A biogas purification system that is compact, efficient and cost effective could help to turn organic waste into valuable streams of methane and carbon dioxide at small scales.
Biogas is a renewable energy source, produced using microbes that break down sewage sludge, agricultural residues or food waste. Biogas is roughly 50% to 70% methane — which can replace natural gas used for cooking, heating, or generating electricity — while the remainder is mostly carbon dioxide.
A method called pressure swing adsorption (PSA) is used to separate these gases, by passing high-pressure biogas over a porous adsorbent material in a separation column. The adsorbent selectively traps carbon dioxide from the mixture, leaving relatively pure methane. Once this methane has been piped away, the pressure is lowered so that the adsorbent releases its carbon dioxide in a stream of ‘tail gas’. Several separation columns can be connected together to improve the purity of each gas stream over multiple adsorption cycles.
However, tail gas often contains traces of methane, which has up to 30 times greater global warming potential than carbon dioxide. This mixture is typically released into the atmosphere, where it contributes to climate change.
Carlos Grande at KAUST, along with his Ph.D. student, Saravanakumar Ganesan, and research scientist, Rafael Canevesi, aimed to design a PSA system that could economically upgrade biogas into purer product streams, even when operating at small scales[1]. This would not only avoid methane emissions in the tail gas, but also deliver carbon dioxide that is sufficiently pure for industrial use, so that it is not merely vented.
“If small units could be made affordable, they could be implemented in farms or small communities, extending the capabilities of producing biomethane as a renewable fuel,” says Grande. “Our studies in this field are targeted to make a profitable case for farm-scale implementation of biogas upgrading while also being environmentally responsible.”
The team simulated different PSA configurations that used a commercially-available carbon molecular sieve as the adsorbent, and found that a dual-stage PSA was the most successful1. In the first stage, four columns produce a high-purity stream of carbon dioxide. Methane-rich gas from this stage is then piped into the second stage, which uses two columns to maximize the methane’s purity. Tail gas from the second stage is recycled back into the first stage, giving any stray methane another opportunity to be extracted.
Then the researchers refined their design, by using industrial balloons to manage the flow of gases through the system. This enabled a simpler PSA configuration with only two columns that achieved more than 97 percent methane purity, and carbon dioxide purity over 99.5 percent — enough to satisfy the most stringent legislation in this area, Grande says. This system also had a lower energy demand than previous designs, and would be cheaper to set up[2].
“The next stage is to reduce the cost by 30 percent in small units,” says Grande. “We can also tailor the PSA units to different biogas sources, adapting the technology to treat different streams available in Saudi Arabia.”
Many plants have developed adaptations to environmental extremes such as drought and high salinity. Plant resilience can enhance the vast community of associated microorganisms, collectively known as the plant microbiome. Among these beneficial bacteria, members of the Pseudomonas genus are known for their plant-growth-promoting properties.
Two strains of the Pseudomonas species, known as E102 and E141, have been the subject of a study to examine how these bacteria interact with plants to promote growth under stress by a team of researchers led by KAUST’s Ramona Marasco, Ikram Blilou and Daniele Daffonchio[1]. The effects of these strains, which were isolated from date palm roots, have been shown to promote drought tolerance and resistance to salinity in date palms and other plants.
Using Arabidopsis as a host plant, the researchers found the presence of the bacteria caused increased root hair elongation and lateral root formation. Under normal conditions, these changes did not result in an increase in root and shoot biomass. However, during mild and severe salt stress, the bacteria were able to promote and protect plant growth. Shoot and root biomass increased significantly after exposure to increasing concentrations of bacterial cells. The stress-dependent effect of these plant-growth-promoting bacteria was also confirmed in lettuce plants grown under severe salt stress.
“This effect significantly increases with the concentration of bacteria used to treat the plant,” says Marasco.
“The changes we observed suggest that the bacteria are improving plant resistance under abiotic stress by increasing the effective root surface available for water and nutrient uptake. These changes give plants an adaptive advantage under stress conditions such as salinity,” she says.
