Simulations of Depletion Interactions in Biology: Collapsing Polymers, Stacking Red Blood Cells, and Bundling Rods

Date and Time


MacN 415



Hendrick de Haan, UOIT


Objects suspended in a solvent that also contains many smaller objects will often stick together even in the absence of anyattractive chemical interactions. The mechanism driving this aggregation is called the depletant force and its form can be derived strictly from entropic considerations. Depletant forces play a critical role in biological systems at cellular and sub-cellular lengths scales where having a number of large biological molecules in an environment crowded with smaller molecules is the norm. They are also used routinely in the lab for purposes such as stabilizing colloids or precipitating out desired cells. In this talk I will provide an introduction to depletion forces and then discuss three different systems that we are investigating with coarse-grained molecular dynamics simulations. In the first, the collapse of polymers from coiled to globular states is induced by the addition of depletants. This work has implications for processes such as the packing of DNA into higher order structures and ultimately into chromosomes. In the second, we show that depletant interactions are sufficient to cause red blood cells to stack into rouleaux. These roll-of-coins like structures appear as a non-specific disease indicator in optical microscopy of blood. For the third project, rod-like molecules are induced to bundle via depletant interactions. Our results indicate that aggregation is a function of both rod length and rod stiffness thus suggesting separation applications.

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