10028
2016
2016
eng
18
article
IOP Publ.
London
Deutsche Physikalische Gesellschaft
1
--
2016-08-18
--
Critical adsorption of polyelectrolytes onto planar and convex highly charged surfaces
We study the adsorption–desorption transition of polyelectrolyte chains onto planar, cylindrical and spherical surfaces with arbitrarily high surface charge densities by massive Monte Carlo computer simulations. We examine in detail how the well known scaling relations for the threshold transition—demarcating the adsorbed and desorbed domains of a polyelectrolyte near weakly charged surfaces—are altered for highly charged interfaces. In virtue of high surface potentials and large surface charge densities, the Debye–Hückel approximation is often not feasible and the nonlinear Poisson–Boltzmann approach should be implemented. At low salt conditions, for instance, the electrostatic potential from the nonlinear Poisson–Boltzmann equation is smaller than the Debye–Hückel result, such that the required critical surface charge density for polyelectrolyte adsorption σc increases. The nonlinear relation between the surface charge density and electrostatic potential leads to a sharply increasing critical surface charge density with growing ionic strength, imposing an additional limit to the critical salt concentration above which no polyelectrolyte adsorption occurs at all. We contrast our simulations findings with the known scaling results for weak critical polyelectrolyte adsorption onto oppositely charged surfaces for the three standard geometries. Finally, we discuss some applications of our results for some physical–chemical and biophysical systems.
New journal of physics : the open-access journal for physics
the nonlinear Poisson–Boltzmann approach
10.1088/1367-2630/18/8/083037
1367-2630
Universität Potsdam, Publikationsfonds
PA 2016_33
1390.30
online registration
083037
<a href="http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-100295">Zweitveröffentlichung in der Schriftenreihe Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe ; 292</a>
Sidney J. de Carvalho
Ralf Metzler
Andrey G. Cherstvy
eng
uncontrolled
polyelectrolyte adsorption
eng
uncontrolled
electrostatic interactions
eng
uncontrolled
critical phenomena
eng
uncontrolled
Debye screening
Physik
Institut für Physik und Astronomie
Referiert
Publikationsfonds der Universität Potsdam
Open Access
Universität Potsdam
10029
2016
2016
eng
17
postprint
1
--
2016-08-18
--
Critical adsorption of polyelectrolytes onto planar and convex highly charged surfaces
We study the adsorption–desorption transition of polyelectrolyte chains onto planar, cylindrical and spherical surfaces with arbitrarily high surface charge densities by massive Monte Carlo computer simulations. We examine in detail how the well known scaling relations for the threshold transition—demarcating the adsorbed and desorbed domains of a polyelectrolyte near weakly charged surfaces—are altered for highly charged interfaces. In virtue of high surface potentials and large surface charge densities, the Debye–Hückel approximation is often not feasible and the nonlinear Poisson–Boltzmann approach should be implemented. At low salt conditions, for instance, the electrostatic potential from the nonlinear Poisson–Boltzmann equation is smaller than the Debye–Hückel result, such that the required critical surface charge density for polyelectrolyte adsorption σc increases. The nonlinear relation between the surface charge density and electrostatic potential leads to a sharply increasing critical surface charge density with growing ionic strength, imposing an additional limit to the critical salt concentration above which no polyelectrolyte adsorption occurs at all. We contrast our simulations findings with the known scaling results for weak critical polyelectrolyte adsorption onto oppositely charged surfaces for the three standard geometries. Finally, we discuss some applications of our results for some physical–chemical and biophysical systems.
