Samuel Kinde Kassegne

Numerical modeling of transport and accumulation of DNA on electronically active biochips

Abstract Transport and accumulation of biomolecules, particularly DNA, in active electronic chips are investigated through numerical modeling and experimental verification. Various geometric and design configurations of electronically active DNA chips are considered. Further, we investigate the effect of electric field distribution on practical design of flow cells and chips. Particular attention is focused on the geometric effects on current and electric field distribution which are well captured by a finite element method-based model. We demonstrate that these geometric effects are observed only in buffers of very low conductivity. We also demonstrate that numerical models which do not include the charge transfer mechanism between electrodes and the buffer solution will fail to predict the reduction of these geometric effects with increased buffer conductivity. The review of the technology is based on computer simulation using a finite element-based computational model and experimental results of electric field distribution, DNA transport and accumulation. Comparison of theoretical results for electrophoretic DNA accumulation with those obtained from experiments and a simple analytical model is presented.

Design issues in SOI-based high-sensitivity piezoresistive cantilever devices

In this work, the mechanical design and optimization of high-sensitivity piezoresistive cantilevers used for detecting changes in surface stresses due to binding and hybridization of biomolecules on the surface of the cantilever is investigated. The silicon-based cantilevers are typically of a micron order thickness doped with boron to introduce piezoresistivity. Microcantilever beams can be built as micro-mechanical arrays which could provide a basis for developing devices capable of performing multi-plexed, low-cost genomic and proteomic analyses. This paper provides several design solutions in optimizing the cantilever mechanical design to address the sensitivity required when approaching recognition of single base pairing of DNA molecules. The sensitivity of such piezoresistive cantilevers to the chemo-mechanical stress induced currents depends not only on the cantilever geometric properties, such as depth and width but also on the depth of the piezo layer (dopant) and its doping characteristics. It is often an expensive exercise to determine the optimum design parameters for increased sensitivity, particularly the dopant characteristics for such MEMS devices. A managed solution or parametric solution algorithm based on a finite element simulation is used to help determine optimum location and depth of this piezoresistive layer in the cantilever that maximizes the piezoresistor signals. Further, novel approaches for increasing the sensitivity of piezoresistive cantilevers through selected structural discontinuities are discussed.

PMN-PT single crystal resonators for sensing acetone vapors

This paper compares frequency measurements in lead magnesium niobate-lead titanate (PMN-PT) resonators with conventional quartz crystal microbalance (QCM) resonators when exposed to acetone vapors under identical test conditions. A pumpless mechanism for driving acetone vapors by convection force was developed in our experimental setup. The frequency shift recorded in response to acetone vapor exposure for the PMN-PT resonator was more than 10,000 times larger than for the QCM resonator. Our experimental results reinforce the notion that PMN-PT resonators could be a superior replacement for QCM resonators in a variety of biosensor applications. The experimental setup heated water to produce acetone vapors, a volatile organic chemical, which were delivered to a sensing chamber to interact with the sensing unit. Chemical vapors were driven toward the sensing unit and circulated through the system via a pumpless mechanism by the principle of convection. Both types of resonators displayed a change in frequency as acetone vapors were applied, but PMN-PT showed a more significant change by several orders of magnitude.

Reactive Current-Activated Tip-Based Sintering of Ni–Al Intermetallics

Current-activated tip-based sintering (CATS) is a new process that imposes local current-activated sintering conditions to consolidate selected areas of a powder compact/bed through the controlled application of a contacting tip electrode. The process has the ability of achieving very high sintering rates and obtaining complex-sintered geometries through the controlled precision motion of the electrically conductive tip. In this study, the high current densities afforded by CATS are utilized to locally activate a macroscopic combustion synthesis type reaction in compacts of reactive mixtures of nickel and aluminum to rapidly form nickel aluminides. The effect of current intensity on the ignition time, microstructure, homogeneity, and properties of the combustion synthesized products is discussed in this article. It was found that ultra-rapid formation of aluminum-rich intermetallics precedes and contributes to the major ignition event. Moreover, time to ignition was found to decrease with an increase in current intensity, also leading to less homogenous microstructures.

Microelectro-optical DNA array sensor

We describe a micro electro-optical DNA array sensor whose main features are that it is rapid, sensitive, highly accurate and capable of detecting more than one analyte. These features are the consequence of electronic control of three key elements of DNA assays, namely: concentration of the target molecules at the analysis sites, hybridization of the DNA targets to capture probes and discrimination of complementary DNA from non-complementary DNA. The assays are monitored using a scanning confocal optical platform for fluorescence detection. A finite-element based computational model for determining electric field distribution at the biochip electrode array and electrophoretic transport of DNA species is built and analyzed. Comparison of theoretical results for electrophoretic DNA accumulation with those obtained from experiments and a simple analytical model is presented.

