Ejection dynamics of semiflexible polymers out of a nanochannel

Using theoretical analysis and three-dimensional Langevin dynamics simulations, we investigate the influence of chain rigidity on the ejection dynamics of polymers from a nanochannel. We find that there exist two distinct dynamical regimes divided by a critical chain length for both flexible and semiflexible chains. At the short chain regime, semiflexible chains eject faster than flexible chains of the same chain length due to the longer occupying length. In contrast, at the long chain regime, semiflexible chains eject slower than flexible ones as the effective entropic driving force decreases. Based on these results, we propose that the nanochannels could be used to separate flexible and semiflexible chains effectively.     

Partitioning of Semiflexible Macromolecules into a Slit in Theta Solvent

Investigation of semiflexible coil‐like chains in the process of partitioning with a slit in a solvent of variable thermodynamic quality has shown two key results. For semiflexible chains in a good solvent, the effect of chain stiffness played a role only at low concentrations. However, the situation is different with interacting chains where the effect of stiffness is also observed at higher concentrations. For theta chains, the partitioning into a slit in dilute solutions is lower for semiflexible than for flexible chains, while for higher concentrations this order is reversed. The packing ability of semiflexible chains at higher concentrations is enhanced in the theta system. Interestingly, stretching of chains on penetration into the slit is observed at higher concentrations. Decomposition of free energy change on partitioning into entropy and energy contributions gives more information on the details of partitioning of these systems, especially the differentiation between dilute and moderate concentration regimes. A positive change of partitioning entropy in the theta solvent in the semidilute regime for both flexible and semiflexible chains is noteworthy. This is related to breaking favorable interactions between chains on penetration into the slit.     

Impact of surface charge density and motor force upon polyelectrolyte packaging in viral capsids

By means of Langevin molecular dynamics simulations, we study the packaging dynamics of flexible and semiflexible polyelectrolytes in spherical cavities that resemble viral capsids. We employ a coarse‐grained model of the polymer–capsid complex that allows us to perform simulations of a 900mer and investigate the influence of surface charges inside the capsid and an additional motor force, acting on the polymer in the portal region of the cavity, on the packaging process. Our results indicate that it is most efficient if surface charges are present that initially promote the formation of an ordered surface layer inside the capsid. Once these charges are screened, the motor force pulls in the remaining part of the chain. Additionally, the simulations also demonstrate that the packaging dynamics depends on the counterion valence. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016 , 54, 1054–1065     

Influence of ions on genome packaging and ejection: a molecular dynamics study

We, theoretically, investigate the effect of ions on the packing and ejection dynamics of flexible and semiflexible polymers from spherical viral capsids. We find that when the polymer charge is less screened, or the Debye length increases (corresponding to a buffer with low concentration of a monovalent salt, such as Na(+)), the packing becomes more difficult and it may stop midway. Ejection, instead, proceeds more easily if the electrostatic screening is small. On the other hand, more screening (corresponding, for example, to the addition of divalent ions such as Mg(2+)) results in easier packing and slower ejection. We interpret this as resulting from electrostatic forces among the various polymer sections, which can be tuned with the type of salt present in the solution. We also discuss how the DNA structure inside the capsid changes due to screened electrostatic interactions.     

Role of chain stiffness on the conformation of single polyelectrolytes in salt solutions

Conformation of single polyelectrolytes in tetravalent salt solutions is investigated under the framework of a coarse-grained model, using Langevin dynamics simulations. The chain size, studied by the radius of gyration, shows three different variational behaviors with salt concentration, depending on the chain stiffness. According to the size variations, polyelectrolytes of fixed chain length are classified into three categories: (1) flexible chain, for which the variation shows a curve similar to a tilted L, (2) semiflexible chain, whose curve resembles U, and (3) rigid chain, for which the curve is a straight line. The wormlike chain model with persistence length predicted by the Odijk-Skolnick-Fixman theory is found to be able to qualitatively describe the end-to-end distance at low salt concentration not only for semiflexible and rigid chains but also for flexible chain. In a low salt region, a flexible polyelectrolyte extends more significantly than a semiflexible chain, in reference of the size of their uncharged counterparts, and in a high salt region, regardless of chain stiffness, a chain attains a dimension comparable to that of its neutral polymer. The chain stiffness influences both the local and the global chain structures. A flexible chain exhibits a zigzagged local structure in the presence of salt ions, and the condensed structure is a disordered, random globule. A semiflexible chain is locally smooth, and the condensed structure is orderly packed, taking a form such as hairpin or toroid. Moreover, the chain stiffness can also affect the nature of the coil-globule transition. The transition occurred in a discrete manner for semiflexible chain, whereas it occurred in a continuous way for flexible chain. This discrete feature happened not only at low salt concentration when a semiflexible chain collapsed but also at high salt concentration when the collapsed chain is reexpanded. At the end, the effects of chain stiffness and salt concentration on the conformation of single polyelectrolytes are summarized in a schematic state diagram.     

