Modeling molecular structure and behavior of microbial extracellular polymeric substances through interacting-particle reaction dynamics

Abstract

Extracellular polymeric substances (EPS) are essential for bacteria to interact with external environments and play a key role in the formation of microbial aggregates. Unveiling the black box of EPS has become an urgent topic in the field of microbiology, medical science and environmental science. Here, we develop an explicit approach to describe the molecular structure and behaviors of EPS using interacting-particle reaction dynamics (iPRD). Three representative states of EPS (i.e., normal EPS layer, metal bridging EPS layer and extracted EPS layer) are qualitatively simulated at molecular scale and validated with previous research results on EPS. Furthermore, an averaged concentration representation method is proposed to quantitatively model the EPS-oriented bioprocesses. Through this method, the contents of protein and polysaccharide in EPS extracted by cation exchange resin are accurately predicted by our model (R2>0.982). This work gives new insights into EPS at the molecular scale and opens up new avenues for further exploring and modeling complex molecular structure and behaviors of EPS.

Keywords

• extracellular polymeric substances
• interacting-particle reaction dynamics
• computational biology
• extraction
• microbial aggregates
• averaged concentration representation method