We consider stochastic reaction networks modeled by continuous-time Markov chains. Such reaction networks often contain many reactions, potentially occurring at different time scales, and have unknown parameters (kinetic rates, total amounts). This makes their analysis complex. We examine stochastic reaction networks with non-interacting species that often appear in examples of interest (e.g. in the two-substrate Michaelis Menten mechanism). Non-interacting species typically appear as intermediate (or transient) chemical complexes that are depleted at a fast rate. We embed the Markov process of the reaction network into a one-parameter family under a two time-scale approach, such that molecules of non-interacting species are degraded fast. We derive simplified reaction networks where the non-interacting species are eliminated and that approximate the scaled Markov process in the limit as the parameter becomes small. Then, we derive sufficient conditions for such reductions based on the reaction network structure for both homogeneous and time-varying stochastic settings, and study examples and properties of the reduction.
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http://dx.doi.org/10.3934/mbe.2022124 | DOI Listing |
Dalton Trans
November 2024
Dipartimento di Scienze Chimiche e Geologiche e UdR INSTM, Università degli Studi di Modena e Reggio Emilia, via G. Campi 103, 41125 Modena, Italy.
First prepared in the late 70s, the pro-ligand 1,3-bis(3,5-dioxo-1-hexyl)benzene (Hbdhb) contains two acetoacetyl terminations linked to a central 1,3-phenylene unit through dimethylene bridges. Since each termination can be either in diketonic or keto-enolic form, in organic solution it exists as a mixture of three spectroscopically resolvable tautomers. In the presence of pyridine, Co and the bdhb anion form a crystalline dimeric compound with formula [Co(bdhb)(py)] (2) and a Co⋯Co separation of more than 11 Å.
View Article and Find Full Text PDFProtein J
February 2024
Machine Intelligence Research Lab, Department of Computer Science, University of Kerala, Thiruvananthapuram, Kerala, India.
Protein-protein interactions are crucial for the entry of viruses into the cell. Understanding the mechanism of interactions is essential in studying human-virus association, developing new biologics and drug candidates, as well as viral infections and antiviral responses. Experimental methods to analyze human-virus protein-protein interactions based on protein sequence data are time-consuming and labor-intensive, so machine learning models are being developed to predict interactions and determine large-scale interactomes between species.
View Article and Find Full Text PDFIUBMB Life
January 2024
Division of Bioinformatics, Bose Institute, Kolkata, India.
Long non-coding RNAs (lncRNAs) play a significant role in various biological processes. Hence, it is utmost important to elucidate their functions in order to understand the molecular mechanism of a complex biological system. This versatile RNA molecule has diverse modes of interaction, one of which constitutes lncRNA-mRNA interaction.
View Article and Find Full Text PDFIEEE Trans Nanobioscience
October 2023
Protein-protein interactions (PPI) are crucial for understanding the behaviour of living organisms and identifying disease associations. This paper proposes DensePPI, a novel deep convolution strategy applied to the 2D image map generated from the interacting protein pairs for PPI prediction. A colour encoding scheme has been introduced to embed the bigram interaction possibilities of Amino Acids into RGB colour space to enhance the learning and prediction task.
View Article and Find Full Text PDFFront Bioinform
December 2022
Department Computer Science, Colorado State University, Fort Collins, CO, United States.
As practitioners of machine learning in the area of bioinformatics we know that the quality of the results crucially depends on the quality of our labeled data. While there is a tendency to focus on the quality of positive examples, the negative examples are equally as important. In this opinion paper we revisit the problem of choosing negative examples for the task of predicting protein-protein interactions, either among proteins of a given species or for host-pathogen interactions and describe important issues that are prevalent in the current literature.
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