| Records |
| Author |
Cuypers, B.; Vermeylen, S.; Hammerschmid, D.; Trashin, S.; Rahemi, V.; Konijnenberg, A.; De Schutter, A.; Cheng, C.-H.C.; Giordano, D.; Verde, C.; De Wael, K.; Sobott, F.; Dewilde, S.; Van Doorslaer, S. |
| Title |
Antarctic fish versus human cytoglobins : the same but yet so different |
Type |
A1 Journal article |
| Year |
2017 |
Publication  |
Journal of inorganic biochemistry |
Abbreviated Journal |
J Inorg Biochem |
| Volume |
173 |
Issue |
|
Pages |
66-78 |
| Keywords |
A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation) |
| Abstract |
The cytoglobins of the Antarctic fish Chaenocephalus aceratus and Dissostichus mawsoni have many features in common with human cytoglobin. These cytoglobins are heme proteins in which the ferric and ferrous forms have a characteristic hexacoordination of the heme iron, i.e. axial ligation of two endogenous histidine residues, as confirmed by electron paramagnetic resonance, resonance Raman and optical absorption spectroscopy. The combined spectroscopic analysis revealed only small variations in the heme-pocket structure, in line with the small variations observed for the redox potential. Nevertheless, some striking differences were also discovered. Resonance Raman spectroscopy showed that the stabilization of an exogenous heme ligand, such as CO, occurs differently in human cytoglobin in comparison with Antarctic fish cytoglobins. Furthermore, while it has been extensively reported that human cytoglobin is essentially monomeric and can form an intramolecular disulfide bridge that can influence the ligand binding kinetics, 3D modeling of the Antarctic fish cytoglobins indicates that the cysteine residues are too far apart to form such an intramolecular bridge. Moreover, gel filtration and mass spectrometry reveal the occurrence of non-covalent multimers (up to pentamers) in the Antarctic fish cytoglobins that are formed at low concentrations. Stabilization of these oligomers by disulfide-bridge formation is possible, but not essential. If intermolecular disulfide bridges are formed, they influence the heme-pocket structure, as is shown by EPR measurements. |
| Address |
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| Corporate Author |
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Thesis |
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| Publisher |
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Place of Publication |
|
Editor |
|
| Language |
|
Wos |
000405159600007 |
Publication Date |
2017-04-28 |
| Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
| Series Volume |
|
Series Issue |
|
Edition |
|
| ISSN |
0162-0134 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| Impact Factor |
3.348 |
Times cited |
7 |
Open Access |
|
| Notes |
; The authors acknowledge the support of the University of Antwerp GOA-BOF funding (28312), FWO funding (G.0687.13) and the Hercules foundation for funding of the Synapt G2 instrument. This study was carried out in the framework of the SCAR program “Antarctic Thresholds – Ecosystem Resilience and Adaptation” (AnT-ERA). It was financially supported by the Italian National Program for Antarctic Research (PNRA). Research of A. De Schutter is funded by a PhD grant of the Agency for Innovation by Science and Technology (121339) (IWT, Belgium). C-H C. Cheng acknowledges funding support from US National Science Foundation Polar Programs (ANT-1142158). ; |
Approved |
Most recent IF: 3.348 |
| Call Number |
UA @ admin @ c:irua:144826 |
Serial |
5474 |
| Permanent link to this record |
| |
|
| |
| Author |
Vandelannoote, R.; Blommaert, W.; Sadurski, A.; Van 'T Dack, L.; Gijbels, R.; Van Grieken, R.; Bosch, B.; Leleu, M.; Rochon, J.; Sarcia, C.; Sureau, J.F.; |
| Title |
Trace-elemental anomalies in surface water near a small lead-zinc mineralization at Menez-Albot (Brittany, France) |
Type |
A1 Journal article |
| Year |
1984 |
Publication |
Journal of geochemical exploration |
Abbreviated Journal |
J Geochem Explor |
| Volume |
20 |
Issue |
1 |
Pages |
33-46 |
| Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation) |
| Abstract |
Sensitive multi-element analysis techniques were applied to water samples collected in the vicinity of a small Zn-Pb-Cu sulfide mineralization in the region of Menez-Albot (Finistère, France). The variation of the trace-element content along a local stream shows the presence of the mineralization, mainly through a simultaneous positive anomaly in solution for a group of about 10 elements (e.g. Ni, Cu, Zn, As, Sb) which are connected with this type of mineralization. The anomaly decreases steeply due to the influx of swamp water rich in Fe, Mn and organic matter. The precipitation barrier is reflected in the stream sediment composition. Contamination from fertilizers was observed in some samples. |
| Address |
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| Corporate Author |
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Thesis |
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| Publisher |
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Place of Publication |
Amsterdam |
Editor |
|
| Language |
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Wos |
A1984SF42900004 |
Publication Date |
2003-08-07 |
| Series Editor |
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Series Title |
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Abbreviated Series Title |
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| Series Volume |
|
Series Issue |
|
Edition |
|
| ISSN |
0375-6742; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| Impact Factor |
2.747 |
Times cited |
4 |
Open Access |
|
| Notes |
|
Approved |
no |
| Call Number |
UA @ lucian @ c:irua:111449 |
Serial |
3695 |
| Permanent link to this record |
| |
|
| |
| Author |
Prituzhalov, V.A.; Ardashnikova, E.I.; Vinogradov, A.A.; Dolgikh, V.A.; Videau, J.-J.; Fargin, E.; Abakumov, A.M.; Tarakina, N.V.; Van Tendeloo, G. |
| Title |
New anion-conducting solid solutions Bi1-xTex(O,F)2+\delta (x > 0.5) and glassceramic material on their base |
Type |
A1 Journal article |
| Year |
2011 |
Publication |
Journal of fluorine chemistry |
Abbreviated Journal |
J Fluorine Chem |
| Volume |
132 |
Issue |
12 |
Pages |
1110-1116 |
| Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
| Abstract |
The anion-excess fluorite-like solid solutions with general composition Bi1−xTex(O,F)2+δ (x > 0.5) have been synthesized by a solid state reaction of TeO2, BiF3 and Bi2O3 at 873 K with following quenching. The homogeneity areas and polymorphism of the I ↔ IV Bi1−xTex(O,F)2+δ phases were investigated. The crystal structure of the low temperature IV-Bi1−xTex(O,F)2+δ phase has been solved using electron diffraction and X-ray powder diffraction (a = 11.53051(9) Å, S.G. Ia-3, RI = 0.046, RP = 0.041). Glass formation area in the Bi2O3BiF3TeO2 (10% TiO2) system was investigated. IVBi1−xTex(O,F)2+δ phase starts to crystallize at short-time (0.53 h) annealing of oxyfluoride glasses at temperatures above Tg (600615 K). The ionic conductivity of the crystalline Bi1−xTex(O,F)2+δ phase and corresponding glass-ceramics was investigated. Activation energy of conductivity Ea = 0.41(2) eV for the IV-Bi1−xTex(O,F)2+δ crystalline samples and Ea = 0.73 eV for the glass-ceramic samples were obtained. Investigation of the oxyfluoride samples with a constant cation ratio demonstrates essential influence of excess fluorine anions on the ionic conductivity. |
| Address |
