131 research outputs found
Driven polymer translocation through nanopores: slow versus fast dynamics
We investigate the dynamics of polymer translocation through nanopores under
external driving by 3D Langevin Dynamics simulations, focusing on the scaling
of the average translocation time versus the length of the polymer,
. For slow translocation, i.e., under low driving force
and/or high friction, we find where
denotes the Flory exponent. In contrast, is observed for
fast translocation due to the highly deformed chain conformation on the trans
side, reflecting a pronounced non-equilibrium situation. The dependence of the
translocation time on the driving force is given by and
for slow and fast translocation, respectively. These
results clarify the controversy on the magnitude of the scaling exponent
for driven translocation.Comment: 6 pages, 7 figures, to appear in EPL (Europhysics Letters
Sequence dependence of DNA translocation through a nanopore
We investigate the dynamics of DNA translocation through a nanopore using 2D
Langevin dynamics simulations, focusing on the dependence of the translocation
dynamics on the details of DNA sequences. The DNA molecules studied in this
work are built from two types of bases and , which has been shown
previously to have different interactions with the pore. We study DNA with
repeating blocks for various values of , and find that the
translocation time depends strongly on the {\em block length} as well as
on the {\em orientation} of which base entering the pore first. Thus, we
demonstrate that the measurement of translocation dynamics of DNA through
nanopore can yield detailed information about its structure. We have also found
that the periodicity of the block sequences are contained in the periodicity of
the residence time of the individual nucleotides inside the pore.Comment: 4 pages, 4 figures, minor change
Minimum energy path for the nucleation of misfit dislocations in Ge/Si(001) heteroepitaxy
A possible mechanism for the formation of a 90{\deg} misfit dislocation at
the Ge/Si(001) interface through homogeneous nucleation is identified from
atomic scale calculations where a minimum energy path connecting the coherent
epitaxial state and a final state with a 90{\deg} misfit dislocation is found
using the nudged elastic band method. The initial path is generated using a
repulsive bias activation procedure in a model system including 75000 atoms.
The energy along the path exhibits two maxima in the energy. The first maximum
occurs as a 60{\deg} dislocation nucleates. The intermediate minimum
corresponds to an extended 60{\deg} dislocation. The subsequent energy maximum
occurs as a second 60{\deg} dislocation nucleates in a complementary, mirror
glide plane, simultaneously starting from the surface and from the first
60{\deg} dislocation. The activation energy of the nucleation of the second
dislocation is 30% lower than that of the first one showing that the formation
of the second 60{\deg} dislocation is aided by the presence of the first one.
The simulations represent a step towards unraveling the formation mechanism of
90{\deg} dislocations, an important issue in the design of growth procedures
for strain released Ge overlayers on Si(100) surfaces, and more generally
illustrate an approach that can be used to gain insight into the mechanism of
complex nucleation paths of extended defects in solids
Dynamics of DNA translocation through an attractive nanopore
We investigate the dynamics of single-stranded DNA translocation through a nanopore driven by an external force using Langevin dynamics simulations in two dimensions to study how the translocation dynamics depend on the details of the DNA sequences. We consider a coarse-grained model of DNA built from two bases A and C, having different base-pore interactions, e.g., a strong (weak) attractive force between the pore and the base A (C) inside the pore. From a series of studies on hetero-DNAs with repeat units AmCn, we find that the translocation time decreases exponentially as a function of the volume fraction fC of the base C. For longer A sequences with fC⩽0.5, the translocation time strongly depends on the orientation of DNA, namely which base enters the pore first. Our studies clearly demonstrate that for a DNA of certain length N with repeat units AmCn, the pattern exhibited by the waiting times of the individual bases and their periodicity can unambiguously determine the values of m, n, and N, respectively. Therefore, a prospective experimental realization of this phenomenon may lead to fast and efficient sequence detection.Peer reviewe
Polymer translocation through a nanopore under a pulling force
