Illustration of the structure of the radium compound characterized in this research. Single crystal X-ray diffraction provided detailed information on the bonding of radium in an organic molecule for the first time. Credit: Christopher Orosco, Oak Ridge National Laboratory
For the first time in history, scientists have measured radium’s bonding interactions with oxygen atoms in an organic molecule. Scientists have not measured this bonding before because radium-226 is available only in small amounts and it is highly radioactive (radium is one million times more radioactive than the same mass of uranium), making it challenging to work with.
The findings are published in the journal Nature Chemistry.
Using oxygen as the donor atom, the researchers developed a way to synthesize and crystallize the radium complex rapidly and on a small scale. Next, they measured the X-ray diffraction pattern of the complex. This pattern is created by the complex’s crystal structure and reveals its structure and bonding characteristics.
Certain radium isotopes show promise for targeted alpha therapy treatment for cancers. For this type of treatment, radium must be bonded to another molecule, called a “chelator,” and delivered directly to tumors in the body. There, the radium gives off powerful radiation that travels only a very short distance to attack the tumor and leaves surrounding cells unharmed.
When developing these chelators, scientists typically use barium because it is chemically similar to radium. However, this study showed that radium is quite different from barium. The result gives scientists information that may help them use radium in future cancer treatments.
Working with radium, which is highly radioactive, required the researchers to develop a process for synthesis and crystallization on a nanogram scale.
Their success using this technique to characterize radium potentially allows scientists to learn exactly how radium binds to other elements—oxygen or nitrogen, for example. Since nitrogen and oxygen are elements typically present in chelators, and radium interacts with them during bonding, this information will be helpful for developing chelators to carry radium to cancer sites in targeted alpha therapy treatment.
This work also demonstrates significant differences between radium and barium in how they interact with chelators, suggesting that barium is not always a good stand-in for radium when developing these chelators. The methods the researchers used to characterize and analyze radium potentially could be used to learn about other challenging radioactive complexes.
Illustration of the sensing principle of the distance-based miRNA assay. Credit: SIBET
Point-of-care testing (POCT) devices show great advantages over conventional diagnostic tests in being accessible to patients and providing timely diagnostic information. The global POCT market has grown remarkably over the past few decades. Distance-based devices are attracting great interest due to their simplicity, affordability, and ease of application.
Researchers at the Suzhou Institute of Biomedical Engineering and Technology (SIBET) of the Chinese Academy of Sciences have proposed a distance-based visual miRNA biosensor based on a DNA hydrogel system. The results of the study, titled “Distance-Based Visual miRNA Biosensor with Strand Displacement Amplification-Mediated DNA Hydrogel Assembly,” were published in ACS Materials Letters.
The target miRNA-initiated strand displacement amplification process will produce abundant single-stranded DNA, which are essential probes for the linking of the three-way junction scaffold of the hydrogel.
The phase transition of the solution is confirmed by elastic and electrochemical techniques. A distance-based paper biosensing method is thus set up by establishing the relationship between the seepage flow distance along the strip and the initial miRNA concentration.
Due to the strand displacement amplification, the biosensor is not only simple but also highly sensitive with a detection limit down to 1 fM.
Since the three-dimensional DNA hydrogel provides abundant binding sites, the detection range is quite wide, according to the researchers.
The biosensor is shown to be highly selective, and the results of human serum analysis are consistent with standard quantitative reverse transcription-PCR.
“This approach has the advantages of convenient operation and low cost, which meets the requirements of point-of-care testing,” said Miao Peng, lead author of the study. “It is promising as a convenient tool for miRNA-related biological studies and clinical diagnosis.”
Graphical abstract. Credit: Journal of the American Chemical Society (2024). DOI: 10.1021/jacs.4c01925
In the movie “Jurassic Park,” scientists extracted DNA that had been preserved in amber for millions of years, and used it to create a population of long-extinct dinosaurs.
Inspired partly by that film, MIT researchers have developed a glassy, amber-like polymer that can be used for long-term storage of DNA, whether entire human genomes or digital files such as photos.
