End-monomer Dynamics in Semiflexible Polymers

Spurred by an experimental controversy in the literature, we investigate the end-monomer dynamics of semiflexible polymers through Brownian hydrodynamic simulations and dynamic mean-field theory. Precise experimental observations over the last few years of end-monomer dynamics in the diffusion of double-stranded DNA have given conflicting results: one study indicated an unexpected Rouse-like scaling of the mean squared displacement (MSD) ?r(2)(t)? ~ t(1/2) at intermediate times, corresponding to fluctuations at length scales larger than the persistence length but smaller than the coil size; another study claimed the more conventional Zimm scaling ?r(2)(t)? ~ t(2/3) in the same time range. Using hydrodynamic simulations, analytical and scaling theories, we find a novel intermediate dynamical regime where the effective local exponent of the end-monomer MSD, α(t) = d log?r(2)(t)?/d log t, drops below the Zimm value of 2/3 for sufficiently long chains. The deviation from the Zimm prediction increases with chain length, though it does not reach the Rouse limit of 1/2. The qualitative features of this intermediate regime, found in simulations and in an improved mean-field theory for semiflexible polymers, in particular the variation of α(t) with chain and persistence lengths, can be reproduced through a heuristic scaling argument. Anomalously low values of the effective exponent α are explained by hydrodynamic effects related to the slow crossover from dynamics on length scales smaller than the persistence length to dynamics on larger length scales.     

The phase behavior of polyethylene ring chains

The equilibrium properties of an isolated polyethylene ring chain are studied by using molecular dynamics (MD) simulations. The results of an 80-bond linear chain are also presented, which are in agreement with previous studies of square-well chains and Lennard-Jones (LJ) homopolymers. Mainly, we focus on the collapse of polyethylene ring chains. At high temperatures, a fully oblate structure is observed for the ring chains with different chain lengths. For such an oblate structure, a shape factor of delta(*)=0.25 and a rodlike scaling relation between the radius of gyration and chain lengths could be deduced easily in theory, and the same results are obtained by our MD simulations. Such an oblate structure can be obtained by Monte Carlo simulation only for sufficient stiff ring chains. When the temperature decreases, an internal energy barrier is observed. This induces a strong peak in the heat capacity, denoting a gas-liquid-like transition. This energy barrier comes mainly from the local monomer-monomer interactions, i.e., the bond-stretching, the bond-bending, and the torsion potentials. A low temperature peak is also observed in the same heat capacity curve, representing a liquid-solid-like transition. These numerical simulation results support a two-stage collapse of polyethylene ring chains; however, the nature should be different from the square-well and LJ ring chains.     

Structure of Adsorbed Polymer Chains: A Monte Carlo Study

The structure of adsorbed polymer chains was studied using simplified lattice models. The model chains were adsorbed on an impenetrable surface with an attractive potential. The dynamic Monte Carlo simulations based in the Metropolis scheme were carried out using these models. The influence of the internal chain architecture (linear, star‐branched and ring chains) and the degree of adsorption on the chain's structure was studied. It was shown that for weakly adsorbed chain regime the ring polymers which exhibit an almost twice as high degree of adsorption compared to linear and star chains have a higher number of adsorbed parts of chain (trains). But the length of such train remains almost the same for all types of a polymer chain. Star‐branched chains exhibit a slightly different change in number and the mean length of trains, loops and tails with the temperature and the chain total length compared to two other types of chain.     

Dynamics of polymer melts confined by smooth walls: crossover from nonentangled region to entangled region

The authors present the results of molecular dynamics simulations of polymer films confined by smooth walls. Simulations were performed for a wide range of chain lengths covering both nonentangled and entangled regions, as well as film thicknesses ranging from the order of unperturbed chain size to the bulk state. The simulation results for the chain size dependence on the film thickness are compared with the prediction of the scaling model. By measuring the correlation function of the end-to-end vectors, we have determined the relaxation time of confined polymer chains in different entangled states. It is shown that there is a minimum in the relaxation time of long chains when decreasing the film thickness, which is partially due to the confinement-induced disentanglement effect.     

