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Hypothesis: Ionic liquids have various applications in catalytic reaction environments. In those systems, their interaction with interfaces is key to their performance as a liquid phase. We hypothesize that the way a monolayer ionic liquid phase interacts with interfaces like a sapphire substrate is significantly dependent on temperature and that critical behavior can be observed in the structural properties of the liquid film. Methods and simulations: We perform molecular dynamics simulations of imidazolium-based ionic liquid monolayers deposited on a sapphire substrate at temperatures from 200K to 400K. We develop computational tools to analyze structural properties of molecular arrangement in the monolayer, the structure of the film and the defects spontaneously forming and healing. Findings: We observe a clear structural phase transition at around 300K from a solid-like to a liquid-like behavior of a film. Below the critical point an alternating crystalline structure of cations and anions with alignment of periodic vectors with the underlying substrate grid is observed, with frozen defects. Above the critical temperature, the pattern becomes isotropic within the contact layer that displays dynamic defects of a characteristic size. Our results highlight the importance of confinement to the phase behavior of the system., Comment: 13 pages, 12 pages pure manuscript, 9 figures, Submitted to JCIS

Hypothesis:Diffusion in confinement is an important fundamental problem with significant implications for applications of supported liquid phases. However, resolving the spatially dependent diffusion coefficient, parallel and perpendicular to interfaces, has been a standing issue and for objects of nanometric size, which structurally fluctuate on a similar time scale as they diffuse, no methodology has been established so far. We hypothesise that the complex, coupled dynamics can be captured and analysed by using a model built on the $2$-dimensional Smoluchowski equation and systematic coarse-graining. Methods and simulations: For large, flexible species, a universal approach is offered that does not make any assumptions about the separation of time scales between translation and other degrees of freedom. The method is validated on Molecular Dynamics simulations of bulk systems of a family of ionic liquids with increasing cation sizes where internal degrees of freedom have little to major effects. Findings: After validation on bulk liquids, where we provide an interpretation of two diffusion constants for each species found experimentally, we clearly demonstrate the anisotropic nature of diffusion coefficients at interfaces. Spatial variations in the diffusivities relate to interface-induced structuring of the ionic liquids. Notably, the length scales in strongly confined ionic liquids vary consistently but differently at the solid-liquid and liquid-vapour interfaces., Comment: 21 pages, 14 figures, 5 tables, pdflatex, submitted to JCIS; This is a follow-up to "Anisotropic molecular diffusion in confinement I: Transport of small particles in potential and density gradients" due to a split of arXiv:archive/2212.09545

Over the last two decades, scientific literature has been blooming with various means of simulating epithelial cell colonies. Each of these simulations can be separated by their respective efficiency (expressed in terms of consumed computational resources), the amount of cells/the size of tissues that can be simulated, the time scale of the simulated dynamics and the coarse grained level of precision. Choosing the right algorithm for the simulation of epithelial cells and tissues is a compromise between each of these key elements. Irrespective of the method, each algorithm includes part, or all, of the following features: short-range membrane-mediated attraction between cells, soft-core repulsion between cells, cell proliferation, cell death, cell motility, fluctuations, etc. We will first give a non-exhaustive overview of commonly used modeling approaches for tissues at a mesoscopic level, giving a rough idea of the coarse-graining decisions made for every one of them. Then we will dive into greater detail on how to implement a relaxation procedure according to the Vertex Model, refreshing aspects of the theoretical groundwork, describing required data structures and simulation steps and pointing out details of the simulation that can present pitfalls to a first-time implementation of the model., Comment: 16 pages, 6 figures, to be published in "Active Matter" edited by Giovanni Volpe, Nuno Ara\'ujo, Giorgio Volpe, Agnese Callegari

Hypothesis: Diffusion in confinement is an important fundamental problem with significant implications for applications of supported liquid phases. However, resolving the spatially dependent diffusion coefficient, parallel and perpendicular to interfaces, has been a standing issue. In the vicinity of interfaces, density fluctuations as a consequence of layering locally impose statistical drift, which impedes the analysis of spatially dependent diffusion coefficients even further. We hypothesise, that we can derive a model to spatially resolve interface-perpendicular diffusion coefficients based on local lifetime statistics with an extension to explicitly account for the effect of local drift using the Smoluchowski equation, that allows us to resolve anisotropic and spatially dependent diffusivity landscapes at interfaces. Methods and simulations: An analytic relation between local crossing times in system slices and diffusivity as well as an explicit term for calculating drift-induced systematic errors is presented. The method is validated on Molecular Dynamics simulations of bulk water and applied to simulations of water in slit pores. Findings: After validation on bulk liquids, we clearly demonstrate the anisotropic nature of diffusion coefficients at interfaces. Significant spatial variations in the diffusivities correlate with interface-induced structuring but cannot be solely attributed to the drift induced by local density fluctuations., Comment: 13 pages, 6 figures, submitted to JCIS, PDFLaTex; updated for submission to new Journal and split in two due to length; second accompanying publication: "Anisotropic molecular diffusion in confinement II: A model for structurally complex particles applied to transport in thin ionic liquid films" (both due to a split of arXiv:archive/2212.09545 )