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Next-reaction method by internal Poisson clocks
Definition
Inputs. A finite state set , a finite-channel time-homogeneous system from Finite-channel reaction propensity systems and their generator, initial state , horizon , and optional reaction-event budget , defaulting to , where . Supply independent unit exponential increments for and . The countable product construction uses Countable Choice and Dependent Choice by Assuming countable and dependent choice, countable products of arbitrary probability spaces; the exponential law assumes Countable Choice by Exponential and Weibull survival specifications define probability laws.
Initialization. Set , , , internal times , threshold indices , and next thresholds for each channel.
Procedure. At each state :
- Compute for every channel. If , return the constant path through with status absorbed.
- If , return the path prefix with status budget-exhausted. For each , set when and when .
- Let . If , return the path held at through with status horizon.
- Let be the least minimizing channel (ties have probability zero). For every channel set . Set , , append the marked event, then set and ; finally set .
On the returned time interval (through unless the budget is exhausted), the internal time is , and almost surely the random-time-change representation is where and . An event at exactly is recorded before returning. If the loop reaches , return the path through with status horizon. With unlimited budget, Finite-state Gillespie and next-reaction methods have the specified CTMC law ↗ proves the Poisson threshold-clock laws and equality with the direct method's reaction path law. The implementation scans all channels at each event; no logarithmic update-tree cost is claimed.
Depends on
- The Axiom of Countable Choice ($\mathrm{AC}_\omega$)
- The axiom of dependent choice: a relation in which every element is related to something admits an $\mathbb{N}$-indexed chain
- Independent random elements
- Law or distribution of a random element
- Random elements and real random variables
- Finite-channel reaction propensity systems and their generator
- Assuming countable and dependent choice, countable products of arbitrary probability spaces
- Exponential and Weibull survival specifications define probability laws
Used by
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Sources
- David F. Anderson, Introduction to Stochastic Processes with Applications to Biology, Chapters 6–7 (standard reference, not scraped)
- David F. Anderson and Thomas G. Kurtz, Continuous Time Markov Chain Models for Chemical Reaction Networks (standard reference, not scraped)