Calcium isotope ratios of pore fluids and solid phase of organic rich sediments

Pore fluid calcium isotope, calcium concentration and strontium concentration data are used to measure the rates of diagenetic dissolution and precipitation of calcite in deep-sea sediments containing abundant clay and organic material. This type of study of deep-sea sediment diagenesis provides unique information about the ultra-slow chemical reactions that occur in natural marine sediments that affect global geochemical cycles and the preservation of paleo-environmental information in carbonate fossils. For this study, calcium isotope ratios (d44/40Ca) of pore fluid calcium from Ocean Drilling Program (ODP) Sites 984 (North Atlantic) and 1082 (off the coast of West Africa) were measured to augment available pore fluid measurements of calcium and strontium concentration. Both study sites have high sedimentation rates and support quantitative sulfate reduction, methanogenesis and anaerobic methane oxidation. The pattern of change of d44/40Ca of pore fluid calcium versus depth at Sites 984 and 1082 differs markedly from that of previously studied deep-sea Sites like 590B and 807, which are composed of nearly pure carbonate sediment. In the 984 and 1082 pore fluids, d44/40Ca remains elevated near seawater values deep in the sediments, rather than shifting rapidly toward the d44/40Ca of carbonate solids. This observation indicates that the rate of calcite dissolution is far lower than at previously studied carbonate-rich sites. The data are fit using a numerical model, as well as more approximate analytical models, to estimate the rates of carbonate dissolution and precipitation and the relationship of these rates to the abundance of clay and organic material. Our models give mutually consistent results and indicate that calcite dissolution rates at Sites 984 and 1082 are roughly two orders of magnitude lower than at previously studied carbonate-rich sites, and the rate correlates with the abundance of clay. Our calculated rates are conservative for these sites (the actual rates could be significantly slower) because other processes that impact the calcium isotope composition of sedimentary pore fluid have not been included. The results provide direct geochemical evidence for the anecdotal observation that the best-preserved carbonate fossils are often found in clay or organic-rich sedimentary horizons. The results also suggest that the presence of clay minerals has a strong passivating effect on the surfaces of biogenic carbonate minerals, slowing dissolution dramatically even in relation to the already-slow rates typical of carbonate-rich sediments.

Concrete Swelling in Two Spanish Dams

Several chemical reactions are able to produce swelling of concrete for decades after its initial curing, a problem that affects a considerable number of concrete dams around the world. Principia has had several contracts to study this problem in recent years, which have required reviewing the state-ofthe-art, adopting appropriate mathematical descriptions, programming them into user routines in Abaqus, determining model parameters on the basis of some parts of the dams’ monitored histories, ensuring reliability using some other parts, and finally predicting the future evolution of the dams and their safety margins. The paper describes some of the above experience, including the programming of sophisticated nonisotropic swelling models, that must be compatible with cracking and other nonlinearities involved in concrete behaviour. The applications concentrate on two specific cases, an arch-gravity dam and a double-curvature arch dam, both with a long history of concrete swelling and which, interestingly, entailed different degrees of success in the modelling efforts

Concrete Swelling in Existing Dams

Several chemical reactions are able to produce swelling of concrete for decades after its initial curing, a problem that affects a considerable number of concrete dams around the world. Principia has had several contracts to study this problem in recent years, which have required reviewing the state-of-the-art, adopting appropriate mathematical descriptions, programming them into user routines in Abaqus, determining model parameters on the basis of some parts of the dams’ monitored histories, ensuring reliability using some other parts, and finally predicting the future evolution of the dams and their safety margins. The paper describes some of the above experience, including the programming of sophisticated non-isotropic swelling models, that must be compatible with cracking and other nonlinearities involved in concrete behaviour. The applications concentrate on two specific cases, an archgravity dam and a double-curvature arch dam, both with a long history of concrete swelling and which, interestingly, entailed different degrees of success in the modelling efforts

