POSTMODERN ALCHEMY

Simulations and experiments meet: Machine learning predicts the structures of gold nanoclusters

University of Jyväskylä - Jyväskylän yliopisto

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Atomistic snapshots describing how two thiolate-protected gold nanoclusters of 144 gold atoms each coalesce producing a single larger cluster matching a size that previously has been synthesized. 

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Credit: Maryam Sabooni Asre Hazer, University of Jyväskylä.

Researchers at University of Jyväskylä (Finland) advance understanding of gold nanocluster behavior at elevated temperatures using machine learning-based simulations. This information is crucial in the design of nanomaterials so that their properties can be modified for use in catalysis and other technological applications.

Thiolate protected gold nanoclusters are hybrid nanomaterials with promising applications in nanomedicine, bioimaging and catalysis. However, understanding how these nanoclusters behave under elevated temperatures, which is critical for their use, has remained largely unexplored due to the prohibitive computational cost of traditional simulation methods. 

Record-long simulations of gold nanoclusters

Researchers at the University of Jyväskylä have successfully employed machine learning-driven simulations to investigate the thermal dynamics of Au₁₄₄(SR)₆₀, one of the most well-studied gold nanoclusters. Using a recently developed atomic cluster expansion (ACE) potential trained on extensive density functional theory data, the researchers conducted molecular dynamics simulations extending up to 0.12 microseconds. This is approximately five orders of magnitude longer than what is feasible with conventional quantum chemical methods.

"This work opens new possibilities for understanding how ligand-protected metal nanoclusters behave under realistic operating conditions," says lead author Dr. Maryam Sabooni Asre Hazer. "Through this work, we can observe in atomistic detail how these clusters transform, fragment, and even merge at elevated temperatures over timescales that are relevant for experimental conditions."

Layer-by-layer thermal transformations revealed

The study revealed that thermal effects induce structural changes in a layer-by-layer fashion, starting from the outermost gold-thiolate protective shell. At temperatures between 300 and 550 K, the researchers observed the spontaneous formation of polymer-like chains and ring structures of gold-thiolate units, which can dynamically detach and reattach to the cluster surface. The remaining cluster compositions closely matched those observed in experimental studies, demonstrating the accuracy of the machine learning potential.

"What's particularly exciting is that we can now see how gold atoms migrate between different layers of the cluster and how the surface restructures under thermal stress," explains Dr. Sabooni Asre Hazer. "These processes are directly relevant to understanding why thermally treated gold nanoclusters become effective catalysts."

Gold clusters joined together in the simulation

In an even more remarkable finding, the researchers successfully simulated the complete coalescence of two Au₁₄₄(SR)₆₀ clusters at 550 K. The fusion process produced a larger cluster with composition Au₂₃₉(SR)₆₉, strikingly similar to a gold nanocluster previously synthesized experimentally. 

"The merged cluster exhibited a twinned face-centered cubic metal core structure, matching the symmetry determined from experimental X-ray diffraction data," says Dr. Sabooni Asre Hazer.

Opening new avenues for nanomaterials research

The methodology enables detailed atomistic studies of processes that were previously inaccessible to computational investigation, including cluster-cluster interactions, catalytic activation mechanisms, thermal stability, and inter-particle reactions.

"Our results provide fundamental insights into how ligand-protected nanoclusters behave as they transition toward larger nanoparticles," explains Professor Hannu Häkkinen, who supervised the research. "This knowledge is instrumental for the rational design of nanomaterials with tailored functionalities for catalysis and other applications.", he continues. 

The research was published in Nature Communications. The publication was recognized as an Editors' Highlight in the Inorganic and Physical Chemistry section of Nature Communications.

The work was supported by the Research Council of Finland and the European Research Council (ERC) through the Advanced Grant project DYNANOINT. Computational resources on supercomputers Puhti and Mahti were provided by the Finnish national supercomputing center CSC. 

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Journal

Nature Communications

DOI

10.1038/s41467-025-67700-w 

Method of Research

Imaging analysis

Subject of Research

Not applicable

Article Title

Thermal dynamics and coalescence of Au144(SR)60 clusters from a machine-learned potential

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POSTMODERN ALCHEMY

Steel making could get a makeover

University of Minnesota

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Ph.D. student, Jae Hyun Nam, worked in the University of Minnesota Characterization Facility to complete these nanometer scale observations.

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Credit: Kalie Pluchel, University of Minnesota

Researchers investigate clean and efficient new method for iron production

MINNEAPOLIS / ST. PAUL (09/29/2025) — A research team at the University of Minnesota Twin Cities has investigated a new method to produce iron, the main component of steel. For the first time, the researchers were able to observe chemical reactions and iron formation in real-time at the nanometer scale. 

