Reduction of dynamical biochemical reaction networks in computational biology

Biochemical networks are used in computational biology, to model the static and dynamical details of systems involved in cell signaling, metabolism, and regulation of gene expression. Parametric and structural uncertainty, as well as combinatorial explosion are strong obstacles against analyzing the dynamics of large models of this type. Multi-scaleness is another property of these networks, that can be used to get past some of these obstacles. Networks with many well separated time scales, can be reduced to simpler networks, in a way that depends only on the orders of magnitude and not on the exact values of the kinetic parameters. The main idea used for such robust simplifications of networks is the concept of dominance among model elements, allowing hierarchical organization of these elements according to their effects on the network dynamics. This concept finds a natural formulation in tropical geometry. We revisit, in the light of these new ideas, the main approaches to model reduction of reaction networks, such as quasi-steady state and quasi-equilibrium approximations, and provide practical recipes for model reduction of linear and nonlinear networks. We also discuss the application of model reduction to backward pruning machine learning techniques

Algorithmic Reduction of Biological Networks With Multiple Time Scales

We present a symbolic algorithmic approach that allows to compute invariant manifolds and corresponding reduced systems for differential equations modeling biological networks which comprise chemical reaction networks for cellular biochemistry, and compartmental models for pharmacology, epidemiology and ecology. Multiple time scales of a given network are obtained by scaling, based on tropical geometry. Our reduction is mathematically justified within a singular perturbation setting using a recent result by Cardin and Teixeira. The existence of invariant manifolds is subject to hyperbolicity conditions, which we test algorithmically using Hurwitz criteria. We finally obtain a sequence of nested invariant manifolds and respective reduced systems on those manifolds. Our theoretical results are generally accompanied by rigorous algorithmic descriptions suitable for direct implementation based on existing off-the-shelf software systems, specifically symbolic computation libraries and Satisfiability Modulo Theories solvers. We present computational examples taken from the well-known BioModels database using our own prototypical implementations

Diffuse Neutron Scattering Study of Magnetic Correlations in half-doped La0.5Ca0.5-xSrxMnO3 (x = 0.1, 0.3 and 0.4) Manganites

The short range ordered magnetic correlations have been studied in half doped La0.5Ca0.5-xSrxMnO3 (x = 0.1, 0.3 and 0.4) compounds by polarized neutron scattering technique. On doping Sr2+ for Ca2+ ion, these compounds with x = 0.1, 0.3, and 0.4 exhibit CE-type, mixture of CE-type and A-type, and A-type antiferromagnetic ordering, respectively. Magnetic diffuse scattering is observed in all the compounds above and below their respective magnetic ordering temperatures and is attributed to magnetic polarons. The correlations are primarily ferromagnetic in nature above T\_N, although a small antiferromagnetic contribution is also evident. Additionally, in samples x = 0.1 and 0.3 with CE-type antiferromagnetic ordering, superlattice diffuse reflections are observed indicating correlations between magnetic polarons. On lowering temperature below T\_N the diffuse scattering corresponding to ferromagnetic correlations is suppressed and the long range ordered antiferromagnetic state is established. However, the short range ordered correlations indicated by enhanced spin flip scattering at low Q coexist with long range ordered state down to 3K. In x = 0.4 sample with A-type antiferromagnetic ordering, superlattice diffuse reflections are absent. Additionally, in comparison to x = 0.1 and 0.3 sample, the enhanced spin flip scattering at low Q is reduced at 310K, and as temperature is reduced below 200K, it becomes negligibly low. The variation of radial correlation function, g(r) with temperature indicates rapid suppression of ferromagnetic correlations at the first nearest neighbor on approaching TN. Sample x = 0.4 exhibits growth of ferromagnetic phase at intermediate temperatures (~ 200K). This has been further explored using SANS and neutron depolarization techniques.Comment: 13 pages, 12 figures, To appear in Physical Review

Effects of early intervention and the moderating effects of brain activity on institutionalized children's social skills at age 8