Concrete Swelling in Two Spanish Dams

Several chemical reactions are able to produce swelling of concrete for decades after its initial curing, a problem that affects a considerable number of concrete dams around the world. Principia has had several contracts to study this problem in recent years, which have required reviewing the state-ofthe-art, adopting appropriate mathematical descriptions, programming them into user routines in Abaqus, determining model parameters on the basis of some parts of the dams’ monitored histories, ensuring reliability using some other parts, and finally predicting the future evolution of the dams and their safety margins. The paper describes some of the above experience, including the programming of sophisticated nonisotropic swelling models, that must be compatible with cracking and other nonlinearities involved in concrete behaviour. The applications concentrate on two specific cases, an arch-gravity dam and a double-curvature arch dam, both with a long history of concrete swelling and which, interestingly, entailed different degrees of success in the modelling efforts.

Agent-based modelling for cement hydration

The Agent-Based Modelling and simulation (ABM) is a rather new approach for studying complex systems withinteracting autonomous agents that has lately undergone great growth in various fields such as biology, physics, social science, economics and business. Efforts to model and simulate the highly complex cement hydration process have been made over the past 40 years, with the aim of predicting the performance of concrete and designing innovative and enhanced cementitious materials. The ABM presented here - based on previous work - focuses on the early stages of cement hydration by modelling the physical-chemical processes at the particle level. The model considers the cement hydration process as a time and 3D space system, involving multiple diffusing and reacting species of spherical particles. Chemical reactions are simulated by adaptively selecting discrete stochastic simulation for the appropriate reaction, whenever that is necessary. Interactions between particles are also considered. The model has been inspired by reported cellular automata?s approach which provides detailed predictions of cement microstructure at the expense of significant computational difficulty. The ABM approach herein seeks to bring about an optimal balance between accuracy and computational efficiency.

Glassy State and Cryopreservation of Mint Shoot Tips

Vitrification refers to the physical process by which a liquid supercools to very low tem- peratures and finally solidifies into a metastable glass, without undergoing crystallization at a practical cooling rate. Thus, vitrification is an effective freeze-avoidance mechanism and living tissue cryopreservation is, in most cases, relying on it. As a glass is exceedingly vis- cous and stops all chemical reactions that require molecular diffusion, its formation leads to metabolic inactivity and stability over time. To investigate glassy state in cryopreserved plant material, mint shoot tips were submitted to the different stages of a frequently used cryopreservation protocol (droplet-vitrification) and evaluated for water content reduction and sucrose content, as determined by ion chromatography, frozen water fraction and glass transitions occurrence by differential scanning calorimetry, and investigated by low-tempera- ture scanning electron microscopy, as a way to ascertain if their cellular content was vitri- fied. Results show how tissues at intermediate treatment steps develop ice crystals during liquid nitrogen cooling, while specimens whose treatment was completed become vitrified, with no evidence of ice formation. The agreement between calorimetric and microscopic observations was perfect. Besides finding a higher sucrose concentration in tissues at the more advanced protocol steps, this level was also higher in plants precultured at 25/21?C than in plants cultivated at 25?C.

Thermal behaviour of bitumen modified by sulphur addition

The most frequent use of bitumen is as binder for pavement applications. The effect of sulphur addition on the properties of the bitumen has been extensively studied several decades ago. Recently, there is a renewed interest in researching the behaviour of sulphur-bitumen combination, because off 1.The future availability of bitumen may be limited and 2. The beneficial consumption of great amounts of sulphur compounds from petroleum refining is advisable. The addition of sulphur to bitumen provokes the beginning of chemical reactions depending on the sulphur content and heating temperature. At heating temperatures T< 140 ºC liquid sulphur reacts with naphthenic-aromatic fraction forming polysulphides. At temperatures above 150 ºC dehydrogenization reactions with emission of hydrogen sulfide take place and naphthenic-aromatic molecules are transformed into asphaltenes. Therefore, the addition of sulphur to bitumen provokes changes in the chemical structure of the bitumen. The objective of this work is to analyze, the thermal behaviour of sulphur-bitumen mixtures of different composition (0-35 %wt sulphur content) prepared at 130 and 140 ºC, by means of differential scanning calorimetry (DSC). Besides, the volatile emissions of the mixtures at high temperature have been estimated from loss weight measurements as a function of stored time