Most current methods for storing DNA require freezing temperatures, so they consume a great deal of energy and are not feasible in many parts of the world. In contrast, the new amber-like polymer can store DNA at room temperature while protecting the molecules from damage caused by heat or water.
The researchers showed that they could use this polymer to store DNA sequences encoding the theme music from Jurassic Park, as well as an entire human genome. They also demonstrated that the DNA can be easily removed from the polymer without damaging it.
“Freezing DNA is the number one way to preserve it, but it’s very expensive, and it’s not scalable,” says James Banal, a former MIT postdoc. “I think our new preservation method is going to be a technology that may drive the future of storing digital information on DNA.”
Banal and Jeremiah Johnson, the A. Thomas Geurtin Professor of Chemistry at MIT, are the senior authors of the study, published in the Journal of the American Chemical Society. Former MIT postdoc Elizabeth Prince and MIT postdoc Ho Fung Cheng are the lead authors of the paper.
Capturing DNA
DNA, a very stable molecule, is well-suited for storing massive amounts of information, including digital data. Digital storage systems encode text, photos, and other kinds of information as a series of 0s and 1s. This same information can be encoded in DNA using the four nucleotides that make up the genetic code: A, T, G, and C. For example, G and C could be used to represent 0 while A and T represent 1.
DNA offers a way to store this digital information at very high density: In theory, a coffee mug full of DNA could store all of the world’s data. DNA is also very stable and relatively easy to synthesize and sequence.
In 2021, Banal and his postdoc advisor, Mark Bathe, an MIT professor of biological engineering, developed a way to store DNA in particles of silica, which could be labeled with tags that revealed the particles’ contents. That work led to a spinout called Cache DNA.
One downside to that storage system is that it takes several days to embed DNA into the silica particles. Furthermore, removing the DNA from the particles requires hydrofluoric acid, which can be hazardous to workers handling the DNA.
To come up with alternative storage materials, Banal began working with Johnson and members of his lab. Their idea was to use a type of polymer known as a degradable thermoset, which consists of polymers that form a solid when heated. The material also includes cleavable links that can be easily broken, allowing the polymer to be degraded in a controlled way.
“With these deconstructable thermosets, depending on what cleavable bonds we put into them, we can choose how we want to degrade them,” Johnson says.
For this project, the researchers decided to make their thermoset polymer from styrene and a cross-linker, which together form an amber-like thermoset called cross-linked polystyrene. This thermoset is also very hydrophobic, so it can prevent moisture from getting in and damaging the DNA. To make the thermoset degradable, the styrene monomers and cross-linkers are copolymerized with monomers called thionolactones. These links can be broken by treating them with a molecule called cysteamine.
Because styrene is so hydrophobic, the researchers had to come up with a way to entice DNA—a hydrophilic, negatively charged molecule—into the styrene.
To do that, they identified a combination of three monomers that they could turn into polymers that dissolve DNA by helping it interact with styrene. Each of the monomers has different features that cooperate to get the DNA out of water and into the styrene. There, the DNA forms spherical complexes, with charged DNA in the center and hydrophobic groups forming an outer layer that interacts with styrene. When heated, this solution becomes a solid glass-like block, embedded with DNA complexes.
The researchers dubbed their method T-REX (Thermoset-REinforced Xeropreservation). The process of embedding DNA into the polymer network takes a few hours, but that could become shorter with further optimization, the researchers say.
To release the DNA, the researchers first add cysteamine, which cleaves the bonds holding the polystyrene thermoset together, breaking it into smaller pieces. Then, a detergent called SDS can be added to remove the DNA from polystyrene without damaging it.
Storing information
Using these polymers, the researchers showed that they could encapsulate DNA of varying length, from tens of nucleotides up to an entire human genome (more than 50,000 base pairs). They were able to store DNA encoding the Emancipation Proclamation and the MIT logo, in addition to the theme music from “Jurassic Park.”
After storing the DNA and then removing it, the researchers sequenced it and found that no errors had been introduced, which is a critical feature of any digital data storage system.
The researchers also showed that the thermoset polymer can protect DNA from temperatures up to 75 degrees Celsius (167 degrees Fahrenheit). They are now working on ways to streamline the process of making the polymers and forming them into capsules for long-term storage.
