Related papers: Coordinated Spatial Pattern Formation in Biomolecu…
Complex spatial patterns in biological systems often arise through self-organization without a central coordination, guided by local interactions and chemical signaling. In this study, we explore how motility-dependent chemical deposition…
Cooperative behaviors arising from bacterial cell-to-cell communication can be modeled by reaction-diffusion equations having only a single diffusible component. This paper presents the following three contributions for the systematic…
Molecular communication (MC) is recently featured as a novel communication tool to connect individual biological nanorobots. It is expected that a large number of nanorobots can form large multi-agent MC systems through MC to accomplish…
Biomolecular condensates help organize the cell cytoplasm and nucleoplasm into spatial compartments with different chemical compositions. A key feature of such compositional patterning is the local enrichment of enzymatically active…
Turing's theory of pattern formation has been used to describe the formation of self-organised periodic patterns in many biological, chemical and physical systems. However, the use of such models is hindered by our inability to predict, in…
Most models of biological pattern formation are simulated on continuous domains even though cells are discrete objects that provide internal boundaries to the diffusion of regulatory components. In our previous papers on simulating…
Spatial and temporal pattern formation in reaction-diffusion systems is typically studied with two or more equations, as scalar reaction-diffusion equations confined to convex domains do not admit stable inhomogeneous states in time or…
This paper is concerned with stochastic reaction-diffusion kinetics governed by the reaction-diffusion master equation. Specifically, the primary goal of this paper is to provide a mechanistic basis of Turing pattern formation that is…
Originating from the pioneering study of Alan Turing, the bifurcation analysis predicting spatial pattern formation from a spatially uniform state for diffusing morphogens or chemical species that interact through nonlinear reactions is a…
Traditional top-down robotic design often lacks the adaptability needed to handle real-world complexities, prompting the need for more flexible approaches. Therefore, this study introduces a novel cellular plasticity model tailored for…
This paper presents a Markov-based system model for microfluidic molecular communication (MC) channels. By discretizing the advection-diffusion dynamics, the proposed model establishes a physically consistent state-space formulation. The…
In this paper, we consider the diffusive molecular communication channel between a transmitter nano-machine and a receiver nano-machine in a fluid environment. The information molecules released by the transmitter nano-machine into the…
Within the domain of molecular communications, researchers mimic the techniques in nature to come up with alternative communication methods for collaborating nanomachines. This work investigates the channel transfer function for molecular…
Quantitatively predictive models of biomolecular circuits are important tools for the design of synthetic biology and molecular communication circuits. The information content of typical time-lapse single-cell data for the inference of…
The activity of biological cells is primarily based on chemical reactions and typically modeled as a reaction-diffusion system. Cells are, however, highly crowded with macromolecules, including a variety of molecular machines such as…
MicroRNAs are extensively known for post-transcriptional gene regulation and pattern formation in the embryonic developmental stage. We explore the origin of these spatio-temporal patterns mathematically, considering three different motifs…
In a diffusion-based molecular communication system, molecules are employed to convey information. When propagation and reception processes are considered in a framework of first passage processes, we need to focus on absorbing receivers.…
Reaction-diffusion systems offer a powerful framework for understanding self-organized patterns in biological systems, yet controlling these patterns remains a significant challenge. As a consequence, we present a rigorous framework of…
Chemically fueled supramolecular systems can exhibit complex, time-dependent behaviors reminiscent of living matter when maintained far from equilibrium by continuous energy or fuel consumption. Here, we introduce a minimal…
We study pattern formation in a chemotaxis model of bacteria and soil carbon dynamics as an example system where transient dynamics can give rise to pattern formation outside of Turing unstable regimes. We use a detailed analysis of the…