“Dynamics of self-organized driven particles with competing range interaction”. Zhao HJ, Misko VR, Peeters FM, Physical review : E : statistical, nonlinear, and soft matter physics 88, 022914 (2013). http://doi.org/10.1103/PhysRevE.88.022914
Abstract: Nonequilibrium self-organized patterns formed by particles interacting through competing range interaction are driven over a substrate by an external force. We show that, with increasing driving force, the preexisted static patterns evolve into dynamic patterns either via disordered phase or depinned patterns or via the formation of nonequilibrium stripes. Strikingly, the stripes are formed either in the direction of the driving force or in the transverse direction, depending on the pinning strength. The revealed dynamical patterns are summarized in a dynamical phase diagram.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 2.366
Times cited: 23
DOI: 10.1103/PhysRevE.88.022914
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“Structure of binary colloidal systems confined in a quasi-one-dimensional channel”. Yang W, Nelissen K, Kong M, Zeng Z, Peeters FM, Physical review : E : statistical physics, plasmas, fluids, and related interdisciplinary topics 79, 041406 (2009). http://doi.org/10.1103/PhysRevE.79.041406
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.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 2.366
Times cited: 11
DOI: 10.1103/PhysRevE.79.041406
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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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“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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“Local and fast relaxation phenomena after laser-induced photodetachment in a strongly electronegative rf discharge”. Yan M, Bogaerts A, Gijbels R, Goedheer WJ, Physical review : E : statistical, nonlinear, and soft matter physics 65, 016408 (2002). http://doi.org/10.1103/PhysRevE.65.016408
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.366
Times cited: 2
DOI: 10.1103/PhysRevE.65.016408
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“Kinetic modeling of relaxation phenomena after photodetachment in a rf electronegative SiH4 discharge”. Yan M, Bogaerts A, Gijbels R, Physical review : E : statistical physics, plasmas, fluids, and related interdisciplinary topics 63 (2001). http://doi.org/10.1103/PhysRevE.63.026405
Abstract: The global relaxation process after pulsed laser induced photodetachment in a rf electronegative SIH4 discharge is studied by a self-consistent kinetic one-dimensional particle-in-cell-Monte Carlo model. Our results reveal a comprehensive physical picture of the relaxation process, including the main plasma variables, after a perturbation up to the full recovery of the steady state. A strong influence of the photodetachment on the discharge is found, which results from an increase of the electron density, leading to a weaker bulk field, and hence to a drop in the high energy tail of the electron energy distribution function (EEDF), a reduction of the reaction rates of electron impact attachment and ionization, and a subsequent decrease of the positive and negative ion densities. All the plasma quantities related to electrons recover synchronously. The recovery time of the ion densities is about 1-2 orders of magnitude longer than that of the electrons due to different recovery mechanisms. The modeled behavior of all the charged particles agrees very well with experimental results from the literature. In addition, our work clarifies some unclear processes assumed in the literature, such as the relaxation of the EEDF, the evolution of the electric field, and the recovery of negative ions.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.366
Times cited: 4
DOI: 10.1103/PhysRevE.63.026405
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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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“Multistep radial melting in small two-dimensional classical clusters”. Tomecka D, Partoens B, Peeters FM, Physical review : E : statistical physics, plasmas, fluids, and related interdisciplinary topics 71, 062401 (2005). http://doi.org/10.1103/PhysRevE.71.062401
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.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 2.366
Times cited: 11
DOI: 10.1103/PhysRevE.71.062401
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“Dynamics of colloids in a narrow channel driven by a nonuniform force”. Tkachenko DV, Misko VR, Peeters FM, Physical review : E : statistical physics, plasmas, fluids, and related interdisciplinary topics 80, 051401 (2009). http://doi.org/10.1103/PhysRevE.80.051401
Abstract: Using Brownian dynamics simulations, we investigate the dynamics of colloids confined in two-dimensional narrow channels driven by a nonuniform force Fdr(y). We considered linear-gradient, parabolic, and deltalike driving-force profiles. This driving force induces melting of the colloidal solid (i.e., shear-induced melting), and the colloidal motion experiences a transition from elastic to plastic regime with increasing Fdr. For intermediate Fdr (i.e., in the transition region) the response of the system, i.e., the distribution of the velocities of the colloidal chains õi(y), in general does not coincide with the profile of the driving force Fdr(y), and depends on the magnitude of Fdr, the width of the channel, and the density of colloids. For example, we show that the onset of plasticity is first observed near the boundaries while the motion in the central region is elastic. This is explained by: (i) (in)commensurability between the chains due to the larger density of colloids near the boundaries, and (ii) the gradient in Fdr. Our study provides a deeper understanding of the dynamics of colloids in channels and could be accessed in experiments on colloids (or in dusty plasma) with, e.g., asymmetric channels or in the presence of a gradient potential field.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 2.366
