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Records |
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Author |
Galván Moya, J.E.; Lucena, D.; Ferreira, W.P.; Peeters, F.M. |
| |
Title |
Magnetic particles confined in a modulated channel : structural transitions tunable by tilting a magnetic field |
Type |
A1 Journal article |
| |
Year |
2014 |
Publication |
Physical review : E : statistical, nonlinear, and soft matter physics |
Abbreviated Journal |
Phys Rev E |
| |
Volume |
89 |
Issue |
3 |
Pages |
032309-9 |
| |
Keywords |
A1 Journal article; Condensed Matter Theory (CMT) |
| |
Abstract |
The ground state of colloidal magnetic particles in a modulated channel are investigated as a function of the tilt angle of an applied magnetic field. The particles are confined by a parabolic potential in the transversal direction while in the axial direction a periodic substrate potential is present. By using Monte Carlo simulations, we construct a phase diagram for the different crystal structures as a function of the magnetic field orientation, strength of the modulated potential, and the commensurability factor of the system. Interestingly, we found first-and second-order phase transitions between different crystal structures, which can be manipulated by the orientation of the external magnetic field. A reentrant behavior is found between two-and four-chain configurations, with continuous second-order transitions. Novel configurations are found consisting of frozen solitons of defects. By changing the orientation and/or strength of the magnetic field and/or the strength and periodicity of the substrate potential, the system transits through different phases. |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
American Institute of Physics |
Place of Publication |
Woodbury (NY) |
Editor |
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Language |
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Wos |
000333702800015 |
Publication Date |
2014-03-31 |
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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 |
|
Edition |
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| |
ISSN  |
1539-3755;1550-2376; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
| |
Impact Factor |
2.366 |
Times cited |
11 |
Open Access |
|
| |
Notes |
; This work was supported by the Flemish Science Foundation (FWO-Vl), the Methusalem programme of the Flemish government, CNPq, CAPES, FUNCAP (Pronex grant), the collaborative program CNPq-FWO-Vl, and the Brazilian program Science Without Borders CsF. Computational resources were provided by HPC infrastructure of University of Antwerp (CalcUA) a division of the Flemish Supercomputer Center (VSC). ; |
Approved |
Most recent IF: 2.366; 2014 IF: 2.288 |
| |
Call Number |
UA @ lucian @ c:irua:117217 |
Serial |
1886 |
| Permanent link to this record |
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Author |
Ferreira, W.P.; Peeters, F.M.; Farias, G.A. |
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Title |
Melting and evaporation in classical two-dimensional clusters confined by a Coulomb potential |
Type |
A1 Journal article |
| |
Year |
2005 |
Publication |
Physical review : E : statistical, nonlinear, and soft matter physics |
Abbreviated Journal |
Phys Rev E |
| |
Volume |
72 |
Issue |
4 Part 1 |
Pages |
041502-41507 |
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Keywords |
A1 Journal article; Condensed Matter Theory (CMT) |
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Abstract |
The thermal properties of a two-dimensional classical cluster of negatively charged particles bound by a punctual positive charge are presented. The melting phenomenon is analyzed and the features which characterize such a solid-liquid transition are highlighted. We found that the presence of metastable states strongly modifies the melting scenario, and that the melting temperature of the system is determined by the height of the saddle point energy separating the ground state and the metastable state. Due to the particular type of confinement potential considered in this paper, we also found that, at sufficiently large temperature, the cluster can become thermally ionized. |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
American Institute of Physics |
Place of Publication |
Woodbury (NY) |
Editor |
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Language |
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Wos |
000232930600030 |
Publication Date |
2005-10-06 |
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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 |
1539-3755;1550-2376; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
| |
Impact Factor |
2.366 |
Times cited |
4 |
Open Access |
|
| |
Notes |
|
Approved |
Most recent IF: 2.366; 2005 IF: 2.418 |
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Call Number |
UA @ lucian @ c:irua:104067 |
Serial |
1983 |
| Permanent link to this record |
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Author |
Apolinario, S.W.S.; Peeters, F.M. |
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Title |
Melting transitions in isotropically confined three-dimensional small Coulomb clusters |
Type |
A1 Journal article |
| |
Year |
2007 |
Publication |
Physical review : E : statistical physics, plasmas, fluids, and related interdisciplinary topics |
Abbreviated Journal |
Phys Rev E |
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Volume |
76 |
Issue |
3 |
Pages |
031107,1-13 |
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Keywords |
A1 Journal article; Condensed Matter Theory (CMT) |
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Abstract |
Molecular dynamic simulations are performed to investigate the melting process of small three-dimensional clusters (i.e., systems with one and two shells) of classical charged particles trapped in an isotropic parabolic potential. The confined particles interact through a repulsive potential. We find that the ground-state configurations for systems with N=6, 12, 13, and 38 particles interacting through a Coulomb potential are magic clusters. Such magic clusters have an octahedral or icosahedral symmetry and are found to have a large stability against intrashell diffusion leading to an intershell melting transition prior to the intrashell and radial melting process. For systems with two shells a local radial melting of subshells is found at low temperatures resulting in a structural transition leading to an increased symmetry of the ordered system. Using Lindemanns criterion the different melting temperatures are determined and the influence of the screening of the interparticle interaction was investigated. A normal mode analysis is performed and some of the normal modes are found to be determinantal for the melting process. |
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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 |
Lancaster, Pa |
Editor |
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Language |
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Wos |
000249785800015 |
Publication Date |
2007-09-10 |
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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 |
1539-3755;1550-2376; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
| |
Impact Factor |
2.366 |
Times cited |
28 |
Open Access |
|
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Notes |
|
Approved |
Most recent IF: 2.366; 2007 IF: 2.483 |
