Note: a 4 ns hardware photon correlator based on a general-purpose field-programmable gate array development board implemented in a compact setup for fluorescence correlation spectroscopy

Variance analysis of dynamic light scattering data

We propose a novel method alternative to the classical Dynamic Light Scattering (DLS) technique for performing particle sizing on diluted dispersions of nanosized particles. Differently from DLS, which works by determining the correlation function of the intensity scattered by the sample, our method does not require the use of a correlator because it exploits the behavior of the variance (VAR) of the scattered signal as a function of the sampling time Δt. By using a wide range of sampling times Δtmin ≪ τc ≪ Δtmax, it is possible to recover the correlation time τc of the scattered field and, in turn (by using the Stokes-Einstein relation), the hydrodynamic diameter of the particles. The new method is endowed with an analytical expression for the error bars associated with to the VAR data. Extensive computer simulations carried out on monodisperse and narrow polydisperse samples show that VAR and DLS techniques provide fairly similar performances. The same results were obtained on calibrated polystyrene spheres and fluorescent perovskite nanoparticles tested with different setups and detection schemes.

Multi-angle in situ dynamic light scattering at a neutron spin echo spectrometer

A new sample environment, called Bio-Oven, has been built for the Neutron Spin Echo (NSE) Spectrometer J-NSE Phoenix. It provides active temperature control and the possibility to perform Dynamic Light Scattering (DLS) measurements during the neutron measurement. DLS provides diffusion coefficients of the dissolved nanoparticles, and thus one can monitor the aggregation state of the sample on a time scale of minutes during the spin echo measurement times on the order of days. This approach helps to validate the NSE data or to replace the sample when its aggregation state influences the spin echo measurement results. The new Bio-Oven is an in situ DLS setup based on optical fibers decoupling the free space optics around the sample cuvette in a lightproof casing from the laser sources and the detectors. It collects light from three scattering angles simultaneously. Six different values of momentum transfer can be accessed by switching between two different laser colors. Test experiments were performed with silica nanoparticles with diameters ranging from 20 nm up to 300 nm. Their hydrodynamic radii were determined from DLS measurements and compared with the ones obtained by a commercial particle sizer. It was demonstrated that also the static light scattering signal can be processed and gives meaningful results. The protein sample apomyoglobin was used for a long-term test and in a first neutron measurement using the new Bio-Oven. The results prove that the aggregation state of the sample can be followed using in situ DLS along with the neutron measurement.

Flexible Sample Environments for the Investigation of Soft Matter at the European Spallation Source: Part I—The In Situ SANS/DLS Setup

As part of the development of the new European Spallation Source (ESS) in Lund (Sweden), which will provide the most brilliant neutron beams worldwide, it is necessary to provide different sample environments with which the potential of the new source can be exploited as soon as possible from the start of operation. The overarching goal of the project is to reduce the downtimes of the instruments related to changing the sample environment by developing plug and play sample environments for different soft matter samples using the same general carrier platform and also providing full software integration and control by just using unified connectors. In the present article, as a part of this endeavor, the sample environment for in situ SANS and dynamic light scattering measurements is introduced.

Reporting on the future of integrative structural biology ORAU workshop

Integrative and hybrid methods have the potential to bridge long-standing knowledge gaps in structural biology. These methods will have a prominent role in the future of the field as we make advances toward a complete, unified representation of biology that spans the molecular and cellular scales. The Department of Physics and Astronomy at Clemson University hosted The Future of Integrative Structural Biology workshop on April 29, 2017 and partially sponsored by partially sponsored by a program of the Oak Ridge Associated Universities (ORAU). The workshop brought experts from multiple structural biology disciplines together to discuss near-term steps toward the goal of a molecular atlas of the cell. The discussion focused on the types of structural data that should be represented, how this data should be represented, and how the time domain might be incorporated into such an atlas. The consensus was that an explorable, map-like Virtual Cell, containing both spatial and temporal data bridging the atomic and cellular length scales obtained by multiple experimental methods, represents the best path toward a complete atlas of the cell.

Diffuse Correlation Spectroscopy Analysis Implemented on a Field Programmable Gate Array

Diffusive correlation spectroscopy (DCS) is an emerging optical technique that measures blood perfusion in deep tissue. In a DCS measurement, temporal changes in the interference pattern of light, which has passed through tissue, are quantified by an autocorrelation function. This autocorrelation function is further parameterized through a non-linear curve fit to a solution to the diffusion equation for coherence transport. The computational load for this non-linear curve fitting is a barrier for deployment of DCS for clinical use, where real-time results, as well as instrument size and simplicity, are important considerations. We have mitigated this computational bottleneck through development of a hardware analyzer for DCS. This analyzer implements the DCS curving fitting algorithm on digital logic circuit using Field Programmable Gate Array (FPGA) technology. The FPGA analyzer is more efficient than a typical software analysis solution. The analyzer module can be easily duplicated for processing multiple channels of DCS data in real-time. We have demonstrated the utility of this analyzer in pre-clinical large animal studies of spinal cord ischemia. In combination with previously described FPGA implementations of auto-correlators, this hardware analyzer can provide a complete device-on-a-chip solution for DCS signal processing. Such a component will enable new DCS applications demanding mobility and real-time processing.

