M.Sc Thesis

M.Sc StudentDagan Ofer
SubjectSimulation Tool Coupling Non-Linear Electrophoresis and
Reaction Kinetics for Developing and Optimizing
New Biosensing Assay
DepartmentDepartment of Mechanical Engineering
Supervisor ASSOCIATE PROF. Moran Bercovici
Full Thesis textFull thesis text - English Version


Electrophoretic separation and concentration techniques are extensively used in a wide range of chemical and biochemical applications, including drug discovery, genetics, and food analysis. The research and development of novel bioanalytical assays and new applications presents challenges in both improving the resolution and sensitivity of these assays on the one hand and lowering R&D costs on the other hand. Using computer simulations for design and optimization of new assays is necessary to address these challenges.

In this dissertation we present the development, formulation, validation, and demonstration of a fast, generic and open source simulation tool, which integrates non-linear electromigration with multispecies non-equilibrium reaction kinetics. The code is particularly useful for the design and optimization of new electrophoresis-based bioanalytical assays, in which electrophoretic transport, separation, or focusing control analyte spatial concentration and subsequent reactions. We decouple    the kinetics solver for the reactants from solver for the electric field, and demonstrate an order of magnitude improvement in total simulation time for a series of 100 reaction simulations, when using a common background electric field. 

The code can efficiently handle complex electrophoretic setups coupling sharp electric field gradients with bulk reactions, surface reactions, and competing reactions. We present validation of the code against published data from the literature, and its use for a range of realistic assays. In the examples we demonstrate that the code can be used both as a design and optimization tool for new assays and as a tool for deeper research into the basic physical mechanisms of electromigation-reaction problems.

The user can define arbitrary initial conditions and reaction rules, and we believe it will be a valuable tool for the design of novel bioanalytical assays. The code is available as an open source for free download at http://microfluidics.technion.ac.il