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Author |
Faraji, F.; Neek-Amal, M.; Neyts, E.C.; Peeters, F.M. |
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Title |
Cation-controlled permeation of charged polymers through nanocapillaries |
Type |
A1 Journal article |
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Year  |
2023 |
Publication |
Physical review E |
Abbreviated Journal |
Phys Rev E |
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Volume |
107 |
Issue |
3 |
Pages |
034501-34510 |
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Keywords |
A1 Journal article; Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
Molecular dynamics simulations are used to study the effects of different cations on the permeation of charged polymers through flat capillaries with heights below 2 nm. Interestingly, we found that, despite being monovalent, Li+ , Na+ , and K+ cations have different effects on polymer permeation, which consequently affects their transmission speed throughout those capillaries. We attribute this phenomenon to the interplay of the cations' hydration free energies and the hydrodynamic drag in front of the polymer when it enters the capillary. Different alkali cations exhibit different surface versus bulk preferences in small clusters of water under the influence of an external electric field. This paper presents a tool to control the speed of charged polymers in confined spaces using cations. |
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Wos |
000955986000006 |
Publication Date |
2023-03-17 |
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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 |
2470-0053 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.4 |
Times cited |
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Open Access |
Not_Open_Access |
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Notes |
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Approved |
Most recent IF: 2.4; 2023 IF: 2.366 |
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Call Number |
UA @ admin @ c:irua:196089 |
Serial |
7586 |
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Author |
Wang, Q.; Lin, S.; Liu, X.; Xu, W.; Xiao, Y.; Liang, C.; Ding, L.; Peeters, F.M. |
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Title |
Photoluminescence and electronic transition behaviors of single-stranded DNA |
Type |
A1 Journal article |
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Year |
2021 |
Publication |
Physical Review E |
Abbreviated Journal |
Phys Rev E |
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Volume |
104 |
Issue |
3 |
Pages |
034412 |
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Keywords |
A1 Journal article; Condensed Matter Theory (CMT) |
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Abstract |
Due to the potential application of DNA for biophysics and optoelectronics, the electronic energy states and transitions of this genetic material have attracted a great deal of attention recently. However, the fluorescence and corresponding physical process of DNA under optical excitation with photon energies below ultraviolet are still not fully clear. In this work, we experimentally investigate the photoluminescence (PL) properties of single-stranded DNA (ssDNA) samples under near-ultraviolet (NUV) and visible excitations (270 similar to 440 nm). Based on the dependence of the PL peak wavelength (lem) upon the excitation wavelength (lex), the PL behaviors of ssDNA can be approximately classified into two categories. In the relatively short excitation wavelength regime, lem is nearly constant due to exciton-like transitions associated with delocalized excitonic states and excimer states. In the relatively long excitation wavelength range, a linear relation of lem = Alex + B with A 0 or A < 0 can be observed, which comes from electronic transitions related to coupled vibrational-electronic levels. Moreover, the transition channels in different excitation wavelength regimes and the effects of strand length and base type can be analyzed on the basis of these results. These important findings not only can give a general description of the electronic energy states and transitional behaviors of ssDNA samples under NUV and visible excitations, but also can be the basis for the application of DNA in nanoelectronics and optoelectronics. |
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Wos |
000703562300002 |
Publication Date |
2021-09-20 |
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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 |
2470-0053 |
ISBN |
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Additional Links |
UA library record; WoS full record |
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Impact Factor |
2.366 |
Times cited |
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Open Access |
OpenAccess |
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Notes |
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Approved |
Most recent IF: 2.366 |
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Call Number |
UA @ admin @ c:irua:182517 |
Serial |
7009 |
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Author |
Jalali, H.; Ghorbanfekr, H.; Hamid, I.; Neek-Amal, M.; Rashidi, R.; Peeters, F.M. |
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Title |
Out-of-plane permittivity of confined water |
Type |
A1 Journal article |
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Year |
2020 |
Publication |
Physical Review E |
Abbreviated Journal |
Phys Rev E |
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Volume |
102 |
Issue |
2 |
Pages |
022803 |
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Keywords |
A1 Journal article; Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
The dielectric properties of confined water is of fundamental interest and is still controversial. For water confined in channels with height smaller than h = 8 angstrom, we found a commensurability effect and an extraordinary decrease in the out-of-plane dielectric constant down to the limit of the dielectric constant of optical water. Spatial resolved polarization density data obtained from molecular dynamics simulations are found to be antisymmetric across the channel and are used as input in a mean-field model for the dielectric constant as a function of the height of the channel for h > 15 angstrom. Our results are in excellent agreement with a recent experiment [L. Fumagalli et al., Science 360, 1339 (2018)]. |
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Language |
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Wos |
000560660400004 |
Publication Date |
2020-08-11 |
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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 |
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Impact Factor |
2.366 |
Times cited |
25 |
Open Access |
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Notes |
; This work was supported by the Flemish Science Foundation (FWO-Vl) and the Methusalem program. ; |
Approved |
Most recent IF: NA |
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Call Number |
