Integrating Ecological and Engineering Concepts of Resilience in Microbial Communities

Many definitions of resilience have been proffered for natural and engineered ecosystems, but a conceptual consensus on resilience in microbial communities is still lacking. We argue that the disconnect largely results from the wide variance in microbial community complexity, which range from compositionally simple synthetic consortia to complex natural communities, and divergence between the typical practical outcomes emphasized by ecologists and engineers. Viewing microbial communities as elasto-plastic systems that undergo both recoverable and unrecoverable transitions, we argue that this gap between the engineering and ecological definitions of resilience stems from their respective emphases on elastic and plastic deformation, respectively. We propose that the two concepts may be fundamentally united around the resilience of function rather than state in microbial communities and the regularity in the relationship between environmental variation and a community\u27s functional response. Furthermore, we posit that functional resilience is an intrinsic property of microbial communities and suggest that state changes in response to environmental variation may be a key mechanism driving functional resilience in microbial communities

Evidence of a Critical time in Constrained Kinetic Ising models

We study the relaxational dynamics of the one-spin facilitated Ising model introduced by Fredrickson and Andersen. We show the existence of a critical time which separates an initial regime in which the relaxation is exponentially fast and aging is absent from a regime in which relaxation becomes slow and aging effects are present. The presence of this fast exponential process and its associated critical time is in agreement with some recent experimental results on fragile glasses.Comment: 20 Pages + 7 Figures, Revte

Shear Alignment and Instability of Smectic Phases

We consider the shear flow of well-aligned one-component smectic phases, such as thermotropic smectics and lamellar diblock copolymers, below the critical region. We show that, as a result of thermal fluctuations of the layers, parallel ($c$) alignment is generically unstable and perpendicular ($a$) alignment is stable against long-wavelength undulations. We also find, surprisingly, that both $a$ and $c$ are stable for a narrow window of values for the anisotropic viscosity.Comment: To appear in PRL. Revtex, 1 figure

Stability of Quasicrystals Composed of Soft Isotropic Particles

Quasicrystals whose building blocks are of mesoscopic rather than atomic scale have recently been discovered in several soft-matter systems. Contrary to metallurgic quasicrystals whose source of stability remains a question of great debate to this day, we argue that the stability of certain soft-matter quasicrystals can be directly explained by examining a coarse-grained free energy for a system of soft isotropic particles. We show, both theoretically and numerically, that the stability can be attributed to the existence of two natural length scales in the pair potential, combined with effective three-body interactions arising from entropy. Our newly gained understanding of the stability of soft quasicrystals allows us to point at their region of stability in the phase diagram, and thereby may help control the self-assembly of quasicrystals and a variety of other desired structures in future experimental realizations.Comment: Revised abstract, more detailed explanations, and better images of the numerical minimization of the free energ

Facilitated spin models: recent and new results

Facilitated or kinetically constrained spin models (KCSM) are a class of interacting particle systems reversible w.r.t. to a simple product measure. Each dynamical variable (spin) is re-sampled from its equilibrium distribution only if the surrounding configuration fulfills a simple local constraint which \emph{does not involve} the chosen variable itself. Such simple models are quite popular in the glass community since they display some of the peculiar features of glassy dynamics, in particular they can undergo a dynamical arrest reminiscent of the liquid/glass transitiom. Due to the fact that the jumps rates of the Markov process can be zero, the whole analysis of the long time behavior becomes quite delicate and, until recently, KCSM have escaped a rigorous analysis with the notable exception of the East model. In these notes we will mainly review several recent mathematical results which, besides being applicable to a wide class of KCSM, have contributed to settle some debated questions arising in numerical simulations made by physicists. We will also provide some interesting new extensions. In particular we will show how to deal with interacting models reversible w.r.t. to a high temperature Gibbs measure and we will provide a detailed analysis of the so called one spin facilitated model on a general connected graph.Comment: 30 pages, 3 figure

