Investigating finite-size effects in molecular dynamics simulations of ion diffusion, heat transport, and thermal motion in superionic materials

Computational Insights into Papaveroline as an In Silico Drug Candidate for Alzheimer's Disease via Fyn Tyrosine Kinase Inhibition

Alzheimer's disease (AD) poses a significant global health challenge, necessitating the exploration of novel therapeutic strategies. Fyn Tyrosine Kinase has emerged as a key player in AD pathogenesis, making it an attractive target for drug development. This study focuses on investigating the potential of Papaveroline as a drug candidate for AD by targeting Fyn Tyrosine Kinase. The research employed high-throughput virtual screening and QSAR analysis were conducted to identify compounds with optimal drug-like properties, emphasizing adherence to ADMET parameters for further evaluation. Molecular dynamics simulations to analyze the binding interactions between Papaveroline and Staurosporine with Fyn Tyrosine Kinase over a 200-ns period. The study revealed detailed insights into the binding mechanisms and stability of the Papaveroline-Fyn complex, showcasing the compound's potential as an inhibitor of Fyn Tyrosine Kinase. Comparative analysis with natural compounds and a reference compound highlighted Papaveroline's unique characteristics and promising therapeutic implications for AD treatment. Overall, the findings underscore Papaveroline's potential as a valuable drug candidate for targeting Fyn Tyrosine Kinase in AD therapy, offering new avenues for drug discovery in neurodegenerative diseases. This study contributes to advancing our understanding of molecular interactions in AD pathogenesis and paves the way for further research and development in this critical area.

Mechanism of Charge Transport in Lithium Thiophosphate

Lithium ortho-thiophosphate (Li3PS4) has emerged as a promising candidate for solid-state electrolyte batteries, thanks to its highly conductive phases, cheap components, and large electrochemical stability range. Nonetheless, the microscopic mechanisms of Li-ion transport in Li3PS4 are far from being fully understood, the role of PS4 dynamics in charge transport still being controversial. In this work, we build machine learning potentials targeting state-of-the-art DFT references (PBEsol, r2SCAN, and PBE0) to tackle this problem in all known phases of Li3PS4 (α, β, and γ), for large system sizes and time scales. We discuss the physical origin of the observed superionic behavior of Li3PS4: the activation of PS4 flipping drives a structural transition to a highly conductive phase, characterized by an increase in Li-site availability and by a drastic reduction in the activation energy of Li-ion diffusion. We also rule out any paddle-wheel effects of PS4 tetrahedra in the superionic phases-previously claimed to enhance Li-ion diffusion-due to the orders-of-magnitude difference between the rate of PS4 flips and Li-ion hops at all temperatures below melting. We finally elucidate the role of interionic dynamical correlations in charge transport, by highlighting the failure of the Nernst-Einstein approximation to estimate the electrical conductivity. Our results show a strong dependence on the target DFT reference, with PBE0 yielding the best quantitative agreement with experimental measurements not only for the electronic band gap but also for the electrical conductivity of β- and α-Li3PS4.

Anomalous Transport of Small Polarons Arises from Transient Lattice Relaxation or Immovable Boundaries

Elucidating transport mechanisms is crucial for advancing material design, yet state-of-the-art theory is restricted to exact simulations of small lattices with severe finite-size effects or approximate ones that assume the nature of transport. We leverage algorithmic advances to tame finite-size effects and exactly simulate small polaron formation and transport in the Holstein model. We further analyze the applicability of the ubiquitously used equilibrium-based Green-Kubo relations and nonequilibrium methods to predict charge mobility. We find that these methods can converge to different values and track this disparity to finite-size dependence and the sensitivity of Green-Kubo relations to the system's topology. Contrary to standard perturbative calculations, our results demonstrate that small polarons exhibit anomalous transport that manifests transiently due to nonequilibrium lattice relaxation or permanently as a signature of immovable boundaries. These findings can offer new interpretations of transport experiments on polymers and transition metal oxides.

Topological Data analysis of Ion Migration Mechanism

Topological data analysis based on persistent homology has been applied to the molecular dynamics simulation for the fast ion-conducting phase (α-phase) of AgI to show its effectiveness on the ion migration mechanism analysis. Time-averaged persistence diagrams of α-AgI, which quantitatively record the shape and size of the ring structures in the given atomic configurations, clearly showed the emergence of the four-membered rings formed by two Ag and two I ions at high temperatures. They were identified as common structures during the Ag ion migration. The averaged potential energy change due to the deformation of the four-membered ring during Ag migration agrees well with the activation energy calculated from the conductivity Arrhenius plot. The concerted motion of two Ag ions via the four-membered ring was also successfully extracted from molecular dynamics simulations by our approach, providing new insight into the specific mechanism of the concerted motion.

Solids that are also liquids: elastic tensors of superionic materials

Superionics are fascinating materials displaying both solid- and liquid-like characteristics: as solids, they respond elastically to shear stress; as liquids, they display fast-ion diffusion at normal conditions. In addition to such scientific interest, superionics are technologically relevant for energy, electronics, and sensing applications. Characterizing and understanding their elastic properties is, e.g., urgently needed to address their feasibility as solid-state electrolytes in all-solid-state batteries. However, static approaches to elasticity assume well-defined reference positions around which atoms vibrate, in contrast with the quasi-liquid motion of the mobile ions in fast ionic conductors. Here, we derive the elastic tensors of superionics from ensemble fluctuations in the isobaric-isothermal ensemble, exploiting extensive Car-Parrinello simulations. We apply this approach to paradigmatic Li-ion conductors, and complement with a block analysis to compute statistical errors. Static approaches sampled over the trajectories often overestimate the response, highlighting the importance of a dynamical treatment in determining elastic tensors in superionics.