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| Author | Yusupov, M.; Bogaerts, A.; Huygh, S.; Snoeckx, R.; van Duin, A.C.T.; Neyts, E.C. | ||||
| Title | Plasma-induced destruction of bacterial cell wall components : a reactive molecular dynamics simulation | Type | A1 Journal article | ||
| Year | 2013 | Publication | The journal of physical chemistry: C : nanomaterials and interfaces | Abbreviated Journal  |
J Phys Chem C |
| Volume | 117 | Issue | 11 | Pages | 5993-5998 |
| Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Nonthermal atmospheric pressure plasmas are gaining increasing attention for biomedical applications. However, very little fundamental information on the interaction mechanisms between the plasma species and biological cells is currently available. We investigate the interaction of important plasma species, such as OH, H2O2, O, O3, as well as O2 and H2O, with bacterial peptidoglycan by means of reactive molecular dynamics simulations, aiming for a better understanding of plasma disinfection. Our results show that OH, O, O3, and H2O2 can break structurally important bonds of peptidoglycan (i.e., CO, CN, or CC bonds), which consequently leads to the destruction of the bacterial cell wall. The mechanisms behind these breakups are, however, dependent on the impinging plasma species, and this also determines the effectiveness of the cell wall destruction. | ||||
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| Publisher | Place of Publication | Washington, D.C. | Editor | ||
| Language | Wos | 000316773000056 | Publication Date | 2013-02-23 | |
| 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 | 59 | Open Access | |
| Notes | Approved | Most recent IF: 4.536; 2013 IF: 4.835 | |||
| Call Number | UA @ lucian @ c:irua:107154 | Serial | 2636 | ||
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| Author | Somers, W.; Bogaerts, A.; van Duin, A.C.T.; Neyts, E.C. | ||||
| Title | Plasma species interacting with nickel surfaces : toward an atomic scale understanding of plasma-catalysis | 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 | 39 | Pages | 20958-20965 |
| Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | The adsorption probability and reaction behavior of CHx plasma species on various nickel catalyst surfaces is investigated by means of reactive molecular dynamics (MD) simulations using the ReaxFF potential. Such catalysts are used in the reforming of hydrocarbons and in the growth of carbon nanotubes, and further insight in the underlying mechanisms of these processes is needed to increase their applicability. Single and consecutive impacts of CHx radicals (x={1,2,3}) were performed on four different Ni surfaces, at a temperature of 400 K. The adsorption probability is shown to be related to the number of free electrons, i.e. a higher number leads to more adsorptions, and the steric hindrance caused by the hydrogen atoms bonded to the impacting CHx species. Furthermore, some of the CH bonds break after adsorption, which generally leads to diffusion of the hydrogen atom over the surface. Additionally, these adsorbed H-atoms can be used in reactions to form new molecules, such as CH4 and C2Hx, although this is dependent on the precise morphology of the surface. New molecules are also formed by subtraction of H-atoms from adsorbed radicals, leading to occasional formation of H2 and C2Hx molecules. | ||||
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| Publisher | Place of Publication | Washington, D.C. | Editor | ||
| Language | Wos | 000309375700040 | Publication Date | 2012-09-10 | |
| 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 | 37 | Open Access | |
| Notes | Approved | Most recent IF: 4.536; 2012 IF: 4.814 | |||
| Call Number | UA @ lucian @ c:irua:101522 | Serial | 2640 | ||
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| Author | Khalilov, U.; Yusupov, M.; Bogaerts, A.; Neyts, E.C. | ||||
| Title | Selective Plasma Oxidation of Ultrasmall Si Nanowires | 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 | 472-477 |
| Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Device performance of Si|SiOx core-shell based nanowires critically depends on the exact control over the oxide thickness. Low-temperature plasma oxidation is a highly promising alternative to thermal oxidation allowing for improved control over the oxidation process, in particular for ultrasmall Si nanowires. We here elucidate the room temperature plasma oxidation mechanisms of ultrasmall Si nanowires using hybrid molecular dynamics / force-bias Monte Carlo simulations. We demonstrate how the oxidation and concurrent water formation mechanisms are a function of the oxidizing plasma species and we demonstrate how the resulting core-shell oxide thickness can be controlled through these species. A new mechanism of water formation is discussed in detail. The results provide a detailed atomic level explanation of the oxidation process of highly curved Si surfaces. These results point out a route toward plasma-based formation of ultrathin core-shell Si|SiOx nanowires at room temperature. | ||||
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| Language | Wos | 000368562200057 | Publication Date | 2015-12-21 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
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| ISSN | 1932-7447 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 4.536 | Times cited | 3 | Open Access | |
| Notes | U.K. and M.Y. gratefully acknowledge financial support from the Research Foundation – Flanders (FWO), Grants 12M1315N and 1200216N. 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. We thank Prof. A. C. T. van Duin for sharing the ReaxFF code. | Approved | Most recent IF: 4.536 | ||
| Call Number | c:irua:130677 | Serial | 4002 | ||
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| 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 | ||
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| Author | Zhang, Y.-R.; Neyts, E.C.; Bogaerts, A. | ||||
