Search

Among lattice configurations of densely packed hard ellipses, Monte Carlo simulations are used to identify the so-called parallel and diagonal lattices as the two favorable states. The free energies of these two states are computed for several system sizes employing the Einstein crystal method. An accurate calculation of the free energy difference between the two states reveals the parallel lattice as the state with the lowest free energy. The origin of the entropic difference between the two states is further elucidated by assessing the roles of the translational and rotational degrees of freedom. [ABSTRACT FROM AUTHOR]

In an effort to illuminate the general principles governing the critical behavior of model fluids, we investigate in this study how the shape and the (attractive) interaction range of the molecule affect the gas–liquid equilibrium and the critical behavior of the system. A combination of Monte Carlo simulations and analytical theory is employed to compute critical properties, i.e., temperature and density, of a system of hard-core ellipses with an attractive square-well potential in two-dimensional space. The critical temperature is found to decrease monotonically as the asphericity of the molecule is increased. This trend can be successfully explained in terms of the strength of the effective attraction acting between molecules measured, for instance, by the second virial coefficient. The critical density shows a complex dependence on both the range of attraction and the asphericity of the molecule. We find that the properties of particle clusters formed in near-critical states reproduce some of the most important features of the critical density, including multiple minima and maxima. It is shown that a model based on the extent of the overlap between attractive shells surrounding the ellipses captures the variation of the size of the clusters. Based on the obtained results, we discuss implications of varying the shape of the attraction potential for critical density. [ABSTRACT FROM AUTHOR]

Several repetitive elements are known to be present in the genome of chickpea (Cicer arietinum L.) including satellite DNA and En/Spm transposons as well as two dispersed, highly repetitive elements, CaRepl and CaRep2. PCR was used to prove that CaRepl, CaRep2, and previously isolated CaRep3 of C. arietinum represent different segments of a highly repetitive Ty3-gypsy-like retrotransposon (Metaviridae) designated CaRep that makes up large parts of the intercalary heterochromatin. The full sequence of this element including the LTRs and untranslated internal regions was isolated by selective amplification. The restriction pattern of CaRep was different within the annual species of the genus Cicer, suggesting its rearrangement during the evolution of the genus during the last 100000 years. In addition to CaRep, another LTR and a non-LTR retrotransposon family were isolated, and their restriction patterns and physical localization in the chickpea genome were characterized. The LINE-like element CaLin is only of comparatively low abundance and reveals a considerable heterogeneity. The Ty1-copia-like element (Pseudoviridae) CaTy is located in the distal parts of the intercalary heterochromatin and adjacent euchromatic regions, but it is absent from the centromeric regions. These results together with earlier findings allow to depict the distribution of retroelements on chickpea chromosomes, which extensively resembles the retroelement landscape of the genome of the model legume Medicago truncatula Gaertn. Key words: Cicer arietinum L., fluorescent in situ hybridization (FISH), repetitive DNA, retrotransposon, Metaviridae, Pseudoviridae. Plusieurs elements repetes sont connus au sein du genome du pois chiche (Cicer arietinum L.) incluant l'ADN satellite, des transposons En/Spm ainsi que deux elements disperses tresrepetes, CaRep1 et CaRep2. Une approche PCR a ete employee pour montrer que CaRep1, CaRep2 ainsi que l'element CaRep3 isole anteerieurement du C. arietinum L. represented divers segments d'un retrotransposon de type Ty3-gypsy (Metaviridae) appele CaRep qui peuple de grands segments de l'heteerochromatine intercalaire. La sequence complete de cet element incluant les LTR et les regions internes non-traduites a ete isolee par amplification selective. Le motif de restriction de CaRep diffeerait au sein des especes annuelles du genre Cicer, ce qui suggere l'occurrence de rearrangements au cours de revolution du genre Cicer lors des 100 000 dernieres anneees. En plus de CaRep, deux autres familles de retrotransoposons, l'une avec LTR et l'autre sans LTR, ont ete; cloneees, caracteriseees par analyse de restriction et par cartographie physique au sein du genome du pois chiche. L'element de type LINE CaLin est relativement peu abondant et presente une heteerogeneeitee considerable. L'element de type Ty1-copia (Pseudoviridae) CaTy est situe dans les portions distales de l'heeterochromatine intercalaire ainsi que dans les regions euchromatiques voisines, mais il est absent des regions centromeiriques. Ajoutes aux resultats anteerieurs (Staginnus et al. 1999, 2001), les resultats de cette etude permettent de depeindre la distribution des retroelements au sein des chromosomes du pois chiche et dressent un portrait qui ressemble grandement a la situation decrite chez la legumineuse modele Medicago truncatula Gaertn. Mots-cles : Cicer arietinum L., hybridation in situ en fluorescence (FISH), ADN repete,retrotransposon, Metaviridae, Pseudoviridae. [Traduit par la Redaction], Introduction Retrotransposons are ubiquitous in plant genomes and contribute significantly to their complexity (Kumar and Bennetzen 1999; Vitte and Panaud 2005). In some genomes such as maize, retrotransposons comprise up [...]