Singularities in ternary mixtures of k-core percolation

Heterogeneous k-core percolation is an extension of a percolation model which has interesting applications to the resilience of networks under random damage. In this model, the notion of node robustness is local, instead of global as in uniform k-core percolation. One of the advantages of k-core percolation models is the validity of an analytical mathematical framework for a large class of network topologies. We study ternary mixtures of node types in random networks and show the presence of a new type of critical phenomenon. This scenario may have useful applications in the stability of large scale infrastructures and the description of glass-forming systems.Comment: To appear in Complex Networks, Studies in Computational Intelligence, Proceedings of CompleNet 201

Prediction of Neighbor-Dependent Microbial Interactions From Limited Population Data

Modulation of interspecies interactions by the presence of neighbor species is a key ecological factor that governs dynamics and function of microbial communities, yet the development of theoretical frameworks explicit for understanding context-dependent interactions are still nascent. In a recent study, we proposed a novel rule-based inference method termed the Minimal Interspecies Interaction Adjustment (MIIA) that predicts the reorganization of interaction networks in response to the addition of new species such that the modulation in interaction coefficients caused by additional members is minimal. While the theoretical basis of MIIA was established through the previous work by assuming the full availability of species abundance data in axenic, binary, and complex communities, its extension to actual microbial ecology can be highly constrained in cases that species have not been cultured axenically (e.g., due to their inability to grow in the absence of specific partnerships) because binary interaction coefficients – basic parameters required for implementing the MIIA – are inestimable without axenic and binary population data. Thus, here we present an alternative formulation based on the following two central ideas. First, in the case where only data from axenic cultures are unavailable, we remove axenic populations from governing equations through appropriate scaling. This allows us to predict neighbor-dependent interactions in a relative sense (i.e., fractional change of interactions between with versus without neighbors). Second, in the case where both axenic and binary populations are missing, we parameterize binary interaction coefficients to determine their values through a sensitivity analysis. Through the case study of two microbial communities with distinct characteristics and complexity (i.e., a three-member community where all members can grow independently, and a four-member community that contains member species whose growth is dependent on other species), we demonstrated that despite data limitation, the proposed new formulation was able to successfully predict interspecies interactions that are consistent with experimentally derived results. Therefore, this technical advancement enhances our ability to predict context-dependent interspecies interactions in a broad range of microbial systems without being limited to specific growth conditions as a pre-requisite

Fractionation of polydisperse systems: multi-phase coexistence

The width of the distribution of species in a polydisperse system is employed in a small-variable expansion, to obtain a well-controlled and compact scheme by which to calculate phase equilibria in multi-phase systems. General and universal relations are derived, which determine the partitioning of the fluid components among the phases. The analysis applies to mixtures of arbitrarily many slightly-polydisperse components. An explicit solution is approximated for hard spheres.Comment: 4 pages, 1 figur

Dynamic charge density correlation function in weakly charged polyampholyte globules

We study solutions of statistically neutral polyampholyte chains containing a large fraction of neutral monomers. It is known that, even if the quality of the solvent with respect to the neutral monomers is good, a long chain will collapse into a globule. For weakly charged chains, the interior of this globule is semi-dilute. This paper considers mainly theta-solvents, and we calculate the dynamic charge density correlation function g(k,t) in the interior of the globules, using the quadratic approximation to the Martin-Siggia-Rose generating functional. It is convenient to express the results in terms of dimensionless space and time variables. Let R be the blob size, and let T be the characteristic time scale at the blob level. Define the dimensionless wave vector q = R k, and the dimensionless time s = t/T. We find that for q<1, corresponding to length scales larger than the blob size, the charge density fluctuations relax according to g(q,s) = q^2(1-s^(1/2)) at short times s < 1, and according to g(q,s) = q^2 s^(-1/2) at intermediate times 1 < s 0.1, where entanglements are unimportant.Comment: 12 pages RevTex, 1 figure ps, PACS 61.25.Hq, reason replacement: Expression for dynamic corr. function g(k,t) in old version was incorrect (though expression for Fourier transform g(k,w) was correct, so the major part of the calculation remains.) Also major textual chang