“Merging Metadynamics into Hyperdynamics: Accelerated Molecular Simulations Reaching Time Scales from Microseconds to Seconds”. Bal KM, Neyts EC, Journal of chemical theory and computation 11, 4545 (2015). http://doi.org/10.1021/acs.jctc.5b00597
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.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 5.245
Times cited: 41
DOI: 10.1021/acs.jctc.5b00597
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“SBH17 : benchmark database of barrier heights for dissociative chemisorption on transition metal surfaces”. Tchakoua T, Gerrits N, Smeets EWF, Kroes G-J, Journal of chemical theory and computation 19, 245 (2023). http://doi.org/10.1021/ACS.JCTC.2C00824
Abstract: Accurate barriers for rate controlling elementary reactions on metal surfaces are key to understanding, controlling, and predicting the rate of heterogeneously catalyzed processes. While barrier heights for gas phase reactions have been extensively benchmarked, dissociative chemisorption barriers for the reactions of molecules on metal surfaces have received much less attention. The first database called SBH10 and containing 10 entries was recently constructed based on the specific reaction parameter approach to density functional theory (SRP-DFT) and experimental results. We have now constructed a new and improved database (SBH17) containing 17 entries based on SRP-DFT and experiments. For this new SBH17 benchmark study, we have tested three algorithms (high, medium, and light) for calculating barrier heights for dissociative chemisorption on metals, which we have named for the amount of computational effort involved in their use. We test the performance of 14 density functionals at the GGA, GGA+vdW-DF, and meta-GGA rungs. Our results show that, in contrast with the previous SBH10 study where the BEEF-vdW-DF2 functional seemed to be most accurate, the workhorse functional PBE and the MS2 density functional are the most accurate of the GGA and meta-GGA functionals tested. Of the GGA+vdW functionals tested, the SRP32-vdW-DF1 functional is the most accurate. Additionally, we found that the medium algorithm is accurate enough for assessing the performance of the density functionals tested, while it avoids geometry optimizations of minimum barrier geometries for each density functional tested. The medium algorithm does require metal lattice constants and interlayer distances that are optimized separately for each functional. While these are avoided in the light algorithm, this algorithm is found not to give a reliable description of functional performance. The combination of relative ease of use and demonstrated reliability of the medium algorithm will likely pave the way for incorporation of the SBH17 database in larger databases used for testing new density functionals and electronic structure methods.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 5.5
DOI: 10.1021/ACS.JCTC.2C00824
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“Reweighted Jarzynski sampling : acceleration of rare events and free energy calculation with a bias potential learned from nonequilibrium work”. Bal KM, Journal Of Chemical Theory And Computation 17, 6766 (2021). http://doi.org/10.1021/ACS.JCTC.1C00574
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.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 5.245
DOI: 10.1021/ACS.JCTC.1C00574
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“Conformational analysis of TMC114, a novel HIV-1 protease inhibitor”. Nivesanond K, Peeters A, Lamoen D, van Alsenoy C, Journal of Chemical Information and Modeling 48, 99 (2008). http://doi.org/10.1021/ci7001318
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 3.76
Times cited: 13
DOI: 10.1021/ci7001318
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“Lipid Oxidation: Role of Membrane Phase-Separated Domains”. Oliveira MC, Yusupov M, Bogaerts A, Cordeiro RM, Journal Of Chemical Information And Modeling 61, 2857 (2021). http://doi.org/10.1021/acs.jcim.1c00104
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.
Keywords: A1 Journal Article; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ;
Impact Factor: 3.76
DOI: 10.1021/acs.jcim.1c00104
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“Effect of Cysteine Oxidation in SARS-CoV-2 Receptor-Binding Domain on Its Interaction with Two Cell Receptors: Insights from Atomistic Simulations”. Ghasemitarei M, Privat-Maldonado A, Yusupov M, Rahnama S, Bogaerts A, Ejtehadi MR, Journal Of Chemical Information And Modeling 62, 129 (2022). http://doi.org/10.1021/acs.jcim.1c00853
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.
Keywords: A1 Journal article; Pharmacology. Therapy; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 5.6
DOI: 10.1021/acs.jcim.1c00853
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“Immobilization of TiO2 into self-supporting photocatalytic foam : influence of calcination temperature”. Tytgat T, Smits M, Lenaerts S, Verbruggen SW, International journal of applied ceramic technology 11, 714 (2014). http://doi.org/10.1111/IJAC.12086
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.
