Glassy dynamics of a binary Voronoi fluid: a mode-coupling analysis.

The binary Voronoi mixture is a fluid model whose interactions are derived from the Voronoi-Laguerre tessellation of the configurations of the system. The resulting interactions are local and many-body. Here we perform molecular-dynamics (MD) simulations of an equimolar mixture that is weakly polydisperse and additive. For the first time we study the structural relaxation of this mixture in the supercooled-liquid regime. From the simulations we determine the time- and temperature-dependent coherent and incoherent scattering functions for a large range of wave vectors, as well as the mean-square displacements of both particle species. We perform a detailed analysis of the dynamics by comparing the MD results with the first-principles-based idealized mode-coupling theory (MCT). To this end, we employ two approaches: fits to the asymptotic predictions of the theory, and fit-parameter-free binary MCT calculations based on static-structure-factor input from the simulations. We find that many-body interactions of the Voronoi mixture do not lead to strong qualitative differences relative to similar analyses carried out for simple liquids with pair-wise interactions. For instance, the fits give an exponent parameter λ ≈ 0.746 comparable to typical values found for simple liquids, the wavevector dependence of the Kohlrausch relaxation time is in good qualitative agreement with literature results for polydisperse hard spheres, and the MCT calculations based on static input overestimate the critical temperature, albeit only by a factor of about 1.2. This overestimation appears to be weak relative to other well-studied supercooled-liquid models such as the binary Kob-Andersen Lennard-Jones mixture. Overall, the agreement between MCT and simulation suggests that it is possible to predict several microscopic dynamic properties with qualitative, and in some cases near-quantitative, accuracy based solely on static two-point structural correlations, even though the system itself is inherently governed by many-body interactions.

Continuous-time random-walk approach to supercooled liquids: Self-part of the van Hove function and related quantities.

From equilibrium molecular dynamics (MD) simulations of a bead-spring model for short-chain glass-forming polymer melts we calculate several quantities characterizing the single-monomer dynamics near the (extrapolated) critical temperature [Formula: see text] of mode-coupling theory: the mean-square displacement g0(t), the non-Gaussian parameter [Formula: see text] and the self-part of the van Hove function [Formula: see text] which measures the distribution of monomer displacements r in time t. We also determine these quantities from a continuous-time random walk (CTRW) approach. The CTRW is defined in terms of various probability distributions which we know from previous analysis. Utilizing these distributions the CTRW can be solved numerically and compared to the MD data with no adjustable parameter. The MD results reveal the heterogeneous and non-Gaussian single-particle dynamics of the supercooled melt near [Formula: see text]. In the time window of the early [Formula: see text] relaxation [Formula: see text] is large and [Formula: see text] is broad, reflecting the coexistence of monomer displacements that are much smaller ("slow particles") and much larger ("fast particles") than the average at time t, i.e. than [Formula: see text]. For large r the tail of [Formula: see text] is compatible with an exponential decay, as found for many glassy systems. The CTRW can reproduce the spatiotemporal dependence of [Formula: see text] at a qualitative to semiquantitative level. However, it is not quantitatively accurate in the studied temperature regime, although the agreement with the MD data improves upon cooling. In the early [Formula: see text] regime we also analyze the MD results for [Formula: see text] via the space-time factorization theorem predicted by ideal mode-coupling theory. While we find the factorization to be well satisfied for small r, both above and below [Formula: see text] , deviations occur for larger r comprising the tail of [Formula: see text]. The CTRW analysis suggests that single-particle "hops" are a contributing factor for these deviations.

Voronoi glass-forming liquids: A structural study.

We introduce a theoretical model of simple fluid, whose interactions, defined in terms of the Voronoi cells of the configurations, are local and many-body. The resulting system is studied both theoretically and numerically. We show that the fluid, though sharing the global features of other models of fluids with soft interactions, has several unusual characteristics, which are investigated and discussed.

Anomalous sound attenuation in Voronoi liquid.

