Modeling electrophoresis of peptides, proteins, DNA, blood cells and colloids is based on classical electrokinetic theory. The coupled field equations-Poisson, Navier-Stokes or Brinkman, and ion transport equations are solved numerically to calculate the electrophoretic mobilities. First, free solution electrophoretic mobility expressions are derived for weakly charged rigid bead arrays. Variables include the number of beads (N), their size (radius), charge, distribution (configuration), salt type, and salt concentration. We apply these mobility expressions to rings, rigid rods, and wormlike chain models and then apply the approach to the electrophoretic mobilities and translational diffusion constants of weakly charged peptides. It is shown that our bead model can predict the electrophoretic mobilities accurately. In order to make the method applicable at higher salt concentrations and/or to models consisting of larger sized subunits, account is taken of the finite size of the beads making up the model structure. For highly charged particles, it is also necessary to account for ion relaxation. This ion relaxation effect is accounted for by correcting "unrelaxed" mobilities on the basis of model size and average electrostatic surface, or "zeta" potential. With these corrections our model can be applied to the system with absolute electrophoretic mobilities exceeding approximately 0.20 cm2/kV sec and also models involving larger subunits. This includes bead models of duplex DNA. Along somewhat different lines, we have investigated the electrophoresis of colloidal particles with an inner hard core and an outer diffusive layer ("hairy" particles). An electrokinetic gel layer model of a spherical, highly charged colloid particle developed previously, is extended in several ways. The charge of the particle is assumed to arise from the deprotonation of acidic groups that are uniformly distributed over a portion (or all) of the gel layer. Free energy considerations coupled with Poisson-Boltzmann theory is used to calculate the change of the local pKa of the acidic groups depending on the local electrostatic environment. Based on the modeling of electrophoresis and viscosity, we predict that the thickness of the gel layer decreases as the salt concentration increases. And only the outermost portion of the gel layer is charged.

Micro- and nano-fluidic devices represent an exciting field with a wide range of possible applications. These devices, typically made of either silica or glass, ionize when placed in contact with water. Upon the application of an electric field parallel to the wall, a flow is produced by the charged walls called the electro-osmotic flow (EOF). Since electric fields are so often used as the driving force in these devices, EOF is an extremely common phenomenon. For this reason it is highly desirable to be able to control EOF in order to optimize the functioning of these devices. One method which is quite common experimentally is the modification of the surface using polymer coatings. These coatings can be either adsorbed or grafted, and charged or neutral. The first part of this thesis looks at the role of neutral adsorbed polymer coatings for the modulation of EOF. Specifically our simulation results show that for adsorbed coatings made from a dilute polymer solution the strongest quenching of EOF is found for an adsorption strength at the phase transition for adsorption of the polymers. Further evidence is presented that shows that by using a high density of polymer solution and a polymer which has a strong attraction to the surface a very thick polymer layer can be created. Next the case of charged grafted polymer coatings is examined. The variation of the EOF with respect to several key parameters which characterize the polymer coating is investigated and compared to theory. The prediction that the electrophoretic velocity of the polymers is the same as the EOF generated by a coating made up of the same polymers is found to be false though the two values are quite close. The last section presents results which show how hydrodynamic interactions in charged polymer systems can be modeled mesoscopically without the use of explicit charges by forcing a slip between monomers and the surrounding fluid. This model is validated by simulating some surprising predictions made in the literature such as an object with no net charge having a non-zero force when subjected to an electric field, and how the velocity can even be perpendicular to the applied electric field. The thesis can be roughly divided into two topics: using polymer coatings to modulate EOF, and the free solution electrophoresis of polyelectrolytes. While EOF and free solution electrophoresis might seem unrelated it will be shown that the concepts are the same in both cases. In fact while not investigated in this thesis, the mesoscopic simulation methods for electrophoresis could be applied to the modulation of EOF with polymer coatings allowing for the simulation of longer length and time scales or more complex systems such as heterogeneously grafted colloids.

Micro- and nano-fluidic devices represent an exciting field with a wide range of possible applications. These devices, typically made of either silica or glass, ionize when placed in contact with water. Upon the application of an electric field parallel to the wall, a flow is produced by the charged walls called the electro-osmotic flow (EOF). Since electric fields are so often used as the driving force in these devices, EOF is an extremely common phenomenon. For this reason it is highly desirable to be able to control EOF in order to optimize the functioning of these devices. One method which is quite common experimentally is the modification of the surface using polymer coatings. These coatings can be either adsorbed or grafted, and charged or neutral. The first part of this thesis looks at the role of neutral adsorbed polymer coatings for the modulation of EOF. Specifically our simulation results show that for adsorbed coatings made from a dilute polymer solution the strongest quenching of EOF is found for an adsorption strength at the phase transition for adsorption of the polymers. Further evidence is presented that shows that by using a high density of polymer solution and a polymer which has a strong attraction to the surface a very thick polymer layer can be created. Next the case of charged grafted polymer coatings is examined. The variation of the EOF with respect to several key parameters which characterize the polymer coating is investigated and compared to theory. The prediction that the electrophoretic velocity of the polymers is the same as the EOF generated by a coating made up of the same polymers is found to be false though the two values are quite close. The last section presents results which show how hydrodynamic interactions in charged polymer systems can be modeled mesoscopically without the use of explicit charges by forcing a slip between monomers and the surrounding fluid. This model is validated by simulating some surprising predictions made in the literature such as an object with no net charge having a non-zero force when subjected to an electric field, and how the velocity can even be perpendicular to the applied electric field. The thesis can be roughly divided into two topics: using polymer coatings to modulate EOF, and the free solution electrophoresis of polyelectrolytes. While EOF and free solution electrophoresis might seem unrelated it will be shown that the concepts are the same in both cases. In fact while not investigated in this thesis, the mesoscopic simulation methods for electrophoresis could be applied to the modulation of EOF with polymer coatings allowing for the simulation of longer length and time scales or more complex systems such as heterogeneously grafted colloids.

