ArticleThe Journal of chemical physics2013
Mechanisms and topology determination of complex chemical and biological network systems from first-passage theoretical approach.
Article in The Journal of chemical physics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Energy Landscapes of Model Knotted Polymers.Journal of chemical theory and computation · 2025Article
- Particle dynamics in biconical cavities: First-passage, direct-transit, and looping time distributions.The Journal of chemical physics · 2025Article
- Transient power-law behaviour following induction distinguishes between competing models of stochastic gene expression.Nature communications · 2025Article
- High-order Michaelis-Menten equations allow inference of hidden kinetic parameters in enzyme catalysis.Nature communications · 2025Article
- Analysing ill-conditioned Markov chains.Philosophical transactions. Series A, Mathematical, physical, and engineering sciences · 2023Article
- Theoretical Tools to Quantify Stochastic Fluctuations in Single-Molecule Catalysis by Enzymes and Nanoparticles.ACS omega · 2022Review
- Dynamical Signatures of Multifunnel Energy Landscapes.The journal of physical chemistry letters · 2022Review
- On distributions of barrier crossing times as observed in single-molecule studies of biomolecules.Biophysical reports · 2021Article
- Inferring phenomenological models of first passage processes.PLoS computational biology · 2021Article
- Direct detection of molecular intermediates from first-passage times.Science advances · 2020Article
- Molecular mechanisms for microtubule length regulation by kinesin-8 and XMAP215 proteins.Interface focus · 2014Article
- Stochastic kinetics on networks: when slow is fast.The journal of physical chemistry. B · 2014Article
- Pathway structure determination in complex stochastic networks with non-exponential dwell times.The Journal of chemical physics · 2014Article
- Unveiling the hidden structure of complex stochastic biochemical networks.The Journal of chemical physics · 2014Article
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Authors and funding
2 authors.
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Abstract
The majority of chemical and biological processes can be viewed as complex networks of states connected by dynamic transitions. It is fundamentally important to determine the structure of these networks in order to fully understand the mechanisms of underlying processes. A new theoretical method of obtaining topologies and dynamic properties of complex networks, which utilizes a first-passage analysis, is developed. Our approach is based on a hypothesis that full temporal distributions of events between two arbitrary states contain full information on number of intermediate states, pathways, and transitions that lie between initial and final states. Several types of network systems are analyzed analytically and numerically. It is found that the approach is successful in determining structural and dynamic properties, providing a direct way of getting topology and mechanisms of general chemical network systems. The application of the method is illustrated on two examples of experimental studies of motor protein systems.
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