Note that engineering problems, based on how we’ve defined them, cannot be solved by a biological resolution because they were concerned with physico-chemical or thermodynamic aspects of the substrates/products. *There is one exception here. We might consider improvement of equilibrium reactions by coupling product removal to a second reaction to be a biological solution if we use a second enzy...

Biological process enrichment is a widely used metric for evaluating the quality of multiprotein modules. In this study, we examine possible optimization criteria for detecting homologous multiprotein modules and quantify their effects on biological process enrichment. We find that modularity, linear density, and module size are the most important criteria considered, complementary to each othe...

A simplified environmental biological model has been developed based on biodegradation kinetics correlation to regulate and optimize wastewater treatment system of activated sludge process. All parameters included in the model are calibrated in accordance with reference data and experimental results and good agreements are achieved between calculated results and reference data or experimental r...

MOTIVATION Cellular processes are not isolated groups of events. Nevertheless, in most microarray analyses, they tend to be treated as standalone units. To shed light on how various parts of the interlocked biological processes are coordinated at the transcription level, there is a need to study the between-unit expressional relationship directly. RESULTS We approach this issue by constructin...

In this paper we present how the process modeling and execution tools iPM and iPE can be used to model and execute biological processes. The main focus of this paper is on the flexibility of iPM and iPE with respect to the customization to the biological application domain. We will demonstrate the flexibility of our modeling methodology by giving two examples: Modeling the invocation semantics ...

The topic of condylar injury in adults has generated more discussion and controversy than any other in the field of maxillofacial trauma. It is an important subject because such injuries are common and complications of trauma to the temporomandibular joint (TMJ) are far-reaching in their effects. Why are there so many different methods to treat this injury? How can seemingly disparate treatment...

The language that Nurse wishes to see is a formal language that can be automatically translated into machine executable code and that enables simulation and analysis techniques for proving properties of biological systems. Although there are many approaches to the formal modeling of living systems, only a few provide executable descriptions that highlight the mechanistic steps that make a syste...

ACTIVATED sludge processes are the dominating wastewater treatment method. Large quantities of hazardous excess sludge are generated in the processes, and elimination of the waste sludge has been a major problem for the last decade worldwide. The disposal of waste sludge is subject to various environmental, social and economic problems; and the cost consists about 50% of the operational cost of...

 Background: Sulfur compounds must be removed from petroleum because they contribute to environmental pollution. A strong alkaline solution such as caustic soda is used to remove these compounds. This spent caustic has high values for chemical oxygen demand (COD) concentration, pH and total sulfur. In this study, the regeneration and treatment methodology of sulfidic spent caustic was inve...