arXiv subjects

Yuansheng Cao

Publications and source records attributed to Yuansheng Cao.

13 recordsLinked to original sources

arXiv2026

Contact-Dependent Ion Gating Explains Directional Asymmetry in the Bacterial Flagellar Motor

The bacterial flagellar motor (BFM) is a rotary molecular machine driven by the ion electrochemical potential across the cell membrane. Recent cryo-EM structures reveal a cogwheel-like architecture in which multiple stators engage a large rotor. A longstanding puzzle is the directional asymmetry of its torque-speed relation: concave in counterclockwise (CCW) rotation but nearly linear in clockwise (CW) rotation. Here, we develop a stochastic mechanochemical model that explicitly incorporates rotor-stator coupling and detailed ion translocation kinetics. By integrating physiological torque-speed data with recent measurements of rotor-stator relative motion, we show that under physiological conditions the motor operates in a tight engagement regime, rendering the torque-speed relation largely insensitive to the specific form of mechanical interactions. This finding rules out differences in rotor-stator mechanics as the origin of CW-CCW asymmetry. Guided by cryo-EM structures, we propose a contact-dependent gating mechanism in which the MotA-FliG interaction modulates the ion release rate of the MotB subunit proximal to the FliG ring. Molecular dynamics simulations indicate tighter MotA-FliG contact in the CW motor, implying a reduced ion release rate compared to CCW. Our model demonstrates that differential gating strength accounts for the observed asymmetry: stronger gating in CCW shortens torque-free waiting phases, enhances torque generation, and produces a concave torque-speed curve, whereas weaker gating in CW yields lower torque and a linear relation. This structure-based framework quantitatively links molecular asymmetry to motor function and identifies specific interfaces for targeted perturbation and mutational studies.

physics.bio-ph↗

arXiv2026

Thermodynamic Limits on Reliable Signaling by Biochemical Traveling Waves

Biochemical traveling waves transmit signals across cells and tissues, but the thermodynamic cost of reliable propagation remains unclear. We develop a stochastic thermodynamic framework for reaction--diffusion systems with stable traveling waves and show that diffusion of the wave position is bounded by the dissipation specifically associated with propagation. The bound follows by projecting noisy field dynamics onto the adjoint translational mode, which maps the wave position to an effective biased random walk. Its tightness is controlled by the non-self-adjoint part of the linearized dynamics, with finite wave speed and antisymmetric reaction dynamics generically producing deviations from equality. For excitable trigger waves in a FitzHugh--Nagumo model, we show that the slow inhibitor dominates the propagation cost, yielding a trade-off among wave speed, inhibitor amplitude, and dissipation. We test these predictions in stochastic simulations of a microscopic Belousov--Zhabotinsky reaction--diffusion system and find consistent signatures in mitotic trigger-wave experiments in \textit{Xenopus} egg extracts. The same relation further imposes an annihilation-limited bound on the reliable signaling rate of wave trains.

physics.bio-ph↗

arXiv2026

Physics-guided curriculum learning for the identification of reaction-diffusion dynamics from partial observations

Reaction-diffusion (RD) systems provide fundamental models for understanding self-organized spatiotemporal patterns across natural and engineered settings, yet reliable parameter estimation remains challenging, particularly when observations are sparse, noisy, and restricted to a subset of state variables. We introduce CLIP (Curriculum Learning Identification via PINNs), a physics-guided framework built on physics-informed neural networks for joint parameter inference and hidden-state reconstruction under partial observability. Leveraging the physical separability of RD systems, the CLIP training progresses from reaction-dominated regimes to full spatiotemporal dynamics using curriculum learning and an anchored widening transfer strategy. Across three canonical reaction-diffusion benchmarks, CLIP achieves more accurate and robust identification than baseline methods. Furthermore, the CLIP framework is successfully applied to infer the dynamics of the Min system in bacteria, where only membrane-bound species are observed and key kinetic rates span multiple orders of magnitude. Ablation experiments and loss-landscape visualizations demonstrate that both the curriculum stages and the anchored transfer are essential for stable convergence.

physics.comp-ph↗

arXiv2026

Optimal Discretization in Hour-Glass Molecular Clocks Driven by Oscillating Free Energy

Hour-glass clocks do not free-run; they keep time by riding an external rhythm. Motivated by the primordial KaiBC system in cyanobacteria, we study a driven, finite-state molecular clock that advances through a small number of biochemical states under an intrinsic driving energy and a rotating energy landscape set by day-night metabolism. In the continuum limit, coherence is maximized at a resonant operating point where the intrinsic drift matches the driving frequency. In realistic clocks with a finite number of states, discreteness matters: as the rotating landscape sweeps over a lattice of states, it generates a small and high frequency vibration of the collective phase that makes timing inaccurate. Combining the resonant cost with this discreteness penalty yields a trade-off in the number of states: few states are energetically cheap but noisy; many states are precise but costly. The optimum lies at moderate discretization (typically five to fifteen states) and an environmental coupling that is strong enough for responsiveness yet weak enough to avoid large discrete-state vibrations. These design rules rationalize why KaiC's hexameric architecture falls near the predicted optimum and suggest a general principle for hour-glass clocks across organisms.