Concrete Swelling in a Double Curvature Dam

Se describe el problema del hinchamiento del hormigón en las presas de doble curvatura. Several chemical reactions are able to produce swelling of concrete for decades after its initial curing, a problem that affects a considerable number of concrete dams around the world. The object of the work reported is to simulate the underlying mechanisms with sufficient accuracy to reproduce the past history and to predict the future evolution reliably. Having studied the available formulations, that considered to be more promising was adopted and introduced via user routines in a commercial finite element code. It is a non isotropic swelling model,compatible with the cracking and other non-linearities displayed by the concrete. The paper concentrates on the work conducted for a double-curvature arch dam. The model parameters were determined on the basis of some parts of the dam’s monitored histories, reliability was then verified using other parts and, finally, predictions were made about the future evolution of the dam and its safety margin.

Enhancing iDynoMiCS framework with a plasmid conjugation module

Actualmente existen aplicaciones que permiten simular el comportamiento de bacterias en distintos hábitats y los procesos que ocurren en estos para facilitar su estudio y experimentación sin la necesidad de un laboratorio. Una de las aplicaciones de software libre para la simulación de poblaciones bacteriológicas mas usada es iDynoMiCS (individual-based Dynamics of Microbial Communities Simulator), un simulador basado en agentes que permite trabajar con varios modelos computacionales de bacterias en 2D y 3D. Este simulador permite una gran libertad al configurar una numerosa cantidad de variables con respecto al entorno, reacciones químicas y otros detalles importantes. Una característica importante es el poder simular de manera sencilla la conjugación de plásmidos entre bacterias. Los plásmidos son moléculas de ADN diferentes del cromosoma celular, generalmente circularles, que se replican, transcriben y conjugan independientemente del ADN cromosómico. Estas están presentes normalmente en bacterias procariotas, y en algunas ocasiones en eucariotas, sin embargo, en este tipo de células son llamados episomas. Dado el complejo comportamiento de los plásmidos y la gama de posibilidades que estos presentan como mecanismos externos al funcionamiento básico de la célula, en la mayoría de los casos confiriéndole distintas ventajas evolutivas, como por ejemplo: resistencia antibiótica, entre otros, resulta importante su estudio y subsecuente manipulación. Sin embargo, el marco operativo del iDynoMiCS, en cuanto a simulación de plásmidos se refiere, es demasiado sencillo y no permite realizar operaciones más complejas que el análisis de la propagación de un plásmido en la comunidad. El presente trabajo surge para resolver esta deficiencia de iDynomics. Aquí se analizarán, desarrollarán e implementarán las modificaciones necesarias para que iDynomics pueda simular satisfactoriamente y mas apegado a la realidad la conjugación de plásmidos y permita así mismo resolver distintas operaciones lógicas, como lo son los circuitos genéticos, basadas en plásmidos. También se analizarán los resultados obtenidos de acuerdo a distintos estudios relevantes y a la comparación de los resultados obtenidos con el código original de iDynomics. Adicionalmente se analizará un estudio comparando la eficiencia de detección de una sustancia mediante dos circuitos genéticos distintos. Asimismo el presente trabajo puede tener interés para el grupo LIA de la Facultad de Informática de la Universidad Politécnica de Madrid, el cual está participando en el proyecto europeo BACTOCOM que se centra en el estudio de la conjugación de plásmidos y circuitos genéticos. --ABSTRACT--Currently there are applications that simulate the behavior of bacteria in different habitats and the ongoing processes inside them to facilitate their study and experimentation without the need for an actual laboratory. One of the most used open source applications to simulate bacterial populations is iDynoMiCS (individual-based Dynamics of Microbial Communities Simulator), an agent-based simulator that allows working with several computer models of 2D and 3D bacteria in biofilms. This simulator allows great freedom by means of a large number of configurable variables regarding environment, chemical reactions and other important details of the simulation. Within these characteristics there exists a very basic framework to simulate plasmid conjugation. Plasmids are DNA molecules physically different from the cell’s chromosome, commonly found as small circular, double-stranded DNA molecules that are replicated, conjugated and transcribed independently of chromosomal DNA. These bacteria are normally present in prokaryotes and sometimes in eukaryotes, which in this case these cells are called episomes. Plasmids are external mechanisms to the cells basic operations, and as such, in the majority of the cases, confer to the host cell various evolutionary advantages, like antibiotic resistance for example. It is mperative to further study plasmids and the possibilities they present. However, the operational framework of the iDynoMiCS plasmid simulation is too simple, and does not allow more complex operations that the analysis of the spread of a plasmid in the community. This project was conceived to resolve this particular deficiency in iDynomics, moreover, in this paper is discussed, developed and implemented the necessary changes to iDynomics simulation software so it can satisfactorily and realistically simulate plasmid conjugation, and allow the possibility to solve various ogic operations, such as plasmid-based genetic circuits. Moreover the results obtained will be analyzed and compared with other relevant studies and with those obtained with the original iDynomics code. Conjointly, an additional study detailing the sensing of a substance with two different genetic circuits will be presented. This work may also be relevant to the LIA group of the Faculty of Informatics of the Polytechnic University of Madrid, which is participating in the European project BACTOCOM that focuses on the study of the of plasmid conjugation and genetic circuits.

