UP Biologists Develop an Aptamer-based Test for Trichomoniasis Detection

UP Biologists Develop an Aptamer-based Test for Trichomoniasis Detection

Published: March 6, 2025
By: Eunice Jean C. Patron

Schematic representation of the assay. (Photo credit: Justo et al., 2024)

The World Health Organization (WHO) aims to eliminate sexually transmitted infection (STI) epidemics as significant public health threats by 2030. One of the four main non-viral and curable STIs, trichomoniasis, stays persistent, affecting 156 million out of 376 million individuals aged 15–49 in 2016. About 70–85% of persons with trichomoniasis show no signs of infection, highlighting the urgent need for accurate, fast, and accessible detection of Trichomonas vaginalis, the parasite that causes the infection.

 

Dr. Christine Aubrey Justo and Dr. Windell Rivera of the University of the Philippines – Diliman College of Science’s Institute of Biology (UPD-CS IB), along with colleagues from Spain, Belgium, and the Democratic Republic of the Congo, developed an alternative detection method for T. vaginalis. Instead of using antibodies, they used aptamers—short DNA strands that form 3D shapes and bind to specific targets, in this case, proteins related to T. vaginalis.

 

“In this research, we conducted a series of sandwich enzyme-linked aptamer-based assays (ELAAs) to determine which of the ten aptamers that were previously selected in another study, can be paired to detect low concentrations of the parasite,” Dr. Justo explained. Sandwich ELAA is a multistep process that can be used to analyze multiple samples at one time. With their study results showing that the combination of a short aptamer (A1_14mer) and a long aptamer (A6) can be used in this process to detect T. vaginalis in clinical samples, the researchers can now adapt the sandwich ELAA to develop more affordable, easy-to-use, and rapid tests for its detection. One such adaptation is the recently reported aptamer-based lateral flow assay. “With the flexible and amplifiable nature of aptamers (unlike antibodies), many more aptamer-based POCTs for trichomoniasis can be created. However, funding and attention to trichomoniasis is very limited. Additional financial and clinical partners are needed before we can start implementing them in healthcare units” Dr. Justo concluded.

 

Using the knowledge gained in the sandwich ELAA study, various aptamer-based tests can be developed to fill the gap on the  low-cost, rapid tests for trichomoniasis, which has been included in the WHO global research priorities for STIs. Having access to rapid and affordable tests for T. vaginalis detection can help identify the impact of trichomoniasis and create effective strategies for controlling its spread, managing complications, and treating the infection.

 

Their research paper, titled “Sandwich Enzyme-Linked Aptamer-Based Assay for the Detection of Trichomonas vaginalis,” was published in the international journal Analytical Biochemistry: Methods in the Biological Sciences. This journal features scientific research on methodologies in different fields of biology, including biochemistry, molecular genetics, cell biology, proteomics, immunology, and bioinformatics.

 

References:

Justo, C. A., Jauset-Rubio, M., Svobodova, M., Skouridou, V., Cools, P., Mulinganya, G., Ibáñez-Escribano, A., Rivera, W. L., & O’Sullivan, C. K. (2024). Sandwich enzyme-linked aptamer-based assay for the detection of trichomonas vaginalis. Analytical Biochemistry, 695, 115656. https://doi.org/10.1016/j.ab.2024.115656

 

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Venomous Jellyfish Found in PH Waters, Biologists Confirm

Venomous Jellyfish Found in PH Waters, Biologists Confirm

Published: February 21, 2025
By: Eunice Jean C. Patron

Box jellyfishes are known for their distinctive box-like appearance and their potent venom, which can cause severe stings and fatalities. In the Philippines, many coastal communities are well aware of the dangers posed by box jellyfishes, but Filipino scientists noted that the government does not have a systematic plan to address this issue.

 

Preserved specimen of C. yamaguchii. (Photo credit: Boco et al., 2025)

Based on previous studies by marine researchers, a team of biologists hypothesized that Chironex yamaguchii, a dangerous species of box jellyfish known from Japan, is also present in Philippine waters. This box jellyfish was found to cause severe stings and even fatalities in the Indo-Pacific and Western Pacific regions. Their tentacles can inflict extreme pain, cause skin injuries with welts, and even trigger heart attacks and death.

 

By closely examining the physical characteristics and DNA of this deadly jellyfish, the team found strong evidence that the species exists in the Coral Triangle, a marine biodiversity hotspot that includes the Philippines. Despite their nearly identical physical characteristics, the scientists discovered small genetic differences between the Philippine and Japanese C. yamaguchii, suggesting that the Philippine C. yamaguchii may be a separate species requiring further research.

