Related papers: In silico transitions to multicellularity
Cells with the same genome can exist in different phenotypes. and can change between distinct phenotypes when subject to specific stimuli and microenvironments. Some examples include cell differentiation during development, reprogramming…
Across biological subdisciplines, the last decade has seen an explosion of high-dimensional datasets, including datasets for cells, species, immune systems, neurons and behaviour. At the ICTS workshop 'Unifying Theories in High-Dimensional…
An invitation to simulation is made into a realizable challenge: the reader is taken from scratch to games with words, to mathematical models, to statistical analysis, to simulation of evolution. No special requirements are needed: we work…
The nucleation of crystals in liquids is one of nature's most ubiquitous phenomena, playing an important role in areas such as climate change and the production of drugs. As the early stages of nucleation involve exceedingly small time and…
Cell deformability is an essential determinant for tissue-scale mechanical nature, such as fluidity and rigidity, and is thus crucial for understanding tissue homeostasis and stable developmental processes. However, numerical simulations…
We explain how hierarchical organization of biological systems emerges naturally during evolution, through a transition in the units of individuality. We will show how these transitions are the result of competing selective forces operating…
Several bacteria and bacteria strands form biofilms in different environmental conditions, e.g. pH, temperature, nutrients, etc. Biofilm growth, therefore, is an extremely robust process. Because of this, while biofilm growth is a complex…
Biological organisms adapt to changes by processing informations from different sources, most notably from their ancestors and from their environment. We review an approach to quantify these informations by analyzing mathematical models of…
The evolution of multicellularity was a major transition in the history of life on earth. Conditions under which multicellularity is favored have been studied theoretically and experimentally. But since the construction of a multicellular…
Dynamics maintaining diversity of cell types in a multi-cellular system are studied in relationship with the plasticity of cellular states. First, we introduce a new theoretical framework, reaction-diffusion system on `chemical species…
Metabolic pathways describe chains of enzymatic reactions. Their modelling is a key point to understand living systems. An enzymatic reaction is an interaction between one or several metabolites (substrates) and an enzyme (simple protein or…
It is still not understood how similar genomic sequences have generated diverse and spectacular forms during evolution. The difficulty to bridge phenotypes and genotypes stems from the complexity of multicellular systems, where thousands of…
Biological systems, from a cell to the human brain, are inherently complex. A powerful representation of such systems, described by an intricate web of relationships across multiple scales, is provided by complex networks. Recently, several…
A theoretical study of cell evolution is presented here. By using a toolbox containing an intracellular catalytic reaction network model and a mutation-selection process, four distinct phases of self-organization were unveiled. First, the…
A modeling formalism is proposed for the description and study of living and life-like systems. It provides an abstract conceptual model framework for real life and evolution of biological organisms. It is proposed, that this model…
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…
We use complexity theory to rigorously investigate the difficulty of classically simulating evolution under many-body localized (MBL) Hamiltonians. Using the defining feature that MBL systems have a complete set of quasilocal integrals of…
Many real-world complex systems are best modeled by multiplex networks of interacting network layers. The multiplex network study is one of the newest and hottest themes in the statistical physics of complex networks. Pioneering studies…
Advances in molecular technologies underlie an enormous growth in the size of data sets pertaining to biology and biomedicine. These advances parallel those in the deep learning subfield of machine learning. Components in the differentiable…
In bacterial populations, cells are able to cooperate in order to yield complex collective functionalities. Interest in population-level cellular behaviour is increasing, due to both our expanding knowledge of the underlying biological…