High level research at the nanoscale

Researchers from the Nanoscience Center, have developed a pioneering machine-learning model capable of predicting how proteins interact with ligand-stabilised gold nanoclusters, materials that are widely used in bioimaging, biosensing, and targeted drug delivery. By combining advanced clustering analysis with atomistic simulations, the model not only identifies which amino acids are most likely or unlikely to bind to the gold nanocluster surface but also reveals the specific chemical groups responsible for these interactions.

Designed to be general and scalable, the framework can be applied beyond peptides, offering broad insights into protein–nanocluster interactions. This capability could accelerate the screening of large numbers of proteins and guide the rational design of more effective and reliable nanomaterials for biomedical applications.

The full study is published in the Aggregate journal.

Article information:

B. Ferrari, Z. Fallah, M. Khatun, and H. Häkkinen, “Development of an Interaction Model of the Protein–Nanocluster Interface by Machine Learning–Assisted Clustering of Amino Acids.” Aggregate (2025): e70213. 

https://doi.org/10.1002/agt2.70213

New metal-organic framework (MOF) materials based on gold nanoclusters have the potential to transform nanoelectronics. Four innovative materials with electrical conductivity and semiconductor-like behaviour were developed through international research cooperation, opening new possibilities for precise control of electronic properties.

Kim, S., Jääskö, H., Park, K. C., Malola, S., Häkkinen, H., & Park, S. S. Tuning the Electrical Properties through Metal-Ion-Mediated Assembly in Au25 Nanocluster- Based Frameworks. Journal of the American Chemical Society Vol. 147, p. 30803 (2025).

https://doi.org/10.1021/jacs.5c06695

Researchers at the Nanoscience Center used machine-learning combined with density-functional theory (DFT) to demonstrate that geometrical smoothness is the key factor governing the energetic and mechanical stability of lateral graphene–metallene interfaces. They demonstrated universal machine-learning capabilities to reproduce DFT-predicted stabilities accurately, enabling faster, more efficient design of metallene interfaces.

They demonstrated universal machine-learning capabilities to accurately reproduce DFT-predicted stabilities accurately, enabling faster, more efficient design of metallene interfaces.

Reference and link to the published article:

M. Bagheri and P. Koskinen, Lateral Graphene-Metallene Interfaces at the Nanoscale, Nanoscale 17, (2025)

https://doi.org/10.1039/D5NR02770E

A new quantum transport theory reveals how femtosecond time scale
thermoelectric fluctuations influence energy control at the nanoscale.

We contributed to the development of a theoretical approach that enables
accurate simulations of temperature differences and electric currents in
nanoscale junctions formed by single molecules. The research opens new
possibilities for designing components used in quantum technologies.

R. Tuovinen and Y. Pavlyukh, Thermoelectric Energy Conversion in
Molecular Junctions Out of Equilibrium, PRX Energy 4, 043003 (2025)

https://doi.org/10.1103/rj3h-8z3g

Image. A computational framework based on non-equilibrium Green's functions enables accurate and efficient predictions for nanoscale thermoelectric optimization.

A new study published in the International Journal of Biological Macromolecules uncovers how the EspF protein from enteropathogenic E. coli (EPEC) manipulates human cells to promote infection. EspF is an intrinsically disordered protein that uses motif mimicry to bind tightly to two human proteins—SNX9 and N-WASP—disrupting normal cell signaling and aiding bacterial attachment.

Key findings:

• EspF contains pre-formed helical motifs that mimic host structures and activate actin polymerization, helping EPEC adhere to intestinal cells.
• Its C-terminal interactions compensate for structural differences compared to EspFU (from EHEC), ensuring strong binding despite lacking an extended domain.
• Researchers identified an extended SH3-binding motif (ϕxPxRxAPxxP) critical for EspF’s interaction with SNX9.
• Unlike EspFU, EspF’s helical structure does not determine binding order or strength, showing EPEC’s unique adaptation strategy.

Using NMR spectroscopy, the research team mapped EspF’s structure and binding dynamics, offering insights that could lead to new treatments targeting these interactions.