 

The international research team was composed of Dr. Sheldon Rey Boco, Christine Gloria Grace Capidos and Dennis Talacay of The Philippine Jellyfish Stings Project together with Raffy Jay Fornillos and Dr. Ian Kendrich Fontanilla of the University of the Philippines – Diliman College of Science’s Institute of Biology, Dr. Phuping Sucharitakul and Dr. Jonathan Lawley of Griffith University’s School of Environment and Science in Queensland, Australia; Dr. Allen Collins of Smithsonian National Museum of Natural History in Washington, DC; Joseph Elliz Comendador of National Museum of Natural History of the National Museum of the Philippines; and Facundo Rey Ladiao of Leyte Normal University.

 

“This study shows genetic differences within C. yamaguchii that we couldn’t see just by looking at them as physical specimens,” the researchers explained. “This finding highlights how important it is to use molecular methods to correctly identify species and understand their genetic variety.”

 

The study’s findings exceeded the team’s expectations, particularly regarding their hypothesis on the species’ presence in the Philippines. “We identified the Philippine population as a potential cryptic species. This means that we are being encouraged to determine if they belong to a new species or if their geographic isolation doesn’t make them entirely distinct from the Japanese population,” the researchers said.

 

The team added that the citizens and tourists of the coastal communities they visited played a significant role in the research. Their images and videos of box jellyfishes, as well as their traditional knowledge of the marine environment, helped confirm that C. yamaguchii is widespread in Philippine waters. “Their insights and experiences have helped us identify and confirm the presence of the box jellyfish in areas that might otherwise be overlooked. This collaboration between scientists and Filipinos or tourists (“the citizens”) highlights the importance of community involvement in scientific research,” they shared.

 

“Knowing the genetic diversity and distribution of C. yamaguchii helps in correctly identifying the jellyfish responsible for stings, which is crucial for effective treatment and management,” the biologists added. “Understanding the presence of jellyfish populations in various regions can also help assess the risk of jellyfish stings in those areas, which can protect local communities and tourists.”

 

Distribution of C. yamaguchii in the Western Pacific and the Philippines. (Image credit: Boco et al., 2025)

The researchers mentioned that the study’s results can also impact healthcare workers, policymakers, and the general public. With better knowledge of the jellyfish’s distribution and genetics, healthcare providers will be better equipped to treat sting cases. Policymakers can implement regulations and guidelines for beach safety, including monitoring and managing jellyfish populations to reduce the risk of stings. Raising awareness of the presence and dangers of C. yamaguchii can lead to better preventive measures, such as avoiding certain areas during peak jellyfish seasons and using protective gear.


Their research, titled “Molecular signatures reveal intra-species divergence, undetectable by traditional morphology, in the deadly box jellyfish, Chironex yamaguchii (Cubozoa; Chirodropidae) of Western Pacific,” was published in Regional Studies in Marine Science, an international journal that features scientifically rigorous studies on maritime and marine resources, including estuaries, coastal zones, continental shelves, seas, and oceans. The research was partially funded by UPD, with open-access funding provided by Griffith University, and was also partly supported by citizen-science participants of the Philippine Jellyfish Stings Project.


References:

Boco, S. R., Capidos, C. G., Fornillos, R. J., Sucharitakul, P., Lawley, J. W., Talacay, D., Collins, A. G., Fontanilla, I. K., Comendador, J. E., & Ladiao, F. R. (2025). Molecular signatures reveal intra-species divergence, undetectable by traditional morphology, in the deadly box jellyfish, Chironex yamaguchii (Cubozoa; Chirodropidae) of western Pacific. Regional Studies in Marine Science, 82, 104033. https://doi.org/10.1016/j.rsma.2025.104033


Verdadero, F. X., Licuanan, W., Ang, J. L., De los Santos Jr, B., & Metillo, E. (2022). Harmful jellyfishes are manageable. The Philippine Journal of Fisheries, 209-216. https://doi.org/10.31398/tpjf/29.2.2021-0032


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UPD-CS Mathematicians Introduce Innovative Matrix Decomposition Framework

UPD-CS Mathematicians Introduce Innovative Matrix Decomposition Framework

Published: February 19, 2025
By: Eunice Jean C. Patron

Matrix decomposition is an area of linear algebra which is focused on expressing a matrix as a product of matrices with prescribed properties. (Photo credit: Merino et al., 2024)

Imagine discovering an ancient treasure chest sealed with a complex dual-lock mechanism, requiring two keys that must work together in a precise way. A matrix—a rectangular array of numbers—is like a locked chest holding valuable information that helps us understand the world around us. Matrices need keys like decompositions, which break them down into simpler components while preserving their essential properties, to help us understand them better. At times, special kinds of decompositions are required to have a deeper understanding of matrices.

