First-passage fingerprints of water diffusion near glutamine surfaces

Abstract

First-passage time statistics of water molecules carries information about their interaction with proteins. This information allows reconstruction of water’s space-dependent mobility near protein surfaces.

"Spectrally gapped" random walks on networks: a Mean First Passage Time formula

“…The MFPT is the average over many realizations of the walk of the "first-passage time" (or "first-hitting time") -defined as the number of steps taken by the walker to reach a target node from a given source node for the first time. Applications range from biology [25,26] to finance [27], ecology [28], kinetic network models [29] and many other fields (see [3,30] for reviews on first-passage problems on networks and other media). More recently, the idea that the most "important" nodes should also be those that are most rapidly reachable by others has been used to rank constituents [31][32][33] and to assess heterogeneity and correlations [34] in complex networks.…”

Statistical physics of inhomogeneous transport: Unification of diffusion laws and inference from first-passage statistics

“…The inferred space-dependent diffusivity is compared with the value obtained using the approach of Ref. [24] which requires additional measurements of the local particle density. Interestingly both methods agree with the diffusion coefficients inferred from the linear regression of local mean-squared displacements (Appendix E).…”

“…Molecular-dynamics methods, which allow for estimation of fluids' space-dependent diffusion coefficients in presence of an external potential, have been a topic of several publications [24,25,[76][77][78]. In particular, some of the latest approaches [24,77,78], which offer a relatively simple computational scheme, rely on the information extracted from statistics of first-passage times-a time elapsed until a certain condition, typically a passage to a given spatial region, is satisfied [79][80][81][82][83]. By combining the theory presented in Sec.…”

“…formulated in Ref. [24] , we develop a new method for measuring the transverse component of a diffusion tensor.…”

“…In a recent work [24] we combined stochastic theory of diffusion with molecular-dynamics simulations to investigate mobility of water molecules near the amino-acid surface of a glutamine crystal, which has been implicated in numerous neurodegenerative diseases. In that study, assuming Eq.…”