Modeling of Biological Processes by Using Membrane Computing Formalism

Abstract

Problem statement: Membrane computing has structural resemblance with the cell structure. This characteristic provides the versatility in the modeling of biological processes. Approach: This study was carried to discuss the membrane computing formalism in modeling biological processes by analyzing two examples: Photosynthesis in chloroplast and Sodium-Potassium exchange pump. Results: The modeling of these two examples showed membrane computing formalism has the capability to capture the fundamental features and elements of biological processes. Conclusion: There are flexibilities and advantages in modeling biological processes with membrane computing but its formalism need further expansion to accommodate complex biological processes.

Modeling A Multi-Compartments Biological System with Membrane Computing

“…The research in this line shows that biological system can be modeled better using membrane computing than the conventional methods using mathematical representation such as Ordinary Differential Equation (ODE) (Bernardini and et al, 2006;Muniyandi and Abdullah, 2009). Simulation strategies based on membrane computing such as Gillespie Algorithm are also used to proof this claim .…”

“…(Somogyi and Stucki, 1991) Modeling: The chemical substances, the structure of the system, the processes that interact between compartments and the parameters assigned to each processes are extracted from ODE model (Somogyi and Stucki, 1991). This information is used in modeling the case study with membrane computing formalism as investigated by Muniyandi and Abdullah (2009).…”

Experimenting the Simulation Strategy of Membrane Computing with Gillespie Algorithm by Using Two Biological Case Studies

“…However, the interest has increased in investigating membrane computing into practical computing applications. Since membrane computing originated from biology, question of why we do not use membrane computing back into where it has originated has arisen (Muniyandi and Abdullah, 2009). Most of mathematical models of biological processes have been done by using continuous mathematics, especially system of Ordinary Differential Equations (ODE) in which the variation of concentration of each chemical substance or object is modeled as a global entity.…”

Model Checking the Biological Model of Membrane Computing with Probabilistic Symbolic Model Checker by Using Two Biological Systems

“…The biological description of membrane computing formalism has been utilized to characterize and preserve the elements in biological systems. The research in this line shows that biological system can be modeled better using membrane computing than the conventional methods using mathematical representation such as Ordinary Differential Equation (ODE) (Bernardini et al, 2006;Muniyandi and Abdullah, 2009;2010). Simulation strategies based on membrane computing such as Gillespie Algorithm are also used to proof this claim.…”

“…The two biological case studies are preypredator population and signal processing in the legendreceptor Networks of protein TGF-β. These two case studies have been modeled in membrane computing formalism and simulated with simulation strategy of membrane computing with Gillespie Algorithm (Muniyandi and Abdullah, 2009;2010). (Kwiatkowska et al, 2002) is probabilistic model checker that represent a technique for formally verifying quantitative properties of a stochastic system.…”