Cache DNA, a company started by Banal and Bathe, with Johnson as a member of the scientific advisory board, is now working on further developing DNA storage technology. The earliest application they envision is storing genomes for personalized medicine, and they also anticipate that these stored genomes could undergo further analysis as better technology is developed in the future.
“The idea is, why don’t we preserve the master record of life forever?” Banal says. “Ten years or 20 years from now, when technology has advanced way more than we could ever imagine today, we could learn more and more things. We’re still in the very infancy of understanding the genome and how it relates to disease.”
High-resolution image of the individual copper atoms (marked in red) of the heterogeneous catalyst (Cu-SAC) using a scanning transmission electron microscope (STEM). Credit: LIKAT
A catalyst developed at LIKAT in Rostock opens up new avenues in the synthesis of fine chemicals for pharmaceuticals, agrochemicals and household chemicals, for example. Its effect is based on isolated copper atoms applied to a solid carrier material around which the reaction solution flows.
This heterogeneous catalysis, so called because the aggregate states of the catalyst (solid) and the starting materials (liquid) differ, is highly unusual in the production of pharmaceuticals, for example. The researchers report on the new approach in the journal Chem.
Hot topic: Heterogeneous instead of homogeneous
In the production of fine chemicals, chemists usually use the classic workhorse, homogeneous catalysis: starting materials, catalyst and end product are in a liquid mix (homogeneous, i.e. in the same aggregate state) in one vessel. One advantage of this catalysis is the mild reaction temperatures, which are gentle on the sensitive structures of these complex molecules.
However, homogeneous catalysis has decisive disadvantages. This is why one of the “hot topics” in chemistry is to replace these processes with heterogeneous procedures. Two Humboldt Fellows at the Leibniz Institute for Catalysis in Rostock have succeeded in doing this for a single step within a multi-stage reaction cascade that fine chemicals usually undergo during their production.
Dr. Qiang Wang and Dr. Haifeng Qi developed a heterogeneous copper catalyst and were able to use it to re-establish important bonds between carbon and other chemical elements in numerous complex molecules at moderate temperatures of 60 degrees Celsius.
Single-atom structure on MOFs
When developing their catalyst, they applied the copper atoms to the carrier material in isolated form, i.e. individually. This so-called single-atom structure enabled Wang and Qi to enormously increase the precision of their catalyst, which chemists refer to as selectivity. Their copper catalyst has also outperformed the homogeneous process in terms of yield.
“Individually, copper atoms offer the reaction environment a much larger surface area than when they are connected in clusters or nanoparticles,” say Dr. Kathrin Junge and Prof. Jagadeesh Rajenahally, explaining the principle.
Junge and Rajenahally are co-authors of the Chem paper and supervised Haifeng Qi and Qiang Wang. The two Humboldt Fellows are now working in other research groups in China and the UK. Kathrin Junge explains the significance of her research, “Active ingredients, vitamins and fragrances are often modeled on nature and are created through total synthesis, which in turn can involve a dozen or more reaction steps.”
After each step, the substances must be separated, purified and prepared for the next reaction stage. However, the catalysts, usually organometallic complexes, are difficult to recover from the homogeneous reaction solutions. And metal impurities represent a real hurdle for the approval of drugs, as the authors write in the original paper.
The two Humboldt fellows circumvented this problem by stably bonding their metal to a solid carrier material. They used organometallic framework structures as carriers, which have been making a name for themselves in chemistry for several years under the name MOFs.
“These MOFs contain structures similar to those of ligands in homogeneous catalysts,” explains Dr. Junge. Their function is simulated to a certain extent with the help of the corresponding structure in the heterogeneous copper catalyst.
Substances selected for specific applications
Qiang Wang and Haifeng Qi demonstrated the functionality of their heterogeneous catalyst using a variety of complex molecules that are used in organic synthesis chemistry. For example, for the production of pharmaceuticals, vitamins in animal feed production and fragrances in household chemistry.
