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

Effect of inelasticity on the phase transitions of a thin vibrated granular layer

We describe an experimental and computational investigation of the ordered and disordered phases of a vibrating thin, dense granular layer composed of identical metal spheres. We compare the results from spheres with different amounts of inelasticity and show that inelasticity has a strong effect on the phase diagram. We also report the melting of an ordered phase to a homogeneous disordered liquid phase at high vibration amplitude or at large inelasticities. Our results show that dissipation has a strong effect on ordering and that in this system ordered phases are absent entirely in highly inelastic materials.Comment: 5 pages, 5 figures, published in Physical Review E. Title of first version slightly change

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

Freezing of parallel hard cubes with rounded edges

The freezing transition in a classical three-dimensional system of parallel hard cubes with rounded edges is studied by computer simulation and fundamental-measure density functional theory. By switching the rounding parameter s from zero to one, one can smoothly interpolate between cubes with sharp edges and hard spheres. The equilibrium phase diagram of rounded parallel hard cubes is computed as a function of their volume fraction and the rounding parameter s. The second order freezing transition known for oriented cubes at s = 0 is found to be persistent up to s = 0.65. The fluid freezes into a simple-cubic crystal which exhibits a large vacancy concentration. Upon a further increase of s, the continuous freezing is replaced by a first-order transition into either a sheared simple cubic lattice or a deformed face-centered cubic lattice with two possible unit cells: body-centered orthorhombic or base-centered monoclinic. In principle, a system of parallel cubes could be realized in experiments on colloids using advanced synthesis techniques and a combination of external fields.Comment: Submitted to JC

Properties of Cyclic-Nucleotide Gated Channels Mediating Olfactory Transduction - Activation, Selectivity, and Blockage

Cyclic nucleotide-gated channels (cng channels) in the sensory membrane of olfactory receptor cells, activated after the odorant-induced increase of cytosolic cAMP concentration, conduct the receptor current that elicits electrical excitation of the receptor neurons. We investigated properties of cng channels from frog and rat using inside-out and outside-out membrane patches excised from isolated olfactory receptor cells. Channels were activated by cAMP and cGMP with activation constants of 2.5-4.0-mu-M for cAMP and 1.0-1.8 for cGMP. Hill coefficients of dose-response curves were 1.4-1.8, indicating cooperativity of ligand binding. Selectivity for monovalent alkali cations and the Na/Li mole-fraction behavior identified the channel as a nonselective cation channel, having a cation-binding site of high field strength in the pore. Cytosolic pH effects suggest the presence of an additional titratable group which, when protonated, inhibits the cAMP-induced current with an apparent pK of 5.0-5.2. The pH effects were not voltage dependent. Several blockers of Ca2+ channels also blocked olfactory cng channels. Amiloride, D 600, and diltiazem inhibited the cAMP-induced current from the cytosolic side. Inhibition constants were voltage dependent with values of, respectively, 0.1, 0.3, and 1 mM at - 60 mV, and 0.03, 0.02, and 0.2 mM at + 60 mV. Our results suggest functional similarity between frog and rat cng channels, as well as marked differences to cng channels from photoreceptors and other tissues

A High-Sensitivity Radon Emanation Detector System for Future Low-Background Experiments

Radioactive radon atoms originating from the long-lived primordial $^{238}\mathrm{U}$ and $^{232}\mathrm{Th}$ decay chains are constantly emanated from the surfaces of most materials. The radon atoms or their radioactive daughter isotopes can significantly contribute to the background of low-background experiments, e.g., the $^{222}\mathrm{Rn}$ progeny $^{214}\mathrm{Pb}$ dominates the background of liquid xenon detectors which are currently leading the direct search for WIMP dark matter. We report on a new detector system to directly quantify the $^{222}\mathrm{Rn}$ surface emanation of materials. Using cryogenic physisorption traps, emanated radon atoms are transferred from an independent emanation vessel and concentrated inside the dedicated detection vessel, where the charged daughter isotopes, most importantly $^{214}\mathrm{Po}$ and $^{218}\mathrm{Po}$, are electrostatically collected and detected on a silicon PIN photodiode. The overall detection efficiency is $\sim 36\,\%$ for both polonium channels. The intrinsic detection vessel background was measured to be $\sim 2.4\,\mathrm{cpd}$ ($28\,\mathrm{\mu Bq}$) and $\sim 1.5\,\mathrm{cpd}$ ($17\,\mathrm{\mu Bq}$) for $^{218}\mathrm{Po}$ and $^{214}\mathrm{Po}$, respectively. The radon emanation activity of the emanation vessel was determined to be $(0.16\pm 0.03)\,\mathrm{mBq}$, resulting in a detection sensitivity of $\sim 59\,\mathrm{\mu Bq}$ (at $90\,\%$ C.L.).Comment: 13 pages, 3 figure

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

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.