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| Corporate Author |
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Thesis |
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| Publisher |
|
Place of Publication |
Lausanne |
Editor |
|
| Language |
|
Wos |
000296936300011 |
Publication Date |
2011-07-07 |
| Series Editor |
|
Series Title |
|
Abbreviated Series Title |
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| Series Volume |
|
Series Issue |
|
Edition |
|
| ISSN |
0022-1139; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| Impact Factor |
2.101 |
Times cited |
2 |
Open Access |
|
| Notes |
|
Approved |
Most recent IF: 2.101; 2011 IF: 2.033 |
| Call Number |
UA @ lucian @ c:irua:93687 |
Serial |
2305 |
| Permanent link to this record |
| |
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| |
| Author |
Loenders, B.; Michiels, R.; Bogaerts, A. |
| Title |
Is a catalyst always beneficial in plasma catalysis? Insights from the many physical and chemical interactions |
Type |
A1 Journal Article |
| Year |
2023 |
Publication |
Journal of Energy Chemistry |
Abbreviated Journal |
Journal of Energy Chemistry |
| Volume |
85 |
Issue |
|
Pages |
501-533 |
| Keywords |
A1 Journal Article; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ; |
| Abstract |
Plasma-catalytic dry reforming of CH4 (DRM) is promising to convert the greenhouse gasses CH4 and CO2 into value-added chemicals, thus simultaneously providing an alternative to fossil resources as feedstock for the chemical industry. However, while many experiments have been dedicated to plasma-catalytic DRM, there is no consensus yet in literature on the optimal choice of catalyst for targeted products, because the underlying mechanisms are far from understood. Indeed, plasma catalysis is very complex, as it encompasses various chemical and physical interactions between plasma and catalyst, which depend on many parameters. This complexity hampers the comparison of experimental results from different studies, which, in our opinion, is an important bottleneck in the further development of this promising research field. Hence, in this perspective paper, we describe the important physical and chemical effects that should be accounted for when designing plasma-catalytic experiments in general, highlighting the need for standardized experimental setups, as well as careful documentation of packing properties and reaction conditions, to further advance this research field. On the other hand, many parameters also create many windows of opportunity for further optimizing plasma-catalytic systems. Finally, various experiments also reveal the lack of improvement in plasma catalysis compared to plasma-only, specifically for DRM, but the underlying mechanisms are unclear. Therefore, we present our newly developed coupled plasma-surface kinetics model for DRM, to provide more insight in the underlying reasons. Our model illustrates that transition metal catalysts can adversely affect plasmacatalytic DRM, if radicals dominate the plasma-catalyst interactions. Thus, we demonstrate that a good understanding of the plasma-catalyst interactions is crucial to avoiding conditions at which these interactions negatively affect the results, and we provide some recommendations for improvement. For instance, we believe that plasma-catalytic DRM may benefit more from higher reaction temperatures, at which vibrational excitation can enhance the surface reactions. |
| Address |
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| Corporate Author |
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Thesis |
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| Publisher |
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Place of Publication |
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Editor |
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| Language |
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Wos |
|
Publication Date |
2023-06-30 |
| Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
| Series Volume |
|
Series Issue |
|
Edition |
|
| ISSN |
2095-4956 |
ISBN |
|
Additional Links |
UA library record |
| Impact Factor |
13.1 |
Times cited |
|
Open Access |
Not_Open_Access |
| Notes |
This research was supported by the FWO-SBO project PlasMa- CatDESIGN (FWO grant ID S001619N), the FWO fellowship of R. Michiels (FWO grant ID 1114921N), and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 810182 – SCOPE ERC Synergy project). 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 Research Foundation – Flanders (FWO) and the Flemish Government. |
Approved |
Most recent IF: 13.1; 2023 IF: 2.594 |
| Call Number |
PLASMANT @ plasmant @c:irua:198159 |
Serial |
8806 |
| Permanent link to this record |
| |
|
| |
| Author |
Wanten, B.; Vertongen, R.; De Meyer, R.; Bogaerts, A. |
| Title |
Plasma-based CO2 conversion: How to correctly analyze the performance? |
Type |
A1 journal article |
| Year |
2023 |
Publication |
Journal of Energy Chemistry |
Abbreviated Journal |
Journal of Energy Chemistry |
| Volume |
86 |
Issue |
|
Pages |
180-196 |
| Keywords |
A1 journal article; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ; |
| Abstract |
|
| Address |
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| Corporate Author |
|
Thesis |
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| Publisher |
|
Place of Publication |
|
Editor |
|
| Language |
|
Wos |
001070885000001 |
Publication Date |
2023-07-22 |
| Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
| Series Volume |
|
Series Issue |
|
Edition |
|
| ISSN |
2095-4956 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| Impact Factor |
13.1 |
Times cited |
|
Open Access |
Not_Open_Access |
| Notes |
We acknowledge financial support from the Fund for Scientific Research (FWO) Flanders (Grant ID 110221N), the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Program (grant agreement No 810182 – SCOPE ERC Synergy project), and the Methusalem funding of the University of Antwerp. We acknowledge the icons from the graphical abstract made by dDara, geotatah, Spashicons and Freepik on www.flaticon.com. We also thank Stein Maerivoet, Joachim Slaets, Elizabeth Mercer, Colín Ó’Modráin, Joran Van Turnhout, Pepijn Heirman, dr. Yury Gorbanev, dr. Fanny Girard-Sahun and dr. Sean Kelly for the interesting discussions and feedback. |
Approved |
Most recent IF: 13.1; 2023 IF: 2.594 |
| Call Number |
PLASMANT @ plasmant @c:irua:198709 |
Serial |
8816 |
| Permanent link to this record |
| |
|
| |
| Author |
Cai, Y.; Mei, D.; Chen, Y.; Bogaerts, A.; Tu, X. |
| Title |
Machine learning-driven optimization of plasma-catalytic dry reforming of methane |
Type |
A1 Journal Article |
| Year |
2024 |
Publication |
Journal of Energy Chemistry |
Abbreviated Journal |
Journal of Energy Chemistry |
| Volume |
96 |
Issue |
|
Pages |
153-163 |
| Keywords |
A1 Journal Article; Plasma catalysis Machine learning Process optimization Dry reforming of methane Syngas production; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ; |
| Abstract |