| Title | Influence of the Material Dielectric Constant on Plasma Generation inside Catalyst Pores | 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 | 25923-25934 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Plasma catalysis is gaining increasing interest for various environmental applications, but the crucial question is whether plasma can be created inside catalyst pores and under which conditions. In practice, various catalytic support materials are used, with various dielectric constants. We investigate here the influence of the dielectric constant on the plasma properties inside catalyst pores and in the sheath in front of the pores, for various pore sizes. The calculations are performed by a two-dimensional fluid model for an atmospheric pressure dielectric barrier discharge in helium. The electron impact ionization rate, electron temperature, electron and ion density, as well as the potential distribution and surface charge density, are analyzed for a better understanding of the discharge behavior inside catalyst pores. The results indicate that, in a 100 μm pore, the electron impact ionization in the pore, which is characteristic for the plasma generation inside the pore, is greatly enhanced for dielectric constants below 300. Smaller pore sizes only yield enhanced ionization for smaller dielectric constants, i.e., up to εr = 200, 150, and 50 for pore sizes of 50, 30, and 10 μm. Thus, the most common catalyst supports, i.e., Al2O3 and SiO2, which have dielectric constants around εr = 8−11 and 4.2, respectively, should allow more easily that microdischarges can be formed inside catalyst pores, even for smaller pore sizes. On the other hand, ferroelectric materials with dielectric constants above 300 never seem to yield plasma enhancement inside catalyst pores, not even for 100 μm pore sizes. Furthermore, it is clear that the dielectric constant of the material has a large effect on the extent of plasma enhancement inside the catalyst pores, especially in the range between εr = 4 and εr = 200. The obtained results are explained in detail based on the surface charge density at the pore walls, and the potential distribution and electron temperature inside and above the pores. The results obtained with this model are important for plasma catalysis, as the production plasma species in catalyst pores might affect the catalyst properties, and thus improve the applications of plasma catalysis. |
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| Language | Wos | 000388429100029 | Publication Date | 2016-11-17 | |
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| ISSN | 1932-7447 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 4.536 | Times cited | 34 | Open Access | |
| Notes | This work was supported by the Fund for Scientific Research Flanders (FWO) (Grant G.0217.14N), the National Natural Science Foundation of China (Grant 11405019), and the China Postdoctoral Science Foundation (Grant 2015T80244). This 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: 4.536 | ||
| Call Number | PLASMANT @ plasmant @ c:irua:138602 | Serial | 4319 | ||
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| Author | Verlackt, C.C.W.; Van Boxem, W.; Dewaele, D.; Lemière, F.; Sobott, F.; Benedikt, J.; Neyts, E.C.; Bogaerts, A. | ||||
| Title | Mechanisms of Peptide Oxidation by Hydroxyl Radicals: Insight at the Molecular Scale | Type | A1 Journal article | ||
| Year | 2017 | Publication | The journal of physical chemistry: C : nanomaterials and interfaces | Abbreviated Journal |
J Phys Chem C |
| Volume | 121 | Issue | 121 | Pages | 5787-5799 |
| Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Molecular dynamics (MD) simulations were performed to provide atomic scale insight in the initial interaction between hydroxyl radicals (OH) and peptide systems in solution. These OH radicals are representative reactive oxygen species produced by cold atmospheric plasmas. The use of plasma for biomedical applications is gaining increasing interest, but the fundamental mechanisms behind the plasma modifications still remain largely elusive. This study helps to gain more insight in the underlying mechanisms of plasma medicine but is also more generally applicable to peptide oxidation, of interest for other applications. Combining both reactive and nonreactive MD simulations, we are able to elucidate the reactivity of the amino acids inside the peptide systems and their effect on their structure up to 1 μs. Additionally, experiments were performed, treating the simulated peptides with a plasma jet. The computational results presented here correlate well with the obtained experimental data and highlight the importance of the chemical environment for the reactivity of the individual amino acids, so that specific amino acids are attacked in higher numbers than expected. Furthermore, the long time scale simulations suggest that a single oxidation has an effect on the 3D conformation due to an increase in hydrophilicity and intra- and intermolecular interactions. | ||||
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| Language | Wos | 000396969900037 | Publication Date | 2017-03-16 | |
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| 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 | 5 | Open Access | OpenAccess |
| Notes | Fonds Wetenschappelijk Onderzoek, G012413N ; | Approved | Most recent IF: 4.536 | ||
| Call Number | PLASMANT @ plasmant @ c:irua:142202 | Serial | 4537 | ||
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| Author | Grubova, I.Y.; Surmeneva, M.A.; Huygh, S.; Surmenev, R.A.; Neyts, E.C. | ||||
| Title | Density functional theory study of interface interactions in hydroxyapatite/rutile composites for biomedical applications | Type | A1 Journal article | ||
| Year | 2017 | Publication | The journal of physical chemistry: C : nanomaterials and interfaces | Abbreviated Journal |
J Phys Chem C |
| Volume | 121 | Issue | 29 | Pages | 15687-15695 |
| Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | To gain insight into the nature of the adhesion mechanism between hydroxyapatite (HA) and rutile (rTiO(2)), the mutual affinity between their surfaces was systematically studied using density functional theory (DFT). We calculated both bulk and surface properties of HA and rTiO(2), and explored the interfacial bonding mechanism of amorphous HA (aHA) surface onto amorphous as well as stoichiometric and nonstoichiometric crystalline rTiO(2). Formation energies of bridging and subbridging oxygen vacancies considered in the rTiO(2)(110) surface were evaluated and compared with other theoretical and experimental results. The interfacial interaction was evaluated through the work of adhesion. For the aHA/rTiO(2)(110) interfaces, the work of adhesion is found to depend strongly on the chemical environment of the rTiO(2)(110) surface. Electronic analysis indicates that the charge transfer is very small in the case of interface formation between aHA and crystalline rTiO(2)(110). In contrast, significant charge transfer occurs between aHA and amorphous rTiO(2) (aTiO(2)) slabs during the formation of the interface. Charge density difference (CDD) analysis indicates that the dominant interactions in the interface have significant covalent character, and in particular the Ti-O and Ca-O bonds. Thus, the obtained results reveal that the aHA/aTiO(2) interface shows a more preferable interaction and is thermodynamically more stable than other interfaces. These results are particularly important for improving the long-term stability of HA-based implants. | ||||
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| Publisher | Place of Publication | Washington, D.C. | Editor | ||
| Language | Wos | 000406726200022 | Publication Date | 2017-06-27 | |
| 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 | 5 | Open Access | Not_Open_Access |
| Notes | Approved | Most recent IF: 4.536 | |||
| Call Number | UA @ lucian @ c:irua:145195 | Serial | 4715 | ||
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| Author | Vets, C.; Neyts, E.C. | ||||
| Title | Stabilities of bimetallic nanoparticles for chirality-selective carbon nanotube growth and the effect of carbon interstitials | Type | A1 Journal article | ||
| Year | 2017 | Publication | The journal of physical chemistry: C : nanomaterials and interfaces | Abbreviated Journal |
J Phys Chem C |
| Volume | 121 | Issue | 28 | Pages | 15430-15436 |
| Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| 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. | ||||
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| Publisher | Place of Publication | Washington, D.C. | Editor | ||
| Language | Wos | 000406355700050 | Publication Date | 2017-06-23 | |
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| ISSN | 1932-7447; 1932-7455 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 4.536 | Times cited | 2 | Open Access | Not_Open_Access |
| Notes | Approved | Most recent IF: 4.536 | |||
| Call Number | UA @ lucian @ c:irua:145206 | Serial | 4725 | ||
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| 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 | |
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| 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 | ||
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| Author | Bal, K.M.; Neyts, E.C. | ||||
| Title | Overcoming Old Scaling Relations and Establishing New Correlations in Catalytic Surface Chemistry: Combined Effect of Charging and Doping | Type | A1 Journal article | ||
| Year | 2019 | Publication | The journal of physical chemistry: C : nanomaterials and interfaces | Abbreviated Journal |
J Phys Chem C |
| Volume | 123 | Issue | 10 | Pages | 6141-6147 |
| Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Optimization of catalytic materials for a given application is greatly constrained by linear scaling relations. Recently, however, it has been demonstrated that it is possible to reversibly modulate the chemisorption of molecules on nanomaterials by charging (i.e., injection or removal of electrons) and hence reversibly and selectively modify catalytic activity beyond structure−activity correlations. The fundamental physical relation between the properties of the material, the charging process, and the chemisorption energy, however, remains unclear, and a systematic exploration and optimization of charge-switchable sorbent materials is not yet possible. Using hybrid DFT calculations of CO2 chemisorption on hexagonal boron nitride nanosheets with several types of defects and dopants, we here reveal the existence of fundamental correlations between the electron affinity of a material and charge-induced chemisorption, show how defect engineering can be used to modulate the strength and efficiency of the adsorption process, and demonstrate that excess electrons stabilize many topological defects. We then show how these insights could be exploited in the development of new electrocatalytic materials and the synthesis of doped nanomaterials. Moreover, we demonstrate that calculated chemical properties of charged materials are highly sensitive to the employed computational methodology because of the self-interaction error, which underlines the theoretical challenge posed by such systems. | ||||
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| Language | Wos | 000461537400035 | Publication Date | 2019-03-14 | |
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| ISSN | 1932-7447 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 4.536 | Times cited | 5 | Open Access | Not_Open_Access: Available from 21.02.2020 |
| Notes | Fonds Wetenschappelijk Onderzoek, 11V8915N ; | Approved | Most recent IF: 4.536 | ||
| Call Number | PLASMANT @ plasmant @UA @ admin @ c:irua:158117 | Serial | 5160 | ||
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| Author | Jafarzadeh, A.; Bal, K.M.; Bogaerts, A.; Neyts, E.C. | ||||
| Title | CO2 activation on TiO2-supported Cu5 and Ni5 nanoclusters : effect of plasma-induced surface charging | Type | A1 Journal article | ||
