Related papers: Embryonic Pattern Scaling Achieved by Oppositely D…
Shape transformations of epithelial tissues in three dimensions, which are crucial for embryonic development or in vitro organoid growth, can result from active forces generated within the cytoskeleton of the epithelial cells. How the…
Position determination in biological systems is often achieved through protein concentration gradients. Measuring the local concentration of such a protein with a spatially-varying distribution allows the measurement of position within the…
Self-organized pattern formation is vital for many biological processes. Reaction-diffusion models have advanced our understanding of how biological systems develop spatial structures, starting from homogeneity. However, biological…
Understanding the spatial organisation of the genome in the cell nucleus is one of the current grand challenges in biophysics. Certain biochemical -- or epigenetic -- marks that are deposited along the genome are thought to play an…
The quantitative description of marine systems is constrained by a major issue of scale separation: most marine biochemical processes occur at sub-centimeter scales, while the contribution to the Earth's biogeochemical cycles is expressed…
A common developmental process, called branching morphogenesis, generates the epithelial trees in a variety of organs, including the lungs, kidneys, and glands. How branching morphogenesis can create epithelial architectures of very…
We consider a free boundary problem for a system of PDEs, modeling the growth of a biological tissue. A morphogen, controlling volume growth, is produced by specific cells and then diffused and absorbed throughout the domain. The geometric…
The problem is solved of describing scale factors of a homogeneous isotropic spaces-time such that the exact solution for the scalar field with a nonconformal coupling to curvature can be obtained from solutions for the conformally coupled…
Gene expression levels carry information about signals that have functional significance for the organism. Using the gap gene network in the fruit fly embryo as an example, we show how this information can be decoded, building a dictionary…
Current state-of-the-art generative models map noise to data distributions by matching flows or scores. A key limitation of these models is their inability to readily integrate available partial observations and additional priors. In…
We study the pairwise annihilation process $A+A\to$ inert of a number of random walkers, which originally are localized in a small region in space. The size of the colony and the typical distance between particles increases with time and,…
Right-handed neutrinos offer an elegant solution to two well established phenomena beyond the Standard Model (SM) - masses and oscillations of neutrinos, as well as the baryon asymmetry of the Universe. It is also a minimalistic solution…
We present a new type of leptogenesis mechanism based on a two-scalar split-fermions framework. At high temperatures the bulk scalar vacuum expectation values (VEVs) vanish and lepton number is strongly violated. Below some temperature,…
Gene expression patterns (GEPs) are established by cross-regulating target genes that interpret morphogen gradients. However, as development progresses, morphogen activity is reduced, leaving the emergent GEP without stabilizing positional…
We study the scale at which one can generate the lepton asymmetry of the universe which could then get converted to a baryon asymmetry during the electroweak phase transition. We consider the possibility that the Yukawa couplings are small…
The development of multicellular organisms proceeds through a series of morphogenetic and cell-state transitions, transforming homogeneous zygotes into complex adults by a process of self-organization. Many of these transitions are achieved…
We propose a physical model for developmental process at cellular level to discuss the mechanism of epigenetic landscape. In our simplified model, a minimal model, the network of the interaction among cells generates the landscape…
The dynamics and processes of urban morphogenesis are a central issue regarding a long-term sustainability of urban systems. They however imply stakeholders and parameters at multiple temporal and spatial scales simultaneously, leading to…
Gene regulatory network (GRN)-based morphogenetic models have recently gained an increasing attention. However, the relationship between microscopic properties of intracellular GRNs and macroscopic properties of morphogenetic systems has…
Scaling describes how a given quantity $Y$ that characterizes a system varies with its size $P$. For most complex systems it is of the form $Y\sim P^\beta$ with a nontrivial value of the exponent $\beta$, usually determined by regression…