Related papers: Spatial structure facilitates evolutionary rescue …
Unlike coffee and cream that homogenize when stirred, growing micro-organisms (e.g., bacteria, baker's yeast) can actively kill each other and avoid mixing. How do such antagonistic interactions impact the growth and survival of competing…
Antimicrobial resistance (AMR) poses a significant threat to public health by increasing mortality, extending hospital stays, and increasing healthcare costs. It affects people of all ages and affects health services, veterinary medicine,…
Variations of transport efficiency in structured environments between distinct individuals in actively self-propelled systems is both hard to study and poorly understood. Here, we study the transport of a non-tumbling {\ecoli} strain, an…
Background: Microbiota have evolved to acclimate themselves to many environments. Humanity is become ever increasingly medicated and many of those medications are antibiotics. Sadly, Microbiota are adapting to medication and with each…
We analyze evolutionary dynamics in a confluent, branching cellular population, such as in a growing duct, vasculature, or in a branching microbial colony. We focus on the coarse-grained features of the evolution and build a statistical…
We study evolutionary processes induced by spatio-temporal dynamics in prebiotic evolution. Using numerical simulations we demonstrate that hypercycles emerge from complex interaction structures in multispecies systems. In this work we also…
In microbial communities, each species often has multiple, distinct phenotypes, but studies of ecological stability have largely ignored this subpopulation structure. Here, we show that such implicit averaging over phenotypes leads to…
The evolution of drug resistance in HIV occurs by the fixation of specific, well-known, drug-resistance mutations, but the underlying population genetic processes are not well understood. By analyzing within-patient longitudinal sequence…
Bacterial communities such as biofilms are widely recognised as being important for survival and persistence of bacteria in harsh environments. Mechanistic models of biofilm growth indicate that the way in which the surface is seeded can…
The mutual influence of dynamics and structure is a central issue in complex systems. In this paper we study by simulation slow evolution of network under the feedback of a local-majority-rule opinion process. If performance-enhancing local…
Environmental heterogeneity can drive genetic heterogeneity in expanding populations; mutant strains may emerge that trade overall growth rate for an improved ability to survive in patches that are hostile to the wild type. This…
Spatial metapopulation models are fundamental to theoretical ecology, enabling to study how landscape structure influences global species dynamics. Traditional models, including recent generalizations, often rely on the deterministic limit…
Studying exoplanet atmospheres is essential for assessing their potential to host liquid water and their capacity to support life (their habitability). Each atmosphere uniquely influences the likelihood of surface liquid water, defining the…
Autocatalysis is thought to have played an important role in the earliest stages of the origin of life. An autocatalytic cycle (AC) is a set of reactions that results in stoichiometric increase in its constituent chemicals. When the…
We study a general setting of neutral evolution in which the population is of finite, constant size and can have spatial structure. Mutation leads to different genetic types ("traits"), which can be discrete or continuous. Under minimal…
Understanding of the evolutionary origins of protein structures represents a key component of the understanding of molecular evolution as a whole. Here we seek to elucidate how the features of an underlying protein structural "space" might…
Collective behavior of bacterial colonies plays critical roles in adaptability, survivability, biofilm expansion and infection. We employ an individual-based model of an interstitial biofilm to study emergent pattern formation based on the…
The sustainable use of multicomponent treatments such as combination therapies, combination vaccines/chemicals, and plants carrying multigenic resistance requires an understanding of how their population-wide deployment affects the speed of…
We use fitness graphs, or directed cube graphs, for analyzing evolutionary reversibility. The main application is antimicrobial drug resistance. Reversible drug resistance has been observed both clinically and experimentally. If drug…
Robustness of spatial pattern against perturbations is an indispensable property of developmental processes for organisms, which need to adapt to changing environments. Although specific mechanisms for this robustness have been extensively…