Gaussian model of explosive percolation in three and higher dimensions

The Gaussian model of discontinuous percolation, recently introduced by Ara\'ujo and Herrmann [Phys. Rev. Lett., 105, 035701 (2010)], is numerically investigated in three dimensions, disclosing a discontinuous transition. For the simple-cubic lattice, in the thermodynamic limit, we report a finite jump of the order parameter, $J=0.415 \pm 0.005$. The largest cluster at the threshold is compact, but its external perimeter is fractal with fractal dimension $d_A = 2.5 \pm 0.2$. The study is extended to hypercubic lattices up to six dimensions and to the mean-field limit (infinite dimension). We find that, in all considered dimensions, the percolation transition is discontinuous. The value of the jump in the order parameter, the maximum of the second moment, and the percolation threshold are analyzed, revealing interesting features of the transition and corroborating its discontinuous nature in all considered dimensions. We also show that the fractal dimension of the external perimeter, for any dimension, is consistent with the one from bridge percolation and establish a lower bound for the percolation threshold of discontinuous models with finite number of clusters at the threshold

Carbon assimilation strategies in ultrabasic groundwater: clues from the integrated study of a serpentinization-influenced aquifer

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Seyler, L. M., Brazelton, W. J., McLean, C., Putman, L. I., Hyer, A., Kubo, M. D. Y., Hoehler, T., Cardace, D., & Schrenk, M. O. . Carbon assimilation strategies in ultrabasic groundwater: clues from the integrated study of a serpentinization-influenced aquifer. mSystems, 5(2), (2020): e00607-00619, doi: 10.1128/mSystems.00607-19.Serpentinization is a low-temperature metamorphic process by which ultramafic rock chemically reacts with water. Such reactions provide energy and materials that may be harnessed by chemosynthetic microbial communities at hydrothermal springs and in the subsurface. However, the biogeochemistry mediated by microbial populations that inhabit these environments is understudied and complicated by overlapping biotic and abiotic processes. We applied metagenomics, metatranscriptomics, and untargeted metabolomics techniques to environmental samples taken from the Coast Range Ophiolite Microbial Observatory (CROMO), a subsurface observatory consisting of 12 wells drilled into the ultramafic and serpentinite mélange of the Coast Range Ophiolite in California. Using a combination of DNA and RNA sequence data and mass spectrometry data, we found evidence for several carbon fixation and assimilation strategies, including the Calvin-Benson-Bassham cycle, the reverse tricarboxylic acid cycle, the reductive acetyl coenzyme A (acetyl-CoA) pathway, and methylotrophy, in the microbial communities inhabiting the serpentinite-hosted aquifer. Our data also suggest that the microbial inhabitants of CROMO use products of the serpentinization process, including methane and formate, as carbon sources in a hyperalkaline environment where dissolved inorganic carbon is unavailable.We thank McLaughlin Reserve, in particular Paul Aigner and Cathy Koehler, for hosting sampling at CROMO and providing access to the wells, A. Daniel Jones and Anthony Schilmiller for their advice regarding metabolite extraction and mass spectrometry, Elizabeth Kujawinski for her guidance in metabolomics data analysis and interpretation, and Julia McGonigle, Christopher Thornton, and Katrina Twing for assistance with metagenomic and computational analyses

Establishment of the Coast Range ophiolite microbial observatory (CROMO): Drilling objectives and preliminary outcomes

Abstract. This project aimed to establish a subsurface microbial observatory in ultramafic rocks, by drilling into an actively serpentinizing peridotite body, characterizing cored rocks, and outfitting the boreholes for a program of long-term observation and experimentation to resolve the serpentinite-hosted subsurface biosphere. We completed drilling in August 2011, drilling two boreholes with core recovery and possibility for down-hole experimentation, and six smaller-diameter monitoring wells arrayed around the two primary holes, in the Coast Range ophiolite (CRO) locality in the UC-Davis McLaughlin Natural Reserve, Lower Lake, CA. Every effort was made during drilling to keep the cores and wells as free of drilling-induced contamination as possible: clean, purified water was used as drilling fluid, fluorescent microbead tracers were suspended in that water for quantification of drilling fluid penetration into the cores, and high resolution next generation sequencing approaches were used to characterize the microbial populations in the drill fluids and core materials. In December 2011, we completed installation of well pumps (slow flow bladder pumps) in the monitoring wells, and have deployed a set of in situ incubation experiments in the two uncased boreholes. Preliminary findings illustrate natural variability in actively serpentinizing strata, and confirm distinct groundwater flow regimes and microbial ecosystems in (a) shallow, surface-impacted soil water horizons and (b) deeper, ultramafic bedrock-sourced formation fluids

Influence of grape rot on the contents of sulfur binding compounds in wine after automated optical grape sorting