| Year | 2019 | Publication | The journal of physical chemistry: C : nanomaterials and interfaces | Abbreviated Journal |
J Phys Chem C |
| Volume | 123 | Issue | 11 | Pages | 6516-6525 |
| Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Surface charging is an often overlooked factor in many plasma-surface interactions and in particular in plasma catalysis. In this study, we investigate the effect of excess electrons induced by a plasma on the adsorption properties of CO2 on titania-supported Cu-5 and Ni-5 clusters using spin-polarized and dispersion-corrected density functional theory calculations. The effect of excess electrons on the adsorption of Ni and Cu pentamers as well as on CO2 adsorption on a pristine anatase TiO2(101) slab is studied. Our results indicate that adding plasma-induced excess electrons to the system leads to further stabilization of the bent CO2 structure. Also, dissociation of CO2 on charged clusters is energetically more favorable than on neutral clusters. We hypothesize that surface charge is a plausible cause for the synergistic effects sometimes observed in plasma catalysis. | ||||
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| Language | Wos | 000462260700024 | Publication Date | 2019-02-21 | |
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| ISSN | 1932-7447; 1932-7455 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 4.536 | Times cited | 4 | Open Access | OpenAccess |
| Notes | Approved | Most recent IF: 4.536 | |||
| Call Number | UA @ admin @ c:irua:159422 | Serial | 5281 | ||
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| Author | Jafarzadeh, A.; Bal, K.M.; Bogaerts, A.; Neyts, E.C. | ||||
| Title | Activation of CO2on Copper Surfaces: The Synergy between Electric Field, Surface Morphology, and Excess Electrons | Type | A1 Journal article | ||
| Year | 2020 | Publication | Journal Of Physical Chemistry C | Abbreviated Journal |
J Phys Chem C |
| Volume | 124 | Issue | 12 | Pages | 6747-6755 |
| Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | In this work, we use density functional theory calculations to study the combined effect of external electric fields, surface morphology, and surface charge on CO2 activation over Cu(111), Cu(211), Cu(110), and Cu(001) surfaces. We observe that the binding energy of the CO2 molecule on Cu surfaces increases significantly upon increasing the applied electric field strength. In addition, rougher surfaces respond more effectively to the presence of the external electric field toward facilitating the formation of a carbonate-like CO2 structure and the transformation of the most stable adsorption mode from physisorption to chemisorption. The presence of surface charges further strengthens the electric field effect and consequently causes an improved bending of the CO2 molecule and C−O bond length elongation. On the other hand, a net charge in the absence of an externally applied electric field shows only a marginal effect on CO2 binding. The chemisorbed CO2 is more stable and further activated when the effects of an external electric field, rough surface, and surface charge are combined. These results can help to elucidate the underlying factors that control CO2 activation in heterogeneous and plasma catalysis, as well as in electrochemical processes. | ||||
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| Language | Wos | 000526396900030 | Publication Date | 2020-03-26 | |
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| ISSN | 1932-7447 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 3.7 | Times cited | Open Access | ||
| Notes | Bijzonder Onderzoeksfonds, 32249 ; The financial support from the TOP research project of the Research Fund of the University of Antwerp (grant ID: 32249) is highly acknowledged by the authors. The computational resources used in this study were provided by the VSC (Flemish Supercomputer Center), funded by the FWO and the Flemish Governmentdepartment EWI. | Approved | Most recent IF: 3.7; 2020 IF: 4.536 | ||
| Call Number | PLASMANT @ plasmant @c:irua:168606 | Serial | 6361 | ||
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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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| 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 | ||
| Permanent link to this record | |||||
| Author | Van de Sompel, P.; Khalilov, U.; Neyts, E.C. | ||||
| Title | Contrasting H-etching to OH-etching in plasma-assisted nucleation of carbon nanotubes | Type | A1 Journal article | ||
| Year | 2021 | Publication | Journal Of Physical Chemistry C | Abbreviated Journal |
J Phys Chem C |
| Volume | 125 | Issue | 14 | Pages | 7849-7855 |
| Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | To gain full control over the growth of carbon nanotubes (CNTs) using plasma-enhanced chemical vapor deposition (PECVD), a thorough understanding of the underlying plasma-catalyst mechanisms is required. Oxygen-containing species are often used as or added to the growth precursor gas, but these species also yield various radicals and ions, which may simultaneously etch the CNT during the growth. At present, the effect of these reactive species on the growth onset has not yet been thoroughly investigated. We here report on the etching mechanism of incipient CNT structures from OH and O radicals as derived from combined (reactive) molecular dynamics (MD) and force-bias Monte Carlo (tfMC) simulations. Our results indicate that the oxygen-containing radicals initiate a dissociation process. In particular, we show how the oxygen species weaken the interaction between the CNT and the nanocluster. As a result of this weakened interaction, the CNT closes off and dissociates from the cluster in the form of a fullerene. Beyond the specific systems studied in this work, these results are generically important in the context of PECVD-based growth of CNTs using oxygen-containing precursors. | ||||
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| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000641307100032 | Publication Date | 2021-04-06 | |
