Publications (53)83.2 Total impact
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ABSTRACT: The conformations of semiflexible polymers in two dimensions confined in a strip of width D are studied by computer simulations, investigating two different models for the mechanism by which chain stiffness is realized. One model (studied by molecular dynamics) is a beadspring model in the continuum, where stiffness is controlled by a bond angle potential allowing for arbitrary bond angles. The other model (studied by Monte Carlo) is a selfavoiding walk chain on the square lattice, where only discrete bond angles (0° and ±90°) are possible, and the bond angle potential then controls the density of kinks along the chain contour. The first model is a crude description of DNAlike biopolymers, while the second model (roughly) describes synthetic polymers like alkane chains. It is first demonstrated that in the bulk the crossover from rods to selfavoiding walks for both models is very similar, when one studies average chain linear dimensions, transverse fluctuations, etc., despite their differences in local conformations. However, in quasionedimensional confinement two significant differences between both models occur: (i) The persistence length (extracted from the average cosine of the bond angle) gets renormalized for the lattice model when D gets less than the bulk persistence length, while in the continuum model it stays unchanged. (ii) The monomer density near the repulsive walls for semiflexible polymers is compatible with a power law predicted for the KratkyPorod model in the case of the beadspring model, while for the lattice case it tends to a nonzero constant across the strip. However, for the density of chain ends, such a constant behavior seems to occur for both models, unlike the power law observed for flexible polymers. In the regime where the bulk persistence length ℓ p is comparable to D, hairpin conformations are detected, and the chain linear dimensions are discussed in terms of a crossover from the Daoud/De Gennes “string of blobs”picture to the flexible rod picture when D decreases and/or the chain stiffness increases. Introducing a suitable further coarsegraining of the chain contours of the continuum model, direct estimates for the deflection length and its distribution could be obtained.  [Show abstract] [Hide abstract]
ABSTRACT: We study the translocation dynamics of a semiflexible polymer through a nanopore from the cis into the trans compartment containing attractive binding particles (BPs) using the Langevin dynamics simulation in two dimensions. The binding particles accelerate the threading process in two ways: (i) reducing the backsliding of the translocated monomer, and (ii) providing the pulling force toward the translocation direction. We observe that for certain binding strength (ε_{c}) and concentration (ρ) of the BPs, the translocation is faster than the ideal ratcheting condition as elucidated by Simon, Peskin, and Oster [M. Simon, C. S. Peskin, and G. F. Oster, Proc. Natl. Acad. Sci. USA 89, 3770 (1992)PNASA60027842410.1073/pnas.89.9.3770]. The asymmetry produced by the BPs at the transside leads to similarities of this process to that of a driven translocation with an applied force inside the pore manifested in various physical quantities. Furthermore, we provide an analytic expression for the force experienced by the translocating chain as well as for the scaled mean first passage time (MFPT), for which we observe that for various combinations of N, ε, and ρ the scaled MFPT (〈τ〉/N^{1.5}ρ^{0.8}) collapses onto the same master plot. Based on the analysis of our simulation data, we provide plausible arguments with regard to how the scaling theory of driven translocation can be generalized for such a directed diffusion process by replacing the externally applied force with an effective force. 
