arXiv subjects

Karol Kolataj

Publications and source records attributed to Karol Kolataj.

9 recordsLinked to original sources

arXiv2026

Sel-assembled Rhodium Nanoantennas for Single-Protein UV SERS

Surface-enhanced Raman scattering (SERS) provides critical insights into analyte structure, dynamic processes, and intermolecular interactions at the single-molecule level. By exploiting the hotspot formation in the vicinity of plasmonic structures, SERS constitutes an established tool for fundamental biological research, particularly for early-stage disease diagnostics. In this context, the DNA Origami technique, with its high addressability, enables both the assembly of plasmonic nanostructures with nanometric accuracy, and the deterministic placement of a single analyte molecule precisely at the generated hotspot within them. To date, most DNA Origami based nanoantennas rely on gold or silver nanoparticles (NPs), whose plasmonic resonances are confined to the visible spectrum, severely limiting their use in other spectral ranges. To extend the operating range, we have recently established a robust strategy for self-assembling programmable ultraviolet (UV)-plasmonic dimer antennas using rhodium nanocubes. Herein, we leverage this tailored architecture to systematically investigate its performance for single-molecule UV-SERS. We demonstrated how biofabricated Rh-dimers can be used to detect the characteristic SERS signal of a single streptavidin molecule linked at the dimer s gap. Our results are validated through polarization dependent measurements that yield the expected signal modulation depending on the the dimer orientation only for the DNA origami with a protein at the hotspot. This work establishes a highly sensitive and polarization-tunable UV-SERS platform, laying a solid foundation for label-free optical investigation and bio-spectroscopy of individual biomolecules in the UV spectral range.

physics.app-ph↗

arXiv2025

Color Routing and Beam Steering of Single-Molecule Emission with a Spherical Silicon Nanoantenna

Single-photon emitters radiate as electric dipoles, which limits light collection efficiency and complicates integration into flat photonic devices. Developing nanophotonic structures capable of directing photon emission with tunable angular distributions in the visible spectrum has been pursued for applications ranging from integrated optical systems to discrimination of molecular species. To date, such directional control has been achieved using components whose overall footprint is larger than the emission wavelength and often rely on lossy plasmonic components. Here, we employ the DNA origami technique for deterministic nanoscale assembly, positioning single fluorophores in nanometric proximity to a single silicon spherical nanoparticle and demonstrate unidirectional emission with forward-to-backward intensity ratios up to ~7 dB. Furthermore, we show that a single silicon nanosphere antenna can function as a color router or a beam steerer depending on its size, emitter spectral range and emitter-nanoparticle distance.

physics.optics↗

arXiv2025

Dynamics of DNA-Templated Ultrafine Silver Nanowires Formation

Recent research on silver nanowires prepared on DNA templates has focused on two fundamental applications: nano-scale circuits and sensors. Despite its broad potential, the formation kinetics of DNA-templated silver nanowires remains unclear. Here, we present an experimental demonstration of the formation of silver nanowires with a diameter of 2.2+0.4 nm at the single-molecule level through chemical reduction. We conducted equilibrium and perturbation kinetic experiments to measure force spectroscopy during the formation of Ag+ -DNA complexes and Ag-DNA complexes, using optical tweezers combined with microfluidics. The addition of AgNO3 resulted in an increase in force of 5.5-7.5 pN within 2 minutes, indicating that Ag+ compacts the DNA structure. In contrast, the addition of hydroquinone caused the force to decrease by 4-5 pN. Morphological characterization confirmed the presence of a dense structure formed by silver atoms bridging the DNA strands, and revealed conformational differences before and after metallization. We compare our experimental data with Brownian dynamics simulations using a coarse-grained double-stranded DNA (dsDNA) model that provides insights on the dependency of the force on the persistence length.

physics.app-ph↗

arXiv2024

Advances and Applications of Dynamic Surface-Enhanced Raman Spectroscopy (SERS) for Single Molecule Studies

Dynamic surface-enhanced Raman spectroscopy (SERS) is nowadays one of the most interesting applications of SERS, in particular for single molecule studies. In fact, it enables the study of real-time processes at the molecular level. This review summarizes the latest developments in dynamic SERS techniques and their applications, focusing on new instrumentation, data analysis methods, temporal resolution and sensitivity improvements, and novel substrates. We highlight the progress and applications of single-molecule dynamic SERS in monitoring chemical reactions, catalysis, biomolecular interactions, conformational dynamics, and real-time sensing and detection. We aim to provide a comprehensive review on its advancements, applications as well as its current challenges and development frontiers.

physics.app-ph↗

arXiv2024

Coupling single-molecules to DNA-based optical antennas with position and orientation control

