Related papers: Embryonic Pattern Scaling Achieved by Oppositely D…
We use inelastic hard sphere molecular dynamics simulations and laboratory experiments to study patterns in vertically oscillated granular layers. The simulations and experiments reveal that {\em phase bubbles} spontaneously nucleate in the…
Reprogramming is a process of transforming differentiated cells into pluripotent stem cells by inducing specific modifying factors in the cells. Reprogramming is a non-equilibrium process involving a collaboration at levels separated by…
Cells in a developing embryo have no direct way of "measuring" their physical position. Through a variety of processes, however, the expression levels of multiple genes come to be correlated with position, and these expression levels thus…
Spatial distributions of morphogens provide positional information in developing systems, but how the distributions are established and maintained remains an open problem. Transport by diffusion has been the traditional mechanism, but…
In the French flag problem, initially uncolored cells on a grid must differentiate to become blue, white or red. The goal is for the cells to color the grid as a French flag, i.e., a three-colored triband, in a distributed manner. To solve…
Complex interactions leading to phase transitions continue to hold a due interest in the scientific community. We charactersize a phase transition in a coupled oscillators model where interactions are not local in nature. At a first order…
We discuss leptogenesis in a majoron model extended by a right-handed $SU(2)_L$ triplet fermion. We study several different parameter assignments and find that the interactions of neutrinos with the new particles in the majoron+triplet…
A new class of matching condition between the atomistic and continuum regions is presented for the multi-scale modeling of crystals. They ensure the accurate passage of large scale information between the atomistic and continuum regions and…
Multicellular tissues, such as the epithelium coating a developing embryo, often combine complex tissue shapes with heterogeneity in the spatial arrangement of individual cells. Discrete approximations, such as the cell vertex model, can…
In this review we summarize our recent efforts in trying to understand the role of heterogeneity in cancer progression by using neural networks to characterise different aspects of the mapping from a cancer cells genotype and environment to…
Different encodings of datapoints in the latent space of latent-vector generative models may result in more or less effective and disentangled characterizations of the different explanatory factors of variation behind the data. Many works…
During mammalian embryo development, reprogramming of DNA methylation plays important roles in the erasure of parental epigenetic memory and the establishment of na\"{i}ve pluripogent cells. Multiple enzymes that regulate the processes of…
Embryonic development leads to the reproducible and ordered appearance of complexity from egg to adult. The successive differentiation of different cell types, that elaborates this complexity, result from the activity of gene networks and…
Establishing sharp and correctly positioned boundaries in spatial gene expression patterns is a central task, both in developmental and synthetic biology. We consider situations where a global morphogen gradient provides positional…
DNA methylation is a primary layer of epigenetic modification that plays a pivotal role in the regulation of development, aging, and cancer. The concurrent activity of opposing enzymes that mediate DNA methylation and demethylation gives…
Optimising probabilistic models is a well-studied field in statistics. However, its connection with the training of generative models remains largely under-explored. In this paper, we show that the evolution of time-varying generative…
Recent advances in generative artificial intelligence have had a significant impact on diverse domains spanning computer vision, natural language processing, and drug discovery. This work extends the reach of generative models into physical…
Infinitely many particles of two types ("plus" and "minus") jump randomly along the one-dimensional lattice $\mathbf{Z}_{\varepsilon}=\varepsilon\mathbf{Z}$. Annihillations occur when two particles of different time occupy the same site.…
It is shown that the renormalized nuclear deformations in different mass regions can be globally scaled by two probability partition factors of Boltzmann-like distribution, which are derived from the competing valence $np$ and like-nucleon…
The biological functions of proteins often depend on dynamic structural ensembles. In this work, we develop a flow-based generative modeling approach for learning and sampling the conformational landscapes of proteins. We repurpose highly…