36426
2011
2011
eng
8
24
135
article
American Institute of Physics
Melville
1
--
--
--
First passage time distribution of chaperone driven polymer translocation through a nanopore homopolymer and heteropolymer cases
Combining the advection-diffusion equation approach with Monte Carlo simulations we study chaperone driven polymer translocation of a stiff polymer through a nanopore. We demonstrate that the probability density function of first passage times across the pore depends solely on the Peclet number, a dimensionless parameter comparing drift strength and diffusivity. Moreover it is shown that the characteristic exponent in the power-law dependence of the translocation time on the chain length, a function of the chaperone-polymer binding energy, the chaperone concentration, and the chain length, is also effectively determined by the Peclet number. We investigate the effect of the chaperone size on the translocation process. In particular, for large chaperone size, the translocation progress and the mean waiting time as function of the reaction coordinate exhibit pronounced sawtooth-shapes. The effects of a heterogeneous polymer sequence on the translocation dynamics is studied in terms of the translocation velocity, the probability distribution for the translocation progress, and the monomer waiting times. (C) 2011 American Institute of Physics.
The journal of chemical physics : bridges a gap between journals of physics and journals of chemistr
10.1063/1.3669427
0021-9606
wos:2011-2013
245102
WOS:000298640500053
Abdolvahab, RH (reprint author), Sharif Univ Technol, Dept Phys, POB 11155-9161, Tehran, Iran., abdolvahab@physics.sharif.edu
CompInt graduate school at TUM; Academy of Finland; Sharif University of
Technology
Rouhollah Haji Abdolvahab
Ralf Metzler
Mohammad Reza Ejtehadi
Institut für Physik und Astronomie
Referiert
36288
2012
2012
eng
8651
8658
8
33
8
article
Royal Society of Chemistry
Cambridge
1
--
--
--
Quantifying supercoiling-induced denaturation bubbles in DNA
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.
Soft matter
10.1039/c2sm26089a
1744-683X
wos:2011-2013
WOS:000307021300014
Metzler, R (reprint author), Tampere Univ Technol, Dept Phys, FI-33101 Tampere, Finland., rmetzler@uni-potsdam.de
Deutsche Forschungsgemeinschaft; Academy of Finland
Jozef Adamcik
Jae-Hyung Jeon
Konrad J. Karczewski
Ralf Metzler
Giovanni Dietler
Institut für Physik und Astronomie
Referiert
52266
2018
2018
eng
6
2
98
article
American Physical Society
College Park
1
--
2018-08-07
--
Ergodicity, rejuvenation, enhancement, and slow relaxation of diffusion in biased continuous-time random walks
Bias plays an important role in the enhancement of diffusion in periodic potentials. Using the continuous-time random walk in the presence of a bias, we report on an interesting phenomenon for the enhancement of diffusion by the start of the measurement in a random energy landscape. When the variance of the waiting time diverges, in contrast to the bias-free case, the dynamics with bias becomes superdiffusive. In the superdiffusive regime, we find a distinct initial ensemble dependence of the diffusivity. Moreover, the diffusivity can be increased by the aging time when the initial ensemble is not in equilibrium. We show that the time-averaged variance converges to the corresponding ensemble-averaged variance; i.e., ergodicity is preserved. However, trajectory-to-trajectory fluctuations of the time-averaged variance decay unexpectedly slowly. Our findings provide a rejuvenation phenomenon in the superdiffusive regime, that is, the diffusivity for a nonequilibrium initial ensemble gradually increases to that for an equilibrium ensemble when the start of the measurement is delayed.
Physical review : E, Statistical, nonlinear and soft matter physics
10.1103/PhysRevE.98.022105
30253516
2470-0045
2470-0053
wos:2018
022105
WOS:000441016100001
Akimoto, T (reprint author), Tokyo Univ Sci, Dept Phys, Noda, Chiba 2788510, Japan., takuma@rs.tus.ac.jp
JSPSMinistry of Education, Culture, Sports, Science and Technology, Japan (MEXT)Japan Society for the Promotion of Science [16KT0021]; DFGGerman Research Foundation (DFG) [ME 1535/6-1, ME 1535/7-1]; Foundation for Polish Science (Humboldt Polish Honorary Research Scholarship)
2021-10-18T07:56:14+00:00
sword
importub
filename=package.tar
af5864ed12895ae8946082892bb5cc7d
CC-BY - Namensnennung 4.0 International
Takuma Akimoto
Andrey G. Cherstvy
Ralf Metzler
Physik
Institut für Physik und Astronomie
Referiert
Import
Hybrid Open-Access
59212
2020
2020
eng
55
102
48
1
23
article
De Gruyter
Berlin ; Boston
1
2020-02-27
2020-02-27
--
Crossover dynamics from superdiffusion to subdiffusion
The Cattaneo or telegrapher's equation describes the crossover from initial ballistic to normal diffusion. Here we study and survey time-fractional generalisations of this equation that are shown to produce the crossover of the mean squared displacement from superdiffusion to subdiffusion. Conditional solutions are derived in terms of Fox H-functions and the dth-order moments as well as the diffusive flux of the different models are derived. Moreover, the concept of the distribution-like is proposed as an alternative to the probability density function.
