Related papers: A Broad Dynamical Model for Pattern Formation by L…
Inferring dynamic biochemical networks is one of the main challenges in systems biology. Given experimental data, the objective is to identify the rules of interaction among the different entities of the network. However, the number of…
Applying steering vectors to large language models (LLMs) is an efficient and effective model alignment technique, but we lack an interpretable explanation for how it works-- specifically, what internal mechanisms steering vectors affect…
The methylation of DNA regulates gene expression. On cell division the methylation state of the DNA is typically inherited from parent to daughter cells. While the chemical bond between the methyl group and the DNA is very strong, changes…
DNA methylation is usually treated as an epigenetic memory mark: transcriptional history is written into regulatory DNA and later stabilizes a chosen cell identity. This picture explains persistence, but it makes memory passive. Here we…
The concept of limiting step gives the limit simplification: the whole network behaves as a single step. However, in its simplest form this idea is applicable only to the simplest linear cycles in steady states. For such the simplest cycles…
Many studies have shown that the excitation and inhibition received by cortical neurons remain roughly balanced across many conditions. A key question for understanding the dynamical regime of cortex is the nature of this balancing.…
Many biological processes are supported by special molecules, called motor proteins or molecular motors, that transport cellular cargoes along linear protein filaments and can reversibly associate to their tracks. Stimulated by these…
Confirming Turing's theory of morphogens in developmental processes is challenging, and synthetic biology has opened new avenues for testing Turing's predictions. Synthetic mammalian pattern formation has been recently achieved through a…
Many natural systems are organized as networks, in which the nodes (be they cells, individuals or populations) interact in a time-dependent fashion. The dynamic behavior of these networks depends on how these nodes are connected, which can…
This paper studies a chemotaxis system where cells move in response to a chemical signal within a confined habitat. The model includes external source terms that combine local and nonlocal growth with dampening effects. The main focus is on…
Delayed interactions are a common property of coupled natural systems and therefore arise in a variety of different applications. For instance, signals in neural or laser networks propagate at finite speed giving rise to delayed…
We introduce and solve a general model of dynamic response under external perturbations. This model captures a wide range of systems out of equilibrium including Ising models of physical systems, social opinions, and population genetics.…
Exchange of molecules allows cells to exchange information. How robust is the information to changes in cell parameters? We use a mapping between the stochastic dynamics of two cells sharing a stimulatory molecule, and parameters akin to an…
All intelligence is collective intelligence, in the sense that it is made of parts which must align with respect to system-level goals. Understanding the dynamics which facilitate or limit navigation of problem spaces by aligned parts thus…
The reaction-diffusion models have been extensively applied to explain the mechanism of pattern formations in early embryogenesis based on geometrically confined microtissues consisting of human pluripotent stem cells. Recently, mechanical…
A high activity of reactions can be confined in a model cell with a semipermeable membrane in the Schl\"ogl model. It is interpreted as a model of primitive metabolism in a cell. We study two generalized models to understand the creation of…
Development in multi-cellular organisms is marked by a high degree of spatial organization of the cells attaining distinct fates in the embryo. We show that receptor-ligand interaction between cells in close physical proximity adaptively…
Linearized catalytic reaction equations modeling e.g. the dynamics of genetic regulatory networks under the constraint that expression levels, i.e. molecular concentrations of nucleic material are positive, exhibit nontrivial dynamical…
Using a lattice string model, a number of peculiar excitation situations related to non-propagating excitations and non-radiating sources are demonstrated. External fields can be used to trap excitations locally but also lead to the ability…
Commonly studied cellular automata are memoryless and have fixed topology of connections between cells. However by allowing updates of links and short-term memory in cells we may potentially discover novel complex regimes of spatio-temporal…