Challenges
Datasets
Workspaces
Papers
Discussions
Leaderboard
Log inSign up
Challenges
Datasets
Workspaces
Papers
Discussions
Leaderboard
Blog
Job Board
Q3AS

© 2026 Aqora Quantum S.A.S.

TermsPrivacyLegal Notice

arXiv:1502.07568 · EPJ Quantum Technology

Single molecule DNA detection with an atomic vapor notch filter

Denis Uhland, Torsten Rendler, Matthias Widmann, Sang-Yun Lee, Jörg Wrachtrup, Ilja Gerhardt

Published Aug 25, 2015• 8 citations
arXivHTMLPDF

Abstract

The detection of single molecules has facilitated many advances in life- and material-science. Commonly the fluorescence of dye molecules is detected, which are attached to a non-fluorescent structure under study. For fluorescence microscopy one desires to maximize the detection efficiency together with an efficient suppression of undesired laser leakage. Here we present the use of the narrow-band filtering properties of hot atomic sodium vapor to selectively filter the excitation light from the red-shifted fluorescence of dye labeled single-stranded DNA molecules. A statistical analysis proves an enhancement in detection efficiency of more than 15% in a confocal and in a wide-field configuration.

DOI
10.1140/epjqt/s40507-015-0033-1

Related papers

An atomic spectrum recorded with a single-molecule light source

Wilhelm Kiefer, Mohammad Rezai, Jörg Wrachtrup +1 more

A single molecule under cryogenic conditions allows one to realize an extremely bright and simultaneously narrow-band single-photon source. We present a review on the different excitation schemes of a single molecule and present the corresponding single-photon nature of the emitted light. Single-molecule spectroscopy has been recently interlinked with atomic spectroscopy. This optical interconnect among the different quantum systems might be enhanced by a so-called Faraday anomalous dispersion optical filter—an ideal tool for many experiments in quantum optics. We introduce our theoretical and experimental approach on these filters which are based on hot atomic sodium vapor. The electrical tunability together with the brightness of a single molecule allows us to record a full atomic spectrum of this filter with the single photons originating from a single-molecular emitter.

Applied Physics B•Feb 1, 2016•22 citations

Single Photons from Single Molecules: Hong-Ou-Mandel Experiments and Beyond

Mohammad Rezai, Jörg Wrachtrup, Ilja Gerhardt

The generation of non-classical light, especially of single photon states, is mostly limited to non-linear optics in crystals and single emitters. Here we perform research on single organic dye molecules under cryogenic conditions. The molecules are well-behaved and do not blink or bleach. Also they exhibit an enormous brightness (>106 detected counts per second) and have narrow-band emission (<15-20MHz). By atomic sodium vapor we are able to suppress unwanted background emission from residual impurities in the sample. This light is now analyzed for the use in all-optical gates and further quantum optical schemes. A first step is the characterization in a Hong-Ou-Mandel type experiment. Different variations of this are possible – reaching from indistinguishable to distinguishable photons impinging on a beam-splitter.

Conference on Lasers and Electro-Optics•Jan 1, 2017•0 citations

How to Build an Optical Filter with an Atomic Vapor Cell

Denis Uhland, Dillmann, Helena, Yijun Wang +1 more

The nature of atomic vapors, their natural alignment with interatomic transitions, and their ease of use make them highly suited for spectrally narrow-banded optical filters. Atomic filters come in two flavors: a filter based on the absorption of light by the Doppler broadened atomic vapor, i.e. a notch filter, and a bandpass filter based on the transmission of resonant light caused by the Faraday effect. The notch filter uses the absorption of resonant photons to filter out a small spectral band around the atomic transition. The off-resonant part of the spectrum is fully transmitted. Atomic vapors based on the Faraday effect allow for suppression of the detuned spectral fraction. Transmission of light originates from the magnetically induced rotation of linear polarized light close to an atomic resonance. This filter constellation allows selective acceptance of specific light frequencies. In this manuscript, we discuss these two types of filters and elucidate the specialties of atomic line filters. We also present a practical guide on building such filter setups from scratch and discuss an approach to achieve an almost perfect atomic spectrum backed by theoretical calculations.

