|   | 
Details
   web
Records
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 (down) 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
Permanent link to this record
 

 
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.
Address
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 (down) 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 Kato, T.; Neyts, E.C.; Abiko, Y.; Akama, T.; Hatakeyama, R.; Kaneko, T.
Title Kinetics of energy selective Cs encapsulation in single-walled carbon nanotubes for damage-free and position-selective doping Type A1 Journal article
Year 2015 Publication The journal of physical chemistry: C : nanomaterials and interfaces Abbreviated Journal J Phys Chem C
Volume 119 Issue 119 Pages 11903-11908
Keywords A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract A method has been developed for damage-free cesium (Cs) encapsulation within single-walled carbon nanotubes (SWNTs) with fine position selectivity. Precise energy tuning of Cs-ion irradiation revealed that there is a clear energy window (2060 eV) for the efficient encapsulation of Cs through the hexagonal network of SWNT sidewalls without causing significant damage. This minimum energy threshold of Cs-ion encapsulation (∼20 eV) matches well with the value obtained by ab initio simulation (∼22 eV). Furthermore, position-selective Cs encapsulation was carried out, resulting in the successful formation of pn-junction SWNT thin films with excellent environmental stability.
Address
Corporate Author Thesis
Publisher Place of Publication Washington, D.C. Editor
Language Wos 000355495600072 Publication Date 2015-05-06
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; WoS citing articles
Impact Factor (down) 4.536 Times cited 3 Open Access
Notes Approved Most recent IF: 4.536; 2015 IF: 4.772
Call Number c:irua:125928 Serial 1760
Permanent link to this record
 

 
Author Khalilov, U.; Pourtois, G.; Huygh, S.; van Duin, A.C.T.; Neyts, E.C.; Bogaerts, A.
Title New mechanism for oxidation of native silicon oxide 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 19 Pages 9819-9825
Keywords A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Continued miniaturization of metal-oxide-semiconductor field-effect transistors (MOSFETs) requires an ever-decreasing thickness of the gate oxide. The structure of ultrathin silicon oxide films, however, critically depends on the oxidation mechanism. Using reactive atomistic simulations, we here demonstrate how the oxidation mechanism in hyperthermal oxidation of such structures may be controlled by the oxidation temperature and the oxidant energy. Specifically, we study the interaction of hyperthermal oxygen with energies of 15 eV with thin SiOx (x ≤ 2) films with a native oxide thickness of about 10 Å. We analyze the oxygen penetration depth probability and compare with results of the hyperthermal oxidation of a bare Si(100){2 × 1} (c-Si) surface. The temperature-dependent oxidation mechanisms are discussed in detail. Our results demonstrate that, at low (i.e., room) temperature, the penetrated oxygen mostly resides in the oxide region rather than at the SiOx|c-Si interface. However, at higher temperatures, starting at around 700 K, oxygen atoms are found to penetrate and to diffuse through the oxide layer followed by reaction at the c-Si boundary. We demonstrate that hyperthermal oxidation resembles thermal oxidation, which can be described by the DealGrove model at high temperatures. Furthermore, defect creation mechanisms that occur during the oxidation process are also analyzed. This study is useful for the fabrication of ultrathin silicon oxide gate oxides for metal-oxide-semiconductor devices as it links parameters that can be straightforwardly controlled in experiment (oxygen temperature, velocity) with the silicon oxide structure.
Address
Corporate Author Thesis
Publisher Place of Publication Washington, D.C. Editor
Language Wos 000319649100032 Publication Date 2013-04-23
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 (down) 4.536 Times cited 24 Open Access
Notes Approved Most recent IF: 4.536; 2013 IF: 4.835
Call Number UA @ lucian @ c:irua:107989 Serial 2321
Permanent link to this record
 

