Related papers: Characterising submonolayer deposition via visibil…
The shape evolution of two-dimensional islands under electromigration-driven periphery diffusion is studied by kinetic Monte Carlo (KMC) simulations and continuum theory. The energetics of the KMC model is adapted to the Cu(100) surface,…
In this thesis we present a kinetic Monte Carlo model for the description of epitaxial graphene growth. Experimental results suggest a growth mechanism by which clusters of 5 carbon atoms are an intermediate species necessary for nucleation…
I show how to construct Monte Carlo algorithms (programs), prove that they are correct and document them. Complicated algorithms are build using a handful of elementary methods. This construction process is transparently illustrated using…
Machine learning techniques have been developed to identify inclusions on the surface of freely suspended smectic liquid crystal films imaged by reflected light microscopy. The experimental images are preprocessed using Canny edge detection…
Using a set of evolution equations [J.G. Amar {\it et al}, Phys. Rev. Lett. {\bf 86}, 3092 (2001)] for the average gap-size between islands, we calculate analytically the asymptotic scaled capture-number distribution (CND) for…
Uncertainty estimation in deep models is essential in many real-world applications and has benefited from developments over the last several years. Recent evidence suggests that existing solutions dependent on simple Gaussian formulations…
If a stochastic system during some periods of its evolution can be divided into non-interacting parts, the kinetics of each part can be simulated independently. We show that this can be used in the development of efficient Monte Carlo…
We are developing an interactive graph exploration system called Graph Playground for making sense of large graphs. Graph Playground offers a fast and scalable edge decomposition algorithm, based on iterative vertex-edge peeling, to…
Computer modeling of multicellular systems has been a valuable tool for interpreting and guiding in vitro experiments relevant to embryonic morphogenesis, tumor growth, angiogenesis and, lately, structure formation following the printing of…
A visibility algorithm maps time series into complex networks following a simple criterion. The resulting visibility graph has recently proven to be a powerful tool for time series analysis. However its straightforward computation is…
Irreversible growth of strained epitaxial nanoislands has been studied with the use of the kinetic Monte Carlo (KMC) technique. It has been shown that the strain-inducing size misfit between the substrate and the overlayer produces long…
This review article is intended as a practical guide for newcomers to the field of kinetic Monte Carlo (KMC) simulations, and specifically to lattice KMC simulations as prevalently used for surface and interface applications. We will…
Visibility algorithms are a family of geometric and ordering criteria by which a real-valued time series of N data is mapped into a graph of N nodes. This graph has been shown to often inherit in its topology non-trivial properties of the…
We report developments of the kinetic Monte Carlo (KMC) method with improved accuracy and increased versatility for the description of atomic diffusivity on metal surfaces. The on-lattice constraint built into our recently proposed…
In our earlier study of Ag island coarsening on Ag(111) surface using kinetic Monte Carlo (KMC) simulations we found that during early stages coarsening proceeds as a sequence of selected island sizes resulting in peaks and valleys in the…
We have performed Kinetic Monte Carlo simulation to study the effect of diffusion anisotropy and bonding anisotropy on island formation at different temperatures during the sub-monolayer film growth in Molecular Beam Epitaxy. We use simple…
Cellular scale decision making is modulated by the dynamics of signalling molecules and their diffusive trajectories from a source to small absorbing sites on the cellular surface. Diffusive capture problems are computationally challenging…
Multi-layer graphs consist of several graphs (layers) over the same vertex set. They are motivated by real-world problems where entities (vertices) are associated via multiple types of relationships (edges in different layers). We chart the…
The simulation of the physical movement of multi-body systems at an atomistic level, with forces calculated from a quantum mechanical description of the electrons, motivates a graph partitioning problem studied in this article. Several…
Many problems require to approximate an expected value by some kind of Monte Carlo (MC) sampling, e.g. molecular dynamics (MD) or simulation of stochastic reaction models (also termed kinetic Monte Carlo (kMC)). Often, we are furthermore…