Optical crosstalk in single photon avalanche diode arrays: a new complete model.

One of the main issues of Single Photon Avalanche Diode arrays is optical crosstalk. Since its intensity increases with reducing the distance between devices, this phenomenon limits the density of integration within arrays. In the past optical crosstalk was ascribed essentially to the light propagating from one detector to another through direct optical paths. Accordingly, reflecting trenches between devices were proposed to prevent it, but they proved to be not completely effective. In this paper we will present experimental evidence that a significant contribution to optical crosstalk comes from light reflected internally off the bottom of the chip, thus being impossible to eliminate it completely by means of trenches. We will also propose an optical model to predict the dependence of crosstalk on the distance between devices.

Dual-color microchip electrophoresis with single-photon avalanche diodes: application to mutation detection.

A novel microchip electrophoresis instrument based on single-photon avalanche diodes was used for the molecular characterization of mutations in disease genes. The identification of the main mutation causing cystic fibrosis, named DeltaF508, by the Amplification Refractory Mutation System was used to validate the technology. In our implemented protocol the wild-type and mutant allele-specific primers are labeled with Cy5 and Cy5.5, respectively. The protocol enables the amplification of the DNA sample in a single PCR. The genotype was deduced from the fluorescence of the amplicons run in the CE microchip. Validation on 15 DNA samples from either homozygous wild-type or heterozygous and homozygous mutated control subjects proved the complete reliability of the system, thus confirming its high diagnostic potential.

Enhanced performance photon-counting time-of-flight sensor.

We describe improvements to a time-of-flight sensor utilising the time-correlated single-photon counting technique employing a commercially-available silicon-based photon-counting module. By making modifications to the single-photon detection circuitry and the data analysis techniques, we experimentally demonstrate improved resolution between multiple scattering surfaces with a minimum resolvable separation of 1.7 cm at ranges in excess of several hundred metres.

Operation of silicon single photon avalanche diodes at cryogenic temperature.

This article reports a complete characterization of single photon avalanche diodes (SPADs) at temperatures down to 120 K. We show that deep cooling of the device by means of a compact liquid-nitrogen Dewar brings several advantages, such as extremely low dark counting rates (down to 1 counts/s), better time resolution, and higher quantum efficiency in the visible range. By using a special current pick-off circuit, we achieved a time resolution of 20 ps full width at half maximum at 120 K for a 50 mum diameter SPAD. Afterpulsing effects are avoided by using a sufficiently long hold-off time (microseconds).

Quantum key distribution system clocked at 2 GHz.

An improved quantum key distribution test system operating at clock rates of up to 2GHz using a specially adapted commercially-available silicon single-photon counting module is presented. The use of an enhanced detector has improved the fiber-based quantum key distribution test system performance in terms of transmission distance and quantum bit error rate.

New silicon technologies enable high-performance arrays of Single Photon Avalanche Diodes.

In order to fulfill the requirements of many applications, we recently developed a new technology aimed at combining the advantages of traditional thin and thick silicon Single Photon Avalanche Diodes (SPAD). In particular we demonstrated single-pixel detectors with a remarkable improvement in the Photon Detection Efficiency at the longer wavelengths (e.g. 40% at 800nm) while maintaining a timing jitter better than 100ps. In this paper we will analyze the factors the currently prevent the fabrication of arrays of SPADs by adopting such a Red-Enhanced (RE) technology and we will propose further modifications to the device structure that will enable the fabrication of high performance RE-SPAD arrays for photon timing applications.

Single-molecule FRET experiments with a red-enhanced custom technology SPAD.

Single-molecule fluorescence spectroscopy of freely diffusing molecules in solution is a powerful tool used to investigate the properties of individual molecules. Single-Photon Avalanche Diodes (SPADs) are the detectors of choice for these applications. Recently a new type of SPAD detector was introduced, dubbed red-enhanced SPAD (RE-SPAD), with good sensitivity throughout the visible spectrum and with excellent timing performance. We report a characterization of this new detector for single-molecule fluorescence resonant energy transfer (smFRET) studies on freely diffusing molecules in a confocal geometry and alternating laser excitation (ALEX) scheme. We use a series of doubly-labeled DNA molecules with donor-to-acceptor distances covering the whole range of useful FRET values. Both intensity-based (µs-ALEX) and lifetime-based (ns-ALEX) measurements are presented and compared to identical measurements performed with standard thick SPADs. Our results demonstrate the great potential of this new detector for smFRET measurements and beyond.