Dr. Junge said, “The two colleagues have thus shown that their research work really does have potential applications in mind.” Or, as the original paper puts it, “The use of more stable heterogeneous materials is a model for future catalysis in the field of organic syntheses.”
Cracking and self-healing of the peptide glass. Credit: Nature (2024). DOI: 10.1038/s41586-024-07408-x
A team of materials scientists from Tel Aviv University and Ben-Gurion University of the Negev, both in Israel, working with a colleague from California Institute of Technology, in the U.S., has found that mixing a certain peptide with water results in the creation of a self-assembling and self-healing glass.
While investigating the properties of other proteins, the group stumbled upon the discovery, which has been published in Nature Communications. Silvia Marchesan, with the University of Trieste, in Italy, has published a News and Views piece in the same journal issue, outlining the newly found glass and possible uses for it.
In this new effort, the research team was investigating the possibility of using short peptides as stand-ins for conventional components of complex macro-molecules. As part of that effort, they worked with a dipeptide molecule that consisted of two phenylalanine residues when they discovered that mixing it with nothing but water led to the creation of a self-assembling type of supramolecular amorphous glass as the water evaporated at room temperature.
What was most surprising about the discovery was that peptide self-assembly in the past has typically led to the creation of materials with a crystalline structure, something that would not be transparent and thus not even close to glass.
Upon discovering the new type of glass, the researchers began investigating its properties. They found that in addition to automatically building itself, the glass was both self-healing and adhesive, despite being highly rigid.
It was also deemed to be extremely strong. The researchers found that it was as transparent as traditional glass, and further investigation showed that the glass could be used to make glass panes and coatings to create hydrophilic surfaces. They also found it could be used to make things that require precision, such as optical lenses that could be used for a wide range of magnification purposes.
The research team suggests that additional testing could lead to a wide variety of uses for the glass, noting that the new type of glass does not require a lot of energy to produce as is typical with most glasses now in commercial use.
Spicy foods taste spicy because they contain a family of compounds called capsaicinoids. Capsaicin is the major culprit. It’s found in chilies, jalapeños, cayenne pepper, and is even the active ingredient in pepper spray.
Capsaicin doesn’t actually physically heat up your mouth. The burning sensation comes from receptors in the mouth reacting to capsaicin and sending a signal to the brain that something is very hot.
That’s why the “hot” chlli sensation feels so real—we even respond by sweating. To alleviate the heat, you need to remove the capsaicin from your mouth.
So why doesn’t drinking water help make that spicy feeling go away? And what would work better instead?
Water-loving and water-hating molecules
To help us choose what might wash the capsaicin away most effectively, it’s helpful to know that capsaicin is a hydrophobic molecule. That means it hates being in contact with water and will not easily mix with it.
Look what happens when you try to mix hydrophobic sand with water.
On the other hand, hydrophilic molecules love water and are very happy to mix with it.
You’ve likely seen this before. You can easily dissolve hydrophilic sugar in water, but it’s hard to wash away hydrophobic oils from your pan using tap water alone.
If you try to wash hydrophobic capsaicin away with water, it won’t be very effective, because hydrophilic and hydrophobic substances don’t mix.
Going for iced water will be even less effective, as hydrophobic capsaicin is even less soluble in water at lower temperatures. You may get a temporary sense of relief while the cold liquid is in your mouth, but as soon as you swallow it, you’ll be back where you started.
Instead, a good choice would be to consume something that is also hydrophobic. This is because of an old-but-true adage in chemistry that “like dissolves like.”
The idea is that generally, hydrophobic substances will not dissolve in something hydrophilic—like water—but will dissolve in something that is also hydrophobic, as the video shows.
My mouth is on fire. What should I drink instead of water?
A swig of oil would likely be effective, but is perhaps not so palatable.
Milk makes for an ideal choice for two reasons.
The first is that milk contains hydrophobic fats, which the capsaicin will more easily dissolve in, allowing it to be washed away.
The second is that dairy products contain a protein called casein. Casein is an emulsifier, a substance that helps oils and water mix, as in this video:
Casein plays a large role in keeping the fat mixed throughout your glass of milk, and it also has a strong affinity for capsaicin. It will readily wrap up and encapsulate capsaicin molecules and assist in carrying them away from the receptor. This relieves the burning sensation.
