I present research in systems of biomedical relevance consisting of agents near or com- prising surfaces using computational approaches. The research topics include formation of bacterial biofilms, behavior of charged species near stacked, like-charged lamellae, and the the conformational behavior of lamellae with strong self-attraction. In chapter 2, I present agent-based simulations and experimental analysis of bacte- rial surface colonization behavior. Results show that the bacterial population exhibits polyphenic motility despite being genetically homogeneous, and that the deposition of a polysaccharide causes the emergence of distinct bacterial subpopulations that specialize separately in microcolony nucleation and surface exploration. Chapter 3 considers aggregation behavior on a much smaller length scale, wherein an attraction between like-charged cellular lamellae is mediated by the antiviral mole- cule squalamine. Free-energy calculations along with structural analysis of the resulting compounds reveals that the squalamine molecules form bridging configurations that are highly effective at condensing membranes, and that the strength of this condensation is sufficient to eject the viral protein Rac1 from the lamellae. In chapter 4, I explore the ability of such condensed, charged lamellae to selectively exclude ions as a means to control ionic current. Simulations and theory of ion-selective graphene-oxide paper in series with a bulk salt solution under an applied field show how this exclusion leads to a nonlinear current–voltage relationship. Additionally, geometrical asymmetries are introduced into the system to achieve ionic current rectification. Chapter 5 studies the behavior of dilute graphene oxide sheets in poor solvent. In such a case, the conformations taken by the sheet are determined by a competition between its intrinsic bending rigidity and effective self-attraction. I show how self-attraction of a finite range and sufficient strength can overcome bending energy barriers of ∼100kBT to allow sheets to spontaneously condense in solution

Last modified

• 02/13/2018

Creator

• Bernard McAlpine Beckerman

DOI

• https://doi.org/10.21985/N2N38G

Subject

• Material Science and Engineering

Keyword

• biophysics
• soft matter
• molecular dynamics
• coarse graining
• self assembly
• computer simulations

Date created

• 2016-01-01

Resource type

• Dissertation

Rights statement

• In Copyright