Biological Water: Static and Dynamic Properties of Water in Atomistic and Continuum Simulations of Polysaccharide Solutions and Gels

Abstract

As the predominant mode of microbial life on Earth, biofilms are the hands by which microorganisms leave their mark on the world. The fingerprints of their existence can be found in the hierarchical structure of healthy soils, in the marine snow that processes organic matter in the ocean, and in the 1000‐fold increase in resistance to antibiotics they confer to their inhabitants. Investigations into the impact of divalent ions on the extracellular polymeric substance (EPS) comprising biofilms suggest that their macroscale properties might be informed by the molecular-scale architecture. To explore this relationship,we created large molecular dynamics (MD) simulations of a model EPS at a range of divalent/monovalent counterion ratios (0, 0.5, 1) and water contents (65 to 95 wt.%). In Chapter 2, we develop a methodology for the generation of equilibrated configurations of explicitly-hydrated EPS gels that utilizes an enhanced sampling technique developed by computational biologists. Measurements of the free energy and enthalpy of hydration show a large barrier to dehydration at water contents below 70 wt.% as well as a metastable regime at intermediate water contents that suggests an entropic driving force for dehydration. In chapter 3, we then use our equilibrated EPS configurations to investigate the structure and dynamics of water within these solutions and gels with particular attention paid to their consistency with continuum models of flow in porous media. These findings are the motivation for chapter 4, where we advance towards a numerical simulation capable of showcasing how ion diffusion in biofilms, and associated osmotic water fluxes, might play a role in the mesoscale structural heterogeneities observed by experimentalists. We conclude chapter 4 with a discussion of how to parameterize our numerical solver according to the findings of chapters 2 and 3.