Simulating stochastic systems with feedback control is challenging due to the complex interplay between the system's dynamics and the feedback-dependent control protocols. We present a single-step-trajectory probability analysis to time-dependent stochastic systems. Based on this analysis, we revisit several time-dependent kinetic Monte Carlo (KMC) algorithms designed for systems under open-loop-control protocols. Our analysis provides a unified alternative proof to these algorithms, summarized into a pedagogical tutorial. Moreover, with the trajectory probability analysis, we present a novel feedback-controlled KMC algorithm that accurately captures the dynamics systems controlled by an external signal based on the measurements of the system's state. Our method correctly captures the system dynamics and avoids the artificial Zeno effect that arises from incorrectly applying the direct Gillespie algorithm to feedback-controlled systems. This work provides a unified perspective on existing open-loop-control KMC algorithms and also offers a powerful and accurate tool for simulating stochastic systems with feedback control.
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Iglesias P. A., 2010, Control theory and systems biology
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Univ Chicago, James Franck Inst, Chicago, IL 60637 USA
Univ Chicago, Dept Phys, Chicago, IL 60637 USA
Univ Chicago, Inst Biophys Dynam, Chicago, IL 60637 USAUniv Chicago, James Franck Inst, Chicago, IL 60637 USA
Li, Ying
;
Qu, Xiaohui
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Univ Chicago, James Franck Inst, Chicago, IL 60637 USA
Univ Chicago, Dept Phys, Chicago, IL 60637 USA
Univ Chicago, Inst Biophys Dynam, Chicago, IL 60637 USAUniv Chicago, James Franck Inst, Chicago, IL 60637 USA
Qu, Xiaohui
;
Ma, Ao
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Albert Einstein Coll Med, Dept Physiol & Biophys, Bronx, NY 10461 USAUniv Chicago, James Franck Inst, Chicago, IL 60637 USA
Ma, Ao
;
Smith, Glenna J.
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Univ Chicago, James Franck Inst, Chicago, IL 60637 USA
Univ Chicago, Inst Biophys Dynam, Chicago, IL 60637 USA
Univ Chicago, Dept Chem, Chicago, IL 60637 USAUniv Chicago, James Franck Inst, Chicago, IL 60637 USA
Smith, Glenna J.
;
Scherer, Norbert F.
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Univ Chicago, James Franck Inst, Chicago, IL 60637 USA
Univ Chicago, Inst Biophys Dynam, Chicago, IL 60637 USA
Univ Chicago, Dept Chem, Chicago, IL 60637 USAUniv Chicago, James Franck Inst, Chicago, IL 60637 USA
Scherer, Norbert F.
;
Dinner, Aaron R.
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Univ Chicago, James Franck Inst, Chicago, IL 60637 USA
Univ Chicago, Inst Biophys Dynam, Chicago, IL 60637 USA
Univ Chicago, Dept Chem, Chicago, IL 60637 USAUniv Chicago, James Franck Inst, Chicago, IL 60637 USA
机构:
Univ Chicago, James Franck Inst, Chicago, IL 60637 USA
Univ Chicago, Dept Phys, Chicago, IL 60637 USA
Univ Chicago, Inst Biophys Dynam, Chicago, IL 60637 USAUniv Chicago, James Franck Inst, Chicago, IL 60637 USA
Li, Ying
;
Qu, Xiaohui
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h-index: 0
机构:
Univ Chicago, James Franck Inst, Chicago, IL 60637 USA
Univ Chicago, Dept Phys, Chicago, IL 60637 USA
Univ Chicago, Inst Biophys Dynam, Chicago, IL 60637 USAUniv Chicago, James Franck Inst, Chicago, IL 60637 USA
Qu, Xiaohui
;
Ma, Ao
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机构:
Albert Einstein Coll Med, Dept Physiol & Biophys, Bronx, NY 10461 USAUniv Chicago, James Franck Inst, Chicago, IL 60637 USA
Ma, Ao
;
Smith, Glenna J.
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机构:
Univ Chicago, James Franck Inst, Chicago, IL 60637 USA
Univ Chicago, Inst Biophys Dynam, Chicago, IL 60637 USA
Univ Chicago, Dept Chem, Chicago, IL 60637 USAUniv Chicago, James Franck Inst, Chicago, IL 60637 USA
Smith, Glenna J.
;
Scherer, Norbert F.
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机构:
Univ Chicago, James Franck Inst, Chicago, IL 60637 USA
Univ Chicago, Inst Biophys Dynam, Chicago, IL 60637 USA
Univ Chicago, Dept Chem, Chicago, IL 60637 USAUniv Chicago, James Franck Inst, Chicago, IL 60637 USA
Scherer, Norbert F.
;
Dinner, Aaron R.
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h-index: 0
机构:
Univ Chicago, James Franck Inst, Chicago, IL 60637 USA
Univ Chicago, Inst Biophys Dynam, Chicago, IL 60637 USA
Univ Chicago, Dept Chem, Chicago, IL 60637 USAUniv Chicago, James Franck Inst, Chicago, IL 60637 USA