Curvature Dependence of Surface Free Energy of Liquid Drops and Bubbles: A Simulation Study

We study the excess free energy due to phase coexistence of fluids by Monte Carlo simulations using successive umbrella sampling in finite LxLxL boxes with periodic boundary conditions. Both the vapor-liquid phase coexistence of a simple Lennard-Jones fluid and the coexistence between A-rich and B-rich phases of a symmetric binary (AB) Lennard-Jones mixture are studied, varying the density rho in the simple fluid or the relative concentration x_A of A in the binary mixture, respectively. The character of phase coexistence changes from a spherical droplet (or bubble) of the minority phase (near the coexistence curve) to a cylindrical droplet (or bubble) and finally (in the center of the miscibility gap) to a slab-like configuration of two parallel flat interfaces. Extending the analysis of M. Schrader, P. Virnau, and K. Binder [Phys. Rev. E 79, 061104 (2009)], we extract the surface free energy gamma (R) of both spherical and cylindrical droplets and bubbles in the vapor-liquid case, and present evidence that for R -> Infinity the leading order (Tolman) correction for droplets has sign opposite to the case of bubbles, consistent with the Tolman length being independent on the sign of curvature. For the symmetric binary mixture the expected non-existence of the Tolman length is confirmed. In all cases {and for a range of radii} R relevant for nucleation theory, gamma(R) deviates strongly from gamma (Infinity) which can be accounted for by a term of order gamma(Infinity)/gamma(R)-1 ~ 1/R^2. Our results for the simple Lennard-Jones fluid are also compared to results from density functional theory and we find qualitative agreement in the behavior of gamma(R) as well as in the sign and magnitude of the Tolman length.Comment: 25 pages, submitted to J. Chem. Phy

TAMMiCol: Tool for analysis of the morphology of microbial colonies.

Many microbes are studied by examining colony morphology via two-dimensional top-down images. The quantification of such images typically requires each pixel to be labelled as belonging to either the colony or background, producing a binary image. While this may be achieved manually for a single colony, this process is infeasible for large datasets containing thousands of images. The software Tool for Analysis of the Morphology of Microbial Colonies (TAMMiCol) has been developed to efficiently and automatically convert colony images to binary. TAMMiCol exploits the structure of the images to choose a thresholding tolerance and produce a binary image of the colony. The images produced are shown to compare favourably with images processed manually, while TAMMiCol is shown to outperform standard segmentation methods. Multiple images may be imported together for batch processing, while the binary data may be exported as a CSV or MATLAB MAT file for quantification, or analysed using statistics built into the software. Using the in-built statistics, it is found that images produced by TAMMiCol yield values close to those computed from binary images processed manually. Analysis of a new large dataset using TAMMiCol shows that colonies of Saccharomyces cerevisiae reach a maximum level of filamentous growth once the concentration of ammonium sulfate is reduced to 200 μM. TAMMiCol is accessed through a graphical user interface, making it easy to use for those without specialist knowledge of image processing, statistical methods or coding

Monte Carlo Methods for Estimating Interfacial Free Energies and Line Tensions

Excess contributions to the free energy due to interfaces occur for many problems encountered in the statistical physics of condensed matter when coexistence between different phases is possible (e.g. wetting phenomena, nucleation, crystal growth, etc.). This article reviews two methods to estimate both interfacial free energies and line tensions by Monte Carlo simulations of simple models, (e.g. the Ising model, a symmetrical binary Lennard-Jones fluid exhibiting a miscibility gap, and a simple Lennard-Jones fluid). One method is based on thermodynamic integration. This method is useful to study flat and inclined interfaces for Ising lattices, allowing also the estimation of line tensions of three-phase contact lines, when the interfaces meet walls (where "surface fields" may act). A generalization to off-lattice systems is described as well. The second method is based on the sampling of the order parameter distribution of the system throughout the two-phase coexistence region of the model. Both the interface free energies of flat interfaces and of (spherical or cylindrical) droplets (or bubbles) can be estimated, including also systems with walls, where sphere-cap shaped wall-attached droplets occur. The curvature-dependence of the interfacial free energy is discussed, and estimates for the line tensions are compared to results from the thermodynamic integration method. Basic limitations of all these methods are critically discussed, and an outlook on other approaches is given

