Paper List
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GOPHER: Optimization-based Phenotype Randomization for Genome-Wide Association Studies with Differential Privacy
This paper addresses the core challenge of balancing rigorous privacy protection with data utility when releasing full GWAS summary statistics, overco...
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Real-time Cricket Sorting By Sex A low-cost embedded solution using YOLOv8 and Raspberry Pi
This paper addresses the critical bottleneck in industrial insect farming: the lack of automated, real-time sex sorting systems for Acheta domesticus ...
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Training Dynamics of Learning 3D-Rotational Equivariance
This work addresses the core dilemma of whether to use computationally expensive equivariant architectures or faster symmetry-agnostic models with dat...
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Fast and Accurate Node-Age Estimation Under Fossil Calibration Uncertainty Using the Adjusted Pairwise Likelihood
This paper addresses the dual challenge of computational inefficiency and sensitivity to fossil calibration errors in Bayesian divergence time estimat...
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Few-shot Protein Fitness Prediction via In-context Learning and Test-time Training
This paper addresses the core challenge of accurately predicting protein fitness with only a handful of experimental observations, where data collecti...
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scCluBench: Comprehensive Benchmarking of Clustering Algorithms for Single-Cell RNA Sequencing
This paper addresses the critical gap of fragmented and non-standardized benchmarking in single-cell RNA-seq clustering, which hinders objective compa...
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Simulation and inference methods for non-Markovian stochastic biochemical reaction networks
This paper addresses the computational bottleneck of simulating and performing Bayesian inference for non-Markovian biochemical systems with history-d...
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Assessment of Simulation-based Inference Methods for Stochastic Compartmental Models
This paper addresses the core challenge of performing accurate Bayesian parameter inference for stochastic epidemic models when the likelihood functio...
ATP Level and Phosphorylation Free Energy Regulate Trigger-Wave Speed and Critical Nucleus Size in Cellular Biochemical Systems
School of Physics, Center for Quantitative Biology, Peking University, Beijing 100871, China
30秒速读
IN SHORT: This work addresses the core challenge of quantitatively predicting how the cellular energy state (ATP level and phosphorylation free energy) governs the speed, direction, and critical initiation size of propagating biochemical trigger waves.
核心创新
- Methodology Develops a thermodynamically consistent reaction-diffusion framework that treats ATP concentration ([ATP]) and the nonequilibrium parameter γ (=[ATP]/(Keq[ADP][Pi])) as independent control variables for analyzing trigger waves.
- Biology Identifies the intracellular energetic state as a direct regulator of trigger-wave behavior, quantitatively linking metabolic conditions (ATP/ADP/Pi ratio) to spatiotemporal propagation dynamics.
- Theory Derives analytical expressions showing that the critical excitation radius (Rc) for sustained wave propagation depends on both [ATP] and γ, with scaling Rc ∝ 1/√[ATP] under specific approximations.
主要结论
- ATP concentration ([ATP]) and the phosphorylation free energy parameter (γ) jointly regulate trigger-wave speed (c0), with a dominant scaling c0 ∝ √[ATP] in the forward propagation regime.
- The sign of the potential difference (ΔF) between bistable states, determined by [ATP] and γ, dictates wave propagation direction (forward for ΔF<0, reverse for ΔF>0), with a stationary interface at ΔF=0.
- The critical nucleus radius (Rc) for sustained spherical wave propagation is inversely related to wave speed (Rc = D(d-1)/c0), leading to the prediction that higher [ATP] reduces the minimum trigger size required (Rc ∝ 1/√[ATP]).
摘要: Trigger waves are self-regenerating propagating fronts that emerge from the coupling of nonlinear reaction kinetics and diffusion. In cells, trigger waves coordinate large-scale processes such as mitotic entry and stress responses. Although the roles of circuit topology and feedback architecture in generating bistability are well established, how nonequilibrium energetic driving shapes wave propagation is less well understood. Here, we employ a thermodynamically consistent reaction–diffusion framework to investigate trigger-wave dynamics in ATP-dependent phosphorylation–dephosphorylation systems. We first recapitulate general expressions for trigger-wave speed in the bistable regime and analyze curvature-induced corrections that determine the minimum critical nucleus required for sustained propagation in higher dimensions. We then apply this framework to two representative systems, treating ATP concentration and the nonequilibrium parameter γ=[ATP]/(Keq[ADP][Pi]) as independent control variables to examine how energetic driving regulates wave propagation. Our results show that ATP and γ not only modulate wave speed, but can also reverse the direction of propagation and reshape the parameter regime supporting trigger waves. The critical excitation radius also depends on both ATP concentration and phosphorylation free energy. These findings identify the intracellular energetic state as a regulator of trigger-wave behavior, linking metabolic conditions to the spatial dynamics of wave propagation. More broadly, this framework connects classical reaction–diffusion theory with ATP-driven biochemical regulation and provides a general perspective on related energy-dependent cellular decision-making processes.