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Records |
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Author |
Ghasemitarei, M.; Privat-Maldonado, A.; Yusupov, M.; Rahnama, S.; Bogaerts, A.; Ejtehadi, M.R. |
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| |
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 |
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| |
Volume |
62 |
Issue |
1 |
Pages |
129-141 |
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| |
Keywords |
A1 Journal article; Pharmacology. Therapy; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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| |
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. |
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Corporate Author |
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Place of Publication |
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Wos |
000740019000001 |
Publication Date |
2022-01-10 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
|
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| |
ISSN |
1549-9596 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
5.6 |
Times cited |
|
Open Access |
Not_Open_Access |
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| |
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 |
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| |
Call Number |
PLASMANT @ plasmant @c:irua:185485 |
Serial |
7050 |
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| Permanent link to this record |
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Author |
Martin, J.M.L.; François, J.P.; Gijbels, R. |
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Title |
Ab initio study of the structure, infrared spectra and heat of formation of C4 |
Type |
A1 Journal article |
| |
Year |
1991 |
Publication |
The journal of chemical physics |
Abbreviated Journal |
J Chem Phys |
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| |
Volume |
94 |
Issue |
|
Pages |
3753-3761 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
New York, N.Y. |
Editor |
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Language |
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Wos |
A1991FA77800052 |
Publication Date |
0000-00-00 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
|
Series Issue |
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Edition |
|
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| |
ISSN |
0021-9606 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
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| |
Impact Factor |
2.952 |
Times cited |
62 |
Open Access |
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Notes |
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Approved |
no |
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| |
Call Number |
UA @ lucian @ c:irua:715 |
Serial |
38 |
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| Permanent link to this record |
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Author |
Taylor, P.R.; Martin, J.M.L.; François, J.P.; Gijbels, R. |
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Title |
An ab initio study of the C3+ cation using multireference methods |
Type |
A1 Journal article |
| |
Year |
1991 |
Publication |
The journal of chemical physics |
Abbreviated Journal |
J Chem Phys |
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| |
Volume |
95 |
Issue |
|
Pages |
6530-6534 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
New York, N.Y. |
Editor |
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Language |
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Wos |
|
Publication Date |
0000-00-00 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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| |
Series Volume |
|
Series Issue |
|
Edition |
|
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| |
ISSN |
0021-9606 |
ISBN |
|
Additional Links |
UA library record |
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| |
Impact Factor |
2.952 |
Times cited |
|
Open Access |
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| |
Notes |
|
Approved |
no |
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| |
Call Number |
UA @ lucian @ c:irua:720 |
Serial |
39 |
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| Permanent link to this record |
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Author |
Lamoen, D.; Persson, B.N.J. |
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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 |
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| |
Volume |
108 |
Issue |
|
Pages |
3332-3341 |
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Keywords |
A1 Journal article; Electron Microscopy for Materials Science (EMAT); |
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Abstract |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
New York, N.Y. |
Editor |
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Language |
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Wos |
000074379600032 |
Publication Date |
2002-07-26 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
0021-9606; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
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| |
Impact Factor |
2.965 |
Times cited |
91 |
Open Access |
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| |
Notes |
|
Approved |
Most recent IF: 2.965; 1998 IF: 3.147 |
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| |
Call Number |
UA @ lucian @ c:irua:19420 |
Serial |
64 |
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| Permanent link to this record |
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Author |
Nikolaev, A.V.; Prassides, K.; Michel, K.H. |
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| |
Title |
Charge transfer and polymer phases in AC60 (A=K, Rb, Cs) fullerides |
Type |
A1 Journal article |
| |
Year |
1998 |
Publication |
The journal of chemical physics |
Abbreviated Journal |
J Chem Phys |
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| |
Volume |
108 |
Issue |
|
Pages |
4912-4923 |
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Keywords |
A1 Journal article; Condensed Matter Theory (CMT) |
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Abstract |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
New York, N.Y. |
Editor |
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Language |
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Wos |
000072588400025 |
Publication Date |
2002-07-26 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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| |
Series Volume |
|
Series Issue |
|
Edition |
|
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| |
ISSN |
0021-9606; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
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| |
Impact Factor |
2.965 |
Times cited |
14 |
Open Access |
|
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| |
Notes |
|
Approved |
Most recent IF: 2.965; 1998 IF: 3.147 |
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| |
Call Number |
UA @ lucian @ c:irua:23985 |