| 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 | 4.536 | Times cited | Open Access | OpenAccess | |
| Notes | Approved | Most recent IF: 4.536 | |||
| Call Number | UA @ admin @ c:irua:178393 | Serial | 7729 | ||
| Permanent link to this record | |||||
| Author | Nematollahi, P.; Ma, H.; Schneider, W.F.; Neyts, E.C. | ||||
| Title | DFT and microkinetic comparison of ru-doped porphyrin-like graphene and nanotubes toward catalytic formic acid decomposition and formation | Type | A1 Journal article | ||
| Year | 2021 | Publication | Journal Of Physical Chemistry C | Abbreviated Journal |
J Phys Chem C |
| Volume | 125 | Issue | 34 | Pages | 18673-18683 |
| Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Immobilization of single metal atoms on a solid host opens numerous possibilities for catalyst designs. If that host is a two-dimensional sheet, sheet curvature becomes a design parameter potentially complementary to host and metal composition. Here, we use a combination of density functional theory calculations and microkinetic modeling to compare the mechanisms and kinetics of formic acid decomposition and formation, chosen for their relevance as a potential hydrogen storage medium, over single Ru atoms anchored to pyridinic nitrogen in a planar graphene flake (RuN4-G) and curved carbon nanotube (RuN4-CNT). Activation barriers are lowered and the predicted turnover frequencies are increased over RuN4-CNT relative to RuN4-CNT. The results highlight the potential of curvature control as a means to achieve high performance and robust catalysts. | ||||
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| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000693413400013 | Publication Date | 2021-08-22 | |
| 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 | Open Access | OpenAccess | |
| Notes | Approved | Most recent IF: 4.536 | |||
| Call Number | UA @ admin @ c:irua:181538 | Serial | 7805 | ||
| Permanent link to this record | |||||
| Author | Nematollahi, P.; Neyts, E.C. | ||||
| Title | Distribution pattern of metal atoms in bimetal-doped pyridinic-N₄ pores determines their potential for electrocatalytic N₂ reduction | Type | A1 Journal article | ||
| Year | 2022 | Publication | Journal Of Physical Chemistry A | Abbreviated Journal |
J Phys Chem A |
| Volume | 126 | Issue | 20 | Pages | 3080-3089 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Doping two single transition-metal (TM) atoms on a substrate host opens numerous possibilities for catalyst design. However, what if the substrate contains more than one vacancy site? Then, the combination of two TMs along with their distribution patterns becomes a design parameter potentially complementary to the substrate itself and the bimetal composition. In this study, we investigate ammonia synthesis under mild electrocatalytic conditions on a transition-metal-doped porous C24N24 catalyst using density functional theory (DFT). The TMs studied include Ti, Mn, and Cu in a 2:4 dopant ratio (Ti2Mn4@C24N24 and Ti2Cu4@N-24(24)). Our computations show that a single Ti atom in both catalysts exhibits the highest selectivity for N-2 fixation at ambient conditions. This work is a good theoretical model to establish the structure-activity relationship, and the knowledge earned from the metal-N-4 moieties may help studies of related nanomaterials, especially those with curved structures. | ||||
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| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000804119800003 | Publication Date | 2022-05-12 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1089-5639; 1520-5215 | ISBN | Additional Links | UA library record; WoS full record | |
| Impact Factor | 2.9 | Times cited | Open Access | OpenAccess | |
| Notes | Approved | Most recent IF: 2.9 | |||
| Call Number | UA @ admin @ c:irua:189023 | Serial | 7146 | ||
| Permanent link to this record | |||||
| 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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| Publisher | Place of Publication | Editor | |||
| 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 | ||
| Permanent link to this record | |||||
| Author | Heyne, M.H.; Chiappe, D.; Meersschaut, J.; Nuytten, T.; Conard, T.; Bender, H.; Huyghebaert, C.; Radu, I.P.; Caymax, M.; de Marneffe, J.F.; Neyts, E.C.; De Gendt, S.; | ||||
| Title | Multilayer MoS2 growth by metal and metal oxide sulfurization | Type | A1 Journal article | ||
| Year | 2016 | Publication | Journal of materials chemistry C : materials for optical and electronic devices | Abbreviated Journal |
J Mater Chem C |
| Volume | 4 | Issue | 4 | Pages | 1295-1304 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | We investigated the deposition of MoS2 multilayers on large area substrates. The pre-deposition of metal or metal oxide with subsequent sulfurization is a promising technique to achieve layered films. We distinguish a different reaction behavior in metal oxide and metallic films and investigate the effect of the temperature, the H2S/H-2 gas mixture composition, and the role of the underlying substrate on the material quality. The results of the experiments suggest a MoS2 growth mechanism consisting of two subsequent process steps. At first, the reaction of the sulfur precursor with the metal or metal oxide occurs, requiring higher temperatures in the case of metallic film compared to metal oxide. At this stage, the basal planes assemble towards the diffusion direction of the reaction educts and products. After the sulfurization reaction, the material recrystallizes and the basal planes rearrange parallel to the substrate to minimize the surface energy. Therefore, substrates with low roughness show basal plane assembly parallel to the substrate. These results indicate that the substrate character has a significant impact on the assembly of low dimensional MoS2 films. | ||||
