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Author:Moisio, Jaakko
Title:Driven translocation of a polymer through a narrow pore in dilute solvent
Polymeerin ajettu translokaatio kapean huokosen läpi laimeassa liuoksessa
Publication type:Master's thesis
Publication year:2014
Pages:viii + 59      Language:   eng
Department/School:Perustieteiden korkeakoulu
Main subject:Laskennallinen tekniikka   (S-114)
Supervisor:Kaski, Kimmo
Instructor:Linna, Riku
Electronic version URL: http://urn.fi/URN:NBN:fi:aalto-201404101661
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Electronic archive copy is available via Aalto Thesis Database.
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Location:P1 Ark Aalto  607   | Archive
Keywords:polymers
driven translocation
computational science
computational physics
stochastic rotation dynamics
molecular dynamics
polymeeri
ajettu translokaatio
laskennallinen tiede
laskennallinen fysiikka
stokastinen rotaatiodynamiikka
molekyylidynamiikka
Abstract (eng): In this work driven translocation of a polymer through a narrow pore in dilute solvent is studied using computational methods.
Stochastic rotation dynamics (SRD) is used for simulating the fluid dynamics and molecular dynamics (MD) for simulating the polymer.
These methods were implemented in a parallel hybrid algorithm.
The results of the simulations are compared to previous theoretical and computational studies.

Scaling of the translocation time tau alpha NalphaF is found for polymers immersed in either good or bad solvent up to the length of 1600 monomers.
The simulations are repeated both with and without hydrodynamic interactions, and the scaling is observed for both cases.
The scaling is observed for a wide range of driving forces in good solvent, but only for small forces in bad solvent.

By studying the evolution of radius of gyration and local straightening during the translocation process, it is shown that in good solvent polymer translocation is a strongly out-of-equilibrium process.
On the cis side the straightening of the polymer is observed as tension propagates through the polymer backbone.
On the trans side monomers crowd near the pore exit as monomers leave the pore faster than the polymer segment on the trans side relaxes into equilibrium.
The out-of-equilibrium effects are more perceptible when hydrodynamic interactions are removed.
In bad solvent the polymer maintains its globulous equilibrium conformation during the whole translocation process.
Abstract (fin): Tässä työssä tutkitaan laimeassa liuoksessa olevan polymeerin ajettua translokaatiota kapean huokosen läpi laskennallisin menetelmin.
Simulaatiot toteutetaan rinnakkaistetulla hybridialgoritmilla, jossa nestedynamiikka toteutetaan käyttäen stokastista rotaatiodynamiikkaa (SRD) ja polymeerin itsensä simulointi tapahtuu molekyylidynamiikan (MD) menetelmiä käyttäen.
Simulaatioiden tuloksia verrataan aiheesta aiemmin esitettyihin teoreettisiin ja laskennallisiin tuloksiin.

Translokaatioaika noudattaa skaalausta tau alfa NalfaF sekä hyvässä että huonossa liuoksessa 1600 monomeerin pituuteen asti.
Simulaatiot toistetaan sekä hydrodynaamisten vuorovaikutusten kanssa että ilman niitä.
Skaalaus havaitaan molemmissa tapauksissa.
Hyvän liuoksen tapauksessa skaalaus havaitaan laajalla ajavan voiman vaihteluvälillä.
Huonossa liuoksessa skaalaus havaitaan vain pienillä voimilla.

Transkolaatio osoitetaan voimakkaaksi epätasapainoprosessiksi tutkimalla gyraatiosäteen muutosta ja polymeerin paikallista suoristumista translokaatioprosessin aikana.
Cis-puolella polymeeri suoristuu jännityksen levitessä pitkin polymeeria.
Trans-puolella havaitaan huokosen suun tukkeutumista, kun huokosesta poistuu monomeereja nopeammin kuin trans-puolella oleva polymeerisegmentti ehtii relaksoitua tasapainoon.
Epätasapaino on selvempää simulaatioissa, jotka ajetaan ilman hydrodynaamisia vuorovaikutuksia.
Huonossa liuoksessa polymeeri säilyttää pallomaisen tasapainomuotonsa koko translokaatioprosessin ajan.
ED:2014-04-04
INSSI record number: 48821
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