Brownian dynamics simulations of a flexible polymer chain which includes continuous resistance and multibody hydrodynamic interactions

Using methods adapted from the simulation of suspension dynamics, we have developed a Brownian dynamics algorithm with multibody hydrodynamic interactions for simulating the dynamics of polymer molecules. The polymer molecule is modeled as a chain composed of a series of inextensible, rigid rods with constraints at each joint to ensure continuity of the chain. The linear and rotational velocities of each segment of the polymer chain are described by the slender-body theory of Batchelor [J. Fluid Mech. 44, 419 (1970)]. To include hydrodynamic interactions between the segments of the chain, the line distribution of forces on each segment is approximated by making a Legendre polynomial expansion of the disturbance velocity on the segment, where the first two terms of the expansion are retained in the calculation. Thus, the resulting linear force distribution is specified by a center of mass force, couple, and stresslet on each segment. This method for calculating the hydrodynamic interactions has been successfully used to simulate the dynamics of noncolloidal suspensions of rigid fibers [O. G. Harlen, R. R. Sundararajakumar, and D. L. Koch, J. Fluid Mech. 388, 355 (1999); J. E. Butler and E. S. G. Shaqfeh, J. Fluid Mech. 468, 204 (2002)]. The longest relaxation time and center of mass diffusivity are among the quantities calculated with the simulation technique. Comparisons are made for different levels of approximation of the hydrodynamic interactions, including multibody interactions, two-body interactions, and the "freely draining" case with no interactions. For the short polymer chains studied in this paper, the results indicate a difference in the apparent scaling of diffusivity with polymer length for the multibody versus two-body level of approximation for the hydrodynamic interactions.     

Brownian dynamics simulations of needle chain and nugget chain polymer models--rigid constraint conditions versus infinitely stiff springs

It is well known that orientational correlations appear in polymer chain models when the subunits are linked by ball-socket joints implemented as rigid constraint conditions. These correlations do not appear when the subunits are connected by springlike potential forces, even in the limit of infinitely stiff springs. In a widely used class of algorithms for Brownian dynamics simulations, inertia effects are ignored. However, in the recently introduced needle chain and nugget chain algorithms, the rigid constraint correlations depend on the mass and moment of inertia. This inconsistency does not appear in the bead-rod (Kramers) polymer chain model, which also has orientational correlations introduced by rigid constraint conditions. Explicit expressions for the correlation functions are given for thermodynamic equilibrium states. Analytical expressions for the associated forces ("metric forces") and simulation results showing how the rigid constraint correlations influence dynamical properties, are also presented. Further we discuss the physical relevance of these correlations and show via simulations that their influence on stationary and dynamical properties depend significantly on chain length. We further show that if the metric forces are removed, algorithms designed with rigid constraint conditions describe a chain of segments connected by infinitely stiff springs. Finally we show that the results presented here for needle chains are relevant also for the bead-rod (Kramers) chain model, making it possible to simulate a bead-spring chain with infinitely stiff springs.     

Brownian dynamics simulation of grafted polymer brushes

We present results of computer simulations by the method of Brownian dynamics of polymeric brushes attached to impenetrable planes. For testing both model and method we have used one polymer brush attached to a repulsive plane and compare some results with Monte Carlo results of Lai and Binder on the bond fluctuation model. We have also studied two polymeric brushes attached to two parallel planes at different distances between planes, and investigate the interplay between the interpenetration of the brushes and the configurational properties of the grafted chains.     

Statistics of polymer capture by a nanopore: A Brownian dynamics simulation study

We investigate the statistics of polymer capture by a nanopore using Brownian dynamics simulations. It is found that when the velocity flux is greater than a critical velocity flux, the capture picture is a random selection process, otherwise it tends to a statistical process governed by energetic considerations. In addition, the chain ends capture probability decreases as the chain length increases and satisfies a power-law scaling of P0(N)~N-0.8.     

Stepwise growth of a single polymer chain

By monitoring the modulation of an ionic current passing through a nanoreactor formed from a protein pore, the step-by-step growth of an individual polymer chain was monitored. The observation of polymer growth at the single-molecule level will be useful for studying the kinetics of chain growth or the movement of polymers under confinement. It might also be used to synthesize "molecular fishing lines" in situ, for applications in stochastic sensing.     