Okay, but I hate drinking milk. What else can I try?
What about raita? This dish, commonly served with Indian curries, is made primarily from yogurt. So aside from being its own culinary experience, raita is rich in fats, and therefore contains plenty of hydrophobic material. It also contains casein, which will again help lock up and remove the capsaicin.
Ice cream would also work, as it contains both casein and large amounts of hydrophobic substances.
This is commonly suggested as a suitable approach to stop the burning. At first glance, this may seem a good idea because capsaicin is highly soluble in alcohol.
However, most beers only contain between 4 and 6% alcohol. The bulk of the liquid in beer is water, which is hydrophilic and cannot wash away capsaicin. The small amount of alcohol in your beer would make it slightly more effective, but not to any great degree.
Your curry and beer may taste great together, but that’s likely the only benefit.
In truth, an alcoholic beverage is not going to help much unless you go for something with a much, much higher alcohol content, which comes with its own problems.
The inhibitor 7,8-dihydroxyflavone (purple) bound to pyridoxal phosphatase (green) Credit: Marian Brenner / JMU
A low vitamin B6 level has negative effects on brain performance. A research team from Würzburg University Medicine has now found a way to delay the degradation of the vitamin.
Vitamin B6 is important for brain metabolism. Accordingly, in various mental illnesses, a low vitamin B6 level is associated with impaired memory and learning abilities, with a depressive mood, and even with genuine depression. In older people, too little vitamin B6 is linked to memory loss and dementia.
Although some of these observations were made decades ago, the exact role of vitamin B6 in mental illness is still largely unclear. What is clear, however, is that an increased intake of vitamin B6 alone, for example in the form of dietary supplements, is insufficient to prevent or treat disorders of brain function.
A research team from Würzburg University Medicine has now discovered another way to increase vitamin B6 levels in cells more effectively: namely by specifically inhibiting its intracellular degradation. Antje Gohla, Professor of Biochemical Pharmacology at the Department of Pharmacology and Toxicology at Julius-Maximilians-Universität Würzburg (JMU), is responsible for this.
Other participants come from the Rudolf Virchow Center for Integrative and Translational Bioimaging at JMU, the Leibniz-Forschungsinstitut für Molekulare Pharmakologie-FMP Berlin and the Institute for Clinical Neurobiology at Würzburg University Hospital. The team has now published the results of their investigations in the journal eLife.
Enzyme blockade improves learning ability
“We were already able to show in earlier studies that genetically switching off the vitamin B6-degrading enzyme pyridoxal phosphatase in mice improves the animals’ spatial learning and memory capacity,” explains Gohla. In order to investigate whether such effects can also be achieved by pharmacological agents, the scientists have now looked for substances that bind and inhibit pyridoxal phosphatase.
“In our experiments, we identified a natural substance that can inhibit pyridoxal phosphatase and thus slow down the degradation of vitamin B6,” explains the pharmacologist. The working group was actually able to increase vitamin B6 levels in nerve cells that are involved in learning and memory processes. The name of this natural substance: 7,8-Dihydroxyflavone.
New approach for drug therapy
7,8-Dihydroxyflavone has already been described in numerous other scientific papers as a molecule that can improve learning and memory processes in disease models for mental disorders. The new knowledge of its effect as an inhibitor of pyridoxal phosphatase now opens up new explanations for the effectiveness of this substance. This could improve the mechanistic understanding of mental disorders and represent a new drug approach for the treatment of brain disorders, the scientists write in their study.
The team also considers it a great success that 7,8-Dihydroxyflavone has been identified as an inhibitor of pyridoxal phosphatase for the first time—after all, this class of enzymes is considered to be particularly challenging for drug development.
A long way to a drug
When will people benefit from this discovery? “It’s too early to say,” explains Marian Brenner, a first author of the study. However, there is much to suggest that it could be beneficial to use vitamin B6 in combination with inhibitors of pyridoxal phosphatase for various mental disorders and neurodegenerative diseases.
