Implementation of dynamical nucleation theory with quantum potentials.

A method is implemented within the context of dynamical nucleation theory in order to efficiently determine the ab initio water dimer evaporation rate constant. The drive for increased efficiency in a Monte Carlo methodology is established by the need to use relatively expensive quantum mechanical interaction potentials. A discussion is presented illustrating the theory, algorithm, and implementation of this method to the water dimer. Hartree-Fock and second order Møller-Plesset perturbation theories along with the Dang-Chang polarizable classical potential are utilized to determine the ab initio water dimer evaporation rate constant.

Temperature scaling method for Markov chains.

The use of ab initio potentials in Monte Carlo simulations aimed at investigating the nucleation kinetics of water clusters is complicated by the computational expense of the potential energy determinations. Furthermore, the common desire to investigate the temperature dependence of kinetic properties leads to an urgent need to reduce the expense of performing simulations at many different temperatures. A method is detailed that allows a Markov chain (obtained via Monte Carlo) at one temperature to be scaled to other temperatures of interest without the need to perform additional large simulations. This Markov chain temperature-scaling (TeS) can be generally applied to simulations geared for numerous applications. This paper shows the quality of results which can be obtained by TeS and the possible quantities which may be extracted from scaled Markov chains. Results are obtained for a 1-D analytical potential for which the exact solutions are known. Also, this method is applied to water clusters consisting of between 2 and 5 monomers, using Dynamical Nucleation Theory to determine the evaporation rate constant for monomer loss. Although ab initio potentials are not utilized in this paper, the benefit of this method is made apparent by using the Dang-Chang polarizable classical potential for water to obtain statistical properties at various temperatures.

Phylogenetically Novel Uncultured Microbial Cells Dominate Earth Microbiomes.

To describe a microbe's physiology, including its metabolism, environmental roles, and growth characteristics, it must be grown in a laboratory culture. Unfortunately, many phylogenetically novel groups have never been cultured, so their physiologies have only been inferred from genomics and environmental characteristics. Although the diversity, or number of different taxonomic groups, of uncultured clades has been studied well, their global abundances, or numbers of cells in any given environment, have not been assessed. We quantified the degree of similarity of 16S rRNA gene sequences from diverse environments in publicly available metagenome and metatranscriptome databases, which we show have far less of the culture bias present in primer-amplified 16S rRNA gene surveys, to those of their nearest cultured relatives. Whether normalized to scaffold read depths or not, the highest abundances of metagenomic 16S rRNA gene sequences belong to phylogenetically novel uncultured groups in seawater, freshwater, terrestrial subsurface, soil, hypersaline environments, marine sediment, hot springs, hydrothermal vents, nonhuman hosts, snow, and bioreactors (22% to 87% uncultured genera to classes and 0% to 64% uncultured phyla). The exceptions were human and human-associated environments, which were dominated by cultured genera (45% to 97%). We estimate that uncultured genera and phyla could comprise 7.3 × 1029 (81%) and 2.2 × 1029 (25%) of microbial cells, respectively. Uncultured phyla were overrepresented in metatranscriptomes relative to metagenomes (46% to 84% of sequences in a given environment), suggesting that they are viable. Therefore, uncultured microbes, often from deeply phylogenetically divergent groups, dominate nonhuman environments on Earth, and their undiscovered physiologies may matter for Earth systems. IMPORTANCE In the past few decades, it has become apparent that most of the microbial diversity on Earth has never been characterized in laboratory cultures. We show that these unknown microbes, sometimes called "microbial dark matter," are numerically dominant in all major environments on Earth, with the exception of the human body, where most of the microbes have been cultured. We also estimate that about one-quarter of the population of microbial cells on Earth belong to phyla with no cultured relatives, suggesting that these never-before-studied organisms may be important for ecosystem functions. Author Video: An author video summary of this article is available.

Silicon radicals in silicon oxynitride: a theoretical ESR study.

Quantum mechanical calculations are performed on a series of silicon radical defects. These are the upward arrow Si[triple bond]O(3-x)Nx, upward arrow Si[triple bond]N(3-x)Si(x), and upward arrow Si[triple bond]Si(3-x)Ox defects, where x takes on values between 0 and 3. The defects under study constitute a central silicon radical, upward arrow Si, with differing first-nearest-neighbor substitution, as may be found at a Si/SiOxNy interface. These first-nearest neighbor atoms are connected to the silicon radical via three single covalent bonds, denoted as " [triple bond] ". A hybrid defect, upward arrow Si[triple bond]ONSi, is also included. Calculations are performed on gas-phase-like cluster models, as well as more-constrained hybrid quantum and molecular mechanical (QM/MM) models. The isotropic hyperfine coupling constants of these defects are calculated via density functional theory (DFT). Trends in these calculated hyperfines are consistent between the different models utilized. Analysis of the electronic structure and geometries of defects correlate well with trends in the electronegativity of the first-nearest-neighbor atoms. Changes in radical hybridization, induced by changes in the first-nearest-neighbor composition, are the primary factor that affects the calculated hyperfines. Furthermore, comparisons to experimental results are encouraging. Agreement is found between experiments on amorphous to crystalline materials.