Serial |
338 |
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| Permanent link to this record |
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Author |
Lamoen, D.; Michel, K.H. |
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Title |
Crystal field, orientational order, and lattice contraction in solid C60 |
Type |
A1 Journal article |
| |
Year |
1994 |
Publication |
The journal of chemical physics |
Abbreviated Journal |
J Chem Phys |
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| |
Volume |
101 |
Issue |
|
Pages |
1435-1443 |
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Keywords |
A1 Journal article; Condensed Matter Theory (CMT) |
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Abstract |
A model of the intermolecular potential in solid C-60, which is based on Born-Mayer repulsions, van der Waals attractions, and electrostatic multipoles, is presented. The potential is expanded in terms of multipolar rotator functions. The orientation-orientation interaction and the crystal field are calculated. The orientational phase transition to the Pa3 phase is studied with the methods of statistical mechanics. The discontinuity of the order parameter at the transition and the temperature evolution of the order parameter are calculated. The lattice contraction at the phase transition is evaluated. The influence of the lattice contraction on the crystal field and on the orientational order is studied. |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
New York, N.Y. |
Editor |
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Language |
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Wos |
A1994NW97900058 |
Publication Date |
2002-07-26 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
0021-9606; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
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| |
Impact Factor |
2.952 |
Times cited |
39 |
Open Access |
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Notes |
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Approved |
CHEMISTRY, PHYSICAL 54/144 Q2 # PHYSICS, ATOMIC, MOLECULAR & CHEMICAL 9/35 Q2 # |
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| |
Call Number |
UA @ lucian @ c:irua:9361 |
Serial |
554 |
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| Permanent link to this record |
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Author |
Verberck, B.; Michel, K.H.; Nikolaev, A.V. |
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Title |
Crystal structures of polymerized fullerides AC60, A=K, Rb, Cs, and alkali-mediated interactions |
Type |
A1 Journal article |
| |
Year |
2002 |
Publication |
The journal of chemical physics |
Abbreviated Journal |
J Chem Phys |
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Volume |
116 |
Issue |
23 |
Pages |
10462-10474 |
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Keywords |
A1 Journal article; Condensed Matter Theory (CMT) |
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Abstract |
Starting from a model of rigid interacting C-60 polymer chains on an orthorhombic lattice, we study the mutual orientation of the chains and the stability of the crystalline structures Pmnn and I2/m. We take into account (i) van der Waals interactions and electric quadrupole interactions between C-60 monomers on different chains as well as (ii) interactions of the monomers with the surrounding alkali atoms. The direct interactions (i) always lead to an antiferrorotational structure Pmnn with alternate orientation of the C-60 chains in planes (001). The interactions (ii) with the alkalis consist of two parts: translation-rotation (TR) coupling where the orientations of the chains interact with displacements of the alkalis, and quadrupolar electronic polarizability (ep) coupling, where the electric quadrupoles on the C-60 monomers interact with induced quadrupoles due to excited electronic d-states of the alkalis. Both interactions (ii) lead to an effective orientation-orientation interaction between the C-60 chains and always favor the ferrorotational structure I2/m, where C-60 chains have a same orientation. The structures Pmnn for KC60 and I2/m for Rb- and CsC60 are the result of a competition between the direct interaction (i) and the alkali-mediated interactions (ii). In Rb- and CsC60 the latter are found to be dominant, the preponderant role being played by the quadrupolar electronic polarizability of the alkali ions. (C) 2002 American Institute of Physics. |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
New York, N.Y. |
Editor |
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Language |
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Wos |
000175905800044 |
Publication Date |
2002-07-26 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
|
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ISSN |
0021-9606; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
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| |
Impact Factor |
2.965 |
Times cited |
12 |
Open Access |
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Notes |
|
Approved |
Most recent IF: 2.965; 2002 IF: 2.998 |
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| |
Call Number |
UA @ lucian @ c:irua:103350 |
Serial |
578 |
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| Permanent link to this record |
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Author |
Singh, S.K.; Neek-Amal, M.; Peeters, F.M. |
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Title |
Electronic properties of graphene nano-flakes : energy gap, permanent dipole, termination effect, and Raman spectroscopy |
Type |
A1 Journal article |
| |
Year |
2014 |
Publication |
The journal of chemical physics |
Abbreviated Journal |
J Chem Phys |
|
| |
Volume |
140 |
Issue |
7 |
Pages |
074304-74309 |
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Keywords |
A1 Journal article; Condensed Matter Theory (CMT) |
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| |
Abstract |
The electronic properties of graphene nano-flakes (GNFs) with different edge passivation are investigated by using density functional theory. Passivation with F and H atoms is considered: C-Nc X-Nx (X = F or H). We studied GNFs with 10 < N-c < 56 and limit ourselves to the lowest energy configurations. We found that: (i) the energy difference Delta between the highest occupied molecular orbital and the lowest unoccupied molecular orbital decreases with N-c, (ii) topological defects (pentagon and heptagon) break the symmetry of the GNFs and enhance the electric polarization, (iii) the mutual interaction of bilayer GNFs can be understood by dipole-dipole interaction which were found sensitive to the relative orientation of the GNFs, (iv) the permanent dipoles depend on the edge terminated atom, while the energy gap is independent of it, and (v) the presence of heptagon and pentagon defects in the GNFs results in the largest difference between the energy of the spin-up and spin-down electrons which is larger for the H-passivated GNFs as compared to F-passivated GNFs. Our study shows clearly the effect of geometry, size, termination, and bilayer on the electronic properties of small GNFs. This study reveals important features of graphene nano-flakes which can be detected using Raman spectroscopy. (C) 2014 AIP Publishing LLC. |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
