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How do living cells achieve sufficient abundances of functional protein complexes while minimizing promiscuous non-functional interactions? Here we study this problem using a first-principle model of the cell whose phenotypic traits are…
Traditionally evolution is seen as a process where from a pool of possible variations of a population (e.g. biological species or industrial goods) a few variations get selected which survive and proliferate, whereas the others vanish.…
Metabolic networks consist of linked functional components, or modules. The mechanism underlying metabolic network modularity is of great interest not only to researchers of basic science but also to those in fields of engineering. Previous…
The folding pathway and rate coefficients of the folding of a knotted protein are calculated for a potential energy function with minimal energetic frustration. A kinetic transition network is constructed using the discrete path sampling…
The fitness landscape metaphor plays a central role on the modeling of optimizing principles in many research fields, ranging from evolutionary biology, where it was first introduced, to management research. Here we consider the ensemble of…
Several growth models have been proposed in the literature for scale-free complex networks, with a range of fitness-based attachment models gaining prominence recently. However, the processes by which such fitness-based attachment behaviour…
Regulatory networks consist of interacting molecules with a high degree of mutual chemical specificity. How can these molecules evolve when their function depends on maintenance of interactions with cognate partners and simultaneous…
Complex systems often exhibit highly structured network topologies that reflect functional constraints. In this work, we investigate how, under varying combinations of system-wide selection rules and special agents, different classes of…
We study a recent model of random networks based on the presence of an intrinsic character of the vertices called fitness. The vertices fitnesses are drawn from a given probability distribution density. The edges between pair of vertices…
Emergent patterns in complex systems are related to many intriguing phenomena in modern science and philosophy. Several conceptions such as weak, strong and robust emergence have been proposed to emphasize different epistemological and…
We propose a new mechanism leading to scale-free networks which is based on the presence of an intrinsic character of a vertex called fitness. In our model, a vertex $i$ is assigned a fitness $x_i$, drawn from a given probability…
Biological evolution of a population is governed by the fitness landscape, which is a map from genotype to fitness. However, a fitness landscape depends on the organisms environment, and evolution in changing environments is still poorly…
We consider the problem of growing multiplex networks with intrinsic fitness and inter-layer coupling. The model comprises two layers; one that incorporates fitness and another in which attachments are preferential. In the first layer,…
In recent years, Evolutionary Algorithms (EAs) have frequently been adopted to evolve instances for optimization problems that pose difficulties for one algorithm while being rather easy for a competitor and vice versa. Typically, this is…
During their evolution, proteins explore sequence space via an interplay between random mutations and phenotypic selection. Here we build upon recent progress in reconstructing data-driven fitness landscapes for families of homologous…
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…
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…
A geometric analysis of the global properties of the energy landscape of a minimalistic model of a polypeptide is presented, which is based on the relation between dynamical trajectories and geodesics of a suitable manifold, whose metric is…
We find an advantage of recombination for a category of complex fitness landscapes. Recent studies of empirical fitness landscapes reveal complex gene interactions and multiple peaks, and recombination can be a powerful mechanism for…
We develop a general method to explore how the function performed by a biological network can constrain both its structural and dynamical network properties. This approach is orthogonal to prior studies which examine the functional…