This study investigates the dry reformation of methane (DRM) over Ni/Al2O3 catalysts in a dielectric barrier discharge (DBD) non-thermal plasma reactor. A novel hybrid machine learning (ML) model is developed to optimize the plasma-catalytic DRM reaction with limited experimental data. To address the non-linear and complex nature of the plasma-catalytic DRM process, the hybrid ML model integrates three well-established algorithms: regression trees, support vector regression, and artificial neural networks. A genetic algorithm (GA) is then used to optimize the hyperparameters of each algorithm within the hybrid ML model. The ML model achieved excellent agreement with the experimental data, demonstrating its efficacy in accurately predicting and optimizing the DRM process. The model was subsequently used to investigate the impact of various operating parameters on the plasma-catalytic DRM performance. We found that the optimal discharge power (20 W), CO2/CH4 molar ratio (1.5), and Ni loading (7.8 wt%) resulted in the maximum energy yield at a total flow rate of 51 mL/min. Furthermore, we investigated the relative significance of each operating parameter on the performance of the plasmacatalytic DRM process. The results show that the total flow rate had the greatest influence on the conversion, with a significance exceeding 35% for each output, while the Ni loading had the least impact on the overall reaction performance. This hybrid model demonstrates a remarkable ability to extract valuable insights from limited datasets, enabling the development and optimization of more efficient and selective plasma-catalytic chemical processes. |
| Address |
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| Corporate Author |
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Thesis |
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| Publisher |
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Place of Publication |
|
Editor |
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| Language |
|
Wos |
|
Publication Date |
2024-04-25 |
| Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
| Series Volume |
|
Series Issue |
|
Edition |
|
| ISSN |
2095-4956 |
ISBN |
|
Additional Links |
|
| Impact Factor |
13.1 |
Times cited |
|
Open Access |
|
| Notes |
This project received funding from the European Union’s Hori- zon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 813393. |
Approved |
Most recent IF: 13.1; 2024 IF: 2.594 |
| Call Number |
PLASMANT @ plasmant @ |
Serial |
9124 |
| Permanent link to this record |
| |
|
| |
| Author |
Bottari, F.; De Wael, K. |
| Title |
Electrodeposition of gold nanoparticles on boron doped diamond electrodes for the enhanced reduction of small organic molecules |
Type |
A1 Journal article |
| Year |
2017 |
Publication |
Journal of electroanalytical chemistry : an international journal devoted to all aspects of electrode kynetics, interfacial structure, properties of electrolytes, colloid and biological electrochemistry. |
Abbreviated Journal |
J Electroanal Chem |
| Volume |
801 |
Issue |
|
Pages |
521-526 |
| Keywords |
A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation) |
| Abstract |
The performance of gold nanoparticles electrodeposited on boron doped diamond (BDD) electrodes was investigated in respect to the reduction of chloramphenicol (CAP), an antibiotic of the phenicols family. The chosen deposition protocol, three nucleation-growing pulses, shows a remarkable surface coverage, with an even distribution of average-sized gold particles (~ 50 nm), and it was proven capable of generating a three-fold increase in the CAP reduction current. A calibration plot for CAP detection was obtained in the micromolar range (535 μM) with good correlation coefficient (0.9959) and an improved sensitivity of 0.053 μA μM− 1 mm− 2 compared to the electrochemistry of CAP at a bare BDD electrode. |
| Address |
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| Corporate Author |
|
Thesis |
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| Publisher |
|
Place of Publication |
|
Editor |
|
| Language |
|
Wos |
000411847500065 |
Publication Date |
2017-08-02 |
| Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
| Series Volume |
|
Series Issue |
|
Edition |
|
| ISSN |
1572-6657 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| Impact Factor |
3.012 |
Times cited |
4 |
Open Access |
|
| Notes |
; This work was financially supported by the University of Antwerp (BOF) and the Research Foundation Flanders (FWO) (project G037415N). ; |
Approved |
Most recent IF: 3.012 |
| Call Number |
UA @ admin @ c:irua:146372 |
Serial |
5600 |
| Permanent link to this record |
| |
|
| |
| Author |
Barich, H.; Cánovas, R.; De Wael, K. |
| Title |
Electrochemical identification of hazardous phenols and their complex mixtures in real samples using unmodified screen-printed electrodes |
Type |
A1 Journal article |
| Year |
2022 |
Publication |
Journal of electroanalytical chemistry : an international journal devoted to all aspects of electrode kynetics, interfacial structure, properties of electrolytes, colloid and biological electrochemistry. |
Abbreviated Journal |
J Electroanal Chem |
| Volume |
904 |
Issue |
|
Pages |
115878 |
| Keywords |
A1 Journal article; Engineering sciences. Technology; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation); Antwerp Electrochemical and Analytical Sciences Lab (A-Sense Lab) |
| Abstract |
The electrochemical behavior of some of the most relevant endocrine-disrupting phenols using unmodified carbon screen-printed electrodes (SPEs) is described for the first time. Experiments were made to assess the electrochemical behavior of phenol (PHOH), pentachlorophenol (PCP), 4-tert octylphenol (OP) and bisphenol A (BPA) and their determination in the most favorable conditions, using voltammetric methods such as cyclic voltammetry (CV), linear sweep voltammetry (LSV) and square wave voltammetry (SWV) in Britton Robinson (BR) buffer. Further, the usefulness of the electrochemical approach was validated with real samples from a local river and was compared to commercial phenols test kit, which is commonly used for on-site screening in industrial streams and wastewaters. Finally, the approach was compared with a lab-bench standard method using real samples, i.e., high-performance liquid chromatography with a photodiode array detector (HPLC-DAD). |
| Address |
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| Corporate Author |
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Thesis |
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| Publisher |
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Place of Publication |
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Editor |
|
| Language |
|
Wos |
000741151200005 |
Publication Date |
2021-11-14 |
| Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
| Series Volume |
|
Series Issue |
|
Edition |
|
| ISSN |
1572-6657; 1873-2569 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| Impact Factor |
4.5 |
Times cited |
|
Open Access |
OpenAccess |
| Notes |
|
Approved |
Most recent IF: 4.5 |
| Call Number |
UA @ admin @ c:irua:184384 |
Serial |
7150 |
| Permanent link to this record |
| |
|
| |
| Author |
Ortiz-Aguayo, D.; De Wael, K.; del Valle, M. |
| Title |
Voltammetric sensing using an array of modified SPCE coupled with machine learning strategies for the improved identification of opioids in presence of cutting agents |
Type |
A1 Journal article |
| Year |
2021 |
Publication |
Journal Of Electroanalytical Chemistry |
Abbreviated Journal |
J Electroanal Chem |
| Volume |
902 |
Issue |
|
Pages |
115770 |
| Keywords |
A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation); Antwerp Electrochemical and Analytical Sciences Lab (A-Sense Lab) |
| Abstract |