This breakthrough has the potential to transform the global iron and steel production industry by improving energy efficiency and lowering costs. The study was recently published in Nature Communications, a peer-reviewed, high impact scientific journal.

According to the paper, the iron and steel industry is the largest industrial emitter of carbon dioxide, responsible for approximately 7 percent of the total global carbon dioxide emissions. Traditional methods for producing iron are pollution-heavy, relying on coke–a type of coal–to remove oxygen from iron ore—a process that has remained largely unchanged for centuries.

This method eliminates the CO2 emissions that have traditionally come from iron-making that can be performed at room temperature. This makes it potentially more efficient and desirable to industry and opens new pathways to innovation in the U.S. based manufacturing industry.

The new process uses hydrogen gas plasma, an ionized gas which dissociates the hydrogen gas producing an abundance of highly reactive hydrogen atoms. When the iron is exposed to this plasma, the highly reactive hydrogen atoms strip the oxygen from the ore producing pure iron and water vapor.

“We developed a new technique that allows us to monitor plasma-material interactions at the nanometer scale, which has never been done before,” said Jae Hyun Nam, first author on the paper and a Ph.D. student in the University of Minnesota Department of Mechanical Engineering.

The team partnered with Hummingbird Scientific, a company that builds products for electron, X-ray and ion microscopy, to create a specialized holder that fits inside of an transmission electron microscope. 

"Overcoming the technical challenges of this research was one of the most difficult experiments we've done," said Peter Bruggeman, a senior author on the paper and University of Minnesota Distinguished McKnight University Professor in the Department of Mechanical Engineering. “Generating plasmas on a scale around the size of a human hair, which is required to obtain the nanometer resolution, creates significant engineering challenges which we collaboratively tackled with Hummingbird Scientific.”

Previous optical methods could only be viewed at a few hundred nanometers—about a thousand times smaller than the diameter of a human hair. This new method will allow researchers to see things at a nanometer resolution, which is 100 times better than previous research. 

“Creating plasma could be energetically a lot more efficient than heating the material," said Andre Mkhoyan, a senior author on the paper and professor and Ray D. and Mary T. Johnson Chair in the University of Minnesota Department of Chemical Engineering and Materials Science. “This innovation could lead to materials being modified with lower energy consumption, ultimately making processes more economically efficient.”

Read the full paper entitled, “Revealing the mechanisms of non-thermal plasma-enabled iron oxide reduction through nanoscale operando TEM” on the Nature Communications website.

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Journal

Nature Communications

DOI

10.1038/s41467-025-62639-4 

Article Title

Revealing the mechanisms of non-thermal plasma-enabled iron oxide reduction through nanoscale operando TEM

POSTMODERN ALCHEMY

Liquid gold: Prototype harvests valuable resource from urine

Stanford University

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A newly developed system transforms human waste into a powerful tool for profitable and sustainable energy and agriculture in resource-limited regions. The prototype, outlined in a Stanford-led study published Aug 19 in Nature Water, recovers a valuable fertilizer from urine, using solar energy that can also provide power for other uses. In the process, the system provides essential sanitation, making wastewater safer to discharge or reuse for irrigation.

“This project is about turning a waste problem into a resource opportunity,” said study senior author William Tarpeh, an assistant professor of chemical engineering in the Stanford School of Engineering. “With this system, we’re capturing nutrients that would otherwise be flushed away or cause environmental damage and turning them into something valuable—fertilizer for crops—and doing it without needing access to a power grid.”

Nitrogen is a key component of commercial fertilizers. Traditionally, it's produced using a carbon-intensive process and distributed globally from large industrial facilities, many of which are located in wealthier nations resulting in higher prices in low- and middle-income countries. Globally, the nitrogen in human urine is equivalent to about 14% of annual fertilizer demand.

The prototype separates ammonia – a chemical compound made up of nitrogen and hydrogen – from urine through a series of chambers separated by membranes, using solar-generated electricity to drive ions across and eventually trap ammonia as ammonium sulfate, a common fertilizer. Warming the system—using waste heat collected from the back of photovoltaic solar panels via an attached copper tube cold plate—helps speed up the process by encouraging ammonia gas production, the final step in the separation process. Solar panels also produce more electricity at lower temperatures, so collecting waste heat helps keep them cool and efficient.   