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Call Number |
UA @ lucian @ c:irua:65693 |
Serial |
1990 |
| Permanent link to this record |
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Author |
Liu, Y.H.; Chen, Z.Y.; Yu, M.Y.; Bogaerts, A. |
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Title |
Multiple void formation in plasmas containing multispecies charged grains |
Type |
A1 Journal article |
| |
Year |
2006 |
Publication |
Physical review : E : statistical physics, plasmas, fluids, and related interdisciplinary topics |
Abbreviated Journal |
Phys Rev E |
| |
Volume |
74 |
Issue |
|
Pages |
056401,1-6 |
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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 |
Lancaster, Pa |
Editor |
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Language |
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Wos |
000242408800037 |
Publication Date |
2006-11-14 |
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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 |
1539-3755;1550-2376; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
| |
Impact Factor |
2.366 |
Times cited |
21 |
Open Access |
|
| |
Notes |
|
Approved |
Most recent IF: 2.366; 2006 IF: 2.438 |
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Call Number |
UA @ lucian @ c:irua:60424 |
Serial |
2233 |
| Permanent link to this record |
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Author |
Tomecka, D.; Partoens, B.; Peeters, F.M. |
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Title |
Multistep radial melting in small two-dimensional classical clusters |
Type |
A1 Journal article |
| |
Year |
2005 |
Publication |
Physical review : E : statistical physics, plasmas, fluids, and related interdisciplinary topics |
Abbreviated Journal |
Phys Rev E |
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Volume |
71 |
Issue |
|
Pages |
062401,1-4 |
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Keywords |
A1 Journal article; Condensed Matter Theory (CMT) |
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Abstract |
We report on a molecular dynamics study of small classical two-dimensional clusters with ringlike configurations. We focus on the particles motion at low temperatures before the radial and angular melting sets in. It is shown that in magic number configurations a local radial melting of subshells occur, which is related to the intershell rotation. |
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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 |
Lancaster, Pa |
Editor |
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Language |
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Wos |
000230274500084 |
Publication Date |
2005-06-23 |
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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 |
1539-3755;1550-2376; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
| |
Impact Factor |
2.366 |
Times cited |
11 |
Open Access |
|
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Notes |
|
Approved |
Most recent IF: 2.366; 2005 IF: 2.418 |
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Call Number |
UA @ lucian @ c:irua:62447 |
Serial |
2241 |
| Permanent link to this record |
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Author |
Kong, M.; Vagov, A.; Partoens, B.; Peeters, F.M.; Ferreira, W.P.; Farias, G.A. |
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Title |
Nonlinear screening in large two-dimensional Coulomb clusters |
Type |
A1 Journal article |
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Year |
2004 |
Publication |
Physical review : E : statistical physics, plasmas, fluids, and related interdisciplinary topics |
Abbreviated Journal |
Phys Rev E |
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Volume |
70 |
Issue |
|
Pages |
051807,1-6 |
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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 |
Lancaster, Pa |
Editor |
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Language |
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Wos |
000225970500071 |
Publication Date |
2004-11-22 |
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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 |
1539-3755;1550-2376; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
| |
Impact Factor |
2.366 |
Times cited |
4 |
Open Access |
|
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Notes |
|
Approved |
Most recent IF: 2.366; 2004 IF: NA |
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Call Number |
UA @ lucian @ c:irua:62444 |
Serial |
2358 |
| Permanent link to this record |
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Author |
Piacente, G.; Peeters, F.M.; Betouras, J.J. |
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Title |
Normal modes of a quasi-one-dimensional multichain complex plasma |
Type |
A1 Journal article |
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Year |
2004 |
Publication |
Physical review : E : statistical physics, plasmas, fluids, and related interdisciplinary topics |
Abbreviated Journal |
Phys Rev E |
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Volume |
70 |
Issue |
3Part 2 |
Pages |
|
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Keywords |
A1 Journal article; Condensed Matter Theory (CMT) |
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Abstract |
We studied equally charged particles, suspended in a complex plasma, which move in a plane and interact with a screened Coulomb potential (Yukawa type) and with an additional external confining parabolic potential in one direction, which makes the system quasi-one-dimensional (Q1D). The normal modes of the system are studied in the presence of dissipation. We also investigated how a perpendicular magnetic field couples the phonon modes with each other. Two different ways of exciting the normal modes are discussed: (1) a uniform excitation of the Q1D lattice, and (2) a local forced excitation of the system in which one particle is driven by, e.g., a laser. Our results are in very good agreement with recent experimental findings on a finite single chain system [Liu , Phys. Rev. Lett. 91, 255003 (2003)]. Predictions are made for the normal modes of multichain structures in the presence of damping. |
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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 |
Lancaster, Pa |
Editor |
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Language |
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Wos |
000224302300081 |
Publication Date |
2004-09-21 |
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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 |
1539-3755;1550-2376; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
| |
Impact Factor |
2.366 |
Times cited |
18 |
Open Access |
|
| |
Notes |
|
Approved |
Most recent IF: 2.366; 2004 IF: NA |
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Call Number |
UA @ lucian @ c:irua:69417 |
Serial |
2369 |
| Permanent link to this record |
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Author |
Sobrino Fernandez, M.; Misko, V.R.; Peeters, F.M. |
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Title |
Self-assembly of Janus particles confined in a channel |
Type |
A1 Journal article |
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Year |
2014 |
Publication |
Physical review : E : statistical, nonlinear, and soft matter physics |
Abbreviated Journal |
