Single Molecule DNA Detection with an Atomic Vapor Notch Filter

The detection of single molecules has facilitated many advances in life- and material-sciences. Commonly, it founds on the fluorescence detection of single molecules, which are for example attached to the structures under study. For fluorescence microscopy and sensing the crucial parameters are the collection and detection efficiency, such that photons can be discriminated with low background from a labeled sample. Here we show a scheme for filtering the excitation light in the optical detection of single stranded labeled DNA molecules. We use the narrow-band filtering properties of a hot atomic vapor to filter the excitation light from the emitted fluorescence of a single emitter. The choice of atomic sodium allows for the use of fluorescent dyes, which are common in life-science. This scheme enables efficient photon detection, and a statistical analysis proves an enhancement of the optical signal of more than 15% in a confocal and in a wide-field configuration.Comment: 9 pages, 5 figure

How to build an optical filter with an atomic vapor cell

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

Cross-calibration of atomic pressure sensors and deviation from quantum diffractive collision universality for light particles

The total room-temperature, velocity-averaged cross section for atom-atom and atom-molecule collisions is well approximated by a universal function depending only on the magnitude of the leading order dispersion coefficient, $C_6$. This feature of the total cross section together with the universal function for the energy distribution transferred by glancing angle collisions ($P_{\rm{QDU}6}$) can be used to empirically determine the total collision cross section and realize a self-calibrating, vacuum pressure standard. This was previously validated for Rb+N$_2$ and Rb+Rb collisions. However, the post-collision energy distribution is expected to deviate from $P_{\rm{QDU}6}$ in the limit of small $C_6$ and small reduced mass. Here we observe this deviation experimentally by performing a direct cross-species loss rate comparison between Rb+H$_2$ and Li+H$_2$ and using the \textit{ab initio} value of $\langle \sigma_{\rm{tot}} \, v \rangle_{\rm{Li+H}_2}$. We find a velocity averaged total collision cross section ratio, $R = \langle \sigma_{\rm{tot}} \, v \rangle_{\rm{Li+H}_2} : \langle \sigma_{\rm{tot}} \, v \rangle_{\rm{Rb+H}_2} = 0.83(5)$. Based on an \textit{ab initio} computation of $\langle \sigma_{\rm{tot}} \, v \rangle_{\rm{Li+H}_2} = 3.13(6)\times 10^{-15}$ m$^3$/s, we deduce $\langle \sigma_{\rm{tot}} \, v \rangle_{\rm{Rb+H}_2} = 3.8(2) \times 10^{-15}$ m$^3$/s, in agreement with a Rb+H$_2$ \textit{ab initio} value of $\langle \sigma_{\mathrm{tot}} v \rangle_{\mathrm{Rb+H_2}} = 3.57 \times 10^{-15} \mathrm{m}^3/\mathrm{s}$.By contrast, fitting the Rb+H$_2$ loss rate as a function of trap depth to the universal function we find $\langle \sigma_{\rm{tot}} \, v \rangle_{\rm{Rb+H}_2} = 5.52(9) \times 10^{-15}$ m$^3$/s. Finally, this work demonstrates how to perform a cross-calibration of sensor atoms to extend and enhance the cold atom based pressure sensor.Comment: 14 pages, 9 figure

How to build an optical filter with an atomic vapor cell

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