Fractional calculus and applied analysis : an international journal for theory and applications
models and solutions
10.1515/fca-2020-0003
1311-0454
1314-2224
outputup:dataSource:Crossref:2020
WOS:000536393200003
Awad, Emad (corresponding author), Alexandria Univ, Dept Math, Fac Educ, Souter St,POB 21526, Alexandria, Egypt., emadawad78@alexu.edu.eg; rmetzler@uni-potsdam.de
Alexander von Humboldt Polish Honorary Research Scholarship from the; Foundation for Polish Science (Fundacja na rzecz Nauki Polskiej)
Awad, Emad
2023-05-15T10:55:35+00:00
sword
importub
filename=package.tar
aabdd21ca00e91ae31046590ad8097bb
2276545-1
1446869-4
false
true
Emad Awad
Ralf Metzler
eng
uncontrolled
Cattaneo equation
eng
uncontrolled
telegrapher's equation
eng
uncontrolled
crossover dynamics
eng
uncontrolled
fractional dynamic equations
eng
uncontrolled
anomalous diffusion
eng
uncontrolled
superdiffusion and
eng
uncontrolled
subdiffusion
eng
uncontrolled
Fox H-functions
Physik
Institut für Physik und Astronomie
Referiert
Import
Bronze Open-Access
61836
2022
2022
eng
29
20
55
article
IOP Publ. Ltd.
Bristol
1
2022-04-21
2022-04-21
--
Closed-form multi-dimensional solutions and asymptotic behaviours for subdiffusive processes with crossovers: II. Accelerating case
Anomalous diffusion with a power-law time dependence vertical bar R vertical bar(2)(t) similar or equal to t(alpha i) of the mean squared displacement occurs quite ubiquitously in numerous complex systems. Often, this anomalous diffusion is characterised by crossovers between regimes with different anomalous diffusion exponents alpha(i). Here we consider the case when such a crossover occurs from a first regime with alpha(1) to a second regime with alpha(2) such that alpha(2) > alpha(1), i.e., accelerating anomalous diffusion. A widely used framework to describe such crossovers in a one-dimensional setting is the bi-fractional diffusion equation of the so-called modified type, involving two time-fractional derivatives defined in the Riemann-Liouville sense. We here generalise this bi-fractional diffusion equation to higher dimensions and derive its multidimensional propagator (Green's function) for the general case when also a space fractional derivative is present, taking into consideration long-ranged jumps (Levy flights). We derive the asymptotic behaviours for this propagator in both the short- and long-time as well the short- and long-distance regimes. Finally, we also calculate the mean squared displacement, skewness and kurtosis in all dimensions, demonstrating that in the general case the non-Gaussian shape of the probability density function changes.
Journal of physics : A, Mathematical and theoretical
10.1088/1751-8121/ac5a90
1751-8113
1751-8121
outputup:dataSource:WoS:2022
205003
WOS:000787001200001
Metzler, R (corresponding author), Univ Potsdam, Inst Phys & Astron, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany., emadawad78@alexu.edu.eg; rmetzler@uni-potsdam.de
German Research Foundation (DFG) [ME 1535/12-1]; Foundation for Polish; Science (Fundacja na rzecz Nauki Polskiej, FNP) within an Alexander von; Humboldt Honorary Polish Research Scholarship
Metzler, Ralf
2023-12-13T08:24:19+00:00
sword
importub
filename=package.tar
056f6ff60fe3be093372d3babe840f94
209217-7
1363010-6
false
true
CC-BY - Namensnennung 4.0 International
Emad Awad
Ralf Metzler
eng
uncontrolled
multidimensional fractional diffusion equation
eng
uncontrolled
continuous time random
eng
uncontrolled
walks
eng
uncontrolled
crossover anomalous diffusion dynamics
eng
uncontrolled
non-Gaussian probability
eng
uncontrolled
density
Physik
Institut für Physik und Astronomie
Referiert
Import
Hybrid Open-Access
53898
2018
2018
eng
278
288
11
490
article
Elsevier
Amsterdam
1
2017-08-18
2017-08-18
--
Wealth distribution, Pareto law, and stretched exponential decay of money
We study by Monte Carlo simulations a kinetic exchange trading model for both fixed and distributed saving propensities of the agents and rationalize the person and wealth distributions. We show that the newly introduced wealth distribution – that may be more amenable in certain situations – features a different power-law exponent, particularly for distributed saving propensities of the agents. For open agent-based systems, we analyze the person and wealth distributions and find that the presence of trap agents alters their amplitude, leaving however the scaling exponents nearly unaffected. For an open system, we show that the total wealth – for different trap agent densities and saving propensities of the agents – decreases in time according to the classical Kohlrausch–Williams–Watts stretched exponential law. Interestingly, this decay does not depend on the trap agent density, but rather on saving propensities. The system relaxation for fixed and distributed saving schemes are found to be different.
