DNA confined in a two-dimensional strip geometry

Semiflexible polymers characterized by the contour length $L$ and persistent length $\ell_p$ confined in a spatial region $D$ have been described as a series of ``{\em spherical blobs}'' and ``{\em deflecting lines}'' by de Gennes and Odjik for $\ell_p < D$ and $\ell_p \gg D$ respectively. Recently new intermediate regimes ({\em extended de Gennes} and {\em Gauss-de Gennes}) have been investigated by Tree {\em et al.} [Phys. Rev. Lett. {\bf 110}, 208103 (2013)]. In this letter we derive scaling relations to characterize these transitions in terms of universal scaled fluctuations in $d$-dimension as a function of $L,\ell_p$, and $D$, and show that the Gauss-de Gennes regime is absent and extended de Gennes regime is vanishingly small for polymers confined in a 2D strip. We validate our claim by extensive Brownian dynamics (BD) simulation which also reveals that the prefactor $A$ used to describe the chain extension in the Odjik limit is independent of physical dimension $d$ and is the same as previously found by Yang {\em et al.}[Y. Yang, T. W. Burkhardt, G. Gompper, Phys. Rev. E {\bf 76}, 011804 (2007)]. Our studies are relevant for optical maps of DNA stretched inside a nano-strip.Comment: 6 pages, 4 figure

Out of Equilibrium Characteristics of a Forced Translocating Chain through a Nanopore

Polymer translocation through a nano-pore in a thin membrane is studied using a coarse-grained bead-spring model and Langevin dynamics simulation with a particular emphasis to explore out of equilibrium characteristics of the translocating chain. We analyze the out of equilibrium chain conformations both at the $cis$ and the $trans$ side separately either as a function of the time during the translocation process or as as function of the monomer index $m$ inside the pore. A detailed picture of translocation emerges by monitoring the center of mass of the translocating chain, longitudinal and transverse components of the gyration radii and the end to end vector. We observe that polymer configurations at the $cis$ side are distinctly different from those at the $trans$ side. During the translocation, and immediately afterwards, the chain is clearly out of equilibrium, as different parts of the chain are characterized by a series of effective Flory exponents. We further notice that immediately after the translocation the last set of beads that have just translocated take a relatively compact structure compared to the first set of beads that translocated earlier, and the chain immediately after translocation is described by an effective Flory exponent $0.45 \pm 0.01$. The analysis of these results is further strengthened by looking at the conformations of chain segments of equal length as they cross from the $cis$ to the $trans$ side, We discuss implications of these results to the theoretical estimates and numerical simulation studies of the translocation exponent reported by various groups.Comment: 35 pages, 16 figures. Submitted to Phys. Rev.

Universal monomer dynamics of a two dimensional semi-flexible chain

We present a unified scaling theory for the dynamics of monomers for dilute solutions of semiflexible polymers under good solvent conditions in the free draining limit. Our theory encompasses the well-known regimes of mean square displacements (MSDs) of stiff chains growing like t^{3/4} with time due to bending motions, and the Rouse-like regime t^{2 \nu / (1+ 2\nu)} where \nu is the Flory exponent describing the radius R of a swollen flexible coil. We identify how the prefactors of these laws scale with the persistence length l_p, and show that a crossover from stiff to flexible behavior occurs at a MSD of order l^2_p (at a time proportional to l^3_p). A second crossover (to diffusive motion) occurs when the MSD is of order R^2. Large scale Molecular Dynamics simulations of a bead-spring model with a bond bending potential (allowing to vary l_p from 1 to 200 Lennard-Jones units) provide compelling evidence for the theory, in D=2 dimensions where \nu=3/4. Our results should be valuable for understanding the dynamics of DNA (and other semiflexible biopolymers) adsorbed on substrates.Comment: 4-page paper with 5 figures. 3-page supplemental information with 3 figure

How capture affects polymer translocation in a solitary nanopore

DNA capture with high fidelity is an essential part of nanopore translocation. We report several important aspects of the capture process and subsequent translocation of a model DNA polymer through a solid-state nanopore in presence of an extended electric field using the Brownian dynamics simulation that enables us to record statistics of the conformations at every stage of the translocation process. By releasing the equilibrated DNAs from different equipotentials, we observe that the capture time distribution depends on the initial starting point and follows a Poisson process. The field gradient elongates the DNA on its way towards the nanopore and favors a successful translocation even after multiple failed threading attempts. Even in the limit of an extremely narrow pore, a fully flexible chain has a finite probability of hairpin-loop capture while this probability decreases for a stiffer chain and promotes single file translocation. Our in silico studies identify and differentiate characteristic distributions of the mean first passage time due to single file translocation from those due to translocation of different types of folds and provide direct evidences of the interpretation of the experimentally observed folds [M. Gershow et al., Nat. Nanotech. 2, 775 (2007) and M. Mihovilovic et al. Phys. Rev. Letts. 110, 028102 (2013)] in a solitary nanopore. Finally, we show a new finding, - that a charged tag attached at the $5^{\prime}$ end of the DNA enhances both the multi-scan rate as well as the uni-directional translocation ($5^{\prime} \rightarrow 3^{\prime}$) probability that would benefit the genomic barcoding and sequencing experiments

