Microscopic Theory for Long Range Spatial Correlations in Lattice Gas Automata

Lattice gas automata with collision rules that violate the conditions of semi-detailed-balance exhibit algebraic decay of equal time spatial correlations between fluctuations of conserved densities. This is shown on the basis of a systematic microscopic theory. Analytical expressions for the dominant long range behavior of correlation functions are derived using kinetic theory. We discuss a model of interacting random walkers with x-y anisotropy whose pair correlation function decays as 1/r^2, and an isotropic fluid-type model with momentum correlations decaying as 1/r^2. The pair correlation function for an interacting random walker model with interactions satisfying all symmetries of the square lattice is shown to have 1/r^4 density correlations. Theoretical predictions for the amplitude of the algebraic tails are compared with the results of computer simulations.Comment: 31 pages, 2 figures, final version as publishe

Renormalized Equilibria of a Schloegl Model Lattice Gas

A lattice gas model for Schloegl's second chemical reaction is described and analyzed. Because the lattice gas does not obey a semi-detailed-balance condition, the equilibria are non-Gibbsian. In spite of this, a self-consistent set of equations for the exact homogeneous equilibria are described, using a generalized cluster-expansion scheme. These equations are solved in the two-particle BBGKY approximation, and the results are compared to numerical experiment. It is found that this approximation describes the equilibria far more accurately than the Boltzmann approximation. It is also found, however, that spurious solutions to the equilibrium equations appear which can only be removed by including effects due to three-particle correlations.Comment: 21 pages, REVTe

Entropy and Correlations in Lattice Gas Automata without Detailed Balance

We consider lattice gas automata where the lack of semi-detailed balance results from node occupation redistribution ruled by distant configurations; such models with nonlocal interactions are interesting because they exhibit non-ideal gas properties and can undergo phase transitions. For this class of automata, mean-field theory provides a correct evaluation of properties such as compressibility and viscosity (away from the phase transition), despite the fact that no H-theorem strictly holds. We introduce the notion of locality - necessary to define quantities accessible to measurements - by treating the coupling between nonlocal bits as a perturbation. Then if we define operationally ``local'' states of the automaton - whether the system is in a homogeneous or in an inhomogeneous state - we can compute an estimator of the entropy and measure the local channel occupation correlations. These considerations are applied to a simple model with nonlocal interactions.Comment: 13 pages, LaTeX, 5 PostScript figures, uses psfig. Submitted to Int. J. Mod. Phys.

Patterns and Long Range Correlations in Idealized Granular Flows

An initially homogeneous freely evolving fluid of inelastic hard spheres develops inhomogeneities in the flow field (vortices) and in the density field (clusters), driven by unstable fluctuations. Their spatial correlations, as measured in molecular dynamics simulations, exhibit long range correlations; the mean vortex diameter grows as the square root of time; there occur transitions to macroscopic shearing states, etc. The Cahn--Hilliard theory of spinodal decomposition offers a qualitative understanding and quantitative estimates of the observed phenomena. When intrinsic length scales are of the order of the system size, effects of physical boundaries and periodic boundaries (finite size effects in simulations) are important.Comment: 13 pages with 7 postscript figures, LaTeX (uses psfig). Submitted to International Journal of Modern Physics

Profiling condition-specific, genome-wide regulation of mRNA stability in yeast

The steady-state abundance of an mRNA is determined by the balance between transcription and decay. Although regulation of transcription has been well studied both experimentally and computationally, regulation of transcript stability has received little attention. We developed an algorithm, MatrixREDUCE, that discovers the position-specific affinity matrices for unknown RNAbinding factors and infers their condition-specific activities, using only genomic sequence data and steady-state mRNA expression data as input. We identified and computationally characterized the binding sites for six mRNA stability regulators in Saccharomyces cerevisiae, which include two members of the Pumilio-homology domain (Puf) family of RNA-binding proteins, Puf3p and Puf4p. We provide computational and experimental evidence that regulation of mRNA stability by these factors is modulated in response to a variety of environmental stimuli

Theoretical approach to two-dimensional traffic flow models

In this paper we present a theoretical analysis of a recently proposed two-dimensional Cellular Automata model for traffic flow in cities with the novel ingredient of turning capability. Numerical simulations of this model show that there is a transition between a freely moving phase with high velocity to a jammed state with low velocity. We study the dynamics of such a model starting with the microscopic evolution equation, which will serve as a basis for further analysis. It is shown that a kinetic approach, based on the Boltzmann assumption, is able to provide a reasonably good description of the jamming transition. We further introduce a space-time continuous phenomenological model leading to a couple of partial differential equations whose preliminary results agree rather well with the numerical simulations.Comment: 15 pages, REVTeX 3.0, 7 uuencoded figures upon request to [email protected]

The promises of inclusive research methodologies: relational design and praxis

This article explores the potential and challenges of inclusive research methodologies when working with older individuals with lower literacy levels. We present inclusive approaches developed during our research and discuss their implications for methodology and individual well-being among older adults with lower literacy levels. Our key insight is that the promise of inclusive research lies in relational design and praxis. Prioritizing meaningful relationships between researchers and participants, we emphasize the importance of considering participants as active contributors rather than mere informants. Creating a safe and supportive environment fosters trust, empowerment, and meaningful contributions from participants. Flexibility and adaptability in research approaches, including phased informed consent and the minimizing of written language, enhance participants' self-confidence and trust in their own voices. This approach empowers participants in co-creating knowledge, which strengthens the trustworthiness and validity of research results. Inclusive research, while promising, requires researchers to navigate ethical dilemmas, invest time in building rapport, and adapt to participants' needs. It challenges traditional research norms, emphasizing ethical engagement, meaningful participation, and tangible outcomes that benefit both researchers and participants. Employing inclusive research strategies, despite their departure from traditional praxis, ensures that the voices of older individuals with lower literacy levels are respected. This shift enhances the validity of knowledge, promotes co-creation, and fosters feelings of inclusiveness and empowerment. These promises underscore the importance of embracing inclusive research methodologies in contemporary research practices.Prevention, Population and Disease management (PrePoD)Public Health and primary car

Mapping of mutation-sensitive sites in protein-like chains

In this work we have studied, with the help of a simple on-lattice model, the distribution pattern of sites sensitive to point mutations ('hot' sites) in protein-like chains. It has been found that this pattern depends on the regularity of the matrix that rules the interaction between different kinds of residues. If the interaction matrix is dominated by the hydrophobic effect (Miyazawa Jernigan like matrix), this distribution is very simple - all the 'hot' sites can be found at the positions with maximum number of closest nearest neighbors (bulk). If random or nonlinear corrections are added to such an interaction matrix the distribution pattern changes. The rising of collective effects allows the 'hot' sites to be found in places with smaller number of nearest neighbors (surface) while the general trend of the 'hot' sites to fall into a bulk part of a conformation still holds.Comment: 15 pages, 6 figure