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Biomedical subjects

Michael D Graham

Publications and source records attributed to Michael D Graham.

11 recordsLinked to original sources
PubMed2006

N log N method for hydrodynamic interactions of confined polymer systems: Brownian dynamics.

A Brownian dynamics simulation technique is presented where a Fourier-based N log N approach is used to calculate hydrodynamic interactions in confined flowing polymer systems between two parallel walls. A self-consistent coarse-grained Langevin description of the polymer dynamics is adopted in which the polymer beads are treated as point forces. Hydrodynamic interactions are therefore included in the diffusion tensor through a Green's function formalism. The calculation of Green's function is based on a generalization of a method developed for sedimenting particles by Mucha et al. [J. Fluid Mech. 501, 71 (2004)]. A Fourier series representation of the Stokeslet that satisfies no-slip boundary conditions at the walls is adopted; this representation is arranged in such a way that the total O(N2) contribution of bead-bead interactions is calculated in an O(N log N) algorithm. Brownian terms are calculated using the Chebyshev polynomial approximation proposed by Fixman [Macromolecules 19, 1195 (1986); 19, 1204 (1986)] for the square root of the diffusion tensor. The proposed Brownian dynamics simulation methodology scales as O(N1.25 log N). Results for infinitely dilute systems of dumbbells are presented to verify past predictions and to examine the performance and numerical consistency of the proposed method.

Algorithms↗
PubMed2006

Cross-stream migration of flexible molecules in a nanochannel.

Molecular dynamics simulations are used to examine the cross-stream chain migration phenomenon in dilute polymer solutions that are flowing in nanochannels. In particular, both uniform planar shear (Couette) and pressure driven (Poiseuille) flows of a dilute polymer solution are studied using a bead-spring representation of polymer chains and a coarse grained model for the solvent. Our results show that three mechanisms govern the migration of deformable molecules in a nanochannel: (1) chain-wall hydrodynamic interactions, (2) thermal diffusion, and (3) gradient in chain mobility. These results are discussed in the context of recent experimental, numerical and theoretical work.

Bacteriophage lambda↗
PubMed2005

Transport and collective dynamics in suspensions of confined swimming particles.

Direct simulations of large populations of confined hydrodynamically interacting swimming particles at low Reynolds number are performed. Hydrodynamic coupling between the swimmers leads to large-scale coherent vortex motions in the flow and regimes of anomalous diffusion that are consistent with experimental observations. At low concentrations, swimmers propelled from behind (like spermatazoa) strongly migrate toward solid surfaces in agreement with simple theoretical considerations; at higher concentrations this localization is disrupted by the large-scale coherent motions.

Journal Article↗
PubMed2005

Role of desorption kinetics in determining marangoni flows generated by using electrochemical methods and redox-active surfactants.

We report quantitative measurements of Marangoni flows generated at the surfaces of aqueous solutions by using water-soluble redox-active surfactants in combination with electrochemical methods. These measurements are interpreted within the framework of a simple model that is based on lubrication theory and the proposition that the kinetics of the desorption of redox-active surfactants from the surfaces of aqueous solutions plays a central role in determining the strength of the Marangoni flow. The model predicts that the leading edge velocity of the Marangoni flow will decay exponentially with time and that the rate constant for the decay of the velocity can yield an estimate of the surfactant desorption rate constant. Good agreement between theory and experiments was found. By interpreting experimental measurements of electrochemically generated Marangoni flows within the framework of the model, we conclude that the desorption rate constant of the redox-active surfactant Fc(CH(2))(11)-N(+)(CH(3))(3)Br(-), where Fc is ferrocene, is 0.07 s(-)(1). We also conclude that the ionic strength of the aqueous solution has little effect on the desorption rate constant of the ferrocenyl surfactant.

Journal Article↗
PubMed2004

A microfluidic system for large DNA molecule arrays.