A Direct Comparison of Glassy Carbon and PEDOT-PSS Electrodes for High Charge Injection and Low Impedance Neural Interfaces

For neural applications, materials able to interface with the brain without harming it while recording high-fidelity signals over long-term implants are still sought after. Glassy Carbon (GC) and Poly (3,4-ethylenedioxythiophene)-poly (styrenesulfonate) (PEDOT-PSS) have proved to be promising materials for neural interfaces as they show – compared to conventional metal electrodes - higher conductivity, better electrochemical stability, very good mechanical properties and therefore seem to be very promising for in vivo applications. We present here, for the first time, a direct comparison between GC and PEDOT-PSS microelectrodes in terms of biocompatibility, electrical and electrochemical properties as well as in vivo recording capabilities, using electrocorticography microelectrode arrays located on flexible polyimide substrate. The GC microelectrodes were fabricated using a traditional negative lithography processes followed by pyrolysis. PEDOT-PSS was selectively electrodeposited on the desired electrodes. Electrochemical performance of the two materials was evaluated through electrochemical impedance spectroscopy and cyclic voltammetry. Biocompatibility was assessed through in-vitro studies evaluating cultured cells viability. The in vivo performance of the GC and PEDOT-PSS electrodes was directly compared by simultaneously recording neuronal activity during somatosensory stimulation in Long-Evans rats. We found that both GC and PEDOT-PSS electrodes outperform metals in terms of electrochemical performance and allow to obtain excellent recordings of somatosensory evoked potentials from the rat brain surface. Furthermore, we found that both GC and PEDOT-PSS substrates are highly biocompatible, confirming that they are safe for neural interface applications.

Buckling characteristic of multi-laminated composite elliptical cylindrical shells

Fiber-reinforced composite materials continue to experience increased adoption in aerospace, marine, automobile, and civil structures due to their high specific strength, high stiffness, and light weight. This increased use has been accompanied by applications involving non-traditional configurations such as compression members with elliptical cross-sections. To model such shapes, we develop and report an improved generalized shell element called 4EAS-FS through a combination of enhanced assumed strain and the substitute shear strain fields. A flat shell element has been developed by combining a membrane element with drilling degree-of-freedom and a plate bending element. We use the element developed to determine specifically buckling loads and mode shapes of composite laminates with elliptical cross-section including transverse shear deformations. The combined influence of shell geometry and elliptical cross-sectional parameters, fiber angle, and lay-up on the buckling loads of an elliptical cylinder is examined. It is hoped that the critical buckling loads and mode shapes presented here will serve as a benchmark for future investigations.

Envisioning a National e-Medicine Network Architecture in a Developing Country: A Case Study

Poor infrastructures in developing countries such as Ethiopia and much of Sub-Saharan Africa have caused these nations to suffer from lack of efficient and effective delivery of basic and extended medical and healthcare services. Often, such limitation is further accompanied by low patient-doctor ratios, resulting in unwarranted rationing of services. Apparently, e-medicine awareness among both governmental policy makers and private health professionals is motivating the gradual adoption of technological innovations in these countries. It is argued, however, that there still is a gap between current e-medicine efforts in developing countries and the existing connectivity infrastructure leading to faulty, inefficient and expensive designs. The particular case of Ethiopia, one such developing country where e-medicine continues to carry significant promises, is investigated and reported in this article.

Work in Progress: Lessons from Virtual Supervision of Engineering and Computer Science Graduate Students - Case of Addis Ababa University

In this paper, we document the case of a virtual/remote graduate student supervision the author carried out at the Addis Ababa University, Ethiopia from the US over a period of two years. The theses of three engineering and two computer science students at the MS level were successfully supervised in this period. At one point, this virtual supervision of students at the computer science department of Addis Ababa University (AAU) by external faculty at the US had accounted to almost one-third of the supervised MS theses in the whole department. Lessons on the adoption of similar collaborations between US universities and overseas universities is also investigated and reported

Mechanical vibration induced electro-spinning of polyvinylidene difluoride (PVDF)

Polyvinylidene difluoride (PVDF) is a piezoelectric polymer with a low-cost, high flexibility and biocompatibility that is suitable for various energy conversion applications between the electrical and mechanical forms of energy. One of the novel techniques to create PVDF fibers is electro-spinning. In the present work, the above technique has been applied to develop electro-spun thin-film based on PVDF with the use of high electric field and a high-frequency mechanical vibratory motion as an electro-spinning setup. The high-frequency vibratory motion is used to create effective fluid viscous forces to achieve a localized fluid spreading and thinning behavior of extremely thin polymer fiber solution.