Abstract:
2026-01-20- Heini Järvinen
In recent years, hierarchical nanostructures have found applications in fields like diagnostics, medicine, nano-optics, and nanoelectronics, especially in challenging applications like the creation of meta surfaces with unique optical properties. One of the promising materials to fabricate such nanostructures has been DNA due to its robust self-assembly properties and plethora of different functionalization schemes.Cross-shaped DNA origami can be used as building blocks, i.e., tiles to form fishnet-type lattices on a substrate. When combined with methods such as DNA assisted lithography (DALI) [1], one can obtain meta surfaces without the need for time-consuming patterning steps i.e., e-beam lithography. Our final goal is to fabricate a multilayered fishnet metamaterial surface with a negative refractive index to enable novel applications such as perfect lensing, optical filters and optical cloaking to name a few in a cost-effective manner. Earlier, we developed a large-scale fabrication methodology to produce a closely spaced two-dimensional fishnet-type lattices on a silicon substrate [2]. Recently, we grew the polycrystalline domain size toward a large single-crystalline lattice (average domain size of ~2 µm) [3] to further advance the optical response from the subsequent meta surface. In addition, we have grown a silicon dioxide mask (DALI step 5) for our fishnet lattice for the following etching step. We require a high precision etch process with high Si/SiO2 selectivity and anisotropic etch profile (no undercut) to avoid the collapse of the mask. Currently, we are optimizing an HBr etching process and finally, we will use the etched pattern as an evaporation mask for the metallic nanostructures.
[1] B. Shen, V. Linko, K. Tapio, et al. Sci. Adv. 4, eaap8978 (2018). [2] K. Tapio, C. Kielar, J.M. Parikka, et al., Chem. Mater. 35, 1961-1971 (2023).
[3] H. Järvinen, J.M. Parikka, R.P.T.N. Rajapaksha, A. Keller, and J.J. Toppari, ”Towards single-crystalline DNA origami lattices on silicon wafers for bottom-up nanofabrication” Submitted to Small Structures
2026-02-03- Gour Das*
The precise manipulation of 2D materials through near-field optical techniques has emerged as a focal point of interest due to its direct relevance in device engineering. Despite the inherent difficulty in fine-tuning properties at the atomic scale, we have recently developed a methodology for achieving super-resolution nanopatterning of 2D materials. This approach combines femtosecond laser pulses with scattering Scanning Near-field Optical Microscopy (SNOM). In this seminar, I will elucidate the recent experimental development, instrumental methodology, resultant findings, encountered challenges, and the prospective trajectory of this innovative technique.
2026-02-18- Santiago Agudelo Gomez
Strong light-matter coupling has emerged as a promising way to precisely control photochemical reactions. However, the main limitation of this application is the lack of a comprehensive understanding of excited states dynamics, which includes a large contribution from dark reservoir states. In recent years, experiments using laser pump-probe techniques in open nanocavities with BODIPY as the photoactive molecule have demonstrated their effectiveness in selectively populating polariton states while avoiding the dark reservoir states. A better understanding of this process requires computational simulations. Unfortunately, the lack of a force field that adequately represents the BODIPY molecule (and especially the lack of bonding parameters involving the boron atom) prevents the experiment from being replicated. For this reason, and because this molecule is widely used in biochemical research, this work aims to parameterise and validate an adequate force field for the BODIPY molecule that will be used in future studies.
2026-03-03- Maryam Naderpour
The fabrication of uniform, ultrathin insulating layers on graphene is crucial for graphene field-effect transistors (GFETs), particularly in sensing applications where high sensitivity, low leakage currents, and reliable operation are required. However, the chemically inert surface of graphene inhibits nucleation during atomic layer deposition (ALD), limiting direct dielectric integration.
To address this challenge, femtosecond laser two-photon oxidation is employed to locally functionalize graphene through direct-write optical patterning. This maskless method introduces oxygen-containing groups in predefined regions, creating reactive sites that enable low-temperature (<250 °C) ALD of ultrathin ZnO dielectric layers, while pristine graphene largely remains uncoated [1]. The resulting films are conformal, electrically insulating, and chemically stable, making them suitable for device and biosensing environments. Post-deposition thermal annealing reduces defect density in graphene, restoring its electronic properties without altering the ZnO layer [2].
This approach provides a framework for integrating spatially patterned gate dielectrics in GFETs, aimed at advancing device functionality and operational stability.
References: [1] J. Aumanen, A. Johansson, J. Koivistoinen, P. Myllyperkiö, M. Pettersson, Nanoscale, 7, 2851–2855 (2015).[2] K. K. Mentel, A. V. Emelianov, A. Philip, A. Johansson, M. Karppinen, M. Pettersson, Adv. Mater. Interfaces, 9, 2201110 (2022).
