Related papers: OxDNA to study species interactions
Network science has become an essential interdisciplinary tool for understanding complex biological systems. However, because these systems undergo continuous, often stimulus-driven changes in both structure and function, traditional static…
Standard models of population dynamics focus on the the interaction, survival, and extinction of the competing species individually. Real ecological systems, however, are characterized by an abundance of species (or strategies, in the…
We analyze a stylized model of co-evolution between any two purely competing species (e.g., host and parasite), both sexually reproducing. Similarly to a recent model of Livnat \etal~\cite{evolfocs14} the fitness of an individual depends on…
Models in evolutionary game theory traditionally assume symmetric interactions in homogeneous environments. Here, we consider populations evolving in a heterogeneous environment, which consists of patches of different qualities that are…
Although networks provide a powerful approach to study a large variety of ecological systems, their formulation does not typically account for multiple interaction types, interactions that vary in space and time, and interconnected systems…
Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution…
The structure of molecular networks derives from dynamical processes on evolutionary time scales. For protein interaction networks, global statistical features of their structure can now be inferred consistently from several…
A central and long-standing issue in evolutionary theory is the origin of the biological variation upon which natural selection acts1. Some hypotheses suggest that evolutionary change represents an adaptation to the surrounding environment…
Developing physics-based models for molecular simulation requires fitting many unknown parameters to diverse experimental datasets. Traditionally, this process is piecemeal and difficult to reproduce, leading to a fragmented landscape of…
Ecological models traditionally explain stability and coexistence through pairwise interactions among species. These interactions can also involve groups of three or more species, higher-order interactions, which recent theory suggests can…
Evolutionary dynamics is often viewed as a subtle process of change accumulation that causes a divergence among organisms and their genomes. However, this interpretation is an inheritance of a gradualistic view that has been challenged at…
Ecologists have long suspected that species are more likely to interact if their traits match in a particular way. For example, a pollination interaction may be more likely if the proportions of a bee's tongue fit a plant's flower shape.…
Along with recent progress in structural biology and genome biology, structural dynamics of molecular systems including nucleic acids has attracted attention in the context of gene regulation. Structure-function relationship is an important…
The analysis of live-cell single-molecule imaging experiments can reveal valuable information about the heterogeneity of transport processes and interactions between cell components. These characteristics are seen as motion changes in the…
Molecular dynamics simulations are often used to provide feedback in the design workflow of DNA nanostructures. However, even with coarse-grained models, convergence of distributions from unbiased simulation is slow, limiting applications…
This research paper delves into the dynamics of a novel ecology model that describes the intricate interplay between radioactivity and cancer cases. Organized into three main sections, the study covers numerical analysis using advanced…
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…
Does an ecological community allow stable coexistence? Identifying the general principles that determine the answer to this question is a central problem of theoretical ecology. Random matrix theory approaches have uncovered the general…
Semi-empirical molecular dynamics is used to simulate several gaseous atomic hydrogen interactions with hydrocarbon grains in space: recoil, adsorption, diffusion, chemisorption and recombination into molecular hydrogen. Their probabilities…
If one isolated species (corporation) is supposed to evolve following the logistic mapping, then we are tempted to think that the dynamics of two species (corporations) can be expressed by a coupled system of two discrete logistic…