A study on the structural transition of a single polymer chain by parallel tempering molecular dynamics simulation

The structural transition of a single polymer chain with chain length of 100,200 and 300 beads was investigated by parallel tempering MD simulation.Our simulation results can capture the structural change from random coil to orientationally ordered structure with decreasing temperature.The clear transition was observed on the curves of radius of gyration and global orientational order parameter P as the function of temperature,which demonstrated structural formation of a single polymer chain.The linear relationships between three components of square radius of gyration R_gx²,R_gx²,R_gz² and global orientational order P can be obtained under the structurally transformational process.The slope of the linear relationship between x（or y-axis） component R_gx²(or R_gy²) and P is negative,while that of RL as the function of P is positive.The absolute value of slope is proportional to the chain length.Once the single polymer chain takes the random coil or ordered configuration,the linear relationship is invalid.The conformational change was also analyzed on microscopic scale.The polymer chain can be treated as the construction of rigid stems connecting by flexible loops.The deviation from exponentially decreased behavior of stem length distribution becomes prominent,indicating a stiffening of the chain arises leading to more and more segments ending up in the trans state with decreasing temperature.The stem length N_tr is about 21 bonds indicating the polymer chain is ordered with the specific fold length.So,the simulation results,which show the prototype of a liquid-crystalline polymer chain,are helpful to understand the crystallization process of crystalline polymers.     

Adsorption of a single polymer chain on a surface: A molecular dynamics simulation study

We performed simulations of the physical adsorption of a single globular chain on a surface of hemispherical shape by means of molecular dynamics simulations. For the chain, we took advantage of a united atom model. Interactions within the chain were limited to stretching, bending, and torsional as well as nonbonded interactions between the nonadjacent atoms. The interaction between each chain element and the surface formation are reigned by a Lennard–Jones potential. In this article, we focused on differences in the behavior of the adsorbed globule to the free unadsorbed one particularly in two different zones of the immediate vicinity of the surface. There were strong indications for a localized acceleration of the dynamics as compared with the bulk that appears in an increase of trans–gauche switches. For explanation we came up with an adsorption scenario. Special attention was given to the shift of the percentage of trans and gauche conformations within the globule in dependence on the strength of the adsorption potential that might be related to crystallization or glass transition. © 2001 John Wiley & Sons, Inc. J Polym Sci Part B: Polym Phys 39: 2333–2339, 2001     

Universal properties of a single polymer chain in slit: Scaling versus molecular dynamics simulations

We revisit the classical problem of a polymer confined in a slit in both of its static and dynamic aspects. We confirm a number of well known scaling predictions and analyze their range of validity by means of comprehensive molecular dynamics simulations using a coarse-grained bead-spring model of a flexible polymer chain. The normal and parallel components of the average end-to-end distance, mean radius of gyration and their distributions, the density profile, the force exerted on the slit walls, and the local bond orientation characteristics are obtained in slits of width D=4/10 (in units of the bead diameter) and for chain lengths N=50/300. We demonstrate that a wide range of static chain properties in normal direction can be described quantitatively by analytic model-independent expressions in perfect agreement with computer experiment. In particular, the observed profile of confinement-induced bond orientation is shown to closely match theory predictions. The anisotropy of confinement is found to be manifested most dramatically in the dynamic behavior of the polymer chain. We examine the relation between characteristic times for translational diffusion and lateral relaxation. It is demonstrated that the scaling predictions for lateral and normal relaxation times are in good agreement with our observations. A novel feature is the observed coupling of normal and lateral modes with two vastly different relaxation times. We show that the impact of grafting on lateral relaxation is equivalent to doubling the chain length.     

Brownian dynamics of polymeric chain in strong external field

The cooperativity of conformational transitions in strained linear polymer chain was investigated by the method of Brownian dynamics. Deformation of a chain consisting of N=32 and 64 bonds was created by strong external field of dipole type. Correlations are discussed in terms of hazard-plot analysis.     

Electrophoresis of a bead-rod chain through a narrow slit: a Brownian dynamics study

We use two-dimensional Brownian dynamics simulations to study the electrophoresis of a bead-rod chain through a narrow slit. A constant electric field is assumed to act inside and outside of the slit, and each bead on the chain is assigned a constant uniform charge. We calculate the dependence of the polymer transit velocity on chain length, slit dimensions (width-to-length ratio), and electric-field strength. For sufficiently narrow slits, the transit velocity increases nonlinearly with the applied field for low-field strengths, whereas it increases linearly for high-field strengths. In the low-field strength region and for sufficiently narrow slits, the transit velocity decreases rapidly for small chain lengths and then decreases slowly beyond a critical chain length. As the slit width increases, the transit velocity decreases with chain length in more continuous manner, and for sufficiently large slits the transit velocity becomes independent of chain length as expected. Distributions of the chain end-to-end distances and the translocation times depend strongly on the relative size of the chain to the slit. These results show the sensitivity of the transit velocity vs chain length relationship to the slit dimensions and applied electric-field strength, and suggest that there may be an optimal slit width for a given field strength and vice versa. The results may be useful for microfluidic separations and for understanding the motion of biological polymers through narrow constrictions.     

