The doctoral dissertations of the former Helsinki University of Technology (TKK) and Aalto University Schools of Technology (CHEM, ELEC, ENG, SCI) published in electronic format are available in the electronic publications archive of Aalto University - Aaltodoc.

Transport Phenomena of Polar Biomolecules and Colloids, Perspectives Through Simulation

Emma Terämä

Dissertation for the degree of Doctor of Science in Technology to be presented with due permission of the Department of Engineering Physics and Mathematics for public examination and debate in Auditorium E at Helsinki University of Technology (Espoo, Finland) on the 3rd of January, 2007, at 12 noon.

Dissertation in PDF format (ISBN 952-10-2963-3)   [14315 KB]
Dissertation is also available in print (ISBN 952-10-2962-5)


The thesis focuses on the transport of polar biomolecules and colloid particles studied through atomistic and coarse-grained simulation techniques. The thesis is comprised of two themes complementing one another. First we concentrate on the structural and dynamical aspects of alcohol molecules in lipid bilayers with varying degree of unsaturation. Second, the thesis employs dielectrophoresis to elucidate the non-equilibrium transport phenomena of nano-sized colloidal particles. The former is an example of simulating a molecular system at the atomic level, providing insight into the mechanism of anesthetics such as alcohols. The latter topic exemplifies the more coarse grained approach of describing surface polarization effects of a colloid coupled to a varying external electric field and subsequent transport of the colloid.

In water solution the lipids self-organize into bilayer structures depicting biological membranes. The effect of ethanol and methanol solvents on the lipid bilayer structure and dynamics was investigated. Simulations show ethanol transport into and through the bilayer, results indicating an undisputable effect of alcohols, esp. ethanol, on membrane properties. Hydrogen bonding between lipid and alcohol molecules is observed, and lipid bilayer pressure profile changes due to alcohol are obtained.

For dielectrophoresis, novel computational models for the transport of (nano-sized) colloidal particles in non-homogeneous electric fields are developed. The model's coupling strength depends on field strength, colloid charge magnitude and charge distribution, which in real life also affect the general characteristics of (surface) conductivity and permittivity that evoke dielectrophoretic behavior of e.g. cells. The colloids in simulation are shown to be affected by their medium via Brownian motion and hydrodynamics. It is demonstrated that aggregation of nano-sized colloids can enhance their transport.

Keywords: lipid membrane, dielectrophoresis, molecular dynamics

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© 2007 Helsinki University of Technology

Last update 2011-05-26