scholarly journals Machine learning deciphers structural features of RNA duplexes measured with solution X-ray scattering

IUCrJ ◽  
2020 ◽  
Vol 7 (5) ◽  
pp. 870-880
Author(s):  
Yen-Lin Chen ◽  
Lois Pollack
Keyword(s):  
Machine Learning ◽  
Structural Information ◽  
Structural Parameters ◽  
Supervised Machine Learning ◽  
Scattering Data ◽  
Length Scales ◽  
X Ray ◽  
X Ray Scattering ◽  
Extreme Gradient Boosting ◽  
Ray Scattering

Macromolecular structures can be determined from solution X-ray scattering. Small-angle X-ray scattering (SAXS) provides global structural information on length scales of 10s to 100s of Ångstroms, and many algorithms are available to convert SAXS data into low-resolution structural envelopes. Extension of measurements to wider scattering angles (WAXS or wide-angle X-ray scattering) can sharpen the resolution to below 10 Å, filling in structural details that can be critical for biological function. These WAXS profiles are especially challenging to interpret because of the significant contribution of solvent in addition to solute on these smaller length scales. Based on training with molecular dynamics generated models, the application of extreme gradient boosting (XGBoost) is discussed, which is a supervised machine learning (ML) approach to interpret features in solution scattering profiles. These ML methods are applied to predict key structural parameters of double-stranded ribonucleic acid (dsRNA) duplexes. Duplex conformations vary with salt and sequence and directly impact the foldability of functional RNA molecules. The strong structural periodicities in these duplexes yield scattering profiles with rich sets of features at intermediate-to-wide scattering angles. In the ML models, these profiles are treated as 1D images or features. These ML models identify specific scattering angles, or regions of scattering angles, which correspond with and successfully predict distinct structural parameters. Thus, this work demonstrates that ML strategies can integrate theoretical molecular models with experimental solution scattering data, providing a new framework for extracting highly relevant structural information from solution experiments on biological macromolecules.

scholarly journals In situ small-angle X-ray scattering reveals solution phase discharge of Li–O2 batteries with weakly solvating electrolytes

2021 ◽  
Vol 118 (14) ◽  
pp. e2021893118
Author(s):  
Christian Prehal ◽  
Aleksej Samojlov ◽  
Manfred Nachtnebel ◽  
Ludek Lovicar ◽  
Manfred Kriechbaum ◽  
...  
Keyword(s):  
Structural Information ◽  
Surface Film ◽  
Phase Evolution ◽  
Scattering Data ◽  
Carbon Surface ◽  
X Ray ◽  
Surface Areas ◽  
X Ray Scattering ◽  
Ray Scattering

Electrodepositing insulating lithium peroxide (Li2O2) is the key process during discharge of aprotic Li–O2 batteries and determines rate, capacity, and reversibility. Current understanding states that the partition between surface adsorbed and dissolved lithium superoxide governs whether Li2O2 grows as a conformal surface film or larger particles, leading to low or high capacities, respectively. However, better understanding governing factors for Li2O2 packing density and capacity requires structural sensitive in situ metrologies. Here, we establish in situ small- and wide-angle X-ray scattering (SAXS/WAXS) as a suitable method to record the Li2O2 phase evolution with atomic to submicrometer resolution during cycling a custom-built in situ Li–O2 cell. Combined with sophisticated data analysis, SAXS allows retrieving rich quantitative structural information from complex multiphase systems. Surprisingly, we find that features are absent that would point at a Li2O2 surface film formed via two consecutive electron transfers, even in poorly solvating electrolytes thought to be prototypical for surface growth. All scattering data can be modeled by stacks of thin Li2O2 platelets potentially forming large toroidal particles. Li2O2 solution growth is further justified by rotating ring-disk electrode measurements and electron microscopy. Higher discharge overpotentials lead to smaller Li2O2 particles, but there is no transition to an electronically passivating, conformal Li2O2 coating. Hence, mass transport of reactive species rather than electronic transport through a Li2O2 film limits the discharge capacity. Provided that species mobilities and carbon surface areas are high, this allows for high discharge capacities even in weakly solvating electrolytes. The currently accepted Li–O2 reaction mechanism ought to be reconsidered.

scholarly journals In situ small angle X-ray scattering reveals solution phase discharge of Li-O2 batteries with weakly solvating electrolytes

2020 ◽  
Author(s):  
Christian Prehal ◽  
Aleksej Samojlov ◽  
Manfred Nachtnebel ◽  
Manfred Kriechbaum ◽  
Heinz Amenitsch ◽  
...  
Keyword(s):  
Structural Information ◽  
Surface Film ◽  
Phase Evolution ◽  
Scattering Data ◽  
Carbon Surface ◽  
X Ray ◽  
Surface Areas ◽  
X Ray Scattering ◽  
Ray Scattering