Times cited: 14
DOI: 10.1103/PhysRevE.80.051401
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“Effect of correlated noise on quasi-one-dimensional diffusion”. Tkachenko DV, Misko VR, Peeters FM, Physical review : E : statistical physics, plasmas, fluids, and related interdisciplinary topics 82, 051102 (2010). http://doi.org/10.1103/PhysRevE.82.051102
Abstract: Single-file diffusion (SFD) of an infinite one-dimensional chain of interacting particles has a long-time mean-square displacement ∝t1/2, independent of the type of interparticle repulsive interaction. This behavior is also observed in finite-size chains, although only for certain intervals of time t depending on the chain length L, followed by the ∝t for t→∞, as we demonstrate for a closed circular chain of diffusing interacting particles. Here, we show that spatial correlation of noise slows down SFD and can result, depending on the amount of correlated noise, in either subdiffusive behavior ∝tα, where 0<α<1/2, or even in a total suppression of diffusion (in the limit N→∞). Spatial correlation can explain the subdiffusive behavior in recent SFD experiments in circular channels.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 2.366
Times cited: 11
DOI: 10.1103/PhysRevE.82.051102
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“Self-assembly of Janus particles confined in a channel”. Sobrino Fernandez M, Misko VR, Peeters FM, Physical review : E : statistical, nonlinear, and soft matter physics 89, 022306 (2014). http://doi.org/10.1103/PhysRevE.89.022306
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.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 2.366
Times cited: 11
DOI: 10.1103/PhysRevE.89.022306
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“Self-assembly of Janus particles into helices with tunable pitch”. Sobrino Fernandez M, Misko VR, Peeters FM, Physical review : E : statistical, nonlinear, and soft matter physics 92, 042309 (2015). http://doi.org/10.1103/PhysRevE.92.042309
Abstract: Janus particles present an important class of building blocks for directional assembly. These are compartmentalized colloids with two different hemispheres. In this work we consider a three-dimensional model of Janus spheres that contain one hydrophobic and one charged hemisphere. Using molecular dynamics simulations, we study the morphology of these particles when confined in a channel-like environment. The interplay between the attractive and repulsive forces on each particle gives rise to a rich phase space where the relative orientation of each particle plays a dominant role in the formation of large-scale clusters. The interest in this system is primarily due to the fact that it could give a better understanding of the mechanisms of the formation of polar membranes. A variety of ordered membranelike morphologies is found consisting of single and multiple connected chain configurations. The helicity of these chains can be chosen by simply changing the salt concentration of the solution. Special attention is given to the formation of Bernal spirals. These helices are composed of regular tetrahedra and are known to exhibit nontrivial translational and rotational symmetry.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 2.366
Times cited: 18
DOI: 10.1103/PhysRevE.92.042309
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“Effect of transport of growing nanoparticles on capacitively coupled rf discharge dynamics”. Schweigert IV, Alexandrov AL, Ariskin DA, Peeters FM, Stefanović, I, Kovačević, E, Berndt J, Winter J, Physical review : E : statistical physics, plasmas, fluids, and related interdisciplinary topics 78, 026410 (2008). http://doi.org/10.1103/PhysRevE.78.026410
Abstract: We present experimental and numerical studies of the properties of a capacitively coupled 13.56 MHz discharge in a mixture of Ar and C2H2 with growing nanosize particles. It is found that at the initial stage of the growth, nanoparticles are accumulated near the sheath-plasma boundaries, where the ionization by electrons is maximal. The nanoparticles suppress the ionization due to the absorbing fast electrons and stimulate a quick change of the plasma parameters followed by a transition between different modes of discharge operation. At that moment the peaked distribution of the dust particles transforms into a flat one.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 2.366
Times cited: 36
DOI: 10.1103/PhysRevE.78.026410
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“Dynamical properties and melting of binary two-dimensional colloidal alloys”. Ramos IRO, Ferreira WP, Munarin FF, Peeters FM, Physical review : E : statistical, nonlinear, and soft matter physics 90, 062311 (2014). http://doi.org/10.1103/PhysRevE.90.062311
Abstract: A two-dimensional (2D) binary colloidal system consisting of interacting dipoles is investigated using an analytical approach. Within the harmonic approximation we obtain the phonon spectrum of the system as a function of the composition, dipole-moment ratio, and mass ratio between the small and big particles. Through a systematic analysis of the phonon spectra we are able to determine the stability region of the different lattice structures of the colloidal alloys. The gaps in the phonon frequency spectrum, the optical frequencies in the long-wavelength limit, and the sound velocity are discussed as well. Using the modified Lindemann criterion and within the harmonic approximation we estimate the melting temperature of the sublattice generated by the big particles.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 2.366