Polymer translocation in solid-state nanopores: dependence of scaling behavior on pore dimensions and applied voltage

We investigate unforced and forced translocation of a Rouse polymer (in the absence of hydrodynamic interactions) through a silicon nitride nanopore by three-dimensional Langevin dynamics simulations, as a function of pore dimensions and applied voltage. Our nanopore model consists of an atomistically detailed nanopore constructed using the crystal structure of β-Si(3)N(4). We also use realistic parameters in our simulation models rather than traditional dimensionless quantities. When the polymer length is much larger than the pore length, we find the translocation time versus chain length scales as τ ～ N(2+ν) for the unforced case and as τ ～ N((1+2ν)/(1+ν)) for the forced case. Our results agree with theoretical predictions which indicate that memory effects and tension on the polymer chain play an important role during the translocation process. We also find that the scaling exponents are highly dependent on the applied voltage (force). When the length of the polymer is on the order of the length of the pore, we do not find a continuous scaling law, but rather scaling exponents that increase as the length of the polymer increases. Finally, we investigate the scaling behavior of translocation time versus applied voltage for different polymer and pore lengths. For long pores, we obtain the theoretical scaling law of τ ～ 1/V(α), where α ? 1 for all voltages and polymer lengths. For short pores, we find that α decreases for very large voltages and/or small polymer lengths, indicating that the value of α = 1 is not universal. The results of our simulations are discussed in the context of experimental measurements made under different conditions and with differing pore geometries.     

Structure of polyelectrolyte complexes by Brownian dynamics simulation: effects of the bond length asymmetry of the polyelectrolytes

Brownian dynamics simulations were performed to study the structure of polyelectrolyte complexes formed by two flexible, oppositely charged polyelectrolyte chains. The distribution of monomers in the complex as well as the radius of gyration and structure factor of complexes and individual polyelectrolytes are reported. These structural properties were calculated for polyelectrolyte chains with equal number of monomers, keeping constant the bond length of the negative chain and increasing the bond length of the positive chain. This introduces an asymmetry in the length of the chains that modulates the final structure of the complexes. In the symmetric case the distribution of positive and negative monomers in the complex are identical, producing clusters that are locally and globally neutral. Deviations from the symmetric case lead to nonuniform, asymmetric monomer distributions, producing net charge oscillations inside the complex and large changes in the radius of gyration of the complex and individual chains. From the radius of gyration of the polyelectrolyte chains it is shown that the positive chain is much more folded than the negative chain when the chains are asymmetric, which is also confirmed through the scaling behavior of the structure factors.     

Molecular dynamics simulations of dendritic polyelectrolytes with flexible spacers in salt free solution

We present the results of molecular dynamics simulations of dendritic polyelectrolytes in dilute salt-free solutions. The dendritic polyelectrolytes are modeled as an ensemble of regular-branched bead-spring chains of neutral and charged Lennard-Jones particles with explicit counterions. A wide range of molecular variables of the dendritic polyelectrolytes such as generation number, spacer length, and charge density were considered in the simulations. The effect of dendrimer size on relaxation time, the conformation of spacers, and the size dependence of the dendrimer on molecular variables are discussed and compared with a Flory type theory. The osmotic coefficients of the dilute dendritic polyelectrolyte solutions, as well as the profiles of monomers and counterions, are calculated directly from the simulations. Our simulation results show that the inner spacers of the dendrimers are extensively stretched, and the size dependence on the molecular weight deviates from the scaling prediction that assumes a Gaussian elasticity of the spacer.     

Persistence lengths and structure factors of wormlike polymers under confinement

The behavior of semiflexible chains modeling wormlike polymers such as DNA and actin in confined spaces was explored by coarse-grained Monte Carlo simulations. The persistence length P, mean end-to-end distance R2, mean radius of gyration Rg2, and the size ratio R2/Rg2 were computed for chains in slits, cylinders, and spheres. It was found that the intrinsic persistence length of a free chain undergoes on confinement substantial alteration into the apparent persistence length. The qualitative differences were found in trends of the apparent persistence lengths between slits and cylinders on one side and spheres on the other side. The quantities P, R2, Rg2, and R2/Rg2 display similar dependences upon squeezing the chains in nanopores. The above quantities change nonmonotonically with confinement in slits and cylinders, whereas they drop smoothly with decreasing radius of a sphere. For elongation of a chain in a cylinder, two regimes corresponding to strong and moderate confinements were found and compared to experiments and predictions of the blob and Odijk theories. In a spherical cavity, the toroidal chain structure with a hole in the center was detected under strong confinements. The scattering form factor S(q) computed for semiflexible confined chains revealed three regimes of behavior in a slit and a cylinder that matched up well with the scaling theory. The complex form of the function S(q) computed for a sphere was interpreted as a sign of the toroidal structure. A reasonable agreement was found between the simulations and measurements of DNA and actin filaments, confined in nano- and microfluidic channels and spherical droplets, pertaining to the changes of the persistence lengths, chain elongation, and toroidal structure formation.     

