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Various multicellular tissues show chiral morphology. Experimental studies have shown this can originate from cell chirality. However, no theory has been proposed to connect the cellular chiral torque and multicellular chiral morphogenesis.…

Fluorescence microscopy has led to impressive quantitative models and new insights gained from richer sets of biomedical imagery. However, there is a dearth of rigorous and established bioimaging strategies for modeling spatiotemporal…

Analyzing the temporal behavior of nodes in time-varying graphs is useful for many applications such as targeted advertising, community evolution and outlier detection. In this paper, we present a novel approach, STWalk, for learning…

Vesicles are becoming a quite popular model for the study of red blood cells (RBCs). This is a free boundary problem which is rather difficult to handle theoretically. Quantitative computational approaches constitute also a challenge. In…

Statistical and mathematical modeling are crucial to describe, interpret, compare and predict the behavior of complex biological systems including the organization of hematopoietic stem and progenitor cells in the bone marrow environment.…

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…

Graph-based techniques emerged as a choice to deal with the dimensionality issues in modeling multivariate time series. However, there is yet no complete understanding of how the underlying structure could be exploited to ease this task.…

The dynamics of flexible filaments entrained in flow, important for understanding many biological and industrial processes, are computationally expensive to model with full-physics simulations. This work describes a data-driven technique to…

We present a continuum model trained on molecular dynamics (MD) simulations for cellular membranes composed of an arbitrary number of lipid types. The model is constructed within the formalism of dynamic density functional theory and can be…

Different cell types aggregate and sort into hierarchical architectures during the formation of animal tissues. The resulting spatial organization depends (in part) on the strength of adhesion of one cell type to itself relative to other…

Cell migration, which is strictly regulated by intracellular and extracellular cues, is crucial for normal physiological processes and the progression of certain diseases. However, there is a lack of an efficient approach to analyze…

Time series modeling has attracted extensive research efforts; however, achieving both reliable efficiency and interpretability from a unified model still remains a challenging problem. Among the literature, shapelets offer interpretable…

The morphogenesis of cells and tissues involves an interplay between chemical signals and active forces on their surrounding surface layers. The complex interaction of hydrodynamics and material flows on such active surfaces leads to…

Neural networks for structured data like graphs have been studied extensively in recent years. To date, the bulk of research activity has focused mainly on static graphs. However, most real-world networks are dynamic since their topology…

Adhesion-independent migration is a prominent mode of cell motility in confined environments, yet the physical principles that guide such movement remain incompletely understood. We present a phase-field model for simulating the motility of…

In biology, cells undergo deformations under the action of flow caused by the fluid surrounding them. These flows lead to shape changes and instabilities that have been explored in detail for single component vesicles. However, cell…

We develop an agent-based model of the motion and pattern formation of vesicles. These intracellular particles can be found in four different modes of (undirected and directed) motion and can fuse with other vesicles. While the size of…

Temporal graphs represent the dynamic relationships among entities and occur in many real life application like social networks, e commerce, communication, road networks, biological systems, and many more. They necessitate research beyond…

During epithelial-mesenchymal transition (EMT), epithelial cells change their morphology, disperse, and gain mesenchymal-like characteristics. Usually, cells are categorized into discrete cell types or states based on gene expression and…

Dynamic graphs are common in real-world systems such as social media, recommender systems, and traffic networks. Existing dynamic graph models for link prediction often fall short in capturing the complexity of temporal evolution. They tend…