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| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000370723300020 | Publication Date | 2016-01-05 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 2050-7526; 2050-7534 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 5.256 | Times cited | Open Access | ||
| Notes | Approved | Most recent IF: 5.256 | |||
| Call Number | UA @ lucian @ c:irua:132327 | Serial | 4211 | ||
| Permanent link to this record | |||||
| Author | Heyne, M.H.; de Marneffe, J.-F.; Nuytten, T.; Meersschaut, J.; Conard, T.; Caymax, M.; Radu, I.; Delabie, A.; Neyts, E.C.; De Gendt, S. | ||||
| Title | The conversion mechanism of amorphous silicon to stoichiometric WS2 | Type | A1 Journal article | ||
| Year | 2018 | Publication | Journal of materials chemistry C : materials for optical and electronic devices | Abbreviated Journal |
J Mater Chem C |
| Volume | 6 | Issue | 15 | Pages | 4122-4130 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | The deposition of ultra-thin tungsten films and their related 2D chalcogen compounds on large area dielectric substrates by gas phase reactions is challenging. The lack of nucleation sites complicates the adsorption of W-related precursors and subsequent sulfurization usually requires high temperatures. We propose here a technique in which a thin solid amorphous silicon film is used as reductant for the gas phase precursor WF6 leading to the conversion to metallic W. The selectivity of the W conversion towards the underlying dielectric surfaces is demonstrated. The role of the Si surface preparation, the conversion temperature, and Si thickness on the formation process is investigated. Further, the in situ conversion of the metallic tungsten into thin stoichiometric WS2 is achieved by a cyclic approach based on WF6 and H2S pulses at the moderate temperature of 450 1C, which is much lower than usual oxide sulfurization processes. | ||||
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| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000430538000036 | Publication Date | 2018-03-20 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 2050-7526 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 5.256 | Times cited | 4 | Open Access | OpenAccess |
| Notes | This work was supported throughout a strategic fundamental research grant for M. H. by the agency Flanders innovation & entrepreneurship (VLAIO). | Approved | Most recent IF: 5.256 | ||
| Call Number | PLASMANT @ plasmant @c:irua:150968 | Serial | 4921 | ||
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| Author | Berdiyorov, G.R.; Khalilov, U.; Hamoudi, H.; Neyts, E.C. | ||||
| Title | Effect of chemical modification on electronic transport properties of carbyne | Type | A1 Journal article | ||
| Year | 2021 | Publication | Journal Of Computational Electronics | Abbreviated Journal |
J Comput Electron |
| Volume | Issue | Pages | |||
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Using density functional theory in combination with the Green’s functional formalism, we study the effect of surface functionalization on the electronic transport properties of 1D carbon allotrope—carbyne. We found that both hydrogenation and fluorination result in structural changes and semiconducting to metallic transition. Consequently, the current in the functionalization systems increases significantly due to strong delocalization of electronic states along the carbon chain. We also study the electronic transport in partially hydrogenated carbyne and interface structures consisting of pristine and functionalized carbyne. In the latter case, current rectification is obtained in the system with rectification ratio up to 50%. These findings can be useful for developing carbyne-based structures with tunable electronic transport properties. | ||||
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| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000617664900001 | Publication Date | 2021-02-13 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1569-8025 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 1.526 | Times cited | Open Access | OpenAccess | |
| Notes | Computational resources were provided by the research computing facilities of Qatar Environment and Energy Research Institute. Calculations are also conducted using the Turing HPC infrastructure of the CalcUA core facility of the Universiteit Antwerpen, a division of the Flemish Supercomputer Centre VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the University of Antwerp. U. Khalilov gratefully acknowledges financial support from the Fund of Scientific Research Flanders (FWO), Belgium, Grant number 12M1315N. | Approved | Most recent IF: 1.526 | ||
| Call Number | PLASMANT @ plasmant @c:irua:176169 | Serial | 6708 | ||
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| Author | Neyts, E.C.; Thijsse, B.J.; Mees, M.J.; Bal, K.M.; Pourtois, G. | ||||
| Title | 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 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| 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 | Merging Metadynamics into Hyperdynamics: Accelerated Molecular Simulations Reaching Time Scales from Microseconds to Seconds | Type | A1 Journal article | ||
| Year | 2015 | Publication | Journal of chemical theory and computation | Abbreviated Journal |
J Chem Theory Comput |
| Volume | 11 | Issue | 11 | Pages | 4545-4554 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | The hyperdynamics method is a powerful tool to simulate slow processes at the atomic level. However, the construction of an optimal hyperdynamics potential is a task that is far from trivial. Here, we propose a generally applicable implementation of the hyperdynamics algorithm, borrowing two concepts from metadynamics. First, the use of a collective variable (CV) to represent the accelerated dynamics gives the method a very large flexibility and simplicity. Second, a metadynamics procedure can be used to construct a suitable history-dependent bias potential on-the-fly, effectively turning the algorithm into a self-learning accelerated molecular dynamics method. This collective variable-driven hyperdynamics (CVHD) method has a modular design: both the local system properties on which the bias is based, as well as the characteristics of the biasing method itself, can be chosen to match the needs of the considered system. As a result, system-specific details are abstracted from the biasing algorithm itself, making it extremely versatile and transparent. The method is tested on three model systems: diffusion on the Cu(001) surface and nickel-catalyzed methane decomposition, as examples of reactive processes with a bond-length-based CV, and the folding of a long polymer-like chain, using a set of dihedral angles as a CV. Boost factors up to 109, corresponding to a time scale of seconds, could be obtained while still accurately reproducing correct dynamics. | ||||