Dataset: 02955075 109 3 38001
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ABSTRACT: We study translocation dynamics of a driven compressible semiflexible chain consisting of alternate blocks of stiff ($S$) and flexible ($F$) segments of size $m$ and $n$ respectively for different chain length $N$. The free parameters in the model are the bending rigidity $\kappa_b$ which controls the three body interaction term, the elastic constant $k_F$ in the FENE (bond) potential between successive monomers, as well as the block lengths $m$ and $n$ and the repeat unit $p$ ($N=m_pn_p$). We demonstrate that the due to change in the entropic barrier and the inhomogeneous friction on the chain a variety of scenario are possible amply manifested in the incremental mean first passage time (IMFPT) or in the waiting time distribution of the translocating chain. These informations can be deconvoluted to extract information about the mechanical properties of the chain at various length scales and thus can be used to nanopore based methods to probe biomolecules, such as DNA, RNA and proteins.  [Show abstract] [Hide abstract]
ABSTRACT: This work shows that in situ reduction of metal ions bound at a polymer surface can form nanoparticles within the polymer matrix as well as at the interface, and the size and distribution of nanoparticles between the interface and subsurface depends upon the choice of reagents and reaction conditions. Tetrachloroaurate ions were bound to crosslinked SU8 films that were functionalized using a variety of multifunctional amines, then reduced using one of several reagents. Reduction using sodium borohydride or sodium citrate generates bands of interspersed gold nanoparticles as much as 40 nm deep within the polymer, indicating that both the Au ions and the reducing agent can penetrate the surface enabling formation of nanoparticles within the polymer matrix. Nanoparticle formation can be confined nearer to the polymer interface by reducing with hydroquinone, or by processing the polymer film in aqueous media using high molecularweight multifunctional amines that confine the gold ions at the interface.  [Show abstract] [Hide abstract]
ABSTRACT: We present a unified scaling theory for the dynamics of monomers of a semiflexible chain under good solvent condition in the free draining limit. We consider both the cases where the contour length $L$ is comparable to the persistence length $\ell_p$ and the case $L\gg \ell_p$. Our theory captures the early time monomer dynamics of a stiff chain characterized by $t^{3/4}$ dependence for the mean square displacement(MSD) of the monomers, but predicts a first crossover to the Rouse regime of $t^{2\nu/{1+2\nu}}$ for $\tau_1 \sim \ell_p^3$, and a second crossover to the purely diffusive dynamics for the entire chain at $\tau_2 \sim L^{5/2}$. We confirm the predictions of this scaling theory by studying monomer dynamics of dilute solution of semiflexible chains under good solvent conditions obtained from our Brownian dynamics (BD) simulation studies for a large choice of chain lengths with number of monomers per chain N = 16  2048 and persistence length $\ell_p = 1  500$ LennardJones (LJ) units. These BD simulation results further confirm the absence of Gaussian regime for a 2d swollen chain from the slope of the plot of $\langle R_N^2 \rangle/2L \ell_p \sim L/\ell_p$ which around $L/\ell_p \sim 1$ changes suddenly from $\left(L/\ell_p \right) \rightarrow \left(L/\ell_p \right)^{0.5} $, also manifested in the power law decay for the bond autocorrelation function disproving the validity of the WLC in 2d. We further observe that the normalized transverse fluctuations of the semiflexible chains for different stiffness $\sqrt{\langle l_{\bot}^2\rangle}/L$ as a function of renormalized contour length $L/\ell_p$ collapse on the same master plot and exhibits power law scaling $\sqrt{\langle l_{\bot}^2\rangle}/L \sim (L/\ell_p)^\eta $ at extreme limits, where $\eta = 0.5$ for extremely stiff chains ($L/\ell_p \gg 1$), and $\eta = 0.25$ for fully flexible chains.  [Show abstract] [Hide abstract]
ABSTRACT: 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 Gaussde 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 Gaussde 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 Burkhardt {\em et al.}[T. W. Burkhardt, Y. Yang, G. Gompper, Phys. Rev. E {\bf 82}, 041801 (2010)]. Our studies are relevant for optical maps of DNA stretched inside a nanostrip.  [Show abstract] [Hide abstract]
ABSTRACT: 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 wellknown regimes of mean square displacements (MSDs) of stiff chains growing like t^{3/4} with time due to bending motions, and the Rouselike 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 beadspring model with a bond bending potential (allowing to vary l_p from 1 to 200 LennardJones 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.  [Show abstract] [Hide abstract]
ABSTRACT: We study translocation dynamics of a semiflexible 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 κb considered in this paper, we observe that the mean first passage time 〈τ〉 increases as 〈τ(κb)〉∼〈τ(κb=0)〉lp (aN) , where κb and lp are the stiffness parameter and persistence length, respectively, and aN is a constant that has a weak N dependence. We monitor the time dependence of the last monomer xN(t) at the cis compartment and calculate the tension propagation time (TP) ttp directly from simulation data for 〈xN(t)〉 ∼ 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. AlaNissila, and W. Sung, Phys. Rev. E 85, 051803 (2012); and J. Chem. Phys. 137, 085101 (2012)] originally developed to study translocation of a fully flexible chain. We also measure ttp 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 semiflexible chains as well. From the simulation data, we determine the dependence of ttp on chain persistence length lp and show that the ratio ttp∕〈τ〉 is independent of the bias F. 
