Related papers: OxDNA to study species interactions
This work proposes to model the space environment as a stochastic dynamic network where each node is a group of objects of a given class, or species, and their relationship is represented by stochastic links. A set of stochastic dynamic…
A fundamental design rule that nature has developed for biological machines is the intimate correlation between motion and function. One class of biological machines is molecular motors in living cells, which directly convert chemical…
We develop a set of equations to describe the population dynamics of many interacting species in food webs. Predator-prey interactions are non-linear, and are based on ratio-dependent functional responses. The equations account for…
Recent work draws attention to community-community encounters ("coalescence") as likely an important factor shaping natural ecosystems. This work builds on MacArthur's classic model of competitive coexistence to investigate such…
Genetic information and environmental factors determine the path of an individuals life and therefore, the evolution of its entire species. We have succeeded in proposing and studying a model that captures this idea. In our model, a…
Understanding the stability of complex communities is a central focus in ecology, many important theoretical advancements have been made to identify drivers of ecological stability. However, previous results often rely on the…
Evolutionary algorithms have been widely applied for solving dynamic constrained optimization problems (DCOPs) as a common area of research in evolutionary optimization. Current benchmarks proposed for testing these problems in the…
The entanglement of population dynamics, evolution, and adaptive radiation for species competing for resources is studied. For resource harvesting, we modify the model used in Ref. Phys. Rev. Lett. 118 048103 and introduce new resource…
Modeling environmental ecosystems is essential for effective resource management, sustainable development, and understanding complex ecological processes. However, traditional methods frequently struggle with the inherent complexity,…
Highly specific spatiotemporal interactions between cognate molecular partners essentially sustain all biochemical transactions in the living matter. That such an exquisite level of accuracy may result from encountering forces solely driven…
It is known that the competitive exclusion principle holds for a large kind of models involving several species competing for a single resource in an homogeneous environment. Various works indicate that the coexistence is possible in an…
Geographic ranges of communities of species evolve in response to environmental, ecological, and evolutionary forces. Understanding the effects of these forces on species' range dynamics is a major goal of spatial ecology. Previous…
Phase separation has emerged as an essential concept for the spatial organization inside biological cells. However, despite the clear relevance to virtually all physiological functions, we understand surprisingly little about what phases…
By creating networks of biochemical pathways, communities of micro-organisms are able to modulate the properties of their environment and even the metabolic processes within their hosts. Next-generation high-throughput sequencing has led to…
In a mathematical model of interacting biological organisms, where external interventions may alter behavior over time, traditional models that assume fixed parameters usually do not capture the evolving dynamics. In oncology, this is…
In this study, we intend to solve a mutual information problem in interacting molecules of any type, such as proteins, nucleic acids, and small molecules. Using machine learning techniques, we accurately predict pairwise interactions, which…
This short paper presents an abstract, tunable model of genomic structural change within the cell lifecycle and explores its use with simulated evolution. A well-known Boolean model of genetic regulatory networks is extended to include…
Cyclic, nonhierarchical interactions among biological species represent a general mechanism by which ecosystems are able to maintain high levels of biodiversity. However, species coexistence is often possible only in spatially extended…
We discuss three different aspects of the quantum dynamics of bio-molecular systems and more generally complex networks in the presence of strongly coupled environments. Firstly, we make a case for the systematic study of fundamental…
The construction of a network of cell-to-cell contacts makes it possible to characterize the patterns and spatial organisation of tissues. Such networks are highly dynamic, depending on the changes of the tissue architecture caused by cell…