Flamelet structures in spray ignition

In typical liquid-fueled burners the fuel is injected as a high-velocity liquid jet that breaks up to form the spray. The initial heating and vaporization of the liquid fuel rely on the relatively large temperatures of the sourrounding gas, which may include hot combustion products and preheated air. The heat exchange between the liquid and the gas phases is enhanced by droplet dispersion arising from the turbulent motion. Chemical reaction takes place once molecular mixing between the fuel vapor and the oxidizer has occurred in mixing layers separating the spray flow from the hot air stream. Since in most applications the injection velocities are much larger than the premixed-flame propagation velocity, combustion stabilization relies on autoignition of the fuel-oxygen mixture, with the combustion stand-off distance being controlled by the interaction of turbulent transport, droplet heating and vaporization, and gas-phase chemical reactions. In this study, conditions are identified under which analyses of laminar flamelets canshed light on aspects of turbulent spray ignition. This study extends earlier fundamental work by Liñan & Crespo (1976) on ignition in gaseous mixing layers to ignition of sprays. Studies of laminar mixing layers have been found to be instrumental in developing un-derstanding of turbulent combustion (Peters 2000), including the ignition of turbulent gaseous diffusion flames (Mastorakos 2009). For the spray problem at hand, the configuration selected, shown in Figure 1, involves a coflow mixing layer formed between a stream of hot air moving at velocity UA and a monodisperse spray moving at velocity USUA. The boundary-layer approximation will be used below to describe the resulting sl ender flow, which exhibits different igniting behaviors depending on the characteristics of t he fuel. In this approximation, consideration of the case U A = U S enables laminar ignition distances to be related to ignition times of unstrained spray flamelets, thereby pro viding quantitative information of direct applicability in regions of low scala r dissipation-rate in turbulent reactive flows (see the discussion in pp. 181–186 of Peters (2000)) . This report is organized as follows. Effects of droplet dispersion dynamics on ignition of sprays in turbulent mixing layers are discussed in Section 2. The formulation f or ignition in laminar mixing layers is outlined in Sections 3 and 4. The results are presented in Section 5. In Section 6, the mixture-fraction field and associated scalar dissipat ion rates for spray ignition are discussed. Finally, some brief conclusions are drawn in Section 7.

BIND—The Biomolecular Interaction Network Database

The Biomolecular Interaction Network Database (BIND; http://binddb.org) is a database designed to store full descriptions of interactions, molecular complexes and pathways. Development of the BIND 2.0 data model has led to the incorporation of virtually all components of molecular mechanisms including interactions between any two molecules composed of proteins, nucleic acids and small molecules. Chemical reactions, photochemical activation and conformational changes can also be described. Everything from small molecule biochemistry to signal transduction is abstracted in such a way that graph theory methods may be applied for data mining. The database can be used to study networks of interactions, to map pathways across taxonomic branches and to generate information for kinetic simulations. BIND anticipates the coming large influx of interaction information from high-throughput proteomics efforts including detailed information about post-translational modifications from mass spectrometry. Version 2.0 of the BIND data model is discussed as well as implementation, content and the open nature of the BIND project. The BIND data specification is available as ASN.1 and XML DTD.