Phys Rev E |
| |
Volume |
89 |
Issue |
2 |
Pages |
022306-6 |
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Keywords |
A1 Journal article; Condensed Matter Theory (CMT) |
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Abstract |
Janus particles present an important class of building blocks for directional assembly. These are compartmentalized colloids with two different hemispheres. Here, we consider a two-dimensional model of Janus disks consisting of a hydrophobic semicircle and an electro-negatively charged one. Placed in a solution, the hydrophobic sides will attract each other while the charged sides will give rise to a repulsive force. Using molecular dynamics simulations, we study the morphology of these particles when confined in a channel-like environment using a one dimensional harmonic confinement potential. The interest to this system is first of all due to the fact that it could serve as a simple model for membrane formation. Indeed, the recently synthesized new class of artificial amphiphiles, known as Janus dendrimers, were shown to self-assemble in bilayer structures mimicking biological membranes. In turn, Janus particles that combine the amphiphilicity and colloidal rigidity serve as a good model for Janus dendrimers. A variety of ordered membrane-like morphologies are found consisting of single and multiple chain configurations with different orientations of the particles with respect to each other that we summarize in a phase diagram. |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
American Institute of Physics |
Place of Publication |
Woodbury (NY) |
Editor |
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Language |
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Wos |
000332179900009 |
Publication Date |
2014-02-21 |
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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 |
1539-3755;1550-2376; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| |
Impact Factor |
2.366 |
Times cited |
11 |
Open Access |
|
| |
Notes |
; This work was supported by the Flemish Science Foundation (FWO-Vl) and by the “Odysseus” program of the Flemish government and FWO-Vl. ; |
Approved |
Most recent IF: 2.366; 2014 IF: 2.288 |
| |
Call Number |
UA @ lucian @ c:irua:115858 |
Serial |
2971 |
| Permanent link to this record |
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Author |
Lucena, D.; Galván Moya, J.E.; Ferreira, W.P.; Peeters, F.M. |
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Title |
Single-file and normal diffusion of magnetic colloids in modulated channels |
Type |
A1 Journal article |
| |
Year |
2014 |
Publication |
Physical review : E : statistical, nonlinear, and soft matter physics |
Abbreviated Journal |
Phys Rev E |
| |
Volume |
89 |
Issue |
3 |
Pages |
032306-32309 |
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Keywords |
A1 Journal article; Condensed Matter Theory (CMT) |
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Abstract |
Diffusive properties of interacting magnetic dipoles confined in a parabolic narrow channel and in the presence of a periodic modulated (corrugated) potential along the unconfined direction are studied using Brownian dynamics simulations. We compare our simulation results with the analytical result for the effective diffusion coefficient of a single particle by Festa and d'Agliano [Physica A 90, 229 (1978)] and show the importance of interparticle interaction on the diffusion process. We present results for the diffusion of magnetic dipoles as a function of linear density, strength of the periodic modulation and commensurability factor. |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
American Institute of Physics |
Place of Publication |
Woodbury (NY) |
Editor |
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Language |
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Wos |
000333646400005 |
Publication Date |
2014-03-13 |
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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 |
1539-3755;1550-2376; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
| |
Impact Factor |
2.366 |
Times cited |
5 |
Open Access |
|
| |
Notes |
; This work was supported by CNPq, CAPES, FUNCAP (Pronex grant), the Flemish Science Foundation (FWO-Vl), the collaborative program CNPq-FWO-Vl, and the Brazilian program Science Without Borders (CsF). D. Lucena acknowledges fruitful discussions with W. A. Munoz, V. F. Becerra, E. C. Euan-Diaz, and M. R. Masir. ; |
Approved |
Most recent IF: 2.366; 2014 IF: 2.288 |
| |
Call Number |
UA @ lucian @ c:irua:116865 |
Serial |
3020 |
| Permanent link to this record |
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Author |
Euán-Díaz, E.C.; Misko, V.R.; Peeters, F.M.; Herrera-Velarde, S.; Castaneda-Priego, R. |
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Title |
Single-file diffusion in periodic energy landscapes : the role of hydrodynamic interactions |
Type |
A1 Journal article |
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Year |
2012 |
Publication |
Physical review : E : statistical, nonlinear, and soft matter physics |
Abbreviated Journal |
Phys Rev E |
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Volume |
86 |
Issue |
3Part 1 |
Pages |
031123 |
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Keywords |
A1 Journal article; Condensed Matter Theory (CMT) |
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Abstract |
We report on the dynamical properties of interacting colloids confined to one dimension and subjected to external periodic energy landscapes. We particularly focus on the influence of hydrodynamic interactions on the mean-square displacement. Using Brownian dynamics simulations, we study colloidal systems with two types of repulsive interparticle interactions, namely, Yukawa and superparamagnetic potentials. We find that in the homogeneous case, hydrodynamic interactions lead to an enhancement of the particle mobility and the mean-square displacement at long times scales as t(alpha), with alpha = 1/2 + epsilon and epsilon being a small correction. This correction, however, becomes much more important in the presence of an external field, which breaks the homogeneity of the particle distribution along the line and, therefore, promotes a richer dynamical scenario due to the hydrodynamical coupling among particles. We provide here the complete dynamical scenario in terms of the external potential parameters: amplitude and commensurability. |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
American Institute of Physics |
Place of Publication |
Woodbury (NY) |
Editor |
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Language |
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Wos |
000308873500002 |
Publication Date |
2012-09-21 |
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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 |
1539-3755;1550-2376; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| |
Impact Factor |
2.366 |
Times cited |
14 |
Open Access |
|
| |
Notes |
; This work was partially supported by the “Odysseus” Program of the Flemish Government, the Flemish Science Foundation (FWO-Vl), and PIFI 3.4-PROMEP and CONACyT (Grant Nos. 61418/2007 and 102339/2008, Ph.D. Scholarship No. 230171/ 2010). ; |
Approved |
Most recent IF: 2.366; 2012 IF: 2.313 |
| |
Call Number |
UA @ lucian @ c:irua:101840 |
Serial |
3021 |
| Permanent link to this record |
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Author |