The present study examined the social skills of previously institutionalized, 8-y-old Romanian children from the Bucharest Early Intervention Project and the influence of attachment security and brain electrical activity (alpha power) on these skills. Participants included children randomized to an intervention involving foster care [Foster Care Group (FCG)], children randomized to remain in institutions [Care As Usual Group (CAUG)], and never-institutionalized children living with their families in the Bucharest community [Never-Institutionalized Group (NIG)]. A continuous rating of children's attachment security to their primary caregiver was assessed at 42 mo of age. When children were 8 y old, teachers rated their social skills, and the children's resting electroencephalogram alpha power was recorded. Teachers rated social skills of FCG children who were placed into foster care before 20 mo of age as no different from NIG children, and both of these groups were higher than CAUG children and FCG children placed after 20 mo. Electroencephalogram alpha power at age 8 significantly moderated the relations between attachment security and social skills. These findings characterize institutionalized children's social skills in middle childhood within the context of a randomized intervention while highlighting the roles of both relational and biological factors in these developmental trajectories

Dense packing on uniform lattices

We study the Hard Core Model on the graphs ${\rm {\bf \scriptstyle G}}$ obtained from Archimedean tilings i.e. configurations in $\scriptstyle \{0,1\}^{{\rm {\bf G}}}$ with the nearest neighbor 1's forbidden. Our particular aim in choosing these graphs is to obtain insight to the geometry of the densest packings in a uniform discrete set-up. We establish density bounds, optimal configurations reaching them in all cases, and introduce a probabilistic cellular automaton that generates the legal configurations. Its rule involves a parameter which can be naturally characterized as packing pressure. It can have a critical value but from packing point of view just as interesting are the noncritical cases. These phenomena are related to the exponential size of the set of densest packings and more specifically whether these packings are maximally symmetric, simple laminated or essentially random packings.Comment: 18 page

XAS signatures of Am(III) adsorbed onto magnetite and maghemite

Trivalent americium was adsorbed on magnetite and maghemite under similar chemical conditions and the local environment probed by EXAFS spectroscopy. In both samples, partially hydrated Am(III) binds the surface but slightly different surface complexes were identified. On Fe3O4, Am(III) forms monomeric tridentate surface complexes similar to that reported for Pu(III) at the (111) surface. In contrast, the lower number of detected Fe atoms may suggest that Am(III) forms monomeric bidentate surface complexes on γ-Fe2O3. Alternatively, the lower Fe coordination number can also be due to the presence of vacancies in maghemite. XPS data imply very similar binding environments for Am at both Fe oxide surfaces

The Johnson-Segalman model with a diffusion term in Couette flow

We study the Johnson-Segalman (JS) model as a paradigm for some complex fluids which are observed to phase separate, or ``shear-band'' in flow. We analyze the behavior of this model in cylindrical Couette flow and demonstrate the history dependence inherent in the local JS model. We add a simple gradient term to the stress dynamics and demonstrate how this term breaks the degeneracy of the local model and prescribes a much smaller (discrete, rather than continuous) set of banded steady state solutions. We investigate some of the effects of the curvature of Couette flow on the observable steady state behavior and kinetics, and discuss some of the implications for metastability.Comment: 14 pp, to be published in Journal of Rheolog

PRIVATE SAVINGS IN TRANSITION ECONOMIES: ARE THERE TERMS OF TRADE SHOCKS?

The paper examines the impact of terms of trade shocks on private savings in the transition economies after accounting for the effect of other determinants. Economic agents in the transition economies are subject to tight credit constraints which are more pronounced during bad state of nature. Thus, adverse shocks to commodity prices in the world market can force them to reduce savings by a larger amount than they would otherwise have. Empirical analysis using a dynamic panel model and data from twenty one transition economies confirm that most of the determinants of savings identified in the literature also apply to the transition economies. Favorable movements in both the permanent and transitory components of the terms of trade have a significant positive impact on private savings with transitory movements having a larger impact than the permanent component. This reflects the lack of access to foreign borrowing that many of the transition economies have faced during the last decade. Although the impact of terms of trade shocks are found to be asymmetric, the magnitude of the impact appears to be small. The results are robust for alternative estimators, determinants, and country groupings.http://deepblue.lib.umich.edu/bitstream/2027.42/39958/3/wp572.pd