Markov processes are widely used models for investigating kinetic networks. Here, we collate and present a variety of results pertaining to kinetic network models in a unified framework. The aim is to lay out explicit links between several important quantities commonly studied in the field, including mean first passage times (MFPTs), correlation functions, and the Kemeny constant. We provide new insights into (i) a simple physical interpretation of the Kemeny constant, (ii) a relationship to infer equilibrium distributions and rate matrices from measurements of MFPTs, and (iii) a protocol to reduce the dimensionality of kinetic networks based on specific requirements that the MFPTs in the coarse-grained system should satisfy. We prove that this protocol coincides with the one proposed by Hummer and Szabo [J. Phys. Chem. B 119, 9029 (2014)], and it leads to a variational principle for the Kemeny constant. Finally, we introduce a modification of this protocol, which preserves the Kemeny constant. Our work underpinning the theoretical aspects of kinetic networks will be useful in applications including milestoning and path sampling algorithms in molecular simulations.
Download full-text PDF |
Source |
---|---|
http://dx.doi.org/10.1063/1.5143504 | DOI Listing |
PLoS One
August 2024
Faculty of Education and Psychology, ELTE Eötvös Loránd University, Budapest, Hungary.
Computational thinking (CT) is a set of problem-solving skills with high relevance in education and work contexts. The present paper explores the role of key cognitive factors underlying CT performance in non-programming university students. We collected data from 97 non-programming adults in higher education in a supervised setting.
View Article and Find Full Text PDFJ Phys Chem B
August 2024
Department of Physics and Astronomy, University College London, London WC1E 6BT, U.K.
The recent trend in using network and graph structures to represent a variety of different data types has renewed interest in the graph partitioning (GP) problem. This interest stems from the need for general methods that can both efficiently identify network communities and reduce the dimensionality of large graphs while satisfying various application-specific criteria. Traditional clustering algorithms often struggle to capture the complex relationships within graphs and generalize to arbitrary clustering criteria.
View Article and Find Full Text PDFProc Natl Acad Sci U S A
March 2024
Department of the Geophysical Sciences, The University of Chicago, Chicago, IL.
Biogeochemical reactions modulate the chemical composition of the oceans and atmosphere, providing feedbacks that sustain planetary habitability over geological time. Here, we mathematically evaluate a suite of biogeochemical processes to identify combinations of reactions that stabilize atmospheric carbon dioxide by balancing fluxes of chemical species among the ocean, atmosphere, and geosphere. Unlike prior modeling efforts, this approach does not prescribe functional relationships between the rates of biogeochemical processes and environmental conditions.
View Article and Find Full Text PDFJ Chem Phys
March 2023
Department of Physics and Astronomy, University College London, WC1E 6BT London, United Kingdom.
Efficiently identifying the most important communities and key transition nodes in weighted and unweighted networks is a prevalent problem in a wide range of disciplines. Here, we focus on the optimal clustering using variational kinetic parameters, linked to Markov processes defined on the underlying networks, namely, the slowest relaxation time and the Kemeny constant. We derive novel relations in terms of mean first passage times for optimizing clustering via the Kemeny constant and show that the optimal clustering boundaries have equal round-trip times to the clusters they separate.
View Article and Find Full Text PDFEnter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!