UA @ admin @ c:irua:171157 |
Serial |
6574 |
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Author |
McNaughton, B.; Milošević, M.V.; Perali, A.; Pilati, S. |
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Title |
Boosting Monte Carlo simulations of spin glasses using autoregressive neural networks |
Type |
A1 Journal article |
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Year |
2020 |
Publication |
Physical Review E |
Abbreviated Journal |
Phys Rev E |
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Volume |
101 |
Issue |
5 |
Pages |
053312 |
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Keywords |
A1 Journal article; Condensed Matter Theory (CMT) |
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Abstract |
The autoregressive neural networks are emerging as a powerful computational tool to solve relevant problems in classical and quantum mechanics. One of their appealing functionalities is that, after they have learned a probability distribution from a dataset, they allow exact and efficient sampling of typical system configurations. Here we employ a neural autoregressive distribution estimator (NADE) to boost Markov chain Monte Carlo (MCMC) simulations of a paradigmatic classical model of spin-glass theory, namely, the two-dimensional Edwards-Anderson Hamiltonian. We show that a NADE can be trained to accurately mimic the Boltzmann distribution using unsupervised learning from system configurations generated using standard MCMC algorithms. The trained NADE is then employed as smart proposal distribution for the Metropolis-Hastings algorithm. This allows us to perform efficient MCMC simulations, which provide unbiased results even if the expectation value corresponding to the probability distribution learned by the NADE is not exact. Notably, we implement a sequential tempering procedure, whereby a NADE trained at a higher temperature is iteratively employed as proposal distribution in a MCMC simulation run at a slightly lower temperature. This allows one to efficiently simulate the spin-glass model even in the low-temperature regime, avoiding the divergent correlation times that plague MCMC simulations driven by local-update algorithms. Furthermore, we show that the NADE-driven simulations quickly sample ground-state configurations, paving the way to their future utilization to tackle binary optimization problems. |
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Thesis |
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Wos |
000535862000014 |
Publication Date |
2020-05-28 |
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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 |
1539-3755; 1550-2376 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.366 |
Times cited |
15 |
Open Access |
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Notes |
; The authors thank I. Murray, G. Carleo, and F. RicciTersenghi for useful discussions. Financial support from the FAR2018 project titled “Supervised machine learning for quantum matter and computational docking” of the University of Camerino and from the Italian MIUR under Project No. PRIN2017 CEnTraL 20172H2SC4 is gratefully acknowledged. S.P. also acknowledges the CINECA award under the ISCRA initiative, for the availability of high performance computing resources and support. M.V.M. gratefully acknowledges the Visiting Professorship program at the University of Camerino that facilitated the collaboration in this work. ; |
Approved |
Most recent IF: NA |
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Call Number |
UA @ admin @ c:irua:170244 |
Serial |
6463 |
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Author |
Domingos, J.L.C.; Peeters, F.M.; Ferreira, W.P. |
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Title |
Self-assembly of rigid magnetic rods consisting of single dipolar beads in two dimensions |
Type |
A1 Journal article |
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Year |
2017 |
Publication |
Physical review E |
Abbreviated Journal |
Phys Rev E |
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Volume |
96 |
Issue |
1 |
Pages |
012603 |
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Keywords |
A1 Journal article; Condensed Matter Theory (CMT) |
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Abstract |
Molecular dynamics simulations are used to investigate the structural properties of a two-dimensional ensemble of magnetic rods, which are modeled as aligned single dipolar beads. The obtained self-assembled configurations can be characterized as (1) clusters, (2) percolated, and (3) ordered structures, and their structural properties are investigated in detail. By increasing the aspect ratio of the magnetic rods, we show that the percolation transition is suppressed due to the reduced mobility of the rods in two dimensions. Such a behavior is opposite to the one observed in three dimensions. A magnetic bulk phase is found with local ferromagnetic order and an unusual nonmonotonic behavior of the nematic order is observed. |
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Corporate Author |
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Thesis |
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Place of Publication |
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Wos |
000405713900014 |
Publication Date |
2017-07-18 |
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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 |
2470-0045;2470-0053; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.366 |
Times cited |
8 |
Open Access |
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Notes |
; This work was supported by the Brazilian agencies FUNCAP, CAPES, program Science without borders, and CNPq (Project No. 400748/2013-4), the joint CNPq-FWO bilateral project, and the Flemish Science Foundation (FWO-V1). ; |
Approved |
Most recent IF: 2.366 |
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Call Number |
UA @ lucian @ c:irua:145210 |
Serial |
4723 |
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Author |
de Araujo, J.L.B.; Munarin, F.F.; Farias, G.A.; Peeters, F.M.; Ferreira, W.P. |
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Title |
Structure and reentrant percolation in an inverse patchy colloidal system |
Type |
A1 Journal article |
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Year |
2017 |
Publication |
Physical Review E |
Abbreviated Journal |
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Volume |
95 |
Issue |
6 |
Pages |
062606 |
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Keywords |
A1 Journal article; Condensed Matter Theory (CMT) |
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Abstract |
Two-dimensional systems of inverse patchy colloids modeled as disks with a central charge and having their surface decorated with oppositely pointlike charged patches are investigated using molecular dynamics simulations. The self-assembly of the patchy colloids leads to diverse ground state configurations ranging from crystalline arrangements of monomers to linear clusters, ramified linear clusters and to percolated configurations. Two structural phase diagrams are constructed: (1) as a function of the net charge and area fraction, and (2) as a function of the net charge and the range of the pair interaction potential. An interesting reentrant percolation transition is obtained as a function of the net charge of the colloids. We identify distinct mechanisms that lead to the percolation transition. |
