arXiv subjects

Maxim Yulikov

Publications and source records attributed to Maxim Yulikov.

5 recordsLinked to original sources

arXiv2026

Direct separation of intra- and inter-molecular contributions in pulse dipolar EPR experiments

We present a direct method of separating intra- (form factor) and inter-molecular (background) contri- butions in pulse EPR dipolar spectroscopy (PDS) experiments. The form factor/background separation is accomplished by rearranging data measured at two different biradical concentrations, without any fitting fundamentally required. This new data processing method allows to analyse PDS data from spin concen- trated samples for which background separation was previously unrealistic. In particular, the presented method would be of high importance for studies of spin labeled biomolecules, especially in respect to the liquid-liquid phase separation (LLPS). Furthermore, we propose a simple measurement and data processing protocol to separate the PDS contributions from each phase in LLPS samples. The protocol for the form factor/background separation for RIDME experiment is also discussed

physics.chem-ph↗

arXiv2025

Quantifying the liquid-liquid transition in cold water/glycerol mixtures by ih-RIDME

Water/glycerol mixtures are common for experiments with biomacromolecules at cryogenic temperatures due to their vitrification properties. Above the glass transition temperature, they undergo liquid-liquid phase separation. Using the novel EPR technique called intermolecular hyperfine Relaxation-Induced Dipolar Modulation Enhancement (ih-RIDME), we quantified the molar composition in frozen water/glycerol mixtures with one or the other component deuterated after the phase transition. Our experiments reveal nearly equal phase composition regardless of the proton/deuterium isotope balance. With the new ih-RIDME data, we can also revisit the already reported body of glass transition data for such mixtures and build a consistent picture for water/glycerol freezing and phase transitions. Our results also indicate that ih-RIDME has the potential for investigating the solvation shells of spin-labelled macromolecules.

cond-mat.soft↗

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↗

arXiv2019

Gd(III)-Gd(III) RIDME for In-Cell EPR Distance Determination

In-cell distance determination by EPR reveals essential structural information about biomacromolecules under native conditions. We demonstrate that the pulsed EPR technique RIDME (relaxation induced dipolar modulation enhancement) can be utilized for such distance determination. The performance of in-cell RIDME has been assessed at Q band using stiff molecular rulers labelled with Gd(III)-PyMTA tags and microinjected into X. laevis oocytes. The overtone coefficients are determined to be the same for protonated aqueous solutions and inside cells. As compared to in-cell DEER (double electron-electron resonance, also abbreviated as PELDOR), in-cell RIDME features approximately 5 times larger modulation depth and does not show artificial broadening in the distance distributions due to the effect of pseudo-secular terms.

cond-mat.mes-hall↗