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How do mammalian cells that share the same genome exist in notably distinct phenotypes, exhibiting differences in morphology, gene expression patterns, and epigenetic chromatin statuses? Furthermore how do cells of different phenotypes…
The mechanisms of infant development are far from understood. Learning about one's own body is likely a foundation for subsequent development. Here we look specifically at the problem of how spontaneous touches to the body in early infancy…
The growth of cities has traditionally been studied from a population perspective, while urban expansion-its spatial growth-has often been approached qualitatively. However, characterizing and modeling this spatial expansion is crucial,…
Mathematical and computational models can assist in gaining an understanding of cell behavior at many levels of organization. Here, we review models in the literature that focus on eukaryotic cell motility at 3 size scales: intracellular…
We examine a variety of numerical methods that arise when considering dynamical systems in the context of physics-based simulations of deformable objects. Such problems arise in various applications, including animation, robotics, control…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
Biological networks have evolved to be highly functional within uncertain environments while remaining extremely adaptable. One of the main contributors to the robustness and evolvability of biological networks is believed to be their…
In order to gain a mechanistic understanding of how tinnitus emerges in the brain, we must build biologically plausible computational models that mimic both tinnitus development and perception, and test the tentative models with brain and…
Statistical mechanics determines the abundance of different arrangements of matter depending on cost-benefit balances. Its formalism and phenomenology percolate throughout biological processes and set limits to effective computation. Under…
Mathematical Modelling has a long history in developmental biology. Advances in experimental techniques and computational algorithms now permit the development of increasingly more realistic models of organogenesis. In particular, 3D…
Bristle-bots are legged robots that can be easily made out of a toothbrush head and a small vibrating engine. Despite their simple appearance, the mechanism enabling them to propel themselves by exploiting friction with the substrate is far…
An intriguing unanswered question about the evolution of bilateral animals with internal skeletons is how an internal skeleton evolved in the first place. Computational modeling of the development of bilateral symmetric organisms suggests…
Biological functions are generated as a result of developmental dynamics that form phenotypes governed by genotypes. The dynamical system for development is shaped through genetic evolution following natural selection based on the fitness…
A novel theory for cell differentiation is proposed, based on simulations with interacting artificial cells which have metabolic networks within, and divide into two when the final product is accumulated. Results of simulations with coupled…
Large language models (LLMs) frequently make errors when handling even simple numerical problems, such as comparing two small numbers. A natural hypothesis is that these errors stem from how LLMs represent numbers, and specifically, whether…
Digital logic forms the functional basics of most modern electronic equipment and as such the creation of novel digital logic circuits is an active area of computer engineering research. This study demonstrates that genetic algorithms can…
A remarkable phenomenon in the time evolution of many networks such as cultural, political, national and economic systems, is the recurrent transition between the states of union and division of nodes. In this work, we propose a…
Ordinary differential equation models are nowadays widely used for the mechanistic description of biological processes and their temporal evolution. These models typically have many unknown and non-measurable parameters, which have to be…
The explosive growth of large language models (LLMs) has created a vast but opaque landscape: millions of models exist, yet their evolutionary relationships through fine-tuning, distillation, or adaptation are often undocumented or unclear,…
Formal modelling provides a toolkit for understanding cultural dynamics, from individual decisions to recurring patterns of change. This chapter explains what models are and why they matter. Using a precise, shared language, they aid…