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The applicability of computational and dynamical systems models to organisms is scrutinized, using examples from developmental biology and cognition. Developmental morphogenesis is dependent on the inherent material properties of developing…
Cellular bioelectricity describes the biological phenomenon in which cells in living tissue generate and maintain patterns of voltage gradients induced by differing concentrations of charged ions. A growing body of research suggests that…
In the fields of computation and neuroscience, much is still unknown about the underlying computations that enable key cognitive functions including learning, memory, abstraction and behavior. This paper proposes a mathematical and…
Growth patterns generated by filamentous organisms (e.g. actinomycetes and fungi) involve spatial and temporal dynamics at different length scales. Several mathematical models have been proposed in the last thirty years to address these…
Biomaterials are becoming an essential tool in the study and application of stem cell research. Various types of biomaterials enable three-dimensional (3D) culture of stem cells, and, more recently, also enable high-resolution patterning…
Mounting evidence shows that oscillatory activity is widespread in cell signaling. Here we review some of this recent evidence, focusing on both the molecular mechanisms that potentially underlie such dynamical behavior, and the potential…
We simulate the electrical response of multiple disjoint biological 3D cells undergoing an electropermeabilization process. Instead of solving the boundary value problem in the unbounded volume, we reduce it to a system of boundary…
Recent developments in lipid membrane models for simulations are reviewed. To reduce computational costs, various coarse-grained molecular models have been proposed. Among them, implicit solvent (solvent-free) molecular models are…
Our knowledge of how individual cells self-organize to form complex multicellular systems is being revolutionized by a data outburst, coming from high-throughput experimental breakthroughs such as single-cell RNA sequencing and spatially…
A cell is polarised when it has developed a main axis of organisation through the reorganisation of its cytosqueleton and its intracellular organelles. Polarisation can occur spontaneously or be triggered by external signals, like gradients…
Modeling cellular states and predicting their responses to perturbations are central challenges in computational biology and the development of virtual cells. Existing foundation models for single-cell transcriptomics provide powerful…
Determining the different conformational states of a protein and the transition paths between them is key to fully understanding the relationship between biomolecular structure and function. This can be accomplished by sampling protein…
We consider the problem of modeling, estimating, and controlling the latent state of a spatiotemporally evolving continuous function using very few sensor measurements and actuator locations. Our solution to the problem consists of two…
We develop a simple computational model for cell boundary evolution in plastic deformation. We study the cell boundary size distribution and cell boundary misorientation distribution that experimentally have been found to have scaling forms…
Signal processing traditionally relies on classical statistical modeling techniques. Such model-based methods utilize mathematical formulations that represent the underlying physics, prior information and additional domain knowledge. Simple…
We construct a homogeneous, nonlinear elastic constitutive law, that models aspects of the mechanical behavior of inhomogeneous fibrin networks. Fibers in such networks buckle when in compression. We model this as a loss of stiffness in…
Spatial agent-based models are increasingly used to investigate the evolution of solid tumours subject to localised cell-cell interactions and microenvironmental heterogeneity. Here we present a non-technical step by step guide to…
Computer simulations are an important tool for studying the mechanics of biological evolution. In particular, in silico work with agent-based models provides an opportunity to collect high-quality records of ancestry relationships among…
This paper introduces a continuous model for Multi-cellular Developmental Design. The cells are fixed on a 2D grid and exchange "chemicals" with their neighbors during the growth process. The quantity of chemicals that a cell produces, as…
Cells in natural environments like tissue or soil sense and respond to extracellular ligands with intricately structured and non-monotonic spatial distributions that are sculpted by processes such as fluid flow and substrate adhesion.…