Related papers: OxDNA to study species interactions
A review of the mechanisms of speciation is performed. The mechanisms of the evolution of species, taking into account the feedback of the state of the environment and mechanisms of the emergence of complexity, are considered. It is shown…
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…
How large ecosystems can create and maintain the remarkable biodiversity we see in nature is probably one of the biggest open questions in science, attracting attention from different fields, from Theoretical Ecology to Mathematics and…
Numerous cellular functions rely on protein$\unicode{x2013}$protein interactions. Efforts to comprehensively characterize them remain challenged however by the diversity of molecular recognition mechanisms employed within the proteome. Deep…
Local coexistence of species in large ecosystems is traditionally explained within the broad framework of niche theory. However, its rationale hardly justifies rich biodiversity observed in nearly homogeneous environments. Here we consider…
The specificity of molecular recognition is important to molecular self-organization. A prominent example is the biological cell where, within a highly crowded molecular environment, a myriad of different molecular receptor pairs recognize…
DNA-interacting proteins have roles multiple processes, many operating as molecular machines which undergo dynamic metastable transitions to bring about their biological function. To fully understand this molecular heterogeneity, DNA and…
In molecular phylogeny, relationships among organisms are reconstructed using DNA or protein sequences and are displayed as trees. A linear increase in the number of sequences results in an exponential increase of possible trees. Thus,…
All living systems can function only far away from equilibrium, and for this reason chemical kinetic methods are critically important for uncovering the mechanisms of biological processes. Here we present a new theoretical method of…
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?…
Competitive interactions represent one of the driving forces behind evolution and natural selection in biological and sociological systems. For example, animals in an ecosystem may vie for food or mates; in a market economy, firms may…
Protein-DNA interactions are vital for many processes in living cells, especially transcriptional regulation and DNA modification. To further our understanding of these important processes on the microscopic level, it is necessary that…
Understanding the behaviors of ecological systems is challenging given their multi-faceted complexity. To proceed, theoretical models such as Lotka-Volterra dynamics with random interactions have been investigated by the dynamical…
For the outcomes and phenotypes of complex diseases, multiple types of molecular (genetic, genomic, epigenetic, etc.) changes, environmental risk factors, and their interactions have been found to have important contributions. In each of…
Protein-DNA interactions are critical for the successful functioning of all natural systems. The key role in these interactions is played by processes of protein search for specific sites on DNA. Although it has been studied for many years,…
Understanding the mechanisms that govern species coexistence and biodiversity represents a fundamental challenge in ecology. This study extends the classic rock-paper-scissors model by introducing a context-dependent higher-order…
Classical models for competition between two species usually predict exclusion or divergent evolution of resource exploitation. However, recent experimental data show that coexistence is possible for very similar species competing for the…
Relations among species in ecosystems can be represented by complex networks where both negative (competition) and positive (mutualism) interactions are concurrently present. Recently, it has been shown that many ecosystems can be cast into…
This paper demonstrates that simple yet important characteristics of coevolution can occur in evolutionary algorithms when only a few conditions are met. We find that interaction-based fitness measurements such as fitness (linear) ranking…
Ecosystems are formed by networks of species and their interactions. Traditional models of such interactions assume a constant interaction strength between a given pair of species. However, there is often significant trait variation among…