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Stochastic Reaction Jump Simulation and Coupling — Examples
1 · Prerequisites
- Absolute and Conditional Convergence; Rearrangement; Products
- Areas of Elementary Plane Figures
- Binary Operations, Monoids, Groups and Subgroups
- Compactness
- Compactness in Metric Spaces
- Complete Metrizability, Čech-Completeness, and Baire Category
- Completeness, Completion, and Uniform Continuity
- Conditional Distributions and Regular Conditional Probability
- Conditional Expectation
- Construction of the Natural Numbers
- Construction of the Real Numbers via Cauchy Sequences
- Construction of the Real Numbers via Dedekind Cuts
- Continuity, IVT, EVT, and Uniform Continuity
- Cosets, Index and Lagrange's Theorem
- Countability and Uncountability
- Countability Axioms and Cardinal Functions
- Divisibility, Euclidean Domains, Principal Ideal Domains and Unique Factorisation
- Event observation, censoring, truncation
- Filters and Ultrafilters
- Finite Counting, Factorials and Binomial Coefficients
- Foundations of the Real Numbers for Analysis
- Ideals, Quotient Rings and the Isomorphism Theorems for Rings
- Independence Borel Cantelli and Zero One Laws
- Infinite Product Measures and Kolmogorov Extension
- Lebesgue Measure on Euclidean Space
- Lebesgue-Stieltjes Measures and Distribution Functions
- Limits of Real Functions
- limsup, liminf, and Subsequential Limits
- Linear Independence, Bases and Dimension
- Linear Transformations, Rank-Nullity and Quotient Spaces
- Markov Kernels and Markov Chains
- Measurable Functions and Simple Approximation
- Measures and Their Basic Properties
- Metric Spaces
- Monotone Functions, Discontinuities, and Continuity Sets
- Monotone Sequences, Bolzano-Weierstrass, and Cauchy Completeness
- Normal Subgroups and Quotient Groups
- Order, Zorn's Lemma, and the Axiom of Choice
- Outer Measure and the Caratheodory Extension Theorem
- Parametric survival and reliability
- Poisson and Cox point processes
- Polynomial Rings, the Division Algorithm and Roots
- Power Series and Real-Analytic Functions
- Probability Spaces Random Variables and Expectation
- Product Measures and the Fubini Tonelli Theorems
- Properties of the Integral and the Working FTC
- Relations, Functions, and Quotients
- Rings, Subrings, Integral Domains and Fields
- Rⁿ as a Normed Space; Vector-Valued Functions
- Roots, Rational Powers, and Classical Inequalities
- Separation Axioms: the Hierarchy
- Sequences and Limits
- Sequences and Series of Functions; Uniform Convergence
- Series: Convergence and the Nonnegative Tests
- Sigma Algebras and Borel Sets
- Signed and Complex Measures Hahn and Jordan
- Simple Field Extensions and the Construction of the Complex Numbers
- Standard-Borel Real Codings and Determining Classes
- Statistical Experiments, Models and Identifiability
- Stochastic Reaction Jump Simulation and Coupling
- Subspaces, Products, and Quotients
- Suprema and Infima
- Temporal intensity and likelihood
- The Cantor Set, Baire Category, and Measure Zero in ℝ
- The Derivative and the Mean Value Theorems
- The Exponential Function
- The Integral Logarithm and the Equivalence of Its Characterisations
- The Lebesgue and Riemann Integrals Compared
- The Lebesgue Integral and the Convergence Theorems
- The Logarithm and General Powers
- The Lᵖ Spaces Holder Minkowski and Riesz Fischer
- The Radon Nikodym Theorem and Lebesgue Decomposition
- The Riemann Integral in Rᵐ and Jordan Content
- The Riemann Integral: Definition and Integrability
- The Topology of Euclidean Space
- The ZFC Axioms and the Basic Set Constructions
- Topological Spaces and Continuity
- Topology of ℝ
- Triangularisation, Generalised Eigenspaces and Jordan Canonical Form
- Vector Spaces, Linear Subspaces, Span and Direct Sums
2 · Summary
Summary
Show finite-rate explosion in the quadratic pure-birth network, compare correct thinning with a clipped invalid envelope, compute an absorbing extinction state and a finite birth-death path law, and work out the shared and residual rates in a two-chain minimum-intensity coupling.
3 · Logical flowchart
4 · Definitions, theorems and proofs
None yet.
5 · Examples, counterexamples and false statements
Quadratic pure-birth rates can explode
Statement
Let , use one increment , and set the propensity . Starting at , the minimal reaction process has explosion time where the independent holding times satisfy . This sum is finite almost surely, so finite per-state rates alone do not prevent explosion. The sufficient criterion in A proper Lyapunov bound prevents reaction-network explosion does not apply with , since its local expression is not bounded by for any finite .
