Related papers: Quasispecies Theory for Evolution of Modularity
Constraints on changes in expression levels across all cell components imposed by the steady growth of cells have recently been discussed both experimentally and theoretically. By assuming a small environmental perturbation and considering…
If two species exhibit different nonlinear responses to a single shared resource, and if each species modifies the resource dynamics such that this favors its competitor, they may stably coexist. This coexistence mechanism, known as…
We study the intermittent fluorescence of a single molecule, jumping from the "light on" to the "light off" state, as a Poisson process modulated by a fluctuating environment. We show that the quasi-periodic and quasi-deterministic…
We study self-replicating molecules under externally varying conditions. Changing conditions such as temperature variations and/or alterations in the environment's resource composition lead to both non-constant replication and decay rates…
A stochastic system under the influence of a stochastic environment is correlated with both present and future states of the environment. Such a system can be seen as implicitly implementing a predictive model of future environmental…
Naturally evolving proteins gradually accumulate mutations while continuing to fold to thermodynamically stable native structures. This process of neutral protein evolution is an important mode of genetic change, and forms the basis for the…
A population evolving in an inhomogeneous environment will adapt differently to different regions. We study the conditions under which such a population can maintain adaptations to a particular region when that region is not stationary, but…
Frequency-dependent selection reflects the interaction between different species as they battle for limited resources in their environment. In a stochastic evolutionary game the species relative fitnesses guides the evolutionary dynamics…
This paper introduces a novel approach to quantifying ecological resilience in biological systems, particularly focusing on noisy systems responding to episodic disturbances with sudden adaptations. Incorporating concepts from…
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…
An integro-differential model for evolutionary dynamics with mutations is investigated by improving the understanding of its behavior using numerical simulations. The proposed numerical approach can handle also density dependent fitness,…
Biological networks have evolved to be highly functional within uncertain environments while remaining extremely adaptable. One of the main contributors to the robustness and evolvability of biological networks is believed to be their…
By generalizing a class of models recently introduced to account for protracted transients in biological systems, we identify a novel mechanism for hyperuniformity. In this model, competition of particles over a shared resource guides the…
Recent research has extended methods from the fields of thermodynamics and statistical mechanics into other disciplines. Most notably, one recent work creates a unified theoretical framework to understand evolutionary biology, machine…
The adaptation rate in theoretical models of biological evolution increases with the mutation rate but only to a point when mutations into lethal states cause extinction. One would expect that removing such states should be beneficial for…
We examine the feasibility of predicting and subsequently managing the future evolution of a Complex Adaptive System. Our archetypal system mimics a competitive population of mechanical, biological, informational or human objects. We show…
We analyse the effect of intrinsic fluctuations on the properties of bistable stochastic systems with time scale separation operating under1 quasi-steady state conditions. We first formulate a stochastic generalisation of the quasi-steady…
We demonstrate with a thought experiment that fitness-based population dynamical approaches to evolution are not able to make quantitative, falsifiable predictions about the long-term behavior of evolutionary systems. A key characteristic…
We extend our study of a simple model of biological coevolution to its statistical properties. Staring with a complete description in terms of a master equation, we provide its relation to the deterministic evolution equations used in…
Microbial ecosystems are commonly modeled by fixed interactions between species in steady exponential growth states. However, microbes often modify their environments so strongly that they are forced out of the exponential state into…