Ultra high-throughput single molecule spectroscopy with a 1024 pixel SPAD.

Single-molecule spectroscopy is a powerful approach to measuring molecular properties such as size, brightness, conformation, and binding constants. Due to the low concentrations in the single-molecule regime, measurements with good statistical accuracy require long acquisition times. Previously we showed a factor of 8 improvement in acquisition speed using a custom-CMOS 8x1 SPAD array. Here we present preliminary results with a 64X improvement in throughput obtained using a liquid crystal on silicon spatial light modulator (LCOS-SLM) and a novel standard CMOS 1024 pixel SPAD array, opening the way to truly high-throughput single-molecule spectroscopy.

Photonics for life.

Light is strictly connected with life, and its presence is fundamental for any living environment. Thus, many biological mechanisms are related to light interaction or can be evaluated through processes involving energy exchange with photons. Optics has always been a precious tool to evaluate molecular and cellular mechanisms, but the discovery of lasers opened new pathways of interactions of light with biological matter, pushing an impressive development for both therapeutic and diagnostic applications in biomedicine. The use of light in different fields has become so widespread that the word photonics has been utilized to identify all the applications related to processes where the light is involved. The photonics area covers a wide range of wavelengths spanning from soft X-rays to mid-infrared and includes all devices related to photons as light sources, optical fibers and light guides, detectors, and all the related electronic equipment. The recent use of photons in the field of telecommunications has pushed the technology toward low-cost, compact, and efficient devices, making them available for many other applications, including those related to biology and medicine where these requirements are of particular relevance. Moreover, basic sciences such as physics, chemistry, mathematics, and electronics have recognized the interdisciplinary need of biomedical science and are translating the most advanced researches into these fields. The Politecnico school has pioneered many of them,and this article reviews the state of the art of biomedical research at the Politecnico in the field internationally known as biophotonics.

High-throughput FCS using an LCOS spatial light modulator and an 8 × 1 SPAD array.

We present a novel approach to high-throughput Fluorescence Correlation Spectroscopy (FCS) which enables us to obtain one order of magnitude improvement in acquisition time. Our approach utilizes a liquid crystal on silicon spatial light modulator to generate dynamically adjustable focal spots, and uses an eight-pixel monolithic single-photon avalanche photodiode array. We demonstrate the capabilities of this system by showing FCS of Rhodamine 6G under various viscosities, and by showing that, with proper calibration of each detection channel, one order of magnitude improvement in acquisition speed is obtained. More generally, our approach will allow higher throughput single-molecule studies to be performed.

High-throughput multispot single-molecule spectroscopy.

Solution-based single-molecule spectroscopy and fluorescence correlation spectroscopy (FCS) are powerful techniques to access a variety of molecular properties such as size, brightness, conformation, and binding constants. However, this is limited to low concentrations, which results in long acquisition times in order to achieve good statistical accuracy. Data can be acquired more quickly by using parallelization. We present a new approach using a multispot excitation and detection geometry made possible by the combination of three powerful new technologies: (i) a liquid crystal spatial light modulator to produce multiple diffraction-limited excitation spots; (ii) a multipixel detector array matching the excitation pattern and (iii) a low-cost reconfigurable multichannel counting board. We demonstrate the capabilities of this technique by reporting FCS measurements of various calibrated samples as well as single-molecule burst measurements.

Time-resolved diffuse reflectance using small source-detector separation and fast single-photon gating.

We demonstrate the feasibility of time-resolved diffuse reflectance measurements at small source-detector separations using a single-photon avalanche diode operated in time-gated mode. Photon time distributions at an interfiber distance of 2 mm were obtained on a homogeneous tissue phantom with a dynamic range of 10(6) and collecting photons at arrival times up to 4 ns. Moreover, we were able to detect a local inhomogeneity deeply buried within a diffusive medium with better spatial resolution, higher signal intensity, and same contrast of a larger (20 mm) interfiber distance. Finally, the proposed approach proved valuable to detect in vivo a task-related brain activation.

