomaterials and interfaces | Abbreviated Journal | J Phys Chem C |
| Volume | 115 | Issue | 15 | Pages | 4818-4823 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Using reactive molecular dynamics simulations, we have investigated the effect of single-impact, low-energy (thermal-100 eV) bombardment of a Si(100){2 × 1} surface by atomic and molecular oxygen. Penetration probability distributions, as well as defect formation distributions, are presented as a function of the impact energy for both species. It is found that at low impact energy, defects are created chemically due to the chemisorption process in the top layers of the surface, while at high impact energy, additional defects are created by a knock-on displacement of Si. These results are of particular importance for understanding device performances of silica-based microelectronic and photovoltaic devices. | ||||
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| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Washington, D.C. | Editor | ||
| Language | Wos | 000288401200060 | Publication Date | 2011-03-02 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1932-7447;1932-7455; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 4.536 | Times cited | 28 | Open Access | |
| Notes | Approved | Most recent IF: 4.536; 2011 IF: 4.805 | |||
| Call Number | UA @ lucian @ c:irua:89858 | Serial | 1543 | ||
| Permanent link to this record | |||||
| Author | Nematollahi, P.; Barbiellini, B.; Bansil, A.; Lamoen, D.; Qingying, J.; Mukerjee, S.; Neyts, E.C. | ||||
| Title |
Identification of a Robust and Durable FeN4CxCatalyst for ORR in PEM Fuel Cells and the Role of the Fifth Ligand | Type | A1 Journal article | ||
| Year | 2022 | Publication | ACS catalysis | Abbreviated Journal | Acs Catal |
| Volume | Issue | Pages | 7541-7549 | ||
| Keywords | A1 Journal article; Electron microscopy for materials research (EMAT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Although recent studies have advanced the understanding of pyrolyzed Fe−N−C materials as oxygen reduction reaction (ORR) catalysts, the atomic and electronic structures of the active sites and their detailed reaction mechanisms still remain unknown. Here, based on first-principles density functional theory (DFT) computations, we discuss the electronic structures of three FeN4 catalytic centers with different local topologies of the surrounding C atoms with a focus on unraveling the mechanism of their ORR activity in acidic electrolytes. Our study brings back a forgotten, synthesized pyridinic Fe−N coordinate to the community’s attention, demonstrating that this catalyst can exhibit excellent activity for promoting direct four-electron ORR through the addition of a fifth ligand such as −NH2, −OH, and −SO4. We also identify sites with good stability properties through the combined use of our DFT calculations and Mössbauer spectroscopy data. |
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| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000823193100001 | Publication Date | 2022-06-10 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 2155-5435 | ISBN | Additional Links | UA library record; WoS full record; WoS full record; WoS citing articles | |
| Impact Factor | 12.9 | Times cited | Open Access | OpenAccess | |
| Notes | Basic Energy Sciences, DE-FG02-07ER46352 ; Fonds Wetenschappelijk Onderzoek, 1261721N ; Opetus- ja Kulttuuriministeri?; Department of Energy, DE-EE0008416 ; | Approved | Most recent IF: 12.9 | ||
| Call Number | EMAT @ emat @c:irua:189000 | Serial | 7073 | ||
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| Author | Nematollahi, P.; Neyts, E.C. | ||||
| Title |
Identification of a unique pyridinic FeN4Cx electrocatalyst for N₂ reduction : tailoring the coordination and carbon topologies | Type | A1 Journal article | ||
| Year | 2022 | Publication | Journal Of Physical Chemistry C | Abbreviated Journal | J Phys Chem C |
| Volume | 126 | Issue | 34 | Pages | 14460-14469 |
| Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Although the heterogeneity of pyrolyzed Fe???N???C materials is known and has been reported previously, the atomic structure of the active sites and their detailed reaction mechanisms are still unknown. Here, we identified two pyridinic Fe???N4-like centers with different local C coordinates, i.e., FeN4C8 and FeN4C10, and studied their electrocatalytic activity for the nitrogen reduction reaction (NRR) based on density functional theory (DFT) calculations. We also discovered the influence of the adsorption of NH2 as a functional ligand on catalyst performance on the NRR. We confirmed that the NRR selectivity of the studied catalysts is essentially governed either by the local C coordination or by the dynamic structure associated with the FeII/FeIII. Our investigations indicate that the proposed traditional pyridinic FeN4C10 has higher catalytic activity and selectivity for the NRR than the robust FeN4C8 catalyst, while it may have outstanding activity for promoting other (electro)catalytic reactions. <comment>Superscript/Subscript Available</comment | ||||
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| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000859545200001 | Publication Date | 2022-08-17 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1932-7447; 1932-7455 | ISBN | Additional Links | UA library record; WoS full record | |
| Impact Factor | 3.7 | Times cited | Open Access | OpenAccess | |
| Notes | Approved | Most recent IF: 3.7 | |||
| Call Number | UA @ admin @ c:irua:191469 | Serial | 7268 | ||
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| Author | Yusupov, M.; Neyts, E.C.; Verlackt, C.C.; Khalilov, U.; van Duin, A.C.T.; Bogaerts, A. | ||||
| Title |
Inactivation of the endotoxic biomolecule lipid A by oxygen plasma species : a reactive molecular dynamics study | Type | A1 Journal article | ||
| Year | 2015 | Publication | Plasma processes and polymers | Abbreviated Journal | Plasma Process Polym |
| Volume | 12 | Issue | 12 | Pages | 162-171 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Reactive molecular dynamics simulations are performed to study the interaction of reactive oxygen species, such as OH, HO2 and H2O2, with the endotoxic biomolecule lipid A of the gram-negative bacterium Escherichia coli. It is found that the aforementioned plasma species can destroy the lipid A, which consequently results in reducing its toxic activity. All bond dissociation events are initiated by hydrogen-abstraction reactions. However, the mechanisms behind these dissociations are dependent on the impinging plasma species, i.e. a clear difference is observed in the mechanisms upon impact of HO2 radicals and H2O2 molecules on one hand and OH radicals on the other hand. Our simulation results are in good agreement with experimental observations. | ||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Weinheim | Editor | ||
| Language | Wos | 000350275400005 | Publication Date | 2014-09-17 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1612-8850; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 2.846 | Times cited | 18 | Open Access | |
| Notes | Approved | Most recent IF: 2.846; 2015 IF: 2.453 | |||
| Call Number | c:irua:123540 | Serial | 1589 | ||
| Permanent link to this record | |||||