“Two-dimensional binary clusters in a hard-wall trap: structural and spectral properties”. Yang W, Kong M, Milošević, MV, Zeng Z, Peeters FM, Physical review E 76, art.041404:part 1 (2007). http://doi.org/10.1103/PhysRevE.76.041404
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 2.366
Times cited: 9
DOI: 10.1103/PhysRevE.76.041404
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“Comment on “Generalized exclusion processes : transport coefficients””. Becker T, Nelissen K, Cleuren B, Partoens B, Van den Broeck C, Physical review E 93, 046101 (2016). http://doi.org/10.1103/PHYSREVE.93.046101
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)].
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 2.366
Times cited: 3
DOI: 10.1103/PHYSREVE.93.046101
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“Artificial living crystals in confined environment”. Yang W, Misko VR, Tempère J, Kong M, Peeters FM, Physical Review E 95, 062602 (2017). http://doi.org/10.1103/PHYSREVE.95.062602
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.
Keywords: A1 Journal article; Theory of quantum systems and complex systems; Condensed Matter Theory (CMT)
Impact Factor: 2.366
Times cited: 10
DOI: 10.1103/PHYSREVE.95.062602
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“Self-assembly of rigid magnetic rods consisting of single dipolar beads in two dimensions”. Domingos JLC, Peeters FM, Ferreira WP, Physical review E 96, 012603 (2017). http://doi.org/10.1103/PHYSREVE.96.012603
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.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 2.366
Times cited: 8
DOI: 10.1103/PHYSREVE.96.012603
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“Boosting Monte Carlo simulations of spin glasses using autoregressive neural networks”. McNaughton B, Milošević, MV, Perali A, Pilati S, Physical Review E 101, 053312 (2020). http://doi.org/10.1103/PHYSREVE.101.053312
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.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 2.366
Times cited: 15
DOI: 10.1103/PHYSREVE.101.053312
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“Out-of-plane permittivity of confined water”. Jalali H, Ghorbanfekr H, Hamid I, Neek-Amal M, Rashidi R, Peeters FM, Physical Review E 102, 022803 (2020). http://doi.org/10.1103/PHYSREVE.102.022803
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)].
Keywords: A1 Journal article; Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.366
Times cited: 38
DOI: 10.1103/PHYSREVE.102.022803
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“Photoluminescence and electronic transition behaviors of single-stranded DNA”. Wang Q, Lin S, Liu X, Xu W, Xiao Y, Liang C, Ding L, Peeters FM, Physical Review E 104, 034412 (2021). http://doi.org/10.1103/PHYSREVE.104.034412
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.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 2.366
DOI: 10.1103/PHYSREVE.104.034412
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“Cation-controlled permeation of charged polymers through nanocapillaries”. Faraji F, Neek-Amal M, Neyts EC, Peeters FM, Physical review E 107, 034501 (2023). http://doi.org/10.1103/PHYSREVE.107.034501
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.
Keywords: A1 Journal article; Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.4
Times cited: 1
DOI: 10.1103/PHYSREVE.107.034501
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“Structure and reentrant percolation in an inverse patchy colloidal system”. de Araujo JLB, Munarin FF, Farias GA, Peeters FM, Ferreira WP, Physical Review E 95, 062606 (2017). http://doi.org/10.1103/PHYSREVE.95.062606
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.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Times cited: 5
DOI: 10.1103/PHYSREVE.95.062606
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