In a next step, Gohla and her team now want to develop improved substances that inhibit this enzyme precisely and highly effectively. Such inhibitors could then be used to specifically test whether increasing cellular vitamin B6 levels is helpful in mental or neurodegenerative diseases.
The study, led by the research groups of Varpu Marjomäki at JYU and Antti Haapala at UEF, investigated the antiviral potential of different wood species against enveloped coronaviruses and non-enveloped enteroviruses. The work has been published in ACS Applied Materials & Interfaces.
The COVID-19 pandemic and recurrent viral outbreaks have underscored the urgent need for innovative strategies to reduce virus transmission.
While wood has been a fundamental material in human environments for centuries, its antiviral properties have not been extensively explored—until now. This research is the first to systematically evaluate the inherent antiviral efficacy of the sawn wood material from various tree species, including both coniferous and deciduous trees, under different environmental conditions.
Key findings
Pine and Spruce: These coniferous species demonstrated excellent antiviral activity against enveloped coronaviruses, significantly reducing viral infectivity within just 10 to 15 minutes. However, their efficacy against non-enveloped enteroviruses was less pronounced.
Oak: This hardwood species was notably effective against non-enveloped enteroviruses, showcasing its potential for broader antiviral applications.
Chemical Composition: Analysis at UEF revealed that the antiviral properties are primarily governed by the chemical composition of the wood, including the presence of resin acids, terpenes, and phenolic compounds. These chemicals vary significantly between species and are influenced by environmental factors such as temperature and humidity.
Porosity and Absorption: While the porosity of wood and the absorption characteristics of viruses play a role, the study highlights that the chemical makeup of the wood is the key determinant in its antiviral functionality.
The research also found that thermal treatments and the addition of plastics to wood, such as in wood-plastic composites, can compromise the antiviral properties of the material. This insight opens new avenues for utilizing untreated or minimally processed wood surfaces in public health applications.
Future directions
The research teams from UEF and JYU will continue their investigation into the most effective antiviral components of wood and their mechanisms of action as part of the ongoing European Doctorate Program DESTINY. This future research aims to identify specific bioactive compounds that can be harnessed to develop sustainable and effective antiviral materials and coatings.
“This study marks a significant step forward in understanding how natural materials can be leveraged to enhance public health,” said Varpu Marjomäki, lead virologist at JYU.
“Our findings suggest that wood, a sustainable and widely available material, could play a crucial role in reducing viral transmission in various settings,” added Antti Haapala, lead material engineer at UEF.
“The synergistic roles between the different chemicals present are a continuing theme of investigation,” states Professor Haapala from Department of Chemistry.
This work introduces a technique for using hydrogen and electricity to create pharmaceuticals. Hydrogen can be made using renewable energy sources such as solar power, making the process more sustainable. Credit: UW–Madison
The world needs greener ways to make chemicals. In a new study, University of Wisconsin–Madison researchers demonstrate one potential path toward this goal by adapting hydrogen fuel cell technologies. These technologies are already used to power some electric vehicles, laptops and cell phones.
“The chemical industry is a massive energy consumer, and there is a big push to decarbonize the industry,” says Shannon Stahl, a professor in the UW–Madison Department of Chemistry who guided much of the research. “Renewable electricity can provide energy to produce chemicals with a much lower carbon footprint than burning fossil fuels.”
The conventional process uses large quantities of zinc metal as the source of electrons, but handling zinc is complicated and generates large amounts of environmentally unfriendly waste. Working with scientists at the pharmaceutical maker Merck & Co. Inc., UW–Madison chemists and engineers sought to develop a more sustainable method to manufacture ingredients needed to make many types of drugs.
In their search for an alternative process, the researchers took inspiration from hydrogen fuel cells, which use hydrogen gas as the source of electrons to generate electricity.
“The process we are working with needs a green source of electrons,” says Stahl. “We realized that fuel cell technology could be modified to make chemicals rather than electricity,”
Hydrogen gas is an ideal choice in many ways, according to Stahl. It can be generated from renewable electricity, and it creates very little waste. Developing a hydrogen-based way to make pharmaceuticals aligns with renewed interest in a “hydrogen economy.”
