A dynamic logic method for determining behaviors of biological networks

TL;DR

This paper introduces a dynamic logic approach combining qualitative and quantitative methods to analyze biological networks, revealing key behaviors like bistability and oscillations, with applications to cell signaling pathways.

Contribution

The paper develops a novel dynamic logic method that integrates logic operations with interaction parameters to analyze biological network behaviors.

Findings

Proved theorems for bistable and oscillatory states

Showed time delays are crucial for oscillations

Single-variable networks do not exhibit chaos

Abstract

A dynamic logic method was developed to analyze molecular networks of cells by combining Kauffman and Thomas's logic operations with molecular interaction parameters. The logic operations characterize the discrete interactions between biological components. The interaction parameters (e.g. response times) describe the quantitative kinetics. The combination of the two quantitatively characterizes the discrete biological interactions. A number of simple networks were analyzed. The main results include: we proved the theorems to determine bistable states and oscillation behaviors of networks, we showed that time delays are essential for oscillation structures, we proved that single variable networks do not have chaotic behaviors, and we explained why one signal can have multiply responses. In addition, we applied the present method to the analysis of the MAPK cascade, feed-forward loops, and mitosis cycle of budding yeast cells.