Optical antennas have been extensively employed to manipulate the photophysical properties of single photon emitters. Coupling between an emitter and a given resonant mode of an optical antenna depends mainly on three parameters: spectral overlap, relative distance, and relative orientation between the emitter's transition dipole moment and the antenna. While the first two have been already extensively demonstrated, achieving full coupling control remains unexplored due to the challenges in manipulating at the same time both the position and orientation of single molecules. Here, we use the DNA origami technique to assemble a dimer optical antenna and position a single fluorescent molecule at the antenna gap with controlled orientation, predominately parallel or perpendicular to the antenna's main axis. We study the coupling for both conditions through fluorescence measurements correlated with scanning electron microscopy images, revealing a 5-fold higher average fluorescence intensity when the emitter is aligned with the antenna's main axis and a maximum fluorescence enhancement of ~ 1400-fold. A comparison to realistic numerical simulations suggests that the observed distribution of fluorescence enhancement arises from small variations in emitter orientation and gap size. This work establishes DNA origami as a versatile platform to fully control the coupling between emitters and optical antennas, trailblazing the way for self-assembled nanophotonic devices with optimized and more homogenous performance.

physics.optics↗

arXiv2024

Giant Purcell broadening and Lamb shift for DNA-assembled near-infrared quantum emitters

Controlling the light emitted by individual molecules is instrumental to a number of novel nanotechnologies ranging from super-resolution bio-imaging and molecular sensing to quantum nanophotonics. Molecular emission can be tailored by modifying the local photonic environment, for example by precisely placing a single molecule inside a plasmonic nanocavity with the help of DNA origami. Here, using this scalable approach, we show that commercial fluorophores experience giant Purcell factors and Lamb shifts, reaching values on par with those recently reported in scanning tip experiments. Engineering of plasmonic modes enables cavity-mediated fluorescence far detuned from the zero-phonon-line (ZPL) - at detunings that are up to two orders of magnitude larger than the fluorescence linewidth of the bare emitter and reach into the near-infrared. Our results evidence a regime where the emission linewidth is dominated by the excited state lifetime, as required for indistinguishable photon emission, baring relevance to the development of nanoscale, ultrafast quantum light sources and to the quest toward single-molecule cavity-QED. In the future, this approach may also allow to design efficient quantum emitters at infrared wavelengths, where standard organic sources have a reduced performance.

physics.optics↗

arXiv2024

Towards full control of molecular exciton energy transfer via FRET in DNA origami assemblies

Controlling the flow of excitons between organic molecules holds immense promise for various applications, including energy conversion, spectroscopy, photocatalysis, sensing, and microscopy. DNA nanotechnology has shown promise in achieving this control by using synthetic DNA as a platform for positioning and, very recently, for also orienting organic dyes. In this study, the orientation of doubly-linked dyes in DNA origami structures was manipulated to control energy transfer. By controlling independently the orientation of single donor and acceptor molecules, the average energy transfer efficiency was doubled. This work demonstrates the potential of DNA nanotechnology for precise control of the excitonic energy transfer with implications for artificial light-harvesting antennas.

cond-mat.soft↗

arXiv2023

Universal click-chemistry approach for the DNA functionalization of nanoparticles

Nanotechnology has revolutionized the fabrication of hybrid species with tailored functionalities. A milestone in this field is the DNA conjugation of nanoparticles, introduced almost 30 years ago, which typically exploits the affinity between thiol groups and metallic surfaces. Over the last decades, developments in colloidal research have enabled the synthesis of an assortment of non-metallic structures, such as high-index dielectric nanoparticles, with unique properties not previously accessible with traditional metallic nanoparticles. However, to stabilize, integrate and provide further functionality to non-metallic nanoparticles, reliable techniques for their functionalization with DNA will be crucial. Here, we combine well-established dibenzylcyclooctyne-azide click-chemistry with a simple freeze-thaw method to achieve the functionalization of silica and silicon nanoparticles, which form exceptionally stable colloids with a high DNA surface density of 0.2 molecules/nm2. Furthermore, we demonstrate that these functionalized colloids can be self-assembled into high-index dielectric optical antennas with a yield of up to 78% via the use of DNA origami. Finally, we extend this method to functionalize other important nanomaterials, including oxides, polymers, core-shell and metal nanostructures. Our results indicate that the method presented herein serves as a crucial complement to conventional thiol functionalization chemistry and thus greatly expands the toolbox of DNA-functionalized nanoparticles currently available.

physics.chem-ph↗

arXiv2023

DNA origami assembled nanoantennas for manipulating single-molecule spectral emission

Optical nanoantennas can affect the decay rates of nearby emitters by modifying the local density of photonic states around them. In the weak-coupling limit, and according to the Fermi's Golden Rule, the emission spectrum of a dye is given by the energy of all the possible radiative transitions weighted by the probability of each of them to occur. By engineering the resonance of a nanoantenna, one can selectively enhance specific vibronic transitions of a dye molecule, thus shaping its emission spectrum. Since interactions between emitters and nanoantennas are known to be position dependent, we make here use of DNA origami to precisely place an individual dye at different positions around a gold nanorod. We show how this relative position between the nanorod and the emitter affects the emission spectrum of the latter. In particular, we observe the appearance of a second fluorescence peak whose wavelength and intensity are correlated with the fundamental plasmonic resonance of the nanorod, which we extract from its photoluminescence spectrum. This second peak results from the selective enhancement of transitions to different vibrational levels of the excitonic ground state, whose energies are in resonance with the plasmonic one. Furthermore, we argue that the drastic alteration of the fluorescence spectrum in some of our samples cannot be accounted for with Kasha's rule, which indicates that radiative and vibrational relaxation dye lifetimes can become comparable through the coupling to the gold nanorods.

physics.optics↗