College of Engineering

Theses and dissertations submitted to the College of Engineering

Items in this Collection

The DNA sequence serves as the fundamental blueprint of life, offering potential for biological discovery through computational analysis. With the continuous decline in sequencing costs, genomic data are being generated at an unprecedented rate—attracting not only researchers but also potential threats from malicious actors. Sensitive genetic information can be exploited in various ways, such as discrimination based on disease predisposition or blackmail involving participation in genomic studies. These concerns highlight the urgent need for secure and efficient DNA data protection. While existing approaches utilize both general-purpose and DNA-specific encryption methods, encryption alone can impose substantial computational overhead, thereby underscoring the necessity of integrating compression techniques to enhance efficiency. This study introduces Biitroot, a novel approach that combines k-mer–based compression with Advanced Encryption Standard (AES) encryption. Compression efficiency is optimized by tuning k-mer lengths, encoding schemes, and key-handling mechanisms across organisms and sequence sizes. Biitroot achieves file size reductions of up to 75%, outperforming the 67% reduction achieved by the reference method, Cryfa. Furthermore, Biitroot supports batch compression with independent per-sample processing, allowing de-compression of individual files without accessing others. Additional capabilities include customizable AES modes, support for the extended DNA alphabet, and secure management
of both compression and encryption keys.


This study explored the valorization of cashew nut shell (CNS) cake, an agro-industrial by-product, through oxidative torrefaction to enhance its performance as a solid biofuel. Despite their abundance, CNS cakes remain underutilized for energy applications. Oxidative torrefaction, a thermal treatment in the presence of limited oxygen, was conducted at 200, 250, and 300°C for 20, 40, and 60 minutes to assess changes in the fuel properties. The process significantly altered the lignocellulose composition: mainly extractives and hemicellulose were reduced, while cellulose and lignin were concentrated, improving the combustion behavior. Fuel quality was enhanced by reductions in moisture and volatile matter (75.64% to 41.40%) along with oxygen and hydrogen, and increased in fixed carbon (22.89% to 55.43%) with carbon. The 300°C for 20 minutes condition was identified as optimal, achieving the highest energy–mass co-benefit index (EMCI) of 20.64%, with a higher heating value (HHV) of 24.34 MJ/kg, energy density ratio (EDR) of 1.28, mass yield (MY) of 72.46%, and energy yield (EY) of 93.10%. Torrefying beyond this point led to marginal HHV gains, but significant losses in fuel mass and energy retention, indicating diminishing returns. Thermogravimetric analysis showed that severe torrefaction improved thermal stability and reduced reactivity, whereas less severe conditions provided better ignitability. These results demonstrate that oxidative torrefaction transformed the structural and physicochemical components of the CNS cake, enhancing the bioenergy potential and combustion profile, while maintaining a substantial portion of usable fuel. This approach offers a much lower ash and emissions alternative to fossil fuels. Moreover, valorizing the CNS cake through torrefaction supports viable waste management and contributes to circular bioenergy systems.


A user’s participation in a study leads to his/her personal and possibly sensitive data to be stored in a statistical database, where data analysts can perform calculations and then extract useful information. Privacy is guaranteed through generic, one-size-fits-all privacy policies defined by service providers, which could still leave the data of the end-users vulnerable. This problem is solved by -differential privacy, wherein noise (as a function of the constant privacy parameter ) is added to the aggregated data to protect individual users and provide them an avenue to deny their participation in the study. However, not all pieces of data have the same weight, and users may also have differing definitions of privacy and how much risk they are willing to take in case their data is exposed. This study looks at -differential privacy when applied locally, or on the side of the users, so that they could have full control over how much of their real data they are actually giving up, before it even reaches the ones collecting the data. By varying the distribution of cautious users (who require more privacy and a lower) to those more tolerant to risk (higher ), we see which local differential privacy mechanisms were as effective as the centralized differential privacy mechanisms when applied to a particular type of variable, and which are not.