 
Author Neyts, E.C.; Bogaerts, A.
Title Numerical study of the size-dependent melting mechanisms of nickel nanoclusters Type A1 Journal article
Year 2009 Publication The journal of physical chemistry: C : nanomaterials and interfaces Abbreviated Journal J Phys Chem C
Volume 113 Issue 7 Pages 2771-2776
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Molecular dynamics simulations were used to investigate the size-dependent melting mechanism of nickel nanoclusters of various sizes. The melting process was monitored by the caloric curve, the overall cluster Lindemann index, and the atomic Lindemann index. Size-dependent melting temperatures were determined, and the correct linear dependence on inverse diameter was recovered. We found that the melting mechanism gradually changes from dynamic coexistence melting to surface melting with increasing cluster size. These findings are of importance in better understanding carbon nanotube growth by catalytic chemical vapor deposition as the phase state of the catalyst nanoparticle codetermines the growth mechanism.
Address
Corporate Author Thesis
Publisher Place of Publication Washington, D.C. Editor
Language Wos Publication Date 0000-00-00
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 (down) 4.536 Times cited Open Access
Notes Approved Most recent IF: 4.536; 2009 IF: 4.224
Call Number UA @ lucian @ c:irua:76495 Serial 2410
Permanent link to this record
 

 
Author Khalilov, U.; Pourtois, G.; van Duin, A.C.T.; Neyts, E.C.
Title On the c-Si\mid a-SiO2 interface in hyperthermal Si oxidation at room 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 41 Pages 21856-21863
Keywords A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract The exact structure and properties of the Si vertical bar SiO2 interface are very important in microelectronics and photovoltaic devices such as metal-oxide-semiconductor field-effect transistors (MOSFETs) and solar cells. Whereas Si vertical bar SiO2 structures are traditionally produced by thermal oxidation, hyperthermal oxidation shows a number of promising advantages. However, the Si vertical bar SiO2 interface induced in hyperthermal Si oxidation has not been properly investigated yet. Therefore, in this work, the interface morphology and interfacial stresses during hyperthermal oxidation at room temperature are studied using reactive molecular dynamics simulations based on the ReaxFF potential. Interface thickness and roughness, as well as the bond length and bond angle distributions in the interface are discussed and compared with other models developed for the interfaces induced by traditional thermal oxidation. The formation of a compressive stress is observed. This compressive stress, which at the interface amounts about 2 GPa, significantly slows down the inward silica growth. This value is close to the experimental value in the Si vertical bar SiO2 interface obtained in traditional thermal oxidation.
Address
Corporate Author Thesis
Publisher Place of Publication Washington, D.C. Editor
Language Wos 000309902100026 Publication Date 2012-09-26
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 (down) 4.536 Times cited 27 Open Access
Notes Approved Most recent IF: 4.536; 2012 IF: 4.814
Call Number UA @ lucian @ c:irua:102167 Serial 2458
Permanent link to this record
 

 
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.
Address
Corporate Author Thesis
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 (down) 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
Permanent link to this record
 

 
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.
Address
Corporate Author Thesis
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 (down) 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
Permanent link to this record
 

 
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.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000368562200057 Publication Date 2015-12-21
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 (down) 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
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.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
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 (down) 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 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.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000388429100029 Publication Date 2016-11-17
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 (down) 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
Permanent link to this record
 

 
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.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000396969900037 Publication Date 2017-03-16
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 (down) 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
Permanent link to this record
 

 
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.
Address
Corporate Author Thesis
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 (down) 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
Permanent link to this record
 

 
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.
Address
Corporate Author Thesis
Publisher Place of Publication Washington, D.C. Editor
Language Wos 000406355700050 Publication Date 2017-06-23
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 (down) 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
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.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
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 (down) 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 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.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000461537400035 Publication Date 2019-03-14
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 (down) 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
Permanent link to this record
 