New York, N.Y. |
Editor |
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Language |
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Wos |
000332039900020 |
Publication Date |
2014-02-20 |
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Series Editor |
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Series Title |
|
Abbreviated Series Title |
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Series Volume |
|
Series Issue |
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Edition |
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ISSN |
0021-9606;1089-7690; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
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| |
Impact Factor |
2.965 |
Times cited |
30 |
Open Access |
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Notes |
; This work was supported by the EU-Marie Curie IIF postdoctoral Fellowship/ 299855 (for M. N.-A.), the ESF-EuroGRAPHENE project CONGRAN, the Flemish Science Foundation (FWO-Vl), and the Methusalem Foundation of the Flemish Government. ; |
Approved |
Most recent IF: 2.965; 2014 IF: 2.952 |
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| |
Call Number |
UA @ lucian @ c:irua:115857 |
Serial |
1002 |
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| Permanent link to this record |
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Author |
Martin, J.M.L.; François, J.P.; Gijbels, R. |
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Title |
First principles computation of thermo-chemical properties beyond the harmonic approximation: 1: method and application to the water molecule and its isotopomers |
Type |
A1 Journal article |
| |
Year |
1992 |
Publication |
The journal of chemical physics |
Abbreviated Journal |
J Chem Phys |
|
| |
Volume |
96 |
Issue |
10 |
Pages |
7633-7645 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
New York, N.Y. |
Editor |
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Language |
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Wos |
A1992HU55700047 |
Publication Date |
0000-00-00 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
0021-9606 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
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| |
Impact Factor |
2.952 |
Times cited |
59 |
Open Access |
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Notes |
|
Approved |
no |
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| |
Call Number |
UA @ lucian @ c:irua:4195 |
Serial |
1206 |
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| Permanent link to this record |
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Author |
Martin, J.M.L.; François, J.P.; Gijbels, R. |
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Title |
First principles computation of thermo-chemical properties beyond the harmonic approximation: 2: application to the amino radical and its isotopomers |
Type |
A1 Journal article |
| |
Year |
1992 |
Publication |
The journal of chemical physics |
Abbreviated Journal |
J Chem Phys |
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| |
Volume |
97 |
Issue |
5 |
Pages |
3530-3536 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
New York, N.Y. |
Editor |
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Language |
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Wos |
A1992JL37200072 |
Publication Date |
0000-00-00 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
0021-9606 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.952 |
Times cited |
22 |
Open Access |
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Notes |
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Approved |
no |
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| |
Call Number |
UA @ lucian @ c:irua:4197 |
Serial |
1207 |
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| Permanent link to this record |
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Author |
Michel, K.H. |
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Title |
Molecular structure and orientational ordering in solid C60 |
Type |
A1 Journal article |
| |
Year |
1992 |
Publication |
The journal of chemical physics |
Abbreviated Journal |
J Chem Phys |
|
| |
Volume |
97 |
Issue |
7 |
Pages |
5155-5162 |
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| |
Keywords |
A1 Journal article; Condensed Matter Theory (CMT) |
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| |
Abstract |
A microscopic theory, which describes the orientational dynamics of C60 molecules in the face-centered cubic phase of C60-fullerite, is formulated or the case of a complex molecular structure. Interaction centers which comprise atoms, double bonds, and single bonds as molecular constituents contribute to the intermolecular potential. Orientation dependent physical properties are described in terms of symmetry-adapted rotator functions. It is found that a same set of rotator functions is sufficient even in the case of a complex molecular structure. Phase transition temperatures are discussed for various models of molecular structure. |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
New York, N.Y. |
Editor |
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Language |
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Wos |
A1992JR33800062 |
Publication Date |
2002-07-26 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
0021-9606; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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| |
Impact Factor |
2.952 |
Times cited |
20 |
Open Access |
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Notes |
|
Approved |
no |
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| |
Call Number |
UA @ lucian @ c:irua:2973 |
Serial |
2185 |
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| Permanent link to this record |
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Author |
Martin, J.M.L.; François, J.P.; Gijbels, R. |
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Title |
On the effect of centrifugal stretching on the rotational partition function of an asymmetric top |
Type |
A1 Journal article |
| |
Year |
1991 |
Publication |
The journal of chemical physics |
Abbreviated Journal |
J Chem Phys |
|
| |
Volume |
95 |
Issue |
|
Pages |
8374-8389 |
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| |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
New York, N.Y. |
Editor |
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Language |
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Wos |
A1991GR66500062 |
Publication Date |
0000-00-00 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
0021-9606 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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| |
Impact Factor |
2.952 |
Times cited |
12 |
Open Access |
|
|
| |
Notes |
|
Approved |
no |
|
| |
Call Number |
UA @ lucian @ c:irua:716 |
Serial |
