Event-driven dynamics of rigid bodies interacting via discretized potentials

A framework for performing event-driven, adaptive time step simulations of systems of rigid bodies interacting under stepped or terraced potentials in which the potential energy is only allowed to have discrete values is outlined. The scheme is based on a discretization of an underlying continuous potential that effectively determines the times at which interaction energies change. As in most event-driven approaches, the method consists of specifying a means of computing the free motion, evaluating the times at which interactions occur, and determining the consequences of interactions on subsequent motion for the terraced potential. The latter two aspects are shown to be simply expressible in terms of the underlying smooth potential. Within this context, algorithms for computing the times of interaction events and carrying out efficient event-driven simulations are discussed. The method is illustrated on a system composed of rigid rods in which the constituents interact via a terraced potential that depends on the relative orientations of the rods.     

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.     

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.     

Monte Carlo simulations of systems of rodlike molecules with semiflexible terminal groups

The results of Monte Carlo simulations of systems of rodlike molecules with semiflexible terminal groups are compared with those of systems with terminal groups at a fixed angle τ with respect to the rigid core and with those of a system containing the rigid cores alone in the same total volume. The nematic/isotropic transition temperature decreases with increasing flexibility or with increasing τ. For semiflexible groups, the transition is coupled with a conformational change favouring more extended conformations in the nematic phase. The results of the simulations are discussed in connection with those obtained for similar models in the recent literature and with the predictions of the Maier‐Saupe and Flory‐Ronca‐Irvine theories.     

Isotropic-nematic spinodals of rigid long thin rodlike colloids by event-driven Brownian dynamics simulations

The isotropic-nematic spinodals of solutions of rigid spherocylindrical colloids with various shape anisotropies L/D in a wide range from 10 to 60 are investigated by means of Brownian dynamics simulations. To make these simulations feasible, we developed a new event-driven algorithm that takes the excluded volume interactions between particles into account as instantaneous collisions, but neglects the hydrodynamic interactions. This algorithm is applied to dense systems of highly elongated rods and proves to be efficient. The calculated isotropic-nematic spinodals lie between the previously established binodals in the phase diagram and extrapolate for infinitely long rods to Onsager's [Ann. N. Y. Acad. Sci. 51, 627 (1949)] theoretical predictions. Moreover, we investigate the shear induced shifts of the spinodals, qualitatively confirming the theoretical prediction of the critical shear rate at which the two spinodals merge and the isotropic-nematic phase transition ceases to exist.     

Ordered Toroid Structures of Nanoparticles in Self-attractive Semi exible Polymer/Nanoparticle Composites

By employing dynamic Monte Carlo simulations, we investigate a coil-to-toroid transition of self-attractive semiflexible polymers and the spatial distributions of nanoparticles in selfattractive semiflexible polymer/nanoparticle composites. The conformation of self-attractive semiflexible polymers depends on bending energy and self-attractive interactions between monomers in polymer chains. A three-stage process of toroid formation for self-attractive semiflexible chains is shown: several isolated toroids, a loose toroid structure, and a compact toroid structure. Utilizing the compact toroid conformations of self-attractive semiflexible chains, we can control effectively the spatial distributions of nanoparticles in self-attractive semiflexible polymer nanocomposites, and an unconventional toroid structure of nanoparticles is observed.     

Diffusion and segmental dynamics of rodlike molecules by fluorescence correlation spectroscopy

The dynamics of weakly bending polymers is analyzed on the basis of a Gaussian semiflexible chain model and the fluorescence correlation spectroscopy (FCS) correlation function is determined. Particular attention is paid to the influence of the rotational motion on the decay of the FCS correlation function. An analytical expression for the correlation function is derived, from which the averaged segmental mean square displacement can be determined independent of any specific model for the polymer dynamics. The theoretical analysis exhibits a strong dependence of the correlation function on the rotational motion for semiflexible polymers with typical lengths and persistence lengths of actin filaments or fd viruses. Hence, FCS allows for a measurement of the rotational motion of such semiflexible polymers. The theoretical results agree well with experimental measurements on actin filaments and confirm the importance of large relaxation times.     

