21 research outputs found
Langevin Dynamics Simulations of Polymer Translocation through Nanopores
We investigate the dynamics of polymer translocation through a nanopore using two-dimensional Langevin dynamics simulations. In the absence of an external driving force, we consider a polymer which is initially placed in the middle of the pore and study the escape time Ļe required for the polymer to completely exit the pore on either side. The distribution of the escape times is wide and has a long tail. We find that Ļe scales with the chain length N as Ļeā¼N1+2Ī½, where Ī½ is the Flory exponent. For driven translocation, we concentrate on the influence of the friction coefficient Ī¾, the driving force E, and the length of the chain N on the translocation time Ļ, which is defined as the time duration between the first monomer entering the pore and the last monomer leaving the pore. For strong driving forces, the distribution of translocation times is symmetric and narrow without a long tail and Ļā¼Eā1. The influence of Ī¾ depends on the ratio between the driving and frictional forces. For intermediate Ī¾, we find a crossover scaling for Ļ with N from Ļā¼N2Ī½ for relatively short chains to Ļā¼N1+Ī½ for longer chains. However, for higher Ī¾, only Ļā¼N1+Ī½ is observed even for short chains, and there is no crossover behavior. This result can be explained by the fact that increasing Ī¾ increases the Rouse relaxation time of the chain, in which case even relatively short chains have no time to relax during translocation. Our results are in good agreement with previous simulations based on the fluctuating bond lattice model of polymers at intermediate friction values, but reveal additional features of dependency on friction.Peer reviewe
Multivariate multi-way analysis of multi-source data
Motivation: Analysis of variance (ANOVA)-type methods are the default tool for the analysis of data with multiple covariates. These tools have been generalized to the multivariate analysis of high-throughput biological datasets, where the main challenge is the problem of small sample size and high dimensionality. However, the existing multi-way analysis methods are not designed for the currently increasingly important experiments where data is obtained from multiple sources. Common examples of such settings include integrated analysis of metabolic and gene expression profiles, or metabolic profiles from several tissues in our case, in a controlled multi-way experimental setup where disease status, medical treatment, gender and time-series are usual covariates
Dynamics and Kinetic Roughening of Interfaces in Two-Dimensional Forced Wetting
We consider the dynamics and kinetic roughening of wetting fronts in the case
of forced wetting driven by a constant mass flux into a 2D disordered medium.
We employ a coarse-grained phase field model with local conservation of
density, which has been developed earlier for spontaneous imbibition driven by
a capillary forces. The forced flow creates interfaces that propagate at a
constant average velocity. We first derive a linearized equation of motion for
the interface fluctuations using projection methods. From this we extract a
time-independent crossover length , which separates two regimes of
dissipative behavior and governs the kinetic roughening of the interfaces by
giving an upper cutoff for the extent of the fluctuations. By numerically
integrating the phase field model, we find that the interfaces are superrough
with a roughness exponent of , a growth exponent of
, and as a function of the
velocity. These results are in good agreement with recent experiments on
Hele-Shaw cells. We also make a direct numerical comparison between the
solutions of the full phase field model and the corresponding linearized
interface equation. Good agreement is found in spatial correlations, while the
temporal correlations in the two models are somewhat different.Comment: 9 pages, 4 figures, submitted to Eur.Phys.J.
Driven polymer translocation through a nanopore: a manifestation of anomalous diffusion
We study the translocation dynamics of a polymer chain threaded through a
nanopore by an external force. By means of diverse methods (scaling arguments,
fractional calculus and Monte Carlo simulation) we show that the relevant
dynamic variable, the translocated number of segments , displays an {\em
anomalous} diffusive behavior even in the {\em presence} of an external force.
The anomalous dynamics of the translocation process is governed by the same
universal exponent , where is the Flory
exponent and - the surface exponent, which was established recently
for the case of non-driven polymer chain threading through a nanopore. A closed
analytic expression for the probability distribution function , which
follows from the relevant {\em fractional} Fokker - Planck equation, is derived
in terms of the polymer chain length and the applied drag force . It is
found that the average translocation time scales as . Also the corresponding time dependent
statistical moments, and reveal unambiguously the anomalous nature of the translocation
dynamics and permit direct measurement of in experiments. These
findings are tested and found to be in perfect agreement with extensive Monte
Carlo (MC) simulations.Comment: 6 pages, 4 figures, accepted to Europhys. Lett; some references were
supplemented; typos were correcte
Chaperone-assisted translocation of a polymer through a nanopore
Using Langevin dynamics simulations, we investigate the dynamics of
chaperone-assisted translocation of a flexible polymer through a nanopore. We
find that increasing the binding energy between the chaperone and
the chain and the chaperone concentration can greatly improve the
translocation probability. Particularly, with increasing the chaperone
concentration a maximum translocation probability is observed for weak binding.
For a fixed chaperone concentration, the histogram of translocation time
has a transition from long-tailed distribution to Gaussian distribution with
increasing . rapidly decreases and then almost saturates with
increasing binding energy for short chain, however, it has a minimum for longer
chains at lower chaperone concentration. We also show that has a minimum
as a function of the chaperone concentration. For different , a
nonuniversal dependence of on the chain length is also observed.
These results can be interpreted by characteristic entropic effects for
flexible polymers induced by either crowding effect from high chaperone
concentration or the intersegmental binding for the high binding energy.Comment: 10 pages, to appear in J. Am. Chem. So
The Potential and Challenges of Nanopore Sequencing
A nanopore-based device provides single-molecule detection and analytical capabilities that are achieved by electrophoretically driving molecules in solution through a nano-scale pore. The nanopore provides a highly confined space within which single nucleic acid polymers can be analyzed at high throughput by one of a variety of means, and the perfect processivity that can be enforced
in a narrow pore ensures that the native order of the nucleobases in a polynucleotide is reflected in the sequence of signals that is detected. Kilobase length polymers (single-stranded genomic DNA or RNA) or small molecules (e.g., nucleosides) can be identified and characterized without amplification or labeling, a unique analytical capability that makes inexpensive, rapid DNA sequencing
a possibility. Further research and development to overcome current challenges to nanopore identification of each successive nucleotide in a DNA strand offers the prospect of āthird generationā instruments that will sequence a diploid mammalian genome for ~$1,000 in ~24 h.Molecular and Cellular BiologyPhysic