Related papers: The two-clock problem in population dynamics
We describe a continuous-time modelling framework for biological population dynamics that accounts for demographic noise. In the spirit of the methodology used by statistical physicists, transitions between the states of the system are…
We study the evolution of a population in a two-locus genotype space, in which the negative effects of two single mutations are overcompensated in a high fitness double mutant. We discuss how the interplay of finite population size, $N$,…
Using a lattice model based on Monte Carlo simulations, we study the role of the reproduction pattern on the fate of an evolving population. Each individual is under the selection pressure from the environment and random mutations. The…
Evolutionary Robotics offers the possibility to design robots to solve a specific task automatically by optimizing their morphology and control together. However, this co-optimization of body and control is challenging, because controllers…
There are many natural, physical, and biological systems that exhibit multiple time scales. For example, the dynamics of a population of ticks can be described in continuous time during their individual life cycle yet discrete time is used…
A calculus based on pointer-mark coincidences is proposed to define, in a mathematically rigorous way, measurements of space and time intervals. The connection between such measurements in different inertial frames according to the Galilean…
The Lorentzian length of a timelike curve connecting both endpoints of a classical computation is a function of the path taken through Minkowski spacetime. The associated runtime difference is due to time-dilation: the phenomenon whereby an…
Owing to the analogies between the problem of wealth redistribution with taxation in a multi-agent society, we introduce and discuss a kinetic model describing the statistical distributions in time of the sizes of groups of biological…
Epigenetics is the study of how people's behavior and environments influence the way their genes are expressed, even though their DNA sequence is itself unchanged. By aggregating age-related epigenetic markers, epigenetic 'clocks' have…
Optimization and expansion are two modes of staged evolution of complex systems where macroscopic observables change at a decreasing, respectively increasing, rate. A prime example of evolutionary expansion, Gross Domestic Product (GDP)…
In exponential population growth, variability in the timing of individual division events and environmental factors (including stochastic inoculation) compound to produce variable growth trajectories. In several stochastic models of…
Linkage disequilibrium (LD) is often summarized using the "LD curve," which relates the LD between pairs of sites to the distance that separates them along the chromosome. This paper shows how the LD curve responds to changes in population…
Explaining the wide range of dynamics observed in ecological communities is challenging due to the large number of species involved, the complex network of interactions among them, and the influence of multiple environmental variables.…
We describe the simulation method of modelling the population evolution using Monte Carlo based on the Penna model. Individuals in the populations are represented by their diploid genomes. Genes expressed after the minimum reproduction age…
The population protocol model describes collections of distributed agents that interact in pairs to solve a common task. We consider a dynamic variant of this prominent model, where we assume that an adversary may change the population size…
Population dynamics on a rugged landscape is studied analytically and numerically within a simple discrete model for evolution of N individuals in one-dimensional fitness space. We reduce the set of master equations to a single Fokker-Plank…
Mutations can arise from the chance misincorporation of nucleotides during DNA replication or from DNA lesions that are not repaired correctly. We introduce a model that relates the source of mutations to their accumulation with cell…
Since steep declines in a population's size also typically alter its composition, population bottlenecks are considered highly important for evolution. However, despite such significance, the mechanisms governing the impact of a given…
Many single-cell observables are highly heterogeneous. A part of this heterogeneity stems from age-related phenomena: the fact that there is a nonuniform distribution of cells with different ages. This has led to a renewed interest in…
Generative models trained on finite data face a fundamental tension: their score-matching or next-token objective converges to the empirical training distribution rather than the population distribution we seek to learn. Using rule-valid…