This work reports the use of modified screen-printed carbon electrodes (SPCEs) for the identification of three drugs of abuse and two habitual cutting agents, caffeine and paracetamol, combining voltammetric sensing and chemometrics. In order to achieve this goal, codeine, heroin and morphine were subjected to Square Wave Voltammetry (SWV) at pH 7, in order to elucidate their electrochemical fingerprints. The optimized SPCEs electrode array, which have a differentiated response for the three oxidizable compounds, was derived from Carbon, Prussian blue, Cobalt (II) phthalocyanine, Copper (II) oxide, Polypyrrole and Palladium nanoparticles ink-modified carbon electrodes. Finally, Principal Component Analysis (PCA) coupled with Silhouette parameter assessment was used to select the most suitable combination of sensors for identification of drugs of abuse in presence of cutting agents. |
| Address |
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| Corporate Author |
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Thesis |
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| Publisher |
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Place of Publication |
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Editor |
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| Language |
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Wos |
000714415500006 |
Publication Date |
2021-10-13 |
| Series Editor |
|
Series Title |
|
Abbreviated Series Title |
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| Series Volume |
|
Series Issue |
|
Edition |
|
| ISSN |
1572-6657; 1873-2569 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| Impact Factor |
3.012 |
Times cited |
|
Open Access |
OpenAccess |
| Notes |
|
Approved |
Most recent IF: 3.012 |
| Call Number |
UA @ admin @ c:irua:184018 |
Serial |
8745 |
| Permanent link to this record |
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| |
| Author |
Martin, J.M.L.; François, J.P.; Gijbels, R. |
| Title |
A critical comparison of MINDO/3, MNDO, AM1 and PM3 for a model problem: carbon clusters C2-C10. An ad hoc reparametrization of MNDO well suited for the accurate prediction of their spectroscopic constants |
Type |
A1 Journal article |
| Year |
1991 |
Publication |
Journal of computational chemistry |
Abbreviated Journal |
J Comput Chem |
| Volume |
12 |
Issue |
|
Pages |
52-70 |
| Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
| Abstract |
|
| Address |
|
| Corporate Author |
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Thesis |
|
| Publisher |
Wiley |
Place of Publication |
New York, N.Y. |
Editor |
|
| Language |
|
Wos |
A1991EQ52200006 |
Publication Date |
0000-00-00 |
| Series Editor |
|
Series Title |
|
Abbreviated Series Title |
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| Series Volume |
|
Series Issue |
|
Edition |
|
| ISSN |
0192-8651; 1096-987x |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| Impact Factor |
3.589 |
Times cited |
76 |
Open Access |
|
| Notes |
|
Approved |
MATERIALS SCIENCE, MULTIDISCIPLINARY 135/271 Q2 # PHYSICS, APPLIED 70/145 Q2 # PHYSICS, CONDENSED MATTER 40/67 Q3 # |
| Call Number |
UA @ lucian @ c:irua:712 |
Serial |
541 |
| Permanent link to this record |
| |
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| |
| Author |
Lemberge, P.; Deraedt, I.; Janssens, K.; van Espen, P. |
| Title |
Quantitative analysis of 16-17th century archaeological glass vessels using PLS regression of EPXMA and μ-XRF data |
Type |
A1 Journal article |
| Year |
2000 |
Publication |
Journal of chemometrics |
Abbreviated Journal |
J Chemometr |
| Volume |
14 |
Issue |
|
Pages |
751-763 |
| Keywords |
A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation); Chemometrics (Mitac 3) |
| Abstract |
|
| Address |
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| Corporate Author |
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Thesis |
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| Publisher |
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Place of Publication |
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Editor |
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| Language |
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Wos |
000090065100026 |
Publication Date |
2002-09-10 |
| Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
| Series Volume |
|
Series Issue |
|
Edition |
|
| ISSN |
0886-9383 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| Impact Factor |
1.884 |
Times cited |
|
Open Access |
|
| Notes |
|
Approved |
Most recent IF: 1.884; 2000 IF: 2.081 |
| Call Number |
UA @ admin @ c:irua:32405 |
Serial |
5793 |
| Permanent link to this record |
| |
|
| |
| 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. |
| Address |
|
| Corporate Author |
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Thesis |
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| Publisher |
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Place of Publication |
|
Editor |
|
| 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. |
| Address |
|
| Corporate Author |
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Thesis |
|
| Publisher |
|
Place of Publication |
|
Editor |
|
| 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 |
| Permanent link to this record |
| |
|
| |
| Author |
Bal, K.M. |
| Title |
Reweighted Jarzynski sampling : acceleration of rare events and free energy calculation with a bias potential learned from nonequilibrium work |
Type |
A1 Journal article |
| Year |
2021 |
Publication |
Journal Of Chemical Theory And Computation |
Abbreviated Journal |
J Chem Theory Comput |
| Volume |
17 |
Issue |
11 |
Pages |
6766-6774 |
| Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
| Abstract |
We introduce a simple enhanced sampling approach for the calculation of free energy differences and barriers along a one-dimensional reaction coordinate. First, a small number of short nonequilibrium simulations are carried out along the reaction coordinate, and the Jarzynski equality is used to learn an approximate free energy surface from the nonequilibrium work distribution. This free energy estimate is represented in a compact form as an artificial neural network and used as an external bias potential to accelerate rare events in a subsequent molecular dynamics simulation. The final free energy estimate is then obtained by reweighting the equilibrium probability distribution of the reaction coordinate sampled under the influence of the external bias. We apply our reweighted Jarzynski sampling recipe to four processes of varying scales and complexities.spanning chemical reaction in the gas phase, pair association in solution, and droplet nucleation in supersaturated vapor. In all cases, we find reweighted Jarzynski sampling to be a very efficient strategy, resulting in rapid convergence of the free energy to high precision. |
| Address |
|
| Corporate Author |
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Thesis |
|
| Publisher |
|
Place of Publication |
|
Editor |
|
| Language |
|
Wos |
000718183600008 |
Publication Date |
2021-10-29 |
| 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 |
|
Open Access |
OpenAccess |
| Notes |
|
Approved |
Most recent IF: 5.245 |
| Call Number |
UA @ admin @ c:irua:184676 |
Serial |
8479 |
| Permanent link to this record |
| |
|
| |
| Author |
Sóti, V.; Jacquet, N.; Apers, S.; Richel, A.; Lenaerts, S.; Cornet, I. |
| Title |
Monitoring the laccase reaction of vanillin and poplar hydrolysate |
Type |
A1 Journal article |
| Year |
2016 |
Publication |
