Modeling and analyzing biomolecular networks

Modeling and analyzing biomolecular networks

The authors argue for the need to model and analyze biological networks at molecular and cellular levels. They propose a computational toolbox for biologists. Central to their approach is the paradigm of hybrid models in which discrete events are combined with continuous differential equations to capture switching behavior. Disciplines Engineering | Mechanical Engineering Comments Suggested Cit...

Modeling and querying biomolecular interaction networks

We introduce a formalism to represent and analyze protein-protein and protein-DNA interaction networks. We illustrate the expressivity of this language, by proposing a formal counterpart of Kohn’s compilation on the mammalian cell cycle control. This effectively turns an otherwise static knowledge into a discrete transition system incorporating a qualitative description of the dynamics. We then...

Hybrid Modeling and Simulation of Biomolecular Networks

In a biological cell, cellular functions and the genetic regulatory apparatus are implemented and controlled by a network of chemical reactions in which regulatory proteins can control genes that produce other regulators, which in turn control other genes. Further, the feedback pathways appear to incorporate switches that result in changes in the dynamic behavior of the cell. This paper describ...

Cellular Automata Modeling of Biomolecular Networks

Modeling and Analyzing Hydrocyclone Performances

Hydrocyclones have been used as an operational tool to separate liquids from solids in different industries for more than 50 years. Considering the importance of this issue, many experimental and numerical attempts have been made to estimate the performance of this tool regarding the resulting pressure drop and the separation efficiency (particles separation limit diameter...