physics.bio-ph↗

arXiv2025

FLDmamba: Integrating Fourier and Laplace Transform Decomposition with Mamba for Enhanced Time Series Prediction

Time series prediction, a crucial task across various domains, faces significant challenges due to the inherent complexities of time series data, including non-stationarity, multi-scale periodicity, and transient dynamics, particularly when tackling long-term predictions. While Transformer-based architectures have shown promise, their quadratic complexity with sequence length hinders their efficiency for long-term predictions. Recent advancements in State-Space Models, such as Mamba, offer a more efficient alternative for long-term modeling, but they cannot capture multi-scale periodicity and transient dynamics effectively. Meanwhile, they are susceptible to data noise issues in time series. This paper proposes a novel framework, FLDmamba (Fourier and Laplace Transform Decomposition Mamba), addressing these limitations. FLDmamba leverages the strengths of both Fourier and Laplace transforms to effectively capture both multi-scale periodicity, transient dynamics within time series data, and improve the robustness of the model to the data noise issue. Our extensive experiments demonstrate that FLDmamba achieves superior performance on time series prediction benchmarks, outperforming both Transformer-based and other Mamba-based architectures. To promote the reproducibility of our method, we have made both the code and data accessible via the following URL:{\href{https://github.com/AI4Science-WestlakeU/FLDmamba}{https://github.com/AI4Science-WestlakeU/\model}.

cs.LG↗

arXiv2025

Optimal Cell Shape for Accurate Chemical Gradient Sensing in Eukaryote Chemotaxis

Accurate gradient sensing is crucial for efficient chemotaxis in noisy environments, but the relationship between cell shape deformations and sensing accuracy is not well understood. Using a theoretical framework based on maximum likelihood estimation, we show that the receptor dispersion, quantified by cell shape convex hull, fundamentally limits gradient sensing accuracy. Cells with a concave shape and isotropic error space achieve optimal performance in gradient detection. This concave shape, resulting from active protrusions or contractions, can significantly improve gradient sensing accuracy at the cost of increased energy expenditure. By balancing sensing accuracy and deformation cost, we predict that a concave, three-branched shape as optimal for cells in shallow gradients. To achieve efficient chemotaxis, our theory suggests that a cell should adopt a repeating "run-and-expansion" cycle. Our theoretical predictions align well with experimental observations, implying that the fast amoeboid cell motion is optimized near the physical limit for chemotaxis. This study highlights the crucial role of active cell shape deformation in facilitating accurate chemotaxis.

physics.bio-ph↗

arXiv2025

An altruistic resource-sharing mechanism for synchronization: The energy-speed-accuracy tradeoff

Synchronization among a group of active agents is ubiquitous in nature. Although synchronization based on direct interactions between agents described by the Kuramoto model is well understood, the other general mechanism based on indirect interactions among agents sharing limited resources are less known. Here, we propose a minimal thermodynamically consistent model for the altruistic resource-sharing (ARS) mechanism wherein resources are needed for individual agent to advance but a more advanced agent has a lower competence to obtain resources. We show that while differential competence in ARS mechanism provides a negative feedback leading to synchronization it also breaks detailed balance and thus requires additional energy dissipation besides the cost of driving individual agents. By solving the model analytically, our study reveals a general tradeoff relation between the total energy dissipation rate and the two key performance measures of the system: average speed and synchronization accuracy. For a fixed dissipation rate, there is a distinct speed-accuracy Pareto front traversed by the scarcity of resources: scarcer resources lead to slower speed but more accurate synchronization. Increasing energy dissipation eases this tradeoff by pushing the speed-accuracy Pareto front outwards. The connections of our work to realistic biological systems such as the KaiABC system in cyanobacterial circadian clock and other theoretical results based on thermodynamic uncertainty relation are also discussed.

cond-mat.stat-mech↗

arXiv2022

Modeling bacterial flagellar motor with new structure information: Rotational dynamics of two interacting protein nano-rings

In this article, we develop a mathematical model for the rotary bacterial flagellar motor (BFM) based on the recently discovered structure of the stator complex (MotA$_5$MotB$_2$). The structure suggested that the stator also rotates. The BFM is modeled as two rotating nano-rings that interact with each other. Specifically, translocation of protons through the stator complex drives rotation of the MotA pentamer ring, which in turn drives rotation of the FliG ring in the rotor via interactions between the MotA ring of the stator and the FliG ring of the rotor. Preliminary results from the structure-informed model are consistent with the observed torque-speed relation. More importantly, the model predicts distinctive rotor and stator dynamics and their load dependence, which may be tested by future experiments. Possible approaches to verify and improve the model to further understanding of the molecular mechanism for torque generation in BFM are also discussed.