Microchips and single-photon avalanche diodes for DNA separation with high sensitivity.

Modern techniques for DNA and protein analysis and separation rely on measurements of LIF and face a trend toward employing progressively smaller samples. The currently employed detectors that provide the required ultrahigh sensitivity, e.g. photomultiplier tubes (PMTs), are bulky and/or costly and delicate, whereas a key issue for the development of compact and economical instruments is the availability of miniaturized, inexpensive, and ultrasensitive photodetectors. The planar epitaxial silicon single-photon avalanche diodes (SPADs) combine the typical advantages of microelectronics (miniaturization, ruggedness, low voltage, low power, low cost, etc.) with high sensitivity, even better than that of PMTs. The suitability of such SPADs to microchip CE has been here ascertained by developing a new apparatus with dual-wavelength LIF detection. The apparatus has been experimented in studies on the EOF suppression and on the coating stability and tested in rapid sizing of DNA fragments. The experimental results obtained in the separation of Cy5-labeled oligonucleotide demonstrate sensitivity better than 3 pM, which corresponds to less than 100 fluorescent molecules in the 50 pL illuminated volume.

Complete single-photon counting and timing module in a microchip.

A complete module for single-photon counting and timing is demonstrated in a single chip. Features comparable with or better than commercially available macroscopic modules are obtained by integration of an active-quenching and active-reset circuit in complementary metal-oxide semiconductor technology together with a single-photon avalanche diode (SPAD). The integrated SPAD has a 12-microm-diameter sensitive area and operates with an overvoltage above breakdown adjustable up to 20 V. With a 5-V overvoltage the photon detection efficiency peaks above 40% around 500 nm, and the dark-counting rate is lower than 600 counts/s at room temperature. The overall counting dead time is 33 ns.

Use of high-molecular-mass polyacrylamides as matrices for microchip electrophoresis of DNA fragments.

DNA fragment analysis requires the use of polymer solutions as sieving matrices. Generally, such matrices are constituted of high-molar-weight polymers employed at a concentration higher than their entanglement threshold concentration. These polymer solutions are highly viscous and difficult to use in the narrow channels of a microchip. Ultralarge polyacrylamides synthesized via a nonconventional method, being the low-temperature plasma-induced polymerization (PIP), were used as DNA sieving matrices for microchip electrophoresis. The distinctive features of these polymers (ultralarge molecular mass and linearity) allow their use at a dilute concentration. Dilute PIP polyacrylamides revealed a constant value of resolution in a broad range of DNA fragment sizes (123 bp-1353 bp), thus proving to be effective in common genotyping applications. Moreover, the low viscosity of the dilute solutions enable it to be easier and faster in filling the channel between runs, thus enhancing the throughput of the microchip devices.

Optical design and evaluation of a three-dimensional imaging and ranging system based on time-correlated single-photon counting.

The design and operation of a noncontact surface profilometry system based on the time-correlated single-photon-counting technique are described. This system has a robust optomechanical design and uses an eye-safe laser that makes it particularly suitable for operation in an uncontrolled industrial environment. The sensitivity of the photon-counting technique permits its use on a variety of target materials, and its mode of operation does not require the continual presence of an operator. The system described has been optimized for a 1-25-m standoff, has a distance repeatability of <30 microm, and has a transverse spatial resolution of approximately 60 microm at a 2-m standoff and approximately 400 microm at a 13-m standoff.

Protein conformational dynamics probed by single-molecule electron transfer.

Electron transfer is used as a probe for angstrom-scale structural changes in single protein molecules. In a flavin reductase, the fluorescence of flavin is quenched by a nearby tyrosine residue by means of photo-induced electron transfer. By probing the fluorescence lifetime of the single flavin on a photon-by-photon basis, we were able to observe the variation of flavin-tyrosine distance over time. We could then determine the potential of mean force between the flavin and the tyrosine, and a correlation analysis revealed conformational fluctuation at multiple time scales spanning from hundreds of microseconds to seconds. This phenomenon suggests the existence of multiple interconverting conformers related to the fluctuating catalytic reactivity.