Coil-globule transition: Self-assembly of a single polymer chain

The coil collapse problem is of interest not only because it represents the simplest model of protein folding, but also because of its fundamental importance as related to polymer nanostructures and fractionation. It is extremely difficult to observe the coil-to-globule transition experimentally because at finite concentrations in a poor solvent, the macromolecules tend to aggregate due to phase separation when the collapsed state is being achieved. In the mid-1980s, two-stage kinetics of a single-chain collapse was proposed theoretically.^1,2 The first successful experimental observation of a two-stage coil-to-globule transition was achieved by quenching a dilute solution of polystyrene (PS) in cyclohexane.³ By using a thinnest capillary tube cell with a wall thickness of 0.01 mm and a diameter of 5 mm for dynamic light scattering, two relaxation times, τ_crum for the crumpled globule state and τ_eq for the compact globule state, were determined⁴ for the first time. The relaxation times were much slower than expected. From the size of the crumpled globule and that of the compact globule and by assuming the intraglobular density to be uniform, the volume fraction of the PS chain in the crumpled globule state, ϕ_crum, and that in the compact globule state, ϕ_comp, can be estimated, with ϕ_crum = 0.02 and ϕ_comp ∼ 0.24-0.4 at 28°C for polystyrene in cyclohexane. The results imply that a single-chain globule contains a large amount of solvent. It should also be noted that ϕ_comp is temperature dependent, i.e., one would have to go to hypothetically low temperatures in order to squeeze out all the solvent (cyclohexane) in the compact PS globule. The single-chain coil collapse state could be achieved under equilibrium conditions by using a high molecular weight, M_w ∼ 1.08 × 10⁷ g/mol; M_w/M_n < 1.06) poly(N-isopropylacrylamide) (PNIPAM) in water,<⁵ even though the ten million molecular weight for PNIPAM was substantially lower than that for polystyrene (M_w ∼ 50 × 10⁶ g/mole).⁶ Under equilibrium conditions, it was feasible to determine both the hydrodynamic radius R_h and the radius of gyration R_g. The ratio of R_g/R_h changed from 1.45 to 0.77, clearly demonstrating the transition from the theta coil state to the compact globule state. At the maximum value of the scaled expansion factor α_s³ |τ| M_w^1/2, R_g/R_h = 1.33 where α_s = R_g/R_g (θ) and τ = |T-θ| / θ with θ being the theta temperature. In the compact globule, R_g/R_h was of the order of 0.7, implying that the PNIPAM compact globule in water still contained ∼80% water, of the same order of magnitude as the PS compact globule in cyclohexane at 7° below its theta temperature (35°C).     

The properties of a single polymer chain in solvent confined in a slit: A molecular dynamics simulation

A single polymer chain in solvent confined in a slit formed by two parallel plates is studied by using molecular dynamics simulation method. The square radii of gyration and diffusion behaviors of polymers are greatly affected by the distance between the two plates, but they do not follow the same way. The chain size decays drastically with increasing h (h is the distance between two plates), until a basin occurs, and a universal h/〈R _g〉₀ dependence for polymer chains with different degrees of polymerization can be obtained. While, for the chain’s diffusion coefficient, it decays monotonously and there is no such basin-like behavior. Furthermore, we studied the radial distribution function of confined polymer chains to explain the reason why there is a difference for the decay behaviors between dynamic properties and static properties. Besides, we also give the degree of confinement dependence of the static scaling exponent for a single polymer chain. Our work provides an efficient way to estimate the dynamics and static properties of confined polymer chains, and also helps us to understand the behavior of polymer chains under confinement.     

Brownian dynamics of grafted polymer chains: time dependent properties

Results of computer simulations of polymer layers consisting of chains grafted by one end on an unpenetrable plane are presented. Characteristics of translational and rotational motion of different chain segments and correlation functions of chain radii were calculated both for single layers at different grafting densities s and for two interacting layers at different distances D between parallel grafting planes. Two values of grafting density were used in the latter case. The behavior of different correlation times as function of s and D and the interplay between the interpenetration of the brushes and rotational and translational motion are discussed. Both relaxation functions and mean square displacements are discussed in terms of stretched exponentials, and the behavior of the resulting “Kohlrausch exponents” γ is presented in detail.     