This research comes amid a surge in E. coli outbreaks across Europe and the US in 2025, emphasizing the urgent need for molecular-level understanding of bacterial virulence.

Figure. (Top) Schematic presentation of EspFU and EspF mediated rewiring of actin polymerization machinery. (Bottom) Solution NMR structures of EspFU R5 and EspF R2’ in complex with N-WASP GBD. Created in BioRender. (2025) https://BioRender.com/1ufv9fi

H. Tossavainen, M. Karjalainen, L. Antenucci, M. Hellman & P. Permi. Intrinsically disordered enteropathogenic E. coli EspF exploits motif mimicry in high-affinity binding to neural Wiskott-Aldrich syndrome protein and sorting nexin 9. International Journal of Biological Macromolecules. Volume 330, Part 3, 2025.

• Link: https://doi.org/10.1016/j.ijbiomac.2025.148227

Researchers recently realised the first de Gennes’ absolute superconducting switch in a EuS/Au/Nb/EuS structure. The key element of the switch is the gold layer between the EuS and Nd, which boosts the large proximity exchange field induced in the sample. This enables absolute on/off switching of superconductivity. This achievement could pave the way for the development of non-volatile superconducting random access memory devices.

The work is a collaboration between the University of Cambridge, the University of the Basque Country and the University of Jyväskylä. The study was published in the prestigious Nature Communications series.

• Realisation of de Gennes’ absolute superconducting switch with a heavy metal interface, Nature Communications 16, 5674 (2025).
• DOI: 10.1038/s41467-025-61267-2

• Link: https://www.nature.com/articles/s41467-025-61267-2

  

Research from the University of Jyväskylä has revealed that lignin, a polyphenol, important for plant structure, has antimicrobial activity against viruses and bacteria. Aqueous-based lignin from birch, wheat, and oat possess broad-spectrum antimicrobial activities against enveloped coronaviruses, non-enveloped enteroviruses, as well as Gram-positive and Gram-negative bacterial strains.

Aqueous-based lignins inactivate microbes by different mechanisms: lignins break the structure of the enveloped coronaviruses, stabilize and prevent genome release of the non-enveloped enteroviruses and directly interact with the internal cellular material of bacteria. The results highlight that lignin, which is also an important by-product from wood industry, has potential as promising green alternative to synthetic antimicrobial agents for coating agents, packaging material, or surface disinfectants.

Liu, J., Haapakoski, M., Sundberg, L.-R., Vähäsalo, L., Vento, P., Pöysti, M., & Marjomäki, V. (2025). Aqueous-based lignin extractions from birch, wheat, and oat exhibit broad antimicrobial activities. International Journal of Biological Macromolecules, 319, 145736. https://doi.org/10.1016/j.ijbiomac.2025.145736

Images of Jyvaskylavirus. The virus particle is about twice the size of influenza or coronavirus.

Viruses are everywhere. Most naturally occurring viruses are harmless to humans and can play an important role in the functioning of ecosystems. In recent years, giant viruses have been discovered that can be as large as bacteria. These viruses infect amoebas and other microscopic organisms. Most of the giant viruses identified so far have been found in Europe and South America, and their life cycles and distribution are poorly understood.

The Finnish giant virus has French relatives

The study, initiated at the University of Jyväskylä, is the first to isolate giant viruses from Finland. The giant virus, named Jyvaskylavirus, was discovered when environmental samples were mixed with a culture of amoeba Acanthamoeba castellanii. The virus particle is 200 nanometres in diameter, about twice the size of influenza or coronavirus.

- Through an international collaboration, we elucidated the genome and structure of the Jyvaskylavirus, which was found to be related to Marseilleviruses previously isolated from France. Other new giant viruses were also detected in environmental samples, rejoices professor Lotta-Riina Sundberg from the University of Jyväskylä.

New giant virus regulates microbial populations in soil

The finding indicates that giant viruses are more prevalent than thought in soil and water, even in northern environments.

- The discovery will help to understand the interactions between microbes and the role of viruses in regulating populations of all living organisms, as well as providing new insights into the structure of giant viruses, says Sundberg.

The study is published in the eLife series.

