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Title: Multitiered computational methodology for extracting three-dimensional rotational diffusion coefficients from x-ray photon correlation spectroscopy data without structural information

Journal Article · · Physical Review. B

X-ray photon correlation spectroscopy (XPCS) is a powerful technique for analyzing particle systems by investigating their dynamics in suspensions across a broad range of temporal and spatial scales. This is done by illuminating samples with coherent x-ray beams and calculating the correlation function of the obtained x-ray scattering images. XPCS is uniquely suited for studying Brownian dynamics, consisting of translational and rotational diffusion. While traditional XPCS image analysis techniques can extract translational diffusion components, they are unable to estimate rotational diffusion coefficients. Here, we introduce a methodology that combines the angular-temporal cross-correlation analysis and a algorithmic framework called Multi-Tiered Estimation for Correlation Spectroscopy in 3D for estimating three-dimensional rotational diffusion coefficients from XPCS images of three-dimensional particle systems. We demonstrate our methodology for extracting rotational diffusion coefficients from XPCS data by applying it to simulated noisy x-ray images of systems of crossing nanotubes and proteins that evolve under translational and rotational Brownian motion for different diffusion rates. Furthermore, our results show that our approach determines rotational diffusion coefficients within a few percent error.

Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Advanced Scientific Computing Research (ASCR); USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF); National Energy Research Scientific Computing Center (NERSC)
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
2481641
Journal Information:
Physical Review. B, Journal Name: Physical Review. B Journal Issue: 21 Vol. 110; ISSN 2469-9969; ISSN 2469-9950
Publisher:
American Physical Society (APS)Copyright Statement
Country of Publication:
United States
Language:
English

References (80)

