Noise driven translocation of short polymers in crowded solutions

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Abstract

In this work we study the noise induced effects on the dynamics ofshort polymers crossing a potential barrier, in the presence of a metastable state.An improved version of the Rouse model for a flexible polymer has been adoptedto mimic the molecular dynamics by both taking into account the interactionsbetween adjacent monomers and introducing a Lennard-Jones potential betweenall beads. A bending recoil torque has also been included in our model. Thepolymer dynamics is simulated in a two-dimensional domain by numericallysolving the Langevin equations of motion with a Gaussian uncorrelated noise.We find a non-monotonic behavior of the mean first-passage time and the mostprobable translocation time of the polymer center of inertia as a function of thepolymer length at low noise intensity. We show how thermal fluctuations influencethe motion of short polymers, by inducing two different regimes of translocationin the molecule transport dynamics. In this context, the role played by the lengthof the molecule in the translocation time is investigated.
Lingua originaleEnglish
Numero di pagine10
RivistaJournal of Statistical Mechanics: Theory and Experiment
VolumeP01011
Stato di pubblicazionePublished - 2009

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Translocation
Polymers
polymers
Polymer Dynamics
Molecules
Lennard-Jones Potential
Mean First Passage Time
Metastable States
Langevin Equation
Gaussian Noise
Molecular Dynamics
Inertia
Torque
Lennard-Jones potential
Equations of Motion
noise intensity
Adjacent
random noise
beads
metastable state

All Science Journal Classification (ASJC) codes

  • Statistical and Nonlinear Physics
  • Statistics and Probability
  • Statistics, Probability and Uncertainty

Cita questo

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title = "Noise driven translocation of short polymers in crowded solutions",
abstract = "In this work we study the noise induced effects on the dynamics ofshort polymers crossing a potential barrier, in the presence of a metastable state.An improved version of the Rouse model for a flexible polymer has been adoptedto mimic the molecular dynamics by both taking into account the interactionsbetween adjacent monomers and introducing a Lennard-Jones potential betweenall beads. A bending recoil torque has also been included in our model. Thepolymer dynamics is simulated in a two-dimensional domain by numericallysolving the Langevin equations of motion with a Gaussian uncorrelated noise.We find a non-monotonic behavior of the mean first-passage time and the mostprobable translocation time of the polymer center of inertia as a function of thepolymer length at low noise intensity. We show how thermal fluctuations influencethe motion of short polymers, by inducing two different regimes of translocationin the molecule transport dynamics. In this context, the role played by the lengthof the molecule in the translocation time is investigated.",
keywords = "Brownian Motion, RNA, bio-polymers) (theory), dynamics (theory), mechanical properties (DNA, membranes",
author = "Alessandro Fiasconaro and Nicola Pizzolato and Bernardo Spagnolo and Alessandro Fiasconaro",
year = "2009",
language = "English",
volume = "P01011",
journal = "Journal of Statistical Mechanics: Theory and Experiment",
issn = "1742-5468",
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TY - JOUR

T1 - Noise driven translocation of short polymers in crowded solutions

AU - Fiasconaro, Alessandro

AU - Pizzolato, Nicola

AU - Spagnolo, Bernardo

AU - Fiasconaro, Alessandro

PY - 2009

Y1 - 2009

N2 - In this work we study the noise induced effects on the dynamics ofshort polymers crossing a potential barrier, in the presence of a metastable state.An improved version of the Rouse model for a flexible polymer has been adoptedto mimic the molecular dynamics by both taking into account the interactionsbetween adjacent monomers and introducing a Lennard-Jones potential betweenall beads. A bending recoil torque has also been included in our model. Thepolymer dynamics is simulated in a two-dimensional domain by numericallysolving the Langevin equations of motion with a Gaussian uncorrelated noise.We find a non-monotonic behavior of the mean first-passage time and the mostprobable translocation time of the polymer center of inertia as a function of thepolymer length at low noise intensity. We show how thermal fluctuations influencethe motion of short polymers, by inducing two different regimes of translocationin the molecule transport dynamics. In this context, the role played by the lengthof the molecule in the translocation time is investigated.

AB - In this work we study the noise induced effects on the dynamics ofshort polymers crossing a potential barrier, in the presence of a metastable state.An improved version of the Rouse model for a flexible polymer has been adoptedto mimic the molecular dynamics by both taking into account the interactionsbetween adjacent monomers and introducing a Lennard-Jones potential betweenall beads. A bending recoil torque has also been included in our model. Thepolymer dynamics is simulated in a two-dimensional domain by numericallysolving the Langevin equations of motion with a Gaussian uncorrelated noise.We find a non-monotonic behavior of the mean first-passage time and the mostprobable translocation time of the polymer center of inertia as a function of thepolymer length at low noise intensity. We show how thermal fluctuations influencethe motion of short polymers, by inducing two different regimes of translocationin the molecule transport dynamics. In this context, the role played by the lengthof the molecule in the translocation time is investigated.

KW - Brownian Motion

KW - RNA

KW - bio-polymers) (theory)

KW - dynamics (theory)

KW - mechanical properties (DNA

KW - membranes

UR - http://hdl.handle.net/10447/46773

M3 - Article

VL - P01011

JO - Journal of Statistical Mechanics: Theory and Experiment

JF - Journal of Statistical Mechanics: Theory and Experiment

SN - 1742-5468

ER -