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Living biological tissue is a complex system, constantly growing and changing in response to external and internal stimuli. These processes lead to remarkable and intricate changes in shape. Modeling and understanding both natural and…
During embryonic development tissue morphogenesis and signaling are tightly coupled. It is therefore important to simulate both tissue morphogenesis and signaling simultaneously in in silico models of developmental processes. The resolution…
The propagation of signalling molecules within cellular networks is affected by network topology, but also by the spatial arrangement of cells in the networks. Understanding the collective reaction--diffusion behaviour in space of signals…
In evolutionary game theory, it is customary to be partial to the dynamical models possessing fixed points so that they may be understood as the attainment of evolutionary stability, and hence, Nash equilibrium. Any show of periodic or…
Organogenesis involves large deformations and complex shape changes that require elaborate mechanical regulation. Models of tissue biomechanics have been introduced to account for the coupling between mechanical response and biochemical…
Models in evolutionary game theory traditionally assume symmetric interactions in homogeneous environments. Here, we consider populations evolving in a heterogeneous environment, which consists of patches of different qualities that are…
Evolution and development operate at different timescales; generations for the one, a lifetime for the other. These two processes, the basis of much of life on earth, interact in many non-trivial ways, but their temporal hierarchy --…
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…
This paper deals with the simulateneous optimization of a subset $\mathcal{O}_0$ of some domain $\Omega$ and its complement $\mathcal{O}_1 = \Omega \setminus \overline{\mathcal{O}}_0$ both considered as separate elastic objects subject to a…
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…
The dynamic interplay between collective cell movement and the various molecules involved in the accompanying cell signalling mechanisms plays a crucial role in many biological processes including normal tissue development and pathological…
Genome-scale stoichiometric modeling of metabolism has become a standard systems biology tool for modeling cellular physiology and growth. Extensions of this approach are also emerging as a valuable avenue for predicting, understanding and…
Results of experimental investigation are presented of evolutionary dynamics of several stochastic pattern formation and growth models designed by modifications of the famous mathematical Game of Life. The modifications are two-fold: Game…
This paper presents the principal challenges and opportunities associated with computational biomechanics research. The underlying cognitive control involved in the process of human motion is inherently complex, dynamic, multidimensional,…
Theoretical models of neuronal function consider different mechanisms through which networks learn, classify and discern inputs. A central focus of these models is to understand how associations are established amongst neurons, in order to…
The surface morphology of the developing mammalian brain is crucial for understanding brain function and dysfunction. Computational modeling offers valuable insights into the underlying mechanisms for early brain folding. Recent findings…
This paper presents a computational model of the processing of dynamic spatial relations occurring in an embodied robotic interaction setup. A complete system is introduced that allows autonomous robots to produce and interpret dynamic…
Understanding the dynamic nature of protein structures is essential for comprehending their biological functions. While significant progress has been made in predicting static folded structures, modeling protein motions on microsecond to…
Spatial omics has transformed our understanding of tissue architecture by preserving spatial context of gene expression patterns. Simultaneously, advances in imaging AI have enabled extraction of morphological features describing the…
The building of mathematical and computer models of cities has a long history. The core elements are models of flows (spatial interaction) and the dynamics of structural evolution. In this article, we develop a stochastic model of urban…