Zobrazeno 1 - 10
of 68
pro vyhledávání: '"Linna, R. P."'
Publikováno v:
Phys. Rev. E 96, 062401 (2017)
Motivated by identifying the origin of the bias dependence of tension propagation we investigate methods for measuring tension propagation quantitatively in computer simulations of driven polymer translocation. Here the motion of flexible polymer cha
Externí odkaz:
http://arxiv.org/abs/1707.06663
Autor:
Suhonen, P. M., Linna, R. P.
Publikováno v:
Phys. Rev. E 93, 012406 (2016)
Polymer translocation through a nanometer-scale pore assisted by chaperones binding to the polymer is a process encountered in vivo for proteins. Studying the relevant models by computer simulations is computationally demanding. Accordingly, previous
Externí odkaz:
http://arxiv.org/abs/1510.05542
Autor:
Piili, J., Linna, R. P.
Publikováno v:
Phys. Rev. E 92, 062715 (2015)
We examine the ejection of an initially strongly confined flexible polymer from a spherical capsid through a nanoscale pore. We use molecular dynamics for unprecedentedly high initial monomer densities. We show that the time for an individual monomer
Externí odkaz:
http://arxiv.org/abs/1504.08158
Publikováno v:
Phys. Rev. E 90, 042702 (2014)
While the characteristics of the driven translocation for asymptotically long polymers are well understood, this is not the case for finite-sized polymers, which are relevant for real-world experiments and simulation studies. Most notably, the behavi
Externí odkaz:
http://arxiv.org/abs/1405.0902
Publikováno v:
Physical Review E 89, 052702 (2014)
Polymer ejection from a capsid through a nanoscale pore is an important biological process with relevance to modern biotechnology. Here, we study generic capsid ejection using Langevin dynamics. We show that even when the ejection takes place within
Externí odkaz:
http://arxiv.org/abs/1309.1355
Publikováno v:
Phys. Rev. E 86, 031107 (2012)
We perform classical non-equilibrium molecular dynamics simulations to calculate heat flow through a microscopic junction connecting two larger reservoirs. In contrast to earlier works, we also include the reservoirs in the simulated region to study
Externí odkaz:
http://arxiv.org/abs/1202.0680
Autor:
Linna, R. P., Kaski, K.
Publikováno v:
Physical Review E, Vol. 85, 041910 (2012)
We present event distributions for the polymer translocation obtained by extensive Langevin dynamics simulations. Such distributions have not been reported previously and they provide new understanding of the stochastic characteristics of the process
Externí odkaz:
http://arxiv.org/abs/1112.5091
We present a numerical study of forced polymer translocation by using two separate pore models. Both of them have been extensively used in previous forced translocation studies. We show that variations in the pore model affect the forced translocatio
Externí odkaz:
http://arxiv.org/abs/1008.3616
Publikováno v:
EPL 85 58006 (2009)
We present results from our simulations of biopolymer translocation in a solvent which explain the main experimental findings. The forced translocation can be described by simple force balance arguments for the relevant range of pore potentials in ex
Externí odkaz:
http://arxiv.org/abs/0905.1014
In forced polymer translocation, the average translocation time, $\tau$, scales with respect to pore force, $f$, and polymer length, $N$, as $\tau \sim f^{-1} N^{\beta}$. We demonstrate that an artifact in Metropolis Monte Carlo method resulting in b
Externí odkaz:
http://arxiv.org/abs/0806.3178