Keywords: A1 Journal article; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL)
Impact Factor: 1.048
Times cited: 2
DOI: 10.1111/IJAC.12086
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“Angular melting scenarios in binary dusty-plasma Coulomb balls : magic versus normal clusters”. Apolinario SWS, Aguiar JA, Peeters FM, Physical review : E : statistical, nonlinear, and soft matter physics 90, 063113 (2014). http://doi.org/10.1103/PhysRevE.90.063113
Abstract: Molecular-dynamic simulations were performed in order to investigate the melting processes of isotropically confined binary systems. We considered two species of particles, which differ by their amount of electric charge. A Lindemann type of criterion was used to determine the angular melting temperature. We demonstrate that the magic-to-normal cluster transition can evolve in two distinct ways, that is, through a structural phase transition of the first order or via a smooth transition where an increase of the shells' width leads to a continuous decreasing mechanical stability of the system. Moreover, for large systems, we demonstrate that the internal cluster exerts a minor effect on the mechanical stability of the external shell. Furthermore, we show that highly symmetric configurations, such as those found for multiple ring structures, have large mechanical stability, i.e., high angular melting temperature.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 2.366
Times cited: 1
DOI: 10.1103/PhysRevE.90.063113
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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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“Binary dusty plasma Coulomb balls”. Apolinario SWS, Peeters FM, Physical review : E : statistical physics, plasmas, fluids, and related interdisciplinary topics 83, 041136 (2011). http://doi.org/10.1103/PhysRevE.83.041136
Abstract: We investigated the mixing and segregation of a system consisting of two different species of particles, having different charges, interacting through a pure Coulomb potential, and confined in a three-dimensional parabolic trap. The structure of the cluster and its normal mode spectrum are analyzed as a function of the relative charge and the relative number of different types of particles. We found that (a) the system can be in a mixed or segregated state depending on the relative charge ratio parameter and (b) the segregation process is mediated by a first or second order structural phase transition which strongly influences the magic cluster properties of the system.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 2.366
Times cited: 10
DOI: 10.1103/PhysRevE.83.041136
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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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“Detailed modeling of hydrocarbon nanoparticle nucleation in acetylene discharges”. de Bleecker K, Bogaerts A, Goedheer W, Physical review : E : statistical physics, plasmas, fluids, and related interdisciplinary topics 73, 026405 (2006). http://doi.org/10.1103/PhysRevE.73.026405
Abstract: The initial stage of nanoparticle formation and growth in radiofrequency acetylene (C2H2) plasmas is investigated by means of a self-consistent one-dimensional fluid model. A detailed chemical kinetic scheme, containing electron impact, ion-neutral, and neutral-neutral reactions, has been developed in order to predict the underlying dust growth mechanisms and the most important dust precursors. The model considers 41 different species (neutrals, radicals, ions, and electrons) describing hydrocarbons (CnHm) containing up to 12 carbon atoms. Possible routes for particle growth are discussed. Both positive and negative ion reaction pathways are considered, as consecutive anion- and cation-molecule reactions seem to lead to a fast build up of the carbon skeleton.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.366
Times cited: 89
DOI: 10.1103/PhysRevE.73.026405
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“Diffusion in a quasi-one-dimensional system on a periodic substrate”. Carvalho JCN, Nelissen K, Ferreira WP, Farias GA, Peeters FM, Physical review : E : statistical, nonlinear, and soft matter physics 85, 021136 (2012). http://doi.org/10.1103/PhysRevE.85.021136
Abstract: The diffusion of charged particles interacting through a repulsive Yukawa potential, exp(-r/lambda)/r, confined by a parabolic potential in the y direction and subjected to a periodic substrate potential in the x direction is investigated. Langevin dynamic simulations are used to investigate the effect of the particle density, the amplitude of the periodic substrate, and the range of the interparticle interaction potential on the diffusive behavior of the particles. We found that in general the diffusion is suppressed with increasing the amplitude of the periodic potential, but for specific values of the strength of the substrate potential a remarkable increase of the diffusion is found with increasing the periodic potential amplitude. In addition, we found a strong dependence of the diffusion on the specific arrangement of the particles, e. g., single-chain versus multichain configuration. For certain particle configurations, a reentrant behavior of the diffusion is found as a function of the substrate strength due to structural transitions in the ordering of the particles.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 2.366
Times cited: 9
DOI: 10.1103/PhysRevE.85.021136
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“Diffusion of interacting particles in discrete geometries: Equilibrium and dynamical properties”. Becker T, Nelissen K, Cleuren B, Partoens B, Van den Broeck C, Physical review : E : statistical, nonlinear, and soft matter physics 90, 052139 (2014). http://doi.org/10.1103/PhysRevE.90.052139
Abstract: We expand on a recent study of a lattice model of interacting particles [Phys. Rev. Lett. 111, 110601 (2013)]. The adsorption isotherm and equilibrium fluctuations in particle number are discussed as a function of the interaction. Their behavior is similar to that of interacting particles in porous materials. Different expressions for the particle jump rates are derived from transition-state theory. Which expression should be used depends on the strength of the interparticle interactions. Analytical expressions for the self-and transport diffusion are derived when correlations, caused by memory effects in the environment, are neglected. The diffusive behavior is studied numerically with kinetic Monte Carlo (kMC) simulations, which reproduces the diffusion including correlations. The effect of correlations is studied by comparing the analytical expressions with the kMC simulations. It is found that the Maxwell-Stefan diffusion can exceed the self-diffusion. To our knowledge, this is the first time this is observed. The diffusive behavior in one-dimensional and higher-dimensional systems is qualitatively the same, with the effect of correlations decreasing for increasing dimension. The length dependence of both the self-and transport diffusion is studied for one-dimensional systems. For long lengths the self-diffusion shows a 1/L dependence. Finally, we discuss when agreement with experiments and simulations can be expected. The assumption that particles in different cavities do not interact is expected to hold quantitatively at low and medium particle concentrations if the particles are not strongly interacting.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 2.366