“Each person produces enough nitrogen in their urine to fertilize a garden, but much of the world is reliant on expensive imported fertilizers instead,” said Orisa Coombs, the study’s lead author and a Ph.D. student in mechanical engineering. “You don’t need a giant chemical plant or even a wall socket. With enough sunshine, you can produce fertilizer right where it’s needed, and potentially even store or sell excess electricity.”

The study shows that integrating the heat generated by the solar panel to warm the liquid used in the electrochemical process and managing the current supplied to the electrochemical system increased power generation by nearly 60% and improved ammonia recovery efficiency by more than 20%, compared to earlier prototypes, which did not integrate these functions. The use of this waste heat is especially promising because there is a lot of it: about 80% of the sun energy that hits solar panels is lost, which could otherwise cause system overheating and efficiency slowdowns.

The researchers also developed a detailed model to predict how changes in sunlight, temperature, and electrical configuration affect system performance and economics. The model showed that in regions such as Uganda, where fertilizer is expensive and energy infrastructure is limited, the system could generate up to $4.13 per kilogram of nitrogen recovered—more than double the potential earnings in the U.S.

The researchers believe the approach could scale to help farmers and communities around the world. Lessons learned about integrating solar panel waste heat could also be applied to industrial facilities, such as wastewater treatment plants, capable of capturing heat produced during electricity generation to power a range of applications.

Coombs is working on a prototype that will have triple the reactor capacity, be capable of processing significantly more urine, and will process faster when more sunlight is available.

Beyond the potential for harvesting a valuable product and generating energy, the approach holds the promise of effective sanitation. More than 80% of wastewater goes untreated – much of it in low- and middle-income countries, according to the UN. Nitrogen in wastewater can contaminate groundwater and drinking water sources, and cause oxygen-depleting algal blooms that kill aquatic plants and animals. By removing nitrogen from urine, the prototype system makes the remaining liquid safer to discharge or reuse for irrigation. The ability to do this with a self-powered system could be a game changer in many countries where only a small percentage of the population is connected to centralized sewage systems.

“We often think of water, food, and energy as completely separate systems, but this is one of those rare cases where engineering innovation can help solve multiple problems at once,” said Coombs. “It’s clean, it’s scalable, and it’s literally powered by the sun.”

 

 

Coauthors of the study also include Taigyu Joo, a postdoctoral scholar in chemical engineering at Stanford; Amilton Barbosa Botelho Junior, a postdoctoral research fellow in chemical engineering at Stanford and the University of Sao Paulo, Brazil at the time of the research; and Divya Chalise, a postdoctoral scholar in mechanical engineering at Stanford.

Tarpeh is also an assistant professor, by courtesy, of civil and environmental engineering in the Stanford School of Engineering and the Stanford Doerr School of Sustainability; a center fellow at the Precourt Institute for Energy; and a center fellow, by courtesy, at the Stanford Woods Institute for the Environment.

The study was funded by the Knight-Hennessy Fellowship, the National Science Graduate Research Fellowship, a Global Health Seed Grant from the Stanford Center for Innovation in Global Health, the Camille Dreyfus Teacher-Scholar Award, the Stanford Sustainability Accelerator, and the Fundação de Amparo à Pesquisa do Estado de São Paulo and Capes.

The researchers’ work to convert urine into fertilizer was supported by the Stanford Sustainability Accelerator in its first round of grants in 2022. The team built a lab-scale electricity-driven reactor that extended to 40 days of operation, which inspired and enabled work on pairing electrochemical water treatment with solar panels. The earliest iterations of this project focused on recovering nitrogen and sulfur from wastewater to enable water reuse and fertilizer production, and was supported by the Stanford Woods Institute for the Environment’s Environmental Venture Projects program.

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Journal

Nature Water

Article Title

Prototyping and Modeling a Photovoltaic/Thermal Electrochemical Stripping System for Distributed Urine Nitrogen Recovery

Article Publication Date

19-Aug-2025

POSTMODERN ALCHEMY

Liquid metal tin is the key to sustainable desalination!

Researchers have developed a solar-powered method that uses liquid tin to purify water and recover valuable metals from seawater brine

Institute of Science Tokyo

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Researchers develop a solar energy-powered desalination system using liquid metal tin to recover valuable metallic elements from seawater

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Credit: Masatoshi Kondo from Institute of Science Tokyo, Japan

Water scarcity remains one of the most pressing global challenges, affecting over two billion people worldwide. With population growth and climate change further exacerbating this problem, scientists are turning to seawater desalination as a promising solution to satisfy the ever-increasing demand for freshwater.

However, current desalination plants discharge massive amounts of brine as waste— approximately 141.5 million cubic meters daily. This solution typically contains concentrated metallic elements. Additionally, existing methods for recovering metals from brine are quite energy-intensive and generate other types of hazardous waste.

