Katharina Keller | Searcharxiv

arXiv2022

Neural networks in pulsed dipolar spectroscopy: a practical guide

This is a methodological guide to the use of deep neural networks in the processing of pulsed dipolar spectroscopy (PDS) data encountered in structural biology, organic photovoltaics, photosynthesis research, and other domains featuring long-lived radical pairs and paramagnetic metal ions. PDS uses distance dependence of magnetic dipolar interactions; measuring a single well-defined distance is straightforward, but extracting distance distributions is a hard and mathematically ill-posed problem requiring careful regularisation and background fitting. Neural networks do this exceptionally well, but their "robust black box" reputation hides the complexity of their design and training - particularly when the training dataset is effectively infinite. The objective of this paper is to give insight into training against simulated databases, to discuss network architecture choices, to describe options for handling DEER (double electron-electron resonance) and RIDME (relaxation-induced dipolar modulation enhancement) experiments, and to provide a practical data processing flowchart.

physics.chem-ph↗

arXiv2020

How accurately defined are the overtone coefficients in the Gd(III)-Gd(III) RIDME?

Relaxation-induced dipolar modulation enhancement (RIDME) is a pulse EPR technique that is particularly suitable to determine distances between paramagnetic centers with a broad EPR spectrum, e.g. metal-ion-based ones. As far as high-spin systems (S > 1/2) are concerned, the RIDME experiment provides not only the basic dipolar frequency but also its overtones, which complicates the determination of interspin distances. An r.m.s.d.-based approach for the calibration of the overtone coefficients is proposed and illustrated for a series of molecular rulers doubly labelled with Gd(III)-PyMTA tags. The constructed 2D total-penalty diagrams clearly show that there is no unique set but rather a certain pool of overtone coefficients, which can be used to extract distance distributions between high-spin paramagnetic centers as determined from the RIDME experiment.

cond-mat.other↗