Fitting multiple small-angle scattering datasets simultaneously: on the optimal use of priors and weights

Small-angle X-ray and neutron scattering (SAXS and SANS) are powerful techniques for elucidating the structure of diverse particles and materials. This study address the challenge of effectively combining SAXS and SANS data for accurate structural parameter determination. Surprisingly, our results demonstrate that equally weighting all data points leads to the most accurate parameter estimation, even when SAXS data significantly outnumber SANS data. We compared this approach with weighting schemes normalized by the number of points and by the derived information content. Furthermore, we assessed the impact of prior knowledge by incorporating Gaussian priors for model parameters. Our findings indicate that Gaussian priors improve the accuracy of refined parameter values compared to uniform priors. When using a minimum and a maximum values for model parameters, which is common practice, uniform priors are implicitely applied. Finally, we show that utilizing information content aids in determining the degrees of freedom, enabling accurate calculation of the goodness of fit. In conclusion, this research provides valuable insights into the optimal combination of SAXS and SANS data, emphasizing the importance of weighting schemes and prior knowledge for enhanced accuracy in structural parameter determination

Experimental noise in small-angle scattering can be assessed and corrected using the Bayesian Indirect Fourier Transformation

Small-angle X-ray and neutron scattering are widely used to investigate soft matter and biophysical systems. The experimental errors are essential when assessing how well a hypothesized model fits the data. Likewise, they are important when weights are assigned to multiple datasets used to refine the same model. Therefore, it is problematic when experimental errors are over- or underestimated. We present a method, using Bayesian Indirect Fourier Transformation for small-angle scattering data, to assess whether or not a given small-angle scattering dataset has over- or underestimated experimental errors. The method is effective on both simulated and experimental data, and can be used assess and rescale the errors accordingly. Even if the estimated experimental errors are appropriate, it is ambiguous whether or not a model fits sufficiently well, as the "true" reduced $\chi^2$ of the data is not necessarily unity. This is particularly relevant for approaches where overfitting is an inherent challenge, such as reweighting of a simulated molecular dynamics trajectory against a small-angle scattering data or ab initio modelling. Using the outlined method, we show that one can determine what reduced $\chi^2$ to aim for when fitting a model against small-angle scattering data. The method is easily accessible via a web interface

Shape2SAS -- a web application to simulate small-angle scattering data and pair distance distributions from user-defined shapes

Shape2SAS is a web application that allows researchers and students to build intuition and understanding of small-angle scattering. It is available at https://somo.chem.utk.edu/shape2sas. The user defines a model of arbitrary shape by combining geometrical subunits, and Shape2SAS then calculates and displays the scattering intensity, the pair distance distribution as well as a visualization of the user-defined shape. Simulated data with realistic noise are also generated. We demonstrate how Shape2SAS can calculate and display the different scattering patterns for various geometrical shapes, such as spheres and cylinders. We also demonstrate how the effect of structure factors can be visualized. Finally, we show how multi-contrast particles can readily be generated, and how the calculated scattering may be used to validate and visualize analytical models generated in analysis software for fitting small-angle scattering data

Optimering af signalstyring i realtid

Denne artikel er baseret på kandidatspecialet, Adaptiv signalstyring i realtid, udarbejdet af Mikkel Færgemand, hvilket er foregået under projektsamarbejdet DiCyPS ved Aalborg Universitet, hvorfor der har været en lang række af bidragsydere.Projektet omhandler udviklingen af en ny og intelligent signalstyring som alternativ til den traditionelle signalstyring. Ved anvendelse af nye principper inden for signalstyring samt objektdetektering, som alternativ til traditionel punktdetektering, realiseres en intelligent og adaptiv signalstyring. Denne signalstyring forventes, at kunne forbedre den overordnede trafikafvikling i og omkring de signalregulerede kryds.På baggrund af mikrosimuleringerne i VISSIM er det dokumenteret, at den intelligente signalstyring realiserer en mere effektiv trafikafvikling. Hvilket medfører en betydeligt reduktion af; middelforsinkelse, kølængde, brændstofforbrug, antal stop samt overordnede rejsetid ved anvendelse af den intelligente signalstyring

Optimering af signalstyring i realtid:Intelligent styring af signalregulerede kryds ved anvendelse af maskinlæring og objektdetektering

Artiklen præsenterer nye principper for styring af signalregulerede kryds. Ved anvendelse af maskinlæring og objektdetektering som erstatning for punktdetektering og samordning er udviklet en kontroller til signal- regulerede kryds, der ved mikrosimulering i VISSIM viser mellem 30% og 50%’s reduktion i middelforsinkel- ser, kølængder og antal stop i 4 samordnede kryds på Hobrovej i Aalborg. Brændstofforbruget og samlet rejsetid på den samordnede strækning er i simuleringsstudiet reduceret med omkring 20%

Structure and Dynamics of the Central Lipid Pool and Proteins of the Bacterial Holo-Translocon

The bacterial Sec translocon, SecYEG, associates with accessory proteins YidC and the SecDF-YajC subcom-plex to form the bacterial holo-translocon (HTL). The HTL is a dynamic and flexible protein transport machine capable of coor-dinating protein secretion across the membrane and efficient lateral insertion of nascent membrane proteins. It has been hypothesized that a central lipid core facilitates the controlled passage of membrane proteins into the bilayer, ensuring the efficient formation of their native state. By performing small-angle neutron scattering on protein solubilized in ‘‘match-out’’ deuterated detergent, we have been able to interrogate a ‘‘naked’’ HTL complex, with the scattering contribution of the sur-rounding detergent micelle rendered invisible. Such an approach has allowed the confirmation of a lipid core within the HTL, which accommodates between 8 and 29 lipids. Coarse-grained molecular dynamics simulations of the HTL also demon-strate a dynamic, central pool of lipids. An opening at this lipid-rich region between YidC and the SecY lateral gate may provide an exit gateway for newly synthesized, correctly oriented, membrane protein helices, or even small bundles of helices, to emerge from the HTL

Mg2+-dependent conformational equilibria in CorA and an integrated view on transport regulation

The CorA family of proteins regulates the homeostasis of divalent metal ions in many bacteria, archaea, and eukaryotic mitochondria, making it an important target in the investigation of the mechanisms of transport and its functional regulation. Although numerous structures of open and closed channels are now available for the CorA family, the mechanism of the transport regulation remains elusive. Here, we investigated the conformational distribution and associated dynamic behaviour of the pentameric Mg2+ channel CorA at room temperature using small-angle neutron scattering (SANS) in combination with molecular dynamics (MD) simulations and solid-state nuclear magnetic resonance spectroscopy (NMR). We find that neither the Mg2+-bound closed structure nor the Mg2+-free open forms are sufficient to explain the average conformation of CorA. Our data support the presence of conformational equilibria between multiple states, and we further find a variation in the behaviour of the backbone dynamics with and without Mg2+. We propose that CorA must be in a dynamic equilibrium between different non-conducting states, both symmetric and asymmetric, regardless of bound Mg2+ but that conducting states become more populated in Mg2+-free conditions. These properties are regulated by backbone dynamics and are key to understanding the functional regulation of CorA.Peer reviewe