A telecommunication approach to modeling cell metabolism.
OPUS 17
Research project number: 2019/33/B/ST6/00875
An overall goal of the project is to develop an in-silico simulation framework to model metabolism of a human cell using interconnected queueing networks. Because of the relative ease of interconnecting queueing networks, such a model would be modular in nature, and allow for addition of new building blocks representing separate metabolic pathways once modules representing them are developed.
The project was financed by National Science Centre Poland
Since the limited timeframe of the project, the proposed research will concentrate on developing simulation models leading to production of ATP through the following specific aims:
Aim 1: Develop an in-silico simulation model for basic glucose metabolism combined with an associated signaling network. The model will include a signaling cascade from the insulin detectors at the cell membrane to glucose intake facilitated by Glut-4 proteins, the whole glycolysis process and then conversion of pyruvate in Krebs Cycle (citrate cycle, TCA cycle) into ATP. The known connections/feedbacks between the metabolic network and the signaling network, e.g. activation/deactivation of mTORC proteins by Glyceraldehyde Phosphate (GAP) molecules.
Aim 2: Develop an in-silico simulation model of Pentose Phosphate metabolic pathway and combine it with the glycolysis-TCA cycle model developed in Aim 1.
Aim 3: Develop an in-silico simulation model of metabolism of triglycerides and amino acids, and connect it with the TCA cycle modeled in Aim 1.
Aim 4: Develop an interactive website for simulation of metabolic fluxes leading to production of ATP.
Publications
Sylwester Kloska, Krzysztof Pałczyński, Tomasz Marciniak, Tomasz Talaśka, Marissa Nitz, Beata J Wysocki, Paul Davis, Tadeusz A Wysocki,
Queueing theory model of Krebs cycle, Bioinformatics, Volume 37, Issue 18, 15 September 2021, Pages 2912–2919,
Sylwester M. Kloska, Krzysztof Pałczyński, Tomasz Marciniak, Tomasz Talaśka, Marissa Miller, Beata J. Wysocki, Paul Davis & Tadeusz A. Wysocki, Queueing theory model of pentose phosphate pathway, Scientific Reports volume 12, 4601 (2022). https://doi.org/10.1038/s41598-022-08463-y
The Research Team
prof. dr hab. inż. Tadeusz Wysocki
Head of the Team
Areas of research:
- Molecular communications
- Indoor propagation of microwaves
- Signal processing for communication system
- Modeling biological processes at nano-scale
dr inż. Tomasz Marciniak, prof.PBS
Researcher
Areas of research:
- Telecommunication
- Networks
- IoT
dr hab. inż. Tomasz Talaśka, prof. PBS
Researcher
Areas of research:
-
Telecommunications
-
Artificial intelligence (AI)
-
Artificial neural networks (ANNs)
mgr inż. Krzysztof Pałczyński
PhD Student
Areas of research:
- Artificial intelligence (AI)
- Artificial neural networks (ANNs)
- C# programmer
mgr Sylwester M. Kloska
PhD Student
Areas of research:
- Systems biology
- Metabolomics
- Genetics
Simulation website
Simulation website is based on simulation framework to model metabolism of a human cell using interconnected queueing networks.
Instruction:
Please select a file, the only acceptable format is .csv, then enter your e-mail address and click send to calculate.
After the simulation is completed, you will be informed via e-mail. The result will be attached to the e-mail.