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Place of Publication |
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Language |
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Wos |
000404545700005 |
Publication Date |
2017-06-27 |
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Series Editor |
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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 |
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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 |
5 |
Open Access |
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Notes |
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Approved |
no |
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Call Number |
UA @ admin @ c:irua:152628 |
Serial |
8587 |
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Author |
Yang, W.; Misko, V.R.; Tempère, J.; Kong, M.; Peeters, F.M. |
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Title |
Artificial living crystals in confined environment |
Type |
A1 Journal article |
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Year |
2017 |
Publication |
Physical Review E |
Abbreviated Journal |
Phys Rev E |
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Volume |
95 |
Issue |
6 |
Pages |
062602 |
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Keywords |
A1 Journal article; Theory of quantum systems and complex systems; Condensed Matter Theory (CMT) |
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Abstract |
Similar to the spontaneous formation of colonies of bacteria, flocks of birds, or schools of fish, “living crystals” can be formed by artificial self-propelled particles such as Janus colloids. Unlike usual solids, these “crystals” are far from thermodynamic equilibrium. They fluctuate in time forming a crystalline structure, breaking apart and re-forming again. We propose a method to stabilize living crystals by applying a weak confinement potential that does not suppress the ability of the particles to perform self-propelled motion, but it stabilizes the structure and shape of the dynamical clusters. This gives rise to such configurations of living crystals as “living shells” formed by Janus colloids. Moreover, the shape of the stable living clusters can be controlled by tuning the potential strength. Our proposal can be verified experimentally with either artificial microswimmers such as Janus colloids, or with living active matter. |
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Wos |
000402667600006 |
Publication Date |
2017-06-06 |
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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 |
2470-0045;2470-0053; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.366 |
Times cited |
10 |
Open Access |
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Notes |
; This work was supported by the “Odysseus” Program of the Flemish Government and the Flemish Research Foundation (FWO-Vl) (Belgium), the Flemish Research Foundation (through Projects No. G.0115.12N, No. G.0119.12N, No. G.0122.12N, and No. G.0429.15N), and the Research Fund of the University of Antwerp. W.Y. acknowledges the support from the National Natural Science Foundation of China under Grants No. 11204199 and No. 51135007, the China Scholarship Council, the 131 project and the Program for the Outstanding Innovative Teams of Higher Learning Institutions of Shanxi, and a project under Grant No. 2016-096 by Shanxi Scholarship Council of China. ; |
Approved |
Most recent IF: 2.366 |
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Call Number |
UA @ lucian @ c:irua:144205 |
Serial |
4641 |
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Author |
Becker, T.; Nelissen, K.; Cleuren, B.; Partoens, B.; Van den Broeck, C. |
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Title |
Comment on “Generalized exclusion processes : transport coefficients” |
Type |
A1 Journal article |
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Year |
2016 |
Publication |
Physical review E |
Abbreviated Journal |
Phys Rev E |
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Volume |
93 |
Issue |
93 |
Pages |
046101 |
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Keywords |
A1 Journal article; Condensed Matter Theory (CMT) |
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Abstract |
In a recent paper, Arita et al. [Phys. Rev. E 90, 052108 (2014)] consider the transport properties of a class of generalized exclusion processes. Analytical expressions for the transport-diffusion coefficient are derived by ignoring correlations. It is claimed that these expressions become exact in the hydrodynamic limit. In this Comment,we point out that (i) the influence of correlations upon the diffusion does not vanish in the hydrodynamic limit, and (ii) the expressions for the self- and transport diffusion derived by Arita et al. are special cases of results derived in Becker et al. [Phys. Rev. Lett. 111, 110601 (2013)]. |
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Wos |
000374962100019 |
Publication Date |
2016-04-25 |
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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 |
2470-0045;2470-0053; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.366 |
Times cited |
3 |
Open Access |
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Notes |
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Approved |
Most recent IF: 2.366 |
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Call Number |
UA @ lucian @ c:irua:141060 |
Serial |
4591 |
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Author |
Yang, W.; Kong, M.; Milošević, M.V.; Zeng, Z.; Peeters, F.M. |
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Title |
Two-dimensional binary clusters in a hard-wall trap: structural and spectral properties |
Type |
A1 Journal article |
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Year |
2007 |
Publication |
Physical review E |
Abbreviated Journal |
Phys Rev E |
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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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Wos |
000250621900066 |
Publication Date |
2007-10-24 |
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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 |
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Impact Factor |
2.366 |
Times cited |
9 |
Open Access |
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Notes |
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Approved |
Most recent IF: 2.366; 2007 IF: 2.483 |
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Call Number |
UA @ lucian @ c:irua:67325 |
Serial |
3772 |
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