相关论文: Fold or die: experimental evolution in vitro
We study the adaptation dynamics of an initially maladapted population evolving via the elementary processes of mutation and selection. The evolution occurs on rugged fitness landscapes which are defined on the multi-dimensional genotypic…
One of the outstanding challenges in comparative genomics is to interpret the evolutionary importance of regulatory variation between species. Rigorous molecular evolution-based methods to infer evidence for natural selection from…
An important problem in evolutionary genomics is to investigate whether a certain trait measured on each sample is associated with the sample phylogenetic tree. The phylogenetic tree represents the shared evolutionary history of the samples…
It has recently been suggested that the fundamental haploid-diploid cycle of eukaryotic sex exploits a rudimentary form of the Baldwin effect. Thereafter the other associated phenomena can be explained as evolution tuning the amount and…
Living species, ranging from bacteria to animals, exist in environmental conditions that exhibit spatial and temporal heterogeneity which requires them to adapt. Risk-spreading through spontaneous phenotypic variations is a known concept in…
The optimal mixing evolutionary algorithms (OMEAs) have recently drawn much attention for their robustness, small size of required population, and efficiency in terms of number of function evaluations (NFE). In this paper, the performances…
This short paper presents an abstract, tunable model of genomic structural change within the cell lifecycle and explores its use with simulated evolution. A well-known Boolean model of genetic regulatory networks is extended to include…
Fluorescence spectroscopy is a fundamental tool in life sciences and chemistry, widely used for applications such as environmental monitoring, food quality control, and biomedical diagnostics. However, analysis of spectroscopic data with…
One of the important questions in biological evolution is to know if certain changes along protein coding genes have contributed to the adaptation of species. This problem is known to be biologically complex and computationally very…
Biological and social systems are structured at multiple scales, and the incentives of individuals who interact in a group may diverge from the collective incentive of the group as a whole. Mechanisms to resolve this tension are responsible…
The use of evolutionary methods in design and art is increasing in diversity and popularity. Approaches to using these methods for creative production typically focus either on optimisation or exploration. In this paper we introduce an…
This computational study introduces a theoretical framework for practical, electrochemical fuel generation displaying exponential product yields as functions of time. Exponential reaction scaling is simulated through an autocatalytic cycle…
Coevolution is expected to follow two alternative dynamics, often called trench warfare and arms races in plant-pathogen systems. Trench warfare situations are stable cycles of allele frequencies at the coevolving loci of both host and…
Evolutionary Algorithms (EAs) are widely used general-purpose optimization methods due to their domain independence. However, under a limited number of function evaluations (#FEs), the performance of EAs is quite sensitive to the quality of…
Physics-informed neural networks (PINNs) are neural networks that embed the laws of dynamical systems modeled by differential equations into their loss function as constraints. In this work, we present a PINN framework applied to oncology.…
Living systems can be understood as organized entities that capture, transform, and reproduce information. Classical gene-centered models explain adaptation through frequency changes driven by differential fitness, yet they often overlook…
This study proposes MCEMOL (Multi-Constrained Evolutionary Molecular Design Framework), a molecular optimization approach integrating rule-based evolution with molecular crossover. MCEMOL employs dual-layer evolution: optimizing…
From the point of view of statistical mechanics, a full characterisation of a molecular system requires the experimental determination of its possible states, their populations and the respective interconversion rates. Well-established…
Experimental evolution has yielded surprising insights into human history and evolution by shedding light on the roles of chance and contingency in history and evolution, and on the deep evolutionary roots of cooperation, conflict and kin…
The evolution processes of complex systems carry key information in the systems' functional properties. Applying machine learning algorithms, we demonstrate that the historical formation process of various networked complex systems can be…