Lagrangian Particle Methods for Biological Systems - Porous Media: Applications in Biological Systems and Biotechnology - page 256

realistic set of interaction parameters can often be obtained by using simple
theoretical concepts.
In general, mesoscale DPD simulations make it possible to study the assem-
bly, equilibrium properties, and dynamics of synthetic and biological lipid
bilayers and other large molecular assemblies. The equilibrium structure and
mechanical properties of membrane patches obtained from DPD simulations
are in agreement with experimental results (Gao et al. 2007).
In addition to computational e ciency, DPD provides a consistent way of
simulating the effects of thermal fluctuations on biological systems, which can
be very important at small scales (Sugii et al. 2007). For instance, lipid bilayer
vesicles usually exhibit a much larger surface area than the spheres of same
volume. A large portion of the lipid bilayer vesicles surface area is folded
because of the thermal fluctuation in the system. This excess surface area
could be very important in certain situations, for example, the deformation
of lipid bilayer vesicles in shear flow (de Haas et al. 1997), and this can be
investigated by DPD simulation.
Dissipative particle dynamics has also been applied to other important
biological phenomena. Examples include platelet-mediated thrombus forma-
tion in blood vessels; the motion, collision, aggregation, and adhesion of acti-
vated platelets (Filipovic et al. 2006, 2007, 2008); modeling of red blood cells
in shear flow (Richardson et al. 2008); and modeling of the conformations
of DNA molecules suspended in a fluid flowing in microchannels (Fan et al.
2006).
Here we describe a DPD model for the growth and deformation of biofilm
in a flowing fluid. The hydrodynamic interactions between the biofilm and
liquid flow are expected to be important in this application, and an impor-
tant advantage of DPD, relative to Brownian dynamics simulations, is that
the hydrodynamic interactions are naturally included in DPD models. Biofilm
can be defined as a microbial community composed of either single or multiple
species embedded in extracellular biopolymer, which adheres to a solid sub-
strate. The modeling of biofilm provides important insight that contributes to
a better understanding of the mechanisms of biofilm formation, growth, and
cell death.
Modeling the effects of nutrient and metabolic waste transport and fluid
flow on biofilm development is very challenging because of the complexity of
the underlying fundamental physical, chemical, and biological processes occur-
ring at various scales (Picioreanu et al. 2000). The interplay and coupling
between those physical, chemical, and biological processes governs the evo-
lution of biofilm structure. Biofilm structure development can be conceptual-
ized as a competition between “positive” and “negative” processes (Picioreanu
et al. 2000). Here “positive” processes refer to processes that lead to biofilm
volume expansion, while “negative” processes refer to processes that lead to
biofilm volume reduction. Typical “positive” processes include cell attach-
ment, cell division, and extracellular polymeric substance (EPS) production
as a result of the transport of dissolved substrate via both advection and