2434 |
|
| Permanent link to this record |
| |
|
| |
|
Author |
Martin, J.M.L.; François, J.P.; Gijbels, R. |
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| |
Title |
On the heat formation of C8 and higher carbon clusters (letter to the editor) |
Type |
A1 Journal article |
| |
Year |
1991 |
Publication |
The journal of chemical physics |
Abbreviated Journal |
J Chem Phys |
|
| |
Volume |
95 |
Issue |
|
Pages |
9420-9421 |
|
| |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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| |
Abstract |
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| |
Address |
|
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| |
Corporate Author |
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Thesis |
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| |
Publisher |
|
Place of Publication |
New York, N.Y. |
Editor |
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| |
Language |
|
Wos |
A1991GV82500076 |
Publication Date |
0000-00-00 |
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| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
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| |
Series Volume |
|
Series Issue |
|
Edition |
|
|
| |
ISSN |
0021-9606 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
| |
Impact Factor |
2.952 |
Times cited |
27 |
Open Access |
|
|
| |
Notes |
|
Approved |
no |
|
| |
Call Number |
UA @ lucian @ c:irua:719 |
Serial |
2437 |
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| Permanent link to this record |
| |
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| |
|
Author |
Bal, K.M.; Neyts, E.C. |
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| |
Title |
On the time scale associated with Monte Carlo simulations |
Type |
A1 Journal article |
| |
Year |
2014 |
Publication |
The journal of chemical physics |
Abbreviated Journal |
J Chem Phys |
|
| |
Volume |
141 |
Issue |
20 |
Pages |
204104 |
|
| |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
|
| |
Abstract |
Uniform-acceptance force-bias Monte Carlo (fbMC) methods have been shown to be a powerful technique to access longer timescales in atomistic simulations allowing, for example, phase transitions and growth. Recently, a new fbMC method, the time-stamped force-bias Monte Carlo (tfMC) method, was derived with inclusion of an estimated effective timescale; this timescale, however, does not seem able to explain some of the successes the method. In this contribution, we therefore explicitly quantify the effective timescale tfMC is able to access for a variety of systems, namely a simple single-particle, one-dimensional model system, the Lennard-Jones liquid, an adatom on the Cu(100) surface, a silicon crystal with point defects and a highly defected graphene sheet, in order to gain new insights into the mechanisms by which tfMC operates. It is found that considerable boosts, up to three orders of magnitude compared to molecular dynamics, can be achieved for solid state systems by lowering of the apparent activation barrier of occurring processes, while not requiring any system-specific input or modifications of the method. We furthermore address the pitfalls of using the method as a replacement or complement of molecular dynamics simulations, its ability to explicitly describe correct dynamics and reaction mechanisms, and the association of timescales to MC simulations in general. |
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| |
Address |
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Corporate Author |
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Thesis |
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| |
Publisher |
|
Place of Publication |
New York, N.Y. |
Editor |
|
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| |
Language |
|
Wos |
000345641400005 |
Publication Date |
2014-11-26 |
|
| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
|
| |
ISSN |
0021-9606;1089-7690; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
| |
Impact Factor |
2.965 |
Times cited |
26 |
Open Access |
|
|
| |
Notes |
|
Approved |
Most recent IF: 2.965; 2014 IF: 2.952 |
|
| |
Call Number |
UA @ lucian @ c:irua:120667 |
Serial |
2459 |
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| Permanent link to this record |
| |
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| |
|
Author |
Verberck, B.; Vliegenthart, G.A.; Gompper, G. |
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| |
Title |
Orientational ordering in solid C60 fullerene-cubane |
Type |
A1 Journal article |
| |
Year |
2009 |
Publication |
The journal of chemical physics |
Abbreviated Journal |
J Chem Phys |
|
| |
Volume |
130 |
Issue |
15 |
Pages |
154510,1-154510,14 |
|
| |
Keywords |
A1 Journal article; Condensed Matter Theory (CMT) |
|
| |
Abstract |
We study the structure and phase behavior of fullerene-cubane C60·C8H8 by Monte Carlo simulation. Using a simple potential model capturing the icosahedral and cubic symmetries of its molecular constituents, we reproduce the experimentally observed phase transition from a cubic to an orthorhombic crystal lattice and the accompanying rotational freezing of the C60 molecules. We elaborate a scheme to identify the low-temperature orientations of individual molecules and to detect a pattern of orientational ordering similar to the arrangement of C60 molecules in solid C60. Our configuration of orientations supports a doubled periodicity along one of the crystal axes. |
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| |
Address |
|
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| |
Corporate Author |
|
Thesis |
|
|
| |
Publisher |
|
Place of Publication |
New York, N.Y. |
Editor |
|
|
| |
Language |
|
Wos |
000265486300036 |
Publication Date |
2009-04-22 |
|
| |
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 |
8 |
Open Access |
|
|
| |
Notes |
|
Approved |
Most recent IF: 2.965; 2009 IF: 3.093 |
|
| |
Call Number |
UA @ lucian @ c:irua:77258 |
Serial |
2519 |
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| Permanent link to this record |
| |
|
| |
|
Author |
Titantah, J.T.; Pierleoni, C.; Ryckaert, J.-P. |
|
| |
Title |
Single chain elasticity and thermoelasticity of polyethylene |
Type |
A1 Journal article |
| |
Year |
2002 |
Publication |
The journal of chemical physics |
Abbreviated Journal |
J Chem Phys |
|
| |
Volume |
117 |
Issue |
19 |
Pages |
9028-9036 |
|
| |
Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
|
| |
Abstract |
Single-chain elasticity of polyethylene at theta point up to 90% of stretching with respect to its contour length is computed by Monte Carlo simulation of an atomistic model in continuous space. The elasticity law together with the free-energy and the internal energy variations with stretching are found to be very well represented by the wormlike chain model up to 65% of the chain elongation, provided the persistence length is treated as a temperature-dependent parameter. Beyond this value of elongation simple ideal chain models are not able to describe the Monte Carlo data in a thermodynamic consistent way. This study reinforces the use of the wormlike chain model to interpret experimental data on the elasticity of synthetic polymers in the finite extensibility regime, provided the chain is not yet in its fully stretched regime. Specific solvent effects on the elasticity law and the partition between energetic and entropic contributions to single chain elasticity are investigated. (C) 2002 American Institute of Physics. |
