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The traditional approach to unraveling functions of a biochemical system is to study isolated enzymes and/or complexes, and to determine their kinetic mechanisms for catalyzing given biochemical reactions along with estimates of the associated parameter values [41,47]. While this reductionist approach has been fruitful, the buzzwords of the present are integration and systems. One of the important...
Summary We study the competition between several advantageous mutants in an asexual population (clonal interference) as a function of the time between the appearance of the mutants ∆t, their selective advantages, and the rate of deleterious mutations. We find that the overall probability of fixation (the probability that at least one of the mutants becomes the ancestor of the entire population) does...
Summary This chapter describes the kinetics of the sodium-potassium exchange pump in terms of the π-calculus process algebra. The π-calculus has the advantage of a software verification tool. We emphasize that this software tool is able to check various properties and to provide confidence in the formal description of the pump. This model checker is used to verify that our model of the pump is deadlock...
Summary We describe a general strategy that enables us to develop kinetic models of large-scale metabolic systems by collecting and using all available metabolic experimental data. Our approach can be used to explore the local and global regulatory properties of selected metabolic pathways, and to predict how cell genome modifications can meet selected biotechnological and biomedical criteria. We...
Summary The gene assembly process that transforms the micronuclear genome to the macronuclear genome in stichotrichs ciliates is a complex DNA processing which is very interesting from the computational point of view. We shall give a survey of the notions and results concerning three molecular operations, known as ld, hi, and dlad, that have been postulated to accomplish the gene assembly process...
Summary According to the author’s view, research in the field of DNA and molecular computing is expanding into broader applications in nanotechnology and biotechnology, and the principles and methods for designing molecular systems with information-processing capability for such applications are considered important. We call research into designing such molecular systems molecular programming. This...
Summary DNA is the foundation stone of molecular information. Therefore, any theory that accounts for the basic molecular properties and behaviours of DNA inside the living cell can be viewed as constituting a molecular information theory. It is posited that the necessary and sufficient conditions for unraveling the workings of DNA are the successful construction of a computer model of the living cell...
Summary We present preliminary results of a new approach to the formal modelling of biological phenomena. The approach stems from the conceptual compatibility of the methods and logic of data collection and analysis in the field of developmental genetics with the languages, methods, and tools of scenario-based reactive system design. In particular, we use the recently developed methodology consisting...
Summary After briefly presenting the basic ideas and types of results of membrane computing, we introduce a widely investigated class of P systems, with a direct biological motivation, the symport/antiport P systems. We recall the generative variants (including the case when the result of a computation is obtained by means of the trace of a specified object in its movement through membranes), as well...
Summary The immune system is the natural defense of an organism. It comprises a network of cells, molecules, and organs whose primary tasks are to defend the organism from pathogens and maintain its integrity. The cooperation between the components of the immune system network realizes effectively and efficiently the processes of pattern recognition, learning, and memory. Our knowledge of the immune...
Biochemical processes, carried out by networks of proteins, underlies the major functions of living cells ([8, 60]). Although such systems are the focus of intensive experimental research, the mountains of knowledge about the function, activity, and interaction of molecular systems in cells remain fragmented. While computational methods are key to addressing this challenge ([8, 60]), they require...
Summary Central notions in evolutionary biology are intrinsically topological. This claim is perhaps most obvious for the discontinuities associated with punctuated equilibrium. Recently, a mathematical framework has been developed that derives the concepts of phenotypic characters and homology from the topological structure of the phenotype space. This structure in turn is determined by the genetic...
Summary The evolutionary theory, “evolution by duplication”, originally proposed by Susumu Ohno in 1970, can now be verified with the available genome sequences. Recently, several mathematical models have been proposed to explain the topology of protein interaction networks that have also implemented the idea of “evolution by duplication”. The power law distribution with its “hubby” topology (e.g...
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