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| Language | Wos | 000362921700004 | Publication Date | 2015-09-02 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1549-9618 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 5.245 | Times cited | 41 | Open Access | |
| Notes | K.M.B. is funded as Ph.D. fellow (aspirant) of the FWOFlanders (Fund for Scientific Research-Flanders), Grant No. 11 V8915N. The computational resources and services used in this work were provided by the VSC (Flemish Supercomputer Center) and the HPC infrastructure of the University of Antwerp (CalcUA), funded by the Hercules Foundation and the Flemish Government−Department EWI. | Approved | Most recent IF: 5.245; 2015 IF: 5.498 | ||
| Call Number | c:irua:128183 | Serial | 3991 | ||
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| Author | Bal, K.M.; Neyts, E.C. | ||||
| Title | On the time scale associated with Monte Carlo simulations | Type | A1 Journal article | ||
| Year | 2014 | Publication | The journal of chemical physics | Abbreviated Journal |
J Chem Phys |
| Volume | 141 | Issue | 20 | Pages | 204104 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Uniform-acceptance force-bias Monte Carlo (fbMC) methods have been shown to be a powerful technique to access longer timescales in atomistic simulations allowing, for example, phase transitions and growth. Recently, a new fbMC method, the time-stamped force-bias Monte Carlo (tfMC) method, was derived with inclusion of an estimated effective timescale; this timescale, however, does not seem able to explain some of the successes the method. In this contribution, we therefore explicitly quantify the effective timescale tfMC is able to access for a variety of systems, namely a simple single-particle, one-dimensional model system, the Lennard-Jones liquid, an adatom on the Cu(100) surface, a silicon crystal with point defects and a highly defected graphene sheet, in order to gain new insights into the mechanisms by which tfMC operates. It is found that considerable boosts, up to three orders of magnitude compared to molecular dynamics, can be achieved for solid state systems by lowering of the apparent activation barrier of occurring processes, while not requiring any system-specific input or modifications of the method. We furthermore address the pitfalls of using the method as a replacement or complement of molecular dynamics simulations, its ability to explicitly describe correct dynamics and reaction mechanisms, and the association of timescales to MC simulations in general. | ||||
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| Publisher | Place of Publication | New York, N.Y. | Editor | ||
| Language | Wos | 000345641400005 | Publication Date | 2014-11-26 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 0021-9606;1089-7690; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 2.965 | Times cited | 26 | Open Access | |
| Notes | Approved | Most recent IF: 2.965; 2014 IF: 2.952 | |||
| Call Number | UA @ lucian @ c:irua:120667 | Serial | 2459 | ||
| 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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| 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 | ||
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| 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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| 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 | Gou, F.; Neyts, E.; Eckert, M.; Tinck, S.; Bogaerts, A. | ||||
| Title | Molecular dynamics simulations of Cl+ etching on a Si(100) surface | Type | A1 Journal article | ||
| Year | 2010 | Publication | Journal of applied physics | Abbreviated Journal |
J Appl Phys |
| Volume | 107 | Issue | 11 | Pages | 113305,1-113305,6 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Molecular dynamics simulations using improved TersoffBrenner potential parameters were performed to investigate Cl+ etching of a {2×1} reconstructed Si(100) surface. Steady-state Si etching accompanying the Cl coverage of the surface is observed. Furthermore, a steady-state chlorinated reaction layer is formed. The thickness of this reaction layer is found to increase with increasing energy. The stoichiometry of SiClx species in the reaction layer is found to be SiCl:SiCl2:SiCl3 = 1.0:0.14:0.008 at 50 eV. These results are in excellent agreement with available experimental data. While elemental Si products are created by physical sputtering, most SiClx (0<x<4) etch products are produced by chemical-enhanced physical sputtering. | ||||
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| Corporate Author | Thesis | ||||
| Publisher | American Institute of Physics | Place of Publication | New York, N.Y. | Editor | |
| Language | Wos | 000278907100018 | Publication Date | 2010-06-04 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 0021-8979; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 2.068 | Times cited | 15 | Open Access | |
| Notes | Approved | Most recent IF: 2.068; 2010 IF: 2.079 | |||
| Call Number | UA @ lucian @ c:irua:82663 | Serial | 2175 | ||
| Permanent link to this record | |||||
| Author | Neyts, E.; Yan, M.; Bogaerts, A.; Gijbels, R. | ||||
| Title | Particle-in-cell/Monte Carlo simulations of a low-pressure capacitively coupled radio-frequency discharge: effect of adding H2 to an Ar discharge | Type | A1 Journal article | ||
