Cellular automaton model of precipitation/dissolution coupled with solute transport

Precipitation/dissolution reactions coupled with solute transport are modelled as a cellular automaton in which solute molecules perform a random walk on a regular lattice and react according to a local probabilistic rule. Stationary solid particles dissolve with a certain probability and, provided solid is already present or the solution is saturated, solute particles have a probability to precipitate. In our simulation of the dissolution of a solid block inside uniformly flowing water we obtain solid precipitation downstream from the original solid edge, in contrast to the standard reaction-transport equations. The observed effect is the result of fluctuations in solute density and diminishes when we average over a larger ensemble. The additional precipitation of solid is accompanied by a substantial reduction in the relatively small solute concentration. The model is appropriate for the study of the r\^ole of intrinsic fluctuations in the presence of reaction thresholds and can be employed to investigate porosity changes associated with the carbonation of cement.Comment: LaTeX file, 13 pages. To appear in Journal of Statistical Physics (Proceedings of Lattice Gas'94, June 1994, Princeton). Figures available from author. Requests may be submitted by E-mail ([email protected]) or ordinary mail (Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland

A reaction-diffusion model for the hydration/setting of cement

We propose a heterogeneous reaction-diffusion model for the hydration and setting of cement. The model is based on diffusional ion transport and on cement specific chemical dissolution/precipitation reactions under spatial heterogeneous solid/liquid conditions. We simulate the spatial and temporal evolution of precipitated micro structures starting from initial random configurations of anhydrous cement particles. Though the simulations have been performed for two dimensional systems, we are able to reproduce qualitatively basic features of the cement hydration problem. The proposed model is also applicable to general water/mineral systems.Comment: REVTeX (12 pages), 4 postscript figures, tarred, gzipped, uuencoded using `uufiles', coming with separate file(s). Figure 1 consists of 6 color plates; if you have no color printer try to send it to a black&white postscript-plotte

Conceptualising the geographic world: the dimensions of negotiation in crowdsourced cartography

In crowdsourced cartographic projects, mappers coordinate their efforts through online tools to produce digital geospatial artefacts, such as maps and gazetteers, which were once the exclusive territory of professional surveyors and cartographers. In order to produce meaningful and coherent data, contributors need to negotiate a shared conceptualisation that defines the domain concepts, such as road, building, train station, forest, and lake, enabling the communi- cation of geographic knowledge. Considering the OpenStreetMap Wiki website as a case study, this article investigates the nature of this negotiation, driven by a small group of mappers in a context of high contribution inequality. De- spite the apparent consensus on the conceptualisation, the negotiation keeps unfolding in a tension between alternative representations, which are often in- commensurable, i.e., hard to integrate and reconcile. In this study, we identify six complementary dimensions of incommensurability that recur in the nego- tiation: (i) ontology, (ii) cartography, (iii) culture and language, (iv) lexical definitions, (v) granularity, and (vi) semantic overload and duplication

Evaluating privacy-preserving record linkage using cryptographic long-term keys and multibit trees on large medical datasets.

Background: Integrating medical data using databases from different sources by record linkage is a powerful technique increasingly used in medical research. Under many jurisdictions, unique personal identifiers needed for linking the records are unavailable. Since sensitive attributes, such as names, have to be used instead, privacy regulations usually demand encrypting these identifiers. The corresponding set of techniques for privacy-preserving record linkage (PPRL) has received widespread attention. One recent method is based on Bloom filters. Due to superior resilience against cryptographic attacks, composite Bloom filters (cryptographic long-term keys, CLKs) are considered best practice for privacy in PPRL. Real-world performance of these techniques using large-scale data is unknown up to now. Methods: Using a large subset of Australian hospital admission data, we tested the performance of an innovative PPRL technique (CLKs using multibit trees) against a gold-standard derived from clear-text probabilistic record linkage. Linkage time and linkage quality (recall, precision and F-measure) were evaluated. Results: Clear text probabilistic linkage resulted in marginally higher precision and recall than CLKs. PPRL required more computing time but 5 million records could still be de-duplicated within one day. However, the PPRL approach required fine tuning of parameters. Conclusions: We argue that increased privacy of PPRL comes with the price of small losses in precision and recall and a large increase in computational burden and setup time. These costs seem to be acceptable in most applied settings, but they have to be considered in the decision to apply PPRL. Further research on the optimal automatic choice of parameters is needed