Nelissen, K.; Matulis, A.; Partoens, B.; Kong, M.; Peeters, F.M. |
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Title |
Spectrum of classical two-dimensional Coulomb clusters |
Type |
A1 Journal article |
| |
Year |
2006 |
Publication |
Physical review : E : statistical physics, plasmas, fluids, and related interdisciplinary topics |
Abbreviated Journal |
Phys Rev E |
| |
Volume |
73 |
Issue |
1 |
Pages |
016607,1-7 |
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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 |
Lancaster, Pa |
Editor |
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Language |
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Wos |
000235008800095 |
Publication Date |
2006-01-17 |
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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 |
1539-3755;1550-2376; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
| |
Impact Factor |
2.366 |
Times cited |
33 |
Open Access |
|
| |
Notes |
|
Approved |
Most recent IF: 2.366; 2006 IF: 2.438 |
| |
Call Number |
UA @ lucian @ c:irua:56611 |
Serial |
3075 |
| Permanent link to this record |
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Author |
Ferreira, W.P.; Partoens, B.; Peeters, F.M.; Farias, G.A. |
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Title |
Structural phase transitions and unusual melting behavior in a classical two-dimensional Coulomb bound cluster |
Type |
A1 Journal article |
| |
Year |
2005 |
Publication |
Physical review : E : statistical physics, plasmas, fluids, and related interdisciplinary topics |
Abbreviated Journal |
Phys Rev E |
| |
Volume |
71 |
Issue |
|
Pages |
021501,1-4 |
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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 |
Lancaster, Pa |
Editor |
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Language |
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Wos |
000228245700023 |
Publication Date |
2005-02-09 |
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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 |
1539-3755;1550-2376; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
| |
Impact Factor |
2.366 |
Times cited |
8 |
Open Access |
|
| |
Notes |
|
Approved |
Most recent IF: 2.366; 2005 IF: 2.418 |
| |
Call Number |
UA @ lucian @ c:irua:62445 |
Serial |
3251 |
| Permanent link to this record |
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| |
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Author |
Apolinario, S.W.S.; Partoens, B.; Peeters, F.M. |
| |
Title |
Structure and spectrum of anisotropically confined two-dimensional clusters with logarithmic interaction |
Type |
A1 Journal article |
| |
Year |
2005 |
Publication |
Physical review : E : statistical physics, plasmas, fluids, and related interdisciplinary topics |
Abbreviated Journal |
Phys Rev E |
| |
Volume |
72 |
Issue |
|
Pages |
046122,1-7 |
| |
Keywords |
A1 Journal article; Condensed Matter Theory (CMT) |
| |
Abstract |
We studied the structural and spectral properties of a classical system consisting of a finite number of particles, moving in two dimensions, and interacting through a repulsive logarithmic potential and held together by an anisotropic harmonic potential. Increasing the anisotropy of the confinement potential can drive the system from a two-dimensional (2D) to a one-dimensional (1D) configuration. This change occurs through a sequence of structural transitions of first and second order which are reflected in the normal mode frequencies. Our results of the ground state configurations are compared with recent experiments and we obtained a satisfactory agreement. The transition from the 1D line structure to the 2D structure occurs through a zigzag transition which is of second order. We found analytical expressions for the eigenfrequencies before the zigzag transition, which allowed us to obtain an analytical expression for the anisotropy parameter at which the zigzag transition occurs as a function of the number of particles in the system. |
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Address |
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Corporate Author |
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Thesis |
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| |
Publisher |
|
Place of Publication |
Lancaster, Pa |
Editor |
|
| |
Language |
|
Wos |
000232931200034 |
Publication Date |
2005-10-18 |
| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
| |
ISSN |
1539-3755;1550-2376; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| |
Impact Factor |
2.366 |
Times cited |
22 |
Open Access |
|
| |
Notes |
|
Approved |
Most recent IF: 2.366; 2005 IF: 2.418 |
| |
Call Number |
UA @ lucian @ c:irua:62448 |
Serial |
3295 |
| Permanent link to this record |
| |
|
| |
|
Author |
Kong, M.; Partoens, B.; Matulis, A.; Peeters, F.M. |
| |
Title |
Structure and spectrum of two-dimensional clusters confined in a hard wall potential |
Type |
A1 Journal article |
| |
Year |
2004 |
Publication |
Physical review : E : statistical physics, plasmas, fluids, and related interdisciplinary topics |
Abbreviated Journal |
Phys Rev E |
| |
Volume |
69 |
Issue |
|
Pages |
036412,1-10 |
| |
Keywords |
A1 Journal article; Condensed Matter Theory (CMT) |
| |
Abstract |
|
| |
Address |
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| |
Corporate Author |
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Thesis |
|
| |
Publisher |
|
Place of Publication |
Lancaster, Pa |
Editor |
|
| |
Language |
|
Wos |
000220729400077 |
Publication Date |
2004-04-01 |
| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
| |
ISSN |
1539-3755;1550-2376; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| |
Impact Factor |
2.366 |
Times cited |
42 |
Open Access |
|
| |
Notes |
|
Approved |
Most recent IF: 2.366; 2004 IF: NA |
| |
Call Number |
UA @ lucian @ c:irua:62442 |
Serial |
3298 |
| Permanent link to this record |
| |
|
| |
|
Author |
Ferreira, W.P.; Munarin, F.F.; Nelissen, K.; Costa, R.N.; Peeters, F.M.; Farias, G.A. |
| |
Title |
Structure, normal mode spectra, and mixing of a binary system of charged particles confined in a parabolic trap |
Type |
A1 Journal article |
| |
Year |
2005 |
Publication |
Physical review : E : statistical, nonlinear, and soft matter physics |
Abbreviated Journal |
Phys Rev E |
| |
Volume |
72 |
Issue |
2 Part 1 |
Pages |
021406-21413 |
| |
Keywords |
A1 Journal article; Condensed Matter Theory (CMT) |
| |
Abstract |
We study the mixing of two different kinds of particles, having different charge and/or mass, interacting through a pure Coulomb potential, and confined in a parabolic trap. The structure of the cluster and its normal mode spectrum are analyzed as a function of the ratio of the charges (mass ratio) of the two types of particles. We show that particles are not always arranged in a shell structure. Mixing of the particles goes hand in hand with a large number of metastable states. The normal modes of the system are obtained, and we find that some of the special modes can be tuned by varying the ratio between the charges (masses) of the two species. The degree of mixing of the two type of particles is summarized in a phase diagram, and an order parameter that describes quantitatively the mixing between particles is defined. |
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Address |
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Corporate Author |
