#30 · Systems biology

Explicit mechanistic models of promoter, stress-response and allosteric dynamics

The shared thread is explicit mechanistic structure used to represent cellular dynamics through discrete states, delays, or network paths. A hybrid Markovian-ODE framework replaces Hill functions with a continuous-time Markov chain over promoter states, parameterized from ChEC-seq dwell times and reported to match stochastic simulation algorithm accuracy. A calibrated Integrated Stress Response model identifies an eIF2 phosphorylation threshold, cascading ATF4/GADD34/CHOP/DR5 delays, and a biphasic amplitude limit. A spanning-tree framework with Burton-Pemantle path weighting quantifies allosteric communication and noise suppression in protein contact networks. What is new is mechanistic state structure either fitted to experimental data or bounded by physical limits.