Induced order and reentrant melting in classical two-dimensional binary clusters

A binary system of classical charged particles interacting through a dipole repulsive potential and confined in a two-dimensional hardwall trap is studied by Brownian dynamics simulations. We found that the presence of small particles \emph{stabilizes} the angular order of the system as a consequence of radial fluctuations of the small particles. There is an optimum in the increased rigidity of the cluster as function of the number of small particles. The small (i.e. defect) particles melt at a lower temperature compared to the big particles and exhibit a \emph{reentrant} behavior in its radial order that is induced by the intershell rotation of the big particles.Comment: 7 pages, 3 figure

Adsorption and desorption in confined geometries: a discrete hopping model

We study the adsorption and desorption kinetics of interacting particles moving on a one-dimensional lattice. Confinement is introduced by limiting the number of particles on a lattice site. Adsorption and desorption are found to proceed at different rates, and are strongly influenced by the concentration-dependent transport diffusion. Analytical solutions for the transport and self-diffusion are given for systems of length 1 and 2 and for a zero-range process. In the last situation the self- and transport diffusion can be calculated analytically for any length.Comment: Published in EPJ ST volume "Brownian Motion in Confined Geometries

Comment on "Generalized exclusion processes: Transport coefficients"

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 [Phys. Rev. Lett. 111, 110601 (2013)].Comment: (citation added, published version

Structural transitions in vertically and horizontally coupled parabolic channels of Wigner crystals

Structural phase transitions in two vertically or horizontally coupled channels of strongly interacting particles are investigated. The particles are free to move in the $x$-direction but are confined by a parabolic potential in the $y$-direction. They interact with each other through a screened power-law potential ($r^{-n}e^{-r/\lambda}$). In vertically coupled systems the channels are stacked above each other in the direction perpendicular to the $(x,y)$-plane, while in horizontally coupled systems both channels are aligned in the confinement direction. Using Monte Carlo (MC) simulations we obtain the ground state configurations and the structural transitions as a function of the linear particle density and the separation between the channels. At zero temperature the vertically coupled system exhibits a rich phase diagram with continuous and discontinuous transitions. On the other hand the vertically coupled system exhibits only a very limited number of phase transitions due to its symmetry. Further we calculated the normal modes for the Wigner crystals in both cases. From MC simulations we found that in the case of vertically coupled systems the zigzag transition is only possible for low densities. A Ginzburg-Landau theory for the zigzag transition is presented, which predicts correctly the behavior of this transition from which we interpret the structural phase transition of the Wigner crystal through the reduction of the Brillouin zone.Comment: 9 pages, 13 figure

Diffusion of interacting particles in discrete geometries

We evaluate the self-diffusion and transport diffusion of interacting particles in a discrete geometry consisting of a linear chain of cavities, with interactions within a cavity described by a free-energy function. Exact analytical expressions are obtained in the absence of correlations, showing that the self-diffusion can exceed the transport diffusion if the free-energy function is concave. The effect of correlations is elucidated by comparison with numerical results. Quantitative agreement is obtained with recent experimental data for diffusion in a nanoporous zeolitic imidazolate framework material, ZIF-8.Comment: 5 pages main text (3 figures); 9 pages supplemental material (2 figures). (minor changes, published version

Hysteresis and re-entrant melting of a self-organized system of classical particles confined in a parabolic trap

A self-organized system composed of classical particles confined in a two-dimensional parabolic trap and interacting through a potential with a short-range attractive part and long-range repulsive part is studied as function of temperature. The influence of the competition between the short-range attractive part of the inter-particle potential and its long-range repulsive part on the melting temperature is studied. Different behaviors of the melting temperature are found depending on the screening length ($\kappa$) and the strength ($B$) of the attractive part of the inter-particle potential. A re-entrant behavior and a thermal induced phase transition is observed in a small region of ($\kappa,B$)-space. A structural hysteresis effect is observed as a function of temperature and physically understood as due to the presence of a potential barrier between different configurations of the system.Comment: 8 pages, 6 figure

Transition from single-file to two-dimensional diffusion of interacting particles in a quasi-one-dimensional channel

Diffusive properties of a monodisperse system of interacting particles confined to a \textit{quasi}-one-dimensional (Q1D) channel are studied using molecular dynamics (MD) 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 (SFD) to the two-dimensional diffusion regime is investigated. This transition (regarding the calculation of the scaling exponent ($\alpha$) of the MSD $$ $\propto t^{\alpha}$) 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/stepwise (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.Comment: 13 pages, 11 figure

RNA interference knockdown of BRASSINOSTEROID INSENSITIVE1 in maize reveals novel functions for brassinosteroid signaling in controlling plant architecture

Brassinosteroids (BRs) are plant hormones involved in various growth and developmental processes. The BR signaling system is well established in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) but poorly understood in maize (Zea mays). BRASSINOSTEROID INSENSITIVE1 (BRI1) is a BR receptor, and database searches and additional genomic sequencing identified five maize homologs including duplicate copies of BRI1 itself. RNA interference (RNAi) using the extracellular coding region of a maize zmbril complementary DNA knocked down the expression of all five homologs. Decreased response to exogenously applied brassinolide and altered BR marker gene expression demonstrate that zmbriI-RNAi transgenic lines have compromised BR signaling. zmbriI-RNAi plants showed dwarf stature due to shortened internodes, with upper internodes most strongly affected. Leaves of zmbriI-RNAi plants are dark green, upright, and twisted, with decreased auricle formation. Kinematic analysis showed that decreased cell division and cell elongation both contributed to the shortened leaves. A BRASSINOSTEROID INSENSITIVE1-ETHYL METHANESULFONATE-SUPPRESSOR1-yellow fluorescent protein (BES1-YFP) transgenic line was developed that showed BR-inducible BES1-YFP accumulation in the nucleus, which was decreased in zmbriI-RNAi. Expression of the BES1-YFP reporter was strong in the auricle region of developing leaves, suggesting that localized BR signaling is involved in promoting auricle development, consistent with the zmbriI-RNAi phenotype. The blade-sheath boundary disruption, shorter ligule, and disrupted auricle morphology of RNAi lines resemble KNOTTED1-LIKE HOMEOBOX (KNOX) mutants, consistent with a mechanistic connection between KNOX genes and BR signaling

Diffusion of interacting particles in discrete geometries: equilibrium and dynamical properties

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 inter-particle 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 one over length 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.Comment: (18 pages, 16 figures, published version