Physica : europhysics journal ; A, Statistical mechanics and its applications
Computer simulations analysis of agent-based models
10.1016/j.physa.2017.08.017
0378-4371
1873-2119
wos:2018
WOS:000415912900024
Aydiner, E (reprint author), Istanbul Univ, Dept Phys, TR-34134 Istanbul, Turkey., ekrem.aydiner@istanbul.edu.tr
University of IstanbulIstanbul University [BEK-3201-55383]; University of Potsdam
2022-02-14T14:00:28+00:00
sword
importub
filename=package.tar
5c555bee70edaa657dcdc20b41b269f4
Aydiner, Ekrem
false
true
Ekrem Aydiner
Andrey G. Cherstvy
Ralf Metzler
eng
uncontrolled
Econophysics
eng
uncontrolled
Wealth and income distribution
eng
uncontrolled
Pareto law
eng
uncontrolled
Scaling exponents
Physik
Institut für Physik und Astronomie
Referiert
Import
49631
2019
2019
eng
4
5
92
article
Springer
New York
1
2019-05-20
2019-05-20
--
Money distribution in agent-based models with position-exchange dynamics
Wealth and income distributions are known to feature country-specific Pareto exponents for their long power-law tails. To propose a rationale for this, we introduce an agent-based dynamic model and use Monte Carlo simulations to unveil the wealth distributions in closed and open economical systems. The standard money-exchange scenario is supplemented with the position-exchange agent dynamics that vitally affects the Pareto law. Specifically, in closed systems with position-exchange dynamics the power law changes to an exponential shape, while for open systems with traps the Pareto law remains valid.
The European physical journal : B, Condensed matter and complex systems
the Pareto paradigm revisited
10.1140/epjb/e2019-90674-0
1434-6028
1434-6036
wos:2019
104
WOS:000468374500007
Aydiner, E (reprint author), Istanbul Univ, Dept Phys, TR-34134 Istanbul, Turkey., ekrem.aydiner@istanbul.edu.tr
Istanbul UniversityIstanbul University [BYP-2018-45662]; Deutsche Forschungsgemeinschaft (DFG)German Research Foundation (DFG) [ME 1535/6-1, ME 1535/7-1]; Foundation for Polish Science within an Alexander von Humboldt Polish Honorary Research Fellowship
2021-02-24T11:07:47+00:00
sword
importub
filename=package.tar
b80edbb01c783a15c9d740d72ce3ef68
Aydiner, Ekrem
false
true
Ekrem Aydiner
Andrey G. Cherstvy
Ralf Metzler
eng
uncontrolled
Statistical and Nonlinear Physics
Physik
Institut für Physik und Astronomie
Referiert
Import
34877
2013
2013
eng
11
11
1
7
66
other
AMER INST PHYSICS
MELVILLE
1
--
--
--
Electrostatic effects in living cells Reply
PHYSICS TODAY
0031-9228
1945-0699
wos:2011-2013
WOS:000327027700008
Barkai, E (reprint author), Bar Ilan Univ, Ramat Gan, Israel.
, rmetzler@uni-potsdam.de
Eli Barkai
Yuval Garini
Ralf Metzler
35732
2012
2012
eng
29
35
7
8
65
article
American Institute of Physics
Melville
1
--
--
--
Strange Kinetics of single molecules in living cells
Physics today
0031-9228
wos:2011-2013
WOS:000307614600020
Barkai, E (reprint author), Bar Ilan Univ, Ramat Gan, Israel.
Israel Science Foundation; Academy of Finland
Eli Barkai
Yuval Garini
Ralf Metzler
Institut für Physik und Astronomie
Referiert
38309
2014
2014
eng
6118
6128
11
13
16
article
Royal Society of Chemistry
Cambridge
1
--
--
--
Diffusion of finite-size particles in two-dimensional channels with random wall configurations
Diffusion of chemicals or tracer molecules through complex systems containing irregularly shaped channels is important in many applications. Most theoretical studies based on the famed Fick-Jacobs equation focus on the idealised case of infinitely small particles and reflecting boundaries. In this study we use numerical simulations to consider the transport of finite-size particles through asymmetrical two-dimensional channels. Additionally, we examine transient binding of the molecules to the channel walls by applying sticky boundary conditions. We consider an ensemble of particles diffusing in independent channels, which are characterised by common structural parameters. We compare our results for the long-time effective diffusion coefficient with a recent theoretical formula obtained by Dagdug and Pineda
Physical chemistry, chemical physics : a journal of European Chemical Societies
10.1039/c3cp55160a
24556939
1463-9076
1463-9084
wos:2014
WOS:000332474700029
Metzler, R (reprint author), Univ Potsdam, Inst Phys & Astron, D-14476 Potsdam, Germany., rmetzler@uni-potsdam.de
German Federal Ministry for Education and Research; Academy of Finland
within the FiDiPro scheme
Maximilian Bauer
Aljaz Godec
Ralf Metzler
Institut für Chemie
Referiert