In order to address these challenges, a research team led by Associate Professor Masatoshi Kondo from Institute of Science Tokyo (Science Tokyo), Japan, has developed an innovative approach using liquid metal tin to simultaneously purify water and recover valuable metals. Their paper was made available online on February 26, 2025, and was published in Volume 15, Issue 1 of the journal Water Reuse on March 01, 2025. The study demonstrates how this technology can transform desalination brine from an environmental liability into a valuable resource. This work was co-authored by doctoral student Toranosuke Horikawa, then-bachelor student Mahiro Masuda, and Assistant Professor Minho Oh, from Science Tokyo.

The proposed strategy is centered around spraying brine onto the surface of liquid tin heated to 300 °C. Upon contact, freshwater is instantly evaporated and thus distilled from the brine, while valuable elements such as sodium, magnesium, calcium, and potassium remain in the tin. “The main energy source for this type of seawater desalination can be concentrated solar power, since heat is the main energy source required for this desalination process. Unlike conventional methods, large consumption of electricity is not necessary, enabling the development of a sustainable process,” explains Dr. Kondo, highlighting the technology’s use of easily accessible and renewable energy.

After minerals are dissolved into the liquid tin, a slow cooling process allows different metal elements to precipitate at specific temperatures, enabling their separate recovery. Through laboratory experiments, the researchers found that potassium begins to precipitate first, followed by sodium, calcium, and finally magnesium, enabling targeted recovery of each resource.

Another important approach that sets it apart is its versatility and efficiency. “The proposed technology for the collection and recovery of metallic elements from seawater desalination brine can also be used to distill groundwater polluted with arsenic without consuming large amounts of energy or producing waste,” notes Dr. Kondo. Groundwater contamination with arsenic is a widespread problem affecting drinking water for millions of people in regions like South Asia, particularly affecting Bangladesh, India, Vietnam, and nearby countries.

Worth noting, this innovative technology aligns with multiple sustainable development goals, providing a pathway to secure both freshwater and metal resources without generating secondary waste or significant carbon emissions. Additionally, liquid metal tin, which has been considered as a challenge due to its reactivity in nuclear fusion reactors, has been utilized to efficiently recover valuable seawater-based resources. Overall, this liquid tin-based approach offers a promising solution that transforms environmental challenges into valuable opportunities, potentially revolutionizing water treatment and desalination practices worldwide.

 

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Reference

Authors: Toranosuke Horikawa1, Mahiro Masuda1, Minho Oh2, and Masatoshi Kondo3

Title: Liquid metal technology for collection of metal resources from seawater desalination brine and polluted groundwater

Journal: Water Reuse

DOI: 10.2166/wrd.2025.100

Affiliations:        

1School of Engineering, Department of Mechanical Engineering, Graduate Major in Nuclear Engineering, Institute of Science Tokyo, Japan

2Department of Materials Science and Engineering, Institute of Science Tokyo, Japan

3Institute of Integrated Research, Laboratory for Zero-Carbon Energy, Institute of Science Tokyo, Japan

 

About Institute of Science Tokyo (Science Tokyo)

Institute of Science Tokyo (Science Tokyo) was established on October 1, 2024, following the merger between Tokyo Medical and Dental University (TMDU) and Tokyo Institute of Technology (Tokyo Tech), with the mission of “Advancing science and human wellbeing to create value for and with society.”

About Associate Professor Masatoshi Kondo from Institute of Science Tokyo (Science Tokyo), Japan

Dr. Masatoshi Kondo is an Associate Professor at the Institute of Integrated Research at Science Tokyo, Japan. His research interests include liquid metals, nuclear fusion reactors, molten salts, and fast breeder reactors. He is affiliated with academic societies such as Japan Society of Plasma Science and Nuclear Fusion Research and Atomic Energy Society of Japan. He is also an honorable awardee of multiple commendations such as Marine Tech Grand Prix 2022, Asahi Yukuzai Award. He has published numerous articles with more than 2,000 citations.

Funding information

This paper is partially based on results obtained from a project, JPNP20004, subsidized by the New Energy and Industrial Technology Development Organization (NEDO). This work was supported by JST SPRING, Japan Grant Number JPMJSP2106 and JPMJSP2180.

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Journal

Water Reuse

DOI

10.2166/wrd.2025.100 

Method of Research

Experimental study

Subject of Research

Not applicable

Article Title

Liquid metal technology for collection of metal resources from seawater desalination brine and polluted groundwater

Article Publication Date

12-Mar-2025