Related papers: Physical constraints on epistasis
We suggest to simulate evolution of complex organisms constrained by the sole requirement of robustness in their expression patterns. This scenario is illustrated by evolving discrete logical networks with epigenetic properties. Evidence…
Rigidity is an emergent property of materials - it is not a feature of individual components that comprise the structure, but instead arises from interactions between many constituent parts. Recently, it has been recognized that…
An elastic spring network is an example of evolvable matter. It can be pruned to couple separated pairs of nodes so that when a strain is applied to one of them, the other responds either in-phase or out-of-phase. This produces two pruned…
The existence of the {\em typical set} is key for data compression strategies and for the emergence of robust statistical observables in macroscopic physical systems. Standard approaches derive its existence from a restricted set of…
The interconnected processes of protein folding, mutations, epistasis, and evolution have all been the subject of extensive analysis throughout the years due to their significance for structural and evolutionary biology. The origin…
Collective decision-making arises from individual agents integrating their own personal observations with information obtained from social partners. In many biological systems that exhibit collective decision-making, the process by which…
Evolution occurs in populations of reproducing individuals. The structure of a biological population affects which traits evolve. Understanding evolutionary game dynamics in structured populations is difficult. Precise results have been…
One of the most challenging problems in microbiology is to understand how a small fraction of microbes that resists killing by antibiotics can emerge in a population of genetically identical cells, the phenomenon known as persistence or…
Epistatic interactions between residues determine a protein's adaptability and shape its evolutionary trajectory. When a protein experiences a changed environment, it is under strong selection to find a peak in the new fitness landscape. It…
We consider the effect of network structure on the evolution of a population. Models of this kind typically consider a population of fixed size and distribution. Here we consider eco-evolutionary dynamics where population size and…
The natural impedance, or dynamic relationship between force and motion, of a human operator can determine the stability of exoskeletons that use interaction-torque feedback to amplify human strength. While human impedance is typically…
Evolution has fascinated quantitative and physical scientists for decades: how can the random process of mutation, recombination, and duplication of genetic information generate the diversity of life? What determines the rate of evolution?…
We generalize the particle-conserving dynamics method of de las Heras et al. [J. Phys. Condens. Matter: 28, 24404 (2016).] to binary mixtures and apply this to hard rods in one dimension. Considering the case of one species consisting of…
The role of the selection pressure and mutation amplitude on the behavior of a single-species population evolving on a two-dimensional lattice, in a periodically changing environment, is studied both analytically and numerically. The…
Most of the DNA that composes a complex organism is non-coding and defined as junk. Even the coding part is composed of genes that affect the phenotype differently. Therefore, a random mutation has an effect on the specimen fitness that…
Ecosystems tend to fluctuate around stable equilibria in response to internal dynamics and environmental factors. Occasionally, they enter an unstable tipping region and collapse into an alternative stable state. Our understanding of how…
Fitness landscapes provide a quantitative framework for understanding how natural selection shapes evolutionary trajectories. A central feature of these landscapes is their number of local optima, which determines whether fitness-increasing…
Our recent interest is focused on establishing the necessary and sufficient conditions that guarantee a long-term stable evolution of both natural and artificial systems. Two necessary conditions, called global and local boundedness, are…
The sequence of a protein is not only constrained by its physical and biochemical properties under current selection, but also by features of its past evolutionary history. Understanding the extent and the form that these evolutionary…
Understanding the stability of complex communities is a central focus in ecology, many important theoretical advancements have been made to identify drivers of ecological stability. However, previous results often rely on the…