 

Researchers in mathematics have uncovered a new approach to matrix decomposition, which could pave the way for significant advances in areas such as signal and image processing, machine learning, and speaker recognition.

 

Drs. Agnes Paras and Jenny Salinasan of the University of the Philippines – Diliman College of Science’s Institute of Mathematics (UPD-CS IM), along with Dr. Dennis Merino of Southeastern Louisiana University, studied the ϕS polar decomposition—a specialized form of polar decomposition.

 

“There are many ways to decompose a given matrix, but in the event that a prescribed decomposition is not always possible, the challenge is to obtain necessary and sufficient conditions for a prescribed decomposition to exist,” the authors explained.

 

Their study identified three conditions to determine whether a square matrix X has a ϕS​ polar decomposition: (1) the matrix product ϕS(X)X must have a square root that exhibits a specific symmetry; (2) ϕS(X)X and another matrix product, XϕS(X), must have the same fundamental properties; and (3) the matrices [XϕS(X)]kX must have even rank for any nonnegative integer k.

 

By identifying these conditions, the mathematicians discovered when a square matrix can be broken down into special types of matrices called symplectic and skew-Hamiltonian. “Symplectic matrices have applications in quantum optics, particularly, in the analysis of squeezed states of light, while skew-Hamiltonian matrices have applications in systems and control theory,” the authors added.

 

The authors noted that previous mathematical research such as that from de la Cruz and Teretenkov, had already provided conditions for complex matrices. “However, the conditions given in the complex case are not sufficient over an arbitrary field, while the conditions given in the real case are not necessary,” they added.

 

Their study, “The ϕS polar decomposition when S is skew-symmetric,” was published in Linear Algebra and its Applications, a journal that publishes articles that contribute new information or new insights to matrix theory and finite dimensional linear algebra. The research was supported by the UP Diliman Natural Sciences Research Institute.

 

References:

Merino, D. I., Paras, A. T., & Salinasan, J. R. (2024). The ϕ polar decomposition when S is skew-symmetric. Linear Algebra and its Applications, 703, 173-186. https://doi.org/10.1016/j.laa.2024.09.005

 

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In Loving Memory of Dr. Joma Escaner: Honoring a Life Well-Lived

In Loving Memory of Dr. Joma Escaner: Honoring a Life Well-Lived

Published: February 14, 2025
By: Eunice Jean C. Patron

Dr. Jose Maria L. Escaner IV, also known as Dr. Joma of the University of the Philippines – Diliman College of Science’s Institute of Mathematics (UPD-CS IM), sadly entered into eternal rest at the beginning of February 2025. His warmth and kindness will be deeply remembered by his students, colleagues, and the rest of the UP Diliman community whom he truly inspired.

 

Unwavering Dedication to Mathematics

 

Dr. Joma’s passion for mathematics was particularly focused on mathematical finance and actuarial science. He completed his Bachelor’s degree in Mathematics in 1990, his Master’s degree in Applied Mathematics with a specialization in Actuarial Science in 1993, and his Doctorate in Mathematics in 2001, all at UPD-CS IM. He was also a research student for two years at Waseda University in the late 1990s, where he conducted part of his PhD research. At the time of his passing, Dr. Joma served as the Academic Head of UPD-CS IM’s Mathematical Finance and Actuarial Science (MFAS) Group and was the President of the Mathematical Society of the Philippines, after having served the organization as Treasurer for two years.

 

Committed to Honor and Excellence

 

Dr. Joma translated his fervor for mathematics into a commitment to serving the people by guiding his undergraduate, Master’s, and PhD students through their academic journeys for more than three decades of teaching. His steadfast commitment to teaching was recognized by the University, which granted him the UP Diliman Gawad Tsanselor para sa Natatanging Guro Award in 2021. Dr. Joma was also the former president of the UP Diliman Mathematics Foundation and served as UPD-CS’ former College Secretary and Associate Dean for Student Affairs. He was a regular member of the DOST National Research Council of the Philippines (NRCP), contributing to the understanding of mathematical models in finance and insurance.

