TY  - JOUR
A1  - Jeon, Jae-Hyung
A1  - Monne, Hector Martinez-Seara
A1  - Javanainen, Matti
A1  - Metzler, Ralf
T1  - Anomalous diffusion of phospholipids and cholesterols in a lipid bilayer and its origins
JF  - Physical review letters
N2  - Combining extensive molecular dynamics simulations of lipid bilayer systems of varying chemical compositions with single-trajectory analyses, we systematically elucidate the stochastic nature of the lipid motion. We observe subdiffusion over more than 4 orders of magnitude in time, clearly stretching into the submicrosecond domain. The lipid motion depends on the lipid chemistry, the lipid phase, and especially the presence of cholesterol. We demonstrate that fractional Langevin equation motion universally describes the lipid motion in all phases, including the gel phase, and in the presence of cholesterol. The results underline the relevance of anomalous diffusion in lipid bilayers and the strong effects of the membrane composition.
Y1  - 2012
U6  - https://doi.org/10.1103/PhysRevLett.109.188103
SN  - 0031-9007
VL  - 109
IS  - 18
PB  - American Physical Society
CY  - College Park
ER  - 
TY  - JOUR
A1  - Jeon, Jae-Hyung
A1  - Metzler, Ralf
T1  - Inequivalence of time and ensemble averages in ergodic systems: exponential versus power-law relaxation in confinement
JF  - Physical review : E, Statistical, nonlinear and soft matter physics
N2  - Single-particle tracking has become a standard tool for the investigation of diffusive properties, especially in small systems such as biological cells. Usually the resulting time series are analyzed in terms of time averages over individual trajectories. Here we study confined normal as well as anomalous diffusion, modeled by fractional Brownian motion and the fractional Langevin equation, and show that even for such ergodic systems time-averaged quantities behave differently from their ensemble-averaged counterparts, irrespective of how long the measurement time becomes. Knowledge of the exact behavior of time averages is therefore fundamental for the proper physical interpretation of measured time series, in particular, for extraction of the relaxation time scale from data.
Y1  - 2012
U6  - https://doi.org/10.1103/PhysRevE.85.021147
SN  - 1539-3755
VL  - 85
IS  - 2
PB  - American Physical Society
CY  - College Park
ER  - 
TY  - JOUR
A1  - Adamcik, Jozef
A1  - Jeon, Jae-Hyung
A1  - Karczewski, Konrad J.
A1  - Metzler, Ralf
A1  - Dietler, Giovanni
T1  - Quantifying supercoiling-induced denaturation bubbles in DNA
JF  - Soft matter
N2  - In both eukaryotic and prokaryotic DNA sequences of 30-100 base-pairs rich in AT base-pairs have been identified at which the double helix preferentially unwinds. Such DNA unwinding elements are commonly associated with origins for DNA replication and transcription, and with chromosomal matrix attachment regions. Here we present a quantitative study of local DNA unwinding based on extensive single DNA plasmid imaging. We demonstrate that long-lived single-stranded denaturation bubbles exist in negatively supercoiled DNA, at the expense of partial twist release. Remarkably, we observe a linear relation between the degree of supercoiling and the bubble size, in excellent agreement with statistical modelling. Furthermore, we obtain the full distribution of bubble sizes and the opening probabilities at varying salt and temperature conditions. The results presented herein underline the important role of denaturation bubbles in negatively supercoiled DNA for biological processes such as transcription and replication initiation in vivo.
Y1  - 2012
U6  - https://doi.org/10.1039/c2sm26089a
SN  - 1744-683X
VL  - 8
IS  - 33
SP  - 8651
EP  - 8658
PB  - Royal Society of Chemistry
CY  - Cambridge
ER  - 
TY  - JOUR
A1  - Metzler, Ralf
A1  - Jeon, Jae-Hyung
T1  - The role of ergodicity in anomalous stochastic processes - analysis of single-particle trajectories
JF  - Physica scripta : an international journal for experimental and theoretical physics
N2  - Single-particle experiments produce time series x(t) of individual particle trajectories, frequently revealing anomalous diffusion behaviour. Typically, individual x(t) are evaluated in terms of time-averaged quantities instead of ensemble averages. Here we discuss the behaviour of the time-averaged mean squared displacement of different stochastic processes giving rise to anomalous diffusion. In particular, we pay attention to the ergodic properties of these processes, i.e. the (non)equivalence of time and ensemble averages.
Y1  - 2012
U6  - https://doi.org/10.1088/0031-8949/86/05/058510
SN  - 0031-8949
VL  - 86
IS  - 5
PB  - IOP Publ. Ltd.
CY  - Bristol
ER  -