The physics of simple fluids in the hydrodynamic limit and notably the connection between the proper microscopic scales and the macroscopic hydrodynamical description are nowadays well understood. In particular, the three peak shape of the dynamical structure factor S(k,ω) is a universal feature, as well as the k-dependence of the peak position (∝k) and width ∝k2, the latter accounting for the sound attenuation rate. In this paper, we present a theoretical model of monodisperse fluid, whose interactions are defined via the Voronoi tessellations of the configurations [called the Voronoi liquid and first studied in Ruscher et al., Europhys. Lett. 112, 66003 (2015)], which displays at low temperatures a marked violation of the universal features of S(k,ω) with a sound attenuation rate only ∝k. This anomalous behaviour, which apparently violates the basic symmetries of the liquid state, is traced back to the existence of a time scale which is both short enough for the viscoelastic features of the liquid to impact the relaxational dynamics and however long enough for the momentum diffusion to be substantially slower than the sound propagation on that characteristic time.

Simulated glass-forming polymer melts: dynamic scattering functions, chain length effects, and mode-coupling theory analysis.

We present molecular-dynamics simulations for a fully flexible model of polymer melts with different chain length N ranging from short oligomers (N = 4) to values near the entanglement length (N = 64). For these systems we explore the structural relaxation of the supercooled melt near the critical temperature T c of mode-coupling theory (MCT). Coherent and incoherent scattering functions are analyzed in terms of the idealized MCT. For temperatures T > T c we provide evidence for the space-time factorization property of the ß relaxation and for the time-temperature superposition principle (TTSP) of the α relaxation, and we also discuss deviations from these predictions for T ≈ T c. For T larger than the smallest temperature where the TTSP holds we perform a quantitative analysis of the dynamics with the asymptotic MCT predictions for the late ß regime. Within MCT a key quantity, in addition to T c, is the exponent parameter λ. For the fully flexible polymer models studied we find that λ is independent of N and has a value (λ = 0.735 ) typical of simple glass-forming liquids. On the other hand, the critical temperature increases with chain length toward an asymptotic value T c (∞) . This increase can be described by T c (∞) - T c(N) ∼ 1/N and may be interpreted in terms of the N dependence of the monomer density ρ, if we assume that the MCT glass transition is ruled by a soft-sphere-like constant coupling parameter Γ c = ρ c T c (-1/4), where ρ c is the monomer density at T c. In addition, we also estimate T c from a Hansen-Verlet-like criterion and MCT calculations based on structural input from the simulation. For our polymer model both the Hansen-Verlet criterion and the MCT calculations suggest T c to decrease with increasing chain length, in contrast to the direct analysis of the simulation data.

Continuous-time random-walk approach to supercooled liquids. I. Different definitions of particle jumps and their consequences.

Single-particle trajectories in supercooled liquids display long periods of localization interrupted by "fast moves." This observation suggests a modeling by a continuous-time random walk (CTRW). We perform molecular dynamics simulations of equilibrated short-chain polymer melts near the critical temperature of mode-coupling theory Tc and extract "moves" from the monomer trajectories. We show that not all moves comply with the conditions of a CTRW. Strong forward-backward correlations are found in the supercooled state. A refinement procedure is suggested to exclude these moves from the analysis. We discuss the repercussions of the refinement on the jump-length and waiting-time distributions as well as on characteristic time scales, such as the average waiting time ("exchange time") and the average time for the first move ("persistence time"). The refinement modifies the temperature (T) dependence of these time scales. For instance, the average waiting time changes from an Arrhenius-type to a Vogel-Fulcher-type T dependence. We discuss this observation in the context of the bifurcation of the α process and (Johari) ß process found in many glass-forming materials to occur near Tc. Our analysis lays the foundation for a study of the jump-length and waiting-time distributions, their temperature and chain-length dependencies, and the modeling of the monomer dynamics by a CTRW approach in the companion paper [J. Helfferich et al., Phys. Rev. E 89, 042604 (2014)].

