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Computational simulations have the potential to assist in liver resection surgeries by facilitating surgical planning, optimizing resection strategies, and predicting postoperative outcomes. The modeling of liver tissue across multiple…
We extend the formulation of position-based rods to include elastic volumetric deformations. We achieve this by introducing an additional degree of freedom per vertex -- isotropic scale (and its velocity). Including scale enriches the space…
Aerotaxis is the particular form of chemotaxis in which oxygen plays the role of both the attractant and the repellent. Aerotaxis occurs without methylation adaptation, and it leads to fast and complete aggregation toward the most favorable…
Polycrystalline materials undergoing coarsening can be represented as evolving networks of grain boundaries, whose statistical characteristics determine macroscopic materials properties. The process of formation of various statistical…
Although deep learning models have had great success in natural language processing and computer vision, we do not observe comparable improvements in the case of tabular data, which is still the most common data type used in biological,…
There are numerous scenarios in which populations of cells migrate in crowded environments. Typical examples include wound healing, cancer growth and embryo development. In these crowded environments cells are able to interact with each…
Local field potentials (LFPs) sampled with extracellular electrodes are frequently used as a measure of population neuronal activity. However, relating such measurements to underlying neuronal behaviour and connectivity is non-trivial. To…
Rule-based modeling is a powerful way to model kinetic interactions in biochemical systems. Rules enable a precise encoding of biochemical interactions at the resolution of sites within molecules, but obtaining an integrated global view…
Phospholipidic membranes and vesicles constitute a basic element in real biological functions. Vesicles are viewed as a model system to mimic basic viscoelastic behaviors of some cells, like red blood cells. Phase field and level-set models…
Vertical Federated Learning (VFL) is a privacy-preserving collaborative learning paradigm that enables multiple parties with distinct feature sets to jointly train machine learning models without sharing their raw data. Despite its…
We introduce a new nonlinear model for classification, in which we model the joint distribution of response variable, y, and covariates, x, non-parametrically using Dirichlet process mixtures. We keep the relationship between y and x linear…
In vivo and in vitro cells rely on the support of an underlying biocompatible substrate, such as the extracellular matrix or a culture substrate, to spread and proliferate. The mechanical and chemical properties of such structures play a…
Experiments and theory have shown that cell monolayers and epithelial tissues exhibit solid-liquid and glass-liquid transitions. These transitions are biologically relevant to our understanding of embryonic development, wound healing, and…
Animals use past experiences to adapt future behavior. To enable this rapid learning, vertebrates and invertebrates have evolved analogous neural structures like the vertebrate cerebellum or insect mushroom body. A defining feature of these…
Relationships in scientific data, such as the numerical and spatial distribution relations of features in univariate data, the scalar-value combinations' relations in multivariate data, and the association of volumes in time-varying and…
Multiphase systems are ubiquitous in engineering, biology, and materials science, where understanding their complex interactions and rheological behavior is crucial for advancing applications ranging from emulsion stability to cellular…
Under an externally applied load, granular packings form force chains that depend on the contact network and moduli of the grains. In this work, we investigate packings of variable modulus (VM) particles, where we can direct force chains by…
Motile biological cells in tissue often display the phenomenon of durotaxis, i.e. they tend to move towards stiffer parts of substrate tissue. The mechanism for this behavior is not completely understood. We consider simplified models for…
In this paper, we derive an effective macroscale description suitable to describe the growth of biological tissue within a porous tissue-engineering scaffold. As in our recent work (Holden \textit{et al.} "A multiphase multiscale model for…
Fluid deformable surfaces are ubiquitous in cell and tissue biology, including lipid bilayers, the actomyosin cortex, or epithelial cell sheets. These interfaces exhibit a complex interplay between elasticity, low Reynolds number…