Related papers: Simulating short- and long-term evolutionary dynam…
The regulation of a gene depends on the binding of transcription factors to specific sites located in the regulatory region of the gene. The generation of these binding sites and of cooperativity between them are essential building blocks…
Evolution depends on the possibility of successfully exploring fitness landscapes via mutation and recombination. With these search procedures, exploration is difficult in "rugged" fitness landscapes, where small mutations can drastically…
Cellular differentiation and evolution are stochastic processes that can involve multiple types (or states) of particles moving on a complex, high-dimensional state-space or "fitness" landscape. Cells of each specific type can thus be…
The natural evolution of life seems to proceed through steps characterized by phases of relatively rapid changes, followed by longer, more stable periods. In the light of the string-theory derived physical scenario proposed in [1], we…
We introduce a new model of evolution on a fitness landscape possessing a tunable degree of neutrality. The model allows us to study the general properties of molecular species undergoing neutral evolution. We find that a number of…
We explore the connection between evolution and large-deviation theory. To do so, we study evolutionary dynamics in which individuals experience mutations, reproduction, and selection using variants of the Moran model. We show that, in the…
A model for the evolution of a finite population in a rugged fitness landscape is introduced and solved. The population is trapped in an evolutionary loop, alternating periods of stasis to periods in which it performs adaptive walks. The…
Although there are some real world applications where the use of variable length representation (VLR) in Evolutionary Algorithm is natural and suitable, an academic framework is lacking for such representations. In this work we propose a…
Emergence is a phenomenon taken for granted in science but also still not well understood. We have developed a model of artificial genetic evolution intended to allow for emergence on genetic, population and social levels. We present the…
Punctuated equilibrium is a mode of evolution in which phenetic change occurs in rapid bursts that are separated by much longer intervals of stasis during which mutations accumulate but no major phenotypic change occurs. Punctuated…
We study the evolution of asexual microorganisms with small mutation rate in fluctuating environments, and develop techniques that allow us to expand the formal solution of the evolution equations to first order in the mutation rate. Our…
We consider the optimal dynamics in the infinite population evolution models with general symmetric fitness landscape. The search of optimal evolution trajectories are complicated due to sharp transitions (like shock waves) in evolution…
Highly-diverse ecosystems exhibit a broad distribution of population sizes and species turnover, where species at high and low abundances are exchanged over time. We show that these two features generically emerge in the fluctuating phase…
What features characterise complex system dynamics? Power laws and scale invariance of fluctuations are often taken as the hallmarks of complexity, drawing on analogies with equilibrium critical phenomena[1-3]. Here we argue that slow,…
We propose a physical model for developmental process at cellular level to discuss the mechanism of epigenetic landscape. In our simplified model, a minimal model, the network of the interaction among cells generates the landscape…
Evolving systems, be it an antibody repertoire in the face of mutating pathogens or a microbial population exposed to varied antibiotics, constantly search for adaptive solutions in time-varying fitness landscapes. Generalists correspond to…
Evolution is simultaneously driven by a number of processes such as mutation, competition and random sampling. Understanding which of these processes is dominating the collective evolutionary dynamics in dependence on system properties is a…
The accumulation of beneficial mutations on many competing genetic backgrounds in rapidly adapting populations has a striking impact on evolutionary dynamics. This effect, known as clonal interference, causes erratic fluctuations in the…
A common view in evolutionary biology is that mutation rates are minimised. However, studies in combinatorial optimisation and search have shown a clear advantage of using variable mutation rates as a control parameter to optimise the…
Understanding the interplay among processes that occur over different timescales is a challenging issue in the physics of systems regulation. In gene regulation, the timescales for changes in chromatin states can differ from those for…