Continuous-time random-walk approach to supercooled liquids. II. Mean-square displacements in polymer melts.

The continuous-time random walk (CTRW) describes the single-particle dynamics as a series of jumps separated by random waiting times. This description is applied to analyze trajectories from molecular dynamics (MD) simulations of a supercooled polymer melt. Based on the algorithm presented by Helfferich et al. [Phys. Rev. E 89, 042603 (2014)], we detect jump events of the monomers. As a function of temperature and chain length, we examine key distributions of the CTRW: the jump-length distribution (JLD), the waiting-time distribution (WTD), and the persistence-time distribution (PTD), i.e., the distribution of waiting times for the first jump. For the equilibrium (polymer) liquid under consideration, we verify that the PTD is determined by the WTD. For the mean-square displacement (MSD) of a monomer, the results for the CTRW model are compared with the underlying MD data. The MD data exhibit two regimes of subdiffusive behavior, one for the early α process and another at later times due to chain connectivity. By contrast, the analytical solution of the CTRW yields diffusive behavior for the MSD at all times. Empirically, we can account for the effect of chain connectivity in Monte Carlo simulations of the CTRW. The results of these simulations are then in good agreement with the MD data in the connectivity-dominated regime, but not in the early α regime where they systematically underestimate the MSD from the MD.

Mode-coupling approach to polymer diffusion in an unentangled melt. I. The effect of density fluctuations.

We quantitatively assess the effect of density fluctuation modes on the dynamics of a tagged polymer in an unentangled melt. To this end, we develop a density-based mode-coupling theory (dMCT) using the Mori-Zwanzig approach and projecting the fluctuating force onto pair-density fluctuation modes. The effect of dynamical density fluctuations on the center-of-mass (c.m.) dynamics is also analyzed based on a perturbative approach and we show that dMCT and perturbation techniques yield identical results. The c.m. velocity autocorrelation function (c.m. VAF) exhibits a slow power law relaxation in the time range between the monomer time t_{1} and the Rouse relaxation time t_{N}. We obtain an analytical expression for the c.m. VAF in terms of molecular parameters. In particular, the c.m. VAF scales as -N^{-1}t^{-5/4} (where N is the number of monomer units per chain) in the relevant time regime. The results are qualitatively accounted for by the dynamical correlation hole effect. The predicted -t^{-5/4} dependence of the c.m. VAF is supported by data of non-momentum-conserving computer simulations. However, the comparison shows that the theory significantly underestimates the amplitude of the effect. This issue is discussed and an alternative approach is addressed in the second part of this series [Farago et al., Phys. Rev. E 85, 051807 (2012), the following paper].

Mode-coupling approach to polymer diffusion in an unentangled melt. II. The effect of viscoelastic hydrodynamic interactions.

A mode-coupling theory (MCT) version (called hMCT thereafter) of a recently presented theory [Farago, Meyer, and Semenov, Phys. Rev. Lett. 107, 178301 (2011)] is developed to describe the diffusional properties of a tagged polymer in a melt. The hMCT accounts for the effect of viscoelastic hydrodynamic interactions (VHIs), that is, a physical mechanism distinct from the density-based MCT (dMCT) described in the first paper of this series. The two versions of the MCT yield two different contributions to the asymptotic behavior of the center-of-mass velocity autocorrelation function (c.m. VAF). We show that in most cases the VHI mechanism is dominant; for long chains and prediffusive times it yields a negative tail ∝-N^{-1/2}t^{-3/2} for the c.m. VAF. The case of non-momentum-conserving dynamics (Langevin or Monte Carlo) is discussed as well. It generally displays a distinctive behavior with two successive relaxation stages: first -N^{-1}t^{-5/4} (as in the dMCT approach), then -N^{-1/2}t^{-3/2}. Both the amplitude and the duration of the first t^{-5/4} stage crucially depend on the Langevin friction parameter γ. All results are also relevant for the early time regime of entangled melts. These slow relaxations of the c.m. VAF, thus account for the anomalous subdiffusive regime of the c.m. mean square displacement widely observed in numerical and experimental works.