The auxin effect
Many aspects of plant growth and development, including root hair elongation and lateral root development, are triggered and regulated by plant hormones known as auxins, the best known of which is indole-3-acetic acid (IAA). IAA plays a critical role in plant growth and development, regulating key processes such as cell elongation, division and differentiation — essential for controlling and modulating root development and architecture.
Many Pseudomonas strains have an ability to produce phytohormone-like molecules, such as IAA. Although their beneficial effects have often been linked to their IAA production, it remained unclear how the bacteria influence auxin signaling and transport and how these changes further contribute to plant growth.
This study showed that the effectiveness of the bacteria in changing root architecture depends on a functional auxin signaling pathway.
“While Arabidopsis mutants defective in the auxin signaling pathway are unable to develop root hairs when exposed to our bacteria, in wild-type plants, the IAA produced by the bacteria can interfere with the plant’s own IAA production,” Blilou explains.
“This interference enhances the activation of the plant-auxin responsive promoter (DR5), leading to alterations in the root system architecture that we observed. These effects are further facilitated by changes in IAA transport, which promote a more rapid redistribution and circulation of the hormone,” she says.
The findings provide a model illustrating how Pseudomonas bacteria can influence root development to promote growth and enhance the adaptation of plants under salinity stress.
“The modifications depend on the plant’s auxin machinery and confer an adaptive advantage to the plant, exclusively under stress conditions, such as mild and severe salinity,” says Daffonchio.
“The results help explain the responses of plants treated with plant-growth-promoting bacteria. In future, these microorganisms could be important in mitigating the negative effects of climate change in agriculture,” he observes.
Advanced carbon fiber materials could be used in applications from wind turbine blades to biomedical implants following the development of a low-cost carbon fiber feedstock.
The carbon fibers were spun from synergistic blends of the low-value heavy oils left over from crude oil refining by members of KAUST’s Clean Energy Research Platform[1]. The work could not only facilitate broader carbon fiber uptake but also create sustainable new uses for residual oils as the world transitions to alternative energy systems.
“Crude oil is a resource with immense potential beyond fuels,” says Edwin Guevara Romero, a researcher in the labs of Mani Sarathy, who led the work. “Using oil residues as feedstocks for carbon materials is an innovative, high-value application of oil-derived resources, paving the way for economic diversification,” he says.
Carbon fiber is in increasing demand across many industries due to its exceptional properties, including high mechanical strength and durability, low weight, thermal stability, and electrical conductivity. One limiting factor is its high cost, which can largely be attributed to the expensive carbon precursor, polyacrylonitrile (PAN), used to make it.
PAN’s high cost has prompted a search for alternative feedstocks. “Oil residues could offer a cost-effective and abundant alternative,” Guevara says. For their research, the team targeted the heaviest, most complex – and traditionally, hardest to process – components of residual oil, called asphaltenes and resins.
Previously, asphaltenes have been trialed as carbon fiber feedstocks. However, efforts to spin these materials into fibers were limited by their tendency to break, and the carbon fiber yield from the final carbonization heat treatment step was relatively low.
“Previous studies of oil residues have suggested that resins stabilize asphaltene molecules, highlighting their strong molecular affinity,” Guevara says. “This led us to hypothesize that blending asphaltenes with resins could create a synergistic feedstock for carbon fiber production.”
The team showed that the blend offered several advantages over asphaltenes alone as carbon fiber feedstocks. It had better flow characteristics and could be spun at a lower temperature, reducing energy consumption. The team also observed fewer strand breakages during spinning and attained a higher yield after the carbonization step. “This improves the viability of the process by maximizing the conversion of the precursor material into the final carbon fiber product,” Guevara says.
The resulting carbon fibers were also of high quality. “The properties of our fibers are comparable to those of ‘isotropic carbon fibers’, which are commonly used in applications requiring moderate-to-high mechanical performance,” Guevara says.
“Traditionally, oil residues have been used in very low-value applications such as road surfacing. By extracting the heaviest asphaltenes and resins for high-value carbon fiber manufacturing, the remaining residual oils can also be more easily processed to produce cleaner fuels or valuable small molecules, further improving the economics of the process,” Sarathy adds.
