Patrick Greussay

Computing with bacterial constituents, cells and populations: from bioputing to bactoputing

The relevance of biological materials and processes to computing—aliasbioputing—has been explored for decades. These materials include DNA, RNA and proteins, while the processes include transcription, translation, signal transduction and regulation. Recently, the use of bacteria themselves as living computers has been explored but this use generally falls within the classical paradigm of computing. Computer scientists, however, have a variety of problems to which they seek solutions, while microbiologists are having new insights into the problems bacteria are solving and how they are solving them. Here, we envisage that bacteria might be used for new sorts of computing. These could be based on the capacity of bacteria to grow, move and adapt to a myriad different fickle environments both as individuals and as populations of bacteria plus bacteriophage. New principles might be based on the way that bacteria explore phenotype space via hyperstructure dynamics and the fundamental nature of the cell cycle. This computing might even extend to developing a high level language appropriate to using populations of bacteria and bacteriophage. Here, we offer a speculative tour of what we term bactoputing, namely the use of the natural behaviour of bacteria for calculating.

Hierarchical routing approach-based energy optimization in wireless sensor networks

We propose a critical improvement of the LEACH (Low-Energy Adaptive Clustering Hierarchy) routing protocol for the optimization of the energy consumption as well as memory occupation of Wireless Sensor Network (WSN). Our protocol LEACH-M uses a cascade of clustering algorithms, every step of which chooses the next one. We expect at best an improvement of 5% of energy consumption and since the lifetime of the application is itself improved the amount of data routed is improved in the same amount. Of course, testing our approach using it along a comparative study with the standard LEACH confirms our expectation.

Object-Oriented Specification of Complex Bio-computing Processes: A Case Study of a Network of Proteolytic Enzymes

We propose a case study where a familiar but very complex and intrinsically woven bio-computing system – the blood clotting cascade – is specified using methods from software design known as object-oriented design (OOD). The specifications involve definition and inheritance of classes and methods and use design techniques from the most widely used OOD-language: the Unified Modeling Language (UML), as well as its Real-Time-UML extension.First, we emphasize the needs for a unified methodology to specify complex enough biological and biochemical processes. Then, using the blood clotting cascade as a example, we define the class diagrams which exhibit the static structure of procoagulant factors of proenzyme-enzyme conversions, and finally we give a dynamic model involving events, collaboration, synchronization and sequencing. We thus show that OOD can be used in fields very much beyond software design, gives the benefit of unified and sharable descriptions and, as a side effect, automatic generation of code templates for simulation software.

Object-oriented wound healing in the liver: a class-structured view of fibrogenesis and a glimpse of its evolution

We describe a very intricate case of highly correlated bio-processes: the liver fibrogenic cascade, by using a set of tools from object-oriented design (OOD). OOD methods were designed for the abstract specification of complex software prior to programming. It appears that OOD methods can be a fruitful tool for the abstract description of biological processes apparently quite far away from software engineering. We give a detailed view of the fibrogenic cascade within the liver using the now standard tool of OOD: Unified Modeling Language (UML) and one extension: Real-Time UML.OOD methods enforce the important role of concepts such as modularity, classes, methods and their inheritance hierarchies as well as primitives for concurrent process synchronization and cooperation. These concepts are surprisingly quite relevant for specifying bio-processes, and unexpectedly, they suggest an extension of the strict evolutionary explanation of the processes involved. As well as describing bio-structures and their interactions, we could consider evolutionary description of classes and processes. In particular, the OOD inheritance concept seems to be significant as an extension to gradualism. It suggests that DNA could encode, in Universal-Turing-Machine like fashion, the hierarchies of classes of molecular structures and perhaps the process templates associated with methods.

Object-oriented design for the specification of the blood clotting cascade: a class-structured view of bio-computing processes

We describe a very intricate case of interlocked bio-processes: the blood clotting cascade, by using a set of tools from object-oriented design (OOD). Originally, OOD has been designed for the abstract specification of complex software prior to programming. OOD brings a handful of concepts such as modularity, classes, methods and their inheritance hierarchies for concurrent process synchronization and cooperation. It appears that the set of OOD methods can be a very fruitful tool for the abstract description of biological processes apparently quite far away from software engineering. We give a moderately detailed view of the blood clotting cascade using the standard tool of OOD: Unified Modeling Language (UML) and its extension: Real-Time UML.