arXiv subjects

Chongbin Zheng

Publications and source records attributed to Chongbin Zheng.

3 recordsLinked to original sources

arXiv2026

Robust topological oscillators govern a tunable phase transition to synchronized circadian rhythms

While synchronization has been well-studied in deterministic oscillators, most underlying oscillators are stochastic in both natural and man-made systems. Yet, the effects of intrinsic stochasticity remain poorly understood. Here, we develop a new mechanism for synchronizing circadian KaiC molecules that have topologically protected cycles. We find a phase transition to synchronization that depends only on the single-oscillator coherence, across a range of molecular changes that determine this coherence. Examining both mesoscopic and macroscopic numbers relevant for cellular and in vitro conditions respectively, we find different scaling properties above and below the phase transition. Our results shed light on several existing experiments and further predict that external changes can be offset by compensatory changes that improve the single-oscillator coherence - demonstrating a tunable pathway between stochastic single oscillators and their robust collective rhythms.

physics.bio-ph↗

arXiv2025

Topological edge currents promote exploratory chromosome capture in microtubule dynamic instability

Microtubules capture chromosomes during mitosis by stochastically switching between growth and shrinkage at catastrophe events. They display strikingly rich biochemistry and dynamics, regulated by a stabilizing cap with distinct conformational states. Microtubule lengths at catastrophe are observed to follow a peaked distribution, while their growth "stutters" briefly before catastrophe. Such complexity makes it hard to capture all these observations without a large number of tunable parameters. Here, we introduce a topological model of the microtubule cap that reproduces the features above through dynamical edge states, that provides a minimal description with just two free parameters. Our approach further provides an analytical description of catastrophes and allows the same features to persist over a wide range of tubulin concentration, consistent with experimental observations.

physics.bio-ph↗

arXiv2024

A topological mechanism for robust and efficient global oscillations in biological networks

Long and stable timescales are often observed in complex biochemical networks, such as in emergent oscillations. How these robust dynamics persist remains unclear, given the many stochastic reactions and shorter time scales demonstrated by underlying components. We propose a topological model that produces long oscillations around the network boundary, reducing the system dynamics to a lower-dimensional current in a robust manner. Using this to model KaiC, which regulates the circadian rhythm in cyanobacteria, we compare the coherence of oscillations to that in other KaiC models. Our topological model localizes currents on the system edge, with an efficient regime of simultaneously increased precision and decreased cost. Further, we introduce a new predictor of coherence from the analysis of spectral gaps, and show that our model saturates a global thermodynamic bound. Our work presents a new mechanism and parsimonious description for robust emergent oscillations in complex biological networks.

physics.bio-ph↗