A punctuated equilibrium model of biological evolution with relative fitness between different species being the fundamental driving force of evolution is introduced. Mutation is modeled as a fitness updating cellular automaton process where the change in fitness after mutation follows a Gaussian distribution with mean x > 0 and standard deviation σ. Scaling behaviors are observed in our numeri...

We present a simple model for biological aging. We studied it through computer simulations and we have found this model to reflect some features of real populations. 1 The problem of aging has been studied recently [1] also by computer simulations, useful in understanding how the survival rates for younger and older individuals evolve in time and affect the preservation of the species [2]–[4]. ...

Probabilistic model checking is a formal verification technique that has been successfully applied to the analysis of systems from a broad range of domains, including security and communication protocols, distributed algorithms and power management. In this paper we illustrate its applicability to a complex biological system: the FGF (Fibroblast Growth Factor) signalling pathway. We give a deta...

This review deals with computer simulation of biological aging, particularly with the Penna model of 1995. They are based on the mutation accumulation theory of half a century ago. The results agree well with demographical reality, and also with the seemingly contradictory influence of predators on the aging of prey.

Important macrodynamical features of the terrestrial ecosystem’s evolution, like the selectivity of extinction events, are reproduced by a mathematical model recently introduced in the literature. We also show that the model is consistent with Kimura’s neutral theory of molecular evolution. @ 1998 Elsevier Science B.V. PACS: 87.lO.+e; 05.4O.+j

Computational biomodelers adopt either of the following approaches: build rich, as complete as possible models in an effort to obtain very realistic models, or on the contrary, build as simple as possible models focusing only on the core aspects of the process, in an effort to obtain a model that is easier to analyze, fit, and validate. When the latter strategy is adopted, the aspects that are ...

A hierarchical architecture for information processing, the hypernetwork model, has recently been implemented. This is a three level model, inspired by biological systems, that includes representation of scale, vertical flow of information, and feedback control. All interactions are based on complementary relationships between molecular subunits. The system is molded to perform desired tasks th...

High-throughput technologies in the field of biology have led to an exponential growth in the amount of data generated over the past several years. This is witnessed in the sequencing of the genomes of mouse, rat, rice, Arabidopsis, human and many bacteria and viruses. Ever increasing computational resources are required to annotate and explore the resulting sequences and to refine our current ...

This Account is focused on computer simulation studies of model biological membrane systems with potential applications in biomedical research. In the past decade, classical molecular dynamics has provided novel insights into the properties of model biomembrane systems, including the nature of the DNA-lipid interactions, the effect of pore-forming transmembrane peptides on the lipid environment...

Much has been written of the facilities for ontology building and reasoning offered for ontologies expressed in the Web Ontology Language (OWL). Less has been written about how the modelling requirements of different areas of interest are met by OWL-DL’s underlying model of the world. In this paper we use the disciplines of biology and bioinformatics to reveal the requirements of a community th...