 

Anecdotes about Dr. Joma

 

Dr. Joma’s colleagues at UPD-CS IM fondly recalled their memories with him. “Even in his last moments, he was dedicated and committed to his work, and was willing to help others who needed him,” said Dr. Lu Kevin Ong, a member of the MFAS Group, as he shared how Dr. Joma did not hesitate to help him construct comprehensive exams the day before he passed away. Dr. Joma was also his professor when he was an undergraduate. “His way of teaching inspired me to study this subject further and I asked him to be my undergraduate thesis adviser,” Dr. Ong added.

 

Dr. Jose Ernie Lope, Director of UPD-CS IM, also recounted how Dr. Joma was persistent in teaching even though he was sick. “Despite showing signs of illness, despite our suggestions that he file for sick leave, he insisted on reporting back to active duty,” said Dr. Lope. “He said that he felt more energized when he was teaching. And indeed, he was teaching until the week before he got hospitalized.”

 

“In our last conversation at the IMath faculty lounge, we caught up and he congratulated me about my successful special problem final defense and wished me well in my PhD studies,” shared Joseph Angelo Samonte, one of Dr. Joma’s undergraduate students who eventually became his thesis advisee and colleague at the MFAS Group. Samonte reminisced about Dr. Joma’s unwavering support for his endeavors beyond mathematics. “I even promised him that he will get a printed copy of my special problem. Oh, speaking of which, I haven’t returned his risk theory actuarial book.”

 

It is indeed unfortunate that we lost a remarkable individual who made a lasting impact in the UPD-CS IM community, but his legacy will still live on in the hearts of the students, colleagues, and loved ones whose lives he touched. You will be dearly missed, Dr. Joma.

 

Some of the information was taken from Dr. Jose Wendell Capili’s post: https://www.facebook.com/wendellcapili/posts/pfbid0vrhTumHBjR5S5npQGr2wQbckg6tJFNp96NmcTiocBiF619NYoJQ2Hi5NADtN1xKLl

UPD-CS Spearheads Workshop on Promoting Innovation and Industry Collaboration

UPD-CS Spearheads Workshop on Promoting Innovation and Industry Collaboration

Published: January 24, 2025
By: Eunice Jean C. Patron

Participants of the OGSM Workshop. (Photo credit: UPD-CS Innovation Committee)

Institutions around the globe are working toward creating scientific innovations to address the challenges faced by humanity. Likewise, Filipino scientists are striving to find solutions to the Philippines’ concerns.

 

The University of the Philippines – Diliman College of Science (UPD-CS) Innovation Committee, under the Science and Society Program (SSP), held an Objectives, Goals, Strategies, and Measures (OGSM) Workshop last year to spark a discussion on innovation.

 

The OGSM workshop aims to help Innovation Committee members and designated individuals from the College of Science, who hold explicit or delegated responsibilities for decisions related to innovative projects within their respective institutes, better propel researchers toward innovation, connect them with industry partners, and develop a system to assist in achieving practical, utilizable outputs from their research.

 

Invited guests include Innovation Committee representatives and Deputy Directors for Research and Extension from each institute. Individuals who have experience in, or plans for, technology transfer within the College were also invited to join.

 

During the workshop, SSP Director Dr. Lerrie Ann Ipulan-Colet introduced SSP’s CAPE Innovation Program for 2023-2025, which stands for Collate and Categorize theses, dissertations, and research publications, Build Awareness, Prepare researchers and students to develop products from their research, and Exposure and Immersion of the College of Science to Innovation Opportunities. The CAPE Innovation Program serves as the UPD-CS’ initiative to promote scientific advancement for nation-building by encouraging its constituents to pursue research, collaborate with institutions, and protect their research outputs.

 

Innovation Committee Consultant Engr. Rolando Lazo facilitated the workshop proper, covering several key topics such as the rationale, statistical insights, and a summary of the pre-workshop meeting held on October 14. Engr. Lazo also helped gauge the participants’ understanding and concerns regarding the current direction of UPD-CS’ innovation efforts.

 

Serving as the final session of the workshop, participants were divided into small groups to share innovation strategies they had encountered, highlighting both effective and challenging experiences, as well as the resources and actions needed to ensure success moving forward.


“The workshop provided in-depth discussion on the experiences of people who have gone through the innovation process,” one attendee said. Another participant expressed their hope that “the fruits of the meeting will be materialized properly into the Innovation Committee.”


The second day of the workshop will be held this year, wherein the participants will dive into the concept of societal impact, exploring its definition and relevance to their innovation initiatives. The workshop will also include a value proposition exercise designed to refine the participants’ understanding of their innovative research.

