Related papers: Finding the center reliably: robust patterns of de…
From the perfect radial symmetries of radiolarian mineral skeletons to the broken symmetry of homochirality, the logic of Nature's regularities has fascinated scientists for centuries. Some of Nature's symmetries are clearly visible in…
A toggle switch consists of two genes that mutually repress each other. This regulatory motif is active during cell differentiation and is thought to act as a memory device, being able to choose and maintain cell fate decisions. In this…
Despite the advent of several novel, synthetic gene drive mechanisms and their potential to one-day control a number of devastating diseases, among other applications, practical use of these systems remains contentious and risky. In…
Tissue deformations during morphogenesis can be active, driven by internal processes, or passive, resulting from stresses applied at their boundaries. Here, we introduce the Drosophila hindgut primordium as a model for studying…
The self-affinity of growing systems with radial symmetry, from tumors to grain-grain displacement, has devoted increasing interest in the last decade. In this work, we analyzed features about the interface scaling of these clusters through…
Novel mathematical models of three different repressilator topologies are introduced. As designable transcription factors have been shown to bind to DNA non-cooperatively, we have chosen models containing non-cooperative elements. The…
Based on a non-equilibrium mechanism for spatial pattern formation we study how position information can be controlled by locally coupled discrete dynamical networks, similar to gene regulation networks of cells in a developing…
Young's cellular automaton, recently applied to study the spatiotemporal evolution of binary patterns for favorable/hostile environments, has now been modified from a different point of view. In this model, each differentiated cell (DC)…
Specific activator and repressor transcription factors which bind to specific regulator DNA sequences, play an important role in gene activity control. Interactions between genes coding such transcription factors should explain the…
Rhythmic and sequential segmentation of the embryonic body plan is a vital developmental patterning process in all vertebrate species. However, a theoretical framework capturing the emergence of dynamic patterns of gene expression from the…
The time required to transcribe genes with long primary transcripts may limit their ability to be expressed in cells with short mitotic cycles, a phenomenon termed intron delay. As such short cycles are a hallmark of the earliest stages of…
We introduce a new model for the dynamics of centroblasts and centrocytes in a germinal center. The model reduces the germinal center reaction to the elements considered as essential and embeds proliferation of centroblasts, point mutations…
Transcription is regulated through binding factors to gene promoters to activate or repress expression, however, the mechanisms by which factors find targets remain unclear. Using single-molecule fluorescence microscopy, we determined in…
Successful biological development via spatial regulation of cell differentiation relies on action of multiple signaling molecules that are known as morphogens. It is now well established that signaling molecules create non-uniform…
We conduct a systematic study of the approximation properties of Transformer for sequence modeling with long, sparse and complicated memory. We investigate the mechanisms through which different components of Transformer, such as the…
This paper proposes a modular framework to generate robust biped locomotion using a tight coupling between an analytical walking approach and deep reinforcement learning. This framework is composed of six main modules which are…
The properties of a front between two different phases in the presence of a smoothly inhomogeneous external field that takes its critical value at the crossing point is analyzed. Two generic scenarios are studied. In the first, the system…
Eukaryotic cells are often exposed to fluctuations in growth conditions as well as endogenous and exogenous stress-related agents. In addition, during development global patterns of gene transcription change dramatically, and these changes…
Systems biology approaches combining theoretical modeling with experiments have been singularly successful in uncovering novel features of cellular phenomena. One such feature is that of binary gene expression in which the expression level…
Practical modifications of deterministic multigrid and conventional relaxation algorithms are discussed. New parameters need not be tuned but are determined by the algorithms themselves. One modification can be thought of as ``updating on a…