Shear thinning in dilute polymer solutions

We use bead-spring models for a polymer coupled to a solvent described by multiparticle collision dynamics to investigate shear thinning effects in dilute polymer solutions. First, we consider the polymer motion and configuration in a shear flow. For flexible polymer models we find a sharp increase in the polymer radius of gyration and the fluctuations in the radius of gyration at a Weissenberg number approximately 1. We then consider the polymer viscosity and the effect of solvent quality, excluded volume, hydrodynamic coupling between the beads, and finite extensibility of the polymer bonds. We conclude that the excluded volume effect is the major cause of shear thinning in polymer solutions. Comparing the behavior of semiflexible chains, we find that the fluctuations in the radius of gyration are suppressed when compared to the flexible case. The shear thinning is greater and, as the rigidity is increased, the viscosity measurements tend to those for a multibead rod.     

Polymer escape from a metastable Kramers potential: path integral hyperdynamics study

We study the dynamics of flexible, semiflexible, and self-avoiding polymer chains moving under a Kramers metastable potential. Due to thermal noise, the polymers, initially placed in the metastable well, can cross the potential barrier, but these events are extremely rare if the barrier is much larger than thermal energy. To speed up the slow rate processes in computer simulations, we extend the recently proposed path integral hyperdynamics method to the cases of polymers. We consider the cases where the polymers' radii of gyration are comparable to the distance between the well bottom and the barrier top. We find that, for a flexible polymers, the crossing rate (R) monotonically decreases with chain contour length (L), but with the magnitude much larger than the Kramers rate in the globular limit. For a semiflexible polymer, the crossing rate decreases with L but becomes nearly constant for large L. For a fixed L, the crossing rate becomes maximum at an intermediate bending stiffness. For the self-avoiding chain, the rate is a nonmonotonic function of L, first decreasing with L, and then, above a certain length, increasing with L. These findings can be instrumental for efficient separation of biopolymers.     

Rigidity effect on phase behavior of symmetric ABA triblock copolymers: A Monte Carlo simulation

The phase behavior of symmetric ABA triblock copolymers containing a semiflexible midblock is studied by lattice Monte Carlo simulation. As the midblock evolves from a fully flexible state to a semiflexible state in terms of increase in its persistence length, different phase behaviors are observed while cooling the system from an infinite high temperature to a temperature below T(ODT) (order-disorder transition temperature). Within the midblock flexibility range we studied (l(p)N(c)相似文献   

Structure of flexible and semiflexible polyelectrolyte chains in confined spaces of slit micro/nanochannels

Understanding the behavior of a polyelectrolyte in confined spaces has direct relevance in design and manipulation of microfluidic devices, as well as transport in living organisms. In this paper, a coarse-grained model of anionic semiflexible polyelectrolyte is applied, and its structure and dynamics are fully examined with Brownian dynamics (BD) simulations both in bulk solution and under confinement between two negatively charged parallel plates. The modeling is based on the nonlinear bead-spring discretization of a continuous chain with additional long-range electrostatic, Lennard-Jones, and hydrodynamic interactions between pairs of beads. The authors also consider the steric and electrostatic interactions between the bead and the confining wall. Relevant model parameters are determined from experimental rheology data on the anionic polysaccharide xanthan reported previously. For comparison, both flexible and semiflexible models are developed accompanying zero and finite intrinsic persistence lengths, respectively. The conformational changes of the polyelectrolyte chain induced by confinements and their dependence on the screening effect of the electrolyte solution are faithfully characterized with BD simulations. Depending on the intrinsic rigidity and the medium ionic strength, the polyelectrolyte can be classified as flexible, semiflexible, or rigid. Confined flexible and semiflexible chains exhibit a nonmonotonic variation in size, as measured by the radius of gyration and end-to-end distance, with changing slit width. For the semiflexible chain, this is coupled to the variations in long-range bond vector correlation. The rigid chain, realized at low ionic strength, does not have minima in size but exhibits a sigmoidal transition. The size of confined semiflexible and rigid polyelectrolytes can be well described by the wormlike chain model once the electrostatic effects are taken into account by the persistence length measured at long length scale.     