 

For interview requests and other concerns, please contact media@science.upd.edu.ph.

UP Geologist Represents Southeast Asia in Global Young Scientists Summit 2025

UP Geologist Represents Southeast Asia in Global Young Scientists Summit 2025

Published: January 17, 2025
By: Eunice Jean C. Patron

Dr. John Dale Dianala of UPD-CS NIGS represented UP Diliman at the GYSS 2025. (Photo credit: Global Young Scientists Summit)

Dr. John Dale Dianala from the University of the Philippines – Diliman College of Science’s National Institute of Geological Sciences (UPD-CS NIGS) presented his research on the earthquake potential of faults using satellites at the recently concluded Global Young Scientists Summit (GYSS) 2025.

 

Organized by the National Research Foundation (NRF) Singapore, GYSS brings together Nobel laureates and top scientists from around the world to discuss how scientific research and innovation can address emerging global issues.

 

Out of 16 young scientists invited to present their research on life sciences, biomedicine, physical sciences, and engineering, Dr. Dianala represented UPD-CS NIGS, making UP the only Southeast Asian university featured on stage. “The GYSS allowed me to see our place in the international science scene,” he said of his GYSS experience.

 

Dr. Dianala is one of 10 Filipino scientists who attended the summit after being nominated by the Department of Science and Technology (DOST). “Compared to scientists from fields such as physics, chemistry, mathematics, biomedicine, and engineering, only a handful of geoscientists were present at the summit; I looked for them and I counted five,” he added.

 

His research utilizes satellite data and technologies such as Interferometric Synthetic Aperture Radar (InSAR) to monitor fault lines, providing a cost-effective solution for areas lacking ground-based data. Dr. Dianala processed InSAR data over Leyte Island to produce a slip model, which is considered one of the most detailed for a fault in the Philippines. His study demonstrated that detailed fault models based on satellite data enables researchers to identify areas of stress accumulation, potential earthquake activity, and patterns in earthquake occurrences, which can be used in developing preparedness plans.

 

In his presentation, Dr. Dianala also emphasized the value of these techniques for research on fault lines in urbanizing regions around Metro Manila and in other parts of the world, where risk will only increase as population grows. He encouraged collaboration and innovation in earthquake research, especially in less-resourced regions, to enhance global understanding of seismic risks.

 

Presenters under the Physical Sciences & Engineering category, which includes Dr. Dianala. (Photo credit: Global Young Scientists Summit)

“Getting to share the work we do at NIGS, and being the sole geologist to take the stage, is a recognition of the global interest and relevance of research done at UP,” he said of this achievement.

 

 

Currently on its 13th iteration, GYSS was held from January 6 to 10, 2025 at the Stephen Riady Centre, National University of Singapore. The week-long summit included plenary talks from Nobel laureates and other award winning scientists, panel discussions on the role of science in addressing emerging global issues such as sustainability, human well-being, and ethics with artificial intelligence, quickfire talks from selected young scientists, and poster sessions.

 

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UPD Experts Determine the Optimal Model for Predicting Algal Blooms

UPD Experts Determine the Optimal Model for Predicting Algal Blooms

Published: January 16, 2025
By: Harvey Sapigao

Graphical abstract of the study (Photo credit: Pilario et. al. 2024).

Algal blooms, which occur when algae overgrow in bodies of water, can not only turn the water green but also kill fish and contaminate the water supply of nearby communities. Laguna Lake, one of Metro Manila’s major sources of bangus and tilapia, as well as drinking water, is particularly prone to algal blooms, especially during El Niño.


A standard method for monitoring the algal population in water is to measure chlorophyll-a, the green pigment produced by algae. However, “If we wait for [the instruments] to indicate high algal content, it may already be too late since the bloom may have already occurred,” explains author Dr. Karl Ezra Pilario of the UPD Department of Chemical Engineering.

 

A more effective approach would be to monitor nitrate and phosphate concentrations in the water, as changes in these concentrations are often linked to increases in chlorophyll-a. Advanced tools such as machine learning (ML) models can be used to establish these complex relationships from data.


Since 1973, the Laguna Lake Development Authority (LLDA) has routinely monitored the lake’s water quality through remote sensing and monthly assessments. More recently, LLDA’s monitoring programs have employed mathematical tools and ML models. However, various models are currently available, and it is unclear which model suits Laguna Lake best.

