Thermal enhancement of PCR using ternary hybrid nanofluids /
Polymerase chain reaction (PCR) is a vital tool in molecular diagnostics. Still, it is challenged with a host of poor yield, low sensitivity, specificity, contamination, non-specific target amplification, time-consuming, higher cost, energy-intensive, etc. In this study, the performance of PCR as a...
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| Format: | Thesis Book |
| Language: | English |
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| Online Access: | http://studentrepo.iium.edu.my/handle/123456789/11167 |
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| Summary: | Polymerase chain reaction (PCR) is a vital tool in molecular diagnostics. Still, it is challenged with a host of poor yield, low sensitivity, specificity, contamination, non-specific target amplification, time-consuming, higher cost, energy-intensive, etc. In this study, the performance of PCR as a thermocycler is enhanced from a mechanical engineering perspective by adding additives leading to the enhancement of thermal conductivity of the reaction. In this study, two types of novel ternary hybrid nanoparticles (THNp) or tri-hybrid nanoparticles (GO-TiO2-Ag and rGO-TiO2-Ag) were synthesized consisting of three different nanoparticles graphene oxide, titanium dioxide, and silver decorated on each other. The two THNp were synthesized and then characterized using various techniques. The THNp were dispersed in lab-grade DDH2O and sonicated substantially to form stable ternary hybrid nanofluids (THNf). Zeta potential of the prepared nanofluids was measured to check their stability, and it was in a range of 25 mV to 35 mV. The nanofluids were then serially diluted to 5 levels.Thermal conductivity measurements were performed, and the measurements showed a significant enhancement of about 66% and 83% for both GO-TiO2-Ag and rGO-TiO2-Ag, respectively, with THNp in the base fluids. The nanofluids' dynamic viscosity measurements show that the ternary hybrid nanofluids behave as Newtonian and non-Newtonian, where the viscosity decreases with the increase in temperature. Rheological investigations of both the ternary hybrid nanofluids exhibit Newtonian behavior with the stock solution. At the same time, it behaves as non-Newtonian, shear-thinning, or pseudo-plastic fluid when the concentration is diluted. At higher temperatures and low shear rates, the viscosity decreases significantly, which indicates shear thinning behavior. Concentration played a vital role in the change of viscosity due to the variation of temperature. Agglomeration is believed to be the reason for such behavior.Effects of concentration, temperature, and stresses applied in the non-linear viscoelastic fluid revealed linear viscoelastic (LVE) region through amplitude and frequency sweep tests. PCR experiments were performed on the extracted DNA. The initial PCR amplicons from the agarose gel electrophoresis showed that a higher concentration of nanoparticles is not of much significance to PCR, while lower concentration (5x10-3 wt.%) of both GO-TiO2-Ag and rGO-TiO2-Ag contribute a significant enhancement of PCR reaction while reducing the number of cycles to about 40% when compared to PCR without nanoparticles (control). Subsequent PCR study showed PCR amplicon yield increased by 16.74-folds and 15.30- folds with the addition of GO-TiO2-Ag and rGO-TiO2-Ag, respectively. Band intensity study corroborated the same, indicating that the addition of THNp contributes to the thermal enhancement in the reactions. Sanger sequencing results showed the presence of a conserved region, and no DNA damage was observed with the addition of THNp. Separately, DNA denaturation tests were performed with and without the use of THNf for all prepared concentrations. The results showed significantly higher absorbance of UV light in the samples with THNf, indicating earlier denaturation of DNA strands due to the enhancement of thermal conductivity of the reaction. Numerical simulations using ANSYS thermal transient model were performed for a PCR setup with and without THNp. The temperature contours showed a significant enhancement of the heat transfer in the PCR reaction with THNp as an additive. They reduced the overall time by about 40%, corroborating our experimental results. |
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| Item Description: | Abstracts in English and Arabic.
"A thesis submitted in fulfilment of the requirement for the degree of Doctor of Philosophy (Engineering)." --On title page. |
| Physical Description: | xvii, 160 leaves : illustrations ; 30 cm. |
| Bibliography: | Includes bibliographical references (leaves 127-148). |