arXiv subjects

Xiongfei Fu

Publications and source records attributed to Xiongfei Fu.

6 recordsLinked to original sources

arXiv2025

Optimal chemotactic navigation in disordered landscapes

Active navigation in disordered media depends on a biased random walk interacting with environmental constraints. Using E. coli chemotactic navigation in agar gels as a model system, we reveal a fundamental trade-off between diffusive exploration and chemotactic directional bias that dictates the optimal strategy for population range expansion. Counter-intuitively, evolution selects for shorter mean run times ({\tau}_f) to achieve faster chemotactic migration in denser environments. Controlled experiments reveal a non-monotonic relationship between chemotactic navigation speed and {\tau}_f, with the optimum shifting according to the density of physical traps in the gel. Single-cell analysis demonstrates that escape from these traps occurs independently of the tumbling mechanism, challenging the classical view that reorientation is essential for navigation in obstructed spaces. Based on these insights, we develop a minimal theoretical model showing that the optimal {\tau}_f emerges from an antagonistic scaling: while the diffusion coefficient increases with {\tau}_f, the chemotactic bias coefficient decreases with it. This work establishes a general principle for optimizing active transport through complex, disordered environments.

cond-mat.soft↗

arXiv2025

Cell State Transitions Beyond the Small-Noise Limit

State transitions are fundamental in biological systems but challenging to observe directly. Here, we present the first single-cell observation of state transitions in a synthetic bacterial genetic circuit. Using a mother machine, we tracked over 1007 cells for 27 hours. First-passage analysis and dynamical reconstruction reveal that transitions occur outside the small-noise regime, challenging the applicability of classical Kramers' theory. The process lacks a single characteristic rate, questioning the paradigm of transitions between discrete cell states. We observe significant multiplicative noise that distorts the effective potential landscape yet increases transition times. These findings necessitate theoretical frameworks for biological state transitions beyond the small-noise assumption.

cond-mat.stat-mech↗

arXiv2022

Stochastic threshold in cell size control

Classic models of cell size control consider cells divide while reaching a threshold, e.g. size, age, or size extension. The molecular basis of the threshold involves multiple layers of regulation as well as gene noises. In this work, we study cell cycle as first-passage problem with stochastic threshold and discover such stochasticity affects the inter-division statistics, which bewilders the criteria to distinguish the types of size control models. The analytic results show the autocorrelation in the threshold can drive a sizer model to the adder-like and even timer-like inter-division statistics, which is supported by simulations. Following the picture that the autocorrelation in the threshold can propagate to the inter-division statistics, we further show that the adder model can be driven to the timer-like one by positive autocorrelated threshold, and even to the sizer-like one when the threshold is negatively autocorrelated. This work highlights the importance to examine gene noise in size control.

cond-mat.stat-mech↗

arXiv2021

Master equation approach to the stochastic accumulation dynamics of bacterial cell cycle

The mechanism of bacterial cell size control has been a mystery for decades, which involves the well-coordinated growth and division in the cell cycle. The revolutionary modern techniques of microfluidics and the advanced live imaging analysis techniques allow long term observations and high-throughput analysis of bacterial growth on single cell level, promoting a new wave of quantitative investigations on this puzzle. Taking the opportunity, this theoretical study aims to clarify the stochastic nature of bacterial cell size control under the assumption of the accumulation mechanism, which is favoured by recent experiments on species of bacteria. Via the master equation approach with properly chosen boundary conditions, the distributions concerned in cell size control are estimated and are confirmed by experiments. In this analysis, the inter-generation Green's function is analytically evaluated as the key to bridge two kinds of statistics used in batch-culture and mother machine experiments. This framework allows us to quantify the noise level in growth and accumulation according to experimental data. As a consequence of non-Gaussian noises of the added sizes, the non-equilibrium nature of bacterial cell size homeostasis is predicted, of which the biological meaning requires further investigation.

cond-mat.stat-mech↗

arXiv2014

Limits of feedback control in bacterial chemotaxis

Inputs to signaling pathways can have complex statistics that depend on the environment and on the behavioral response to previous stimuli. Such behavioral feedback is particularly important in navigation. Successful navigation relies on proper coupling between sensors, which gather information during motion, and actuators, which control behavior. Because reorientation conditions future inputs, behavioral feedback can place sensors and actuators in an operational regime different from the resting state. How then can organisms maintain proper information transfer through the pathway while navigating diverse environments? In bacterial chemotaxis, robust performance is often attributed to the zero integral feedback control of the sensor, which guarantees that activity returns to resting state when the input remains constant. While this property provides sensitivity over a wide range of signal intensities, it remains unclear how other parameters affect chemotactic performance, especially when considering that the swimming behavior of the cell determines the input signal. Using analytical models and simulations that incorporate recent experimental evidences about behavioral feedback and flagellar motor adaptation we identify an operational regime of the pathway that maximizes drift velocity for various environments and sensor adaptation rates. This optimal regime is outside the dynamic range of the motor response, but maximizes the contrast between run duration up and down gradients. In steep gradients, the feedback from chemotactic drift can push the system through a bifurcation. This creates a non-chemotactic state that traps cells unless the motor is allowed to adapt. Although motor adaptation helps, we find that as the strength of the feedback increases individual phenotypes cannot maintain the optimal operational regime in all environments, suggesting that diversity could be beneficial.

q-bio.MN↗

arXiv2012

Stripe formation in bacterial systems with density-suppressed motility

Engineered bacteria in which motility is reduced by local cell density generate periodic stripes of high and low density when spotted on agar plates. We study theoretically the origin and mechanism of this process in a kinetic model that includes growth and density-suppressed motility of the cells. The spreading of a region of immotile cells into an initially cell-free region is analyzed. From the calculated front profile we provide an analytic ansatz to determine the phase boundary between the stripe and the no-stripe phases. The influence of various parameters on the phase boundary is discussed.

cond-mat.soft↗