 

Researchers from the University of the Philippines Diliman (UPD) recently published a study comparing the robustness and accuracy of eight common ML models for predicting algal blooms. Along with Dr. Pilario, Dr. Maria Pythias Espino of the UP Diliman College of Science Institute of Chemistry (UPD-CS IC), and Dr. Aurelio de los Reyes V and Eric Jan Escober of the UPD-CS Institute of Mathematics (IM) used water quality data from Laguna Lake and historical data from global lakes to train these models.

 

Of the eight, they discovered that two models called the Kernel Ridge Regression (KRR) and Gaussian Process Regression (GPR), performed better than others. These models both belong to a class called similarity-based models, which “use the philosophy that similar-looking inputs must give similar-looking outputs,” explained Dr. Pilario.


The other models included tree-based models, which function like a decision-making flowchart, and artificial neural nets, a framework inspired by our brains’ neural networks.

 

Although all models achieved high accuracy, KRR was the most accurate for Laguna Lake, while GPR was the best for global lakes. Moreover, KRR and GPR were more robust than the other models, allowing them to handle noisy data more effectively.


“Now that we have an accurate, robust, and explainable predictor of chlorophyll-a, we can deploy the model for rapid detection of impending algal blooms,” said Dr. Pilario. “We can take a water sample from the lake at any time, bring it to the lab to obtain the current nitrate ion and phosphate ion content, then estimate the chlorophyll-a from these values using KRR or GPR.”

“We recommend monthly monitoring of these values so that if an impending algal bloom is detected, there is ample time to prepare for interventions or mitigation strategies,” added Dr. Pilario.

 

While KRR and GPR can now be used for algal bloom prediction, the researchers noted that there are still many ways to improve the models. For instance, they are considering additional predictors like weather conditions, land cover types, and other effects caused by humans. Since samples from Laguna Lake were collected in just one season, they also plan to test the models with samples taken at different times of the year.


“Lastly, on the modeling side, we need to test more models that might be more accurate than KRR or GPR,” concluded Dr. Pilario. “In the future, we encourage researchers to test for the robustness and explainability of their machine learning models, and not just for accuracy, because it helps make the results more believable for policy-making.”

 

For interview requests and other concerns, please contact media@science.upd.edu.ph

 

References:

Pilario, K. E., Escober, E. J., De Los Reyes, A., V., & Espino, M. P. (2024). Robust Prediction of Chlorophyll-a from Nitrogen and Phosphorus Content in Philippine and Global Lakes Using Fine-Tuned, Explainable Machine Learning. Environmental Challenges, 101056. https://doi.org/10.1016/j.envc.2024.101056 

UP Physicists Extend Condensed-Matter Principle in Realistic Set-Ups

UP Physicists Extend Condensed-Matter Principle in Realistic Set-Ups

Published: January 06, 2025
By: Harvey Sapigao

Liquid helium in superfluid phase. (Photo credit: Alfred Leitner)

At extremely cold temperatures, things become fascinating. Much like how water turns into ice, some matter undergoes phase transitions that give them interesting properties. Just above absolute zero, for example, aluminum transforms into a superconductor, while helium isotopes change from gas to superfluid. A foundational principle, known as the Kibble-Zurek mechanism (KZM), explains how these materials behave as they cool at different rates.

 

The KZM has been largely validated for closed systems, or systems confined to the effects of the environment. However, it remains unclear whether the mechanism applies in more realistic scenarios where the environment is at play.

 

New research by UPD physicists proves that KZM is applicable to a general class of open systems. Moreover, they uncovered subtleties in how phase transitions are studied in laboratories, illuminating possibilities for more precise experiments in condensed matter physics.

 

“Our work provides a new perspective on how we detect and identify phase transitions in realistic set-ups, in which their interaction with the environment gives us little control over how they will evolve in time,” said Dr. Jayson Cosme and Roy Jara Jr. of the UPD College of Science National Institute of Physics (UPD-CS NIP).

 

In glassblowing, hot glass is placed in annealers to slow down the cooling process and prevent cracks, while some are briefly dipped in water to create a crackled look. This is similar to materials that follow the KZM: those cooled slowly become homogeneous, while those cooled quickly result in more cracks, or “topological defects.”

 

In their research, Dr. Cosme and Jara investigated an open system where the cooling rate, or quench speed, is influenced by the environment. “We found that for these systems, the KZM remains valid when the tuning parameter that controls the phase of the system is modified sufficiently slowly,” the researchers said.

 

However, they observed that KZM breaks down at faster quench speeds. This insight led to a key discovery that a standard laboratory method for detecting phase transitions might not be reliable for open systems undergoing rapid cooling. In the standard method, a threshold is used to infer whether a material has transitioned to a new phase. Dr. Cosme and Jara, however, found that an apparent lag exists between reaching the threshold and the actual phase transition, leading to inconsistencies with the time at which the transition is detected.

