Related papers: Some mathematical tools for the Lenski experiment
We use the lac operon in Escherichia coli as a prototype system to illustrate the current state, applicability, and limitations of modeling the dynamics of cellular networks. We integrate three different levels of description -molecular,…
We propose a stochastic model for evolution. Births and deaths of species occur with constant probabilities. Each new species is associated with a fitness sampled from the uniform distribution on [0,1]. Every time there is a death event…
The ability to absorb mutations while retaining structure and function, or mutational robustness, is a remarkable property of natural proteins. In this Letter, we use a computational model of organismic evolution [Zeldovich et al, PLOS Comp…
Time evolution of number of species (genera, families, and others), population of them, and size distribution of present ones and life times are studied in terms of a new model, where population of each genetic taxon increases by a (random)…
We report a new system of artificial life called Lenia (from Latin lenis "smooth"), a two-dimensional cellular automaton with continuous space-time-state and generalized local rule. Computer simulations show that Lenia supports a great…
In an ecological context, panel data arise when time series measurements are made on a collection of ecological processes. Each process may correspond to a spatial location for field data, or to an experimental ecosystem in a designed…
Growing living cultures of Escherichia coli bacteria were investigated using real-time in situ rheology and rheo-imaging measurements. In the early stages of growth (lag phase), and when subjected to a constant stationary shear, the…
In this report, I will review some of the most used models in theoretical ecology along with appealing reformulations and recent results in terms of diversity, stability, and functioning of large well-mixed ecological communities.
100 years after Smoluchowski introduces his approach to stochastic processes, they are now at the basis of mathematical and physical modeling in cellular biology: they are used for example to analyse and to extract features from large…
Cell growth and gene expression, essential elements of all living systems, have long been the focus of biophysical interrogation. Advances in single-cell methods have invigorated theoretical studies into these processes. However, until…
Ecological and evolutionary dynamics have been historically regarded as unfolding at broadly separated timescales. However, these two types of processes are nowadays well documented to much more tightly than traditionally assumed,…
Large language models (LLMs) are stochastic, and not all models give deterministic answers, even when setting temperature to zero with a fixed random seed. However, few benchmark studies attempt to quantify uncertainty, partly due to the…
In a series of recent papers and in a book, this author put forward a mathematical model capable of embracing the search for extra-terrestrial intelligence (SETI), Darwinian Evolution and Human History into a single, unified statistical…
For the model of periodic chronic myelogenous leukemia considered by Pujo-Menjouet, Mackey et al., model consisting of two delay differential equations, the equation for the density of so-called "resting cells" was studied from numerical…
Reproducibility is imperative for any scientific discovery. More often than not, modern scientific findings rely on statistical analysis of high-dimensional data. At a minimum, reproducibility manifests itself in stability of statistical…
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…
Statistical systems are conceived from the standpoint of statistical mechanics, as made of a (generally large) number of identical units and exhibiting a (generally large) number of different configurations (microstates), among which only…
Central to the artificial life endeavour is the creation of artificial systems spontaneously generating properties found in the living world such as autopoiesis, self-replication, evolution and open-endedness. While numerous models and…
Biological cells replicate their genomes in a well-planned manner. The DNA replication program of an organism determines the timing at which different genomic regions are replicated, with fundamental consequences for cell homeostasis and…
The original Kelly criterion provides a strategy to maximize the long-term growth of winnings in a sequence of simple Bernoulli bets with an edge, that is, when the expected return on each bet is positive. The objective of this work is to…