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We investigate a two-dimensional system of active Brownian dumbbells using molecular dynamics simulations. In this model, each dumbbell is driven by an active force oriented perpendicular to the axis connecting its two constituent beads. We…
Background: The evolution of microRNA regulation in metazoans is a mysterious process: MicroRNA sequences are highly conserved among distal organisms, but on the other hand, there is no evident conservation of their targets. Results: We…
We examine immunostaining experimental data for the formation of the strip 2 of $even-skipped$ ($eve$) transcripts on $D.$ $melanogaster$ embryos. An estimate of the factor converting immunofluorescence intensity units into molecular…
We present a technique to characterize differentially expressed genes in terms of their position in a high-dimensional co-expression network. The set-up of Gaussian graphical models is used to construct representations of the co-expression…
Gene networks exhibiting oscillatory dynamics are widespread in biology. The minimal regulatory designs giving rise to oscillations have been implemented synthetically and studied by mathematical modeling. However, most of the available…
An analytic reversible Hamiltonian system with two degrees of freedom is studied in a neighborhood of its symmetric heteroclinic connection made up of a symmetric saddle-center, a symmetric orientable saddle periodic orbit lying in the same…
Biological motor control provides highly effective solutions to difficult control problems in spite of the complexity of the plant and the significant delays in sensory feedback . Such delays are expected to lead to non trivial stability…
The persistence of life requires populations to adapt at a rate commensurate with the dynamics of their environment. Successful populations that inhabit highly variable environments have evolved mechanisms to increase the likelihood of…
Polar patterns and topological defects are ubiquitous in active matter. In this paper, we study a paradigmatic polar active dumbbell system through numerical simulations, to clarify how polar patterns and defects emerge and shape evolution.…
A fundamental problem in protobiological dynamics is to understand how chemically generated polymers can form persistent sequence distributions before the emergence of replication. We study deterministic polymer growth in which each finite…
Steering vectors offer a training-free mechanism for controlling reasoning behaviors in large language models, but constructing effective vectors requires identifying genuine behavioral signals in the model's hidden states. For behaviors…
In a recent article [Vetter and Iber, Nat. Commun. 13, 1145 (2022)], we demonstrated that single morphogen gradients in the developing mouse neural tube can carry sufficient positional accuracy to explain the patterning precision of…
Convergent extension of epithelial tissue is a key motif of animal morphogenesis. On a coarse scale, cell motion resembles laminar fluid flow; yet in contrast to a fluid, epithelial cells adhere to each other and maintain the tissue layer…
Organisms are equipped with regulatory systems that display a variety of dynamical behaviours ranging from simple stable steady states, to switching and multistability, to oscillations. Earlier work has shown that oscillations in protein…
In this contribution, a design of a synthetic calibration genetic circuit to characterize the relative strength of different sensing promoters is proposed and its specifications and performance are analyzed via an effective mathematical…
During early development, the establishment of gradients of transcriptional factors determines the patterning of cell fates. The case of Bicoid (Bcd) in {\it Drosophila melanogaster} embryos is well documented and studied. There are still…
A repressilator consists of a loop made up of three repressively interacting genes. We construct a hexagonal lattice with repressilators on each triangle, and use this as a model system for multiple interacting feedback loops. Using…
Ring topologies of repressing genes have qualitatively different long-term dynamics if the number of genes is odd (they oscillate) or even (they exhibit bistability). However, these attractors may not fully explain the observed behavior in…
Mitosis in the early syncytial Drosophila embryo is highly correlated in space and time, as manifested in mitotic wavefronts that propagate across the embryo. In this paper we investigate the idea that the embryo can be considered a…
High auditory sensitivity, sharp frequency selectivity, and otoacoustic emissions are signatures of active amplification of the cochlea. The human ear can also detect very large amplitude sound without being damaged as long as the exposed…