Semiflexible amphiphilic polymers: cylindrical-shaped, collagenlike, and toroidal structures

A coarse-grained model is used to study the conformational properties of semiflexible polymers with amphiphilic monomer units containing both hydrophilic and hydrophobic interaction sites. The hydrophobically driven conformational transitions are studied using molecular dynamics simulations for the chains of varying stiffness, as characterized by intrinsic Kuhn segment lengths that vary over a decade. It is shown that the energy of hydrophobic attraction required for the realization of the coil-to-globule transition increases with increasing chain stiffness. For rather stiff backbone, the coil-to-globule transition corresponds to a first order phase transition. We find that depending on the chain stiffness, a variety of thermodynamically stable anisometric chain morphologies are possible in a solvent selectively poor for hydrophobic sites of amphiphilic monomer units. For flexible chains, the amphiphilic polymer forms a cylindrical globule having blob structure with nearly spherical blobs. With increasing stiffness, the number of blobs composing the globule decreases and the shape of blobs transforms into elongated cylinder. Further increase in stiffness leads to compaction of macromolecules into a collagenlike structure when the chain folds itself several times and different strands wind round each other. In this state, the collagenlike structures coexist with toroidal globules, both conformations having approximately equal energies.     

Adsorption of semiflexible block copolymers on homogeneous surfaces

We present the results of extensive numerical off-lattice Monte Carlo simulations of semiflexible block-copolymer chains adsorbed onto flat homogeneous surfaces. We have compared the behavior of several chain structures, such as homopolymers, diblocks, (A(alpha)B(alpha)) block copolymers, and random heteropolymers. In all the cases studied, we have found the adsorption process to be favored with an increase of the chain rigidity. Particularly, the adsorption of diblock structures becomes a two-step process characterized by two different adsorbing temperatures that depend on the chain stiffness kappa, the chain length N, and the adsorbing energies epsilon(A) and epsilon(B). This twofold adsorbing process changes to a single one for copolymers of reduced block size alpha. Each block of the stiff copolymer chain is found to satisfy the classical scaling laws for flexible chains, however, we found the scaling exponent phi to depend on the chain stiffness. The measurement of the radius of gyration exhibits a typical behavior of a polymer chain composed of Nl(p) blobs whose persistence length follows l(p) approximately (kappa/k(B)T)(0.5) for large stiff chains.     

Isotropic-nematic phase transition in athermal solutions of rod-coil diblock copolymers

We present a hybrid method to investigate the isotropic-nematic (I-N) transition in athermal solutions of rod-coil copolymers. This method incorporates the scaled-particle theory for semiflexible chains with two-chain Monte Carlo simulation for the osmotic second virial coefficient and for the angle-dependent excluded volume. We compare the theoretical prediction with Monte Carlo simulations for fused rod-coil copolymers and find good agreement for both the equation of state and the orientational order parameter. The theory is also used to examine the effects of the bond length, the chain length, and the chain composition on orientational ordering in athermal solutions of rod-coil block copolymers. It predicts I-N transition in rod-coil copolymers with fixed rod length but a variable flexible tail in good agreement with experiments.     

Partitioning of Semiflexible Macromolecules into a Slit in Good Solvents

We investigate by Monte Carlo simulations the partitioning of semiflexible chains into slits the sizes of which are in the range of coil dimensions. The investigated chains have variable rigidities within the coil regime not reaching the rigid rod limit. Noticeable deviations of the commonly used approximate persistence length from its exact counterpart are reported. The partitioning of semiflexible chains in the reduced plot of partitioning coefficient versus confinement is located between the results for the partitioning of a sphere and for a rigid rod. At large confinement, and for the most rigid chains investigated, the scaling law for partitioning approaches that of the rigid rods. We advocate presenting results based both on the reduced and absolute plots for drawing the correct conclusions. On increasing concentration, it is apparent that the differences in partitioning resulting from variable chain rigidity appear only in the dilute solution. At higher concentrations the differences vanish. The weak‐to‐strong penetration transition on an increase of concentration is explained using the scaling approach by the change of the mobility unit from the coil dimension to a concentration correlation length, similarly to that of flexible chains. The microscopic picture of partitioning represented by various concentration profiles in the slit leads to the conclusion that stiffer chains are able to fill the depletion layer at the walls more readily.     

Conformational behavior of polymers adsorbed on nanotubes

The importance of hydrophobic interactions in determining polymer adsorption and wrapping of carbon nanotubes is still under debate. In this work, we concentrate on the effect of short-ranged weakly attractive hydrophobic interactions between polymers and nanotubes (modeled as an infinitely long and smooth cylindrical surface), neglecting all other interactions apart for chain flexibility. Using coarse-grained Monte Carlo simulation of such simplified systems, we find that uniform adsorption and wrapping of the nanotube occur for all degrees of chain flexibility for tubes with sufficiently large outer radii. However, the adsorbed conformations depend on chain stiffness, ranging from randomly adsorbed conformations of the flexible chain to perfect helical or multihelical conformations (in the case of more concentrated solutions) of the rigid chains. Adsorption appears to occur in a sequential manner, wrapping the nanotube nearly one monomer at a time from the point of contact. Once adsorbed, the chains travel on the surface of the cylinder, retaining their helical conformations for the semiflexible and rigid chains. Our findings may provide additional insight to experimentally observed ordered polymer wrapping of carbon nanotubes.     