the nonlinear Poisson–Boltzmann approach
urn:nbn:de:kobv:517-opus4-100295
online registration
New journal of physics 18 (2016). - DOI: 10.1088/1367-2630/18/8/083037
PA 2016_33
Universität Potsdam, Publikationsfonds
1392
<a href="http://publishup.uni-potsdam.de/opus4-ubp/frontdoor/index/index/docId/10028">Bibliographieeintrag der Originalveröffentlichung/Quelle</a>
Sidney J. de Carvalho
Ralf Metzler
Andrey G. Cherstvy
Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
292
eng
uncontrolled
polyelectrolyte adsorption
eng
uncontrolled
electrostatic interactions
eng
uncontrolled
critical phenomena
eng
uncontrolled
Debye screening
Physik
open_access
Institut für Physik und Astronomie
Referiert
Open Access
Universität Potsdam
https://publishup.uni-potsdam.de/opus4-ubp/files/10029/pmnr292_online.pdf
35261
2013
2013
eng
8
1
8
article
PLoS
San Fransisco
1
--
--
--
In vivo facilitated diffusion model
Under dilute in vitro conditions transcription factors rapidly locate their target sequence on DNA by using the facilitated diffusion mechanism. However, whether this strategy of alternating between three-dimensional bulk diffusion and one-dimensional sliding along the DNA contour is still beneficial in the crowded interior of cells is highly disputed. Here we use a simple model for the bacterial genome inside the cell and present a semi-analytical model for the in vivo target search of transcription factors within the facilitated diffusion framework. Without having to resort to extensive simulations we determine the mean search time of a lac repressor in a living E. coli cell by including parameters deduced from experimental measurements. The results agree very well with experimental findings, and thus the facilitated diffusion picture emerges as a quantitative approach to gene regulation in living bacteria cells. Furthermore we see that the search time is not very sensitive to the parameters characterizing the DNA configuration and that the cell seems to operate very close to optimal conditions for target localization. Local searches as implied by the colocalization mechanism are only found to mildly accelerate the mean search time within our model.
PLoS one
10.1371/journal.pone.0053956
1932-6203 (print)
wos:2011-2013
e53956
WOS:000313872800019
Metzler, R (reprint author), Univ Potsdam, Inst Phys & Astron, Potsdam, Germany., rmetzler@uni-potsdam.de
Academy of Finland (FiDiPro scheme); German Federal Ministry for
Education and Research
Maximilian Bauer
Ralf Metzler
Institut für Physik und Astronomie
Referiert
Open Access
35268
2013
2013
eng
5
2
110
article
American Physical Society
College Park
1
--
--
--
Finite-Time effects and ultraweak ergodicity breaking in superdiffusive dynamics
We study the ergodic properties of superdiffusive, spatiotemporally coupled Levy walk processes. For trajectories of finite duration, we reveal a distinct scatter of the scaling exponents of the time averaged mean squared displacement (delta x(2)) over bar around the ensemble value 3 - alpha (1 < alpha < 2) ranging from ballistic motion to subdiffusion, in strong contrast to the behavior of subdiffusive processes. In addition we find a significant dependence of the average of (delta x(2)) over bar over an ensemble of trajectories as a function of the finite measurement time. This so-called finite-time amplitude depression and the scatter of the scaling exponent is vital in the quantitative evaluation of superdiffusive processes. Comparing the long time average of the second moment with the ensemble mean squared displacement, these only differ by a constant factor, an ultraweak ergodicity breaking.
Physical review letters
10.1103/PhysRevLett.110.020603
0031-9007 (print)
wos:2011-2013
020603
WOS:000313421800002
Godec, A (reprint author), Univ Potsdam, Inst Phys & Astron, D-14476 Potsdam, Germany., aljaz.godec@ki.si; rmetzler@uni-potsdam.de
Academy of Finland; German Federal Ministry for Science and Education
Aljaz Godec
Ralf Metzler
Institut für Physik und Astronomie
Referiert
35271
2013
2013
eng
5
2
110
article
American Physical Society
College Park
1
--
--
--
Aging effects and population splitting in single-particle trajectoryaverages
We study time averages of single particle trajectories in scale-free anomalous diffusion processes, in which the measurement starts at some time t(a) > 0 after initiation of the process at t = 0. Using aging renewal theory, we show that for such nonstationary processes a large class of observables are affected by a unique aging function, which is independent of boundary conditions or the external forces. Moreover, we discuss the implications of aging induced population splitting: with growing age ta of the process, an increasing fraction of particles remains motionless in a measurement of fixed duration. Consequences for single biomolecule tracking in live cells are discussed.
Physical review letters
10.1103/PhysRevLett.110.020602
0031-9007 (print)
1079-7114 (online)
wos:2011-2013
020602
WOS:000313336500003
Schulz, JHP (reprint author), Tech Univ Munich, Phys Dept T30G, D-85747 Garching, Germany.