Commercial counterboard for 10 ns software correlator for photon and fluorescence correlation spectroscopy

A 10 ns time resolution, multi-tau software correlator, capable of computing simultaneous autocorrelation (A-A, B-B) and cross (A-B) correlation functions at count rates up to ∼10 MHz, with no data loss, has been developed in LabVIEW and C++ by using the National Instrument timer/counterboard (NI PCIe-6612) and a fast Personal Computer (PC) (Intel Core i7-4790 Processor 3.60 GHz ). The correlator works by using two algorithms: for large lag times (τ ≳ 1 μs), a classical time-mode scheme, based on the measure of the number of pulses per time interval, is used; differently, for τ ≲ 1 μs a photon-mode (PM) scheme is adopted and the correlation function is retrieved from the sequence of the photon arrival times. Single auto- and cross-correlation functions can be processed online in full real time up to count rates of ∼1.8 MHz and ∼1.2 MHz, respectively. Two autocorrelation (A-A, B-B) and a cross correlation (A-B) functions can be simultaneously processed in full real time only up to count rates of ∼750 kHz. At higher count rates, the online processing takes place in a delayed modality, but with no data loss. When tested with simulated correlation data and latex spheres solutions, the overall performances of the correlator appear to be comparable with those of commercial hardware correlators, but with several nontrivial advantages related to its flexibility, low cost, and easy adaptability to future developments of PC and data acquisition technology.

Note: Design of a full photon-timing recorder down to 1-ns resolution for fluorescence fluctuation measurements

A photon timing recorder was realized in a field programmable gate array to capture all timing data of photons on multiple channels with down to a 1-ns resolution and to transfer all data to a host computer in real-time through universal serial bus with more than 10 M events/s transfer rate. The main concept is that photon time series can be regarded as a serial communication data stream. This recorder was successfully applied for simultaneous measurements of fluorescence fluctuation and lifetime of near-infrared dyes in solution. This design is not only limited to the fluorescence fluctuation measurement but also applicable to any kind of photon counting experiments in a nanosecond time range because of the simple and easily modifiable design.

A 32-channel photon counting module with embedded auto/cross-correlators for real-time parallel fluorescence correlation spectroscopy

Fluorescence correlation spectroscopy (FCS) is a well-established technique to study binding interactions or the diffusion of fluorescently labeled biomolecules in vitro and in vivo. Fast FCS experiments require parallel data acquisition and analysis which can be achieved by exploiting a multi-channel Single Photon Avalanche Diode (SPAD) array and a corresponding multi-input correlator. This paper reports a 32-channel FPGA based correlator able to perform 32 auto/cross-correlations simultaneously over a lag-time ranging from 10 ns up to 150 ms. The correlator is included in a 32 × 1 SPAD array module, providing a compact and flexible instrument for high throughput FCS experiments. However, some inherent features of SPAD arrays, namely afterpulsing and optical crosstalk effects, may introduce distortions in the measurement of auto- and cross-correlation functions. We investigated these limitations to assess their impact on the module and evaluate possible workarounds.

The performance of 2D array detectors for light sheet based fluorescence correlation spectroscopy

Single plane illumination microscopy based fluorescence correlation spectroscopy (SPIM-FCS) is a new method for imaging FCS in 3D samples, providing diffusion coefficients, transport, flow velocities and concentrations in an imaging mode. SPIM-FCS records correlation functions over a whole plane in a sample, which requires array detectors for recording the fluorescence signal. Several types of image sensors are suitable for FCS. They differ in properties such as effective area per pixel, quantum efficiency, noise level and read-out speed. Here we compare the performance of several low light array detectors based on three different technologies: (1) Single-photon avalanche diode (SPAD) arrays, (2) passive-pixel electron multiplying charge coupled device (EMCCD) and (3) active-pixel scientific-grade complementary metal oxide semiconductor cameras (sCMOS). We discuss the influence of the detector characteristics on the effective FCS observation volume, and demonstrate that light sheet based SPIM-FCS provides absolute diffusion coefficients. This is verified by parallel measurements with confocal FCS, single particle tracking (SPT), and the determination of concentration gradients in space and time. While EMCCD cameras have a temporal resolution in the millisecond range, sCMOS cameras and SPAD arrays can extend the time resolution of SPIM-FCS down to 10 μs or lower.

Analyzing Förster resonance energy transfer with fluctuation algorithms

Fluorescence correlation spectroscopy (FCS) in combination with Förster resonance energy transfer (FRET) has been developed to a powerful statistical tool, which allows for the analysis of FRET fluctuations in the huge time of nanoseconds to seconds. FRET-FCS utilizes the strong distance dependence of the FRET efficiency on the donor (D)-acceptor (A) distance so that it developed to a perfect method for studying structural fluctuation in biomolecules involved in conformational flexibility, structural dynamics, complex formation, folding, and catalysis. Structural fluctuations thereby result in anticorrelated donor and acceptor signals, which are analyzed by FRET-FCS in order to characterize underlying structural dynamics. Simulated and experimental examples are discussed. First, we review experimental implementations of FRET-FCS and present theory for a two-state interconverting system. Additionally, we consider a very common case of FRET dynamics in the presence of donor-only labeled species. We demonstrate that the mean relaxation time for the structural dynamics can be easily obtained in most of cases, whereas extracting meaningful information from correlation amplitudes can be challenging. We present a strategy to avoid a fit with an underdetermined model function by restraining the D and A brightnesses of the at least one involved state, so that both FRET efficiencies and both rate constants (i.e., the equilibrium constant) can be determined. For samples containing several fluorescent species, the use of pulsed polarized excitation with multiparameter fluorescence detection allows for filtered FCS (fFCS), where species-specific correlation functions can be obtained, which can be directly interpreted. The species selection is achieved by filtering using fluorescence decays of individual species. Analytical functions for species auto- and cross-correlation functions are given. Moreover, fFCS is less affected by photophysical artifacts and often offers higher contrast, which effectively increases its time resolution and significantly enhances its capability to resolve multistate kinetics. fFCS can also differentiate between species even when their brightnesses are the same and thus opens up new possibilities to characterize complex dynamics. Alternative fluctuation algorithms to study FRET dynamics are also briefly reviewed.