The researchers are now fine-tuning the residual oil blend to maximize the chemical interaction between the components to improve the fibers’ physical attributes further. They are also collaborating with Saudi Aramco to scale up the process. “Our primary objective is to generate high-performance carbon fibers and then scale towards an industrial process,” Sarathy says. “This will give Saudi Arabia a unique, economically competitive product that can be marketed globally.”
Imagine editing a manuscript, only to find random paragraphs from other books slipping into the text. That is the risk revealed in a new study of the celebrated genome-editing tool called CRISPR-Cas9: various unintended snippets of DNA sometimes get inserted in the edited region where they do not belong.
KAUST scientists uncovered this side effect in a detailed analysis of human embryonic stem cells edited with different types of donor DNA, whereby helper sequences provide a template for fixing the genome during the CRISPR process. They found that the genome editing platform, while efficient in cutting DNA, can sometimes leave behind large fragments of genetic material that were not part of the plan[1].
These stray pieces of DNA included repetitive sequences, regulatory elements and chunks from other parts of the genome. Though relatively rare — occurring in less than 1% of all edited cells — these large insertions could have significant consequences, especially in medical applications where accuracy is critical.
“This unexpected finding highlights the complexity of Cas9-editing outcomes,” says KAUST bioscientist Mo Li, who led the study.
Unlike large deletions, which typically result in the loss of gene functions, large insertions can lead to more complex and unpredictable genetic disruptions, including the activation of cellular pathways linked to cancer and other diseases. “While we cannot directly link these insertions to cancer risk yet, the presence of such sequences raises significant safety concerns for clinical applications,” Li says.
Li and his colleagues discovered that the type of donor DNA used plays a significant role in these outcomes. Linear donor DNA, for example, was more prone to causing unintended donor insertions compared to circular templates. The DNA repair process itself, which relies on the cell’s natural machinery, may also introduce these fragments when it mistakenly incorporates surrounding DNA into the repair site.
There is a simple fix. By chemically tweaking the donor DNA template with phosphorylation — a process that adds phosphate groups to the two ends of DNA — the researchers found that the likelihood of unintended large insertions dropped two-fold without compromising the efficiency of the intended edits.
“Phosphorylation of donor DNA is simple, does not alter experimental design or workflow, and reduces the risk of unintended structural variants without affecting gene-editing efficiency,” explains Chongwei Bi, a postdoc researcher in Li’s research group and the first author of the new study. “However, further validation is required in other settings to confirm the clinical impact and scalability of this approach.”
Without sounding alarms, the study authors emphasize the importance of refining CRISPR technology to make it even safer and more reliable — and of using ultra-sensitive DNA sequencing techniques like those developed in Li’s lab to systematically evaluate gene-editing products for rare unintended events.
“Additionally, designing editing strategies that minimize double-strand breaks or using alternative gene-editing tools without DNA breaks could further reduce these risks,” Li says. As gene editing moves into mainstream use, he points out, understanding and managing these subtleties will be crucial.
“During a research trip to Palmyra Atoll, we made a surprising discovery: a whole network of rhodolith beds[1],” says Lena Li, a recent graduate of KAUST. “No one knew rhodolith beds even existed in the tropical central Pacific.”
Despite years of research, there are still many mysteries to uncover in and around the world’s coral reefs. Rhodolith beds are one example. Scientists have limited understanding of these calcareous nodules made by coralline red algae, which accumulate in shallow seas close to coral reefs.
Rhodoliths are not fixed to the seabed like corals; rather they accumulate over time into ‘beds’ made up of separate nodules, some of which are living, and others dead. These distinctive, pink-colored aggregations provide a unique, highly diverse habitat for multiple creatures in shallow seas. Rhodolith beds may serve as an indicator of wider reef resilience, because they provide a foundation for reef regeneration following periods of stress. However, scientists know little about how rhodoliths respond to stressors such as warming oceans.
Following their exciting discovery, the team improvised to gather as much data as they could on location.
“Palmyra Atoll is located within the largest marine protected area on Earth,” says Li, who was supervised by faculty member, Maggie Johnson. “It is as close to pristine and untouched as we can get, with no permanent human population and no local stressors. This allows us to get an idea of a baseline, healthy rhodolith ecosystem structure and function, without human activities clouding our view.”