 

“This result is significant as it sheds light on the possible limitations of threshold-based criterion in identifying phase transition when applied to open systems with strong dissipation,” they explained.

 

As an alternative to threshold-based experiments, they propose using other techniques, such as examining parameters that reach a steady state as the system undergoes phase transition.

 

While their study applies to a broad class of open systems, they acknowledge that it focuses solely on large systems where quantum effects can be ignored. Since quantum effects may become more relevant for smaller systems, they plan to extend their study to investigate these types as well.

 

“We also plan to extend our work to driven systems, where the systems can transition from a stationary to a dynamical phase like the newly discovered phase of matter called time crystals,” they concluded.

 

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References:

Jara R.D., Cosme J.G. (1 August 2024). Apparent delay of the Kibble-Zurek mechanism in quenched open systems. Physical Review B, 110 (6), Article number 064317. https://doi.org/10.1103/PhysRevB.110.064317

UP Geologists Report Subsidence Rates in Select PH Metropolitan Cities

UP Geologists Report Subsidence Rates in Select PH Metropolitan Cities

Published: December 05, 2024
By: Eunice Jean C. Patron

Land subsidence, or the gradual sinking of the ground, threatens not only Metro Manila but also other cities.

 

Extreme damage running along the length of a road in Marilao, Bulacan is visible. (Photo credit: Sulapas et. al., 2024)

Excessive groundwater extraction, rapid urbanization, tectonic motion, and the natural compaction of sediments contribute to land subsidence worldwide. This issue is worsened by rising sea levels due to climate change, leading to frequent and severe flooding especially during high tides or typhoons, as well as local contexts of hazard management regulations.

 

Jolly Joyce Sulapas, Audrei Anne Ybañez, and Dr. Alfredo Mahar Francisco Lagmay of the University of the Philippines – Diliman College of Science (UPD-CS), along with Kayla Milcah Marasigan and Julian Marie Bernice Grageda of the UP Resilience Institute Nationwide Operational Assessment of Hazards (UPRI-NOAH) analyzed land subsidence in major Philippine cities from 2014 to 2020.

 

Their land subsidence analysis showed that Bulacan, which is located in Greater Manila, has the highest sinking rate at 109 millimeters (mm) per year. This was also the first study to examine land subsidence in other cities, with rates of 11 mm per year in Metro Cebu, 38 mm per year in Metro Davao, 9 mm per year in Metro Iloilo, and 29 mm per year in Legazpi City. “The high population density of cities makes the information more relevant to the public, as its impact on people is greater,” Sulapas said. “Cities are also more vulnerable to land subsidence because the subsurface strata, or the rocks beneath the cities, are relatively younger.”

 

These sinking areas are mostly found in industrial and commercial zones, where large and expansive man-made structures intensify subsidence. Monitoring these areas is crucial, as subsidence increases flood risks, damages buildings and infrastructure, and causes economic losses. This hazard also increases the vulnerability of residents in coastal communities to high tides and storm surges aggravated by climate change.

 

“It seems like industrial complexes require a lot of water to keep their operations running. The same can be said for residential areas,” Sulapas noted.

 

A reconnaissance fieldwork near the trace of the West Valley Fault showing cracks on the road with vertical displacements of 5-7 cm and an aperture of 12 cm (Photo credit: Sulapas et. al., 2024)

The study recommends sustainable groundwater use and improved water management practices. Sulapas mentioned that previous studies on land subsidence were recognized by the National Water Resources Board (NWRB). “The Board then identified zones where groundwater usage would be restricted,” she said.

 

“My co-authors were part of a previous study on subsidence in Metro Manila and surrounding provinces. This was during the year 2010,” Sulapas added. “So more than a decade later, what we wanted to do is to update the deformation data. In the case of the Greater Manila area, what happened after more than a decade?”

 

Moving forward, the team of researchers plans to incorporate additional data, such as groundwater extraction in the major Philippine metropolitan cities covered in their study, and correlate it with existing information. They also intend to continuously update their data to include the years 2021 to the present, collaborating with other researchers interested in contributing to the study over the next decade and beyond.

 

The research, titled “Ground subsidence in major Philippine metropolitan cities from 2014 to 2020,” was published in the International Journal of Applied Earth Observation and Geoinformation, which publishes original papers that apply earth observation data to the inventory and management of natural resources and the environment.