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Thesis |
|
| |
Publisher |
American Institute of Physics |
Place of Publication |
Woodbury (NY) |
Editor |
|
| |
Language |
|
Wos |
000231564000031 |
Publication Date |
2005-08-18 |
| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
| |
ISSN |
1539-3755;1550-2376; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| |
Impact Factor |
2.366 |
Times cited |
25 |
Open Access |
|
| |
Notes |
|
Approved |
Most recent IF: 2.366; 2005 IF: 2.418 |
| |
Call Number |
UA @ lucian @ c:irua:103149 |
Serial |
3306 |
| Permanent link to this record |
| |
|
| |
|
Author |
Yang, W.; Nelissen, K.; Kong, M.; Zeng, Z.; Peeters, F.M. |
| |
Title |
Structure of binary colloidal systems confined in a quasi-one-dimensional channel |
Type |
A1 Journal article |
| |
Year |
2009 |
Publication |
Physical review : E : statistical physics, plasmas, fluids, and related interdisciplinary topics |
Abbreviated Journal |
Phys Rev E |
| |
Volume |
79 |
Issue |
4 |
Pages |
041406,1-041406,6 |
| |
Keywords |
A1 Journal article; Condensed Matter Theory (CMT) |
| |
Abstract |
The structural properties of a binary colloidal quasi-one-dimensional system confined in a narrow channel are investigated through modified Monte Carlo simulations. Two species of particles with different magnetic moment interact through a repulsive dipole-dipole force are confined in a quasi-one-dimensional channel. The impact of three decisive parameters (the density of particles, the magnetic-moment ratio, and the fraction between the two species) on the transition from disordered phase to crystal-like phases and the transitions among the different mixed phases are summarized in a phase diagram. |
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Address |
|
| |
Corporate Author |
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Thesis |
|
| |
Publisher |
|
Place of Publication |
Lancaster, Pa |
Editor |
|
| |
Language |
|
Wos |
000265941300077 |
Publication Date |
2009-04-23 |
| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
| |
ISSN |
1539-3755;1550-2376; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| |
Impact Factor |
2.366 |
Times cited |
11 |
Open Access |
|
| |
Notes |
|
Approved |
Most recent IF: 2.366; 2009 IF: 2.400 |
| |
Call Number |
UA @ lucian @ c:irua:77021 |
Serial |
3308 |
| Permanent link to this record |
| |
|
| |
|
Author |
Liu, Y.H.; Chen, Z.Y.; Yu, M.Y.; Wang, L.; Bogaerts, A. |
| |
Title |
Structure of multispecies charged particles in a quadratic trap |
Type |
A1 Journal article |
| |
Year |
2006 |
Publication |
Physical review : E : statistical physics, plasmas, fluids, and related interdisciplinary topics |
Abbreviated Journal |
Phys Rev E |
| |
Volume |
73 |
Issue |
|
Pages |
047402,1-4 |
| |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
| |
Abstract |
|
| |
Address |
|
| |
Corporate Author |
|
Thesis |
|
| |
Publisher |
|
Place of Publication |
Lancaster, Pa |
Editor |
|
| |
Language |
|
Wos |
000237146800099 |
Publication Date |
2006-04-17 |
| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
| |
ISSN |
1539-3755;1550-2376; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| |
Impact Factor |
2.366 |
Times cited |
25 |
Open Access |
|
| |
Notes |
|
Approved |
Most recent IF: 2.366; 2006 IF: 2.438 |
| |
Call Number |
UA @ lucian @ c:irua:57859 |
Serial |
3312 |
| Permanent link to this record |
| |
|
| |
|
Author |
Lucena, D.; Tkachenko, D.V.; Nelissen, K.; Misko, V.R.; Ferreira, W.P.; Farias, G.A.; Peeters, F.M. |
| |
Title |
Transition from single-file to two-dimensional diffusion of interacting particles in a quasi-one-dimensional channel |
Type |
A1 Journal article |
| |
Year |
2012 |
Publication |
Physical review : E : statistical, nonlinear, and soft matter physics |
Abbreviated Journal |
Phys Rev E |
| |
Volume |
85 |
Issue |
3:1 |
Pages |
031147-031147,12 |
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Keywords |
A1 Journal article; Condensed Matter Theory (CMT) |
| |
Abstract |
Diffusive properties of a monodisperse system of interacting particles confined to a quasi-one-dimensional channel are studied using molecular dynamics simulations. We calculate numerically the mean-squared displacement (MSD) and investigate the influence of the width of the channel (or the strength of the confinement potential) on diffusion in finite-size channels of different shapes (i.e., straight and circular). The transition from single-file diffusion to the two-dimensional diffusion regime is investigated. This transition [ regarding the calculation of the scaling exponent (alpha) of the MSD <Delta x(2)(t)> proportional to t(alpha)] as a function of the width of the channel is shown to change depending on the channel's confinement profile. In particular, the transition can be either smooth (i.e., for a parabolic confinement potential) or rather sharp (i.e., for a hard-wall potential), as distinct from infinite channels where this transition is abrupt. This result can be explained by qualitatively different distributions of the particle density for the different confinement potentials. |
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Address |
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Corporate Author |
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Thesis |
|
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Publisher |
American Institute of Physics |
Place of Publication |
Woodbury (NY) |
Editor |
|
| |
Language |
|
Wos |
000302117900003 |
Publication Date |
2012-03-29 |
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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 |
|
| |
ISSN |
1539-3755;1550-2376; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| |
Impact Factor |
2.366 |
Times cited |
38 |
Open Access |
|
| |
Notes |
; This work was supported by CNPq, FUNCAP (Pronex grant), the “Odysseus” program of the Flemish Government, the Flemish Science Foundation (FWO-Vl), the bilateral program between Flanders and Brazil, and the collaborative program CNPq-FWO-Vl. ; |
Approved |
Most recent IF: 2.366; 2012 IF: 2.313 |
| |
Call Number |
UA @ lucian @ c:irua:97784 |
Serial |
3699 |
| Permanent link to this record |
| |
|
| |
|
Author |
Lucena, D.; Ferreira, W.P.; Munarin, F.F.; Farias, G.A.; Peeters, F.M. |
| |
Title |
Tunable diffusion of magnetic particles in a quasi-one-dimensional channel |
Type |
A1 Journal article |
| |
Year |
2013 |
Publication |
Physical review : E : statistical, nonlinear, and soft matter physics |
Abbreviated Journal |
Phys Rev E |
| |
Volume |
87 |
Issue |
1 |
Pages |
012307-12309 |
| |
Keywords |
A1 Journal article; Condensed Matter Theory (CMT) |
| |
Abstract |
The diffusion of a system of ferromagnetic dipoles confined in a quasi-one-dimensional parabolic trap is studied using Brownian dynamics simulations. We show that the dynamics of the system is tunable by an in-plane external homogeneous magnetic field. For a strong applied magnetic field, we find that the mobility of the system, the exponent of diffusion, and the crossover time among different diffusion regimes can be tuned by the orientation of the magnetic field. For weak magnetic fields, the exponent of diffusion in the subdiffusive regime is independent of the orientation of the external field. DOI: 10.1103/PhysRevE.87.012307 |
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Address |
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Corporate Author |
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Thesis |
|
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Publisher |