The area where they found the rhodolith beds was quite inaccessible and had not yet been explored thoroughly. The team had to maneuver a small boat through tiny cuts between islands and could only reach the beds when the tides were just right.
“We hadn’t come prepared to study rhodoliths, so we used the equipment we had – namely myself, a pair of fins, a snorkel and a handheld GPS unit on a float,” says Johnson. “I swam around the edges of all the beds and further out to survey their full extent, and took a GPS point every two fin kicks. Exhausting, but worth it!”
The team mapped 15 different rhodolith beds, collectively covering 1.5 hectares. Together with the surrounding coral reefs, the whole ecosystem stretched to around 15 hectares. The beds revealed a distinctive ecosystem from the neighboring coral reef, providing food and shelter for large marine mammals, alongside numerous fish, mollusks, echinoderms and sponges.
The team also found an abundance of cryptic invertebrates there, compared with the surrounding coral rubble.
“Rhodoliths provide many of their ecosystem services because of their structural complexity, which is dependent on both their species and local environmental conditions,” explains Li. “Integrating molecular, morpho-anatomical and environmental data allowed us to understand some of the factors driving their complexity.”
“We also discovered two new rhodolith species,” says Li
The team are now further sequencing their samples in collaboration with researchers in Italy. They have also been working closer to home, examining rhodoliths and encrusting coralline algae in the central Red Sea for the first time.
“Rhodoliths are particularly sensitive to both local and global human impacts, so it is vital that we understand them and establish effective conservation policies to protect them,” concludes Johnson.
The glacier-fed streams (GFS) of the world’s highest mountains contain a diverse range of microorganisms but until recently, little was known about them.
A remarkable biodiversity in these streams has been revealed in a major study by a large international team, led by the Swiss Federal Technology Institute of Lausanne, and including KAUST researchers Ramona Marasco and Daniele Daffonchio[1].
The study involved collecting and analyzing samples from 152 GFS across Earth’s major mountain ranges, as part of the Vanishing Glaciers project.
Glacier-fed streams are largely restricted to mountain tops, where they initiate the flow of water for some of the world’s largest rivers. Glacier shrinkage due to climate change affects these streams, putting their ecosystem services and biodiversity at risk. “The shrinking of mountain glaciers in many parts of the world leads to decreasing freshwater supply to downstream areas,” says Daffonchio.
Microbial biofilms (the microbial communities attached to streambed sediments) that dominate life in the GFS have an important role in regulating the glacier and river biogeochemical cycles and the downstream water cycle, but very little is known about their ecology, biology and functions.
This research helps to fill the gap by presenting a biogeography and ecological analysis of the GFS microbiomes from the Earth’s major high mountain ranges,” says Daffonchio.
Using next-generation sequencing (NGS) technology, Marasco and the team sequenced the bacteria to create the dataset needed to describe the bacterial diversity. A challenge was ensuring sufficient sequencing depth and maintaining high-quality standards throughout the process.
“This was critical to guarantee that we could compare data from the different sequencing and libraries, as well as to define a final dataset that could accurately characterize the bacterial diversity and ecology of the GFS,” Marasco explains.
“We were also dealing with a diverse and complex environmental sample, with varying biomass (or microbial load) so we needed to ensure that the DNA sequencing was comprehensive enough to capture rare and abundant taxa alike,” she says.
The high-quality data generated enabled the researchers to construct a robust and comprehensive picture of the bacterial communities associated with these fragile ecosystems.
GFS are characterized by near-zero temperatures, low nutrient concentrations, and periods of either diminished light or strong UV radiation. Given these inhospitable conditions, the scientists were surprised to find such a wealth of microbial biodiversity.
The survey uncovered bacteria from 44 phyla, including many previously unclassified, with genetic diversity decreasing with elevation. It showed a bacterial microbiome that is taxonomically and functionally distinct from other cryospheric (frozen) microbiomes, characterized by both high regional specificity and local uniqueness.
“The GFS harbor a wide variety of bacterial lineages with many not previously characterized, highlighting their resilience and adaptability in extreme environments,” says Marasco.