Electrodepositing insulating and insoluble Li2O2 is the key process during discharge of aprotic Li-O2 batteries and determines rate, capacity, and reversibility. Current understanding states that the partition between surface adsorbed and dissolved LiO2 governs whether Li2O2 grows as a conformal surface film or larger particles, leading to low or high capacities, respectively. However, governing factors for Li2O2 packing density and capacity need better understanding, requiring in situ metrologies with structural sensitivity from the atomic to sub-micron scale. Here, we establish in situ small and wide angle X-ray scattering as a suitable method to record the Li2O2 phase evolution with atomic to sub-micrometer resolution during cycling a custom-built in situ Li-O2 cell. Combined with sophisticated data analysis, SAXS allows retrieving rich quantitative structural information from complex multi-phase systems. Surprisingly, we find that features are absent that would point at a Li2O2 surface film formed via two consecutive electron transfers, even in poorly solvating electrolytes thought to be prototypical for surface growth. All scattering data can be modeled by stacks of thin Li2O2 platelets eventually forming large toroidal particles. Higher discharge overpotentials (high currents) lead to smaller Li2O2 particles, but there is no transition to an electronically passivating, conformal Li2O2 coating. This implies that mass transport of reactive species rather than electronic transport through a Li2O2 film limits the discharge capacity. Provided that species mobilities and carbon surface areas are high, this allows for high discharge capacities even in poorly solvating electrolytes. The currently accepted Li-O2 reaction mechanism ought to be reconsidered.<br>

scholarly journals Restoring structural parameters of lipid mixtures from small-angle X-ray scattering data

2021 ◽  
Vol 54 (1) ◽  
pp. 169-179 ◽  
Author(s):  
Petr V. Konarev ◽  
Andrey Yu. Gruzinov ◽  
Haydyn D. T. Mertens ◽  
Dmitri I. Svergun
Keyword(s):  
Form Factor ◽  
Small Angle ◽  
Structural Parameters ◽  
Lipid Vesicles ◽  
Delivery Systems ◽  
Scattering Data ◽  
X Ray ◽  
X Ray Scattering ◽  
Lipid Mixtures ◽  
Ray Scattering

Small-angle X-ray scattering (SAXS) is widely utilized to study soluble macromolecules, including those embedded into lipid carriers and delivery systems such as surfactant micelles, phospholipid vesicles and bilayered nanodiscs. To adequately describe the scattering from such systems, one needs to account for both the form factor (overall structure) and long-range-order Bragg reflections emerging from the organization of bilayers, which is a non-trivial task. Presently existing methods separate the analysis of lipid mixtures into distinct procedures using form-factor fitting and the fitting of the Bragg peak regions. This article describes a general approach for the computation and analysis of SAXS data from lipid mixtures over the entire angular range of an experiment. The approach allows one to restore the electron density of a lipid bilayer and simultaneously recover the corresponding size distribution and multilamellar organization of the vesicles. The method is implemented in a computer program, LIPMIX, and its performance is demonstrated on an aqueous solution of layered lipid vesicles undergoing an extrusion process. The approach is expected to be useful for the analysis of various types of lipid-based systems, e.g. for the characterization of interactions between target drug molecules and potential carrier/delivery systems.

scholarly journals Three-dimensional Pt-nanoparticle networks studied by anomalous small-angle X-ray scattering and X-ray absorption spectroscopy

2002 ◽  
Vol 35 (4) ◽  
pp. 459-470 ◽  
Author(s):  
T. Vad ◽  
H.-G. Haubold ◽  
N. Waldöfner ◽  
H. Bönnemann
Keyword(s):  
Small Angle ◽  
Structural Information ◽  
Hard Spheres ◽  
Multicomponent System ◽  
Three Dimensional ◽  
Scattering Data ◽  
X Ray ◽  
X Ray Scattering ◽  
X Ray Absorption ◽  
Ray Scattering

Anomalous small-angle X-ray scattering (ASAXS) experiments with synchrotron radiation were performed to study the three-dimensional nanostructures of metal/organic hybrids formed by crosslinking aluminium-organic-stabilized platinum nanoparticles with various bifunctional organic spacer molecules. The advantage of ASAXS is the possibility of separating the particle scattering from that of the organic components, thus providing unbiased information about particle size distributions and interparticle correlation. In order to obtain the structural information from the scattering data, a model function based on Vrij's analytical solution for a multicomponent system of hard spheres is proposed. The model is applied to three different samples and the results are compared with those obtained from the application of Fourier methods (characteristic function) and X-ray absorption measurements.