Volatile organic compound (VOC) emissions have become a key air pollution concern due to adverse health and environmental effects. The refractory nature of organic compounds combined with the toxicity of secondary metabolites limit the physical-chemical treatment processes and conventional biological processes. To overcome these drawbacks, the development of innovative advanced oxidation processes (AOPs) for the degradation of gaseous organic compounds is of major interest.
This work presents the results of two AOPs in the degradation of gaseous VOCs (toluene as a representative compound) – UV irradiation with ozonation (UV/O3) and ultrasonication (US) – considering various operating parameters such as initial toluene concentration, ozone dosage, and ultrasound frequency. For the UV/O3 process, increase in inlet concentration resulted to a decrease in toluene removal while increase in ozone dosage lead to a higher removal. An additional water scrubbing step for the UV/O3 process enhanced the abatement up to 99% due to solubilization of ozone and further oxidation of contaminants. For the US process, increase in inlet concentration had varying effects at different frequencies. Increase in US frequency and additional water recirculation lead to an increase in the removal efficiency. However, addition of ozone proved to be inhibitory for the process. In comparison, UV/O3 proved to be more efficient in terms of toluene removal at lower inlet load while US resulted to higher elimination at higher loading.


Hydrocarbon underground contamination particularly LNAPL remains a significant challenge in the regulation of subsurface pollution in the Philippines. On July 12, 2010, residents of West Tower Condominium (WTC) in Bgy. Bangkal, Makati City detected water leakage contaminated with gasoline fuel in its 4-level basement. Efforts to recover the oil from the extracted LNAPL-water mixture was done, potentially for reuse, using an oil-water separator system. In the recovery efforts, approximately 322,000 liters (equivalent to 1,610 drums) of LNAPL-water mixture were extracted. Monitoring wells were installed to measure LNAPL thickness, oil concentration of the groundwater, and map the contaminant plumes. The plumes demonstrate the behavior of LNAPL using data from 45 monitoring wells and give the extent of the contaminant area.
After Environmental Site Assessments, FPIC and UP-NIGS developed the following hypotheses:1.) Fuel was dissolved by added volumes of groundwater and spread laterally; 2.) Fuel hid beneath the soil water column.; 3.) LNAPL portions were attached to the vadose zone and the unsaturated soil forming the solid phase component. A major unresolved issue is determining the fate of the estimated one million liters of spilled LNAPL, especially after groundwater levels rose due to rainfall—an event that coincided with a sudden contraction of the contaminant plume. And how long will it take to fully remediate the subsurface of the contaminated site.
The study used the GMS AQUAVEO Modelling solution to investigate the LNAPL behavior underground and compare the results from the FPIC and UP-NIGS findings, and satisfy the following objectives: To analyze and explain the behavior of LNAPL plumes in relation to predicted values; To assess the performance and reliability of computer simulation models in replicating LNAPL plume behavior through quantitative comparison with field data; To analyze and characterize the movement and distribution of LNAPL plumes in the subsurface by integrating field observations with predictive model results; To validate the accuracy of the model by comparing its predicted values with observed field data; To describe the spill episode and highlight novel insights that enhance understanding of LNAPL behavior, contributing to advancements in groundwater contamination research; and To estimate the remaining volume of LNAPL and possible clean-up time frame under a business-as-usual scenario.
The LNAPL plumes at different time series follow advection and dispersion patterns influenced by groundwater flow. Findings also indicate that dissolved BTEX compounds remained subsurface until the activation of the Multi-Phase Extraction (MPE) system. Model-calculated LNAPL volumes suggest that a significant portion of the contaminant remains undissolved within the aquifer, emphasizing the need to focus remediation efforts on soil contamination. Of the estimated 253,500 liters of LNAPL released in June 2011, approximately 236,736 liters are still retained in the soil. The undissolved LNAPL, along with oil
adsorbed onto the solid matrix, will be recovered through MPE. Any remaining residues may be further treated through bioremediation. The timeline for complete remediation will depend on the residual BTEX concentrations, which will be regularly monitored to ensure they remain below the regulatory threshold of 5 ppb for benzene.