 
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.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000462260700024 Publication Date 2019-02-21
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 (down) 4.536 Times cited 4 Open Access OpenAccess
Notes Approved Most recent IF: 4.536
Call Number UA @ admin @ c:irua:159422 Serial 5281
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.
Address
Corporate Author Thesis
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 (down) 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.
Address
Corporate Author Thesis
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 (down) 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 Amini, M.N.; Altantzis, T.; Lobato, I.; Grzelczak, M.; Sánchez-Iglesias, A.; Van Aert, S.; Liz-Marzán, L.M.; Partoens, B.; Bals, S.; Neyts, E.C.
Title Understanding the Effect of Iodide Ions on the Morphology of Gold Nanorods Type A1 Journal article
Year 2018 Publication Particle and particle systems characterization Abbreviated Journal Part Part Syst Char
Volume 35 Issue 35 Pages 1800051
Keywords A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT); Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract The presence of iodide ions during the growth of gold nanorods strongly affects the shape of the final products, which is proposed to be due to selective iodide adsorption on certain crystallographic facets. Therefore, a detailed structural and morphological characterization of the starting rods is crucial toward understanding this effect. Electron tomography is used to determine the crystallographic indices of the lateral facets of gold nanorods, as well as those present at the tips. Based on this information, density functional theory calculations are used to determine the surface and interface energies of the observed facets and provide insight into the relationship between the amount of iodide ions in the growth solution and the final morphology of anisotropic gold nanoparticles.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000441893400002 Publication Date 2018-06-10
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0934-0866 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor (down) 4.474 Times cited 6 Open Access OpenAccess
Notes This work was supported by the European Research Council (grant 335078 COLOURATOM to S.B.). T.A., S.V.A. S.B. and E.C.N., acknowledge funding from the Research Foundation Flanders (FWO, Belgium), through project funding (G.0218.14N and G.0369.15N) and a postdoctoral grant to T.A. L.M.L.-M. and M.G. acknowledge funding from the Spanish Ministerio de Economía y Competitividad (grant MAT2013-46101-R). Mozhgan N. Amini and Thomas Altantzis contributed equally to this work. (ROMEO:yellow; preprint:; postprint:restricted ; pdfversion:cannot); ecas_sara Approved Most recent IF: 4.474
Call Number EMAT @ emat @c:irua:152998UA @ admin @ c:irua:152998 Serial 5010
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.
Address
Corporate Author Thesis
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 (down) 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 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.
Address
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 (down) 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 Hoon Park, J.; Kumar, N.; Hoon Park, D.; Yusupov, M.; Neyts, E.C.; Verlackt, C.C.W.; Bogaerts, A.; Ho Kang, M.; Sup Uhm, H.; Ha Choi, E.; Attri, P.;
Title A comparative study for the inactivation of multidrug resistance bacteria using dielectric barrier discharge and nano-second pulsed plasma Type A1 Journal article
Year 2015 Publication Scientific reports Abbreviated Journal Sci Rep-Uk
Volume 5 Issue 5 Pages 13849
Keywords A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Bacteria can be inactivated through various physical and chemical means, and these have always been the focus of extensive research. To further improve the methodology for these ends, two types of plasma systems were investigated: nano-second pulsed plasma (NPP) as liquid discharge plasma and an Argon gas-feeding dielectric barrier discharge (Ar-DBD) as a form of surface plasma. To understand the sterilizing action of these two different plasma sources, we performed experiments with Staphylococcus aureus (S. aureus) bacteria (wild type) and multidrug resistant bacteria (Penicillum-resistant, Methicillin-resistant and Gentamicin-resistant). We observed that both plasma sources can inactivate both the wild type and multidrug-resistant bacteria to a good extent. Moreover, we observed a change in the surface morphology, gene expression and β-lactamase activity. Furthermore, we used X-ray photoelectron spectroscopy to investigate the variation in functional groups (C-H/C-C, C-OH and C=O) of the peptidoglycan (PG) resulting from exposure to plasma species. To obtain atomic scale insight in the plasma-cell interactions and support our experimental observations, we have performed molecular dynamics simulations to study the effects of plasma species, such as OH, H2O2, O, O3, as well as O2 and H2O, on the dissociation/formation of above mentioned functional groups in PG.
Address
Corporate Author Thesis
Publisher Nature Publishing Group Place of Publication London Editor
Language Wos 000360909000001 Publication Date 2015-09-09
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 (down) 4.259 Times cited 32 Open Access
Notes Approved Most recent IF: 4.259; 2015 IF: 5.578
Call Number c:irua:127410 Serial 419
Permanent link to this record
 