Journal of chemical technology and biotechnology |
Abbreviated Journal |
J Chem Technol Biot |
| Volume |
91 |
Issue |
6 |
Pages |
1914-1922 |
| Keywords |
A1 Journal article; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL); Biochemical Wastewater Valorization & Engineering (BioWaVE) |
| Abstract |
BACKGROUND Laccase is an intensively researched enzyme for industrial use. Except for decolorisation measurements, HPLC analysis is the conventional method for monitoring the phenolic removal during laccase enzyme reaction. This paper reports an investigation of the continuous UV absorbance follow-up of the laccase reaction with steam pretreated poplar hydrolysate. RESULTS Vanillin was used as a model substrate and lignocellulose xylose rich fraction (XRF) as a biologically complex substrate for laccase detoxification. The reaction was followed by HPLC-UV as well as by UV spectrometric measurements. Results suggest that the reaction can be successfully monitored by measuring the change of UV absorbance at 280 nm, without previous compound separation. In case of XRF experiments the spectrophotometric follow-up is especially useful, as HPLC analysis takes a long time and provides less information than in case of single substrates. The method seems to be suitable for optimization and process control. CONCLUSION The obtained results can help to construct a fast, easy and straightforward monitoring system for laccase-phenolic substrate reactions. |
| Address |
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| Corporate Author |
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Thesis |
|
| Publisher |
|
Place of Publication |
|
Editor |
|
| Language |
|
Wos |
000375768300040 |
Publication Date |
2015-07-29 |
| Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
| Series Volume |
|
Series Issue |
|
Edition |
|
| ISSN |
0268-2575; 1097-4660 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| Impact Factor |
3.135 |
Times cited |
3 |
Open Access |
|
| Notes |
; This research is financed by the University of Antwerp (project number 15 FA100 002). ; |
Approved |
Most recent IF: 3.135 |
| Call Number |
UA @ admin @ c:irua:127694 |
Serial |
5972 |
| Permanent link to this record |
| |
|
| |
| Author |
Lamoen, D.; Persson, B.N.J. |
| Title |
Adsorption of potassium and oxygen on graphite: a theoretical study |
Type |
A1 Journal article |
| Year |
1998 |
Publication |
Journal Of Chemical Physics |
Abbreviated Journal |
J Chem Phys |
| Volume |
108 |
Issue |
|
Pages |
3332-3341 |
| Keywords |
A1 Journal article; Electron Microscopy for Materials Science (EMAT); |
| Abstract |
|
| Address |
|
| Corporate Author |
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Thesis |
|
| Publisher |
|
Place of Publication |
New York, N.Y. |
Editor |
|
| Language |
|
Wos |
000074379600032 |
Publication Date |
2002-07-26 |
| 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 |
2.965 |
Times cited |
91 |
Open Access |
|
| Notes |
|
Approved |
Most recent IF: 2.965; 1998 IF: 3.147 |
| Call Number |
UA @ lucian @ c:irua:19420 |
Serial |
64 |
| Permanent link to this record |
| |
|
| |
| Author |
Leys, F.E.; March, N.H.; Lamoen, D. |
| Title |
Thermodynamic consistency and integral equations for the liquid structure |
Type |
A1 Journal article |
| Year |
2002 |
Publication |
Journal Of Chemical Physics |
Abbreviated Journal |
J Chem Phys |
| Volume |
117 |
Issue |
|
Pages |
10726 |
| Keywords |
A1 Journal article; Electron Microscopy for Materials Science (EMAT); |
| Abstract |
|
| Address |
|
| Corporate Author |
|
Thesis |
|
| Publisher |
|
Place of Publication |
New York, N.Y. |
Editor |
|
| Language |
|
Wos |
000179495000031 |
Publication Date |
2002-12-02 |
| Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
| Series Volume |
|
Series Issue |
|
Edition |
|
| ISSN |
0021-9606; |
ISBN |
|
Additional Links |
UA library record; WoS full record; |
| Impact Factor |
2.965 |
Times cited |
|
Open Access |
|
| Notes |
|
Approved |
Most recent IF: 2.965; 2002 IF: 2.998 |
| Call Number |
UA @ lucian @ c:irua:41406 |
Serial |
3634 |
| 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 |
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| Corporate Author |
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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 |
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 |
Baskurt, M.; Yagmurcukardes, M.; Peeters, F.M.; Sahin, H. |
| Title |
Stable single-layers of calcium halides (CaX₂, X = F, Cl, Br, I) |
Type |
A1 Journal article |
| Year |
2020 |
Publication |
Journal Of Chemical Physics |
Abbreviated Journal |
J Chem Phys |
| Volume |
152 |
Issue |
16 |
Pages |
164116-164118 |
| Keywords |
A1 Journal article; Condensed Matter Theory (CMT) |
| Abstract |
By means of density functional theory based first-principles calculations, the structural, vibrational, and electronic properties of 1H- and 1T-phases of single-layer CaX2 (X = F, Cl, Br, or I) structures are investigated. Our results reveal that both the 1H- and 1T-phases are dynamically stable in terms of their phonon band dispersions with the latter being the energetically favorable phase for all single-layers. In both phases of single-layer CaX2 structures, significant phonon softening occurs as the atomic radius increases. In addition, each structural phase exhibits distinctive Raman active modes that enable one to characterize either the phase or the structure via Raman spectroscopy. The electronic band dispersions of single-layer CaX2 structures reveal that all structures are indirect bandgap insulators with a decrease in bandgaps from fluorite to iodide crystals. Furthermore, the calculated linear elastic constants, in-plane stiffness, and Poisson ratio indicate the ultra-soft nature of CaX2 single-layers, which is quite important for their nanoelastic applications. Overall, our study reveals that with their dynamically stable 1T- and 1H-phases, single-layers of CaX2 crystals can be alternative ultra-thin insulators. |
| Address |
|
| Corporate Author |
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Thesis |
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| Publisher |
|
Place of Publication |
|
Editor |
|
| Language |
|
Wos |
000531819100001 |
Publication Date |
2020-04-29 |
| 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 |
14 |
Open Access |
|
| Notes |
; Computational resources were provided by TUBITAK ULAKBIM, High Performance and Grid Computing Center (TR-Grid e-Infrastructure). H.S. acknowledges financial support from the TUBITAK under Project No. 117F095. H.S. acknowledges support from the Turkish Academy of Sciences under the GEBIP program. M.Y. was supported by a postdoctoral fellowship from the Flemish Science Foundation (FWO-Vl). ; |
Approved |
Most recent IF: 4.4; 2020 IF: 2.965 |
| Call Number |
UA @ admin @ c:irua:169543 |
Serial |
6615 |
| Permanent link to this record |
| |
|
| |
| Author |
Payne, L.M.; Masia, F.; Zilli, A.; Albrecht, W.; Borri, P.; Langbein, W. |
| Title |
Quantitative morphometric analysis of single gold nanoparticles by optical extinction microscopy: Material permittivity and surface damping effects |
Type |
A1 Journal article |
| Year |
2021 |
Publication |
Journal Of Chemical Physics |
Abbreviated Journal |
J Chem Phys |
| Volume |
154 |
Issue |
4 |
Pages |
044702 |
| Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
| Abstract |
|
| Address |
|
| Corporate Author |
|
Thesis |
|
| Publisher |
|
Place of Publication |
|
Editor |
