Modeling Cellular Processes

Modeling Cellular Processes

Cellular processes can be simulated in many ways. The way it is simulated is called cellular modeling.
These two are types of modeling
  1. Non-computational modeling.
  2. Computational modeling.
To mimic a process occurring in the cell. To simulate it.
The biochemical model mimics the environment.


The requirements to build a non-computational model are fulfilled by answering the following questions.
  1. What are the chemical reactions to be modified?
  2. What are the kinetics of system & reactions? 
  3. What are the parameters & initial conditions for the system and reaction?
Developing the non-computational model involves creating all the reactions to the flow of these reactions and the requirements of the system. For example, the first step in glycolysis is the phosphorylation of glucose which requires kinase. Kinetic details of kinase should know to know that as a result of which reaction glucose 6 phosphate will form.

How computational model from the non-computational model can be created?
When the computational model of glycolysis is made the glycolytic reactions and mechanism of kinetics are given the name of oscillations. Parameter for completion and mechanism etc.
In a reaction


Thus reactions are developed one by one in a computational model. The whole cycle is put one by one.
Modeling oscillations are the set of conditions under which reactions occur and are used to develop a model.

For developing a model of glycolysis, glycolytic oscillations are used. These depend on the concentration of metabolites/reactants, pH, temperature & enzyme concentration, initial conditions to complete reactions i.e.to convert product x into y at each step.

If glucose is present in initial conditions then how it will break, ATP utilization, and alternative pathways of glycolysis (available in prokaryotes) how alternative pathways will initiate. When one has the answers to the questions from the non-computational model then the computational model can be developed.
In glycolytic oscillations, two things are involved
  1. ATP generation & utilization ATP ⇌ ADP
  2. NAD & NADH conversion NAD ⇌ NADH
Certain mathematical formulas are also implemented. From reactants to products all computational events are involved i.e with what concentration of sugar under the available environmental condition in what time reaction will complete & how much product will form Quantitative values are used.

Different databases are available to see the metabolic process. The two major metabolic pathway databases having comprehensive details of various organisms are
  • BioCyc
  • KεGG
Different software is also available. A characterization pathway is given whose environmental conditions are used. By altering these another pathway can be formed. The eldest software is Gepasi.

Software selection involves a mathematical model/equation to develop a pathway that is most suitable. The purpose of it is that detail about everything has been provided & by changing conditions expected change can be seen. Computation is basically prediction hence it is seen that which change may occur. As natural processes are biased (there isn't randomness) so expected and observed are different. Thus, all these things can be computed via computational models. The ultimate benefit is that in various assays the induced changes in metabolic engineering can be seen i.e to produce a product more out of a metabolic pathway which changes will cause more production.

Conditions of every step are computed until the final step is reached Programs/Softwares for cellular modeling processes can be utilized to check the effect of metabolic engineering even at a single step level to see optimum levels of conditions & processes out of various sets of conditions generated. Then, the one giving optimum value is put in the experiment.

KεGG can be used to see the feasibility of a process in an organism based on genomic screening i.e either the genes to be induced are present or not in that organism.

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