Times cited: 8
DOI: 10.1103/PhysRevE.90.052139
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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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“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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“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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“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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“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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“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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“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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“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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“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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“Influence of electron recapture by the cathode upon the discharge characteristics in dc planar magnetrons”. Kolev I, Bogaerts A, Gijbels R, Physical review : E : statistical physics, plasmas, fluids, and related interdisciplinary topics 72, 056402 (2005). http://doi.org/10.1103/PhysRevE.72.056402
Abstract: In dc magnetrons the electrons emitted from the cathode may return there due to the applied magnetic field. When that happens, they can be recaptured or reflected back into the discharge, depending on the value of the reflection coefficient (RC). A 2d3v (two-dimensional in coordinate and three-dimensional in velocity space) particle-in-cellMonte Carlo model, including an external circuit, is developed to determine the role of the electron recapture in the discharge processes. The detailed discharge structure as a function of RC for two pressures (4 and 25mtorr) is studied. The importance of electron recapture is clearly manifested, especially at low pressures. The results indicate that the discharge characteristics are dramatically changed with varying RC between 0 and 1. Thus, the electron recapture at the cathode appears to be a significant mechanism in magnetron discharges and RC a very important parameter in their correct quantitative description that should be dealt with cautiously.
Keywords: A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Impact Factor: 2.366
Times cited: 29
DOI: 10.1103/PhysRevE.72.056402
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“Inhomogeneous melting in anisotropically confined two-dimensional clusters”. Apolinario SWS, Partoens B, Peeters FM, Physical review : E : statistical physics, plasmas, fluids, and related interdisciplinary topics 74, 031107 (2006). http://doi.org/10.1103/PhysRevE.74.031107
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 2.366
Times cited: 25
DOI: 10.1103/PhysRevE.74.031107
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“Interplay of model ingredients affecting aggregate shape plasticity in diffusion-limited aggregation”. Duarte-Neto P, Stosic T, Stosic B, Lessa R, Milošević, MV, Physical review : E : statistical, nonlinear, and soft matter physics 90, 012312 (2014). http://doi.org/10.1103/PhysRevE.90.012312
Abstract: We analyze the combined effect of three ingredients of an aggregation model-surface tension, particle flow and particle source-representing typical characteristics of many aggregation growth processes in nature. Through extensive numerical experiments and for different underlying lattice structures we demonstrate that the location of incoming particles and their preferential direction of flow can significantly affect the resulting general shape of the aggregate, while the surface tension controls the surface roughness. Combining all three ingredients increases the aggregate shape plasticity, yielding a wider spectrum of shapes as compared to earlier works that analyzed these ingredients separately. Our results indicate that the considered combination of effects is fundamental for modeling the polymorphic growth of a wide variety of structures in confined geometries and/or in the presence of external fields, such as rocks, crystals, corals, and biominerals.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 2.366
Times cited: 3
DOI: 10.1103/PhysRevE.90.012312
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“Magnetic particles confined in a modulated channel : structural transitions tunable by tilting a magnetic field”. Galván Moya JE, Lucena D, Ferreira WP, Peeters FM, Physical review : E : statistical, nonlinear, and soft matter physics 89, 032309 (2014). http://doi.org/10.1103/PhysRevE.89.032309
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.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 2.366
Times cited: 11
DOI: 10.1103/PhysRevE.89.032309
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“Melting and evaporation in classical two-dimensional clusters confined by a Coulomb potential”. Ferreira WP, Peeters FM, Farias GA, Physical review : E : statistical, nonlinear, and soft matter physics 72, 041502 (2005). http://doi.org/10.1103/PhysRevE.72.041502
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.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 2.366
Times cited: 4
DOI: 10.1103/PhysRevE.72.041502
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“Melting transitions in isotropically confined three-dimensional small Coulomb clusters”. Apolinario SWS, Peeters FM, Physical review : E : statistical physics, plasmas, fluids, and related interdisciplinary topics 76, 031107 (2007). http://doi.org/10.1103/PhysRevE.76.031107
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.
Keywords: A1 Journal article; Condensed Matter Theory (CMT)
Impact Factor: 2.366
Times cited: 28
DOI: 10.1103/PhysRevE.76.031107
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