Facts & Assumptions
Given: Countable Choice, Dependent Choice, the reaction system above, and an independent stream of unit exponential variables.
A reaction system permits countable , a finite set of increments and finite total rate at each state, with active poststates in . (Finite-channel reaction propensity systems and their generator)
A unit exponential law has density for and survival ; rescaling by gives an exponential holding time with rate . (Exponential and Weibull survival specifications define probability laws)
Expectation is integration against the probability measure. (Expectation of a nonnegative or integrable random variable)
Increasing limits of nonnegative measurable functions pass through the integral. (Monotone convergence for the integral)
On bounded intervals, the Lebesgue integral of a continuous function equals its Riemann integral, and the fundamental theorem evaluates that integral from an antiderivative. (A bounded Riemann integrable function on a closed bounded interval is Lebesgue measurable and has the same integral, The second fundamental theorem: if is differentiable on with and is integrable, then )
The derivative of is ; for , the exponential series has nonnegative terms and dominates . (Exponential and Weibull survival specifications define probability laws, The real exponential function and the number by a power series, A series of nonnegative terms converges iff its partial sums are bounded, and then the sum is their supremum)
A proper with the local generator bound is a sufficient hypothesis for countable-state nonexplosion. (A proper Lyapunov bound prevents reaction-network explosion)
Countable Choice supplies the exponential law. (The Axiom of Countable Choice ())
Dependent Choice is used for the countable product probability space of holding-time inputs. (The axiom of dependent choice: a relation in which every element is related to something admits an -indexed chain, Assuming countable and dependent choice, countable products of arbitrary probability spaces)
Proof
At state , the only active channel has finite rate and moves to , so [F1] defines a valid countable-state network. With independent unit exponentials , its th holding time is ; [F2] gives the stated law and the recursive path visits until its limiting time.
The density of is for . For , [F5] and differentiation of the displayed antiderivative give As , : setting , the exponential series gives , so . Applying [F4] to the increasing truncations yields .
For , . Therefore . Since the partial sums increase, [F4] gives . If , then for every integer , contradicting this finite bound. Thus almost surely.
For , the finite local generator sum is . If for all , then for all positive integers, impossible; thus [F7] does not apply although step 3.1 proves explosion.
Clipping an understated thinning envelope changes the waiting-time law
Statement
Assume Countable Choice and Dependent Choice. Consider the one-state system with one zero-increment channel and constant propensity . Its first marked reaction time has survival . If an implementation incorrectly uses the understated envelope and clips the acceptance probability to , it accepts every rate-one candidate, so its first marked reaction time has survival . These laws differ for every . The specified algorithm requires a valid envelope and does not clip: a detected violation returns invalid-envelope, and the exact-thinning theorem asserts no law under a failed envelope.
Facts & Assumptions
Given: Countable Choice, Dependent Choice, and the one-state time-dependent propensity system above and the candidate-thinning algorithm.
A zero increment is an allowed marked reaction that leaves the state unchanged, while its propensity still contributes to the total event rate. (Finite-channel reaction propensity systems and their generator)
The thinning algorithm requires a supplied envelope certificate, reports a detected violation as invalid-envelope, and does not clip propensities. (Dominating thinning for bounded time-varying propensities)
Under Countable Choice and Dependent Choice, exact thinning conclusions require the certified envelope; if it fails, the theorem asserts no path law. (Dominating thinning has the prescribed reaction law)
Under Countable Choice and Dependent Choice, for a finite-state reaction system with a specified initial state and unlimited event budget, the Gillespie direct method uses an exponential holding time with parameter equal to the total propensity. (Finite-state Gillespie and next-reaction methods have the specified CTMC law)
Proof
The target system has constant total rate ; [F4] therefore gives its first marked-event survival . This is an event even though , by [F1].
A rate-one candidate process has no candidate by time with probability . The clipped rule accepts every candidate, hence its first accepted-event survival is ; for , . Thus clipping changes the event law.
Here , so the required certificate is false. The specified procedure therefore lies outside the theorem's hypothesis and, whenever the violation is evaluated at a candidate, returns invalid-envelope; [F2] expressly forbids continuing by clipping.
A zero-total-hazard state is absorbing
Statement
Assume Countable Choice and Dependent Choice. Let with one death channel of increment , propensity , and . Starting from , the process waits an time , moves to , and remains there forever. In particular, state has total hazard zero and is absorbing.
Facts & Assumptions
Given: Countable Choice (The Axiom of Countable Choice ()), Dependent Choice (The axiom of dependent choice: a relation in which every element is related to something admits an -indexed chain), the finite-state reaction system above and the exact Gillespie method with unlimited event budget.