Length-scale dependent relaxation shear modulus and viscoelastic hydrodynamic interactions in polymer liquids.

A quantitative theory of hydrodynamic interactions in unentangled polymer melts and concentrated solutions is presented. The study is focussed on the pre-Rouse transient time regimes (t < τ(R), the Rouse relaxation time) where the hydrodynamic response is governed mainly by the viscoelastic effects. It is shown that transient viscoelastic hydrodynamic interactions are not suppressed (screened) at large distances and are virtually independent of polymer molecular mass. A number of transient regimes of unusual and qualitatively different behavior of isotropic and anisotropic hydrodynamic response functions are elucidated. The regimes are characterized in terms of two main length-scale dependent characteristic times: momentum spreading time τ(i) ∝ r(4∕3) and viscoelastic time τ(∗) ∝ r(4). It is shown that for t > τ(i) the viscoelastic hydrodynamic interactions can be described in terms of the time or length scale dependent effective viscosity which, for t < τ(R) and/or for r < R(coil), turns out to be much lower than the macroscopic "polymer" viscosity η(m). The theory also involves a quantitative analysis of the length-scale dependent stress relaxation in polymer melts. The general predictions for hydrodynamic interactions in thermostated systems with Langevin friction are obtained as well.

Hydrodynamic and viscoelastic effects in polymer diffusion.

We develop a fluctuating hydrodynamics approach to study the impact of the hydrodynamic and viscoelastic interactions on the motion of the center of mass of a polymer as well as on the relaxation of Rouse modes, either in a Θ solvent or in a melt of identical unentangled chains. We show that this method allows us to describe the effect of hydrodynamic interactions beyond the Zimm (for a single chain in a Θ solvent) or the Rouse models (for an unentangled melt). In the latter case, we recover the same important effect of the viscoelastic hydrodynamic interactions on the center-of-mass diffusion, first described in Farago et al (2011 Phys. Rev. Lett. 107 178301).

Anomalous diffusion of a polymer chain in an unentangled melt.

Contrary to common belief, hydrodynamic interactions in polymer melts are not screened beyond the monomer length and are important in transient regimes. We show that viscoelastic hydrodynamic interactions (VHIs) lead to anomalous dynamics of a tagged chain in an unentangled melt at t

Scale-free center-of-mass displacement correlations in polymer melts without topological constraints and momentum conservation: a bond-fluctuation model study.

By Monte Carlo simulations of a variant of the bond-fluctuation model without topological constraints, we examine the center-of-mass (COM) dynamics of polymer melts in d = 3 dimensions. Our analysis focuses on the COM displacement correlation function C(N)(t)≈∂(t) (2)h(N)(t)/2, measuring the curvature of the COM mean-square displacement h(N)(t). We demonstrate that C(N)(t) ≈ -(R(N)∕T(N))(2)(ρ∗/ρ) f(x = t/T(N)) with N being the chain length (16 ≤ N ≤ 8192), R(N) ∼ N(1/2) is the typical chain size, T(N) ∼ N(2) is the longest chain relaxation time, ρ is the monomer density, ρ(*)≈N/R(N) (d) is the self-density, and f(x) is a universal function decaying asymptotically as f(x) ∼ x(-ω) with ω = (d + 2) × α, where α = 1/4 for x ≪ 1 and α = 1/2 for x ≫ 1. We argue that the algebraic decay NC(N)(t) ∼ -t(-5/4) for t ≪ T(N) results from an interplay of chain connectivity and melt incompressibility giving rise to the correlated motion of chains and subchains.

Static Rouse modes and related quantities: corrections to chain ideality in polymer melts.