Article information:

G. M. D. F.  Almeida, I. Arriaga, B. L. de Azevedo, M. Leppänen, J. S.Abrahao, J.Andreani, Davide Zabeo, J. Ravantti, N. G. A. Abrescia, L.-R. Sundberg: Genomic and structural insights into Jyvaskylavirus, the first giant virus isolated from Finland. eLife13:RP103492

Doi number: https://doi.org/10.7554/eLife.103492.3

Researchers from the Nanoscience Center (NSC), have developed an innovative, label-free ratiometric fluorosensor for the selective and sensitive detection of enteroviral RNA. This cutting-edge sensor leverages the unique properties of carbon dots (CDs) functionalized with a probe (single stranded complementary oligonucleotide fragment) and ethidium bromide (EB) to achieve high sensitivity and selectivity, allowing for real-time detection of viral RNA and providing crucial spatiotemporal information about virus genome release during infection. The sensor significantly outperforms traditional methods by covalently bonding CDs with a probe, enhancing charge transfer and fluorescence changes upon hybridization with target DNA or RNA, resulting in ultrasensitive detection capabilities. This breakthrough offers a powerful tool for early detection and identification of viral infections, which is essential for preventing outbreaks and improving global health responses.

A. Pathak, A. Raj, S. Larsson, A. B. Patil, A. K. Singh, Mira Laajala, T. Kumpulainen, V. S. Marjomäki, and J. J. Toppari. "Ultrasensitive ratiometric fluorosensor for enteroviral RNA detection based on improved electron transfer between carbon dots and ethidium bromide." Carbon 2025, 238, 120222.

Figure: Pictorial representation of the working principle of a functionalized Carbon Dots (CDs) and Ethidium Bromide (EB) based ratiometric fluorosensor (Func sensor). (Figure drawn by Toppari)

University of Jyväskylä researchers achieve direct-write nanoscale modification of graphene with ~10 nm precision using ultrafast laser pulses under ambient conditions, unlocking new opportunities for quantum devices, optoelectronics, and sensing technologies.

The key innovation lies in using a sharp metallic s-SNOM tip to concentrate ultrafast laser pulses into a nanoscale volume, initiating controlled oxidation reactions in targeted regions and nanohole formation at higher exposures. Importantly, the team employed nanoscale infrared spectroscopy (nano-FTIR) to verify the chemical changes at the pattern sites. These measurements confirmed that the laser exposure selectively converts graphene into graphene oxide, validating the chemical precision of the nanopatterning process.

The study was published in Small Science on 30 June 2025 and was selected for the back cover of the journal.

Publication: Near-Field Optical Nanopatterning of Graphene, Gour Mohan Das, Eero Hulkko, Pasi Myllyperkiö, Andreas Johansson, Mika Pettersson, Small Science, 2025 https://doi.org/10.1002/smsc.202500184

Contact for more information: Prof. Mika Pettersson (mika.j.pettersson@jyu.fi)

Organic photovoltaics are a promising alternative to conventional silicon-based solar cells. However, it’s development is severely hampered due to short distances over which charge carriers can propagate. Placing organic molecules between the mirrors of an optical cavity can boost these distances due to hybrydization of the charge carriers with light confined by the mirrors into fast moving polaritons. To understand the reason for such enhancement, the researchers performed atomistic molecular dynamics simulations on the high performance computing facilities of CSC-IT of over a thousand organic molecules in a cavity. The results of the simulations not only confirm recent experimental observations, but also provide a detailed explanation for the molecular mechanism of the polaritonic transport process in terms of extremely high velocities of polaritons and large densities of molecules in a cavity. These insights can pave the way towards rational design of a new class of organic solar cells based on strong light-matter coupling.