2026-03-17- Roosa Vanhatalo
Finding a maximum photoisomerization yield of phytochrome constructs
Phytochromes are photoreceptor proteins that are familiar, for example from how plants avoid shade and thus grow in the direction of light, or from seed germination and flowering at right times of the year and day. Phytochromes have been the interest of research due to their red-light absorbing nature and understanding the phytochrome functionality is important for developing applications where induction of different cellular events can be controlled with light.
Photoactivation of phytochromes begins with an absorption of a photon by the biliverdin IXα molecule, which is covalently bound to the protein. This absorption triggers an isomerization of the chromophore, leading to protein scaffold changes and conversion between red light-absorbing and far-red light-absorbing states. These changes then eventually affect the activity of the phytochromes, which makes it possible for cells to respond to light stimuli. The photocycle of phytochromes, and the intermediates of it, can be studied, for example with time-resolved UV-Vis spectroscopy, better known as pump-probe spectroscopy, tr-IR spectroscopy [1], or serial femtosecond crystallography (SFX) [2,3]. However, these ultrafast methods come with the risk of using too high excitation powers, which in turn lead to photophysics deviating from single excited state dynamics. This has been of concern, especially in SFX, in which laser-induced structural movements of protein crystals can be followed.
We applied pump-probe spectroscopy to follow the ultrafast photoisomerization reaction. Here, we present how changing the excitation wavelength and increasing the excitation power may affect the kinetics of the photoreaction. We observed that the full-length phytochrome withstands higher power and provides a higher photoreaction yield compared to the truncated constructs typically studied in these SFX studies. This observation could be used in studying phytochromes in further detail and help with improving the signal to noise ratio, facilitating the spectral features of the photoisomerized state. This work brings us closer to our goal to rigorously visualize the photoisomerization reaction of phytochrome proteins either by applying femtosecond circular dichroism spectroscopy or SFX techniques.
References: [1] Ihalainen, J. A. et al, “Chromophore–Protein Interplay during the Phytochrome Photocycle Revealed by Step-Scan FTIR Spectroscopy,” J. Am. Chem. Soc. 140 12396–12404, 2018 [2] Claesson, E. et al, “The primary structural photoresponse of phytochrome proteins captured by a femtosecond X-ray laser,” eLife 9, e53514, 2020 [3] Shankar, M. K. et al, “Ultrafast, remote-controlled protonation reaction enables structural changes in a phytochrome,” Science Advances 11, eady0499, 2025
2026-03-31- Shivani Verma
Introducing vibrational quantization in classical molecular dynamics under strong light-matter coupling
Recent experiments have shown that vibrational strong coupling (VSC), a cavity quantum electrodynamics phenomenon, can alter chemical reactivity by changing kinetics, mechanisms, and product distributions.[1-4] VSC arises from the formation of hybrid light–matter states when molecular vibrations couple to photonic cavity modes, enabling modification of molecular wavefunctions without external illumination. While this possibility of controlling reactivity has generated major excitement, no predictive theoretical framework exists. Despite growing experimental evidence, it remains unclear when and how VSC affects reactions, posing a key fundamental challenge and limiting potential applications.
Our work aims to model VSC with atomistic details using a classical molecular dynamics (MD) approach. Since vibrational degrees of freedom are not quantized in classical mechanics, we propose to overcome that limitation by combining classical molecular mechanics (MM) or semi-classical quantum mechanics/molecular mechanics (QM/MM) potentials with a biasing potential, effectively imposing quantization on the relevant vibrational transitions in MD simulations. In my talk, I will present benchmark results demonstrating the introduction of vibrational quantization in classical MD simulations in the absence of a cavity. These results show that the biasing potential can successfully reproduce quantized vibrational behavior within a classical framework. This methodology provides a foundation for extending the approach to systems inside optical cavities, enabling the study of chemical reactivity under VSC conditions.
1. Garcia-Vidal, F. J., Ciuti, C. & Ebbesen, T. W. Science 373, eabd0336 (2021). 2. Thomas, A. et al. Science 363, 615–619 (2019). 3. Xiang, B. et al. Science 368, 665–667 (2020). 4. Pang, Y. et al. Angew. Chem. Int. Ed. 59, 10436–10440 (2020).
2026-04-14- Arpan Dutta*
Title: Optical constants of materials and their physical meanings
Abstract: Optical constants of a material play key role in light-matter interaction. In nanostructures and artificial materials, i.e., so-called 'metamaterials', novel photonic effects are achieved by modifying the effective optical constants of the nanophotonic systems. In addition, materials (natural to artificial ) are categorized based on the magnitude and sign of their optical constants. Therefore, a basic understanding on the physical meaning of optical constants of materials is important in multidisciplinary research.
