Browse
Submit Data
Databases
API
Help

Dataset Information

34 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Cross-correlation analysis of X-ray photon correlation spectroscopy to extract rotational diffusion coefficients.

ABSTRACT: Coefficients for translational and rotational diffusion characterize the Brownian motion of particles. Emerging X-ray photon correlation spectroscopy (XPCS) experiments probe a broad range of length scales and time scales and are well-suited for investigation of Brownian motion. While methods for estimating the translational diffusion coefficients from XPCS are well-developed, there are no algorithms for measuring the rotational diffusion coefficients based on XPCS, even though the required raw data are accessible from such experiments. In this paper, we propose angular-temporal cross-correlation analysis of XPCS data and show that this information can be used to design a numerical algorithm (Multi-Tiered Estimation for Correlation Spectroscopy [MTECS]) for predicting the rotational diffusion coefficient utilizing the cross-correlation: This approach is applicable to other wavelengths beyond this regime. We verify the accuracy of this algorithmic approach across a range of simulated data.

SUBMITTER: Hu Z

PROVIDER: S-EPMC8403868 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Ferroelectric domain wall dynamics characterized with X-ray photon correlation spectroscopy.

Project description:Technologically important properties of ferroic materials are determined by their intricate response to external stimuli. This response is driven by distortions of the crystal structure and/or by domain wall motion. Experimental separation of these two mechanisms is a challenging problem which has not been solved so far. Here, we apply X-ray photon correlation spectroscopy (XPCS) to extract the contribution of domain wall dynamics to the overall response. Furthermore, we show how to distinguish the dynamics related to the passing of domain walls through the periodic (Peierls) potential of the crystal lattice and through the random potential caused by lattice defects (pinning centers). The approach involves the statistical analysis of correlations between X-ray speckle patterns produced by the interference of coherent synchrotron X-rays scattered from different nanosize volumes of the crystal and identification of Poisson-type contribution to the statistics. We find such a contribution in the thermally driven response of the monoclinic phase of a ferroelectric PbZr0.55Ti0.45O3 crystal and calculate the number of domain wall jumps in the studied microvolume.

| S-EPMC6055152 | biostudies-literature

Variations in Plasma Membrane Topography Can Explain Heterogenous Diffusion Coefficients Obtained by Fluorescence Correlation Spectroscopy.

Project description:Fluorescence correlation spectroscopy (FCS) is frequently used to study diffusion in cell membranes, primarily the plasma membrane. The diffusion coefficients reported in the plasma membrane of the same cell type and even within single cells typically display a large spread. We have investigated whether this spread can be explained by variations in membrane topography throughout the cell surface, that changes the amount of membrane in the FCS focal volume at different locations. Using FCS, we found that diffusion of the membrane dye DiI in the apical plasma membrane was consistently faster above the nucleus than above the cytoplasm. Using live cell scanning ion conductance microscopy (SICM) to obtain a topography map of the cell surface, we demonstrate that cell surface roughness is unevenly distributed with the plasma membrane above the nucleus being the smoothest, suggesting that the difference in diffusion observed in FCS is related to membrane topography. FCS modeled on simulated diffusion in cell surfaces obtained by SICM was consistent with the FCS data from live cells and demonstrated that topography variations can cause the appearance of anomalous diffusion in FCS measurements. Furthermore, we found that variations in the amount of the membrane marker DiD, a proxy for the membrane, but not the transmembrane protein TCRζ or the lipid-anchored protein Lck, in the FCS focal volume were related to variations in diffusion times at different positions in the plasma membrane. This relationship was seen at different positions both at the apical cell and basal cell sides. We conclude that it is crucial to consider variations in topography in the interpretation of FCS results from membranes.

| S-EPMC7443568 | biostudies-literature

CONTIN XPCS: Software for Inverse Transform Analysis of X-Ray Photon Correlation Spectroscopy Dynamics.

Project description:X-ray photon correlation spectroscopy (XPCS) and dynamic light scattering (DLS) both reveal dynamics using coherent scattering, but X-rays permit investigating of dynamics in a much more diverse array of materials. Heterogeneous dynamics occur in many such materials, and we showed how classic tools employed in analysis of heterogeneous DLS dynamics extend to XPCS, revealing additional information that conventional Kohlrausch exponential fitting obscures. This work presents the software implementation of inverse transform analysis of XPCS data called CONTIN XPCS, an extension of traditional CONTIN that accommodates dynamics encountered in equilibrium XPCS measurements.

| S-EPMC5986106 | biostudies-other

Rotational and translational diffusion of peptide-coated CdSe/CdS/ZnS nanorods studied by fluorescence correlation spectroscopy.

Project description:CdSe/CdS/ZnS nanorods (NRs) of three aspect ratios were coated with phytochelatin-related peptides and studied using fluorescence correlation spectroscopy (FCS). Theoretical predictions of the NRs' rotational diffusion contribution to the correlation curves were experimentally confirmed. We monitored rotational and translational diffusion of NRs and extracted hydrodynamic radii from the extracted diffusion constants. Translational and rotational diffusion constants (D(trans) and D(rot)) for NRs were in good agreement with Tirado and Garcia de la Torre's as well as with Broersma's theories when accounting for the ligand dimensions. NRs fall in the size range where rotational diffusion can be monitored with higher sensitivity than translational diffusion due to a steeper length dependence, D(rot) approximately L(-)(3) versus D(trans) approximately L(-)(1). By titrating peptide-coated NRs with bovine serum albumin, we monitored (nonspecific) binding through rotational diffusion and showed that D(rot) is an advantageous observable for monitoring binding. Monitoring rotational diffusion of bioconjugated NRs using FCS might prove to be useful for observing binding and conformational dynamics in biological systems.

| S-EPMC2535805 | biostudies-literature

Nanosecond X-ray photon correlation spectroscopy using pulse time structure of a storage-ring source.