I. Sokolovskii, R.H. Tichauer, D. Morozov, J. Feist, G. Groenhof. "Multi-scale molecular dynamics simulations of enhanced energy transfer in organic molecules under strong coupling". Nat. Commun, 2023, 14, 6613

The properties of a crystal are, at its most fundamental level, described by the many-particle Schrödinger equation in which the electrons and atomic nuclei interact via Coulombic interactions. It has been a long- standing open problem how to extract from this fundamental equation a physical description of the system in terms of electrons and phonons, in which the latter are collective vibrations of the nuclear subsystem. A collaboration of researchers from the University of Rome “Tor Vergata” and the University of Jyväskylä has now provided a precise derivation of a new set of equations that achieves this goal, whereby the concept of phonons is shown to appear as a sound concept only in infinite order in perturbation theory. The resulting new equations for the interactions between the electrons and phonons also lead to a first principles way to calculate electron-phonon couplings which are relevant for many physical phenomena such as phonon decay and superconductivity. The theory incorporates a full non-equilibrium description which is particularly relevant for strong field time-resolved laser techniques to study dynamical phenomena in crystals.

G. Stefanucci, R. van Leeuwen and E. Perfetto. "In and Out-of-Equilibrium Ab Initio Theory of Electrons and Phonons." Phys. Rev. X 2023, 13, 031026. Viewpoint on Physics

In a recent publication they show that in some cases a sound wave can jump or “tunnel” fully across a vacuum gap between two solids if the materials in question are piezoelectric. In such materials, vibrations (sound waves) produce an electrical response, as well, and since an electric field can exist in vacuum, it can transmit the sound waves across. The requirement is that the size of the gap is smaller than the wavelength of the sound wave. This effect works not only in audio range of frequencies (Hz-kHz), but also in ultrasound (MHz) and hypersound (GHz) frequencies, as long as the vacuum gap is made smaller as the frequencies increase. In most cases the effect is small but situations, where the full energy of the wave jumps across the vacuum with 100 % efficiency, without any reflections, were also found. As such, the phenomenon could find applications in microelectromechanical components (MEMS, smartphone technology) and in the control of heat.

Z. Geng and I. Maasilta. "Complete tunneling of acoustic waves between piezoelectric crystals." Commun Phys 2023, 6, 178. JYU Press Release.

Marjomäki group in NSC has just published a study that explains the mechanism of an antiviral molecule, vemurafenib. This kinase inhibitor is an FDA approved drug that has been used to treat melanoma which carries a specific mutation V600E in BRAF kinase. Such a mutation is present in 60% of melanoma cases. Unexpectedly, we found this drug to be an efficient antiviral against enteroviruses in a drug screen of about 450 kinase inhibitors and metabolic modifiers. This screen was performed in FIMM, Helsinki. After realizing that this drug very effectively reduced the infection of various enteroviruses (poliovirus, rhinovirus, coxsackieviruses, etc.), we and University of Jyväskylä patented this drug as a repurposed drug against enteroviruses (WO2020070390A1). However, for some time, the mechanism of action was a mystery. Namely, the infection was not prevented by blocking that mutated BRAF kinase. In contrast, we realized that the target had to be a completely different. This prompted us to study several cellular as well as viral targets. After long list of experiments, we finally found the right mechanism: vemurafenib inhibits another kinase, phosphatidyl kinase type 4B, which acts in a completely different signaling cascade on cells. We found out that, during infection, PI4KB affects the accumulation of phosphatidyl lipids in the replication structures that are crucial for virus production inside the cell. Vemurafenib blocks the synthesis of a lipid important for virus replication. This action is also linked to the function of the virus's own protein 3A, which attracts that kinase to the sites of viral replication. In our experiments, we demonstrated that vemurafenib totally blocks enterovirus infection, also in vivo, in mouse tissues. Importantly, vemurafenib can also completely eradicate the so-called silent (persistent) infection of cells. This gives hope that both difficult acute infections but also the so-called chronic infections could be tamed in the future. The drug has been approved for limited use, i.e. for the treatment of certain melanoma, and, before use for enteroviruses, detailed studies should therefore been carried out on the harmfulness of the drug. Hopefully vemurafenib could help patients against difficult infections that presently do not have any approved drug to fight against.