CompInt graduate school; Academy of Finland (FiDiPro scheme); Israel
Science Foundation
Johannes H. P. Schulz
Eli Barkai
Ralf Metzler
Institut für Physik und Astronomie
Referiert
35203
2013
2013
eng
12
2
87
article
American Physical Society
College Park
1
--
--
--
Anomalous statistics of random relaxations in random environments
We comprehensively analyze the emergence of anomalous statistics in the context of the random relaxation ( RARE) model [Eliazar and Metzler, J. Chem. Phys. 137, 234106 ( 2012)], a recently introduced versatile model of random relaxations in random environments. The RARE model considers excitations scattered randomly across a metric space around a reaction center. The excitations react randomly with the center, the reaction rates depending on the excitations' distances from this center. Relaxation occurs upon the first reaction between an excitation and the center. Addressing both the relaxation time and the relaxation range, we explore when these random variables display anomalous statistics, namely, heavy tails at zero and at infinity that manifest, respectively, exceptionally high occurrence probabilities of very small and very large outliers. A cohesive set of closed-form analytic results is established, determining precisely when such anomalous statistics emerge.
Physical review : E, Statistical, nonlinear and soft matter physics
10.1103/PhysRevE.87.022141
1539-3755 (print)
1550-2376 (online)
wos:2011-2013
022141
WOS:000315380200001
Eliazar, I (reprint author), Holon Inst Technol, POB 305, IL-58102 Holon, Israel., eliazar@post.tau.ac.il; rmetzler@uni-potsdam.de
Academy of Finland within the FiDiPro scheme
Iddo Eliazar
Ralf Metzler
Institut für Physik und Astronomie
Referiert
37424
2014
2014
eng
32
article
IOP Publ. Ltd.
Bristol
1
--
--
--
Space-fractional Fokker-Planck equation and optimization of random search processes in the presence of an external bias
Based on the space-fractional Fokker-Planck equation with a delta-sink term, we study the efficiency of random search processes based on Levy flights with power-law distributed jump lengths in the presence of an external drift, for instance, an underwater current, an airflow, or simply the preference of the searcher based on prior experience. While Levy flights turn out to be efficient search processes when the target is upstream relative to the starting point, in the downstream scenario, regular Brownian motion turns out to be advantageous. This is caused by the occurrence of leapovers of Levy flights, due to which Levy flights typically overshoot a point or small interval. Studying the solution of the fractional Fokker-Planck equation, we establish criteria when the combination of the external stream and the initial distance between the starting point and the target favours Levy flights over the regular Brownian search. Contrary to the common belief that Levy flights with a Levy index alpha = 1 (i.e. Cauchy flights) are optimal for sparse targets, we find that the optimal value for alpha may range in the entire interval (1, 2) and explicitly include Brownian motion as the most efficient search strategy overall.
Journal of statistical mechanics: theory and experiment
10.1088/1742-5468/2014/11/P11031
1742-5468 (print)
wos:2014
P11031
WOS:000345747600031
Palyulin, VV (reprint author), Univ Potsdam, Inst Phys & Astron, D-14476 Potsdam, Germany., rmetzler@uni-potsdam.de
Deutsche Forschungsgemeinschaft [PA 2042/1-1]; Academy of Finland within
the FiDiPro scheme; DAAD
Vladimir V. Palyulin
Aleksei V. Chechkin
Ralf Metzler
eng
uncontrolled
driven diffusive systems (theory)
eng
uncontrolled
fluctuations (theory)
eng
uncontrolled
stochastic processes (theory)
eng
uncontrolled
diffusion
Institut für Physik und Astronomie
Referiert
37388
2014
2014
eng
14
16
article
IOP Publ. Ltd.
Bristol
1
--
--
--
Severe slowing-down and universality of the dynamics in disordered interacting many-body systems: ageing and ultraslow diffusion
Low-dimensional, many-body systems are often characterized by ultraslow dynamics. We study a labelled particle in a generic system of identical particles with hard-core interactions in a strongly disordered environment. The disorder is manifested through intermittent motion with scale-free sticking times at the single particle level. While for a non-interacting particle we find anomalous diffusion of the power-law form < x(2)(t)> similar or equal to t(alpha) of the mean squared displacement with 0 < alpha < 1, we demonstrate here that the combination of the disordered environment with the many-body interactions leads to an ultraslow, logarithmic dynamics < x(2)(t)> similar or equal to log(1/2)t with a universal 1/2 exponent. Even when a characteristic sticking time exists but the fluctuations of sticking times diverge we observe the mean squared displacement < x(2)(t)> similar or equal to t(gamma) with 0 < gamma < 1/2, that is slower than the famed Harris law < x(2)(t)> similar or equal to t(1/2) without disorder. We rationalize the results in terms of a subordination to a counting process, in which each transition is dominated by the forward waiting time of an ageing continuous time process.