 


For interview requests and other concerns, please contact media@science.upd.edu.ph.

 

References:

Sulapas, J. J., Ybañez, A. A., Marasigan, K. M., Grageda, J. M., & Lagmay, A. M. (2024). Ground subsidence in major Philippine metropolitan cities from 2014 to 2020. International Journal of Applied Earth Observation and Geoinformation. https://doi.org/10.2139/ssrn.4779261

CS Researchers Receive UPD 2024 REPS Chair and REPS Awards

CS Researchers Receive UPD 2024 REPS Chair and REPS Awards

Published: December 04, 2024
By: Eunice Jean C. Patron

Researchers from the University of the Philippines – Diliman College of Science (UPD-CS) are recipients of the University’s first-ever recognition for its Research, Extension, and Professional Staff (REPS).

 

Researchers from UPD-CS will be recognized at UP Diliman’s first-ever recognition focused on its Research, Extension, and Professional Staff (REPS).

The UP Diliman REPS Chair and REPS Awards aims to recognize the achievements of the REPS in the fields of research and creative work, extension services, and professional public service. These awards also aim to encourage REPS to advance knowledge and learning in their respective fields, establish scientific and thought laboratories, and develop collaborative programs that support UP’s mandate as the nation’s leading research university.

 

Three researchers from the UPD-CS Natural Sciences Research Institute (NSRI) earned the REPS Chair Awards. Meanwhile, one researcher each from NSRI, UPD-CS Marine Science Institute (MSI) and the UPD-CS National Institute of Physics (NIP), along with two from the UPD-CS Institute of Biology (IB), received the REPS Awards.

 

REPS Chair Awards Recipients

 

Dr. Charita S. Kwan is the head of NSRI’s Research and Analytical Services Laboratory. She has over 20 years of experience in projects related to environmental and analytical chemistry, with a focus on the distribution, fate, and transport of organic micropollutants.

 

Dr. Pierangeli G. Vital is the head of NSRI’s Biological Research and Services Laboratory. She has over a decade of experience in research and teaching within the field of environmental microbiology and food safety, publishing multiple articles in international peer-reviewed journals and papers.

 

Dr. Maria Corazon A. De Ungria is the head of NSRI’s DNA Analysis Laboratory. Her research focuses on human genetic diversity and leveraging DNA as a tool for human identification in criminal investigations, prosecuting sexual offenders and preventing wrongful convictions.


REPS Awards Recipients

 

Mary Ann Cielo R. San Diego is a registered microbiologist of NSRI’s Microbiological Research and Services Laboratory. Her research centers on wastewater microbiology, specifically the community and functional profiling of microorganisms in wastewater treatment plants.

 

John Michael L. Lastimoso is an Assistant Herbarium Curator of the Gregorio T. Velasquez Phycological Herbarium and a member of the Marine Phycology Laboratory at MSI, where he conducts biodiversity and systematics research on Indo-West Pacific macroalgae.

 

Dr. Hannah R. Bardolaza assists with the operation and maintenance of equipment in NIP’s Femtosecond Laser Laboratory. Her research focuses on materials science, specifically materials and devices for terahertz science and technology applications.

 

Melizar V. Duya is a university researcher in IB’s Biodiversity Research Laboratory. She has authored and co-authored publications on Philippine wildlife, including new species descriptions, and contributed to developing and identifying Key Biodiversity Areas in the country.

 

Mae Ashley G. Nacario is a university researcher in IB’s Pathogen-Host-Environment Interactions Research Laboratory. Her focus is on Environmental Microbiology, with a specialization in Microbial Source Tracking. She has already published 7 manuscripts in various Scopus-indexed journals.


Harriet Jane R. Caleja-Ballesteros is the sole staff member of IC’s Nuclear Magnetic Resonance (NMR) Facility.  Since 2019, she has managed to run around 3000 NMR samples for clients while doing research projects, mainly on quantitative NMR spectroscopy.


Joel I. Ballesteros is one of the three REPS of IC’s Analytical Services Laboratory (ASL). He got his BS and MS degrees from the same Institute and is currently finishing his dissertation on spectroscopy and chemometrics while working as a full-time university research associate.


The REPS Chair and REPS Awards ceremony will be held on Tuesday, December 10, 2024, at 9:00 AM, at the GT Toyota Auditorium, Asian Center, as part of the REPS Colloquium and General Assembly program. The recipients will be awarded with a plaque of recognition and a cash prize.

 

For interview requests and other concerns, please contact media@science.upd.edu.ph.