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Cell sorting, whereby a heterogeneous cell mixture segregates and forms distinct homogeneous tissues, is one of the main collective cell behaviors at work during development. Although differences in interfacial energies are recognized to be…
Totally asymmetric simple exclusion processes (TASEP) with particles which occupy more than one lattice site and with a local inhomogeneity far away from the boundaries are investigated. These non-equilibrium processes are relevant for the…
We investigate the dynamics of a nonlinear model for tumor growth within a cellular medium. In this setting the "tumor" is viewed as a multiphase flow consisting of cancerous cells in either proliferating phase or quiescent phase and a…
Strong experimental evidence has indicated that tumor growth belongs to the molecular beam epitaxy universality class. This type of growth is characterized by the constraint of cell proliferation to the tumor border, and surface diffusion…
Phase separation drives the formation of biomolecular condensates in cells, which comprise many components and sometimes possess multiple phases. The equilibrium physics of phase separation is well understood, but many components in…
The intratumor heterogeneity has been recognized to characterize cancer cells impairing the efficacy of cancer treatments. We here propose an extension of constraint-based modeling approach in order to simulate metabolism of cell…
Mechanical interactions among cells in a growing microbial colony can significantly influence the colony's spatial genetic structure and, thus, evolutionary outcomes such as the fates of rare mutations. Here, we computationally investigate…
Recent studies have suggested a new phase in the extended Bose-Hubbard model in one dimension at integer filling [1,2]. In this work, we show that this new phase is phase-separated into a supersolid and superfluid part, generated by…
This paper introduces NN-STNE, a neural network using t-distributed stochastic neighbor embedding (t-SNE) as a hidden layer to reduce input dimensions by mapping long time-series data into shapelet membership probabilities. A Gaussian…
We deal with a small enough tumor section to consider it homogeneous, such that populations of lymphocytes and cancer cells are independent of spatial coordinates. A stochastic model based in one step processes is developed to take into…
Analysis of invasion front has been widely used to decipher biological properties, as well as the growth dynamics of the corresponding populations. Likewise, the invasion front of tumors has been investigated, from which insights into the…
Tissue self-organization into defined and well-controlled three-dimensional structures is essential during development for the generation of organs. A similar, but highly deranged process might also occur during the aberrant growth of…
Proliferation and motility are ubiquitous drivers of activity in biological systems. Here, we study a dense binary mixture of motile and proliferating particles with exclusively repulsive interactions, where homeostasis in the proliferating…
Phase segregation, the process by which the components of a binary mixture spontaneously separate, is a key process in the evolution and design of many chemical, mechanical, and biological systems. In this work, we present a data-driven…
The coordination of the immune system and its components is essential for the body to maintain a healthy status. Recent clinical studies show that breast cancer patients with high Dendritic cell clustering in tumour draining lymph nodes…
We have extended our previously developed 3D multi-scale agent-based brain tumor model to simulate cancer heterogeneity and to analyze its impact across the scales of interest. While our algorithm continues to employ an epidermal growth…
t-SNE is one of the most commonly used force-based nonlinear dimensionality reduction methods. This paper has two contributions: the first is forceful colorings, an idea that is also applicable to other force-based methods (UMAP,…
The totally asymmetric simple exclusion process (TASEP) is a paradigmatic stochastic model for non-equilibrium physics, and has been successfully applied to describe active transport of molecular motors along cytoskeletal filaments.…
A fundamental task in machine learning involves visualizing high-dimensional data sets that arise in high-impact application domains. When considering the context of large imbalanced data, this problem becomes much more challenging. In this…
This paper presents an interesting experimental example of voter-model statistics in biology. In recent work on mouse tail-skin, where proliferating cells are confined to a two-dimensional layer, we showed that cells proliferate and…