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Address |
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Corporate Author |
|
Thesis |
|
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| |
Publisher |
|
Place of Publication |
New York, N.Y. |
Editor |
|
|
| |
Language |
|
Wos |
000178934700046 |
Publication Date |
2002-10-31 |
|
| |
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 |
5 |
Open Access |
|
|
| |
Notes |
|
Approved |
Most recent IF: 2.965; 2002 IF: 2.998 |
|
| |
Call Number |
UA @ lucian @ c:irua:103862 |
Serial |
3018 |
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| Permanent link to this record |
| |
|
| |
|
Author |
Euan-Diaz, E.; Herrera-Velarde, S.; Misko, V.R.; Peeters, F.M.; Castaneda-Priego, R. |
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| |
Title |
Structural transitions and long-time self-diffusion of interacting colloids confined by a parabolic potential |
Type |
A1 Journal article |
| |
Year |
2015 |
Publication |
The journal of chemical physics |
Abbreviated Journal |
J Chem Phys |
|
| |
Volume |
142 |
Issue |
142 |
Pages |
024902 |
|
| |
Keywords |
A1 Journal article; Condensed Matter Theory (CMT) |
|
| |
Abstract |
We report on the ordering and dynamics of interacting colloidal particles confined by a parabolic potential. By means of Brownian dynamics simulations, we find that by varying the magnitude of the trap stiffness, it is possible to control the dimension of the system and, thus, explore both the structural transitions and the long-time self-diffusion coefficient as a function of the degree of confinement. We particularly study the structural ordering in the directions perpendicular and parallel to the confinement. Further analysis of the local distribution of the first-neighbors layer allows us to identify the different structural phases induced by the parabolic potential. These results are summarized in a structural state diagram that describes the way in which the colloidal suspension undergoes a structural re-ordering while increasing the confinement. To fully understand the particle dynamics, we take into account hydrodynamic interactions between colloids; the parabolic potential constricts the available space for the colloids, but it does not act on the solvent. Our findings show a non-linear behavior of the long-time self-diffusion coefficient that is associated to the structural transitions induced by the external field. (C) 2015 AIP Publishing LLC. |
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| |
Address |
|
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| |
Corporate Author |
|
Thesis |
|
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| |
Publisher |
|
Place of Publication |
New York, N.Y. |
Editor |
|
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| |
Language |
|
Wos |
000348129700053 |
Publication Date |
2015-01-10 |
|
| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
|
| |
ISSN |
0021-9606;1089-7690; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
| |
Impact Factor |
2.965 |
Times cited |
7 |
Open Access |
|
|
| |
Notes |
; This work was partially supported by the “Odysseus” Program of the Flemish Government, the Flemish Science Foundation (FWO-Vl), PIFI 3.4 – PROMEP, and CONACyT (Grant Nos. 61418/2007, 102339/2008, Ph.D. scholarship 230171/2010). R.C.-P. also acknowledges financial support provided by the Marcos Moshinsky fellowship 2013-2014. The authors also thank to the General Coordination of Information and Communications Technologies (CGSTIC) at Cinvestav for providing HPC resources on the Hybrid Cluster Super-computer Xiuhcoatl, which have contributed partially to the research results reported in this paper. ; |
Approved |
Most recent IF: 2.965; 2015 IF: 2.952 |
|
| |
Call Number |
c:irua:123832 |
Serial |
3267 |
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| Permanent link to this record |
| |
|
| |
|
Author |
Nikolaev, A.V.; Michel, K.H. |
|
| |
Title |
Superexchange and electron correlations in alkali fullerides AC60, A=K, Rb, Cs |
Type |
A1 Journal article |
| |
Year |
2005 |
Publication |
The journal of chemical physics |
Abbreviated Journal |
J Chem Phys |
|
| |
Volume |
122 |
Issue |
6 |
Pages |
064310-64314 |
|
| |
Keywords |
A1 Journal article; Condensed Matter Theory (CMT) |
|
| |
Abstract |
Superexchange interactions in alkali fullerides AC(60) are derived for C-60 molecular ions separated by interstitial alkali-metal ions. We use a multiconfiguration approach which comprises the lowest molecular orbital states of the C-60 molecule and the excited s and d states of the alkali-metal atom A. Interactions are described by the valence bond (Heitler-London) method for a complex (C-60 – A – C-60) – with two valence electrons. The electronic charge transfer between the alkali-metal atom and a neighboring C-60 molecule is not complete. The occupation probability of excited d and s states of the alkali atom is not negligible. In correspondence with the relative positions of the C-60 molecules and A atoms in the polymer crystal, we consider 180degrees and 90degrees (angle) superexchange pathways. For the former case the ground state is found to be a spin singlet separated from a triplet at similar to20 K. For T < 20 K there appear strong spin correlations for the 180degrees superexchange pathway. The results are related to spin lattice relaxation experiments on CsC60 in the polymerized and in the quenched cubic phase. (C) 2005 American Institute of Physics. |
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| |
Address |
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Corporate Author |
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Thesis |
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| |
Publisher |
|
Place of Publication |
New York, N.Y. |
Editor |
|
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| |
Language |
|
Wos |
000226918100018 |
Publication Date |
2005-02-02 |
|
| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
|
| |
ISSN |
0021-9606; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
| |
Impact Factor |
2.965 |
Times cited |
11 |
Open Access |
|
|
| |
Notes |
|
Approved |
Most recent IF: 2.965; 2005 IF: 3.138 |
|
| |
Call Number |
UA @ lucian @ c:irua:102740 |
Serial |
3377 |
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| Permanent link to this record |
| |
|
| |
|
Author |
Michel, K.H.; Verberck, B.; Hulman, M.; Kuzmany, H.; Krause, M. |
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| |
Title |
Superposition of quantum and classical rotational motions in Sc2C2@C84 fullerite |
Type |
A1 Journal article |
| |
Year |
2007 |
Publication |
The journal of chemical physics |
Abbreviated Journal |
J Chem Phys |
|
| |
Volume |
126 |
Issue |
6 |
Pages |
064304,1-15 |
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| |