Project description:X-ray photon correlation spectroscopy (XPCS) is a routine technique to study slow dynamics in complex systems at storage-ring sources. Achieving nanosecond time resolution with the conventional XPCS technique is, however, still an experimentally challenging task requiring fast detectors and sufficient photon flux. Here, the result of a nanosecond XPCS study of fast colloidal dynamics is shown by employing an adaptive gain integrating pixel detector (AGIPD) operated at frame rates of the intrinsic pulse structure of the storage ring. Correlation functions from single-pulse speckle patterns with the shortest correlation time of 192 ns have been calculated. These studies provide an important step towards routine fast XPCS studies at storage rings.

| S-EPMC7792991 | biostudies-literature

Noise reduction in X-ray photon correlation spectroscopy with convolutional neural networks encoder-decoder models.

Project description:Like other experimental techniques, X-ray photon correlation spectroscopy is subject to various kinds of noise. Random and correlated fluctuations and heterogeneities can be present in a two-time correlation function and obscure the information about the intrinsic dynamics of a sample. Simultaneously addressing the disparate origins of noise in the experimental data is challenging. We propose a computational approach for improving the signal-to-noise ratio in two-time correlation functions that is based on convolutional neural network encoder-decoder (CNN-ED) models. Such models extract features from an image via convolutional layers, project them to a low dimensional space and then reconstruct a clean image from this reduced representation via transposed convolutional layers. Not only are ED models a general tool for random noise removal, but their application to low signal-to-noise data can enhance the data's quantitative usage since they are able to learn the functional form of the signal. We demonstrate that the CNN-ED models trained on real-world experimental data help to effectively extract equilibrium dynamics' parameters from two-time correlation functions, containing statistical noise and dynamic heterogeneities. Strategies for optimizing the models' performance and their applicability limits are discussed.

| S-EPMC8292438 | biostudies-literature

Quantitative evaluation of macromolecular crowding environment based on translational and rotational diffusion using polarization dependent fluorescence correlation spectroscopy.

Project description:Macromolecular crowding (MMC) in cells is a hot topic in biology; therefore, well-characterized measurement standards for the evaluation of the nano-environment in MMC solutions are necessary. We propose to use polarization-dependent fluorescence correlation spectroscopy (Pol-FCS) for evaluation of macromolecular crowding in solutions. Pol-FCS can simultaneously measure the relaxation times of rotational and translational diffusion of fluorescent molecules at the same position, even in living cells with low damage. In this report, the differences in the nano-environment among solutions of small molecules, gels, and MMC solutions were evaluated by comparing their rotational and translational diffusion using Pol-FCS. Moreover, this method could distinguish the phase shift in the polyethylene glycol solution. Finally, we separately evaluated the nano-environment in the cytosol and nucleus of living cells in different cell lines and cell cycles. We expect this evaluation method to be useful in characterizing the nano-environment in MMC studies. In addition, the proposed method may be useful for other nano-environments such as liquid-liquid phase separation.

| S-EPMC8134472 | biostudies-literature

Towards ultrafast dynamics with split-pulse X-ray photon correlation spectroscopy at free electron laser sources.

Project description:One of the important challenges in condensed matter science is to understand ultrafast, atomic-scale fluctuations that dictate dynamic processes in equilibrium and non-equilibrium materials. Here, we report an important step towards reaching that goal by using a state-of-the-art perfect crystal based split-and-delay system, capable of splitting individual X-ray pulses and introducing femtosecond to nanosecond time delays. We show the results of an ultrafast hard X-ray photon correlation spectroscopy experiment at LCLS where split X-ray pulses were used to measure the dynamics of gold nanoparticles suspended in hexane. We show how reliable speckle contrast values can be extracted even from very low intensity free electron laser (FEL) speckle patterns by applying maximum likelihood fitting, thus demonstrating the potential of a split-and-delay approach for dynamics measurements at FEL sources. This will enable the characterization of equilibrium and, importantly also reversible non-equilibrium processes in atomically disordered materials.

| S-EPMC5923200 | biostudies-literature

Split-pulse X-ray photon correlation spectroscopy with seeded X-rays from X-ray laser to study atomic-level dynamics.

Project description:With their brilliance and temporal structure, X-ray free-electron laser can unveil atomic-scale details of ultrafast phenomena. Recent progress in split-and-delay optics (SDO), which produces two X-ray pulses with time-delays, offers bright prospects for observing dynamics at the atomic-scale. However, their insufficient pulse energy has limited its application either to phenomena with longer correlation length or to measurement with a fixed delay-time. Here we show that the combination of the SDO and self-seeding of X-rays increases the pulse energy and makes it possible to observe the atomic-scale dynamics in a timescale of picoseconds. We show that the speckle contrast in scattering from water depends on the delay-time as expected. Our results demonstrate the capability of measurement using the SDO with seeded X-rays for resolving the dynamics in temporal and spatial scales that are not accessible by other techniques, opening opportunities for studying the atomic-level dynamics.

| S-EPMC7718898 | biostudies-literature

Multidimensional photon correlation spectroscopy of cavity polaritons.

Project description:The strong coupling of atoms and molecules to radiation field modes in optical cavities creates dressed matter/field states known as polaritons with controllable dynamical and energy transfer properties. We propose a multidimensional optical spectroscopy technique for monitoring polariton dynamics. The response of a two-level atom to the time-dependent coupling to a single-cavity mode is monitored through time-and-frequency-resolved single-photon coincidence measurements of spontaneous emission. Polariton population and coherence dynamics and its variation with cavity photon number and controlled by gating parameters are predicted by solving the Jaynes-Cummings model.

| S-EPMC5816200 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data