New journal of physics : the open-access journal for physics
10.1088/1367-2630/16/11/113050
1367-2630 (print)
wos:2014
113050
WOS:000346764000002
Sanders, LP (reprint author), Lund Univ, Dept Astron & Theoret Phys, Lund, Sweden.
Swedish Research Council [2009-2924, 2012-4526]; Academy of Finland
(FiDiPro scheme)
Lloyd P. Sanders
Michael A. Lomholt
Ludvig Lizana
Karl Fogelmark
Ralf Metzler
Tobias Ambjoernsson
eng
uncontrolled
single-file diffusion
eng
uncontrolled
continuous time random walks
eng
uncontrolled
ageing
Institut für Physik und Astronomie
Referiert
Open Access
37932
2014
2014
eng
1
14
140
other
American Institute of Physics
Melville
1
--
--
--
Breathing dynamics based parameter sensitivity analysis of hetero-polymeric DNA
We study the parameter sensitivity of hetero-polymeric DNA within the purview of DNA breathing dynamics. The degree of correlation between the mean bubble size and the model parameters is estimated for this purpose for three different DNA sequences. The analysis leads us to a better understanding of the sequence dependent nature of the breathing dynamics of hetero-polymeric DNA. Out of the 14 model parameters for DNA stability in the statistical Poland-Scheraga approach, the hydrogen bond interaction epsilon(hb)(AT) for an AT base pair and the ring factor. turn out to be the most sensitive parameters. In addition, the stacking interaction epsilon(st)(TA-TA) for an TA-TA nearest neighbor pair of base-pairs is found to be the most sensitive one among all stacking interactions. Moreover, we also establish that the nature of stacking interaction has a deciding effect on the DNA breathing dynamics, not the number of times a particular stacking interaction appears in a sequence. We show that the sensitivity analysis can be used as an effective measure to guide a stochastic optimization technique to find the kinetic rate constants related to the dynamics as opposed to the case where the rate constants are measured using the conventional unbiased way of optimization.
The journal of chemical physics : bridges a gap between journals of physics and journals of chemistr
10.1063/1.4871297
0021-9606 (print)
1089-7690 (online)
wos:2014
149901
WOS:000334836600041
Chaudhury, P (reprint author), Univ Calcutta, Dept Chem, 92 A P C Rd, Kolkata 700009, India., rmetzler@uni-potsdam.de; skbanik@jcbose.ac.in; pinakc@rediffmail.com
Srijeeta Talukder
Shrabani Sen
Prantik Chakraborti
Ralf Metzler
Suman K. Banik
Pinaki Chaudhury
Institut für Physik und Astronomie
Referiert
37923
2014
2014
eng
5
4
89
article
American Physical Society
College Park
1
--
--
--
First-passage statistics for aging diffusion in systems with annealed and quenched disorder
Aging, the dependence of the dynamics of a physical process on the time t(a) since its original preparation, is observed in systems ranging from the motion of charge carriers in amorphous semiconductors over the blinking dynamics of quantum dots to the tracer dispersion in living biological cells. Here we study the effects of aging on one of the most fundamental properties of a stochastic process, the first-passage dynamics. We find that for an aging continuous time random walk process, the scaling exponent of the density of first-passage times changes twice as the aging progresses and reveals an intermediate scaling regime. The first-passage dynamics depends on t(a) differently for intermediate and strong aging. Similar crossovers are obtained for the first-passage dynamics for a confined and driven particle. Comparison to the motion of an aged particle in the quenched trap model with a bias shows excellent agreement with our analytical findings. Our results demonstrate how first-passage measurements can be used to unravel the age t(a) of a physical system.
Physical review : E, Statistical, nonlinear and soft matter physics
10.1103/PhysRevE.89.040101
24827169
1539-3755 (print)
1550-2376 (online)
wos:2014
040101
WOS:000339888000001
Krusemann, H (reprint author), Univ Potsdam, Inst Phys & Astron, D-14776 Potsdam Golm, Germany., rmetzler@uni-potsdam.de
Alexander von Humboldt Fellowship; Academy of Finland (FiDiPro scheme)
Henning Krüsemann
Aljaz Godec
Ralf Metzler
Institut für Physik und Astronomie
Referiert