 
Author Khosravian, N.; Kamaraj, B.; Neyts, E.C.; Bogaerts, A.
Title Structural modification of P-glycoprotein induced by OH radicals: Insights from atomistic simulations Type A1 Journal article
Year 2016 Publication Scientific reports Abbreviated Journal Sci Rep-Uk
Volume 6 Issue 6 Pages 19466
Keywords A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract This study reports on the possible effects of OH radical impact on the transmembrane domain 6 of P-glycoprotein, TM6, which plays a crucial role in drug binding in human cells. For the first time, we employ molecular dynamics (MD) simulations based on the self-consistent charge density functional tight binding (SCC-DFTB) method to elucidate the potential sites of fragmentation and mutation in this domain upon impact of OH radicals, and to obtain fundamental information about the underlying reaction mechanisms. Furthermore, we apply non-reactive MD simulations to investigate the long-term effect of this mutation, with possible implications for drug binding. Our simulations indicate that the interaction of OH radicals with TM6 might lead to the breaking of C-C and C-N peptide bonds, which eventually cause fragmentation of TM6. Moreover, according to our simulations, the OH radicals can yield mutation in the aromatic ring of phenylalanine in TM6, which in turn affects its structure. As TM6 plays an important role in the binding of a range of cytotoxic drugs with P-glycoprotein, any changes in its structure are likely to affect the response of the tumor cell in chemotherapy. This is crucial for cancer therapies based on reactive oxygen species, such as plasma treatment.
Address Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
Corporate Author Thesis
Publisher Place of Publication Editor
Language English Wos 000369573900001 Publication Date 2016-02-09
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 (down) 4.259 Times cited 7 Open Access
Notes The authors acknowledge financial support from the Fund for Scientific 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: 4.259
Call Number c:irua:131610 Serial 4031
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.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
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 (down) 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 Yusupov, M.; Wende, K.; Kupsch, S.; Neyts, E.C.; Reuter, S.; Bogaerts, A.
Title Effect of head group and lipid tail oxidation in the cell membrane revealed through integrated simulations and experiments Type A1 Journal article
Year 2017 Publication Scientific reports Abbreviated Journal Sci Rep-Uk
Volume 7 Issue 7 Pages 5761
Keywords A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract We report on multi-level atomistic simulations for the interaction of reactive oxygen species (ROS) with the head groups of the phospholipid bilayer, and the subsequent effect of head group and lipid tail oxidation on the structural and dynamic properties of the cell membrane. Our simulations are validated by experiments using a cold atmospheric plasma as external ROS source. We found that plasma treatment leads to a slight initial rise in membrane rigidity, followed by a strong and persistent increase in fluidity, indicating a drop in lipid order. The latter is also revealed by our simulations. This study is important for cancer treatment by therapies producing (extracellular) ROS, such as plasma treatment. These ROS will interact with the cell membrane, first oxidizing the head groups, followed by the lipid tails. A drop in lipid order might allow them to penetrate into the cell interior (e.g., through pores created due to oxidation of the lipid tails) and cause intracellular oxidative damage, eventually leading to cell death. This work in general elucidates the underlying mechanisms of ROS interaction with the cell membrane at the atomic level.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000405746500072 Publication Date 2017-07-12
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 (down) 4.259 Times cited 27 Open Access OpenAccess
Notes M.Y. gratefully acknowledges financial support from the Research Foundation – Flanders (FWO), grant number 1200216 N. The computational work was carried out 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. S.R. and S.K. acknowledge funding by the BMBF (FKZ: 03Z2DN12). S.R. acknowledges funding by the Ministry of Education, Science and Culture of the State of Mecklenburg-Vorpommern (AU 15001). The authors thank M. Hammer for the support and discussion in the biophysical studies and J. Van der Paal for the interesting discussions. Approved Most recent IF: 4.259
Call Number PLASMANT @ plasmant @ c:irua:144627 Serial 4630
Permanent link to this record
 