X-ray Photon Correlation Spectroscopy Studies of Surfaces and Thin Films journal September 2014
Time-dependent fluorescence depolarization and Brownian rotational diffusion coefficients of macromolecules journal November 1969
The Expression of a Tensor or a Polyadic as a Sum of Products journal April 1927
Multiple Invariants and Generalized Rank of a P-Way Matrix or Tensor journal April 1928
Diffusion in Solids: Fundamentals, Methods, Materials, Diffusion-Controlled Processes book January 2007
Analysis of individual differences in multidimensional scaling via an n-way generalization of “Eckart-Young” decomposition journal September 1970
Generalized harmonic analysis journal January 1930
Contribution À ĽÉtude de la reprÉsentation D’une fonction arbitraire par des intÉgrales dÉfinies journal December 1910
Variable projection for nonlinear least squares problems journal August 2012
Optimisation of NMR dynamic models II. A new methodology for the dual optimisation of the model-free parameters and the Brownian rotational diffusion tensor journal December 2007
Optimisation of NMR dynamic models I. Minimisation algorithms and their performance within the model-free and Brownian rotational diffusion spaces journal December 2007
Dynamic light scattering: a practical guide and applications in biomedical sciences journal October 2016
A review on the applications of nuclear magnetic resonance (NMR) in the oil and gas industry: laboratory and field-scale measurements journal March 2022
Millisecond dynamics of colloidal suspension studied by X-ray photon correlation spectroscopy at the Shanghai Synchrotron Radiation Facility journal December 2023
Coupling between the translational and rotational brownian motions of rigid particles of arbitrary shape journal March 1967
Coupling between the translational and rotational brownian motions of rigid particles of arbitrary shape I. Helicoidally isotropic particles journal February 1965
Calculation of Hydrodynamic Properties of Globular Proteins from Their Atomic-Level Structure journal February 2000
Myoglobin and hemoglobin rotational diffusion in the cell journal November 1997
Aliasing error of the exp ⁡ ( β 1 − z 2 ) kernel in the nonuniform fast Fourier transform journal March 2021
XPCS: Nanoscale motion and rheology journal February 2012
A review of X-ray intensity fluctuation spectroscopy journal June 2008
Neutron scattering: A subsurface application review journal October 2021
Parameter estimation for exponential sums by approximate Prony method journal May 2010
Dynamics of proteins in solution journal January 2019
Structure Determination from Multiple-Scattering Electron Crystallography journal August 2022
Interplay between Kinetics and Dynamics of Liquid–Liquid Phase Separation in a Protein Solution Revealed by Coherent X-ray Spectroscopy journal July 2021
Dynamics and Time Scales of Higher-Order Correlations in Supercooled Colloidal Systems journal May 2023
Insights into the Water Transport Mechanism in Polymeric Membranes from Neutron Scattering journal February 2020
Structural Determinants of Protein Dynamics: Analysis of 15N NMR Relaxation Measurements for Main-Chain and Side-Chain Nuclei of Hen Egg White Lysozyme journal March 1995
Refined Structure of an Intact IgG2a Monoclonal Antibody, journal February 1997
Neutron Scattering Study on Dynamics of Water Molecules in MCM-41. 2. Determination of Translational Diffusion Coefficient journal June 2005
Protein Diffusion Coefficients Determined by Macroscopic-Gradient Rayleigh Interferometry and Dynamic Light Scattering journal November 2005
Predicting Effective Diffusion Coefficients in Mudrocks Using a Fractal Model and Small-Angle Neutron Scattering Measurements journal September 2018
Atomic diffusion studied with coherent X-rays journal July 2009
Reaction–diffusion processes at the nano- and microscales journal April 2016
Ionicity of deep eutectic solvents by Walden plot and pulsed field gradient nuclear magnetic resonance (PFG-NMR) journal January 2020
Towards molecular movies with X-ray photon correlation spectroscopy journal January 2020
Spatial programming of self-organizing chemical systems using sustained physicochemical gradients from reaction, diffusion and hydrodynamics journal January 2022
Mouvement brownien d'un ellipsoide - I. Dispersion diélectrique pour des molécules ellipsoidales journal January 1934
Mouvement Brownien d'un ellipsoide (II). Rotation libre et dépolarisation des fluorescences. Translation et diffusion de molécules ellipsoidales journal January 1936
The structure of casein aggregates during renneting studied by indirect Fourier transformation and inverse Laplace transformation of static and dynamic light scattering data, respectively journal August 1995
Probing nonlinear velocity profiles of shear-thinning, nematic platelet dispersions in Couette flow using x-ray photon correlation spectroscopy journal June 2021
X-ray cross correlation analysis uncovers hidden local symmetries in disordered matter journal June 2009
Iterative phasing for fluctuation X-ray scattering journal August 2015
Reconstruction from limited single-particle diffraction data via simultaneous determination of state, orientation, intensity, and phase journal June 2017
Ab initio structure determination from experimental fluctuation X-ray scattering data journal October 2018
Cross-correlation analysis of X-ray photon correlation spectroscopy to extract rotational diffusion coefficients journal August 2021
Fluctuations in polarized fluorescence: evidence that muscle cross bridges rotate repetitively during contraction. journal December 1979
Traceable size determination of nanoparticles, a comparison among European metrology institutes journal November 2012
Method of moments for 3D single particleab initiomodeling with non-uniform distribution of viewing angles journal February 2020
Relaxation and vibrational properties in metal alloys and other disordered systems journal February 2020
Time scale of diffusion in molecular and cellular biology journal April 2014
Molecular dynamics simulation of diffusion in Mg-Al system under pressure journal December 2020
A Simplex Method for Function Minimization journal January 1965
The Protein Data Bank journal January 2000
Isotropic Rotational Brownian Motion journal July 1957
Theory of the Rotational Brownian Motion of a Free Rigid Body journal July 1960
X-ray cross-correlation analysis and local symmetries of disordered systems: General theory journal September 2010
Collective pinning dynamics of charge-density waves in 1 T -TaS 2 journal November 2012
Nuclear magnetic resonance relaxometry as a method of measuring translational diffusion coefficients in liquids journal February 2012
Slow Aging Dynamics and Avalanches in a Gold-Cadmium Alloy Investigated by X-Ray Photon Correlation Spectroscopy journal September 2011
Entanglement-Controlled Subdiffusion of Nanoparticles within Concentrated Polymer Solutions journal August 2012
Jamming Behavior of Domains in a Spiral Antiferromagnetic System journal May 2013
Particle Dynamics in a Diblock-Copolymer-Based Dodecagonal Quasicrystal and Its Periodic Approximant by X-Ray Photon Correlation Spectroscopy journal April 2024
X-Ray Intensity Fluctuation Spectroscopy Studies on Phase-Ordering Systems journal February 2005
Anisotropic dynamics of magnetic colloidal cubes studied by x-ray photon correlation spectroscopy journal March 2021
High resolution strain measurements in highly disordered materials journal February 2021
Coupling x-ray photon correlation spectroscopy and dynamic coherent x-ray diffraction imaging: Particle motion analysis from nano-to-micrometer scale journal November 2023
Introduction to the dynamical theory of X-ray diffraction journal January 1969
Inverse transformation: unleashing spatially heterogeneous dynamics with an alternative approach to XPCS data analysis journal February 2018
X-ray photon correlation spectroscopy journal August 2014
Direct measurement of Stokes–Einstein diffusion of Cowpea mosaic virus with 19 µs-resolved XPCS journal October 2022
X-ray-induced piezoresponse during X-ray photon correlation spectroscopy of PbMg1/3Nb2/3O3 journal January 2024
Communication in the Presence of Noise journal January 1949
Tensor Decompositions and Applications journal August 2009
A Parallel Nonuniform Fast Fourier Transform Library Based on an “Exponential of Semicircle" Kernel journal January 2019
Transforms and Applications Handbook book September 2018
Precise Measurement of Diffusion Coefficients using Scanning Fluorescence Correlation Spectroscopy journal February 2008
A Comprehensive Review of Fluorescence Correlation Spectroscopy journal April 2021
Angular X-ray Cross-Correlation Analysis (AXCCA): Basic Concepts and Recent Applications to Soft Matter and Nanomaterials journal October 2019