Monte Carlo studies of adsorption of a sequenced polyelectrolyte to patterned surfaces By using off-lattice Monte Carlo simulations, the conditions of adsorption of a uniformly charged polyelectrolyte onto oppositely charged planar and spherical surfaces have been investigated. These conditions are functions of the strength of the electrostatic interaction, Debye screening length, chain length, and charge density and curvature of the surface. The adsorption can be tuned by using any one of these parameters. The chain's conformation, adsorption energy and thickness of the adsorbed polymer are obtained under different adsorption conditions. We find the Monte Carlo simulation data to be in good agreement with the theoretical prediction derived previously by using the assumptions of ground state dominance and separability.

Following our previous study of a Gaussian chain translocation, we have investigated the transport of a self-avoiding chain from one sphere to another sphere through a narrow pore, using the self-consistent field theory formalism. The free energy landscape for polymer translocation is significantly modified by excluded volume interactions among monomers. The free energy barrier for the placement of one of the chain ends at the pore depends on the chain length N nonmonotonically, in contrast to the N-independence for Gaussian chains. This results in a nonmonotonic dependence of the average arrival time [tau0] on N for self-avoiding chains. When the polymer chain is partitioned between the donor and recipient spheres, a local free energy minimum develops, depending on the strength w of the excluded volume interaction and the relative sizes of the donor and recipient spheres. If the sizes of spheres are comparable, the average translocation time tau (the average time taken by the polymer, after the arrival at the pore, to convert from the donor to the recipient) increases with an increase in w for a fixed N value. On the other hand, for the highly asymmetric sizes of the donor and recipient spheres, tau decreases with an increase in w. As in the case of Gaussian chains, tau depends nonmonotonically on the pore length.

A modeling algorithm is presented to compute simultaneously polymer conformations and ionic current, as single polymer molecules undergo translocation through protein channels. The method is based on a combination of Langevin dynamics for coarse-grained models of polymers and the Poisson-Nernst-Planck formalism for ionic current. For the illustrative example of ssDNA passing through the ␣-hemolysin pore, vivid details of conformational fluctuations of the polymer inside the vestibule and ␤-barrel compartments of the protein pore, and their consequent effects on the translocation time and extent of blocked ionic current are presented. In addition to yielding insights into several experimentally reported puzzles, our simulations offer experimental strategies to sequence polymers more efficiently.T ranslocation of polymers through biological channels is very complex involving many machineries and is a fundamental step in many life processes. Although several essential features of translocation are richly documented in systems such as mRNP complex through nuclear pores (1-3), a simple system has only recently been identified for following the single-file passage of one isolated polymer through one channel (4-11). In this system, the channel is constituted by self-assembling heptamers of the Staphylococcus aureus ␣-hemolysin (␣HL) protein. The channel is assembled in a phospholipid bilayer, which offers a physical barrier, and the channel has an opening diameter of Ϸ1.4 nm at the narrowest constriction (12). A single-stranded polynucleotide, such as poly(deoxyadenylate) and poly(deoxycytidylate), is pulled through the channel by an externally applied voltage gradient across the channel in a solution of a strong electrolyte. The idea is that the ionic current through the channel caused by the passage of small ions of the electrolyte is blocked to a certain extent during the event of translocation of the polymer. It has been hoped that the extent and duration of the current blockade are unique signatures of the identity of the polymer, both in terms of the polymer's chemical characteristics and physical length.Even this simplest setup, where identical molecules undergo translocation, has generated several puzzling results. The distribution, P( ), of the duration of blockade of ionic current I b is very broad and appears to exhibit at least two peaks. In addition, there are several levels of ionic current blockade I b for the same molecule. It is standard practice in experimental investigations to combine the histograms of and I b (8). The resultant scatter plots always yield two groups of data even for monodisperse homopolymers.To gain insight into these puzzles, we have developed the following simulation. It is complementary to a flurry of theoretical activity (13-21), based on entropic barrier dynamics (22), all of which lead to a generic P( ) unlike in experiments. Although it is indeed desirable to perform the computation ab initio, the size of the system to be simulated is forbiddingly large to enable such a compu...

In an effort to understand recent experiments, we have performed Brownian dynamics simulations of polymer translocation through nanometer-scale protein pores under the influence of an external applied electric field. Multiple peaks in the translocation time distribution are observed in agreement with experiments. Under the same conditions, but replacing the protein pore with a rigid cylindrical tube of comparable size, only a single peak is observed in the translocation time distribution. These results directly show that the geometry of the protein pores is mainly responsible for multiple peaks observed in experiments. In the case of alpha-hemolysin channel, we find the vestibule, by confining many conformations of the translocating polymer, to be responsible for the second peak with longer translocation time.

The adsorption transition of a uniformly charged polyelectrolyte onto heterogeneously charged surfaces has been investigated using off-lattice Monte Carlo simulations. Each of these surfaces contains both positive and negative charges. In addition to the usual case of adsorption of a polyelectrolyte to a surface with net charge opposite to that of the polymer, we show that a polyelectrolyte can adsorb onto a surface with net surface charge density similar to that of the polyelectrolyte. This adsorption is caused by the spatial inhomogeneity of the surface charges, which creates attractive regions with charge density different from the overall charge density of the surface. The spatial inhomogeneity of the surface charges also leads to differences in the conformation of the adsorbed polyelectrolyte. The critical conditions of strength and range of electrostatic interactions and chain length necessary for adsorption of a polyelectrolyte to a heterogeneously charged surface are demonstrated.