In this context, the seminar will first discuss the 'basics' of optical constants, especially which are relevant for the research in Molecular Electronics and Plasmonics (MEP) group, the classification of materials based on optical constants, and their physical meanings. After that, the seminar will briefly showcase the research in MEP involving metamaterials and modification of optical constants.
2026-04-28- Satu Sutinen
Graphene is a single‑atom‑thick, flexible, and biocompatible form of pure carbon with excellent electrical properties, making it an intriguing material for biosensing applications. However, functionalization of graphene is required for selective sensing and for enabling strong and specific biological coupling. Two‑photon oxidation is a direct laser‑writing method that introduces oxygen‑rich functional groups onto graphene with micrometer precision using femtosecond pulses [1]. The degree of oxidation and the resulting chemical composition can be controlled by tuning the laser parameters [2]. These oxidized regions provide chemically active surface sites that can be further functionalized, for example with molecules acting as selective sensing elements in graphene‑based biosensors or as biochemical cues for investigating cellular coupling [3,4].
Here, we compare oxidized and pristine graphene areas using both non‑covalent and covalent protein functionalization strategies, focusing on applications in neurochemical detection and neuronal guidance. Our goal is to develop a highly selective and sensitive graphene field‑effect transistor sensor for detecting neurotransmitters such as acetylcholine. Ongoing work investigates how laser‑induced oxidation influences protein deposition under both functionalization strategies.
We employ nanodisc‑embedded receptor proteins as sensing elements and have successfully deposited them non‑covalently on the graphene surface. In parallel, we examine how oxidation parameters and subsequent functionalization conditions affect the covalent deposition of proteins on oxidized graphene regions using a Mitsunobu reaction, with particular emphasis on proteins relevant for guiding axonal growth. References 1. J. Aumanen, A. Johansson, J. Koivistoinen, P. Myllyperkiö and M. Pettersson “Patterning and tuning of electrical and optical properties of graphene by laser induced two-photon oxidation” Nanoscale 7, 2015 2. A. Johansson, H-C. Tsai, J. Aumanen, J. Koivistoinen, P. Myllyperkiö, Y-Z. Hung, M-C. Chuang, C-H. Chen, W-Y. Woon and M. Pettersson “Chemical composition of two-photon oxidized graphene” Carbon 115, 2015 3. A. Lampinen, A. Emelianov, E. See, A. Johansson and M. Pettersson “Effect of two-photon oxidation and calmodulin functionalization on the performance of graphene field-effect transistor biosensors” RSC Applied Interfaces 2, 2025 4. M. Wolf, W. Vickery, W. Swift-Ramirez, A. Arnold, J. Orlando, S. Schmidt, Y. Liu, J. Er, R. Schusterbauer, R. Ahmed, P. Nickl, J. Radnik, I. Donskyi, S. Sydlik “The Mitsunobu reaction for the gentle covalent attachment of biomolecules to graphene oxide” Carbon 238, 2025
2026-05-12- Pratheek Malol
Quantum dots as charge sensors for donor spin readout
Silicon is a promising platform for scalable quantum technologies due to its compatibility with existing semiconductor fabrication and its potential for integrating qubits, control electronics, and photonic components on a single chip. Among the various silicon-based qubit implementations, donor spins in silicon offer long coherence times and high control fidelities [1]. However, donor spin readout remains challenging with existing techniques.
In this work, we explore the use of silicon quantum dots as charge sensors for donor spin readout. The proposed readout scheme is based on a spin-selective donor-bound exciton transition under an applied magnetic field [2]. The exciton state relaxes via Auger recombination, leading to the ionization of the donor. This ionization can then be detected electrically using nearby quantum dots as charge sensors, enabling donor spin readout.
To ensure scalability of the proposed readout approach, we use gate defined silicon quantum dot devices developed by Semiqon. These devices are fabricated on silicon-on-insulator platforms and incorporate on-chip multiplexing architectures, enabling the operation and characterization of multiple quantum dot structures on a single chip [3]. In this presentation, we will discuss the electrical characterization of these devices and evaluate their suitability as charge sensors for donor-based quantum systems.
Muhonen, J. et al. Storing quantum information for 30 seconds in a nanoelectronic device. Nature Nanotech 9, 986–991 (2014).
Loippo, T et al. Strain effects in phosphorus bound exciton transitions in silicon, Phys. Rev. Materials 7, 016202 (2023).
Bohuslavskyi, H. et al. Scalable on-chip multiplexing of silicon single and double quantum dots. Commun Phys 7, 323 (2024).
2026-05-26- Daniel Rodriguez
2026-06-02- Louise Miton/ Prachi Verma
2026-09-08- Aleix Gomez
2026-09-29- Harsh Kashyap
2026-10-13- Amar Raj*
2026-10-27- Thiwangi Rajapaksha
2026-11-10- Priyam De*
2026-11-24- Nima Nematimansur
2026-12-08-Udit Paramanik