Noise Contributions in an Inducible Genetic Switch: A Whole-Cell Simulation Study

Stochastic expression of genes produces heterogeneity in clonal populations of bacteria under identical conditions. We analyze and compare the behavior of the inducible lac genetic switch using well-stirred and spatially resolved simulations for Escherichia coli cells modeled under fast and slow-growth conditions. Our new kinetic model describing the switching of the lac operon from one phenotype to the other incorporates parameters obtained from recently published in vivo single-molecule fluorescence experiments along with in vitro rate constants. For the well-stirred system, investigation of the intrinsic noise in the circuit as a function of the inducer concentration and in the presence/absence of the feedback mechanism reveals that the noise peaks near the switching threshold. Applying maximum likelihood estimation, we show that the analytic two-state model of gene expression can be used to extract stochastic rates from the simulation data. The simulations also provide mRNA–protein probability landscapes, which demonstrate that switching is the result of crossing both mRNA and protein thresholds. Using cryoelectron tomography of an E. coli cell and data from proteomics studies, we construct spatial in vivo models of cells and quantify the noise contributions and effects on repressor rebinding due to cell structure and crowding in the cytoplasm. Compared to systems without spatial heterogeneity, the model for the fast-growth cells predicts a slight decrease in the overall noise and an increase in the repressors rebinding rate due to anomalous subdiffusion. The tomograms for E. coli grown under slow-growth conditions identify the positions of the ribosomes and the condensed nucleoid. The smaller slow-growth cells have increased mRNA localization and a larger internal inducer concentration, leading to a significant decrease in the lifetime of the repressor–operator complex and an increase in the frequency of transcriptional bursts

Lithographie par faisceaux d'ions : simulations et résultats expérimentaux

The advantages offered by Ion Beam Lithography compared to other lithographic techniques in use today are discussed. The lithographic resolution achievable with light (H+) and heavy (Ga+) ions is studied experimentally. Patterns of dimensions less than 100 nm are transferred in a resist (PMMA) by exposure to light and heavy ions through special thin-membrane masks. The effect of recoil atoms created by focused heavy ion beams in the resist on lithographic resolution is demonstrated with the aid of a computer simulation program of ionstopping in amorphous materials. Computer-simulated developed profiles in resist after ion exposure are pre sented. The use of focused ion-beam systems employing liquid metal sources for lithographic applications is discussed.Cet article décrit une nouvelle technique de lithographie qui utilise des faisceaux d'ions. Les avantages de cette technique sont discutés, et comparés à ceux présentés par d'autres méthodes lithographiques couramment utilisées. La résolution de la lithographie ionique est étudiée expérimentalement par irradiation de résine PMMA à l'aide d'ions légers (H+) et d'ions lourds (Ga+). Des motifs géométriques de dimensions inférieures à 100 nm ont été transférés dans la résine (PMMA) à partir de masques adaptés (membranes minces à trous). L'effet, sur la résolution, des atomes de recul créés pendant l'irradiation est mis en évidence à l'aide d'un programme de simulation du freinage des ions dans la matière amorphe. Des profils de développement de la résine après irradiation aux ions Ga+ sont simulés sur ordinateur. L'utilisation, pour la lithographie, de machines ioniques à sources d'ions à métaux liquides est discutée

Lithographie par faisceaux d'ions : simulations et résultats expérimentaux

Cet article décrit une nouvelle technique de lithographie qui utilise des faisceaux d'ions. Les avantages de cette technique sont discutés, et comparés à ceux présentés par d'autres méthodes lithographiques couramment utilisées. La résolution de la lithographie ionique est étudiée expérimentalement par irradiation de résine PMMA à l'aide d'ions légers (H+) et d'ions lourds (Ga+). Des motifs géométriques de dimensions inférieures à 100 nm ont été transférés dans la résine (PMMA) à partir de masques adaptés (membranes minces à trous). L'effet, sur la résolution, des atomes de recul créés pendant l'irradiation est mis en évidence à l'aide d'un programme de simulation du freinage des ions dans la matière amorphe. Des profils de développement de la résine après irradiation aux ions Ga+ sont simulés sur ordinateur. L'utilisation, pour la lithographie, de machines ioniques à sources d'ions à métaux liquides est discutée