Related papers: OxDNA to study species interactions
Modern biological tools have made it possible to unequivocally demonstrate the deep relationship among species in terms of genes and basic molecular mechanisms. In addition, results from genetic, physical and physiological approaches…
This paper is concerned with a mathematical model of competition for resource where species consume noninteracting resources. This system of differential equations is formally obtained by renormalizing the MacArthur's competition model at…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…
Coexistence of individuals with different species or phenotypes is often found in nature in spite of competition between them. Stable coexistence of multiple types of individuals have implications for maintenance of ecological biodiversity…
Proteins play crucial roles in every cellular process by interacting with each other, with nucleic acids, metabolites, and other molecules. The resulting assemblies can be very large and intricate and pose challenges to experimental…
Gene regulation is one of the most important fundamental biological processes in living cells. It involves multiple protein molecules that locate specific sites on DNA and assemble gene initiation or gene repression multi-molecular…
Explaining biodiversity in nature is a fundamental problem in ecology. An outstanding challenge is embodied in the so-called Competitive Exclusion Principle: two species competing for one limiting resource cannot coexist at constant…
Evolutionary and ecosystem dynamics are often treated as different processes --operating at separate timescales-- even if evidence reveals that rapid evolutionary changes can feed back into ecological interactions. A recent long-term field…
Ecological systems are emergent features of ecological and adaptive dynamics of a community of interacting species. By natural selection through the abiotic environment and by co-adaptation within the community, species evolve, thereby…
The main topic of this thesis is the analysis of evolution equations reflecting issues in ecology and population dynamics. In mathematical modelling, the impact of environmental elements and the interaction between species is read into the…
Empirical observations show that ecological communities can have a huge number of coexisting species, also with few or limited number of resources. These ecosystems are characterized by multiple type of interactions, in particular…
Empirical observations show that ecological communities can have a huge number of coexisting species, also with few or limited number of resources. These ecosystems are characterized by multiple type of interactions, in particular…
Quantitative predictions about the processes that promote species coexistence are a subject of active research in ecology. In particular, competitive interactions are known to shape and maintain ecological communities, and situations where…
A fundamental problem in ecology is to understand how competition shapes biodiversity and species coexistence. Historically, one important approach for addressing this question has been to analyze consumer resource models using geometric…
Mutualistic networks are formed when the interactions between two classes of species are mutually beneficial. They are important examples of cooperation shaped by evolution. Mutualism between animals and plants plays a key role in the…
Protein-DNA interactions are crucial for all biological processes. One of the most important fundamental aspects of these interactions is the process of protein searching and recognizing specific binding sites on DNA. A large number of…
Understanding the rules underlying organismal development is a major unsolved problem in biology. Each cell in a developing organism responds to signals in its local environment by dividing, excreting, consuming, or reorganizing, yet how…
In an ecological context, panel data arise when time series measurements are made on a collection of ecological processes. Each process may correspond to a spatial location for field data, or to an experimental ecosystem in a designed…
In this review we focus on the idea of establishing connections between the mechanical properties of DNAligand complexes and the physical chemistry of DNA-ligand interactions. This type of connection is interesting because it opens the…
Ecological systems comprise an astonishing diversity of species that cooperate or compete with each other forming complex mutual dependencies. The minimum requirements to maintain a large species diversity on long time scales are in general…