Monte Carlo Simulation Studies of the Size and Shape of Ring Polymers

The present work gives a comparison between the properties of athermal ring polymers and those of linear chains. Based on bond fluctuation (BF) and pivot algorithm (PIV) for the construction of molecules, a new algorithm was developed, which proved most efficient due to large acceptance fractions and small (integral) auto‐correlation times of global properties, in addition having the advantage of a large set of different bond vectors. While the topological state of ring polymers remains unchanged by exclusive use of BF, knotted structures (which were identified with the help of Alexander polynomials) can by formed and removed by the use of PIV. In accordance with previous work, it turned out that the probability of unknotted rings (in principle) exponentially decreases with an increasing number of segments, however, so slowly that the appearance of knotted structures (ca. 0.1% for N = 512) is a rare event in the range of chain‐lengths evaluated (N = 32 – 8192). The chain‐length dependence of global quantities of ring polymers are described by the use of scaling relations with proper short chain corrections, in analogy to linear chains. The instantaneous shape of ring polymers is more symmetric than that of linear chains. Local quantities, i.e., mean squared bond lengths and mean bond angles are the same for both systems, at least in the limit of an infinite number of segments.     

A molecular dynamics study on universal properties of polymer chains in different solvent qualities. Part I. A review of linear chain properties

This paper investigates the conformational and scaling properties of long linear polymer chains. These investigations are done with the aid of Monte Carlo (MC) and molecular dynamics (MD) simulations. Chain lengths that comprise several orders of magnitude to reduce errors of finite size scaling, including the effect of solvent quality, ranging from the athermal limit over the theta-transition to the collapsed state of chains are investigated. Also the effect of polydispersity on linear chains is included which is an important issue in the real fabrication of polymers. A detailed account of the hybrid MD and MC simulation model and the exploited numerical methods is given. Many results of chain properties in the extrapolated limit of infinite chain lengths are documented and universal properties of the chains within their universality class are given. An example of the difference between scaling exponents observed in actual solvents and those observed in the extremes of "good solvents" and "theta-solvents" in simulations is provided by comparing simulation results with experimental data on low density polyethylene. This paper is concluded with an outlook on the extension of this study to branched chain systems of many different branching types.     

Translocation of α-helix chains through a nanopore

The translocation of α-helix chains through a nanopore is studied through Langevin dynamics simulations. The α-helix chains exhibit several different characteristics about their average translocation times and the α-helix structures when they transport through the nanopores under the driving forces. First, the relationship between average translocation times τ and the chain length N satisfies the scaling law, τ～N(α), and the scaling exponent α depends on the driving force f for the small forces while it is close to the Flory exponent (ν) in the other force regions. For the chains with given chain lengths, it is observed that the dependence of the average translocation times can be expressed as τ～f(-1/2) for the small forces while can be described as τ～f in the large force regions. Second, for the large driving force, the average number of α-helix structures N(h) decreases first and then increases in the translocation process. The average waiting time of each bead, especially of the first bead, is also dependent on the driving forces. Furthermore, an elasticity spring model is presented to reasonably explain the change of the α-helix number during the translocation and its elasticity can be locally damaged by the large driving forces. Our results demonstrate the unique behaviors of α-helix chains transporting through the pores, which can enrich our insights into and knowledge on biopolymers transporting through membranes.     

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.     

Computer Simulation of Adsorbed Polymer Chains with a Different Molecular Architecture

Simulations of simple models of polymer chains were carried out by the means of the dynamic Monte Carlo method. The model chains were confined to a simple cubic lattice. Three different chain architectures were studied: linear, star‐branched and ring chains. The polymer model chain interacted with an impenetrable surface with a simple contact attractive potential. It was found that size parameters of all these polymers obey scaling laws. The temperatures of the transitions from weakly to strongly adsorbed chain were determined. It was shown for weakly adsorbed chains that ring polymers are always ca. 50% more adsorbed than linear and star‐branched ones. The properties of adsorbed linear and star‐branched polymers are very similar in the length of chain and the strength of adsorption studied. Strongly adsorbed ring polymers are still more adsorbed but differences between all kinds of chains become less pronounced.     

Conformational statistics of polymer chain terminally attached to wall (II)

The SAW tail chains were studied. The permitted conformational number and the mean square end-to-end distance as a function of the chain length N for such a model tail chain were obtained by computer simulations, including the exact enumeration and Monte Carlo method. These two basic quantities obeyed the relations deduced from the scaling law. The critical exponents and the lattice indexes were given by fitting the data of the computer experiments. It has been shown that there is a certain extension in the size of the SAW tail chains as well as the NRW tail chains in the direction normal to the wall. The normal component of the mean square end-to-end distance is almost twice as large as the parallel component of the short chain SAW. However, as N →∞, the effect of the wall on the chain conformation becomes a little weak because of the self-avoiding behavior for the model. That is quite different from the case of the NRW tail chain. Project supported by the National Natural Science Foundation of China     