Positive propensity requires the poststate to lie in the state set; the reaction event and generator use the stated increment and rate. (Finite-channel reaction propensity systems and their generator)
Under Countable Choice and Dependent Choice, at positive total rate the finite-state Gillespie process with a fixed initial state and unlimited event budget has exponential holding time and the channel probabilities are propensity divided by total rate; zero total rate is absorbing. (Finite-state Gillespie and next-reaction methods have the specified CTMC law)
If the direct method reaches its zero-propensity test before the horizon, it returns the constant continuation with status absorbed; a proposed event at or beyond the horizon instead gives status horizon without recording that event. (Gillespie direct method with horizon and budget statuses)
Proof
The only positive rate is , and its poststate lies in , so the system is admissible. At , [F2] gives ; at , the total rate is .
Once the first event occurs, the state is and every propensity is zero. By [F2] the process remains at at all later times. In an unlimited-budget call with finite horizon , if , the event is recorded and the next zero-propensity test returns status absorbed; if , [F3] returns status horizon without recording the event. The underlying process therefore satisfies and for , independently of the call's horizon censoring.
The generator is and for every bounded , so the zero-hazard state has no outgoing transition and the example satisfies the operator convention.
Gillespie simulation of a finite birth-death reaction network
Statement
Assume Countable Choice and Dependent Choice. Let with a birth channel , , and a death channel , . From every state the total rate is . Starting at , the first holding time is ; the event is a birth if and a death otherwise. With unlimited event budget, the direct method generates the exact finite-state reaction path law on every finite horizon.
Facts & Assumptions
Given: Countable Choice (The Axiom of Countable Choice ()), Dependent Choice (The axiom of dependent choice: a relation in which every element is related to something admits an -indexed chain), the finite state set, two reaction channels, initial state , unlimited event budget, and independent exact exponential and uniform inputs.
Each active channel must have its poststate in , and the generator is the finite rate-weighted increment sum on bounded functions. (Finite-channel reaction propensity systems and their generator)
Assuming Countable Choice and Dependent Choice, the direct and next-reaction methods with fixed initial state and unlimited event budgets have the recursively specified finite-state CTMC law; the generator is the reaction rate sum. (Finite-state Gillespie and next-reaction methods have the specified CTMC law)
Proof
For , the birth rate is positive and ; at its rate is zero. For , the death rate is positive and ; at its rate is zero. Thus both channels are admissible, and for all .
At state the two propensities are each . The direct method's waiting time is , and its cumulative selection rule makes the first event a birth exactly when ; after each event the same calculation applies at the new state.
The generator is , , and , obtained from the active channels without evaluating outside . The rates are bounded by , so the finite-state theorem identifies the direct method with the exact path law and gives .
Minimum-intensity coupling of two birth-death chains
Statement
Assume Countable Choice and Dependent Choice. On , let both chains have birth increment and death increment . Set Starting from and using unlimited candidate budget, the minimum-intensity coupling has at the first paired event three possibilities, each at rate : shared birth to , shared death to , or -only death to . Thus its uncensored first paired-event time is and each possibility has probability ; a finite-horizon call records it only when it occurs before the horizon. The coordinate path marginals remain the exact and reaction laws.
Facts & Assumptions
Given: Countable Choice (The Axiom of Countable Choice ()), Dependent Choice (The axiom of dependent choice: a relation in which every element is related to something admits an -indexed chain), the two finite-state birth-death systems, initial pair , and the minimum-intensity coupling with unlimited candidate budget.
The propensity definition requires active poststates to lie in the finite state set, and rates determine the reaction generator. (Finite-channel reaction propensity systems and their generator)
The coupling constructs shared events at the minimum channel rate and residual events at the positive rate differences. (Minimum-intensity coupling of reaction networks)
Under Countable Choice and Dependent Choice and with unlimited candidate budget, both coupled coordinate processes have the exact path laws of their respective Gillespie chains. (The minimum-intensity reaction coupling preserves both marginals)
Under Countable Choice and Dependent Choice, for a fixed state, pairwise-disjoint accepted mark sets with product-measurable time-mark regions and total measure under a rate- candidate stream give first-event survival and channel-specific event probabilities proportional to the set measures. The algorithm's event portions here are fixed intervals, so these regions are product-measurable. (Dominating thinning has the prescribed reaction law)
Proof
For both systems, a positive birth rate occurs only at and moves to ; a positive death rate occurs only at and moves to . All rates are nonnegative and finite, so [F1] gives valid finite-state systems.
At the birth rates are , hence [F2] gives shared birth rate . The death rates are , hence shared death rate and -only death rate ; the -only death rate is . There are no other event types, so the total paired-event rate is .
The algorithm's birth envelope is , and its death envelope is , so the total candidate rate is . At the fixed pair the three disjoint event-mark portions have total length ; [F4] gives first-event survival and assigns each equal-length portion probability conditional on an event. Their state updates are respectively , , and .
The marginal theorem [F3] applies because the budget is unlimited and the finite rates supply the bounds and . It identifies each coordinate path with its own Gillespie reaction law, completing the example.