A role for intermolecular disulfide bonds in prion diseases?

The key event in prion diseases seems to be the conversion of the prion protein PrP from its normal cellular isoform (PrPC) to an aberrant “scrapie” isoform (PrPSc). Earlier studies have detected no covalent modification in the scrapie isoform and have concluded that the PrPC → PrPSc conversion is a purely conformational transition involving no chemical reactions. However, a reexamination of the available biochemical data suggests that the PrPC → PrPSc conversion also involves a covalent reaction of the (sole) intramolecular disulfide bond of PrPC. Specifically, the data are consistent with the hypothesis that infectious prions are composed of PrPSc polymers linked by intermolecular disulfide bonds. Thus, the PrPC → PrPSc conversion may involve not only a conformational transition but also a thiol/disulfide exchange reaction between the terminal thiolate of such a PrPSc polymer and the disulfide bond of a PrPC monomer. This hypothesis seems to account for several unusual features of prion diseases.

Femtochemistry

The topic of femtochemistry is surveyed from both theoretical and experimental points of view. A time-dependent wave packet description of the photodissociation of the O—C—S molecule reveals vibrational motion in the transition-state region and suggests targets for direct experimental observation. Theoretical approaches for treating femtosecond chemical phenomena in condensed phases are featured along with prospects for laser-controlled chemical reactions by using tailored ultrashort chirped pulses. An experimental study of the photoisomerization of retinal in the protein bacteriorhodopsin is discussed with an aim to gain insight into the potential energy surfaces on which this remarkably efficient and selective reactions proceeds. Finally, a prospective view of new frontiers in femtochemistry is given.

Manganese oxide minerals: Crystal structures and economic and environmental significance

Manganese oxide minerals have been used for thousands of years—by the ancients for pigments and to clarify glass, and today as ores of Mn metal, catalysts, and battery material. More than 30 Mn oxide minerals occur in a wide variety of geological settings. They are major components of Mn nodules that pave huge areas of the ocean floor and bottoms of many fresh-water lakes. Mn oxide minerals are ubiquitous in soils and sediments and participate in a variety of chemical reactions that affect groundwater and bulk soil composition. Their typical occurrence as fine-grained mixtures makes it difficult to study their atomic structures and crystal chemistries. In recent years, however, investigations using transmission electron microscopy and powder x-ray and neutron diffraction methods have provided important new insights into the structures and properties of these materials. The crystal structures for todorokite and birnessite, two of the more common Mn oxide minerals in terrestrial deposits and ocean nodules, were determined by using powder x-ray diffraction data and the Rietveld refinement method. Because of the large tunnels in todorokite and related structures there is considerable interest in the use of these materials and synthetic analogues as catalysts and cation exchange agents. Birnessite-group minerals have layer structures and readily undergo oxidation reduction and cation-exchange reactions and play a major role in controlling groundwater chemistry.

Putting ion channels to work: Mechanoelectrical transduction, adaptation, and amplification by hair cells

As in other excitable cells, the ion channels of sensory receptors produce electrical signals that constitute the cellular response to stimulation. In photoreceptors, olfactory neurons, and some gustatory receptors, these channels essentially report the results of antecedent events in a cascade of chemical reactions. The mechanoelectrical transduction channels of hair cells, by contrast, are coupled directly to the stimulus. As a consequence, the mechanical properties of these channels shape our hearing process from the outset of transduction. Channel gating introduces nonlinearities prominent enough to be measured and even heard. Channels provide a feedback signal that controls the transducer's adaptation to large stimuli. Finally, transduction channels participate in an amplificatory process that sensitizes and sharpens hearing.