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In this study, we employ the fractional Fokker\u2013Planck equation and continuous-time random walk models to investigate the anomalous diffusion of particles within rough confining potentials, drawing inspiration from protein internal dynamics. Our analysis reveals that the dynamics exhibit three distinct regimes: initial free subdiffusion, an intermediate regime where roughness markedly impacts motion, and a long-term thermal plateau due to confinement effects. We derive approximate expressions for the mean displacement and the ensemble-averaged mean squared displacement in the low-roughness limit, revealing good agreement with simulation results. Furthermore, our examination of the ergodic properties of the dynamics indicates that systems with high roughness exhibit enhanced weak ergodicity breaking. As a consequence, the time-averaged mean squared displacement does not reach a plateau but shows a power-law increase in time and individual trajectories intrinsically exhibit an amplitude scatter. In addition, we demonstrate that the mean maximal excursion effectively quantifies the extent of confinement, offering a robust measure for characterizing subdiffusive dynamics in complex systems.<\/jats:p>","DOI":"10.1063\/5.0299850","type":"journal-article","created":{"date-parts":[[2025,12,22]],"date-time":"2025-12-22T13:02:07Z","timestamp":1766408527000},"update-policy":"https:\/\/doi.org\/10.1063\/aip-crossmark-policy-page","source":"Crossref","is-referenced-by-count":1,"title":["Internal protein motion in a rough model potential"],"prefix":"10.1063","volume":"163","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5329-7755","authenticated-orcid":false,"given":"P.","family":"Jangid","sequence":"first","affiliation":[{"name":"Department of Chemistry, Indian Institute of Science Education and Research 1 , Pune 411008, Maharashtra,","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6013-7020","authenticated-orcid":false,"given":"R.","family":"Metzler","sequence":"additional","affiliation":[{"name":"University of Potsdam, Institute of Physics and Astronomy 2 , Karl-Liebknecht-Str. 24\/25, 14476 Potsdam,","place":["Germany"]},{"name":"Asia Pacific Center for Theoretical Physics 3 , Pohang 37673,","place":["Republic of Korea"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6718-8886","authenticated-orcid":false,"given":"S.","family":"Chaudhury","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Indian Institute of Science Education and Research 1 , Pune 411008, Maharashtra,","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"317","published-online":{"date-parts":[[2025,12,22]]},"reference":[{"key":"2025122208020339600_c1","volume-title":"The Physics of Protein Folding","year":"2010"},{"key":"2025122208020339600_c2","doi-asserted-by":"publisher","first-page":"762","DOI":"10.1039\/c4cp03058c","volume":"17","year":"2015","journal-title":"Phys. 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