M. Laajala, M. Zwaagstra, M. Martikainen, M. P. Nekoua, M. Benkahla, F. Sane, E. Gervais, G. Campagnola, A. Honkimaa, A.-B. Sioofy-Khojine, H. Hyöty, R. Ojha, M. Bailliot, G. Balistreri, O. Peersen, D. Hober, F. Van Kuppeveld, and V. Marjomäki. "Vemurafenib Inhibits Acute and Chronic Enterovirus Infection by Affecting Cellular Kinase Phosphatidylinositol 4-Kinase Type IIIβ". Microbiology Spectrum, 2023, 11, e00552-23

In a groundbreaking study, researchers from Nanoscience Center at the University of Jyväskylä, Finland, have uncovered detailed dynamics of Förster Resonance Energy Transfer (FRET) in fluorophore-functionalized nanomaterials. The research focuses on the interaction between azadioxotriangulenium dye (KU) and a specific gold nanocluster (Au25(p-MBA)18). Advanced experimental and computational methods were utilized to elucidate the energy transfer mechanism. Time-resolved fluorescence experiments revealed the true energy-transfer-limited lifetime of the dye and identified two distinct subpopulations involved in the process. Further, molecular dynamics simulations showed that KU is bound to the nanocluster's surface by interacting with its ligands both as a monomer and as a π-π stacked dimer. In the dimer, one of the KU dyes was ~0.2 nm closer to the gold cluster than the other KU. This discovery explained the experimental observations of the two subpopulations. For last, the observed energy transfer rates agreed with the established 1/R6 distance dependence for FRET. These findings provide new insights into the energy transfer mechanisms of fluorophore-functionalized nanomaterials. This could enhance their applications in biomedical imaging and optical sensing. 

K. Pyo, M.F. Matus, E. Hulkko, P. Myllyperkiö, S. Malola, T. Kumpulainen, H. Häkkinen, M. Pettersson. "Atomistic View of the Energy Transfer in a Fluorophore-Functionalized Gold Nanocluster" J. Am. Chem. Soc. 2023, 145 (27), 14697–14704

We demonstrate a methodology to obtain well-ordered DNA origami lattices on a silicon substrate, which allows further nanofabrication process steps, such as metallization by DNA-assisted lithography (DALI). The obtained surface coverage is very high over large areas and extendable even up to the wafer scale. This concept could be further used to fabricate metasurfaces.

K. Tapio, C. Kielar, J. M. Parikka, A. Keller, H. Järvinen, K. Fahmy, and J. J. Toppari. "Large-Scale Formation of DNA Origami Lattices on Silicon". Chem. Mater. 2023, 35, 1961

In a recent comprehensive review article, researchers from the Nanoscience Center at the University of Jyväskylä, Finland, discuss the unique properties of nanometer-size metal clusters that make them suitable for various applications in catalysis, bioimaging, sensing and targeted drug delivery. This wide variety of applications is made possible by the tunable, atomically precise structure of the nanoclusters which allows for modifications of their physical and chemical properties via tight connection between computational modeling and experimental characterization. The review article was selected as the cover article in June 2023 issue of Nature Reviews Materials.

M. F. Matus and H. Häkkinen. "Understanding ligand-protected noble metal nanoclusters at work." Nat Rev Mater 2023, 8, 372–389. JYU Press release.

Recent decade has seen a lot of research in metamaterials - nanostructured materials with properties not found in Nature. Metamaterials have been used most often in the control of electromagnetic radiation (light) and acoustic waves. In a recent publication, Tuomas Puurtinen and Ilari Maasilta from the Nanoscience Center and Department of Physics have developed a theory for a thermal metamaterial, which can be used to strongly modify the heat capacity, the capacity to store heat.

The derived analytic theory describes a nanoscale periodic holey plate with the help of effective elastic parameters. It describes the thermal response in the temperature range where the holey material looks continuous, but with modified elastic properties and density because of the structuring. The modified elastic properties in turn change the vibrational spectrum of the material (phonon energies), which directly affects the capacity to store heat. The study was funded by the Academy of Finland and was published in the widely known journal of materials science, Communications Materials, on 5th Jan 2023.

T. A. Puurtinen and I. J. Maasilta. "Effective medium theory for the low-temperature heat capacity of a metasolid plate." Commun. Mater. 2023, 4, 1. UNO Internal bulletin.