Abstract: The pantropical genus Vigna (Leguminosae) comprises 7 cultivated species that are adapted to a wide range of extreme agroclimatic conditions. Few data are available on the relationships among these [...]

Using non-equilibrium molecular dynamics simulations we study the yielding behaviour of a model cluster crystal formed by ultrasoft particles under shear. We investigate the evolution of stress as a function of strain for different shear rates, γ, and temperatures. The stress-strain relation displays a pronounced maximum at the yielding point; the height of this maximum, σp, increases via a power law with an increasing shear range and tends to saturate to a finite value if the limit shear rate goes to zero (at least within the considered temperature range). Interestingly, this behaviour can be captured by the Herschel-Bulkley type model which, for a given temperature, allows us to predict a static yield stress σp0 (in the shear rate tending to zero limit), a characteristic timescale τc, and the exponent α of the above-mentioned power-law decay of the σp at high shear rates. Furthermore, for different temperatures, the σp can be scaled as functions of onto a single master curve when scaled by corresponding τc and σp0. Moreover, for a given shear rate, σp displays a logarithmic dependence on temperature. Again, the σp-T curves for different shear rates can be scaled on a single logarithmic master curve when scaled by a corresponding fitting parameters. [ABSTRACT FROM AUTHOR]

We present a theoretical analysis of the structural properties and phase behavior of spherical, loosely cross-linked ionic microgels that possess a low monomer concentration. The analysis is based on the recently derived effective interaction potential between such particles [A. R. Denton, Phys. Rev. E 67, 011804 (2003)]. By employing standard tools from the theory of the liquid state, we quantitatively analyze the pair correlations in the fluid and find anomalous behavior above the overlap concentration, similar to the cases of star-branched neutral and charged polymers. We also employ an evolutionary algorithm in order to predict the crystalline phases of the system without any a priori assumptions regarding their symmetry class. A very rich phase diagram is obtained, featuring two reentrant melting transitions and a number of unusual crystal structures. At high densities, both the Hansen–Verlet freezing criterion [J.-P. Hansen and L. Verlet, Phys. Rev. 184, 151 (1969)] and the Lindemann melting criterion [F. A. Lindemann, Phys. Z. 11, 609 (1910)] lose their validity. The topology of the phase diagram is altered when the steric interactions between the polymer segments become strong enough, in which case the lower-density reentrant melting disappears and the region of stability of the fluid is split into two disconnected domains, separated by intervening fcc and bcc regions. [ABSTRACT FROM AUTHOR]

In a previous paper, we described a fast and reliable numerical method for obtaining the optical absorption spectrum of a fluid of nonpolar linearly polarizable molecules. The fluid is modeled by a generalization of the microscopic classical Yvon–Kirkwood equations, which yields the same dynamic response as the much-studied quantum Drude oscillator model. Numerical results were presented based on a linear closure relation to the central Ornstein–Zernike analog equation. In the present paper, we consider a nonlinear closure which includes but goes beyond the previously studied linear closure. We display the absorption spectrum, as implied by the renormalized polarizability and the dynamic dielectric constant, for both hard sphere and Lennard-Jones fluids. Comparison with available simulation results shows that the nonlinear closure performs well over a wide density range, and in particular corrects the poor low-density behavior of the linear theory. © 1994 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Numerical results are presented for a classical model describing optical absorption in a fluid of nonpolar linearly polarizable molecules. The model corresponds to the microscopic Yvon–Kirkwood equations with frequency-dependent molecular polarizability. The dynamic response of the model system to an externally applied electric field is identical to that predicted by the much-studied quantum Drude oscillator model. A fast and reliable numerical method is described, based on that proposed by Gillan for the solution of the Ornstein–Zernike equation of classical liquid state theory, which allows more sophisticated results than those obtained to date. In particular, the evolution of the optical absorption band is studied for hard sphere and Lennard-Jones fluids, in which the molecular center-of-mass positions are described by realistic pair distribution functions. Both neat fluids and impurity systems are considered. A number of spectroscopic properties are calculated, including the renormalized dynamic polarizability and the dynamic dielectric constant. [ABSTRACT FROM AUTHOR]

We present a single superchain/effective medium approximation calculation of the electronic density of states for an sp3 fluid in a tight-binding Hamiltonian approximation, with parameters roughly chosen to represent liquid Hg. Comparison with direct diagonalization of the Hamiltonian using quenched liquid configurations generated by molecular dynamics shows that the performance of the theory is more than acceptable for moderate to high densities. Localization is estimated from the inverse participation ratio calculated from the simulation an in a second order renormalized perturbation theory proposed by Winn and Logan. Analysis of the results indicate that by increasing density the metal nonmetal transition occurs well after the band crossing transition. The major weakness of the theory as far as the density of states is concerned can very likely be coped with by inclusion of nonlinear corrections. © 1996 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Studies the band structure of liquid carbon and silicon modelled in a tight-binding Hamiltonian approximation by means of an integral equation approximation that includes non-linear corrections. Non-linear corrections to the frequency spectrum of a fluid of coupled vector drude oscillators.