scholarly journals In situ small angle X-ray scattering reveals solution phase discharge of Li-O2 batteries with weakly solvating electrolytes

2020 ◽  
Author(s):  
Christian Prehal ◽  
Aleksej Samojlov ◽  
Manfred Nachtnebel ◽  
Manfred Kriechbaum ◽  
Heinz Amenitsch ◽  
...  
Keyword(s):  
Structural Information ◽  
Surface Film ◽  
Phase Evolution ◽  
Scattering Data ◽  
Carbon Surface ◽  
X Ray ◽  
Surface Areas ◽  
X Ray Scattering ◽  
Ray Scattering

Electrodepositing insulating and insoluble Li2O2 is the key process during discharge of aprotic Li-O2 batteries and determines rate, capacity, and reversibility. Current understanding states that the partition between surface adsorbed and dissolved LiO2 governs whether Li2O2 grows as a conformal surface film or larger particles, leading to low or high capacities, respectively. However, governing factors for Li2O2 packing density and capacity need better understanding, requiring in situ metrologies with structural sensitivity from the atomic to sub-micron scale. Here, we establish in situ small and wide angle X-ray scattering as a suitable method to record the Li2O2 phase evolution with atomic to sub-micrometer resolution during cycling a custom-built in situ Li-O2 cell. Combined with sophisticated data analysis, SAXS allows retrieving rich quantitative structural information from complex multi-phase systems. Surprisingly, we find that features are absent that would point at a Li2O2 surface film formed via two consecutive electron transfers, even in poorly solvating electrolytes thought to be prototypical for surface growth. All scattering data can be modeled by stacks of thin Li2O2 platelets eventually forming large toroidal particles. Higher discharge overpotentials (high currents) lead to smaller Li2O2 particles, but there is no transition to an electronically passivating, conformal Li2O2 coating. This implies that mass transport of reactive species rather than electronic transport through a Li2O2 film limits the discharge capacity. Provided that species mobilities and carbon surface areas are high, this allows for high discharge capacities even in poorly solvating electrolytes. The currently accepted Li-O2 reaction mechanism ought to be reconsidered.<br>

Analysis of time-resolved X-ray scattering data from solution-state systems

2010 ◽  
Vol 66 (2) ◽  
pp. 261-269 ◽  
Author(s):  
Kristoffer Haldrup ◽  
Morten Christensen ◽  
Martin Meedom Nielsen
Keyword(s):  
Excited States ◽  
Structural Parameters ◽  
Scattering Data ◽  
Platinum Compound ◽  
Time Resolved ◽  
X Ray ◽  
The Past ◽  
X Ray Scattering ◽  
Liquid Systems ◽  
Ray Scattering

As ultrafast time-resolved studies of liquid systems with the laser pump/X-ray scattering probe method have come of age over the past decade, several groups have developed methods for the analysis of such X-ray scattering data. The present article describes a method developed primarily with a focus on determining structural parameters in the excited states of medium-sized molecules (~30 atoms) in solution. The general methodology is set in a maximum-likelihood framework and is introduced through the analysis of the photoactive platinum compound PtPOP, in particular the structure of its lowest triplet excited state (3A2u). Emphasis is put on structure determination in terms of model comparisons and on the information content of difference scattering signals as well as the related experimental variables. Several suggestions for improving the accuracy of these types of measurements are presented.

Small angle X-ray scattering study of porosity variation in a styrene-divinylbenzene copolymer

1981 ◽  
Vol 46 (7) ◽  
pp. 1675-1681 ◽  
Author(s):  
Josef Baldrian ◽  
Božena N. Kolarz ◽  
Henrik Galina
Keyword(s):  
Small Angle ◽  
Structural Parameters ◽  
Two Phase ◽  
X Ray ◽  
Porosity Variation ◽  
Swelling Agent ◽  
X Ray Scattering ◽  
Styrene Divinylbenzene ◽  
Ray Scattering

Porosity variations induced by swelling agent exchange were studied in a styrene-divinylbenzene copolymer. Standard methods were used in the characterization of copolymer porosity in the dry state and the results were compared with related structural parameters derived from small angle X-ray scattering (SAXS) measurements as developed for the characterization of two-phase systems. The SAXS method was also used for porosity determination in swollen samples. The differences in the porosity of dry samples were found to be an effect of the drying process, while in the swollen state the sample swells and deswells isotropically.

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