A Generalized Spatial Measure for Resilience of Microbial Systems

The emergent property of resilience is the ability of a system to return to an original state after a disturbance. Resilience may be used as an early warning system for significant or irreversible community transition; that is, a community with diminishing or low resilience may be close to catastrophic shift in function or an irreversible collapse. Typically, resilience is quantified using recovery time, which may be difficult or impossible to directly measure in microbial systems. A recent study in the literature showed that under certain conditions, a set of spatial-based metrics termed recovery length, can be correlated to recovery time, and thus may be a reasonable alternative measure of resilience. However, this spatial metric of resilience is limited to use for step-change perturbations. Building upon the concept of recovery length, we propose a more general form of the spatial metric of resilience that can be applied to any shape of perturbation profiles (for example, either sharp or smooth gradients). We termed this new spatial measure “perturbation-adjusted spatial metric of resilience” (PASMORE). We demonstrate the applicability of the proposed metric using a mathematical model of a microbial mat

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

Percolation of Immobile Domains in Supercooled Thin Polymeric Films

We present an analysis of heterogeneous dynamics in molecular dynamics simulations of a thin polymeric film, supported by an absorbing structured surface. Near the glass transition "immobile" domains occur throughout the film, yet the probability of their occurrence decreasing with larger distance from the surface. Still, enough immobile domains are located near the free surface to cause them to percolate in the direction perpendicular to surface, at a temperature near the glass transition temperature. This result is in agreement with a recent theoretical model of glass transition

Melting and Rippling Phenomenan in Two Dimensional Crystals with localized bonding

We calculate Root Mean Square (RMS) deviations from equilibrium for atoms in a two dimensional crystal with local (e.g. covalent) bonding between close neighbors. Large scale Monte Carlo calculations are in good agreement with analytical results obtained in the harmonic approximation. When motion is restricted to the plane, we find a slow (logarithmic) increase in fluctuations of the atoms about their equilibrium positions as the crystals are made larger and larger. We take into account fluctuations perpendicular to the lattice plane, manifest as undulating ripples, by examining dual layer systems with coupling between the layers to impart local rigidly (i.e. as in sheets of graphene made stiff by their finite thickness). Surprisingly, we find a rapid divergence with increasing system size in the vertical mean square deviations, independent of the strength of the interplanar coupling. We consider an attractive coupling to a flat substrate, finding that even a weak attraction significantly limits the amplitude and average wavelength of the ripples. We verify our results are generic by examining a variety of distinct geometries, obtaining the same phenomena in each case.Comment: 17 pages, 28 figure

Electronic structure and the glass transition in pnictide and chalcogenide semiconductor alloys. Part II: The intrinsic electronic midgap states

We propose a structural model that treats in a unified fashion both the atomic motions and electronic excitations in quenched melts of pnictide and chalcogenide semiconductors. In Part I (submitted to J. Chem. Phys.), we argued these quenched melts represent aperiodic $pp\sigma$-networks that are highly stable and, at the same time, structurally degenerate. These networks are characterized by a continuous range of coordination. Here we present a systematic way to classify these types of coordination in terms of discrete coordination defects in a parent structure defined on a simple cubic lattice. We identify the lowest energy coordination defects with the intrinsic midgap electronic states in semiconductor glasses, which were argued earlier to cause many of the unique optoelectronic anomalies in these materials. In addition, these coordination defects are mobile and correspond to the transition state configurations during the activated transport above the glass transition. The presence of the coordination defects may account for the puzzling discrepancy between the kinetic and thermodynamic fragility in chalcogenides. Finally, the proposed model recovers as limiting cases several popular types of bonding patterns proposed earlier, including: valence-alternation pairs, hypervalent configurations, and homopolar bonds in heteropolar compounds.Comment: 17 pages, 15 figures, revised version, final version to appear in J. Chem. Phy

Theory of Structural Glasses and Supercooled Liquids

We review the Random First Order Transition Theory of the glass transition, emphasizing the experimental tests of the theory. Many distinct phenomena are quantitatively predicted or explained by the theory, both above and below the glass transition temperature $T_g$. These include: the viscosity catastrophe and heat capacity jump at $T_g$, and their connection; the non-exponentiality of relaxations and their correlation with the fragility; dynamic heterogeneity in supercooled liquids owing to the mosaic structure; deviations from the Vogel-Fulcher law, connected with strings or fractral cooperative rearrangements; deviations from the Stokes-Einstein relation close to $T_g$; aging, and its correlation with fragility; the excess density of states at cryogenic temperatures due to two level tunneling systems and the Boson Peak.Comment: submitted to Ann. Rev. Phys. Che

Wall turbulence control

A variety of wall turbulence control devices which were experimentally investigated are discussed; these include devices for burst control, alteration of outer flow structures, large eddy substitution, increased heat transfer efficiency, and reduction of wall pressure fluctuations. Control of pre-burst flow was demonstrated with a single, traveling surface depression which is phase-locked to elements of the burst production process. Another approach to wall turbulence control is to interfere with the outer layer coherent structures. A device in the outer part of a boundary layer was shown to suppress turbulence and reduce drag by opposing both the mean and unsteady vorticity in the boundary layer. Large eddy substitution is a method in which streamline curvature is introduced into the boundary layer in the form of streamwise vortices. Riblets, which were already shown to reduce turbulent drag, were also shown to exhibit superior heat transfer characteristics. Heat transfer efficiency as measured by the Reynolds Analogy Factor was shown to be as much as 36 percent greater than a smooth flat plate in a turbulent boundary layer. Large Eddy Break-Up (LEBU) which are also known to reduce turbulent drag were shown to reduce turbulent wall pressure fluctuation

Free energies, vacancy concentrations and density distribution anisotropies in hard--sphere crystals: A combined density functional and simulation study

We perform a comparative study of the free energies and the density distributions in hard sphere crystals using Monte Carlo simulations and density functional theory (employing Fundamental Measure functionals). Using a recently introduced technique (Schilling and Schmid, J. Chem. Phys 131, 231102 (2009)) we obtain crystal free energies to a high precision. The free energies from Fundamental Measure theory are in good agreement with the simulation results and demonstrate the applicability of these functionals to the treatment of other problems involving crystallization. The agreement between FMT and simulations on the level of the free energies is also reflected in the density distributions around single lattice sites. Overall, the peak widths and anisotropy signs for different lattice directions agree, however, it is found that Fundamental Measure theory gives slightly narrower peaks with more anisotropy than seen in the simulations. Among the three types of Fundamental Measure functionals studied, only the White Bear II functional (Hansen-Goos and Roth, J. Phys.: Condens. Matter 18, 8413 (2006)) exhibits sensible results for the equilibrium vacancy concentration and a physical behavior of the chemical potential in crystals constrained by a fixed vacancy concentration.Comment: 17 pages, submitted to Phys. Rev.

Extension of PRISM by Synthesis of Optimal Timeouts in Fixed-Delay CTMC

We present a practically appealing extension of the probabilistic model checker PRISM rendering it to handle fixed-delay continuous-time Markov chains (fdCTMCs) with rewards, the equivalent formalism to the deterministic and stochastic Petri nets (DSPNs). fdCTMCs allow transitions with fixed-delays (or timeouts) on top of the traditional transitions with exponential rates. Our extension supports an evaluation of expected reward until reaching a given set of target states. The main contribution is that, considering the fixed-delays as parameters, we implemented a synthesis algorithm that computes the epsilon-optimal values of the fixed-delays minimizing the expected reward. We provide a performance evaluation of the synthesis on practical examples