arXiv:2305.00570•Jan 1, 2023•0 citations

Direct detection of single molecules by optical absorption

Michele Celebrano, Philipp Kukura, Alois Renn +1 more

The advent of single molecule optics has had a profound impact in fields ranging from biophysics to material science, photophysics, and quantum optics. However, all existing room-temperature single molecule methods have been based on fluorescence detection of highly efficient emitters. Here we demonstrate that standard, modulation-free measurements known from conventional absorption spectrometers can indeed detect single molecules. We report on quantitative measurements of the absorption cross section of single molecules under ambient condition even in their dark state, for example during photoblinking or strong quenching. Our work extends single-molecule microscopy and spectroscopy to a huge class of materials that absorb light but do not fluoresce efficiently.

arXiv:1007.3457•Jul 20, 2010•2 citations

How to build an optical filter with an atomic vapor cell

Denis Uhland, Helena Dillmann, Yijun Wang +1 more

Abstract The nature of atomic vapors, their natural alignment with interatomic transitions, and their ease of use make them highly suited for spectrally narrow-banded optical filters. Atomic filters come in two flavors: a filter based on the absorption of light by the Doppler broadened atomic vapor, i.e. a notch filter, and a bandpass filter based on the transmission of resonant light caused by the Faraday effect. The notch filter uses the absorption of resonant photons to filter out a small spectral band around the atomic transition. The off-resonant part of the spectrum is fully transmitted. Atomic vapors based on the Faraday effect allow for suppression of the detuned spectral fraction. Transmission of light originates from the magnetically induced rotation of linear polarized light close to an atomic resonance. This filter constellation allows selective acceptance of specific light frequencies. In this manuscript, we discuss these two types of filters and elucidate the specialties of atomic line filters. We also present a practical guide on building such filter setups from scratch and discuss an approach to achieve an almost perfect atomic spectrum backed by theoretical calculations.

New Journal of Physics•Nov 24, 2023•14 citations

Mapping molecules quantitatively in confocal fluorescence microscopy (Conference Presentation)

Marcelle Koenig, Caroline Berlage, Paja Reisch +4 more

Single-molecule fluorescence microscopy has been established in life science as an essential tool for studying the characteristics and dynamics of individual fluorescent emitters both in vitro as well as in vivo. Acquiring quantitative information from the confocal observation volume is still a challenging task and knowing the absolute number or concentration of proteins in, e.g., cellular structures can significantly improve our understanding of cell biology, which is an important step towards quantitative microscopy. In this talk, a new quantitative analytical tool called Counting by Photon Statistics (CoPS) will be presented. The approach relies on a statistical analysis of detected photon coincidences to estimate the number of independent fluorescent labels in the observation volume [1]. CoPS does exploit the photon antibunching effect: a single photon emitter can only generate one photon at a time. Originally developed for point measurements, CoPS has recently been extended to an imaging scheme [2]. Using a confocal fluorescence microscopy setup with pulsed excitation, four single-photon, detectors and parallellized time-correlated single photon counting electronics (MicroTime 200, PicoQuant), we prove the applicability of the method with artificial model systems (immobilized DNA origami) and present first steps towards biological samples. [1] Ta, H., Wolfrum, J., Herten, D.-P., An extended scheme for counting fluorescent molecules by photon-antibunching Laser Phys. 20:119 (2010). [2] Ta, H. et al., Mapping molecules in scanning far-field fluorescence nanoscopy. Nat. Commun. 6:7977 (2015).