The results showed that GFS microbial communities have a remarkable niche specialization. Certain taxa appear to be specific to particular environmental conditions; for instance, more than half were specific to a mountain range, some unique to a single stream, while a few were both cosmopolitan and abundant.
“This diversity and specificity provide new insights into the complex ecological interactions that drive these ecosystems,” says Marasco.
The team has now compiled the first global atlas of microbes in glacier-fed streams, which provides a baseline for future studies on the vanishing GFS ecosystem.
“We show that GFS microorganisms are distinct from the other microbial communities of the cryosphere and present high biodiversity and strong biogeographical patterns. The large dataset and the information presented in the study provide a novel reference on these important but vanishing microbiomes,” concludes Daffonchio.
Accurate assessment of the land surface damage (such as small-scale fracturing and inelastic deformation) from two major earthquakes in 2023 can help scientists assess future earthquake hazards and therefore minimize risk to people and infrastructure. However, attaining precise extensive measurements in earthquake zones remains challenging.
The two earthquakes that struck on 6 February 2023 were devastating: they were of magnitude 7.8 and 7.6 and occurred in quick succession near the border between Syria and Turkey. They caused widespread infrastructure destruction and resulted in tens of thousands of deaths across multiple provinces.
Using the two Kahramanmaraş earthquakes as a case study, KAUST researchers have demonstrated that the surface damage and inelastic deformation away from main faults probably extend more widely than previously thought[1].
“The Kahramanmaraş earthquakes offered us a unique opportunity to gain insights into details of the co-seismic surface displacement,” says Jihong Liu, postdoctoral fellow in KAUST’s Crustal Deformation and InSAR Group, who carried out the study in collaboration with colleagues from KAUST and IPGP in France. “Our results suggest that the width of the crustal damage zone can reach up to five kilometers from the fault itself, rather than just a few hundred meters as suggested by previous case studies.”
Large earthquakes occur when two tectonic plates that are stuck together move suddenly, instead of moving steadily past one another a few centimeters per year. This sudden slip, which yields meter-scale movement within seconds, causes extensive crustal damage. This damage is not just in the immediate vicinity of a plate boundary or fault, but also “off-fault damage” (OFD) away from the main fault. Measuring OFD accurately is a critical element of estimating fault slip rates and earthquake cycles, yet most case studies of major earthquakes appear to have significantly underestimated OFD.
The team used image data from Synthetic Aperture Radar (SAR) satellites to quantify the OFD and 3D surface displacement caused by the two earthquakes. They used images taken before and after the two earthquakes.
“Radar satellites have transformed the study of earthquake zones, enabling us to visualize and analyze large areas in depth without requiring field observations,” says Liu.
Liu developed the SM-VCE method, an advanced co-seismic 3D surface displacement measurement technique, which the team used to precisely determine the 3D motion, OFD and surface deformation across a wide area around the two earthquakes. They showed that OFD consumed up to 35% of the co-seismic displacement, suggesting that slip rates in different parts of the world could be underestimated by as much as one-third. They also found that geometrically complex fault sections experienced a higher level of OFD than simple straight fault sections.
“Our results hold implications for geologic measurements of fault slip rates. If the OFD is larger than previously thought, it means that the plate boundary may be moving faster and could trigger more large earthquakes than anticipated,” says Sigurjón Jónsson, who led the team. “This increases the estimated earthquake hazard, with serious implications for planned infrastructure, buildings and decision making. Accurate OFD should also be factored into computer models of earthquake zones.”
“We will conduct OFD measurements on other typical earthquake cases to further validate and support the findings of this study,” concludes Liu.
Phytoplankton communities form the basis of the marine food web and are essential for nutrient cycling in the world’s oceans. However, both natural and human activities can easily disrupt the balance and functioning of these essential microalgae communities. Understanding how phytoplankton respond to external pressures over time can provide useful insights for safeguarding these vital ecosystem components in the future.
Now, a study of sediment cores taken from the western Arabian Gulf to examine centennial and decadal trends in phytoplankton communities in the region has been undertaken by KAUST researchers in collaboration with King Fahd University of Petroleum and Minerals (KFUPHM)[1].
