Comment on ``Phase ordering in chaotic map lattices with conserved dynamics''

Angelini, Pellicoro, and Stramaglia [Phys. Rev. E {\bf 60}, R5021 (1999), cond-mat/9907149] (APS) claim that the phase ordering of two-dimensional systems of sequentially-updated chaotic maps with conserved ``order parameter'' does not belong, for large regions of parameter space, to the expected universality class. We show here that these results are due to a slow crossover and that a careful treatment of the data yields normal dynamical scaling. Moreover, we construct better models, i.e. synchronously-updated coupled map lattices, which are exempt from these crossover effects, and allow for the first precise estimates of persistence exponents in this case.Comment: 3 pages, to be published in Phys. Rev.

Lamellae Stability in Confined Systems with Gravity

The microphase separation of a diblock copolymer melt confined by hard walls and in the presence of a gravitational field is simulated by means of a cell dynamical system model. It is found that the presence of hard walls normal to the gravitational field are key ingredients to the formation of well ordered lamellae in BCP melts. To this effect the currents in the directions normal and parallel to the field are calculated along the interface of a lamellar domain, showing that the formation of lamellae parallel to the hard boundaries and normal to the field correspond to the stable configuration. Also, it is found thet the field increases the interface width.Comment: 4 pages, 2 figures, submitted to Physical Review

Temporal patterns of gene expression via nonmetric multidimensional scaling analysis

Motivation: Microarray experiments result in large scale data sets that require extensive mining and refining to extract useful information. We have been developing an efficient novel algorithm for nonmetric multidimensional scaling (nMDS) analysis for very large data sets as a maximally unsupervised data mining device. We wish to demonstrate its usefulness in the context of bioinformatics. In our motivation is also an aim to demonstrate that intrinsically nonlinear methods are generally advantageous in data mining. Results: The Pearson correlation distance measure is used to indicate the dissimilarity of the gene activities in transcriptional response of cell cycle-synchronized human fibroblasts to serum [Iyer et al., Science vol. 283, p83 (1999)]. These dissimilarity data have been analyzed with our nMDS algorithm to produce an almost circular arrangement of the genes. The temporal expression patterns of the genes rotate along this circular arrangement. If an appropriate preparation procedure may be applied to the original data set, linear methods such as the principal component analysis (PCA) could achieve reasonable results, but without data preprocessing linear methods such as PCA cannot achieve a useful picture. Furthermore, even with an appropriate data preprocessing, the outcomes of linear procedures are not as clearcut as those by nMDS without preprocessing.Comment: 11 pages, 6 figures + online only 2 color figures, submitted to Bioinformatic

Selection, Stability and Renormalization

We illustrate how to extend the concept of structural stability through applying it to the front propagation speed selection problem. This consideration leads us to a renormalization group study of the problem. The study illustrates two very general conclusions: (1) singular perturbations in applied mathematics are best understood as renormalized perturbation methods, and (2) amplitude equations are renormalization group equations.Comment: 38 pages, LaTeX, two PostScript figures available by anonymous ftp to gijoe.mrl.uiuc.edu (128.174.119.153) files /pub/front_kkfest_fig

Accurate effective pair potentials for polymer solutions

Dilute or semi-dilute solutions of non-intersecting self-avoiding walk (SAW) polymer chains are mapped onto a fluid of ``soft'' particles interacting via an effective pair potential between their centers of mass. This mapping is achieved by inverting the pair distribution function of the centers of mass of the original polymer chains, using integral equation techniques from the theory of simple fluids. The resulting effective pair potential is finite at all distances, has a range of the order of the radius of gyration, and turns out to be only moderately concentration-dependent. The dependence of the effective potential on polymer length is analyzed in an effort to extract the scaling limit. The effective potential is used to derive the osmotic equation of state, which is compared to simulation data for the full SAW segment model, and to the predictions of renormalization group calculations. A similar inversion procedure is used to derive an effective wall-polymer potential from the center of mass density profiles near the wall, obtained from simulations of the full polymer segment model. The resulting wall-polymer potential turns out to depend strongly on bulk polymer concentration when polymer-polymer correlations are taken into account, leading to a considerable enhancement of the effective repulsion with increasing concentration. The effective polymer-polymer and wall-polymer potentials are combined to calculate the depletion interaction induced by SAW polymers between two walls. The calculated depletion interaction agrees well with the ``exact'' results from much more computer-intensive direct simulation of the full polymer-segment model, and clearly illustrates the inadequacy -- in the semi-dilute regime -- of the standard Asakura-Oosawa approximation based on the assumption of non-interacting polymer coils.Comment: 18 pages, 24 figures, ReVTeX, submitted to J. Chem. Phy

The role of the alloy structure in the magnetic behavior of granular systems

The effect of grain size, easy magnetization axis and anisotropy constant distributions in the irreversible magnetic behavior of granular alloys is considered. A simulated granular alloy is used to provide a realistic grain structure for the Monte Carlo simulation of the ZFC-FC curves. The effect of annealing and external field is also studied. The simulation curves are in good agreement with the FC and ZFC magnetization curves measured on melt spun Cu-Co ribbons.Comment: 13 pages, 10 figures, submitted to PR

The law of action and reaction for the effective force in a nonequilibrium colloidal system

We study a nonequilibrium Langevin many-body system containing two 'test' particles and many 'background' particles. The test particles are spatially confined by a harmonic potential, and the background particles are driven by an external driving force. Employing numerical simulations of the model, we formulate an effective description of the two test particles in a nonequilibrium steady state. In particular, we investigate several different definitions of the effective force acting between the test particles. We find that the law of action and reaction does not hold for the total mechanical force exerted by the background particles, but that it does hold for the thermodynamic force defined operationally on the basis of an idea used to extend the first law of thermodynamics to nonequilibrium steady states.Comment: 13 page

Scaling in Late Stage Spinodal Decomposition with Quenched Disorder

We study the late stages of spinodal decomposition in a Ginzburg-Landau mean field model with quenched disorder. Random spatial dependence in the coupling constants is introduced to model the quenched disorder. The effect of the disorder on the scaling of the structure factor and on the domain growth is investigated in both the zero temperature limit and at finite temperature. In particular, we find that at zero temperature the domain size, $R(t)$, scales with the amplitude, $A$, of the quenched disorder as $R(t) = A^{-\beta} f(t/A^{-\gamma})$ with $\beta \simeq 1.0$ and $\gamma \simeq 3.0$ in two dimensions. We show that $\beta/\gamma = \alpha$, where $\alpha$ is the Lifshitz-Slyosov exponent. At finite temperature, this simple scaling is not observed and we suggest that the scaling also depends on temperature and $A$. We discuss these results in the context of Monte Carlo and cell dynamical models for phase separation in systems with quenched disorder, and propose that in a Monte Carlo simulation the concentration of impurities, $c$, is related to $A$ by $A \sim c^{1/d}$.Comment: RevTex manuscript 5 pages and 5 figures (obtained upon request via email [email protected]