Single Molecule Spectroscopy and Superresolution Imaging•Mar 4, 2019•0 citations
The detection of single molecules has facilitated many advances in life- and material-science. Commonly the fluorescence of dye molecules is detected, which are attached to a non-fluorescent structure under study. For fluorescence microscopy one desires to maximize the detection efficiency together with an efficient suppression of undesired laser leakage. Here we present the use of the narrow-band filtering properties of hot atomic sodium vapor to selectively filter the excitation light from the red-shifted fluorescence of dye labeled single-stranded DNA molecules. A statistical analysis proves an enhancement in detection efficiency of more than 15% in a confocal and in a wide-field configuration.
A single molecule under cryogenic conditions allows one to realize an extremely bright and simultaneously narrow-band single-photon source. We present a review on the different excitation schemes of a single molecule and present the corresponding single-photon nature of the emitted light. Single-molecule spectroscopy has been recently interlinked with atomic spectroscopy. This optical interconnect among the different quantum systems might be enhanced by a so-called Faraday anomalous dispersion optical filter—an ideal tool for many experiments in quantum optics. We introduce our theoretical and experimental approach on these filters which are based on hot atomic sodium vapor. The electrical tunability together with the brightness of a single molecule allows us to record a full atomic spectrum of this filter with the single photons originating from a single-molecular emitter.
The generation of non-classical light, especially of single photon states, is mostly limited to non-linear optics in crystals and single emitters. Here we perform research on single organic dye molecules under cryogenic conditions. The molecules are well-behaved and do not blink or bleach. Also they exhibit an enormous brightness (>106 detected counts per second) and have narrow-band emission (<15-20MHz). By atomic sodium vapor we are able to suppress unwanted background emission from residual impurities in the sample. This light is now analyzed for the use in all-optical gates and further quantum optical schemes. A first step is the characterization in a Hong-Ou-Mandel type experiment. Different variations of this are possible – reaching from indistinguishable to distinguishable photons impinging on a beam-splitter.
The nature of atomic vapors, their natural alignment with interatomic transitions, and their ease of use make them highly suited for spectrally narrow-banded optical filters. Atomic filters come in two flavors: a filter based on the absorption of light by the Doppler broadened atomic vapor, i.e. a notch filter, and a bandpass filter based on the transmission of resonant light caused by the Faraday effect. The notch filter uses the absorption of resonant photons to filter out a small spectral band around the atomic transition. The off-resonant part of the spectrum is fully transmitted. Atomic vapors based on the Faraday effect allow for suppression of the detuned spectral fraction. Transmission of light originates from the magnetically induced rotation of linear polarized light close to an atomic resonance. This filter constellation allows selective acceptance of specific light frequencies. In this manuscript, we discuss these two types of filters and elucidate the specialties of atomic line filters. We also present a practical guide on building such filter setups from scratch and discuss an approach to achieve an almost perfect atomic spectrum backed by theoretical calculations.
The advent of single molecule optics has had a profound impact in fields ranging from biophysics to material science, photophysics, and quantum optics. However, all existing room-temperature single molecule methods have been based on fluorescence detection of highly efficient emitters. Here we demonstrate that standard, modulation-free measurements known from conventional absorption spectrometers can indeed detect single molecules. We report on quantitative measurements of the absorption cross section of single molecules under ambient condition even in their dark state, for example during photoblinking or strong quenching. Our work extends single-molecule microscopy and spectroscopy to a huge class of materials that absorb light but do not fluoresce efficiently.
Abstract The nature of atomic vapors, their natural alignment with interatomic transitions, and their ease of use make them highly suited for spectrally narrow-banded optical filters. Atomic filters come in two flavors: a filter based on the absorption of light by the Doppler broadened atomic vapor, i.e. a notch filter, and a bandpass filter based on the transmission of resonant light caused by the Faraday effect. The notch filter uses the absorption of resonant photons to filter out a small spectral band around the atomic transition. The off-resonant part of the spectrum is fully transmitted. Atomic vapors based on the Faraday effect allow for suppression of the detuned spectral fraction. Transmission of light originates from the magnetically induced rotation of linear polarized light close to an atomic resonance. This filter constellation allows selective acceptance of specific light frequencies. In this manuscript, we discuss these two types of filters and elucidate the specialties of atomic line filters. We also present a practical guide on building such filter setups from scratch and discuss an approach to achieve an almost perfect atomic spectrum backed by theoretical calculations.
Single-molecule fluorescence microscopy has been established in life science as an essential tool for studying the characteristics and dynamics of individual fluorescent emitters both in vitro as well as in vivo. Acquiring quantitative information from the confocal observation volume is still a challenging task and knowing the absolute number or concentration of proteins in, e.g., cellular structures can significantly improve our understanding of cell biology, which is an important step towards quantitative microscopy. In this talk, a new quantitative analytical tool called Counting by Photon Statistics (CoPS) will be presented. The approach relies on a statistical analysis of detected photon coincidences to estimate the number of independent fluorescent labels in the observation volume [1]. CoPS does exploit the photon antibunching effect: a single photon emitter can only generate one photon at a time. Originally developed for point measurements, CoPS has recently been extended to an imaging scheme [2]. Using a confocal fluorescence microscopy setup with pulsed excitation, four single-photon, detectors and parallellized time-correlated single photon counting electronics (MicroTime 200, PicoQuant), we prove the applicability of the method with artificial model systems (immobilized DNA origami) and present first steps towards biological samples. [1] Ta, H., Wolfrum, J., Herten, D.-P., An extended scheme for counting fluorescent molecules by photon-antibunching Laser Phys. 20:119 (2010). [2] Ta, H. et al., Mapping molecules in scanning far-field fluorescence nanoscopy. Nat. Commun. 6:7977 (2015).