Random copolymers at a selective interface: saturation effects

Combining scaling arguments and Monte Carlo simulations using the bond fluctuation method we have studied concentration effects for the adsorption of symmetric AB-random copolymers at selective, symmetric interfaces. For the scaling analysis we consider a hierarchy of two length scales given by the excess (adsorption) blobs and by two dimensional thermal blobs in the semidilute surface regime. When both length scales match, a densely packed array of adsorption blobs is formed (saturation). We show that for random copolymer adsorption the interface concentration can be further increased (oversaturation) due to reorganization of excess blobs. Crossing over this threshold results in a qualitative change in the behavior of the adsorption layer which involves a change in the average shape of the adsorbed chains towards a hairpinlike form. We have analyzed the distribution of loops and tails of adsorbed chains in the various concentration regimes as well as the chain order parameter, concentration profiles, and the exchange rate of individual chains. We emphasized the role of saturation scaling which dominates the behavior of static and dynamic quantities at higher surface concentration.     

高分子相分离的分子动力学模拟

用粗粒化分子动力学(MD)模拟方法从分子层次研究两组分聚合物共混体系相分离过程中的动力学. 在相分离初期, 相区尺寸不随时间增加而变化; 在相分离中期, 相区尺寸与时间有很好的标度关系, 标度指数(α=1/3)符合Lifshiz-Slyozov提出的以扩散为主导的蒸发-凝聚机理的标度预测; 在相分离后期, 体系实现宏观相分离, 相区尺寸不再随时间改变而变化. 体积分数小的高分子链尺寸在相分离过程中先收缩再扩张, 在实现宏观相分离后, 高分子链尺寸又回到本体状态尺寸.     

Excluded volume scaling for polymers

The excluded volume of several polymers in the dilute solution regime is calculated using the Monte Carlo integration. The calculated scaling exponent, λ, for the excluded volume for a polymer chain with another chain of the same length is 1.74±0.02. This exponent is consistent with the idea that the interaction of chains with one another in a good solvent is similiar to the interaction of two hard spheres. The effective radius of the hard sphere is proportional to the radius of gyration which has a scaling exponent of ν=0.595±0.005. This result is close to the theoretical value of 0.589. This study establishes the relationship λ=3ν.     

Computer simulation of DNA orientation and deformation in a shear flow field

The structure and orientation of semiflexible chain molecules in a shear flow field were studied by Brownian dynamics simulation. Molecules in the size range 200 nm to 1 μm were modeled as chains of spherical subunits with parameters chosen to mimic the size and persistence length of B-DNA. The analysis of the steady-state orientation showed a rather broad and asymmetric distribution. The simulations also showed that the orientation of the largest main axis of the moment of inertia tensor is significantly higher compared to the orientation obtained from averaging over the individual bonds in the molecules, the latter procedure being the relevant case when comparing with, e.g., linear dichroism experiments.     

Influence of molecular topology on the static and dynamic properties of single polymer chain in solution

The influence of molecular topology on the structural and dynamic properties of polymer chain in solution with ring structure, three-arm branched structure, and linear structure are studied by molecular dynamics simulation. At the same degree of polymerization (N), the ring-shaped chain possesses the smallest size and largest diffusion coefficient. With increasing N, the difference of the radii of gyration between the three types of polymer chains increases, whereas the difference of the diffusion coefficients among them decreases. However, the influence of the molecular topology on the static and the dynamic scaling exponents is small. The static scaling exponents decrease slightly, and the dynamic scaling exponents increase slightly, when the topology of the polymer chain is changed from linear to ring-shaped or three-arm branched architecture. The dynamics of these three types of polymer chain in solution is Zimm-like according to the dynamic scaling exponents and the dynamic structure factors.     

Self-assembly of patchy particles into polymer chains: a parameter-free comparison between Wertheim theory and Monte Carlo simulation

The authors numerically study a simple fluid composed of particles having a hard-core repulsion, complemented by two short-ranged attractive (sticky) spots at the particle poles, which provides a simple model for equilibrium polymerization of linear chains. The simplicity of the model allows for a close comparison, with no fitting parameters, between simulations and theoretical predictions based on the Wertheim perturbation theory. This comparison offers a unique framework for the analytic prediction of the properties of self-assembling particle systems in terms of molecular parameters and liquid state correlation functions. The Wertheim theory has not been previously subjected to stringent tests against simulation data for ordering across the polymerization transition. The authors numerically determine many of the thermodynamic properties governing this basic form of self-assembly (energy per particle, order parameter or average fraction of particles in the associated state, average chain length, chain length distribution, average end-to-end distance of the chains, and the static structure factor) and find that predictions of the Wertheim theory accord remarkably well with the simulation results.