“People may be surprised to learn that phytoplankton produce nearly half of the oxygen on the planet,” says Sdena Nunes, postdoc at KAUST, who worked on the study with KAUST faculty Carlos M. Duarte and Susana Agusti. “However, when agricultural run-off, urban wastewater discharge and industrial effluents enter the marine environment, the water becomes enriched with nutrients such as phosphorus and nitrogen. This ‘eutrophication’ process fuels the rapid growth of phytoplankton, leading to harmful algal blooms (HABs).”
As these blooms decay, the decomposition process consumes large amounts of oxygen, creating hypoxic zones, or “dead zones,” where marine life cannot survive. Instead of producing oxygen and feeding wider ecosystems, the phytoplankton suffocate habitats.
HABs also pose health risks to humans. Scientists are concerned about the visible rise in eutrophication and HABs in the Arabian Gulf in recent years.
To learn more about the historical trends in phytoplankton in the region, the team analyzed the phytoplankton pigments present in the layers of sediment that have built up over centuries on the seafloor.
“Pigments are colored compounds present in all photosynthetic organisms, including phytoplankton. They are naturally preserved in seafloor sediments after the phytoplankton die,” says Nunes. “These pigments can indicate what species were present and their prevalence over different decades.”
The team’s results show clear evidence of widespread eutrophication in the Arabian Gulf, which has intensified since the 1980s. Chlorophyll-a concentrations increased in all the sediment cores over the last 40 years, reflecting a steady rise in phytoplankton abundance. Over time, the phytoplankton community has shifted from cyanobacteria and prasinophytes, which dominated in the early 20th century, to diatoms and dinoflagellates.
“These changes align with the region’s rapid urbanization and industrialization, and with rising nutrient inputs into the Gulf’s waters,” says Nunes. “The frequency and intensity of HABs have increased rapidly since the early 2000s, and there are also seasonal phytoplankton variations that are influenced by other factors, such as coastal wastewater discharges.”
Cyanobacteria experienced a sharp decline during the 1990s, coinciding with oil spills from the Gulf War. Oil pollutants inhibit the growth, metabolism and photosynthesis processes of cyanobacteria.
“These findings underscore the widespread and ongoing impact of eutrophication — compounded by anthropogenic pressures — on the region’s marine ecosystems,” says Agusti. “By mapping these changes on a centennial scale, we’ve gained insights into how phytoplankton dynamics respond to environmental pressures.”
The team hope these findings can guide the development of national and regional monitoring and management strategies to reduce nutrient in-flows and control pollution in the Arabian Gulf.
A better understanding of how tiny airborne pollutant particles, or aerosols, promotes sulfate formation could help improve management of air quality, a KAUST-led team[1] has shown. The findings could improve models used to predict and reduce secondary pollution.
Aerosols pose serious environmental and health threats, especially in Asia and the Middle East and North Africa region. Primary aerosols are generated by outdoor and household sources, such as power plants, industries, agriculture, automobiles, wildfires, dust storms, cooking activities, and incense burning. Secondary aerosols result from chemical reactions in the atmosphere.
Together, primary and secondary aerosols cause respiratory and cardiovascular disorders that lead to seven million premature deaths annually. Air pollution in Saudi Arabia, with one of the world’s highest aerosol concentrations, has shortened life expectancy by almost 1.5 years.
Aerosols from burning biomass represent 60 to 85 percent of the total primary organic aerosols emitted annually and are likely to increase as wildfires become more frequent and severe with intensifying climate change. They also absorb sunlight and worsen haze, which accelerates the warming of the Earth’s atmosphere.
Sulfate is a major aerosol component that results from the oxidation of sulfur dioxide during haze events. The Middle East emits more than 15 percent of global sulfur dioxide. Conventional air quality models have attributed this reaction to oxidants present in the gas phase, yet fail to explain the elevated sulfate levels observed when haze occurs.
Some molecules in the wildfire smoke absorb light and can transition to long-lived high-energy states called triplet excited states when exposed to light. In a triplet state, the molecules show unique reactivity and can initiate reactions with other compounds.
Inspired by the ability of these brown carbon molecules to form reactive species inside atmospheric particles, a team led by Chak Chan, and post-doc Zhancong Liang, has now proposed that triplet states generated in burning-biomass organic aerosols account for the ‘missing sulfate’.
