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The method of averaging is used to investigate the phenomenon of capture into resonance for a model that describes a Keplerian binary system influenced by radiation damping and external normally incident periodic gravitational radiation.…
We propose a model that explains the hierarchical organization of proteins in fold families. The model, which is based on the evolutionary selection of proteins by their native state stability, reproduces patterns of amino acids conserved…
The preclinical stage of many neurodegenerative diseases can span decades before symptoms become apparent. Understanding the sequence of preclinical biomarker changes provides a critical opportunity for early diagnosis and effective…
The automatic design of robots has existed for 30 years but has been constricted by serial non-differentiable design evaluations, premature convergence to simple bodies or clumsy behaviors, and a lack of sim2real transfer to physical…
Despite the greater functional importance of protein levels, our knowledge of gene expression evolution is based almost entirely on studies of mRNA levels. In contrast, our understanding of how translational regulation evolves has lagged…
Observations of glassy dynamics in experiments on confluent cellular tissue have inspired a wealth of computational and theoretical research to model their emergent collective behavior. Initial studies of the physical properties of several…
Single-cell gene expression measurements encode variability spanning molecular noise, cell-to-cell heterogeneity, and technical artifacts. Mechanistic stochastic models provide powerful approaches to disentangle these sources, yet inferring…
A key problem in computational biology is discovering the gene expression changes that regulate cell fate transitions, in which one cell type turns into another. However, each individual cell cannot be tracked longitudinally, and cells at…
Previous research using evolutionary computation in Multi-Agent Systems indicates that assigning fitness based on team vs.\ individual behavior has a strong impact on the ability of evolved teams of artificial agents to exhibit teamwork in…
We present a model of the evolution of control systems in a genome under environmental constraints. The model conceptually follows the Jacob and Monod model of gene control. Genes contain control elements which respond to the internal state…
A substantial body of research has focused on developing systems that assist medical professionals during labor-intensive early screening processes, many based on convolutional deep-learning architectures. Recently, multiple studies…
The two most fundamental processes describing change in biology, development and evolu-tion, occur over drastically different timescales, difficult to reconcile within a unified framework. Development involves temporal sequences of cell…
A self-adaptive system can modify its own structure and behavior at runtime based on its perception of the environment, of itself and of its requirements. To develop a self-adaptive system, software developers codify knowledge about the…
Eco-evolutionary dynamics, or eco-evolution for short, are thought to involve rapid demography (ecology) and equally rapid phenotypic changes (evolution) leading to novel, emergent system behaviours. This focus on contemporary dynamics is…
Self-organisation of individuals within large collectives occurs throughout biology. Mathematical models can help elucidate the individual-level mechanisms behind these dynamics, but analytical tractability often comes at the cost of…
Animals often exhibit changes in their behavior during migration. Telemetry data provide a way to observe geographic position of animals over time, but not necessarily changes in the dynamics of the movement process. Continuous-time models…
We investigate the evolutionary dynamics of an age-structured population under weak frequency-dependent selection. It turns out that the weak selection is affected in a non-trivial way by the life-history trait. We can disentangle the…
In many clustering scenes, data samples' attribute values change over time. For such data, we are often interested in obtaining a partition for each time step and tracking the dynamic change of partitions. Normally, a smooth change is…
Textual analysis of typical microbial genomes reveals that they have the statistical characteristics of a DNA sequence of a much shorter length. This peculiar property supports an evolutionary model in which a genome evolves by random…
Cell division timing is critical for cell fate specification and morphogenesis during embryogenesis. How division timings are regulated among cells during development is poorly understood. Here we focus on the comparison of asynchrony of…