Characterizing the shape patterns of dimorphic yeast pseudohyphae

© 2018 The Authors. Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.Pseudohyphal growth of the dimorphic yeast Saccharomyces cerevisiae is analysed using two-dimensional top-down binary images. The colony morphology is characterized using clustered shape primitives (CSPs), which are learned automatically from the data and thus do not require a list of predefined features or a priori knowledge of the shape. The power of CSPs is demonstrated through the classification of pseudohyphal yeast colonies known to produce different morphologies. The classifier categorizes the yeast colonies considered with an accuracy of 0.969 and standard deviation 0.041, demonstrating that CSPs capture differences in morphology, while CSPs are found to provide greater discriminatory power than spatial indices previously used to quantify pseudohyphal growth. The analysis demonstrates that CSPs provide a promising avenue for analysing morphology in high-throughput assays

Freezing of Spinodal Decompostion by Irreversible Chemical Growth Reaction

We present a description of the freezing of spinodal decomposition in systems, which contain simultaneous irreversible chemical reactions, in the hydrodynamic limit approximation. From own results we conclude, that the chemical reaction leads to an onset of spinodal decomposition also in the case of an initial system which is completely miscible and can lead to an extreme retardation of the dynamics of the spinodal decomposition, with the probability of a general freezing of this process, which can be experimetally observed in simultaneous IPN formation.Comment: 10 page

An evaluation of survey designs and model-based inferences of fish aggregations using active acoustics

“Star” survey designs have become an increasingly popular alternative to parallel line designs in fisheries-independent sampling of areas with isolated fish aggregations, such as artificial reefs, seamounts, fish aggregating devices, and spawning aggregation sites. In this study, we simulated three scenarios of fish aggregating around a feature of interest with variations in the size and complexity of aggregations as well as their location relative to the habitat feature. Simulated and empirical data representing goliath grouper (Epinephalus itajara) spawning aggregations at artificial reefs were utilized as a case study, and scenarios were generated in relation to both a single habitat feature and a reef complex with multiple structures. Seven variations of survey design using both star and parallel transects were examined and compared by geostatistical and generalized additive models (GAMs) to identify the most robust approach to quantify fish aggregations in each scenario. In most scenarios, precision in the mean and variability of backscatter estimates is not significantly affected by the number of transects passing over the habitat feature as long as at least one pass is made. Estimation error is minimized using the GAM approach, and is further reduced when sampling variance is high, which was better accomplished by parallel designs overall. These results will help inform surveyors on the best overall approach to improve precision in quantifying fish aggregations given basic knowledge of their behavior around an established habitat feature and help them to adapt their survey designs based on common difficulties in sampling these populations simulated below

Diffusion-Limited Growth of Microbial Colonies.

The emergence of diffusion-limited growth (DLG) within a microbial colony on a solid substrate is studied using a combination of mathematical modelling and experiments. Using an agent-based model of the interaction between microbial cells and a diffusing nutrient, it is shown that growth directed towards a nutrient source may be used as an indicator that DLG is influencing the colony morphology. A continuous reaction-diffusion model for microbial growth is employed to identify the parameter regime in which DLG is expected to arise. Comparisons between the model and experimental data are used to argue that the bacterium Bacillus subtilis can undergo DLG, while the yeast Saccharomyces cerevisiae cannot, and thus the non-uniform growth exhibited by this yeast must be caused by the pseudohyphal growth mode rather than limited nutrient availability. Experiments testing directly for DLG features in yeast colonies are used to confirm this hypothesis