Automatic construction of Petri net models for computational simulations of molecular interaction network DOI Creative Commons
Xuefei Lin, Xiao Chang, Yizheng Zhang

et al.

npj Systems Biology and Applications, Journal Year: 2024, Volume and Issue: 10(1)

Published: Nov. 9, 2024

Petri nets are commonly applied in modeling biological systems. However, construction of a net model for complex systems is often time consuming, and requires expertise the research area, limiting their application. To address this challenge, we developed GINtoSPN, an R package that automates conversion multi-omics molecular interaction network extracted from Global Integrative Network (GIN) into GraphML format. These files can be directly used Signaling Net (SPN) simulation. demonstrate utility tool, built neurofibromatosis type I. Simulation NF1 gene knockout, compared to normal skin fibroblast cells, revealed persistent accumulation Ras-GTPs as expected. Additionally, identified several other genes substantially affected by loss NF1's function, exhibiting individual-specific variability. results highlight effectiveness GINtoSPN streamlining simulation

Language: Английский

Hybrid modeling of methanol to olefin fluidized bed reactor corrected by artificial neural network DOI
C. Wang, Wei Wang,

Yanji Sun

et al.

Chemical Engineering Science, Journal Year: 2025, Volume and Issue: unknown, P. 121323 - 121323

Published: Feb. 1, 2025

Language: Английский

Citations

0
Methanol to Olefins (MTO): Understanding and Regulating Dynamic Complex Catalysis DOI
Shanfan Lin, Hua Li, Peng Tian

et al.

Journal of the American Chemical Society, Journal Year: 2025, Volume and Issue: unknown

Published: March 26, 2025

The research and development of methanol conversion into hydrocarbons have spanned more than 40 years. past four decades witnessed mutual promotion successive breakthroughs in both fundamental industrial process to olefins (MTO), demonstrating that MTO is an extremely dynamic, complex catalytic system. This Perspective summarizes the endeavors achievements Dalian Institute Chemical Physics, Chinese Academy Sciences, continuous study reaction mechanisms engineering It elucidates chemical issues concerning essence dynamic evolution cross-talk among diffusion, reaction, catalyst (coke modification), which are crucial for technology optimization. By integrating principles, reaction-diffusion model, coke formation kinetics MTO, a mechanism- model-driven modulation processes has been achieved. acquisition deepening understanding chemistry facilitated optimization upgrading catalysts processes.

Language: Английский

Citations

0
Automatic construction of Petri net models for computational simulations of molecular interaction network DOI Creative Commons
Xuefei Lin, Xiao Chang, Yizheng Zhang

et al.

npj Systems Biology and Applications, Journal Year: 2024, Volume and Issue: 10(1)

Published: Nov. 9, 2024

Petri nets are commonly applied in modeling biological systems. However, construction of a net model for complex systems is often time consuming, and requires expertise the research area, limiting their application. To address this challenge, we developed GINtoSPN, an R package that automates conversion multi-omics molecular interaction network extracted from Global Integrative Network (GIN) into GraphML format. These files can be directly used Signaling Net (SPN) simulation. demonstrate utility tool, built neurofibromatosis type I. Simulation NF1 gene knockout, compared to normal skin fibroblast cells, revealed persistent accumulation Ras-GTPs as expected. Additionally, identified several other genes substantially affected by loss NF1's function, exhibiting individual-specific variability. results highlight effectiveness GINtoSPN streamlining simulation

Language: Английский

Citations

0