“This work is connected to a broader effort to create a hydrogen infrastructure that goes beyond fuel cells and energy production,” says Mathew Johnson, a postdoctoral researcher in the chemistry department who led the study. “This work shows that hydrogen can be combined with electricity to make new drugs.”
The researchers developed a system that uses a type of organic compound called a quinone to pull electrons away from hydrogen. An important feature of this process is that it works well in the absence of water. Fuel cells typically need water to operate effectively, but water can interfere with steps used to make the drug ingredients.
The system then uses electricity to supercharge the electrons, giving the electrons more energy than hydrogen could normally provide.
The team, which included postdoctoral researcher Jack Twilton, chemistry professor Daniel Weix and chemical and biological engineering professor Thatcher Root, described their new system in a paper published Aug. 21 in the journal Nature. They show how it can be used to make dozens of important organic molecules, including a large batch of a pharmaceutical ingredient.
The team is now working to improve the process so it can be used for industrial-scale production. And Stahl and his collaborators see even bigger opportunities for this technology.
“This is a broadly applicable technology for chemical production,” says Johnson. “Many chemical processes need electrons. This is not limited to pharmaceuticals. It should be a very versatile technology.”
More information: Jack Twilton et al, Quinone-mediated hydrogen anode for non-aqueous reductive electrosynthesis, Nature (2023). DOI: 10.1038/s41586-023-06534-2
Calculated results using the persistent homology method (persistence diagram) for amorphous carbon structures and the resulting energy predictions. Credit: 2023 Minamitani et al., Persistent homology-based descriptor for machine-learning potential of amorphous structures. The Journal of Chemical Physics
How is a donut similar to a coffee cup? This question often serves as an illustrative example to explain the concept of topology. Topology is a field of mathematics that examines the properties of objects that remain consistent even when they are stretched or deformed—provided they are not torn or stitched together. For instance, both a donut and a coffee cup have a single hole. This means, theoretically, if either were pliable enough, it could be reshaped into the other.
This branch of mathematics provides a more flexible way to describe shapes in data, such as the connections between individuals in a social network or the atomic coordinates of materials. This understanding has led to the development of a novel technique: topological data analysis.
In a study, titled “Persistent homology-based descriptor for machine-learning potential of amorphous structures,” in The Journal of Chemical Physics, researchers from SANKEN (The Institute of Scientific and Industrial Research) at Osaka University and two other universities have used topological data analysis and machine learning to formulate a new method to predict the properties of amorphous materials.
A standout technique in the realm of topological data analysis is persistent homology. This method offers insights into topological features, specifically the “holes” and “cavities” within data. When applied to material structures, it allows us to identify and quantify their crucial structural characteristics.
Now, these researchers have employed a method that combines persistent homology and machine learning to predict the properties of amorphous materials. Amorphous materials, which include substances like glass, consist of disordered particles that lack repeating patterns.
A crucial aspect of using machine-learning models to predict the physical properties of amorphous substances lies in finding an appropriate method to convert atomic coordinates into a list of vectors. Merely utilizing coordinates as a list of vectors is inadequate because the energies of amorphous systems remain unchanged with rotation, translation, and permutation of the same type of atoms.
Consequently, the representation of atomic configurations should embody these symmetry constraints. Topological methods are inherently well-suited for such challenges. “Using conventional methods to extract information about the connections between numerous atoms characterizing amorphous structures was challenging. However, the task has become more straightforward with the application of persistent homology,” explains Emi Minamitani, the lead author of the study.
The researchers discovered that by integrating persistent homology with basic machine-learning models, they could accurately predict the energies of disordered structures composed of carbon atoms at varying densities. This strategy demands significantly less computational time compared to quantum mechanics-based simulations of these amorphous materials.
The techniques showcased in this study hold potential for facilitating more efficient and rapid calculations of material properties in other disordered systems, such as amorphous glasses or metal alloys.
More information: Emi Minamitani et al, Persistent homology-based descriptor for machine-learning potential of amorphous structures, The Journal of Chemical Physics (2023). DOI: 10.1063/5.0159349
