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Implementation of Time-Averaged Restraints with UNRES Coarse-Grained Model of Polypeptide Chains.

J Chem Theory Comput

January 2025

Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland.

Time-averaged restraints from nuclear magnetic resonance (NMR) measurements have been implemented in the UNRES coarse-grained model of polypeptide chains in order to develop a tool for data-assisted modeling of the conformational ensembles of multistate proteins, intrinsically disordered proteins (IDPs) and proteins with intrinsically disordered regions (IDRs), many of which are essential in cell biology. A numerically stable variant of molecular dynamics with time-averaged restraints has been introduced, in which the total energy is conserved in sections of a trajectory in microcanonical runs, the bath temperature is maintained in canonical runs, and the time-average-restraint-force components are scaled up with the length of the memory window so that the restraints affect the simulated structures. The new approach restores the conformational ensembles used to generate ensemble-averaged distances, as demonstrated with synthetic restraints.

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The intercalation of metal chlorides, and particularly iron chlorides, into graphitic carbon structures has recently received lots of attention, as it can not only protect this two-dimensional (2D) magnetic system from the effects of the environment but also substantially alter the magnetic, electronic, and optical properties of both the intercalant and host material. At the same time, intercalation can result in the formation of structural defects or defects can appear under external stimuli, which can affect materials performance. These aspects have received so far little attention in dedicated experiments.

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The substantia nigra pars compacta (SNc), one of the main dopaminergic nuclei of the brain, exerts a regulatory function on the basal ganglia circuitry via the nigro-striatal pathway but its possible dopaminergic innervation of the thalamus has been only investigated in non-human primates. The impossibility of tract-tracing studies in humans has boosted advanced MRI techniques and multi-shell high-angular resolution diffusion MRI (MS-HARDI) has promised to shed more light on the structural connectivity of subcortical structures. Here, we estimated the possible dopaminergic innervation of the human thalamus via an MS-HARDI tractography of the SNc in healthy human young adults.

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Objective: To investigate the altered characteristics of cortical morphology and individual-based morphological brain networks in type 2 diabetes mellitus (T2DM), as well as the neural network mechanisms underlying cognitive impairment in T2DM.

Methods: A total of 150 T2DM patients and 130 healthy controls (HCs) were recruited in this study. The study used voxel- and surface-based morphometric analyses to investigate morphological alterations (including gray matter volume, cortical thickness, cortical surface area, and localized gyrus index) in the brains of T2DM patients.

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In this work, using first-principles calculations, we predict a promising class of two-dimensional ferromagnetic semiconductors, namely Janus PrXY (X ≠ Y = Cl, Br, I) monolayers. Through first-principles calculations, we found that PrXY monolayers have excellent dynamic and thermal stability, and their band structures, influenced by magnetic exchange and spin-orbital coupling, exhibit significant valley polarization. Between and - valleys, the Berry curvature values are opposite to each other, resulting in the anomalous valley Hall effect.

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