In-silico modeling of early-stage biofilm formation

Abstract

Several bacteria and bacteria strands form biofilms in different environmental conditions, e.g. pH, temperature, nutrients, etc. Biofilm growth, therefore, is an extremely robust process. Because of this, while biofilm growth is a complex process affected by several variables, insights into biofilm formation could be obtained studying simple schematic models. In this manuscript, we describe a hybrid molecular dynamics and Monte Carlo model for the simulation of the early stage formation of a biofilm, to explicitly demonstrate that it is possible to account for most of the processes expected to be relevant. The simulations account for the growth and reproduction of the bacteria, for their interaction and motility, for the synthesis of extracellular polymeric substances and Psl trails. We describe the effect of these processes on the early stage formation of biofilms, in two dimensions, and also discuss preliminary three-dimensional results.

A mechanistic understanding of biofilm morphogenesis: Coexistence of mobile and sessile aggregates and phase-separated patterns

“…The sparseness value is larger for colonies with higher cell motility forces. The underlying reason of compact to sparse colony organization with increasing values of motility can be understood by considering two velocities [36]: (i) a growth-induced velocity ( v g ) and (ii) the self-propeling velocity ( v mot ) and their competition. For larger values of motility force, self-propulsion velocity v mot dominates over v g , developing more sparse colony with less order compared to the smaller values of motility force where v g dominate over v mot .…”

“…On the other hand, in a dense bacterial colony, where mechanical interactions among the bacterial cells and the surroundings appear to be a crucial factor in driving the colony expansion and morphogenesis, alternative approaches have been employed to gain insights at the mesoscopic level interactions among the components. In this context, several studies have utilized agent-based/particle-based models or a hybrid type model which can capture the individual-level interactions among the bacterial cells inside a colony [18, 19, 30, 36, 37]. Although these pre-existing studies illuminate several aspects of the occurence of collective phases, a considerable effort is needed to understand the influence of the two significant aspects of a growing bacterial colony: cell motility and physicochemical properties of self-produced EPS.…”

A mechanistic understanding of microcolony morphogenesis: coexistence of mobile and sessile aggregates

“…In this context, several studies have utilized agent-based/particlebased models or a hybrid type model which can capture the individual-level interactions among the bacterial cells inside a colony. 22,23,34,42,43 Although these pre-existing studies illuminate several aspects of the occurrence of collective phases, considerable effort is needed to understand the influence of the two significant aspects of a growing bacterial colony: cell motility and physicochemical properties of self-produced EPS. In particular, how and to what extent these two aspects in conjugation with each other regulate the microcolony morphogenesis is yet to be explored.…”

Interplay of cell motility and self-secreted extracellular polymeric substance induced depletion effects on spatial patterning in a growing microbial colony

“…Bacteria are a well-known example of living active matter that exhibit a variety of complex morphodynamics in their lifestyles. They can show a broad spectrum of nonequilibrium collective phenomena, such as patterned colonies, [1][2][3][4][5][6][7] biofilm formation, [8][9][10][11][12][13][14][15][16] swarming, and turbulent motions, [17][18][19][20][21] depending on the species and environmental conditions. The interplay of growth, division, motions, and local interactions of individual components plays a crucial role in controlling such phenomena.…”