arXiv subjects

Luca Maggi

Publications and source records attributed to Luca Maggi.

3 recordsLinked to original sources

arXiv2025

Investigation on non-ergodicity of protein dynamics

The study of microscopic protein dynamics has historically presented significant challenges to researchers seeking to develop a comprehensive and detailed description of its diverse and intriguing features. Recent experimental and theoretical studies have proposed the hypothesis that protein dynamics may be non-ergodic. The implications of this finding are of paramount importance from both a practical and theoretical standpoint. In this study, we employ all-atom molecular dynamics simulations to examine these results over a time window spanning from picoseconds to nanoseconds. To this end, we utilize widely used statistical tools. Our findings challenge the conclusions of previous studies, which suggested that proteins exhibit non-ergodic dynamics. Instead, we demonstrate that deviations from ergodic behavior are due to incomplete convergence of the investigated quantities. Additionally, we discuss the implications of findings that suggest a potential breaking of the ergodic hypothesis over larger time windows, which were not directly investigated in this study.

cond-mat.soft↗

arXiv2023

The main role of fractal-like nature of conformational space in subdiffusion in protein

Protein dynamics is a fundamental element to comprehend their biological functions. However, a theoretical picture providing microscopic-detail explanation of its relevant features is still missing. One of the outmost relevant properties exhibited by this dynamic is its subdiffusivity, whose origins are still unknown. Here, by directly comparing all-atom molecular dynamics simulations and theory we show that this behavior mainly arises from the fractal nature of the network of metastable state of conformational state over which protein dynamics, thought as diffusion process, takes place. This process is assumed to be Markovian by the employed theoretical picture. Therefore, to further support its validity, we built a simple Markov state model starting from the simulations outcome and show that it exhibits a subdiffusive behavior, in quantitative agreement with the one associated to the molecular dynamics. Moreover, Molecular dynamics gives direct access to relevant quantities which allowed us to rule out the possibility the Continuous Time Random Walk can explain the protein subdiffusivity.

cond-mat.soft↗

arXiv2019

How superlocalization affects Vibrational Energy Exchange process in proteins

Recent experimental findings on a protein showed the diffusion of vibrational energy does not occur along the backbone interaction,as it might be expected, but prevalently on non-bonded contacts. These results are explained presenting a theoretical picture, supported by computational calculations, that accounts for these different behaviors in vibrational energy exchange process showing the collective motions on the backbone present a $superlocalized$ nature as their decay with the distance $r$ is $exp(-r^{d})$ with $d \sim 1.8$, whereas those associated to non-bonded contacts result simply localized with $d \sim 1$.

cond-mat.soft↗