Keywords |
A1 Journal article; Condensed Matter Theory (CMT) |
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| |
Abstract |
|
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| |
Address |
|
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| |
Corporate Author |
|
Thesis |
|
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| |
Publisher |
|
Place of Publication |
New York, N.Y. |
Editor |
|
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| |
Language |
|
Wos |
000244250200008 |
Publication Date |
2007-02-09 |
|
| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
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| |
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 |
14 |
Open Access |
|
|
| |
Notes |
|
Approved |
Most recent IF: 2.965; 2007 IF: 3.044 |
|
| |
Call Number |
UA @ lucian @ c:irua:63628 |
Serial |
3381 |
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| Permanent link to this record |
| |
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| |
|
Author |
Leys, F.E.; March, N.H.; Lamoen, D. |
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| |
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 |
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| |
Keywords |
A1 Journal article; Electron Microscopy for Materials Science (EMAT); |
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| |
Abstract |
|
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| |
Address |
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Corporate Author |
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Thesis |
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| |
Publisher |
|
Place of Publication |
New York, N.Y. |
Editor |
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| |
Language |
|
Wos |
000179495000031 |
Publication Date |
2002-12-02 |
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| |
Series Editor |
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Series Title |
|
Abbreviated Series Title |
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| |
Series Volume |
|
Series Issue |
|
Edition |
|
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| |
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 |
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| Permanent link to this record |
| |
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| |
|
Author |
Verberck, B.; Popov, V.N.; Nikolaev, A.V.; Lamoen, D. |
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| |
Title |
Valence electronic charge density of distorted C60-monomers in polymerized KC60 and RbC60 |
Type |
A1 Journal article |
| |
Year |
2004 |
Publication |
The journal of chemical physics |
Abbreviated Journal |
J Chem Phys |
|
| |
Volume |
121 |
Issue |
|
Pages |
321 |
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| |
Keywords |
A1 Journal article; Condensed Matter Theory (CMT) |
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| |
Abstract |
|
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| |
Address |
|
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| |
Corporate Author |
|
Thesis |
|
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| |
Publisher |
|
Place of Publication |
New York, N.Y. |
Editor |
|
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| |
Language |
|
Wos |
000222112100035 |
Publication Date |
2004-06-16 |
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| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
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| |
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 |
7 |
Open Access |
|
|
| |
Notes |
|
Approved |
Most recent IF: 2.965; 2004 IF: 3.105 |
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| |
Call Number |
UA @ lucian @ c:irua:47380 |
Serial |
3830 |
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| Permanent link to this record |
| |
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| |
|
Author |
Nikolaev, A.V.; Lamoen, D.; Partoens, B. |
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| |
Title |
Extension of the basis set of linearized augmented plane wave (LAPW) method by using supplemented tight binding basis functions |
Type |
A1 Journal article |
| |
Year |
2016 |
Publication |
The journal of chemical physics |
Abbreviated Journal |
J Chem Phys |
|
| |
Volume |
145 |
Issue |
145 |
Pages |
014101 |
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| |
Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT); Condensed Matter Theory (CMT) |
|
| |
Abstract |
In order to increase the accuracy of the linearized augmented plane wave (LAPW) method, we present a new approach where the plane wave basis function is augmented by two different atomic radial components constructed at two different linearization energies corresponding to two different electron bands (or energy windows). We demonstrate that this case can be reduced to the standard treatment within the LAPW paradigm where the usual basis set is enriched by the basis functions of the tight binding type, which go to zero with zero derivative at the sphere boundary. We show that the task is closely related with the problem of extended core states which is currently solved by applying the LAPW method with local orbitals (LAPW+LO). In comparison with LAPW+LO, the number of supplemented basis functions in our approach is doubled, which opens up a new channel for the extension of the LAPW and LAPW+LO basis sets. The appearance of new supplemented basis functions absent in the LAPW+LO treatment is closely related with the existence of the ul-component in the canonical LAPW method. We discuss properties of additional tight binding basis functions and apply the extended basis set for computation of electron energy bands of lanthanum (face and body centered structures) and hexagonal close packed lattice of cadmium. We demonstrate that the new treatment gives lower total energies in comparison with both canonical LAPW and LAPW+LO, with the energy difference more pronounced for intermediate and poor LAPW basis sets. |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
|
Place of Publication |
|
Editor |
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| |
Language |
|
Wos |
000379584700003 |
Publication Date |
2016-07-05 |
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| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
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| |
Series Volume |
|
Series Issue |
|
Edition |
|
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| |
ISSN |
0021-9606 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
| |
Impact Factor |
2.965 |
Times cited |
11 |
Open Access |
|
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| |
Notes |
A.V.N. acknowledges useful discussions with B. Verberck, E. V. Tkalya, and A. V. Bibikov. |
Approved |
Most recent IF: 2.965 |
|
| |
Call Number |
c:irua:134290 |
Serial |
4099 |
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| Permanent link to this record |
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| |
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Author |
Kandemir, A.; Peeters, F.M.; Sahin, H. |