American Institute of Physics |
Place of Publication |
Woodbury (NY) |
Editor |
|
| |
Language |
|
Wos |
000314152300005 |
Publication Date |
2013-01-15 |
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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 |
|
| |
ISSN |
1539-3755;1550-2376; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| |
Impact Factor |
2.366 |
Times cited |
11 |
Open Access |
|
| |
Notes |
; This work was supported by CNPq, CAPES, FUNCAP (Pronex grant), the Flemish Science Foundation (FWO-Vl), the bilateral program between Flanders and Brazil, the collaborative program CNPq – FWO-Vl, and the Brazilian program Science Without Borders (CsF). Discussions with V. R. Misko are gratefully acknowledged. ; |
Approved |
Most recent IF: 2.366; 2013 IF: 2.326 |
| |
Call Number |
UA @ lucian @ c:irua:110089 |
Serial |
3739 |
| Permanent link to this record |
| |
|
| |
|
Author |
Yang, W.; Kong, M.; Milošević, M.V.; Zeng, Z.; Peeters, F.M. |
| |
Title |
Two-dimensional binary clusters in a hard-wall trap: structural and spectral properties |
Type |
A1 Journal article |
| |
Year |
2007 |
Publication |
Physical review E |
Abbreviated Journal |
Phys Rev E |
| |
Volume |
76 |
Issue |
4 |
Pages |
art.041404:part 1 |
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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 |
|
Editor |
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Language |
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Wos |
000250621900066 |
Publication Date |
2007-10-24 |
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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 |
|
| |
ISSN |
1539-3755;1550-2376; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| |
Impact Factor |
2.366 |
Times cited |
9 |
Open Access |
|
| |
Notes |
|
Approved |
Most recent IF: 2.366; 2007 IF: 2.483 |
| |
Call Number |
UA @ lucian @ c:irua:67325 |
Serial |
3772 |
| Permanent link to this record |
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| |
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Author |
Tytgat, T.; Smits, M.; Lenaerts, S.; Verbruggen, S.W. |
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Title |
Immobilization of TiO2 into self-supporting photocatalytic foam : influence of calcination temperature |
Type |
A1 Journal article |
| |
Year |
2014 |
Publication |
International journal of applied ceramic technology |
Abbreviated Journal |
Int J Appl Ceram Tec |
| |
Volume |
11 |
Issue |
4 |
Pages |
714-722 |
| |
Keywords |
A1 Journal article; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL) |
| |
Abstract |
Immobilization of photocatalytic powder is crucial to obtain industrially relevant purification processes. To achieve this goal, self-supporting TiO2 foams were manufactured by a polyacrylamide gel process. These gels were calcined at different temperatures to study the effect of the calcination temperature on foam characteristics (rigidity, crystallinity, and porosity) and its influence on photocatalytic activity. The results show that an optimal degradation is achieved for those foams calcined between 700 and 800°C. Calcination at higher temperatures results in a steep decrease in activity, explained by stability issues of the material due to formation of Na2SO4 phases and a larger rutile fraction. |
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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 |
|
Editor |
|
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Language |
|
Wos |
000339051500012 |
Publication Date |
2013-04-24 |
| |
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 |
1546-542x |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| |
Impact Factor |
1.048 |
Times cited |
2 |
Open Access |
|
| |
Notes |
; This work was supported by a PhD grant from the Institute of Innovation by Science and Technology in Flanders (IWT). ; |
Approved |
Most recent IF: 1.048; 2014 IF: 1.320 |
| |
Call Number |
UA @ admin @ c:irua:117295 |
Serial |
5960 |
| Permanent link to this record |
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| |
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Author |
Oliveira, M.C.; Yusupov, M.; Bogaerts, A.; Cordeiro, R.M. |
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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 |
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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. |
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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 |
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Editor |
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Language |
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Wos |
000669541400034 |
Publication Date |
2021-06-28 |
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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 |
|
Series Issue |
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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 |
| |
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| |
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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. |
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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 |
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Editor |
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Language |
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Wos |
000740019000001 |
Publication Date |
2022-01-10 |
| |
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 |
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 |
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| |
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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) |
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Abstract |
The hyperdynamics method is a powerful tool to simulate slow processes at the atomic level. However, the construction of an optimal hyperdynamics potential is a task that is far from trivial. Here, we propose a generally applicable implementation of the hyperdynamics algorithm, borrowing two concepts from metadynamics. First, the use of a collective variable (CV) to represent the accelerated dynamics gives the method a very large flexibility and simplicity. Second, a metadynamics procedure can be used to construct a suitable history-dependent bias potential on-the-fly, effectively turning the algorithm into a self-learning accelerated molecular dynamics method. This collective variable-driven hyperdynamics (CVHD) method has a modular design: both the local system properties on which the bias is based, as well as the characteristics of the biasing method itself, can be chosen to match the needs of the considered system. As a result, system-specific details are abstracted from the biasing algorithm itself, making it extremely versatile and transparent. The method is tested on three model systems: diffusion on the Cu(001) surface and nickel-catalyzed methane decomposition, as examples of reactive processes with a bond-length-based CV, and the folding of a long polymer-like chain, using a set of dihedral angles as a CV. Boost factors up to 109, corresponding to a time scale of seconds, could be obtained while still accurately reproducing correct dynamics. |
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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 |
000362921700004 |
Publication Date |
2015-09-02 |