Micro- and nano-fluidic devices represent an exciting field with a wide range of possible applications. These devices, typically made of either silica or glass, ionize when placed in contact with water. Upon the application of an electric field parallel to the wall, a flow is produced by the charged walls called the electro-osmotic flow (EOF). Since electric fields are so often used as the driving force in these devices, EOF is an extremely common phenomenon. For this reason it is highly desirable to be able to control EOF in order to optimize the functioning of these devices. One method which is quite common experimentally is the modification of the surface using polymer coatings. These coatings can be either adsorbed or grafted, and charged or neutral. The first part of this thesis looks at the role of neutral adsorbed polymer coatings for the modulation of EOF. Specifically our simulation results show that for adsorbed coatings made from a dilute polymer solution the strongest quenching of EOF is found for an adsorption strength at the phase transition for adsorption of the polymers. Further evidence is presented that shows that by using a high density of polymer solution and a polymer which has a strong attraction to the surface a very thick polymer layer can be created. Next the case of charged grafted polymer coatings is examined. The variation of the EOF with respect to several key parameters which characterize the polymer coating is investigated and compared to theory. The prediction that the electrophoretic velocity of the polymers is the same as the EOF generated by a coating made up of the same polymers is found to be false though the two values are quite close. The last section presents results which show how hydrodynamic interactions in charged polymer systems can be modeled mesoscopically without the use of explicit charges by forcing a slip between monomers and the surrounding fluid. This model is validated by simulating some surprising predictions made in the literature such as an object with no net charge having a non-zero force when subjected to an electric field, and how the velocity can even be perpendicular to the applied electric field. The thesis can be roughly divided into two topics: using polymer coatings to modulate EOF, and the free solution electrophoresis of polyelectrolytes. While EOF and free solution electrophoresis might seem unrelated it will be shown that the concepts are the same in both cases. In fact while not investigated in this thesis, the mesoscopic simulation methods for electrophoresis could be applied to the modulation of EOF with polymer coatings allowing for the simulation of longer length and time scales or more complex systems such as heterogeneously grafted colloids.

Micro- and nano-fluidic devices represent an exciting field with a wide range of possible applications. These devices, typically made of either silica or glass, ionize when placed in contact with water. Upon the application of an electric field parallel to the wall, a flow is produced by the charged walls called the electro-osmotic flow (EOF). Since electric fields are so often used as the driving force in these devices, EOF is an extremely common phenomenon. For this reason it is highly desirable to be able to control EOF in order to optimize the functioning of these devices. One method which is quite common experimentally is the modification of the surface using polymer coatings. These coatings can be either adsorbed or grafted, and charged or neutral. The first part of this thesis looks at the role of neutral adsorbed polymer coatings for the modulation of EOF. Specifically our simulation results show that for adsorbed coatings made from a dilute polymer solution the strongest quenching of EOF is found for an adsorption strength at the phase transition for adsorption of the polymers. Further evidence is presented that shows that by using a high density of polymer solution and a polymer which has a strong attraction to the surface a very thick polymer layer can be created. Next the case of charged grafted polymer coatings is examined. The variation of the EOF with respect to several key parameters which characterize the polymer coating is investigated and compared to theory. The prediction that the electrophoretic velocity of the polymers is the same as the EOF generated by a coating made up of the same polymers is found to be false though the two values are quite close. The last section presents results which show how hydrodynamic interactions in charged polymer systems can be modeled mesoscopically without the use of explicit charges by forcing a slip between monomers and the surrounding fluid. This model is validated by simulating some surprising predictions made in the literature such as an object with no net charge having a non-zero force when subjected to an electric field, and how the velocity can even be perpendicular to the applied electric field. The thesis can be roughly divided into two topics: using polymer coatings to modulate EOF, and the free solution electrophoresis of polyelectrolytes. While EOF and free solution electrophoresis might seem unrelated it will be shown that the concepts are the same in both cases. In fact while not investigated in this thesis, the mesoscopic simulation methods for electrophoresis could be applied to the modulation of EOF with polymer coatings allowing for the simulation of longer length and time scales or more complex systems such as heterogeneously grafted colloids.