cond-mat.soft↗

arXiv2020

Nonequilibrium thermodynamics of coupled molecular oscillators: The energy cost and optimal design for synchronization

A model of coupled molecular oscillators is proposed to study nonequilibrium thermodynamics of synchronization. We find that synchronization of nonequilibrium oscillators costs energy even when the oscillator-oscillator coupling is conservative. By solving the steady state of the many-body system analytically, we show that the system goes through a nonequilibrium phase transition driven by energy dissipation, and the critical energy dissipation depends on both the frequency and strength of the exchange reactions. Moreover, our study reveals the optimal design for achieving maximum synchronization with a fixed energy budget. We apply our general theory to the Kai system in Cyanobacteria circadian clock and predict a relationship between the KaiC ATPase activity and synchronization of the KaiC hexamers. The theoretical framework can be extended to study thermodynamics of collective behaviors in other extended nonequilibrium active systems.

physics.bio-ph↗

arXiv2019

Cell Motility Dependence on Adhesive Wetting

Adhesive cell-substrate interactions are crucial for cell motility and are responsible for the necessary traction that propels cells. These interactions can also change the shape of the cell, analogous to liquid droplet wetting on adhesive substrates. To address how these shape changes affect cell migration and cell speed we model motility using deformable, 2D cross-sections of cells in which adhesion and frictional forces between cell and substrate can be varied separately. Our simulations show that increasing the adhesion results in increased spreading of cells and larger cell speeds. We propose an analytical model which shows that the cell speed is inversely proportional to an effective height of the cell and that increasing this height results in increased internal shear stress. The numerical and analytical results are confirmed in experiments on motile eukaryotic cells.

physics.bio-ph↗

arXiv2018

Design principles and optimal performance for molecular motors under realistic constraints

The performance of a molecular motor, characterized by its power output and energy efficiency, is investigated in the motor design space spanned by the stepping rate function and the motor-track interaction potential. Analytic results and simulations show that a gating mechanism that restricts forward stepping in a narrow window in configuration space is needed for generating high power at physiologically relevant loads. By deriving general thermodynamics laws for nonequilibrium motors, we find that the maximum torque (force) at stall is less than its theoretical limit for any realistic motor-track interactions due to speed fluctuations. Our study reveals a tradeoff for the motor- track interaction: while a strong interaction generates a high power output for forward steps, it also leads to a higher probability of wasteful spontaneous back steps. Our analysis and simulations show that this tradeoff sets a fundamental limit to the maximum motor efficiency in the presence of spontaneous back steps, i.e., loose-coupling. Balancing this tradeoff leads to an optimal design of the motor-track interaction for achieving a maximum efficiency close to 1 for realistic motors that are not perfectly coupled with the energy source.Comparison with existing data and suggestions for future experiments are discussed.

cond-mat.soft↗

arXiv2015

The free energy cost of accurate biochemical oscillations

Oscillation is an important cellular process that regulates timing of different vital life cycles. However, in the noisy cellular environment, oscillations can be highly inaccurate due to phase fluctuations. It remains poorly understood how biochemical circuits suppress phase fluctuations and what is the incurred thermodynamic cost. Here, we study four different types of biochemical oscillations representing three basic oscillation motifs shared by all known oscillatory systems. We find that the phase diffusion constant follows the same inverse dependence on the free energy dissipation per period for all systems studied. This relationship between the phase diffusion and energy dissipation is shown analytically in a model of noisy oscillation. Microscopically, we find that the oscillation is driven by multiple irreversible cycles that hydrolyze the fuel molecules such as ATP; the number of phase coherent periods is proportional to the free energy consumed per period. Experimental evidence in support of this universal relationship and testable predictions are also presented.

physics.bio-ph↗

arXiv2015

Thermodynamics of Information Processing Based on Enzyme Kinetics: an Exactly Solvable Model of Information Pump

Motivated by the recent proposed models of the information engine [D. Mandal and C. Jarzynski, Proc. Natl. Acad. Sci. 109, 11641 (2012)] and the information refrigerator [D. Mandal, H. T. Quan, and C. Jarzynski, Phys. Rev. Lett. 111, 030602 (2013)], we propose a minimal model of the information pump and the information eraser based on enzyme kinetics. This device can either pump molecules against the chemical potential gradient by consuming the information encoded in the bit stream or (partially) erase the information encoded in the bit stream by consuming the Gibbs free energy. The dynamics of this model is solved exactly, and the "phase diagram" of the operation regimes is determined. The efficiency and the power of the information machine is analyzed. The validity of the second law of thermodynamics within our model is clarified. Our model offers a simple paradigm for the investigating of the thermodynamics of information processing involving the chemical potential in small systems.

cond-mat.stat-mech↗