|
| Language |
|
Wos |
000630495600001 |
Publication Date |
2021-01-28 |
| 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 |
2.965 |
Times cited |
|
Open Access |
OpenAccess |
| Notes |
This work was supported by the Welsh Government Life Sciences Bridging Fund (Grant No. LSBF/R6-005), the UK EPSRC (Grant Nos. EP/I005072/1 and EP/M028313/1), and the European Commission (Grant No. EUSMI E191000350). P.B. acknowledges the Royal Society for her Wolfson research merit award (Grant No. WM140077). F.M. acknowledges the Ser Cymru II programme (Case ID 80762-CU-148) which is part-funded by Cardiff University and the European Regional Development Fund through the Welsh Government. W.A. acknowledges an Individual Fellowship from the Marie Skłodowska-Curie actions (MSCA) under the EU’s Horizon 2020 program (Grant No. 797153, SOPMEN) and Sara Bals for supporting the STEM measurements. The brightfield TEM was performed by Thomas Davies at Cardiff University. We acknowledge Iestyn Pope for technical support of the optical equipment. |
Approved |
Most recent IF: 2.965 |
| Call Number |
EMAT @ emat @c:irua:177566 |
Serial |
6748 |
| Permanent link to this record |
| |
|
| |
| Author |
Hamid, I.; Jalali, H.; Peeters, F.M.; Neek-Amal, M. |
| Title |
Abnormal in-plane permittivity and ferroelectricity of confined water : from sub-nanometer channels to bulk |
Type |
A1 Journal article |
| Year |
2021 |
Publication |
Journal Of Chemical Physics |
Abbreviated Journal |
J Chem Phys |
| Volume |
154 |
Issue |
11 |
Pages |
114503 |
| Keywords |
A1 Journal article; Condensed Matter Theory (CMT) |
| Abstract |
Dielectric properties of nano-confined water are important in several areas of science, i.e., it is relevant in the dielectric double layer that exists in practically all heterogeneous fluid-based systems. Molecular dynamics simulations are used to predict the in-plane dielectric properties of confined water in planar channels of width ranging from sub-nanometer to bulk. Because of suppressed rotational degrees of freedom near the confining walls, the dipole of the water molecules tends to be aligned parallel to the walls, which results in a strongly enhanced in-plane dielectric constant (epsilon (parallel to)) reaching values of about 120 for channels with height 8 angstrom < h < 10 angstrom. With the increase in the width of the channel, we predict that epsilon (parallel to) decreases nonlinearly and reaches the bulk value for h > 70 angstrom. A stratified continuum model is proposed that reproduces the h > 10 angstrom dependence of epsilon (parallel to). For sub-nanometer height channels, abnormal behavior of epsilon (parallel to) is found with two orders of magnitude reduction of epsilon (parallel to) around h similar to 7.5 angstrom, which is attributed to the formation of a particular ice phase that exhibits long-time (similar to mu s) stable ferroelectricity. This is of particular importance for the understanding of the influence of confined water on the functioning of biological systems. |
| Address |
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| Corporate Author |
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Thesis |
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| Publisher |
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Place of Publication |
|
Editor |
|
| Language |
|
Wos |
000629831900001 |
Publication Date |
2021-03-17 |
| 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 |
2.965 |
Times cited |
13 |
Open Access |
OpenAccess |
| Notes |
|
Approved |
Most recent IF: 2.965 |
| Call Number |
UA @ admin @ c:irua:177579 |
Serial |
6967 |
| 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 |
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| Corporate Author |
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Thesis |
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| Publisher |
|
Place of Publication |
|
Editor |
|
| Language |
|
Wos |
000885260600002 |
Publication Date |
2022-11-14 |
| Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
| Series Volume |
|
Series Issue |
|
Edition |
|
| ISSN |
0021-9606 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| Impact Factor |
4.4 |
Times cited |
|
Open Access |
OpenAccess |
| Notes |
|
Approved |
Most recent IF: 4.4 |
| Call Number |
UA @ admin @ c:irua:192076 |
Serial |
7266 |
| Permanent link to this record |
| |
|
| |
| Author |
Bal, K.M. |
| Title |
Nucleation rates from small scale atomistic simulations and transition state theory |
Type |
A1 Journal article |
| Year |
2021 |
Publication |
Journal Of Chemical Physics |
Abbreviated Journal |
J Chem Phys |
| Volume |
155 |
Issue |
14 |
Pages |
144111 |
| Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
| Abstract |
The evaluation of nucleation rates from molecular dynamics trajectories is hampered by the slow nucleation time scale and impact of finite size effects. Here, we show that accurate nucleation rates can be obtained in a very general fashion relying only on the free energy barrier, transition state theory, and a simple dynamical correction for diffusive recrossing. In this setup, the time scale problem is overcome by using enhanced sampling methods, in casu metadynamics, whereas the impact of finite size effects can be naturally circumvented by reconstructing the free energy surface from an appropriate ensemble. Approximations from classical nucleation theory are avoided. We demonstrate the accuracy of the approach by calculating macroscopic rates of droplet nucleation from argon vapor, spanning 16 orders of magnitude and in excellent agreement with literature results, all from simulations of very small (512 atom) systems. |
| Address |
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| Corporate Author |
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Thesis |
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| Publisher |
|
Place of Publication |
|
Editor |
|
| Language |
|
Wos |
000755502100008 |
Publication Date |
2021-09-30 |
| 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 |
2.965 |
Times cited |
|
Open Access |
OpenAccess |
| Notes |
|
Approved |
Most recent IF: 2.965 |
| Call Number |
UA @ admin @ c:irua:184937 |
Serial |
8320 |
| Permanent link to this record |
| |
|
| |
| Author |
Nivesanond, K.; Peeters, A.; Lamoen, D.; van Alsenoy, C. |
| Title |
Conformational analysis of TMC114, a novel HIV-1 protease inhibitor |
Type |
A1 Journal article |
| Year |
2008 |
Publication |
Journal of Chemical Information and Modeling |
Abbreviated Journal |
J Chem Inf Model |
| Volume |
48 |
Issue |
1 |
Pages |
99-108 |
| Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
| Abstract |
|
| Address |
|
| Corporate Author |
|
Thesis |
|
| Publisher |
|
Place of Publication |
|
Editor |
|
| Language |
|
Wos |
000252713700009 |
Publication Date |
2008-01-04 |
| Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
| Series Volume |
|
Series Issue |
|
Edition |
|
| ISSN |
1549-9596;1549-960X; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| Impact Factor |
3.76 |
Times cited |
13 |
Open Access |
|
| Notes |
|
Approved |
Most recent IF: 3.76; 2008 IF: 3.643 |
| Call Number |
UA @ lucian @ c:irua:67463 |
Serial |
491 |
| Permanent link to this record |
| |
|
| |
| Author |
Oliveira, M.C.; Yusupov, M.; Bogaerts, A.; Cordeiro, R.M. |
| Title |
Lipid Oxidation: Role of Membrane Phase-Separated Domains |
Type |
A1 Journal Article |
| Year |
2021 |
Publication |
Journal Of Chemical Information And Modeling |