Single molecule approaches offer the promise of large, exquisitely miniature ensembles for the generation of equally large data sets. Although microfluidic devices have previously been designed to manipulate single DNA molecules, many of the functionalities they embody are not applicable to very large DNA molecules, normally extracted from cells. Importantly, such microfluidic devices must work within an integrated system to enable high-throughput biological or biochemical analysis-a key measure of any device aimed at the chemical/biological interface and required if large data sets are to be created for subsequent analysis. The challenge here was to design an integrated microfluidic device to control the deposition or elongation of large DNA molecules (up to millimeters in length), which would serve as a general platform for biological/biochemical analysis to function within an integrated system that included massively parallel data collection and analysis. The approach we took was to use replica molding to construct silastic devices to consistently deposit oriented, elongated DNA molecules onto charged surfaces, creating massive single molecule arrays, which we analyzed for both physical and biochemical insights within an integrated environment that created large data sets. The overall efficacy of this approach was demonstrated by the restriction enzyme mapping and identification of single human genomic DNA molecules.

DNA↗
PubMed2004

An externally driven magnetic microstirrer.

In this paper, an inexpensive, easy-to-fabricate active magnetic mixer is presented. This mixer functions on top of a common magnetic stir plate and is capable of mixing two streams, each at flow rates up to 5 ml min(-1). A liquid-phase photopolymerization technique is used to fabricate the device. An analysis of mixing efficiency is based on greyscale intensity measurements of two coloured streams passing through the mixer. A brief hypothesis of the mechanism of mixing is also presented.

Complex Mixtures↗
PubMed2004

Shear-induced migration in flowing polymer solutions: simulation of long-chain DNA in microchannels [corrected].

We simulate dilute solution dynamics of long flexible polymer molecules in pressure driven flow in channels with widths of roughly 0.1-10 times the polymer bulk radius of gyration. This is done using a self-consistent coarse-grained Langevin description of the polymer dynamics and a numerical simulation of the flow in the confined geometry that is generated by the motions of polymer segments. Results are presented for a model of DNA molecules of approximately 10-100 microm contour length in micron-scale channels. During flow, the chains migrate toward the channel centerline, in agreement with well-known experimental observations. The thickness of the resulting hydrodynamic depletion layer increases with molecular weight at constant flow strength; higher molecular weight chains therefore move with a higher average axial velocity than lower molecular weight chains. In contrast, if the hydrodynamic effects of the confining geometry are neglected, depletion of concentration is observed in the center of the channel rather than at the walls, contradicting experimental observations. The mechanisms for migration are illustrated using a simple kinetic theory dumbbell model of a confined flexible polymer. The simple theory correctly predicts the trends observed in the detailed simulations. We also examine the steady-state stretch of DNA chains as a function of channel width and flow strength. The flow strength needed to stretch a highly confined chain away from its equilibrium length is shown to increase with decreasing channel width, independent of molecular weight; this is fairly well explained using a simple blob picture.

Computer Simulation↗
PubMed2003

DNA dynamics in a microchannel.

An extended Brownian dynamics simulation method is used to characterize the dynamics of long DNA molecules flowing in microchannels. The relaxation time increases due to confinement in agreement with scaling predictions. During flow the molecules migrate toward the channel center line, and thereby segregate according to molecular weight. Capturing these effects requires the detailed incorporation of solvent flow in the simulation method, demonstrating the importance of hydrodynamic effects in the dynamics of confined macromolecules.

Computer Simulation↗
PubMed2002

Toward a structural understanding of turbulent drag reduction: nonlinear coherent states in viscoelastic shear flows.

Nontrivial steady flows have recently been found that capture the main structures of the turbulent buffer layer. We study the effects of polymer addition on these "exact coherent states" (ECS) in plane Couette flow. Despite the simplicity of the ECS flows, these effects closely mirror those observed experimentally: Structures shift to larger length scales, wall-normal fluctuations are suppressed while streamwise ones are enhanced, and drag is reduced. The mechanism underlying these effects is elucidated. These results suggest that the ECS are closely related to buffer layer turbulence.

Journal Article↗
PubMed2002

Pattern formation in flowing electrorheological fluids.

A two-fluid continuum model is developed to describe mass transport in electro- and magnetorheological suspensions. The particle flux is related to the field-induced stresses. Solutions of the resulting mass balance show column formation in the absence of flow, and stripe formation when a suspension is subjected simultaneously to an applied electric field and shear flow.

Journal Article↗