M.Sc Thesis Defense

Date: 18 August 2015

Modeling and simulation of biomolecular flow in microchannel

Sunitha Marikundil

Supervisors: Prof. D. Roy Mahapatra

Abstract

Microfluidics deal with the behavior, control and manipulation of fluids which are confined at micrometer length scale. It has important application in lab-on-a chip technology, micro-propulsion, additive manufacturing, micro-thermal technologies etc. Microfluidics has been widely used in detection, separation, transportation and mixing of fluids and particles.

Microfluidic modeling and simulation studies are carried out in the present thesis. The interaction behavior of organic molecular structure such as DNA strands with the fluid in a microchannel is studied. Multiple scales are involved in this problem which is not fully understood. Numerical simulations are carried out using a coupled multiphysics finite element scheme. A new approach has been developed to model DNA in the microchannel by assuming DNA as an elastic chain with its characteristic Young's modulus, Poisson's ratio, and density. The interactive behavior of the DNA strands (length scale >1micrometer) under the forces resulting from the fluid dynamic pressure and viscous forces in the channel are analyzed. Simulations are done for rectangular microchannels of varying aspect ratio, containing an incompressible fluid. In the channel, dependence of DNA mobility on factors like channel aspect ratio, velocity distribution, DNA statistical parameters (counter length and end-to-end length) are studied. Straight and coiled DNAs are studied considering their different configurations in the channel. Studies are conducted for different fluid properties, DNA statistical properties, and results are analyzed. For a coiled DNA, mobility is found to be more when its end-to-end length is approximately half the width of the channel. For both coiled and straight DNAs, a higher mobility is observed when the ratio of DNA contour length to channel width approaches unity.

Study of behavior involving measurements of both the biomolecule and the solution simultaneously becomes challenging. An experimental method has been employed to study the distinctive nature of the background solution in the channel by tracing the particle motion in the fluid. An attempt is made to quantify the viscous forces on the DNA strands upon varying concentration of the background fluid. Due to measurement limitation, experimental characterization was done for various different red blood cell (RBC) concentrations (104-108cells/ml) in bovine serum albumin and a power law constitutive model was used. The fluid viscosity was found to increase with the increasing concentration of RBCs. The dependence of viscosity on concentration was studied and a transition regime was detected (106-107 cells/ml), where the fluid changes its behavior from shear thickening to shear thinning. Dimensionless numbers which are important in the micro-regime were calculated from the experimental data. Results were analyzed by simulating the experimental condition. Results obtained can be used for other biomolecules such as DNA with similar length scales. Potential application of these modeling and simulation are in molecular screening processes to improve the performance of microfluidic DNA chips, and in design of microchannel structures of microfluidic devices.