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*
2026-04-28- Satu Sutinen
2026-05-12- Charles Rambo
2026-05-12- Pratheek Malol
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