The researchers assessed the photochemical reactivity of the aerosol particles in the multiphase oxidation of sulfur dioxide. They burned typical biomass to produce particles and then used an aerosol flow reactor to better mimic the reactions of submicron particulates in the atmosphere.
The team discovered that biomass smoke contained photosensitizers and generated triplet states that were key in stimulating the oxidation of sulfur dioxide into sulfate in the aerosol particles. Aerosol particles also displayed oxidation rates three orders of magnitude higher than bulk solution.
Simulations further indicated that triplet-state-driven sulfate formation enhances sulfate levels in wildfire-prone regions that are rich in biomass-burning organic aerosols. “Incorporating our kinetic parameters into atmospheric models can improve predictions of secondary pollution and help improve understanding of the environmental impact of global warming,” Liang says.
Next, the researchers plan to develop a predictive framework for the reactivity of various biomass-burning organic aerosols using their chemical structures. “The diversity and mechanistic ambiguity of organic aerosols make it complex to parameterize and predict triplet-state-driven reactions,” Liang says, noting the need to use samples with diverse compositions to investigate interactions with different atmospheric molecules, such as volatile organic compounds.
The team also collaborates with Imed Gallouzi, Chair of the KAUST Center of Excellence for Smart Health, on health impacts of atmospheric particles.
A mathematical proof established more than 140 years ago provided the key for a KAUST-led team to develop a computational method for accurately simulating complex biophysical processes, such as the spread of disease and the growth of tumors[1].
Reaction-diffusion equations are widely used to model the dynamics of complex systems by providing a macroscopic mathematical description of the interplay between local interactions and random motion.
“Reaction-diffusion equations play a crucial role in many clinical applications, including computational epidemiology — an interdisciplinary field that combines mathematics and computational science — to enhance our understanding and control of the spatiotemporal spread of diseases in real time,” says Rasha Al Jahdali from the KAUST research team.
“This discipline is vital for informing health policy decisions worldwide. Since studying epidemiological phenomena is often complex and sometimes unfeasible, it is important to develop efficient, robust, and predictive algorithms for reaction-diffusion processes.”
These equations capture real physical mechanisms in the form of continuous ‘partial differential’ equations that describe rates of change over space and time. While mathematically ideal, such equations can be very difficult to solve for the purposes of simulating complex biophysical processes because computers require numerical methods involving discrete calculations of real numbers.
“Discretizing continuous reaction-diffusion equations using numerical schemes allows us to use computers to solve them numerically,” says Al Jahdali. “This involves approximating continuous variables and their derivatives or rates of change at specific points in space and time. The problem is that existing discretization methods often lack the ability to maintain stability and accuracy when simulating complex, nonlinear interactions like those inherent in biological systems.”
That means existing numerical schemes often produce ‘unphysical’ results or break down, particularly with spatially varying reaction-diffusion equations, which limits their utility for making reliable predictions in a clinical context.
To solve this problem, Al Jahdali and her colleagues turned to an old mathematical proof, called the Lyapunov direct method, that tests for the existence of a stable solution of time-varying system without needing to solve the underlying partial differential equations.
“Our computational framework leverages the Lyapunov’s direct method to develop fully discrete and ‘smart’ self-adapting schemes of arbitrary accuracy in space and time,” says Al Jahdali. “This new computational framework provides robust and accurate solutions suitable for applications in complex environments, capturing correctly the dynamics of phenomena, which is crucial for accurately modeling real-world scenarios in biological and clinical applications.”
The researchers applied their method to a commonly used spatially varying ‘susceptible-infected’ model for predicting the endemic spread of disease, showing that their numerical approach stayed consistent with the original physically accurate reaction-diffusion solution. They also used their approach to model the treatment of a tumor in the brain using virotherapy, involving complex interactions in space and time based on known biochemical processes.
“Our approach demonstrates superior performance compared to traditional numerical methods for solving reaction-diffusion partial differential equations, which will enable more reliable and physically consistent results,” says Al Jahdali. “This represents a significant step in developing computational methods that are not only theoretically sound, but practically useful for addressing pressing global problems.”