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| |
Title |
Monitoring the effect of asymmetrical vertical strain on Janus single layers of MoSSe via spectrum |
Type |
A1 Journal article |
| |
Year |
2018 |
Publication |
The journal of chemical physics |
Abbreviated Journal |
J Chem Phys |
|
| |
Volume |
149 |
Issue |
8 |
Pages |
084707 |
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| |
Keywords |
A1 Journal article; Condensed Matter Theory (CMT) |
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| |
Abstract |
Using first principles calculations, we study the structural and phononic properties of the recently synthesized Janus type single layers of molybdenum dichalcogenides. The Janus MoSSe single layer possesses 2H crystal structure with two different chalcogenide sides that lead to out-of-plane anisotropy. By virtue of the asymmetric structure of the ultra-thin Janus type crystal, we induced the out-of-plane anisotropy to show the distinctive vertical pressure effect on the vibrational properties of the Janus material. It is proposed that for the corresponding Raman active optical mode of the Janus structure, the phase modulation and the magnitude ratio of the strained atom and its first neighbor atom adjust the distinctive change in the eigen-frequencies and Raman activity. Moreover, a strong variation in the Raman activity of the Janus structure is obtained under bivertical and univertical strains. Not only eigen-frequency shifts but also Raman activities of the optical modes of the Janus structure exhibit distinguishable features. This study reveals that the vertical anisotropic feature of the Janus structure under Raman measurement allows us to distinguish which side of the Janus crystal interacts with the externals (substrate, functional adlayers, or dopants). Published by AIP Publishing. |
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Address |
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Corporate Author |
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Thesis |
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| |
Publisher |
|
Place of Publication |
New York, N.Y. |
Editor |
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| |
Language |
|
Wos |
000444035800044 |
Publication Date |
2018-08-30 |
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| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
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| |
Series Volume |
|
Series Issue |
|
Edition |
|
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| |
ISSN |
0021-9606 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
| |
Impact Factor |
2.965 |
Times cited |
11 |
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 TUBITAK under Project No. 117F095. F.M.P. was supported by the FLAG-ERA-TRANS<INF>2D</INF>TMD. ; |
Approved |
Most recent IF: 2.965 |
|
| |
Call Number |
UA @ lucian @ c:irua:153711UA @ admin @ c:irua:153711 |
Serial |
5115 |
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| Permanent link to this record |
| |
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| |
|
Author |
Bal, K.M.; Fukuhara, S.; Shibuta, Y.; Neyts, E.C. |
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| |
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 |
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Volume |
153 |
Issue |
11 |
Pages |
114118 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
Atomistic simulation methods for the quantification of free energies are in wide use. These methods operate by sampling the probability density of a system along a small set of suitable collective variables (CVs), which is, in turn, expressed in the form of a free energy surface (FES). This definition of the FES can capture the relative stability of metastable states but not that of the transition state because the barrier height is not invariant to the choice of CVs. Free energy barriers therefore cannot be consistently computed from the FES. Here, we present a simple approach to calculate the gauge correction necessary to eliminate this inconsistency. Using our procedure, the standard FES as well as its gauge-corrected counterpart can be obtained by reweighing the same simulated trajectory at little additional cost. We apply the method to a number of systems—a particle solvated in a Lennard-Jones fluid, a Diels–Alder reaction, and crystallization of liquid sodium—to demonstrate its ability to produce consistent free energy barriers that correctly capture the kinetics of chemical or physical transformations, and discuss the additional demands it puts on the chosen CVs. Because the FES can be converged at relatively short (sub-ns) time scales, a free energy-based description of reaction kinetics is a particularly attractive option to study chemical processes at more expensive quantum mechanical levels of theory. |
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Wos |
000574665600004 |
Publication Date |
2020-09-21 |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
0021-9606 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
4.4 |
Times cited |
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Open Access |
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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 |
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Call Number |
PLASMANT @ plasmant @c:irua:172456 |
Serial |
6420 |
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Author |
Baskurt, M.; Yagmurcukardes, M.; Peeters, F.M.; Sahin, H. |
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Title |
Stable single-layers of calcium halides (CaX₂, X = F, Cl, Br, I) |
Type |
A1 Journal article |
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Year |
2020 |
Publication |
Journal Of Chemical Physics |
Abbreviated Journal |
J Chem Phys |
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Volume |
152 |
Issue |
16 |
Pages |
164116-164118 |
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Keywords |
A1 Journal article; Condensed Matter Theory (CMT) |
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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. |
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Wos |
000531819100001 |
Publication Date |
2020-04-29 |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
0021-9606 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
4.4 |
Times cited |
10 |
Open Access |
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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 |
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Call Number |
UA @ admin @ c:irua:169543 |
Serial |
6615 |
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Author |
Payne, L.M.; Masia, F.; Zilli, A.; Albrecht, W.; Borri, P.; Langbein, W. |
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Title |
Quantitative morphometric analysis of single gold nanoparticles by optical extinction microscopy: Material permittivity and surface damping effects |
Type |
A1 Journal article |
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Year |
2021 |
Publication |
Journal Of Chemical Physics |
Abbreviated Journal |
J Chem Phys |