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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 |
1549-9618 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
5.245 |
Times cited |
41 |
Open Access |
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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 |
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Call Number |
c:irua:128183 |
Serial |
3991 |
| Permanent link to this record |
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Author |
Bal, K.M. |
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Title |
Reweighted Jarzynski sampling : acceleration of rare events and free energy calculation with a bias potential learned from nonequilibrium work |
Type |
A1 Journal article |
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Year |
2021 |
Publication |
Journal Of Chemical Theory And Computation |
Abbreviated Journal |
J Chem Theory Comput |
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Volume |
17 |
Issue |
11 |
Pages |
6766-6774 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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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. |
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Corporate Author |
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Thesis |
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Place of Publication |
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Language |
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Wos |
000718183600008 |
Publication Date |
2021-10-29 |
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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 |
1549-9618 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
5.245 |
Times cited |
|
Open Access |
OpenAccess |
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Notes |
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Approved |
Most recent IF: 5.245 |
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Call Number |
UA @ admin @ c:irua:184676 |
Serial |
8479 |
| Permanent link to this record |
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Author |
Neyts, E.C.; Thijsse, B.J.; Mees, M.J.; Bal, K.M.; Pourtois, G. |
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Title |
Establishing uniform acceptance in force biased Monte Carlo simulations |
Type |
A1 Journal article |
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Year |
2012 |
Publication |
Journal of chemical theory and computation |
Abbreviated Journal |
J Chem Theory Comput |
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Volume |
8 |
Issue |
6 |
Pages |
1865-1869 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
Uniform acceptance force biased Monte Carlo (UFMC) simulations have previously been shown to be a powerful tool to simulate atomic scale processes, enabling one to follow the dynamical path during the simulation. In this contribution, we present a simple proof to demonstrate that this uniform acceptance still complies with the condition of detailed balance, on the condition that the characteristic parameter lambda = 1/2 and that the maximum allowed step size is chosen to be sufficiently small. Furthermore, the relation to Metropolis Monte Carlo (MMC) is also established, and it is shown that UFMC reduces to MMC by choosing the characteristic parameter lambda = 0 [Rao, M. et al. Mol. Phys. 1979, 37, 1773]. Finally, a simple example compares the UFMC and MMC methods. |
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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 |
000305092400002 |
Publication Date |
2012-05-16 |
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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 |
1549-9618;1549-9626; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
5.245 |
Times cited |
20 |
Open Access |
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Notes |
|
Approved |
Most recent IF: 5.245; 2012 IF: 5.389 |
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Call Number |
UA @ lucian @ c:irua:99090 |
Serial |
1082 |
| Permanent link to this record |
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Author |
Abakumov, M.A.; Nukolova, N.V.; Sokolsky-Papkov, M.; Shein, S.A.; Sandalova, T.O.; Vishwasrao, H.M.; Grinenko, N.F.; Gubsky, I.L.; Abakumov, A.M.; Kabanov, A.V.; Chekhonin, V.P.; |
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Title |
VEGF-targeted magnetic nanoparticles for MRI visualization of brain tumor |
Type |
A1 Journal article |
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Year |
2015 |
Publication |
Nanomedicine: nanotechnology, biology and medicine |
Abbreviated Journal |
Nanomed-Nanotechnol |
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Volume |
11 |
Issue |
11 |
Pages |
825-833 |
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Keywords |
A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT) |
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Abstract |
This work is focused on synthesis and characterization of targeted magnetic nanoparticles as magnetic resonance imaging (MRI) agents for in vivo visualization of gliomas. Ferric oxide (Fe3O4) cores were synthesized by thermal decomposition and coated with bovine serum albumin (BSA) to form nanoparticles with D-eff of 53 +/- 9 nm. The BSA was further cross-linked to improve colloidal stability. Monoclonal antibodies against vascular endothelial growth factor (mAbVEGF) were covalently conjugated to BSA through a polyethyleneglycol linker. Here we demonstrate that 1) BSA coated nanoparticles are stable and non-toxic to different cells at concentration up to 2.5 mg/mL; 2) conjugation of monoclonal antibodies to nanoparticles promotes their binding to VEGF-positive glioma C6 cells in vitro; 3) targeted nanoparticles are effective in MRI visualization of the intracranial glioma. Thus, mAbVEGF-targeted BSA-coated magnetic nanoparticles are promising MRI contrast agents for glioma visualization. (C) 2015 Elsevier Inc. All rights reserved. |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
S.l. |
Editor |
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Language |
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Wos |
000354559600004 |
Publication Date |
2015-01-31 |
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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 |
1549-9634; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
5.72 |
Times cited |
62 |
Open Access |
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Notes |
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Approved |
Most recent IF: 5.72; 2015 IF: 6.155 |
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Call Number |
c:irua:126351 |
Serial |
3838 |
| Permanent link to this record |
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Author |
Ding, F.; Li, B.; Akopian, N.; Perinetti, U.; Chen, Y.H.; Peeters, F.M.; Rastelli, A.; Zwiller, V.; Schmidt, O.G. |
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Title |
Single neutral excitons confined in AsBr3 in situ etched InGaAs quantum rings |
Type |
A1 Journal article |
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Year |
2011 |
Publication |
Journal of nanoelectronics and optoelectronics |
Abbreviated Journal |
J Nanoelectron Optoe |
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Volume |
6 |
Issue |
1 |
Pages |
51-57 |
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Keywords |
A1 Journal article; Engineering sciences. Technology; Condensed Matter Theory (CMT) |