 
Author Schoeters, B.; Neyts, E.C.; Khalilov, U.; Pourtois, G.; Partoens, B.
Title Stability of Si epoxide defects in Si nanowires : a mixed reactive force field/DFT study Type A1 Journal article
Year 2013 Publication Physical chemistry, chemical physics Abbreviated Journal Phys Chem Chem Phys
Volume 15 Issue 36 Pages 15091-15097
Keywords A1 Journal article; Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Modeling the oxidation process of silicon nanowires through reactive force field based molecular dynamics simulations suggests that the formation of Si epoxide defects occurs both at the Si/SiOx interface and at the nanowire surface, whereas for flat surfaces, this defect is experimentally observed to occur only at the interface as a result of stress. In this paper, we argue that the increasing curvature stabilizes the defect at the nanowire surface, as suggested by our density functional theory calculations. The latter can have important consequences for the opto-electronic properties of thin silicon nanowires, since the epoxide induces an electronic state within the band gap. Removing the epoxide defect by hydrogenation is expected to be possible but becomes increasingly difficult with a reduction of the diameter of the nanowires.
Address
Corporate Author Thesis
Publisher Place of Publication Cambridge Editor
Language Wos 000323520600029 Publication Date 2013-07-16
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1463-9076;1463-9084; ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor (down) 4.123 Times cited 3 Open Access
Notes ; BS gratefully acknowledges financial support of the IWT, Institute for the Promotion of Innovation by Science and Technology in Flanders, via the SBO project “SilaSol”. This work was carried out 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 and the Universiteit Antwerpen. ; Approved Most recent IF: 4.123; 2013 IF: 4.198
Call Number UA @ lucian @ c:irua:110793 Serial 3130
Permanent link to this record
 

 
Author Ali, S.; Myasnichenko, V.S.; Neyts, E.C.
Title Size-dependent strain and surface energies of gold nanoclusters Type A1 Journal article
Year 2016 Publication Physical chemistry, chemical physics Abbreviated Journal Phys Chem Chem Phys
Volume 18 Issue 18 Pages 792-800
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract Gold nanocluster properties exhibit unique size-dependence. In this contribution, we employ reactive molecular dynamics simulations to calculate the size- and temperature-dependent surface energies, strain energies and atomic displacements for icosahedral, cuboctahedral, truncated octahedral and decahedral Au-nanoclusters. The calculations demonstrate that the surface energy decreases with increasing cluster size at 0 K but increases with size at higher temperatures. The calculated melting curves as a function of cluster size demonstrate the Gibbs-Thomson effect. Atomic displacements and strain are found to strongly depend on the cluster size and both are found to increase with increasing cluster size. These results are of importance for understanding the size-and temperature-dependent surface processes on gold nanoclusters.
Address
Corporate Author Thesis
Publisher Place of Publication Cambridge Editor
Language Wos 000369480600017 Publication Date 2015-11-18
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1463-9076 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor (down) 4.123 Times cited 37 Open Access
Notes Approved Most recent IF: 4.123
Call Number UA @ lucian @ c:irua:131626 Serial 4243
Permanent link to this record
 

