Non-equilibrium thermodynamic properties and internal dynamics of 32-residue beta amyloid fibrils

Non-equilibrium molecular dynamics simulations have been applied to investigate the biologically relevant, yet unmapped mechanism of energy transfer and internal dynamics of 32-residue beta amyloid fibrils. Thermal conductivity of the fibril estimated via coupling it to a colder bath has been found to be much larger than those of the normal and denatured biological tissue proteins. The decaying trend of behavior obtained for the fibril temperature is also found to be exactly governed by the series solution of the heat diffusion equation of macroscopic solids in spherical coordinates. Probing internal dynamics of the fibril on the picosecond time scale within the normal mode description of proteins via applying temperature quenches has led to a characteristic dephasing time far below the valid range for echo dephasing of native globular proteins, exhibiting accordingly a significant anharmonicity as well as an overall structural stiffness. (C) 2020 Elsevier B.V. All rights reserved.