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Diatoms are microscopic algae found in all of Earths water courses. They produce frustules, porous silica exoskeletons, grown by precipitation of silicic acid from water. Frustule components, known as girdles, from some diatom species also…
We measure different contributions to entropy production in a living functional epithelial tissue. We do this by extracting the functional dynamics of development while at the same time quantifying fluctuations. Using the translucent…
Voronoi diagrams appear in many areas in science and technology and have numerous applications. They have been the subject of extensive investigation during the last decades. Roughly speaking, they are a certain decomposition of a given…
Seeds of sunflowers are often modelled by the map $n\longmapsto \varphi_\theta(n)=\sqrt{n}e^{2i\pi n\theta}$ leading to a roughly uniform repartition with two consecutive seeds separated by the divergence angle $2\pi\theta$ for $\theta$ the…
Cells exhibit qualitatively different behaviors on substrates with different rigidities. The fact that cells are more polarized on the stiffer substrate motivates us to construct a two-dimensional cell with the distribution of focal…
The protein folding problem must ultimately be solved on all length scales from the atomic up through a hierarchy of complicated structures. By analyzing the stability of the folding process using physics and mathematics, this paper shows…
An oritatami system (OS) is a theoretical model of self-assembly via co-transcriptional folding. It consists of a growing chain of beads which can form bonds with each other as they are transcribed. During the transcription process, the…
The topology of large scale structure is studied as a function of galaxy type using the genus statistic. In hydrodynamical cosmological CDM simulations, galaxies form on caustic surfaces (Zeldovich pancakes) then slowly drain onto filaments…
A foliation on a manifold M can be informally thought of as a partition of M into injectively immersed submanifolds, called leaves. In this thesis we study foliations whose leaves carry some specific geometric structures. The thesis…
Numerous cell-types have shown a remarkable ability to detect and move along gradients in stiffness of an underlying substrate -- a process known as durotaxis. The mechanisms underlying durotaxis are still unresolved, but generally believed…
Biological cells are able to adapt their behaviour in response to environmental cues. Durotaxis is a phenomenon in which cells adjust their migration depending on the mechanical properties of a surrounding substrate. Although durotaxis has…
Green algae of the $Volvocine$ lineage, spanning from unicellular $Chlamydomonas$ to vastly larger $Volvox$, are models for the study of the evolution of multicellularity, flagellar dynamics, and developmental processes. Phototactic…
Phototaxis is an important reaction to light displayed by a wide range of motile microorganisms. Flagellated eukaryotic microalgae in particular, like the model organism Chlamydomonas reinhardtii, steer either towards or away from light by…
The epitaxy of MoO2 on c_plane sapphire substrates is examined. A theoretical approach, based on density functional theory calculations of the strain energy, allowed to predict the preferred layer/substrate epitaxial relationships. To test…
Phylogenetics is a widely used concept in evolutionary biology. It is the reconstruction of evolutionary history by building trees that represent branching patterns and sequences. These trees represent shared history, and it is our…
A geophylogeny is a phylogenetic tree (or dendrogram) where each leaf (e.g. biological taxon) has an associated geographic location (site). To clearly visualize a geophylogeny, the tree is typically represented as a crossing-free drawing…
Phylogenetic networks are becoming of increasing interest to evolutionary biologists due to their ability to capture complex non-treelike evolutionary processes. From a combinatorial point of view, such networks are certain types of rooted…
Certain bacteria form filamentous colonies when the cells fail to separate after dividing. In Bacillus subtilis, Bacillus thermus, and cyanobacteria, the filaments can wrap into complex supercoiled structures as the cells grow. The…
Recent experiments suggest that the interplay between cells and the mechanics of their substrate gives rise to a diversity of morphological and migrational behaviors. Here, we develop a Cellular Potts Model of polarizing cells on a…
The purpose of this paper is to present a model of a phenomenon of plant stem morphogenesis observed by Cesar Gomez-Campo in 1970. We consider a simplified model of auxin dynamics in plant stems, showing that, after creation of the original…