Times cited: 4
DOI: 10.1103/PhysRevE.90.062311
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“Bilayer crystals of charged magnetic dipoles : structure and phonon spectrum”. Ramos IRO, Ferreira WP, Munarin FF, Farias GA, Peeters FM, Physical review : E : statistical, nonlinear, and soft matter physics 85, 051404 (2012). http://doi.org/10.1103/PhysRevE.85.051404
Abstract: We study the structure and phonon spectrum of a two-dimensional bilayer system of classical charged dipoles oriented perpendicular to the plane of the layers for equal density in each layer. This system can be tuned through six different crystalline phases by changing the interlayer separation or the charge and/or dipole moment of the particle. The presence of the charge on the dipole particles is responsible for the nucleation of five staggered phases and a disordered phase which are not found in the magnetic dipole bilayer system. These extra phases are a consequence of the competition between the repulsive Coulomb and the attractive dipole interlayer interaction. We present the phase diagram and determine the order of the phase transitions. The phonon spectrum of the system was calculated within the harmonic approximation, and a nonmonotonic behavior of the phonon spectrum is found as a function of the effective strength of the interparticle interaction. The stability of the different phases is determined.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 2.366
Times cited: 8
DOI: 10.1103/PhysRevE.85.051404
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“Normal modes of a quasi-one-dimensional multichain complex plasma”. Piacente G, Peeters FM, Betouras JJ, Physical review : E : statistical physics, plasmas, fluids, and related interdisciplinary topics 70 (2004). http://doi.org/10.1103/PhysRevE.70.036406
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.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 2.366
Times cited: 18
DOI: 10.1103/PhysRevE.70.036406
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“Dynamics of scattering on a classical two-dimensional artificial atom”. Peelaers H, Partoens B, Tatyanenko DV, Peeters FM, Physical review : E : statistical physics, plasmas, fluids, and related interdisciplinary topics 75, 036606 (2007). http://doi.org/10.1103/PhysRevE.75.036606
Abstract: A classical two-dimensional (2D) model for an artificial atom is used to make a numerical exact study of elastic and nonelastic scattering. Interesting differences in the scattering angle distribution between this model and the well-known Rutherford scattering are found in the small energy and/or small impact parameter scattering regime. For scattering off a classical 2D hydrogen atom different phenomena such as ionization, exchange of particles, and inelastic scattering can occur. A scattering regime diagram is constructed as function of the impact parameter (b) and the initial velocity (v) of the incoming particle. In a small regime of the (b,v) space the system exhibits chaos, which is studied in more detail. Analytic expressions for the scattering angle are given in the high impact parameter asymptotic limit.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 2.366
Times cited: 1
DOI: 10.1103/PhysRevE.75.036606
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“Electron anisotropic scattering in gases: a formula for Monte Carlo simulations”. Okhrimovskyy A, Bogaerts A, Gijbels R, Physical review : E : statistical, nonlinear, and soft matter physics 65, 037402 (2002). http://doi.org/10.1103/PhysRevE.65.037402
Abstract: The purpose of this Brief Report is to point out the mistake in a formula for anisotropic electron scattering, previously published in Phys. Rev. A 41, 1112 (1990), which is widely used in Monte Carlo models of gas discharges. Anisotropic electron scattering is investigated based on the screened Coulomb potential between electrons and neutral atoms. The approach is also applied for electron scattering by nonpolar neutral molecules. Differential cross sections for electron scattering by Ar, N2, and CH4 are constructed on the basis of momentum and integrated cross sections. The formula derived in this paper is useful for Monte Carlo simulations of gas discharges.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.366
Times cited: 57
DOI: 10.1103/PhysRevE.65.037402
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“Bubble, stripe, and ring phases in a two-dimensional cluster with competing interactions”. Nelissen K, Partoens B, Peeters FM, Physical review : E : statistical physics, plasmas, fluids, and related interdisciplinary topics 71, 066204 (2005). http://doi.org/10.1103/PhysRevE.71.066204
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 2.366
Times cited: 30
DOI: 10.1103/PhysRevE.71.066204
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“Influence of a defect particle on the structure of a classical two-dimensional cluster”. Nelissen K, Partoens B, Peeters FM, Physical review : E : statistical physics, plasmas, fluids, and related interdisciplinary topics 69, 046605 (2004). http://doi.org/10.1103/PhysRevE.69.046605
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 2.366
Times cited: 27
DOI: 10.1103/PhysRevE.69.046605
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“Influence of an ellipsoid on the angular order in a two-dimensional cluster”. Nelissen K, Partoens B, Peeters FM, Physical review : E : statistical physics, plasmas, fluids, and related interdisciplinary topics 84, 031405 (2011). http://doi.org/10.1103/PhysRevE.84.031405