QUALITATIVE SCREENING OF PHYTOCHEMICAL AND COMPARATIVE STUDY OF DIETARY ANTIOXIDATIVE PROPERTIES OF THREE COMMONLY USED LEAFY VEGETABLES OF WEST BENGAL

Objective:The study was carried out to evaluate the phytochemical constituents of three very commonly used leafy vegetables of West Bengal namely&nbsp;Bacopa monnieri&nbsp;(Brahmi sak),&nbsp;Lagenaria siceraria&nbsp;(Lau sak) and&nbsp;Spinacia oleracea&nbsp;(Palong sak). Antioxidant potential of leaf and stem in raw and boiled forms was studied. Methods:Aqueous, methanolic and ethanolic extract of the three leafy vegetables were prepared. Qualitative detection of phytochemical constituents from the extracts was done. Phenol, Flavonoid, vitamin C, vitamin E, content and DPPH assay were done using standard protocols from methanolic extracts. Results:Leaf samples of the vegetables under consideration contain higher amount of phenol, flavonoid, vitamin C, vitamin E, than the stem samples. Considering raw and boiled condition, raw samples contain higher amount of flavonoid, vitamin C, vitamin E, from their boiled counterpart whereas boiled samples contain higher amount of phenols. The total antioxidant capacity was positively correlated with total phenolic content and flavonoid content. Conclusion:Cooking reduced the free radical scavenging activities with certainty to varying extent. Among the three leafy vegetables under consideration,&nbsp;Spinacia&nbsp;oleracea&nbsp;was richest in phenol, flavonoid and vitamin E content and was more active as a free radical scavenger with low IC50&nbsp;radical scavenging activity

Scaling theory of driven polymer translocation

We present a theoretical argument to derive a scaling law between the mean translocation time $\tau$ and the chain length $N$ for driven polymer translocation. This scaling law explicitly takes into account the pore-polymer interactions, which appear as a correction term to asymptotic scaling and are responsible for the dominant finite size effects in the process. By eliminating the correction-to-scaling term we introduce a rescaled translocation time and show, by employing both the Brownian Dynamics Tension Propagation theory [Ikonen {\it et al.}, Phys. Rev. E {\bf 85}, 051803 (2012)] and molecular dynamics simulations that the rescaled exponent reaches the asymptotic limit in a range of chain lengths that is easily accessible to simulations and experiments. The rescaling procedure can also be used to quantitatively estimate the magnitude of the pore-polymer interaction from simulations or experimental data. Finally, we also consider the case of driven translocation with hydrodynamic interactions (HIs). We show that by augmenting the BDTP theory with HIs one reaches a good agreement between the theory and previous simulation results found in the literature. Our results suggest that the scaling relation between $\tau$ and $N$ is retained even in this case.Comment: 5 pages, 4 figure

Driven translocation of a semi-flexible chain through a nanopore: A Brownian dynamics simulation study in two dimensions

We study translocation dynamics of a semi-flexible polymer chain through a nanoscopic pore in two dimensions using Langevin dynamics simulation in presence of an external bias F inside the pore. For chain length N and stiffness parameter kappa(b) considered in this paper, we observe that the mean first passage time \u3c tau \u3e increases as \u3c tau(kappa(b)) \u3e similar to \u3c tau(kappa(b) = 0) \u3e l(p)(aN), where kappa(b) and l(p) are the stiffness parameter and persistence length, respectively, and a(N) is a constant that has a weak N dependence. We monitor the time dependence of the last monomer x(N)(t) at the cis compartment and calculate the tension propagation time (TP) t(tp) directly from simulation data for \u3c x(N)(t) \u3e similar to t as alluded in recent nonequlibrium TP theory [T. Sakaue, Phys. Rev. E 76, 021803 (2007)] and its modifications to Brownian dynamics tension propagation theory [T. Ikonen, A. Bhattacharya, T. Ala-Nissila, and W. Sung, Phys. Rev. E 85, 051803 (2012); J. Chem. Phys. 137, 085101 (2012)] originally developed to study translocation of a fully flexible chain. We also measure t(tp) from peak position of the waiting time distribution W(s) of the translocation coordinate s (i.e., the monomer inside the pore), and explicitly demonstrate the underlying TP picture along the chain backbone of a translocating chain to be valid for semi-flexible chains as well. From the simulation data, we determine the dependence of t(tp) on chain persistence length l(p) and show that the ratio t(tp)/\u3c tau \u3e is independent of the bias F