Abstract
Metabolic P (MP) systems are a class of P systems and are based on metabolic process which is used by living organisms. We review for the purpose of experimental research the MP system development, implementation and modeling. To implement MP systems in dedicated hardware, some specifications need to be determined. We look into the possibility of modeling MP systems in fixed point arithmetic capable hardware and determine the minimal needed bit count for selected MP system model. A way to improve the accuracy of fixed point calculations is proposed, which includes the modification of MP grammar. This modification is done using a simple rule to multiply and divide constants in MP grammar equations. The resulting calculations have more than 250 times smaller error when compared to original calculations. When investigating the performance of MP calculations, it is determined that the time needed for all calculations to finish depends linearly on the number of modeled systems. Metabolinė P sistema yra P sistemos klasė, pagrįsta metabolinio proceso, būdingo gyviesiems organizmams, taikymu. Siekiant pasirengti įgyvendinti MP sistemas aparatine įranga, pateikiama MP sistemų kūrimo, įgyvendinimo ir modeliavimo literatūros analitinė apžvalga. Įvertinama galimybė modeliuoti MP sistemas taikant fiksuotojo kablelio aritmetiką. Imitaciniais eksperimentais nustatytas minimalus pasirinktam MP sistemos modeliui taikyti reikiamas žodžių ilgis. Pasiūlytas būdas fiksuotosios aritmetikos skaičiavimo tikslumui padidinti. Šio būdo esmė yra MP gramatikos modifikavimas pagal konstantų daugybos ir dalybos taisyklę. Skaičiavimus atliekant modifikuota sistema, paklaida esti daugiau nei 250 kartų mažesnė. Tiriant MP sistemų našumą nustatyta, kad skaičiavimo trukmė tiesiškai priklauso nuo modeliuojamų sistemų skaičiaus.
Highlights
The simplest natural living organism is a cell
We have reviewed Metabolic P (MP) system development and implementation and selected an appropriate model and tools for our experimental investigation
After performing simulation of the MP system of Brusselator reaction we have concluded the following: 1. Bit count in fixed point arithmetic has a major impact on MP system modeling accuracy
Summary
The simplest natural living organism is a cell. It has evolved through natural ways for billions of years to do one simple operation – consume substances, transform them to new substances by chemical reactions and remove excess substances from the cell. In this paper it was proposed to observe rewriting rules in membranes from a different viewpoint than in P systems It is done by defining a metabolic algorithm for computing the evolution of P systems when some initial state and some reaction parameters are given. We need this to be able to simulate fixed point environment To do this in earlier described systems it would require substantial modifications to Java code and it would not be productive because we only intend to use one relatively simple MP system model. MP systems, modeled by (7) in 32 bit fixed point calculations, precision is decreasing over time (Figure 3). When using modified MP grammar the difference, shown, between floating and fixed point calculations is more than 250 times lower This results in greatly increased accuracy and prevents the oscillation from amplifying the error.
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