Article: Nanoscale characterization of gold nanoparticles created by in situ reduction at a polymeric surface
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ABSTRACT: Transmission Electron Microscopy is used as a quantitative method to measure the shapes, sizes and volumes of gold nanoparticles created at a polymeric surface by three different in situ synthesis methods. The atomic number contrast (Zcontrast) imaging technique reveals nanoparticles which are formed on the surface of the polymer. However, with certain reducing agents, the gold nanoparticles are additionally found up to 20 nm below the polymer surface. In addition, planview highangle annular darkfield scanning transmission electron microscopy images were statistically analyzed on one sample to measure the volume, height and effective diameter of the gold nanoparticles and their size distributions. Depth analysis from highangle annular darkfield scanning transmission electron microscopy micrographs also gives information on the dominant shape of the nanoparticles.  [Show abstract] [Hide abstract]
ABSTRACT: Conformation, dynamics, and escape of semiflexible biopolymers confined in narrowslits are studied using Langevin dynamics simulation in two dimensions (2D). Along with chain the length and the slit width, we vary the chain stiffness and study how internal modes of the individual chain segments are affected by chain stiffness. In addition to the usual measurements of gyration radii, end to end distance, persistence length, etc., we plan to report a detailed analysis of the subchain conformations and relaxation of the confined biopolymers both in de Gennes and Odjik limit We also study escape of confined semiflexible biopolymers through narrow slits. 
Article: How tension propagates for a driven semiflexible chain while translocating through a nanopore
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ABSTRACT: Driven translocation of a stiff chain through a nanopore is studied using Langevin dynamics in two dimension (2D). We observe that for a given chain length N the mean first passage time (MFPT) <τ> increases for a stiffer chain and the translocation exponent α (<τ>˜N^α) satisfies the inequality 2ν< α< 1+ν, where ν is the equilibrium Flory exponent for a given chain stiffness. We calculate the residence time of the individual monomers and observe that the peak position of the residence time W(m) as a function of the monomer index m shifts at a lower mvalue with increasing chain stiffness κb. Finally, we provide qualitative physical explanation for dependence of various quantities on chain stiffness κb by using ideas from Sakaue's tension propagation(TP) theory [Phys. Rev. E 76, 021803 (2007)] and its recent implementation into a Brownian dynamics tension propagation (BDTP) scheme for a finite chain by Ikonen et al. [J. Chem. Phys. 137, 085101 (2012); Phys. Rev. E 85, 051803 (2012)]for a semiflexible chain.  [Show abstract] [Hide abstract]
ABSTRACT: 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 porepolymer 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 correctiontoscaling 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 porepolymer 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.  [Show abstract] [Hide abstract]
ABSTRACT: We report on the quantitative analysis of electrolessly deposited Au and Ag nanoparticles (NPs) on SU8 polymer with the help of HighAngle Annular DarkField Scanning Transmission Electron Microscopy (HAADFSTEM) in tilt series. Au NPs act as nucleating agents for the electroless deposition of silver. Au NPs were prepared by attachingAu^3+cations to amine functionalized SU8 polymeric surfaces and then reducing it with aqueous NaBH4. The nanoscale morphology of the deposited NPs on the surface of polymer has been studied from the dark field TEM cross sectional images. Ag NPs were deposited on the crosslinked polymeric surface from a silver citrate solution reduced by hydroquinone. HAADFSTEM enables us to determine the distances between the NPs and their exact locations at and near the surface. The particle distribution, sizes and densities provide us with the data necessary to control the parameters for the development of the electroless deposition technique for emerging nanoscale technologies. 