Abbreviated Journal |
J Chem Inf Model |
| Volume |
61 |
Issue |
6 |
Pages |
2857-2868 |
| Keywords |
A1 Journal Article; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ; |
| Abstract |
Lipid oxidation is associated with several inflammatory and neurodegenerative diseases, but many questions to unravel its effects on biomembranes are still open due to the complexity of the topic. For instance, recent studies indicated that phase-separated domains can have a significant effect on membrane function. It is reported that domain interfaces are “hot spots” for pore formation, but the underlying mechanisms and the effect of oxidation-induced phase separation on membranes remain elusive. Thus, to evaluate the permeability of the membrane coexisting of liquid-ordered (Lo) and liquid-disordered (Ld) domains, we performed atomistic molecular dynamics simulations. Specifically, we studied the membrane permeability of nonoxidized or oxidized homogeneous membranes (single-phase) and at the Lo/Ld domain interfaces of heterogeneous membranes, where the Ld domain is composed of either oxidized or nonoxidized lipids. Our simulation results reveal that the addition of only 1.5% of lipid aldehyde molecules at the Lo/Ld domain interfaces of heterogeneous membranes increases the membrane permeability, whereas their addition at homogeneous membranes does not have any effect. This study is of interest for a better understanding of cancer treatment methods based on oxidative stress (causing among others lipid oxidation), such as plasma medicine and photodynamic therapy. |
| Address |
|
| Corporate Author |
|
Thesis |
|
| Publisher |
|
Place of Publication |
|
Editor |
|
| Language |
|
Wos |
000669541400034 |
Publication Date |
2021-06-28 |
| Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
| Series Volume |
|
Series Issue |
|
Edition |
|
| ISSN |
1549-9596 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| Impact Factor |
3.76 |
Times cited |
|
Open Access |
OpenAccess |
| Notes |
Fonds Wetenschappelijk Onderzoek, 1200219N ; Coordenação de Aperfeiçoamento de Pessoal de NÃvel Superior; We thank Universidade Federal do ABC for providing the computational resources needed for completion of this work and CAPES for the scholarship granted. M.Y. acknowledges the Flanders Research Foundation (grant 1200219N) for financial support. |
Approved |
Most recent IF: 3.76 |
| Call Number |
PLASMANT @ plasmant @c:irua:179766 |
Serial |
6806 |
| Permanent link to this record |
| |
|
| |
| Author |
Ghasemitarei, M.; Privat-Maldonado, A.; Yusupov, M.; Rahnama, S.; Bogaerts, A.; Ejtehadi, M.R. |
| Title |
Effect of Cysteine Oxidation in SARS-CoV-2 Receptor-Binding Domain on Its Interaction with Two Cell Receptors: Insights from Atomistic Simulations |
Type |
A1 Journal article |
| Year |
2022 |
Publication |
Journal Of Chemical Information And Modeling |
Abbreviated Journal |
J Chem Inf Model |
| Volume |
62 |
Issue |
1 |
Pages |
129-141 |
| Keywords |
A1 Journal article; Pharmacology. Therapy; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
| Abstract |
Binding of the SARS-CoV-2 S-glycoprotein to cell receptors is vital for the entry of the virus into cells and subsequent infection. ACE2 is the main cell receptor for SARS-CoV-2, which can attach to the C-terminal receptor-binding domain (RBD) of the SARS-CoV-2 S-glycoprotein. The GRP78 receptor plays an anchoring role, which attaches to the RBD and increases the chance of other RBDs binding to ACE2. Although high levels of reactive oxygen and nitrogen species (RONS) are produced during viral infections, it is not clear how they affect the RBD structure and its binding to ACE2 and GRP78. In this research, we apply molecular dynamics simulations to study the effect of oxidation of the highly reactive cysteine (Cys) amino acids of the RBD on its binding to ACE2 and GRP78. The interaction energy of both ACE2 and GRP78 with the whole RBD, as well as with the RBD main regions, is compared in both the native and oxidized RBDs. Our results show that the interaction energy between the oxidized RBD and ACE2 is strengthened by 155 kJ/mol, increasing the binding of the RBD to ACE2 after oxidation. In addition, the interaction energy between the RBD and GRP78 is slightly increased by 8 kJ/mol after oxidation, but this difference is not significant. Overall, these findings highlight the role of RONS in the binding of the SARS-CoV-2 S-glycoprotein to host cell receptors and suggest an alternative mechanism by which RONS could modulate the entrance of viral particles into the cells. |
| Address |
|
| Corporate Author |
|
Thesis |
|
| Publisher |
|
Place of Publication |
|
Editor |
|
| Language |
|
Wos |
000740019000001 |
Publication Date |
2022-01-10 |
| Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
| Series Volume |
|
Series Issue |
|
Edition |
|
| ISSN |
1549-9596 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| Impact Factor |
5.6 |
Times cited |
|
Open Access |
Not_Open_Access |
| Notes |
Fonds Wetenschappelijk Onderzoek, 1200219N ; Binding of the SARS-CoV-2 S-glycoprotein to cell receptors is vital for the entry of the virus into cells and subsequent infection. ACE2 is the main cell receptor for SARS-CoV-2, which can attach to the C-terminal receptor-binding domain (RBD) of the SARS-CoV-2 S-glycoprotein. The GRP78 receptor plays an anchoring role, which attaches to the RBD and increases the chance of other RBDs binding to ACE2. Although high levels of reactive oxygen and nitrogen species (RONS) are produced during viral infections, it is not clear how they affect the RBD structure and its binding to ACE2 and GRP78. In this research, we apply molecular dynamics simulations to study the effect of oxidation of the highly reactive cysteine (Cys) amino acids of the RBD on its binding to ACE2 and GRP78. The interaction energy of both ACE2 and GRP78 with the whole RBD, as well as with the RBD main regions, is compared in both the native and oxidized RBDs. Our results show that the interaction energy between the oxidized RBD and ACE2 is strengthened by 155 kJ/mol, increasing the binding of the RBD to ACE2 after oxidation. In addition, the interaction energy between the RBD and GRP78 is slightly increased by 8 kJ/mol after oxidation, but this difference is not significant. Overall, these findings highlight the role of RONS in the binding of the SARS-CoV-2 S-glycoprotein to host cell receptors and suggest an alternative mechanism by which RONS could modulate the entrance of viral particles into the cells. |
Approved |
Most recent IF: 5.6 |
| Call Number |
PLASMANT @ plasmant @c:irua:185485 |
Serial |
7050 |
| Permanent link to this record |
| |
|
| |
| Author |
Kummamuru, N.B.; Eimer, D.A.; Idris, Z. |
| Title |
Viscosity measurement and correlation of unloaded and CO₂-loaded aqueous solutions of N-methyldiethanolamine + 2-amino-2-methyl-1-propanol |
Type |
A1 Journal article |
| Year |
2020 |
Publication |
Journal Of Chemical And Engineering Data |
Abbreviated Journal |
J Chem Eng Data |
| Volume |
65 |
Issue |
6 |
Pages |
3072-3078 |
| Keywords |
A1 Journal article; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL) |
| Abstract |