Complexation of semiflexible chains with oppositely charged cylinder

We study the complexation of long thin semiflexible polymer chains with an oppositely charged cylinder. Starting from the linear Poisson-Boltzmann equation, we calculate the electrostatic potential and the energy of such a charge distribution. We find that sufficiently flexible chains prefer to wrap around the cylinder in a helical manner, when their charge density is smaller than that of the cylinder. The optimal value of the helical pitch is found by minimization of the sum of electrostatic and bending energies. The dependence of the pitch on the number of chains, their rigidity, and salt concentration in solution is analyzed. We discuss our results in the light of recent experiments on DNA complexation with cylindrical dendronized polymers.     

Semiflexible polymers in a random environment

We present using simple scaling arguments and one step replica symmetry breaking a theory for the localization of semiflexible polymers in a quenched random environment. In contrast to completely flexible polymers, localization of semiflexible polymers depends not only on the details of the disorder but also on the ease with which polymers can bend. The interplay of these two effects can lead to the delocalization of a localized polymer with an increase in either the disorder density or the stiffness. Our theory provides a general criterion for the delocalization of polymers with varying degrees of flexibility and allows us to propose a phase diagram for the highly folded (localized) states of semiflexible polymers as a function of the disorder strength and chain rigidity.     

Viscoelastic properties of an isolated polymer chain with arbitrary flexibility,chain length and hydrodynamic interactions from 4‐dimensional Dirac propagator

Kholodenko's theory of semiflexible polymer chains, the conformation and properties of which are obtained from the Dirac propagator, shows applicability to dilute solutions of semiflexible polymers of arbitrary persistence and contour lengths by calculating the static scattering function and the squared end‐to‐end distance of the polymer chain. In the present work, the theory is extended and applied to obtain the intrinsic viscosity with consideration of hydrodynamic interactions. The intrinsic viscosity formula is derived as function of chain length and persistence length. The hydrodynamic interactions are also taken into account following the Kirkwood and Riseman scheme. From this calculation, we obtain the general expression for the intrinsic viscosity and diffusion coefficients covering the whole range of chain flexibilities without confusion with the excluded volume effects. Calculated limiting values of hydrodynamical observables are in complete agreement with those known for random coils and rigid rods.     

Structure and dynamics of liquid-crystalline polymers with different molecular architectures

The structure and dynamics of liquid-crystalline polymers with different molecular architectures as revealed by multidimensional NMR Is described. Specific examples discussed Include semiflexible, rigid-rod, calamitic, and discotic systems. Structural aspects addressed are the determination of high rank order parameters, the micro-order in frozen liquid crystals and the packing of flexible side chains. Local dynamics In the glassy state, conformational dynamics and collective phenomena such as the development of convective director structures are discussed. It is demonstrated that advanced NMR spectroscopy yields highly specific information not available from conventional scattering, microscopic and relaxation techniques.     

A Monte Carlo simulation study of branched polymers

Monte Carlo simulations are presented for the static properties of highly branched polymer molecules. The molecules consist of a semiflexible backbone of hard-sphere monomers with semiflexible side chains, also composed of hard-sphere monomers, attached to either every backbone bead or every other backbone bead. The conformational properties and structure factor of this model are investigated as a function of the stiffness of the backbone and side chains. The average conformations of the side chains are similar to self-avoiding random walks. The simulations show that there is a stiffening of the backbone as degree of crowding is increased, for example, if the branch spacing is decreased or side chain length is increased. The persistence length of the backbone is relatively insensitive to the stiffness of the side chains over the range investigated. The simulations reproduce most of the qualitative features of the structure factor observed in experiment, although the magnitude of the stiffening of the backbone is smaller than in experiment.     

Theoretical analysis of polydispersity in the nematic phase of self-assembled semiflexible chains

In recent simulations of semiflexible equilibrium polymers [X. Lu and J. T. Kindt, J. Chem. Phys. 120, 10328 (2004)] a roughly biexponential distribution of chain lengths was observed in the nematic phase. In this study, we show that a theory representing the nematic phase as an equilibrium mixture of randomly oriented chains below a critical length Lc and chains above Lc obeying a Gaussian orientational distribution reproduces this distribution qualitatively. The agreement between predicted and simulated phase boundaries is improved, with a narrower isotropic-nematic coexistence region, compared with a monoexponential chain distribution. We find, furthermore, that the critical length Lc scales as the inverse of monomer concentration, irrespective of the bond strength of the chains, but that at the phase boundary, the fraction of monomers found in disordered chains peaks at a certain bond strength.