Comparing proteins by their internal dynamics: Exploring structure–function relationships beyond static structural alignments

C Micheletti - Physics of life reviews, 2013 - Elsevier
The growing interest for comparing protein internal dynamics owes much to the realisation
that protein function can be accompanied or assisted by structural fluctuations and …

Models of anomalous diffusion in crowded environments

IM Sokolov - Soft Matter, 2012 - pubs.rsc.org
A particle's motion in crowded environments often exhibits anomalous diffusion, whose
nature depends on the situation at hand and is formalized within different physical models …

Identification of slow molecular order parameters for Markov model construction

G Pérez-Hernández, F Paul, T Giorgino… - The Journal of …, 2013 - pubs.aip.org
A goal in the kinetic characterization of a macromolecular system is the description of its
slow relaxation processes via (i) identification of the structural changes involved in these …

Markov models of molecular kinetics: Generation and validation

JH Prinz, H Wu, M Sarich, B Keller, M Senne… - The Journal of …, 2011 - pubs.aip.org
Markov state models of molecular kinetics (MSMs), in which the long-time statistical
dynamics of a molecule is approximated by a Markov chain on a discrete partition of …

Ever-fluctuating single enzyme molecules: Michaelis-Menten equation revisited

BP English, W Min, AM Van Oijen, KT Lee… - Nature chemical …, 2006 - nature.com
Enzymes are biological catalysts vital to life processes and have attracted century-long
investigation. The classic Michaelis-Menten mechanism provides a highly satisfactory …

Binding of small-molecule ligands to proteins:“what you see” is not always “what you get”

DL Mobley, KA Dill - Structure, 2009 - cell.com
We review insights from computational studies of affinities of ligands binding to proteins. The
power of structural biology is in translating knowledge of protein structures into insights …

[图书][B] Fractional calculus view of complexity: tomorrow's science

BJ West - 2016 - books.google.com
This book explains the quantitative reasoning required by the fractional calculus applied to
complex physical, social, and biological phenomena. Fractional calculus is inextricably …

Single particle tracking in systems showing anomalous diffusion: the role of weak ergodicity breaking

S Burov, JH Jeon, R Metzler, E Barkai - Physical Chemistry Chemical …, 2011 - pubs.rsc.org
Anomalous diffusion has been widely observed by single particle tracking microscopy in
complex systems such as biological cells. The resulting time series are usually evaluated in …

Fractional langevin equation

E Lutz - Physical Review E, 2001 - APS
We investigate fractional Brownian motion with a microscopic random-matrix model and
introduce a fractional Langevin equation. We use the latter to study both subdiffusion and …

Fractional Brownian Motion Versus the Continuous-Time Random Walk:<? format?> A Simple Test for Subdiffusive Dynamics

M Magdziarz, A Weron, K Burnecki, J Klafter - Physical review letters, 2009 - APS
Fractional Brownian motion with Hurst index less then 1/2 and continuous-time random walk
with heavy tailed waiting times (and the corresponding fractional Fokker-Planck equation) …