Related papers: Emergence simulation of cell-like morphologies wit…
To survive in ever-changing environments, living organisms need to continuously combine the ongoing external inputs they receive, representing present conditions, with their dynamical internal state, which includes influences of past…
There is increasing interest in the analysis of biological tissue, its organization and its dynamics with the help of mathematical models. In the ideal case emergent properties on the tissue scale can be derived from the cellular scale.…
Many systems involve numerous interacting parts and the whole system can have properties that the individual parts do not. I take this novelty as the defining characteristic of an emergent property. Other characteristics associated with…
The fundamental understanding of how cells physically interact with each other and their environment is key to understanding their organisation in living tissues. Over the past decades several computational methods have been developed to…
Due to recent advances in synthetic biology and artificial life, the origin of life is currently a hot topic of research. We review the literature and argue that the two traditionally competing "replicator-first" and "metabolism-first"…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
Essential life processes take place across multiple space and time scales in living organisms but understanding their mechanistic interactions remains an ongoing challenge. Advanced multiscale modeling techniques are providing new…
We describe a 3D percolation-type approach to modeling of the processes of aging and certain other properties of tissues analyzed as systems consisting of interacting cells. Lattice sites are designated as regular (healthy) cells, senescent…
Cellular life requires the presence of a set of biochemical mechanisms in order to maintain a predictable process of growth and division. Several attempts have been made towards the building of minimal protocells from a top-down approach,…
Microscopic models of reaction-diffusion processes on the cell membrane can link local spatiotemporal effects to macroscopic self-organized patterns often observed on the membrane. Simulation schemes based on the microscopic lattice method…
Deriving emergent patterns from models of biological processes is a core concern of mathematical biology. In the context of partial differential equations (PDEs), these emergent patterns sometimes appear as local minimisers of a…
Protocells are supposed to have played a key role in the self-organizing processes leading to the emergence of life. Existing models either (i) describe protocell architecture and dynamics, given the existence of sets of collectively…
Understanding the mechanisms of interactions within cells, tissues, and organisms is crucial to driving developments across biology and medicine. Mathematical modeling is an essential tool for simulating biological systems and revealing…
To unveil the logic of cell from a level of chemical reaction dynamics, we need to clarify how ensemble of chemicals can autonomously produce the set of chemical, without assuming a specific external control echanism. A cell consists of a…
The simulation of morphogenetic problems requires the simultaneous and coupled simulation of signalling and tissue dynamics. A cellular resolution of the tissue domain is important to adequately describe the impact of cell-based events,…
Active systems across scales, ranging from molecular machines to human crowds, are usually modeled as assemblies of self-propelled particles driven by internally generated forces. However, these models often assume memoryless dynamics and…
It is well known that life on Earth alters its environment over evolutionary and geological timescales. An important open question is whether this is a result of evolutionary optimization or a universal feature of life. In the latter case,…
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…
The interactions between diffusing molecules and membrane-bound receptors drive numerous cellular processes. In this work, we develop a spatial model of molecular interactions with membrane receptors by homogenizing the cell membrane and…
A great number of biological organisms live in aqueous environments. Major evolutionary transitions, including the emergence of life itself, likely occurred in such environments. While the chemical aspects of the role of water in biology…