DOI: 10.5281/zenodo.17451504
title: Cell Behavior Science (CBS): A Physically Grounded Framework Integrating Non-Equilibrium Thermodynamics, Active Matter Theory, Mechanobiology, Gene Regulatory Networks, Metabolic Fluxes, and Extracellular Matrix Remodeling

description: ### Abstract Summary of "Cell Behavior Science (CBS): A Unified, Physically-Grounded, Multiscale Framework for Predictive Cellular Dynamics and Therapeutic Design"

Cell Behavior Science (CBS) introduces a rigorous, predictive framework for cellular dynamics, integrating non-equilibrium thermodynamics, active matter hydrodynamics, cytoskeletal mechanobiology, gene regulatory networks (GRNs), dynamic metabolic flux balance analysis (dFBA), and extracellular matrix (ECM) remodeling. By modeling the cell as an open, far-from-equilibrium dissipative structure driven by ATP hydrolysis, CBS spans femtosecond-scale molecular processes to organotypic morphogenesis, enabling quantitative forecasts of ontogenesis, homeostasis, and pathological states such as oncogenesis and fibrosis.

The framework is anchored in two falsifiable hypotheses: (1) the Coherent Vibrational Network (CVN), where ultrafast anharmonic oscillations (10 fs–1.2 ps) in hydrophobic protein cores enhance energy delocalization and enzymatic efficiency, validated by 2D-IR spectroscopy with coherence times exceeding 0.8 ps; and (2) Mechano-Geometric Memory (MGM), in which prestressed cytoskeletal lattices encode deformation histories into low-frequency eigenmodes, modulating chromatin accessibility via LINC complexes and YAP/TAZ signaling, quantifiable through ATAC-seq and traction force microscopy with correlations r > 0.85.

These elements converge in the Entropic Flux Model (EFM), a continuum field theory derived from mesoscopic stochastic thermodynamics, which quantifies local entropy reduction amid global irreversibility while incorporating mechanotransductive feedbacks (e.g., Rho GTPases), metabolic constraints (e.g., Warburg shifts under prestress), and durotactic ECM kinetics. EFM ensures second-law compliance (σ ≥ 0) and permits transient ordering via dissipative fluxes, with couplings such as CVN-modulated entropy currents (η ∈ [0.1, 0.5]) and MGM-altered production rates (α ≈ 0.2 Pa⁻¹).

Implementation fuses agent-based modeling (ABM) with graph neural networks (GNNs) for GRN inference, parameterized on synthetic finite-element datasets and empirical multi-omics (n=120,000 samples from CCLE/HTAN). Benchmarks across 3D tumor invasion, organoid engraftment, antibiotic resistance phylogenies, cardiomyocyte contractility, and fibrosis durotaxis achieve 85–94% fidelity (e.g., RMSE 1.45 ± 0.07 μm/h for invasion), outperforming PhysiCell, CellOracle, DeepCell, Chaste, and Morpheus by 16–46% in RMSE, AUC, and accuracy (p < 10⁻⁴, Cohen's d > 1.5). Ablations confirm modular contributions, with MGM excision degrading mechanosensitive tasks by up to 23%.

CBS's open-source codebase (MIT license, GitHub/Zenodo) promotes reproducibility, falsifiability (e.g., τ_c < 0.8 ps refutes CVN), and extensibility, bridging molecular quanta to multicellular ensembles. Translational impacts include 27% gains in AAV transduction via ECM tuning and 35% invasion reductions through YAP inhibitors, advancing precision oncology, regenerative engineering, and mechanomedicines. Future refinements target kinetic dFBA, in vivo 2D-IR, and multicellular cadherin dynamics for enhanced scalability and clinical deployment.