Coupling thermodynamics and digital image models to simulate hydration and microstructure development of portland cement pastes

Equilibrium thermodynamic calculations, coupled to a kinetic model for the dissolution rates of clinker phases, have been used in recent years to predict time-dependent phase assemblages in hydrating cement pastes. We couple this approach to a 3D microstructure model to simulate microstructure development during the hydration of ordinary portland cement pastes. The combined simulation tool uses a collection of growth/dissolution rules to approximate a range of growth modes at material interfaces, including growth by weighted mean curvature and growth by random aggregation. The growth rules are formulated for each type of material interface to capture the kinds of cement paste microstructure changes that are typically observed. We make quantitative comparisons between simulated and observed microstructures for two ordinary portland cements, including bulk phase analyses and two-point correlation functions for various phases. The method is also shown to provide accurate predictions of the heats of hydration and 28 day mortar cube compressive strengths. The method is an attractive alternative to the cement hydration and microstructure model CEMHYD3D because it has a better thermodynamic and kinetic basis and because it is transferable to other cementitious material system

Genome, Functional Gene Annotation, and Nuclear Transformation of the Heterokont Oleaginous Alga \u3ci\u3eNannochloropsis oceanica\u3c/i\u3e CCMP1779

Unicellular marine algae have promise for providing sustainable and scalable biofuel feedstocks, although no single species has emerged as a preferred organism. Moreover, adequate molecular and genetic resources prerequisite for the rational engineering of marine algal feedstocks are lacking for most candidate species. Heterokonts of the genus Nannochloropsis naturally have high cellular oil content and are already in use for industrial production of high-value lipid products. First success in applying reverse genetics by targeted gene replacement makes Nannochloropsis oceanica an attractive model to investigate the cell and molecular biology and biochemistry of this fascinating organism group. Here we present the assembly of the 28.7 Mb genome of N. oceanica CCMP1779. RNA sequencing data from nitrogen-replete and nitrogendepleted growth conditions support a total of 11,973 genes, of which in addition to automatic annotation some were manually inspected to predict the biochemical repertoire for this organism. Among others, more than 100 genes putatively related to lipid metabolism, 114 predicted transcription factors, and 109 transcriptional regulators were annotated. Comparison of the N. oceanica CCMP1779 gene repertoire with the recently published N. gaditana genome identified 2,649 genes likely specific to N. oceanica CCMP1779. Many of these N. oceanica–specific genes have putative orthologs in other species or are supported by transcriptional evidence. However, because similarity-based annotations are limited, functions of most of these species-specific genes remain unknown. Aside from the genome sequence and its analysis, protocols for the transformation of N. oceanica CCMP1779 are provided. The availability of genomic and transcriptomic data for Nannochloropsis oceanica CCMP1779, along with efficient transformation protocols, provides a blueprint for future detailed gene functional analysis and genetic engineering of Nannochloropsis species by a growing academic community focused on this genus

GENE-Counter: A Computational Pipeline for the Analysis of RNA-Seq Data for Gene Expression Differences

GENE-counter is a complete Perl-based computational pipeline for analyzing RNA-Sequencing (RNA-Seq) data for differential gene expression. In addition to its use in studying transcriptomes of eukaryotic model organisms, GENE-counter is applicable for prokaryotes and non-model organisms without an available genome reference sequence. For alignments, GENE-counter is configured for CASHX, Bowtie, and BWA, but an end user can use any Sequence Alignment/Map (SAM)-compliant program of preference. To analyze data for differential gene expression, GENE-counter can be run with any one of three statistics packages that are based on variations of the negative binomial distribution. The default method is a new and simple statistical test we developed based on an over-parameterized version of the negative binomial distribution. GENE-counter also includes three different methods for assessing differentially expressed features for enriched gene ontology (GO) terms. Results are transparent and data are systematically stored in a MySQL relational database to facilitate additional analyses as well as quality assessment. We used next generation sequencing to generate a small-scale RNA-Seq dataset derived from the heavily studied defense response of Arabidopsis thaliana and used GENE-counter to process the data. Collectively, the support from analysis of microarrays as well as the observed and substantial overlap in results from each of the three statistics packages demonstrates that GENE-counter is well suited for handling the unique characteristics of small sample sizes and high variability in gene counts

Cement hydration: the role of adsorption and crystal growth

Portland cement is a fundamental structural and binding material for industry and society. Its structural and physical properties at different scales show a complexity that can presently be barely managed through experimental and computational methods. State of the art problems and trends in cement studies will be briefly assessed from the point of view of the processes at the molecular scale

Dionchus Postoncomiracidia (Monogenea: Dionchidae) from the Skin of Blacktip Sharks, \u3ci\u3eCarcharhinus limbatus\u3c/i\u3e (Carcharhinidae)

Postoncomiracidia of Dionchus sp, are described from specimens collected from the skin of 2 blacktip sharks Carcharhinus limbatus, captured in the northern Gulf of Mexico. The parasites resemble nonciliated oncomiracidia hatched from eggs laid by Dionchus sp, on gills of a cobia Rachycentron canadum and adults of Dionchus remorae that were collected from gills of a common sharksucker Echeneis naucrates, captured in association with a third blacktip shark. The hamuli of the postoncomiracidia were morphologically similar to those of adult D. remorae. This is the first report of dionchids from an elasmobranch and from a location other than the gills. These findings support the idea that some dionchid oncomiracidia colonize the skin of sharks or other aquatic vertebrates that sponsor remoras, prior to transferring to other remoras and maturing

Dissolution Kinetics of Cubic Tricalcium Aluminate Measured by Digital Holographic Microscopy

In situ digital holographic microscopy is used to characterize the dissolution flux of polycrystalline cubic tricalcium aluminate (C₃A-c). The surface dissolves at rates that vary considerably with time and spatial location. This implies a statistical distribution of fluxes, but an approximately steady-state median rate was obtained by using flowing solutions and by reducing the water activity in the solution. The dissolution flux from highly crystalline C₃A-c depends on the water activity raised to an empirically derived exponent of 5.2 and extrapolates to a median flux of – 2.1 μmol m^–2 s^–1 in pure water with an interquartile range of 3.2 μmol m^–2 s^–1. The flux from a less crystalline source of C₃A-c has an empirical water activity exponent of 4.6 and an extrapolated median flux of only −1.4 μmol m^–2 s^–1 in pure water with an interquartile range of 1.9 μmol m^–2 s^–1. These data suggest that the bulk dissolution rate of C₃A-c can vary by at least 30% from one source to another and that variability in the local rate within a single material is even greater because of the heterogeneous spatial distribution of structural characteristics (i.e., degree of crystallinity, chemical impurities, and defects)