Article: Nonequilibrium tension propagation as a unifying description of driven polymer translocation
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ABSTRACT: We present results from a new Brownian dynamics model of driven polymer translocation^1, in which nonequilibrium memory effects due to tension propagation (TP) along the cis side subchain are included as a timedependent friction. To solve the effective friction, we develop a finite chain length TP formalism, expanding on the work of Sakaue^1,2. The model yields results in excellent quantitative agreement with molecular dynamics simulations in a wide range of parameters. Our results show that nonequilibrium TP along the cis side subchain dominates the dynamics of driven translocation. In addition, the model explains the different scaling of translocation time with chain length observed both in experiments and simulations as a combined effect of finite chain length and porepolymer interactions. ^1T. Ikonen, A. Bhattacharya, T. AlaNissila and W. Sung, submitted.^2T. Sakaue, Phys. Rev. E 76, 021803 (2007)^3T. Sakaue, Phys. Rev. E 81, 041808 (2010). 
Article: Morphologies of an anisotropic diffusion limited growth model to study electroless deposition
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ABSTRACT: We report results of Monte Carlo simulation of a model which mimics certain aspects of electroless deposition of metals on polymeric surfaces. In the proposed model growth germinates from certain ``active'' particles residing on a flat surface. Further growth occurs via sticking of a diffusing particle while it is within the range of one of these active particles. Once within the attractive range of an ``active'' particle, the motion of the approaching particle is considered ballistic. This newly adsorbed particle then acts as an ``active'' site for further growth and the process continues. We monitor the layer by layer density variation, the pair correlation function and the structure factor as a function of the initial density of the particles and the range of the reaction, and comment on the fractal aspect of the morphology.  [Show abstract] [Hide abstract]
ABSTRACT: We study translocation dynamics of a semiflexible chain through a nanopore in two dimensions (2D) using Langevin dynamics simulation. Specifically, we show how the mean first passage time (MFPT) and the probability distribution of the MFPT are both influenced by the bending rigidity of the chain. Furthermore, we monitor the chain conformations both at the cis and the trans sides and relate these results with recent theories and experiments for a translocating chain through a nanopore.  [Show abstract] [Hide abstract]
ABSTRACT: We present a Brownian dynamics model of driven polymer translocation, in which nonequilibrium memory effects arising from tension propagation (TP) along the cis side subchain are incorporated as a timedependent friction. To solve the effective friction, we develop a finite chain length TP formalism, expanding on the work of Sakaue [Sakaue, PRE 76, 021803 (2007)]. The model, solved numerically, yields results in excellent agreement with molecular dynamics simulations in a wide range of parameters. Our results show that nonequilibrium TP along the cis side subchain dominates the dynamics of driven translocation. In addition, the model explains the different scaling of translocation time w.r.t chain length observed both in experiments and simulations as a combined effect of finite chain length and porepolymer interactions. 
Article: Morphologies from slippery ballistic deposition model: A bottomup approach for nanofabrication
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ABSTRACT: We report pattern formation using a slippery ballistic deposition (SBD) model where growth germinates from a single site or from sites distributed periodically on a lattice. By changing the sticking probability p(s) and choosing systems with different lattice constants and symmetries, we demonstrate that a variety of patterns can be generated. These patterns can be further used as scaffolds for nanofabrication. We also demonstrate that by choosing a lateral sticking probability p(l) at the base that is different than p(s), one can control both the early and late time morphologies originating from a seed. Furthermore, we indicate a possible generalization of preparing patterns to higher dimensions that in principle can have potential technological applications for preparing grooves and scaffolds of specific shapes and periodicities.  [Show abstract] [Hide abstract]
ABSTRACT: Motivated by electroless deposition of metals on polymeric surfaces we plan to study evolving morphologies of deposited particles from a surface using Monte Carlo simulation in continuum which shares characteristics of both diffusive and ballistic behavior. In the proposed model we assume that the particles residing at the surface of a growing pattern are capable of attracting particles those are within a certain range. Once one of these seed particles attracts a particle it transfers its attractive characteristics to the newly adsorbed particle which then acquires this characteristics for further growth. The motion of the particles in the bulk is diffusive. However, once they are within the range of an "active" particle they move ballistically along a straight line and gets adsorbed to a cluster unless hindered by other particles on its way. We plan to report the characteristics of the evolving patterns as a function of density of the diffusive particles, the range of the attractive particles, and the speed of ballistic moves.
Publication Stats
735  Citations  
83.20  Total Impact Points  
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20022015

University of Central Florida
 Department of Physics
Orlando, Florida, United States