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Volume |
154 |
Issue |
4 |
Pages |
044702 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
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Abstract |
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Wos |
000630495600001 |
Publication Date |
2021-01-28 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
0021-9606 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.965 |
Times cited |
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Open Access |
OpenAccess |
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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 |
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Call Number |
EMAT @ emat @c:irua:177566 |
Serial |
6748 |
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Author |
Hamid, I.; Jalali, H.; Peeters, F.M.; Neek-Amal, M. |
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Title |
Abnormal in-plane permittivity and ferroelectricity of confined water : from sub-nanometer channels to bulk |
Type |
A1 Journal article |
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Year |
2021 |
Publication |
Journal Of Chemical Physics |
Abbreviated Journal |
J Chem Phys |
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Volume |
154 |
Issue |
11 |
Pages |
114503 |
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Keywords |
A1 Journal article; Condensed Matter Theory (CMT) |
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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. |
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Wos |
000629831900001 |
Publication Date |
2021-03-17 |
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Series Issue |
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Edition |
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ISSN |
0021-9606 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.965 |
Times cited |
9 |
Open Access |
OpenAccess |
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Notes |
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Approved |
Most recent IF: 2.965 |
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Call Number |
UA @ admin @ c:irua:177579 |
Serial |
6967 |
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Author |
Bal, K.M.; Neyts, E.C. |
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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 |
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Year |
2022 |
Publication |
Journal Of Chemical Physics |
Abbreviated Journal |
J Chem Phys |
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Volume |
157 |
Issue |
18 |
Pages |
184113-10 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
We calculate bubble nucleation rates in a Lennard-Jones fluid through explicit molecular dynamics simulations. Our approach-based on a recent free energy method (dubbed reweighted Jarzynski sampling), transition state theory, and a simple recrossing correction-allows us to probe a fairly wide range of rates in several superheated and cavitation regimes in a consistent manner. Rate predictions from this approach bridge disparate independent literature studies on the same model system. As such, we find that rate predictions based on classical nucleation theory, direct brute force molecular dynamics simulations, and seeding are consistent with our approach and one another. Published rates derived from forward flux sampling simulations are, however, found to be outliers. This study serves two purposes: First, we validate the reliability of common modeling techniques and extrapolation approaches on a paradigmatic problem in materials science and chemical physics. Second, we further test our highly generic recipe for rate calculations, and establish its applicability to nucleation processes. |
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Wos |
000885260600002 |
Publication Date |
2022-11-14 |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
0021-9606 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
4.4 |
Times cited |
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Open Access |
OpenAccess |
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Notes |
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Approved |
Most recent IF: 4.4 |
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Call Number |
UA @ admin @ c:irua:192076 |
Serial |
7266 |
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Author |
Bal, K.M. |
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Title |
Nucleation rates from small scale atomistic simulations and transition state theory |
Type |
A1 Journal article |
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Year |
2021 |
Publication |
Journal Of Chemical Physics |
Abbreviated Journal |
J Chem Phys |
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Volume |
155 |
Issue |
14 |
Pages |
144111 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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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. |
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Wos |
000755502100008 |
Publication Date |
2021-09-30 |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
0021-9606 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.965 |
Times cited |
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Open Access |
OpenAccess |
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Notes |
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Approved |
Most recent IF: 2.965 |
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Call Number |
UA @ admin @ c:irua:184937 |
Serial |
8320 |
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Author |
Colomer, J.-F.; Piedigrosso, P.; Willems, I.; Journet, C.; Bernier, P.; Van Tendeloo, G.; Fonseca, A.; Nagy, J.B. |
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Title |
Purification of catalytically produced multi-wall nanotubes |
Type |
A1 Journal article |
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Year |
1998 |
Publication |
Journal of the Chemical Society : Faraday transactions: physical chemistry and chemical physics |
Abbreviated Journal |
J Chem Soc Faraday T |
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Volume |
94 |
Issue |
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Pages |
3753-3758 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
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Place of Publication |
London |
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Wos |
000077634100034 |
Publication Date |
2002-07-26 |
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Edition |
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ISSN |
0956-5000;1364-5455; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
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Times cited |
92 |
Open Access |
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Notes |
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Approved |
Most recent IF: NA |
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Call Number |
UA @ lucian @ c:irua:25685 |
Serial |
2740 |
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