We investigate polymer translocation through a nanopore under a pulling force using Langevin dynamics simulations. We concentrate on the influence of the chain length N and the pulling force F on the translocation time τ. The distribution of τ is symmetric and narrow for strong F. We find that τ∼N2 and translocation velocity v∼N−1 for both moderate and strong F. For infinitely wide pores, three regimes are observed for τ as a function of F. With increasing F, τ is independent of F for weak F, and then τ∼F−2+ν−1 for moderate F, where ν is the Flory exponent, which finally crosses over to τ∼F−1 for strong force. For narrow pores, even for moderate force τ∼F−1. Finally, the waiting time, for monomer s and monomer s+1 to exit the pore, has a maximum for s close to the end of the chain, in contrast to the case where the polymer is driven by an external force within the pore.Peer reviewe
Heteropolymer translocation through nanopores
We investigate the translocation dynamics of heteropolymers driven through a
nanopore using a constant temperature Langevin thermostat. Specifically, we
consider heteropolymers consisting of two types of monomers labeled A and B,
which are distinguished by the magnitude of the driving force that they
experience inside the pore. From a series of studies on polymers with sequences
AnBn+m we identify both universal as well as sequence specific properties of
the translocating chains. We find that the scaling of the average translocation
time as a function of the chain length N remains unaffected by the
heterogeneity, while the residence time of each bead is a strong function of
the sequence for short repeat units. We further discover that for a symmetric
heteropolymer AnBn of fixed length, the pattern exhibited by the residence time
of the individual monomer has striking similarity with an interference pattern
for an optical grating with N/(2n) slits. These results are relevant for
designing nanopore based sequencing techniques.Comment: 13 Pages, 6 Figure
Electronic Noise of a Single Skyrmion
To enable the practical use of skyrmion-based devices, it is essential to
achieve a balance between energy efficiency and thermal stability, while also
ensuring reliable electrical detection against noise. Understanding how a
skyrmion interacts with material disorder and external perturbations is thus
essential. Here we investigate the electronic noise of a single skyrmion under
the influence of thermal fluctuations and spin currents in a magnetic thin
film. We detect the thermally induced noise with a 1/f signature in the strong
pinning regime but a random telegraph noise in the intermediate pinning regime.
Both the thermally dominated and current-induced telegraph-like signals are
detected in the weak pinning regime. Our results provide a comprehensive
electronic noise picture of a single skyrmion, demonstrating the potential of
noise fluctuation as a valuable tool for characterizing the pinning condition
of a skyrmion. These insights could also aid in the development of low-noise
and reliable skyrmion-based devices
Translocation Dynamics with Attractive Nanopore-Polymer Interactions
Using Langevin dynamics simulations, we investigate the influence of
polymer-pore interactions on the dynamics of biopolymer translocation through
nanopores. We find that an attractive interaction can significantly change the
translocation dynamics. This can be understood by examining the three
components of the total translocation time
corresponding to the initial filling of the pore, transfer of polymer from the
\textit{cis} side to the \textit{trans} side, and emptying of the pore,
respectively. We find that the dynamics for the last process of emptying of the
pore changes from non-activated to activated in nature as the strength of the
attractive interaction increases, and becomes the dominant
contribution to the total translocation time for strong attraction. This leads
to a new dependence of as a function of driving force and chain length.
Our results are in good agreement with recent experimental findings, and
provide a possible explanation for the different scaling behavior observed in
solid state nanopores {\it vs.} that for the natural -hemolysin
channel.Comment: 8 pages, 11 figure
Influence of polymer-pore interactions on translocation
We investigate the influence of polymer-pore interactions on the
translocation dynamics using Langevin dynamics simulations. An attractive
interaction can greatly improve translocation probability. At the same time, it
also increases translocation time slowly for weak attraction while exponential
dependence is observed for strong attraction. For fixed driving force and chain
length the histogram of translocation time has a transition from Gaussian
distribution to long-tailed distribution with increasing attraction. Under a
weak driving force and a strong attractive force, both the translocation time
and the residence time in the pore show a non-monotonic behavior as a function
of the chain length. Our simulations results are in good agreement with recent
experimental data.Comment: 4 pages, 5 figures, Submitted to Phys. Rev. Let
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