@article{SchwarzeMertensMuelleretal.2017,
  author    = {Schwarze, Thomas and Mertens, Monique and Mueller, Peter and Riemer, Janine and Wessig, Pablo and Holdt, Hans-J{\"u}rgen},
  title     = {Highly K+-Selective Fluorescent Probes for Lifetime Sensing of K+ in Living Cells},
  series = {Chemistry - a European journal},
  volume    = {23},
  journal   = {Chemistry - a European journal},
  publisher = {Wiley-VCH},
  address   = {Weinheim},
  issn      = {0947-6539},
  doi       = {10.1002/chem.201704368},
  pages     = {17186 -- 17190},
  year      = {2017},
  abstract  = {The new K+-selective fluorescent probes 1 and 2 were obtained by Cu-I-catalyzed 1,3-dipolar azide alkyne cycloaddition (CuAAC) reactions of an alkyne-substituted [1,3]dioxolo[4,5-f][1,3]benzodioxole (DBD) ester fluorophore with azido-functionalized N-phenylaza-18-crown-6 ether and N-(o-isopropoxy) phenylaza-18-crown-6 ether, respectively. Probes 1 and 2 allow the detection of K+ in the presence of Na+ in water by fluorescence enhancement (2.2 for 1 at 2000mm K+ and 2.5 for 2 at 160mm K+). Fluorescence lifetime measurements in the absence and presence of K+ revealed bi-exponential decay kinetics with similar lifetimes, however with different proportions changing the averaged fluorescence decay times ((f(av))). For 1 a decrease of (f(av)) from 12.4 to 9.3ns and for 2 an increase from 17.8 to 21.8ns was observed. Variation of the substituent in ortho position of the aniline unit of the N-phenylaza-18-crown-6 host permits the modulation of the K-d value for a certain K+ concentration. For example, substitution of H in 1 by the isopropoxy group (2) decreased the K-d value from >300mm to 10mm. 2 was chosen for studying the efflux of K+ from human red blood cells (RBC). Upon addition of the Ca2+ ionophor ionomycin to a RBC suspension in a buffer containing Ca2+, the fluorescence of 2 slightly rose within 10min, however, after 120min a significant increase was observed.},
  language  = {en}
}
@article{GhoshCherstvyMetzler2014,
  author    = {Ghosh, Surya K. and Cherstvy, Andrey G. and Metzler, Ralf},
  title     = {Non-universal tracer diffusion in crowded media of non-inert obstacles},
  series = {Physical Chemistry Chemical Physics},
  volume    = {3},
  journal   = {Physical Chemistry Chemical Physics},
  number    = {17},
  editor    = {Metzler, Ralf},
  publisher = {The Royal Society of Chemistry},
  address   = {Cambridge},
  issn      = {1463-9076},
  pages     = {1847 -- 1858},
  year      = {2014},
  abstract  = {We study the diffusion of a tracer particle, which moves in continuum space between a lattice of excluded volume, immobile non-inert obstacles. In particular, we analyse how the strength of the tracer-obstacle interactions and the volume occupancy of the crowders alter the diffusive motion of the tracer. From the details of partitioning of the tracer diffusion modes between trapping states when bound to obstacles and bulk diffusion, we examine the degree of localisation of the tracer in the lattice of crowders. We study the properties of the tracer diffusion in terms of the ensemble and time averaged mean squared displacements, the trapping time distributions, the amplitude variation of the time averaged mean squared displacements, and the non-Gaussianity parameter of the diffusing tracer. We conclude that tracer-obstacle adsorption and binding triggers a transient anomalous diffusion. From a very narrow spread of recorded individual time averaged trajectories we exclude continuous type random walk processes as the underlying physical model of the tracer diffusion in our system. For moderate tracer-crowder attraction the motion is found to be fully ergodic, while at stronger attraction strength a transient disparity between ensemble and time averaged mean squared displacements occurs. We also put our results into perspective with findings from experimental single-particle tracking and simulations of the diffusion of tagged tracers in dense crowded suspensions. Our results have implications for the diffusion, transport, and spreading of chemical components in highly crowded environments inside living cells and other structured liquids.},
  language  = {en}
}
@article{ShinCherstvyMetzler2014,
  author    = {Shin, Jaeoh and Cherstvy, Andrey G. and Metzler, Ralf},
  title     = {Kinetics of polymer looping with macromolecular crowding: effects of volume fraction and crowder size},
  series = {Soft Matter},
  journal   = {Soft Matter},
  editor    = {Metzler, Ralf},
  publisher = {The Royal Society of Chemistry},
  address   = {Cambridge},
  issn      = {1744-683X},
  pages     = {472 -- 488},
  year      = {2014},