Abstract: The influence of an ellipsoid on the angular order of two-dimensional classical clusters is investigated through Brownian dynamics simulations. We found the following: (1) The presence of an ellipsoid does not influence the start of the angular melting, but reduces the rate at which the inner rings can rotate with respect to each other. (2) Even a small eccentricity of the ellipsoid leads to a stabilization of the angular order of the system. (3) Depending on the position of the ellipsoid in the cluster, a reentrant behavior in the angular order is observed before full radial melting of the cluster sets in. (4) The ellipsoid can lead to a two-step angular melting process: First, the rotation of the inner rings with respect to each other is hindered by the ellipsoid, but on further increasing the kinetic energy of the system, the ellipsoid just starts to behave as a spherical particle with different mobility. The effect of an ellipsoid on the molten system does not depend crucially on the interparticle interaction, but a softer parabolic confinement reduces the angular stabilization.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 2.366
DOI: 10.1103/PhysRevE.84.031405
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“Spectrum of classical two-dimensional Coulomb clusters”. Nelissen K, Matulis A, Partoens B, Kong M, Peeters FM, Physical review : E : statistical physics, plasmas, fluids, and related interdisciplinary topics 73, 016607 (2006). http://doi.org/10.1103/PhysRevE.73.016607
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 2.366
Times cited: 33
DOI: 10.1103/PhysRevE.73.016607
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“Hysteresis and reentrant melting of a self-organized system of classical particles confined in a parabolic trap”. Munarin FF, Nelissen K, Ferreira WP, Farias GA, Peeters FM, Physical review : E : statistical physics, plasmas, fluids, and related interdisciplinary topics 77, 031608 (2008). http://doi.org/10.1103/PhysRevE.77.031608
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 2.366
Times cited: 11
DOI: 10.1103/PhysRevE.77.031608
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“Ground state and normal-mode spectra of a two-dimensional system of dipole particles confined in a parabolic trap”. Munarin FF, Ferreira WP, Farias GA, Peeters FM, Physical review : E : statistical, nonlinear, and soft matter physics 78, 031405 (2008). http://doi.org/10.1103/PhysRevE.78.031405
Abstract: The ordered configurations of a monolayer of interacting magnetic dipoles confined in a circular parabolic potential are investigated as a function of the dipole moment of the particles. Despite the circular confinement, we find very asymmetric ordered structures like chains and Y-shaped configurations when a magnetic field is applied parallel to the plane of the particles. The normal-mode spectrum of the particles and its dependence on the magnetic field and the strength of the dipole moment of the particles are studied. The vibrational and rotational modes of the spectrum, which are associated with the stability of the system, are investigated in detail. The number of particles is varied and we found different ordering of the particles for different values of the dipole moment and the magnetic field. A ring structure with a large number of particles is observed for high values of the dipole moment of the particles.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 2.366
Times cited: 5
DOI: 10.1103/PhysRevE.78.031405
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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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“Transition from single-file to two-dimensional diffusion of interacting particles in a quasi-one-dimensional channel”. Lucena D, Tkachenko DV, Nelissen K, Misko VR, Ferreira WP, Farias GA, Peeters FM, Physical review : E : statistical, nonlinear, and soft matter physics 85, 031147 (2012). http://doi.org/10.1103/PhysRevE.85.031147
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.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 2.366
Times cited: 38
DOI: 10.1103/PhysRevE.85.031147
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“Single-file and normal diffusion of magnetic colloids in modulated channels”. Lucena D, Galván Moya JE, Ferreira WP, Peeters FM, Physical review : E : statistical, nonlinear, and soft matter physics 89, 032306 (2014). http://doi.org/10.1103/PhysRevE.89.032306
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.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 2.366
Times cited: 5
DOI: 10.1103/PhysRevE.89.032306
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“Tunable diffusion of magnetic particles in a quasi-one-dimensional channel”. Lucena D, Ferreira WP, Munarin FF, Farias GA, Peeters FM, Physical review : E : statistical, nonlinear, and soft matter physics 87, 012307 (2013). http://doi.org/10.1103/PhysRevE.87.012307
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
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 2.366
Times cited: 11
DOI: 10.1103/PhysRevE.87.012307
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“Structure of multispecies charged particles in a quadratic trap”. Liu YH, Chen ZY, Yu MY, Wang L, Bogaerts A, Physical review : E : statistical physics, plasmas, fluids, and related interdisciplinary topics 73, 047402 (2006). http://doi.org/10.1103/PhysRevE.73.047402
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.366
Times cited: 25
DOI: 10.1103/PhysRevE.73.047402
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“Multiple void formation in plasmas containing multispecies charged grains”. Liu YH, Chen ZY, Yu MY, Bogaerts A, Physical review : E : statistical physics, plasmas, fluids, and related interdisciplinary topics 74, 056401 (2006). http://doi.org/10.1103/PhysRevE.74.056401
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.366
Times cited: 21
DOI: 10.1103/PhysRevE.74.056401
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