In the last years, climate change has played an important role in some wine growing regions because of the increasing hazard of different kinds of bunch rot. Botrytis cinerea is the most important kind of rot on grapes. Beside sensory effects, this rot can influence the content of yeast nutrients, e.g. thiamine, in the must and thus affect the alcoholic fermentation. To get insight into the influence of Botrytis cinerea on the content of sulfur binding compounds formed during the fermentation process in wine, tons of grapes from the Mosel valley were sorted by an automated optical grape sorter, an innovative possibility of grape sorting, in 2011. Wine samples before sulfurisation of the four sorting fractions, namely control (unsorted berries), free-run (juice from opened berries), positive (healthy, intact berries) and negative (rotten berries) were analysed for the sulfur-binding compounds acetaldehyde, pyruvic acid, 2-oxoglutaric acid and for bound sulfur dioxide. The results show that acetaldehyde concentrations were not affected by rot, while pyruvic acid and 2-oxoglutaric acid levels were significantly higher in the negative fractions and lower in the positive fractions. Accordingly, bound sulfur levels were significantly higher in wines from the negative fraction. In conclusion, it could be shown that fractionation of the berries can efficiently help to reduce sulfur binding compounds in wine and thus reduce the addition of sulfur dioxide

Turning intractable counting into sampling: Computing the configurational entropy of three-dimensional jammed packings.

We present a numerical calculation of the total number of disordered jammed configurations Ω of N repulsive, three-dimensional spheres in a fixed volume V. To make these calculations tractable, we increase the computational efficiency of the approach of Xu et al. [Phys. Rev. Lett. 106, 245502 (2011)10.1103/PhysRevLett.106.245502] and Asenjo et al. [Phys. Rev. Lett. 112, 098002 (2014)10.1103/PhysRevLett.112.098002] and we extend the method to allow computation of the configurational entropy as a function of pressure. The approach that we use computes the configurational entropy by sampling the absolute volume of basins of attraction of the stable packings in the potential energy landscape. We find a surprisingly strong correlation between the pressure of a configuration and the volume of its basin of attraction in the potential energy landscape. This relation is well described by a power law. Our methodology to compute the number of minima in the potential energy landscape should be applicable to a wide range of other enumeration problems in statistical physics, string theory, cosmology, and machine learning that aim to find the distribution of the extrema of a scalar cost function that depends on many degrees of freedom.We acknowledge useful discussions with Daniel Asenjo, Carl Goodrich, Silke Henkes, and Fabien Paillusson. S.M. acknowledges financial support by the Gates Cambridge Scholarship. K.J.S. acknowledges support by the Swiss National Science Foundation under Grant No. P2EZP2-152188 and No. P300P2-161078. J.D.S. acknowledges support by Marie Curie Grant 275544. D.F. and D.J.W. acknowledge support by EPSRC Programme Grant EP/I001352/1, by EPSRC grant EP/I000844/1 (D.F.) and ERC Advanced Grant RG59508 (D.J.W.)This is the author accepted manuscript. The final version is available from the American Physical Society via http://dx.doi.org/10.1103/PhysRevE.93.01290

Abiotic and biotic processes that drive carboxylation and decarboxylation reactions

© 2020 Walter de Gruyter GmbH, Berlin/Boston 2020. Carboxylation and decarboxylation are two fundamental classes of reactions that impact the cycling of carbon in and on Earth's crust. These reactions play important roles in both long-term (primarily abiotic) and short-term (primarily biotic) carbon cycling. Long-term cycling is important in the subsurface and at subduction zones where organic carbon is decomposed and outgassed or recycled back to the mantle. Short-term reactions are driven by biology and have the ability to rapidly convert CO2 to biomass and vice versa. For instance, carboxylation is a critical reaction in primary production and metabolic pathways like photosynthesis in which sunlight provides energy to drive carbon fixation, whereas decarboxylation is a critical reaction in metabolic pathways like respiration and the tricarboxylic acid cycle. Early life and prebiotic chemistry on Earth likely relied heavily upon the abiotic synthesis of carboxylic acids. Over time, life has diversified (de)carboxylation reactions and incorporated them into many facets of cellular metabolism. Here we present a broad overview of the importance of carboxylation and decarboxylation reactions from both abiotic and biotic perspectives to highlight the importance of these reactions and compounds to planetary evolution

Monte Carlo sampling for stochastic weight functions

Conventional Monte Carlo simulations are stochastic in the sense that the acceptance of a trial move is decided by comparing a computed acceptance probability with a random number, uniformly distributed between 0 and 1. Here, we consider the case that the weight determining the acceptance probability itself is fluctuating. This situation is common in many numerical studies. We show that it is possible to construct a rigorous Monte Carlo algorithm that visits points in state space with a probability proportional to their average weight. The same approach may have applications for certain classes of high-throughput experiments and the analysis of noisy datasets.D. F. acknowledges support by EPSRC Programme Grant EP/I001352/1 and EPSRC grant EP/I000844/1. K. J. S. acknowledges support by the Swiss National Science Foundation (Grant No. P2EZP2-152188 and No. P300P2-161078). S. M. acknowledges financial support from the Gates Cambridge Scholarship