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Author:Suhonen, Pauli
Title:Langevin Dynamics Study of the Effects of cis and trans Side Polymer Segments on Translocation
Langevin dynamiikka tutkimus polymeerin cis ja trans puolisten osien vaikutuksesta translokaatioon
Publication type:Master's thesis
Publication year:2014
Pages:viii + 68      Language:   eng
Department/School:Lääketieteellisen tekniikan ja laskennallisen tieteen laitos
Main subject:Biologinen tekniikka   (F3013)
Supervisor:Kaski, Kimmo
Instructor:Linna, Riku
Electronic version URL: http://urn.fi/URN:NBN:fi:aalto-201406262252
OEVS:
Electronic archive copy is available via Aalto Thesis Database.
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Location:P1 Ark Aalto  1620   | Archive
Keywords:polymer
translocation
cell biology
sequencing
Langevin dynamics
polymeeri
translokaatio
DNA
solubiologia
sekvensointi
Langevin-dynamiikka
Abstract (eng):Polymer translocation through a pore in a membrane is an essential process in cellular biophysics.
It is important in understanding both nucleic acid and protein transportation between different cellular compartments.
In addition, DNA translocation has a potential technological application in the field of DNA sequencing.
In this thesis we study the dynamics of driven polymer translocation computationally by using Langevin dynamics simulations.
We verify that the trans side segment of the translocating polymer is strongly out of equilibrium and packed near the pore entrance.
In contrast to common belief, we show that the effect of the trans side on scaling relations diminishes in the regime of high driving forces.
We also show that collision-based local effects near the pore entrance can significantly alter the dynamics of the translocation process.
These effects are found to depend on multiple factors such as the driving force, polymer length, and the pore model.
Finally, we study how the cis side polymer segment dominates the dynamics of the translocation process.
We extract by far the most accurate tension propagation plots to date from our simulations.
With these plots we demonstrate the dominance of the initial conformation of the translocating polymer to the overall process.
We also show how tension propagation is connected to the translocation times in a simple way.
Abstract (fin):Polymeeritranslokaatio kalvossa olevan kanavan läpi on olennainen prosessi solunsisäisessä biofysiikassa.
Prosessin tutkiminen on tärkeää sekä nukleiinihappojen että proteiinien solunsisäisen kuljetuksen ymmärtämiseksi.
Lisäksi DNA:n translokaatiolle on löydetty tarpeellinen teknologinen sovellus DNA:n sekvensointiin liittyen.
Tässä diplomityössä tutkimme ajetun translokaation dynamiikkaa Langevin-dynamiikka simulaatioiden avulla.
Vahvistamme tuloksen, että polymeerin trans-puolinen osa on huomattavasti epätasapainossa ja pakkautuneena kanavan aukon lähellä.
Vastoin yleistä käsitystä osoitamme, että trans-puolen vaikutus skaalaukseen katoaa riittävän suurilla ajavilla voimilla.
Näytämme myös, että lokaalit törmäysefektit kanavan aukon suulla voivat huomattavasti muuttaa translokaatioprosessin dynamiikkaa.
Näiden efektien huomataan riippuvan monista tekijöistä kuten ajavasta voimasta, polymeerin pituudesta sekä kanavan mallista.
Lopuksi tutkimme polymeerin cis-puolisen osan dominoivaa vaikutusta translokaation dynamiikkaan.
Tarkastelemme simulaatioiden pohjalta jännityksen leviämistä tarkemmin kuin mihin aiemmin on pystytty.
Tarkastelun pohjalta havainnollistamme, kuinka tärkeä polymeerin konformaatio translokaation alussa on koko prosessille.
Näytämme myös kuinka jännityksen leviäminen kytkeytyy translokaatioaikoihin yksinkertaisella tavalla.
ED:2014-08-03
INSSI record number: 49415
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