Following the Flory ideality hypothesis intrachain and interchain excluded-volume interactions are supposed to compensate each other in dense polymer systems. Multichain effects should thus be neglected and polymer conformations may be understood from simple phantom chain models. Here we provide evidence against this phantom chain, mean-field picture. We analyze numerically and theoretically the static correlation function of the Rouse modes. Our numerical results are obtained from computer simulations of two coarse-grained polymer models for which the strength of the monomer repulsion can be varied, from full excluded volume ("hard monomers") to no excluded volume ("phantom chains"). For nonvanishing excluded volume we find the simulated correlation function of the Rouse modes to deviate markedly from the predictions of phantom chain models. This demonstrates that there are nonnegligible correlations along the chains in a melt. These correlations can be taken into account by perturbation theory. Our simulation results are in good agreement with these new theoretical predictions.

Evaluation of abundance of aerobic bacteria in the rhizosphere of transgenic and non-transgenic alfalfa lines.

Fourteen genetically modified lines of alfalfa (Medicago sativa) containing the gene Ov from Japanese quail, coding for a methionine-rich protein ovalbumin, were evaluated for nodulation ability and concentration of aerobic bacteria in the rhizosphere. The transgenic lines were derived from a highly regenerable genotype Rg9/I-14-22, selected from cv. Lucia. On selective media, a higher concentration of ammonifying bacteria, bacterial spores, denitrifying and nitrifying bacteria were observed in the rhizosphere of transgenic clonesand, on the other hand, lower concentration of cellulolytic bacteria and Azotobacter spp. compared with the rhizosphere of non-transgenic clone SE/22-GT2. A statistically significant difference in the concentration of all the bacterial types was found between samples taken from two types of substrates (i.e. sterile vs. nonsterile). Higher bacterial concentration (measured as colony forming units per g soil dry mass) were observed for all tested groups of culturable bacteria in the non-sterile substrate. The presence of Azotobacter spp. was found only in the rhizosphere of plants grown in non-sterile soil in which the highest number of fertile soil particles (97 %) was observed in transgenic clones SE/22-9-1-12 and SE/22-11-1-1S.1. Concentration of bacteria involved in the N cycle in the soil was increased in the rhizosphere of transgenic clones and decreased in the rhizosphere of non-transgenic plants compared with the average value. In spite of some differences in colony numbers in samples isolated from the root rhizosphere of transgenic and nontransgenic alfalfa plants, we could not detect any statistically significant difference between individual lines.

Dissipative particle dynamics simulations of polymer melts. I. Building potential of mean force for polyethylene and cis-polybutadiene.

We present the derivation of coarse-grained force fields for two types of polymers, polyethylene (PE), and cis-polybutadiene (cis-PB), using the concept of potential of mean force. Coarse-grained force fields were obtained from microscopic simulations for several coarse-graining levels, i.e., different number of monomers lambda per mesoscopic unit called "bead." These force fields are then used in dissipative particle dynamics (DPD) simulations to study structural and dynamical properties of polymer melts of PE and cis-PB. The radial distribution functions g(R), the end-to-end distance R0, the end-to-end vector relaxation time tau, and the chain center of mass self-diffusion D(CM), are computed for different chain lengths at different coarse-graining factor lambda. Scaling laws typical of the Rouse regime are obtained for both polymers for chain lengths ranging from 6 to 50 beads. It is found that the end-to-end distance R0 obtained from DPD simulations agree well with values obtained from both microscopic simulations and experiments. The dependence of the friction coefficient used in DPD simulations versus the coarse-graining level is discussed in view of the overall scaling of the dynamical properties.

[Isolated right ventricular infarction]. / Izolált jobb kamrai infarctus.

Generally, right ventricle infarction is accompanied by left ventricle infarction. Isolated right ventricle necrosis is rare. Among 1707 patients with 6-week-old myocardial infarction there were 2 cases with isolated right ventricle infarction. Diagnosis based on pathologic Q waves in right precordial chest wall leads, radionuclide and echocardiographic observations. In one case, diagnosis was supported by coronary angiography, too.