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Abstract |
We observe the evolution of single self-assembled semiconductor quantum dots into quantum rings during AsBr3 in situ etching. The direct three-dimensional imaging of In(Ga)As nanostructures embedded in GaAs matrix is demonstrated by selective wet chemical etching combined with atomic force microscopy. Single neutral excitons confined in these quantum rings are studied by magneto-photoluminescence. Oscillations in the exciton radiative recombination energy and in the emission intensity are observed under an applied magnetic field. Further, we demonstrate that the period of the oscillations can be tuned by a gate potential that modifies the exciton confinement. The experimental results, combined with calculations, indicate that the exciton Aharonov-Bohm effect may account for the observed effects. |
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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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Language |
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Wos |
000290692200005 |
Publication Date |
2011-04-18 |
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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 |
1555-130X;1555-1318; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
0.497 |
Times cited |
3 |
Open Access |
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Notes |
; We acknowledge L. P. Kouwenhoven and Z. G. Wang for support, C. C. Bof Bufon, C. Deneke, V. Fomin, A. Govorov, S. Kiravittaya, and Wen-Hao Chang for their help and discussions. We are grateful for the financial support of NWO (VIDI), the CAS-MPG programm, the DFG (FOR730), BMBF (No. 01BM459), NSFC China (60625402), and Flemish Science Foundation (FWO-V1). ; |
Approved |
Most recent IF: 0.497; 2011 IF: 0.556 |
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Call Number |
UA @ lucian @ c:irua:90187 |
Serial |
3025 |
| Permanent link to this record |
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Author |
Roose, D.; Leroux, F.; de Vocht, N.; Guglielmetti, C.; Pintelon, I.; Adriaensen, D.; Ponsaerts, P.; van der Linden, A.-M.; Bals, S. |
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Title |
Multimodal imaging of micron-sized iron oxide particles following in vitro and in vivo uptake by stem cells: down to the nanometer scale |
Type |
A1 Journal article |
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Year |
2014 |
Publication |
Contrast media and molecular imaging |
Abbreviated Journal |
Contrast Media Mol I |
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Volume |
9 |
Issue |
6 |
Pages |
400-408 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT); Bio-Imaging lab |
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Abstract |
In this study, the interaction between cells and micron-sized paramagnetic iron oxide (MPIO) particles was investigated by characterizing MPIO in their original state, and after cellular uptake in vitro as well as in vivo. Moreover, MPIO in the olfactory bulb were studied 9months after injection. Using various imaging techniques, cell-MPIO interactions were investigated with increasing spatial resolution. Live cell confocal microscopy demonstrated that MPIO co-localize with lysosomes after in vitro cellular uptake. In more detail, a membrane surrounding the MPIO was observed by high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM). Following MPIO uptake in vivo, the same cell-MPIO interaction was observed by HAADF-STEM in the subventricular zone at 1week and in the olfactory bulb at 9months after MPIO injection. These findings provide proof for the current hypothesis that MPIO are internalized by the cell through endocytosis. The results also show MPIO are not biodegradable, even after 9months in the brain. Moreover, they show the possibility of HAADF-STEM generating information on the labeled cell as well as on the MPIO. In summary, the methodology presented here provides a systematic route to investigate the interaction between cells and nanoparticles from the micrometer level down to the nanometer level and beyond. Copyright (c) 2014 John Wiley Sons, Ltd. |
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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 |
S.l. |
Editor |
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Language |
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Wos |
000346172100001 |
Publication Date |
2014-04-24 |
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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 |
1555-4309; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
3.307 |
Times cited |
5 |
Open Access |
Not_Open_Access |
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Notes |
; The authors would like to thank Sofie Thys for her technical support. The UltraVIEW VoX spinning disk confocal microscope was purchased with support of the Hercules Foundation (Hercules Type 1: AUHA 09/001 and AUHA 11/01). The authors also appreciate financial support from the European Union under the Seventh Framework Program (Integrated Infrastructure Initiative no. 262348 European Soft Matter Infrastructure, ESMI), the Fund for Scientific Research- Flanders and the Flemish Institute for Science and Technology and the Belgian government through the Interuniversity Attraction Pole Program (IAP- PAI). ; |
Approved |
Most recent IF: 3.307; 2014 IF: 2.923 |
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Call Number |
UA @ lucian @ c:irua:122750 |
Serial |
2222 |
| Permanent link to this record |
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Author |
Zarenia, M.; Pereira, J.M.; Peeters, F.M.; Farias, G. de A. |
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Title |
Topological confinement in an antisymmetric potential in bilayer graphene in the presence of a magnetic field |
Type |
A1 Journal article |
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Year |
2011 |
Publication |
Nanoscale research letters |
Abbreviated Journal |
Nanoscale Res Lett |
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Volume |
6 |
Issue |
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Pages |
452,1-452,10 |
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Keywords |
A1 Journal article; Condensed Matter Theory (CMT) |
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Abstract |
We investigate the effect of an external magnetic field on the carrier states that are localized at a potential kink and a kink-antikink in bilayer graphene. These chiral states are localized at the interface between two potential regions with opposite signs. |
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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 |
000293299800001 |
Publication Date |
2011-07-14 |
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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 |
1556-276X; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.833 |
Times cited |
4 |
Open Access |
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Notes |
; This work was supported by the Brazilian agency CNPq (Pronex), the Flemish Science Foundation (FWO-Vl), the Belgian Science Policy (IAP), and the bilateral projects between Flanders and Brazil and FWO-CNPq. ; |
Approved |
Most recent IF: 2.833; 2011 IF: NA |
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Call Number |
UA @ lucian @ c:irua:91745 |
Serial |
3674 |
| Permanent link to this record |