| Year | 2003 | Publication | Journal of applied physics | Abbreviated Journal |
J Appl Phys |
| Volume | 93 | Issue | Pages | 5025-5033 | |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | |||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | American Institute of Physics | Place of Publication | New York, N.Y. | Editor | |
| Language | Wos | 000182296700010 | Publication Date | 2003-04-17 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 0021-8979; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 2.068 | Times cited | 15 | Open Access | |
| Notes | Approved | Most recent IF: 2.068; 2003 IF: 2.171 | |||
| Call Number | UA @ lucian @ c:irua:44012 | Serial | 2562 | ||
| Permanent link to this record | |||||
| Author | Neyts, E.; Bogaerts, A.; van de Sanden, M.C.M. | ||||
| Title | Unraveling the deposition mechanism in a-C:H thin-film growth: a molecular-dynamics study for the reaction behavior of C3 and C3H radicals with a-C:H surfaces | Type | A1 Journal article | ||
| Year | 2006 | Publication | Journal of applied physics | Abbreviated Journal |
J Appl Phys |
| Volume | 99 | Issue | 1 | Pages | 014902,1-8 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | |||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | American Institute of Physics | Place of Publication | New York, N.Y. | Editor | |
| Language | Wos | 000234607200071 | Publication Date | 2006-01-23 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 0021-8979; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 2.068 | Times cited | 25 | Open Access | |
| Notes | Approved | Most recent IF: 2.068; 2006 IF: 2.316 | |||
| Call Number | UA @ lucian @ c:irua:55831 | Serial | 3815 | ||
| Permanent link to this record | |||||
| Author | Neyts, E.C.; van Duin, A.C.T.; Bogaerts, A. | ||||
| Title | Changing chirality during single-walled carbon nanotube growth : a reactive molecular dynamics/Monte Carlo study | Type | A1 Journal article | ||
| Year | 2011 | Publication | Journal of the American Chemical Society | Abbreviated Journal |
J Am Chem Soc |
| Volume | 133 | Issue | 43 | Pages | 17225-17231 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | The growth mechanism and chirality formation of a single-walled carbon nanotube (SWNT) on a surface-bound nickel nanocluster are investigated by hybrid reactive molecular dynamics/force-biased Monte Carlo simulations. The validity of the interatomic potential used, the so-called ReaxFF potential, for simulating catalytic SWNT growth is demonstrated. The SWNT growth process was found to be in agreement with previous studies and observed to proceed through a number of distinct steps, viz., the dissolution of carbon in the metallic particle, the surface segregation of carbon with the formation of aggregated carbon clusters on the surface, the formation of graphitic islands that grow into SWNT caps, and finally continued growth of the SWNT. Moreover, it is clearly illustrated in the present study that during the growth process, the carbon network is continuously restructured by a metal-mediated process, thereby healing many topological defects. It is also found that a cap can nucleate and disappear again, which was not observed in previous simulations. Encapsulation of the nanoparticle is observed to be prevented by the carbon network migrating as a whole over the cluster surface. Finally, for the first time, the chirality of the growing SWNT cap is observed to change from (11,0) over (9,3) to (7,7). It is demonstrated that this change in chirality is due to the metal-mediated restructuring process. | ||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Washington, D.C. | Editor | ||
| Language | Wos | 000297380900026 | Publication Date | 2011-10-06 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 0002-7863;1520-5126; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 13.858 | Times cited | 116 | Open Access | |
| Notes | Approved | Most recent IF: 13.858; 2011 IF: 9.907 | |||
| Call Number | UA @ lucian @ c:irua:92043 | Serial | 309 | ||
| Permanent link to this record | |||||
| Author | Neyts, E.C.; van Duin, A.C.T.; Bogaerts, A. | ||||
| Title | Insights in the plasma-assisted growth of carbon nanotubes through atomic scale simulations : effect of electric field | Type | A1 Journal article | ||
| Year | 2012 | Publication | Journal of the American Chemical Society | Abbreviated Journal |
J Am Chem Soc |
| Volume | 134 | Issue | 2 | Pages | 1256-1260 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | Carbon nanotubes (CNTs) are nowadays routinely grown in a thermal CVD setup. State-of-the-art plasma-enhanced CVD (PECVD) growth, however, offers advantages over thermal CVD. A lower growth temperature and the growth of aligned freestanding single-walled CNTs (SWNTs) makes the technique very attractive. The atomic scale growth mechanisms of PECVD CNT growth, however, remain currently entirely unexplored. In this contribution, we employed molecular dynamics simulations to focus on the effect of applying an electric field on the SWNT growth process, as one of the effects coming into play in PECVD. Using sufficiently strong fields results in (a) alignment of the growing SWNTs, (b) a better ordering of the carbon network, and (c) a higher growth rate relative to thermal growth rate. We suggest that these effects are due to the small charge transfer occurring in the Ni/C system. These simulations constitute the first study of PECVD growth of SWNTs on the atomic level. | ||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Washington, D.C. | Editor | ||
| Language | Wos | 000301084300086 | Publication Date | 2011-11-30 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 0002-7863;1520-5126; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 13.858 | Times cited | 56 | Open Access | |
| Notes | Approved | Most recent IF: 13.858; 2012 IF: 10.677 | |||
| Call Number | UA @ lucian @ c:irua:97163 | Serial | 1673 | ||
| Permanent link to this record | |||||