This work contributes to new and complementary experimental viscosity data for blended amine mixtures of aqueous N-methyldiethanolamine + 2-amino-2-methyl-1-propanol (MDEA + AMP) solutions with and without CO2 at different temperatures and mass fractions. For the unloaded MDEA + AMP solutions, measurements were conducted with total amine mass fractions ranging from 0.30 to 0.60. In the case of CO2-loaded aqueous MDEA + AMP solutions, experiments were performed at CO2 loadings ranging from 0.11 to 0.80. Proposed correlations were used to represent viscosity at the unloaded and CO2-loaded solutions within experimental uncertainty. |
| Address |
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| Corporate Author |
|
Thesis |
|
| Publisher |
|
Place of Publication |
|
Editor |
|
| Language |
|
Wos |
000541740100016 |
Publication Date |
2020-05-18 |
| Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
| Series Volume |
|
Series Issue |
|
Edition |
|
| ISSN |
0021-9568; 1520-5134 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| Impact Factor |
2.6 |
Times cited |
|
Open Access |
|
| Notes |
|
Approved |
Most recent IF: 2.6; 2020 IF: 2.323 |
| Call Number |
UA @ admin @ c:irua:180363 |
Serial |
8737 |
| Permanent link to this record |
| |
|
| |
| Author |
Kamaraj, B.; Purohit, R. |
| Title |
Mutational Analysis on Membrane Associated Transporter Protein (MATP) and Their Structural Consequences in Oculocutaeous Albinism Type 4 (OCA4)A Molecular Dynamics Approach |
Type |
A1 Journal article |
| Year |
2016 |
Publication |
Journal of cellular biochemistry |
Abbreviated Journal |
J Cell Biochem |
| Volume |
117 |
Issue |
11 |
Pages |
2608-2619 |
| Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
| Abstract |
|
| Address |
|
| Corporate Author |
|
Thesis |
|
| Publisher |
|
Place of Publication |
New York, N.Y. |
Editor |
|
| Language |
|
Wos |
000383626800017 |
Publication Date |
2016-03-28 |
| Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
| Series Volume |
|
Series Issue |
|
Edition |
|
| ISSN |
0730-2312 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| Impact Factor |
3.085 |
Times cited |
28 |
Open Access |
|
| Notes |
|
Approved |
Most recent IF: 3.085 |
| Call Number |
UA @ lucian @ c:irua:144634 |
Serial |
4671 |
| Permanent link to this record |
| |
|
| |
| Author |
Trashin, S.; De Jong, M.; Luyckx, E.; Dewilde, S.; De Wael, K. |
| Title |
Electrochemical evidence for neuroglobin activity on NO at physiological concentrations |
Type |
A1 Journal article |
| Year |
2016 |
Publication |
Journal of biological chemistry |
Abbreviated Journal |
J Biol Chem |
| Volume |
291 |
Issue |
36 |
Pages |
18959-18966 |
| Keywords |
A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation) |
| Abstract |
The true function of neuroglobin (Ngb) and, particularly, human Ngb (NGB) has been under debate since its discovery 15 years ago. It has been expected to play a role in oxygen binding/supply, but a variety of other functions have been put forward, including NO dioxygenase activity. However, in vitro studies that could unravel these potential roles have been hampered by the lack of an Ngb-specific reductase. In this work, we used electrochemical measurements to investigate the role of an intermittent internal disulfide bridge in determining NO oxidation kinetics at physiological NO concentrations. The use of a polarized electrode to efficiently interconvert the ferric (Fe3+) and ferrous (Fe2+) forms of an immobilized NGB showed that the disulfide bridge both defines the kinetics of NO dioxygenase activity and regulates appearance of the free ferrous deoxy-NGB, which is the redox active form of the protein in contrast to oxy-NGB. Our studies further identified a role for the distal histidine, interacting with the hexacoordinated iron atom of the heme, in oxidation kinetics. These findings may be relevant in vivo, for example in blocking apoptosis by reduction of ferric cytochrome c, and gentle tuning of NO concentration in the tissues. |
| Address |
|
| Corporate Author |
|
Thesis |
|
| Publisher |
|
Place of Publication |
|
Editor |
|
| Language |
|
Wos |
000383242300031 |
Publication Date |
2016-07-12 |
| Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
| Series Volume |
|
Series Issue |
|
Edition |
|
| ISSN |
0021-9258; 1083-351x |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| Impact Factor |
4.125 |
Times cited |
11 |
Open Access |
|
| Notes |
; This work was supported by Fonds Wetenschappelijk Onderzoek (FWO) Grant G.0687.13 and Universiteit Antwerpen GOA BOF 28312. The authors declare that they have no conflicts of interest with the contents of this article. ; |
Approved |
Most recent IF: 4.125 |
| Call Number |
UA @ admin @ c:irua:134340 |
Serial |
5590 |
| Permanent link to this record |
| |
|
| |
| Author |
Pacquets, L.; Irtem, E.; Neukermans, S.; Daems, N.; Bals, S.; Breugelmans, T. |
| Title |
Size-controlled electrodeposition of Cu nanoparticles on gas diffusion electrodes in methanesulfonic acid solution |
Type |
A1 Journal article |
| Year |
2020 |
Publication |
Journal Of Applied Electrochemistry |
Abbreviated Journal |
J Appl Electrochem |
| Volume |
51 |
Issue |
2 |
Pages |
|
| Keywords |
A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT); Applied Electrochemistry & Catalysis (ELCAT) |
| Abstract |
In this paper electrodeposition is used to obtain Cu nanoparticles, as it allows good control over particle size and distribution. These Cu particles were deposited onto a gas diffusion electrode which increased the resulting surface area. Prior to deposition, the surface was pre-treated with NaOH, HNO3, MQ and TX100 to investigate the influence on the electrodeposition of Cu on the gas diffusion electrode (GDE). When using HNO3, the smallest particles with the most homogeneous distribution and high particle roughness were obtained. Once the optimal substrate was determined, we further demonstrated that by altering the electrodeposition parameters, the particle size and density could be tuned. On the one hand, increasing the nucleation potential led to a higher particle density resulting in smaller particles because of an increased competition between particles. Finally, the Cu particle size increased when applying a greater growth charge and growth potential. This fundamental study thus opens up a path towards the synthesis of supported Cu materials with increased surface areas, which is interesting from a catalytic point of view. Larger surface areas are generally correlated with a better catalyst performance and thus higher product yields. This research can contributed in obtaining new insides into the deposition of metallic nanoparticles on rough surfaces. [GRAPHICS] . |
| Address |
|
| Corporate Author |
|
Thesis |
|
| Publisher |
|
Place of Publication |
|
Editor |
|
| Language |
|
Wos |
000568651000001 |
Publication Date |
2020-09-12 |
| Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
| Series Volume |
|
Series Issue |
|
Edition |
|
| ISSN |
0021-891x |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| Impact Factor |
2.9 |
Times cited |
3 |
Open Access |
OpenAccess |
| Notes |
; L. Pacquets was supported through a PhD fellowship strategic basic research (1S56918N) of the Research Foundation-Flanders (FWO). N. Daems was supported through a postdoctoral fellowship (12Y3919N-ND) of the Research Foundation-Flanders (FWO). S. Neukermans was supported through an FWO project grant (G093317N). This research was financed by the research counsel of the university of Antwerp (BOF-GOA 33928). The authors recognize the contribution of Thomas Kenis for analytical validation and methodology. ; |
Approved |
Most recent IF: 2.9; 2020 IF: 2.235 |
| Call Number |
UA @ admin @ c:irua:171588 |
Serial |
6603 |
| Permanent link to this record |
