Design and fabrication of a dna electrophoresis chip based on mems technology

Sukas, Sertan
This thesis reports design, fabrication, and implementation of two different micro electrophoresis system architectures for DNA analyses. The first architecture is traditional single channel layout with several design alternatives for size-based separation of DNA fragments. The second one is novel double channel architecture specialized for rapid mutation detection using heteroduplex analysis (HDA) method with an application of a newly designed injection technique. Besides achieving high resolution separations within the length of 1 mm with single channel arrangement, HDA was successfully applied for 590 base pair (bp) long PCR sample with 3 bp mutations in a separation length of 50 m in less than 3 minutes with double channel structure. Microchannels were formed using parylene-C due to its conformal deposition, no surface treatment requirement, transparency, biocompatibility, low background fluorescence, etc. Using the advantage of parylene in fabrication, the microchannels were fabricated with an only three-mask process. New double channel architecture is obtained by dividing the 200 m-wide separation channel into two parts by a 20 m-thick wall between them. For sample injection, various techniques, such as traditional cross, double-T, and double-L were investigated and optimized for single channel architecture assisting with pullback injection method. For double channel architecture, a novel, u-turn injection technique was applied. Precise control of sample amount by adjusting the injection time was accomplished by this new technique. Using high resolution cross-linked polyacrylamide gel as sieving material, separations were achieved in a very short length and time. Electrophoresis was performed in both channels of the double channel microchips simultaneously under the same conditions. This gives the chance of having a control channel in microchip format, which is very critical for the accuracy and reliability of the results in genetic analyses.


Design and analysis of filament wound composite tubes
Balya, Bora; Parnas, Kemal Levend; Department of Mechanical Engineering (2004)
This thesis is for the investigation of the design and analysis processes of filament wound composite tubes under combined loading. The problem is studied by using a computational tool based on the Finite Element Method (FEM). Filament wound tubes are modeled as multi layered orthotropic tubes. Several analyses are performed on layered orthotropic tubes by using FEM. Results of the FEM are examined in order to investigate characteristics of filament wound tubes under different combined loading conditions. W...
Development of a shell finite element for large deformation analysis of laminated composites
Yıldız, Tuba; Darendeliler, Haluk; Department of Mechanical Engineering (2008)
The objective of the present work is to investigate the behavior of laminated fiber -reinforced polymer matrix composite shell structures under bending load with the help of a modified finite element computer code which was previously developed for the analysis of pseudo-layered single material shells. The laminates are assumed to be orthotropic and the formulation is adapted to first order shear deformation theory. The aim is to determine the large deformation characteristics numerically, and to predict th...
A genetic algorithmfor structural optimization
Taşkınoğlu, Evren Eyüp; Oral, Süha; Department of Mechanical Engineering (2006)
In this study, a design procedure incorporating a genetic algorithm (GA) is developed for optimization of structures. The objective function considered is the total weight of the structure. The objective function is minimized subjected to displacement and strength requirements. In order to evaluate the design constraints, finite element analysis are performed either by using conventional finite element solvers (i.e. MSC/NASTRAN®) or by using in-house codes. The application of the algorithm is shown by a num...
Analysis of thin walled open section tapered beams using hybrid stress finite element method
Akman, Mehmet Nazım; Oral, Süha; Department of Mechanical Engineering (2008)
In this thesis, hybrid stress finite element is formulated for the analysis of the isotropic, thin walled, open section beams with variable cross sections. The beam element has two nodes each having seven degrees of freedom. Assumption of stress field is sufficient to determine the element stiffness matrix. Axial, flexural and torsional effects are taken into account in the analysis. The methodology can be applied both to the tapered and the uniform beams. Throughout this study, firstly element cross-sectio...
Development of test structures and methods for characterization of MEMS materials
Yıldırım, Ender; Arıkan, Mehmet Ali Sahir; Department of Mechanical Engineering (2005)
This study concerns with the testing methods for mechanical characterization at micron scale. The need for the study arises from the fact that the mechanical properties of materials at micron scale differ compared to their bulk counterparts, depending on the microfabrication method involved. Various test structures are designed according to the criteria specified in this thesis, and tested for this purpose in micron scale. Static and fatigue properties of the materials are aimed to be extracted through the ...
Citation Formats
S. Sukas, “Design and fabrication of a dna electrophoresis chip based on mems technology,” M.S. - Master of Science, Middle East Technical University, 2007.