A case for using randomly labeled polymers to study long-range polymer chain dynamics by fluorescence

The process of excimer formation was studied for a series of pyrene end-labeled polystyrenes (PS(X)-Py 2 where X is the polymer molecular weight equal to 3, 4.5, 8, 12.7, and 14.6 K) and two series of polystyrenes randomly labeled with pyrene (CoE-PS and CoA-PS) in seven different solvents. The solvent viscosities ranged from 0.41 to 1.92 mPa x s, while the solvent quality ranged from good to poor solvents for polystyrene, as determined by intrinsic viscosity measurements. Steady-state fluorescence spectra of the pyrene-labeled polymers were acquired, and the excimer to monomer ratios showed that excimer formation increased strongly with a decrease in solvent viscosity. The monomer and excimer time-resolved fluorescence decays were also acquired and fitted globally to either the Birks' scheme or the fluorescence blob model (FBM) for the end- or randomly labeled polymers, respectively. All parameters reporting on the long-range polymer chain dynamics (LRPCD) obtained from the analysis of the fluorescence data acquired with the PS(X)-Py 2, CoE-PS, and CoA-PS series yielded virtually identical trends, demonstrating that these fluorescence experiments yield results that are internally consistent with one another. Considering the substantial advantages associated with the preparation and study of randomly labeled polymers, this report presents an appealing case for the use of randomly labeled polymers in the study of LRPCD.     

Brownian dynamics algorithm for bead-rod semiflexible chain with anisotropic friction

A model of semiflexible bead-rod chain with anisotropic friction can mimic closely the hydrodynamics of a slender filament. We present an efficient algorithm for Brownian dynamics simulations of this model with configuration dependent anisotropic bead friction coefficients. The algorithm is an extension of that given previously for the case of configuration independent isotropic friction coefficients by Grassia and Hinch [J. Fluid Mech. 308, 255 (1996)]. We confirm that the algorithm yields predicted values for various equilibrium properties. We also present a stochastic algorithm for evaluation of the stress tensor, and we show that in the limit of stiff chains the algorithm recovers the results of Kirkwood and Plock [J. Chem. Phys. 24, 665 (1956)] for rigid rods with hydrodynamic interactions.     

New directions in single polymer dynamics

Single polymer techniques are a powerful set of molecular-level tools that enable the direct observation of polymer chain dynamics under highly non-equilibrium conditions. In this way, single polymer methods have been used to uncover fundamentally new information regarding the static and dynamic properties of polymeric materials. However, to achieve the full potential of these new methods, single polymer techniques must be further advanced to enable the study of polymers with complex architectures, heterogeneous chemistries, flexible backbones, and intermolecular interactions in entangled solutions, which reaches far beyond the current state-of-the-art. In this article, we explore recent developments in the area of single polymer physics, including single molecule force spectroscopy and fluorescence microscopy, and we further highlight exciting new directions in the field. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2013     

The chain sucker: translocation dynamics of a polymer chain into a long narrow channel driven by longitudinal flow

Using analytical techniques and Langevin dynamics simulations, we investigate the dynamics of polymer translocation into a narrow channel of width R embedded in two dimensions, driven by a force proportional to the number of monomers in the channel. Such a setup mimics typical experimental situations in nano/microfluidics. During the translocation process if the monomers in the channel can sufficiently quickly assume steady state motion, we observe the scaling τ ～ N∕F of the translocation time τ with the driving force F per bead and the number N of monomers per chain. With smaller channel width R, steady state motion cannot be achieved, effecting a nonuniversal dependence of τ on N and F. From the simulations we also deduce the waiting time distributions under various conditions for the single segment passage through the channel entrance. For different chain lengths but the same driving force, the curves of the waiting time as a function of the translocation coordinate s feature a maximum located at identical s(max), while with increasing the driving force or the channel width the value of s(max) decreases.     

Morphological variation in a toroid generated from a single polymer chain

A single semiflexible polymer chain folds into a toroidal object under poor solvent conditions. In this study, we examined the morphological change in such a toroidal state as a function of the cross-sectional area and stiffness of the chain together with the surface energy, which characterizes the segmental interaction parameter. Changes in the thickness and outer/inner radius on a toroid are interpreted in terms of these parameters. Our theoretical expectation corresponds to the actual morphological changes in a single giant DNA molecule as observed by electron microscopy.