  abstract  = {The looping of polymers such as DNA is a fundamental process in the molecular biology of living cells, whose interior is characterised by a high degree of molecular crowding. We here investigate in detail the looping dynamics of flexible polymer chains in the presence of different degrees of crowding. From the analysis of the looping-unlooping rates and the looping probabilities of the chain ends we show that the presence of small crowders typically slows down the chain dynamics but larger crowders may in fact facilitate the looping. We rationalise these non-trivial and often counterintuitive effects of the crowder size on the looping kinetics in terms of an effective solution viscosity and standard excluded volume. It is shown that for small crowders the effect of an increased viscosity dominates, while for big crowders we argue that confinement effects (caging) prevail. The tradeoff between both trends can thus result in the impediment or facilitation of polymer looping, depending on the crowder size. We also examine how the crowding volume fraction, chain length, and the attraction strength of the contact groups of the polymer chain affect the looping kinetics and hairpin formation dynamics. Our results are relevant for DNA looping in the absence and presence of protein mediation, DNA hairpin formation, RNA folding, and the folding of polypeptide chains under biologically relevant high-crowding conditions.},
  language  = {en}
}
@article{JeonChechkinMetzler2014,
  author    = {Jeon, Jae-Hyung and Chechkin, Aleksei V. and Metzler, Ralf},
  title     = {Scaled Brownian motion: a paradoxical process with a time dependent diffusivity for the description of anomalous diffusion},
  series = {Physical chemistry, chemical physics : PCCP},
  volume    = {30},
  journal   = {Physical chemistry, chemical physics : PCCP},
  number    = {16},
  publisher = {The Royal Society of Chemistry},
  address   = {Cambridge},
  doi       = {10.1039/C4CP02019G},
  pages     = {15811 -- 15817},
  year      = {2014},
  abstract  = {Anomalous diffusion is frequently described by scaled Brownian motion (SBM){,} a Gaussian process with a power-law time dependent diffusion coefficient. Its mean squared displacement is ?x2(t)? [similar{,} equals] 2K(t)t with K(t) [similar{,} equals] t[small alpha]-1 for 0 < [small alpha] < 2. SBM may provide a seemingly adequate description in the case of unbounded diffusion{,} for which its probability density function coincides with that of fractional Brownian motion. Here we show that free SBM is weakly non-ergodic but does not exhibit a significant amplitude scatter of the time averaged mean squared displacement. More severely{,} we demonstrate that under confinement{,} the dynamics encoded by SBM is fundamentally different from both fractional Brownian motion and continuous time random walks. SBM is highly non-stationary and cannot provide a physical description for particles in a thermalised stationary system. Our findings have direct impact on the modelling of single particle tracking experiments{,} in particular{,} under confinement inside cellular compartments or when optical tweezers tracking methods are used.},
  language  = {en}
}
@article{CherstvyChechkinMetzler2014,
  author    = {Cherstvy, Andrey G. and Chechkin, Aleksei V. and Metzler, Ralf},
  title     = {Particle invasion, survival, and non-ergodicity in 2D diffusion processes with space-dependent diffusivity},
  series = {Soft matter},
  volume    = {2014},
  journal   = {Soft matter},
  number    = {10},
  publisher = {Royal Society of Chemistry},
  issn      = {2046-2069},
  doi       = {10.1039/c3sm52846d},
  pages     = {1591 -- 1601},
  year      = {2014},
  abstract  = {We study the thermal Markovian diffusion of tracer particles in a 2D medium with spatially varying diffusivity D(r), mimicking recently measured, heterogeneous maps of the apparent diffusion coefficient in biological cells. For this heterogeneous diffusion process (HDP) we analyse the mean squared displacement (MSD) of the tracer particles, the time averaged MSD, the spatial probability density function, and the first passage time dynamics from the cell boundary to the nucleus. Moreover we examine the non-ergodic properties of this process which are important for the correct physical interpretation of time averages of observables obtained from single particle tracking experiments. From extensive computer simulations of the 2D stochastic Langevin equation we present an in-depth study of this HDP. In particular, we find that the MSDs along the radial and azimuthal directions in a circular domain obey anomalous and Brownian scaling, respectively. We demonstrate that the time averaged MSD stays linear as a function of the lag time and the system thus reveals a weak ergodicity breaking. Our results will enable one to rationalise the diffusive motion of larger tracer particles such as viruses or submicron beads in biological cells.},
  language  = {en}
}