 
Author Dabaghmanesh, S.; Neyts, E.C.; Partoens, B.
Title van der Waals density functionals applied to corundum-type sesquioxides : bulk properties and adsorption of CH3 and C6H6 on (0001) surfaces Type A1 Journal article
Year 2016 Publication Physical chemistry, chemical physics Abbreviated Journal Phys Chem Chem Phys
Volume 18 Issue 18 Pages 23139-23146
Keywords A1 Journal article; Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract van der Waals (vdW) forces play an important role in the adsorption of molecules on the surface of solids. However, the choice of the most suitable vdW functional for different systems is an essential problem which must be addressed for different systems. The lack of a systematic study on the performance of the vdW functionals in the bulk and adsorption properties of metal-oxides motivated us to examine different vdW approaches and compute the bulk and molecular adsorption properties of alpha-Cr2O3, alpha-Fe2O3, and alpha-Al2O3. For the bulk properties, we compared our results for the heat of formation, cohesive energy, lattice parameters and bond distances between the different vdW functionals and available experimental data. Next we studied the adsorption of benzene and CH3 molecules on top of different oxide surfaces. We employed different approximations to exchange and correlation within DFT, namely, the Perdew-Burke-Ernzerhof (PBE) GGA, (PBE)+U, and vdW density functionals [ DFT(vdW-DF/DF2/optPBE/optB86b/optB88)+U] as well as DFT-D2/D3(+U) methods of Grimme for the bulk calculations and optB86b-vdW(+U) and DFT-D2(+U) for the adsorption energy calculations. Our results highlight the importance of vdW interactions not only in the adsorption of molecules, but importantly also for the bulk properties. Although the vdW contribution in the adsorption of CH3 (as a chemisorption interaction) is less important compared to the adsorption of benzene (as a physisorption interaction), this contribution is not negligible. Also adsorption of benzene on ferryl/chromyl terminated surfaces shows an important chemisorption contribution in which the vdW interactions become less significant.
Address
Corporate Author Thesis
Publisher Place of Publication Cambridge Editor
Language Wos 000382109300040 Publication Date 2016-07-27
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1463-9076; 1463-9084 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor (down) 4.123 Times cited 6 Open Access
Notes ; This work was supported by the Strategic Initiative Materials in Flanders (SIM). The computational resources and services used in this work were provided by the Vlaams Supercomputer Centrum (VSC) and the HPC infrastructure of the University of Antwerp. ; Approved Most recent IF: 4.123
Call Number UA @ lucian @ c:irua:135701 Serial 4311
Permanent link to this record
 

 
Author Shirazi, M.; Bogaerts, A.; Neyts, E.C.
Title A DFT study of H-dissolution into the bulk of a crystalline Ni(111) surface: a chemical identifier for the reaction kinetics Type A1 Journal article
Year 2017 Publication Physical chemistry, chemical physics Abbreviated Journal Phys Chem Chem Phys
Volume 19 Issue 19 Pages 19150-19158
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract In this study, we investigated the diffusion of H-atoms to the subsurface and their further diffusion into the bulk of a Ni(111) crystal by means of density functional theory calculations in the context of thermal and plasma-assisted catalysis. The H-atoms at the surface can originate from the dissociative adsorption of H2 or CH4 molecules, determining the surface H-coverage. When a threshold H-coverage is passed, corresponding to 1.00 ML for the crystalline Ni(111) surface, the surface-bound H-atoms start to diffuse to the subsurface. A similar threshold coverage is observed for the interstitial H-coverage. Once the interstitial sites are filled up with a coverage above 1.00 ML of H, dissolution of interstitial H-atoms to the layer below the interstitial sites will be initiated. Hence, by applying a high pressure or inducing a reactive plasma and high temperature, increasing the H-flux to the surface, a large amount of hydrogen can diffuse in a crystalline metal like Ni and can be absorbed. The formation of metal hydride may modify the entire reaction kinetics of the system. Equivalently, the H-atoms in the bulk can easily go back to the surface and release a large amount of heat. In a plasma process, H-atoms are formed in the plasma, and therefore the energy barrier for dissociative adsorption is dismissed, thus allowing achievement of the threshold coverage without applying a high pressure as in a thermal process. As a result, depending on the crystal plane and type of metal, a large number of H-atoms can be dissolved (absorbed) in the metal catalyst, explaining the high efficiency of plasma-assisted catalytic reactions. Here, the mechanism of H-dissolution is established as a chemical identifier for the investigation of the reaction kinetics of a chemical process.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000406334300034 Publication Date 2017-06-22
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1463-9076 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor (down) 4.123 Times cited 10 Open Access OpenAccess
Notes Financial support from the Reactive Atmospheric Plasma processIng – eDucation (RAPID) network, through the EU 7th Framework Programme (grant agreement no. 606889), is gratefully acknowledged. The calculations were performed 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 Universiteit Antwerpen. Approved Most recent IF: 4.123
Call Number PLASMANT @ plasmant @ c:irua:144794 Serial 4633
Permanent link to this record