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.     

Kinetics of interior loop formation in semiflexible chains

Loop formation between monomers in the interior of semiflexible chains describes elementary events in biomolecular folding and DNA bending. We calculate analytically the interior distance distribution function for semiflexible chains using a mean field approach. Using the potential of mean force derived from the distance distribution function we present a simple expression for the kinetics of interior looping by adopting Kramers theory. For the parameters, that are appropriate for DNA, the theoretical predictions in comparison with the case are in excellent agreement with explicit Brownian dynamics simulations of wormlike chain (WLC) model. The interior looping times (tauIC) can be greatly altered in the cases when the stiffness of the loop differs from that of the dangling ends. If the dangling end is stiffer than the loop then tauIC increases for the case of the WLC with uniform persistence length. In contrast, attachment of flexible dangling ends enhances rate of interior loop formation. The theory also shows that if the monomers are charged and interact via screened Coulomb potential then both the cyclization (tauc) and interior looping (tauIC) times greatly increase at low ionic concentration. Because both tauc and tauIC are determined essentially by the effective persistence length [lp(R)] we computed lp(R) by varying the range of the repulsive interaction between the monomers. For short range interactions lp(R) nearly coincides with the bare persistence length which is determined largely by the backbone chain connectivity. This finding rationalizes the efficacy of describing a number of experimental observations (response of biopolymers to force and cyclization kinetics) in biomolecules using WLC model with an effective persistence length.     

Constraint dynamics algorithm for simulation of semiflexible macromolecules

Semiflexible models are often used to study macromolecules containing stable structural elements. Based on rigid body dynamics, we developed a rigid fragment constraint dynamics algorithm for the simulation of semiflexible macromolecules. Stable structural elements are treated as rigid fragments. Rigid fragment constraints, defined as combinations of distance constraints and position constraints, are introduced to limit internal molecular motion to the required mode. The constraint forces are solved separately for each rigid fragment constraint and iteratively until all constraint conditions are satisfied within a given tolerance at each time step, as is done for the bond length constraint in the SHAKE algorithm. The orientation of a rigid fragment is represented by the quaternion parameters, and both translation and rotation are solved by the leap-frog formulation. We tested the algorithm with molecular dynamics simulations of a series of peptides and a small protein. The computation cost for the constraints is roughly proportional to the size of the molecule. In the microcanonical ensemble simulation of polyvalines, the total energy was conserved satisfactorily with time steps as large as 20 fs. A helix folding simulation of a synthetic peptide was carried out to show the efficiency of the algorithm in a conformational search. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1555–1566, 1998     

Periodic orientational motions of rigid liquid-crystalline polymers in shear flow

The collective periodic motions of liquid-crystalline polymers in a nematic phase in shear flow have, for the first time, been simulated at the particle level by Brownian dynamics simulations. A wide range of parameter space has been scanned by varying the aspect ratio L/D between 10 and 60 at three different scaled volume fractions Lphi/D and an extensive series of shear rates. The influence of the start configuration of the box on the final motion has also been studied. Depending on these parameters, the motion of the director is either characterized as tumbling, kayaking, log-rolling, wagging, or flow-aligning. The periods of kayaking and wagging motions are given by T=4.2(Lphi/D)gamma(-1) for high aspect ratios. Our simulation results are in agreement with theoretical predictions and recent shear experiments on fd viruses in solution. These calculations of elongated rigid rods have become feasible with a newly developed event-driven Brownian dynamics algorithm.     

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.     

Relaxation of a semiflexible grafted polymer

The relaxation of single grafted semiflexible chains freely rotating around the grafting point is investigated by means of two dimensional computer simulations and scaling arguments. Both free chains and chains surrounded by topological obstacles are considered. We compute the autocorrelation of the end-to-end vector for the whole chain and for terminal sections of various lengths. Our results are relevant for the relaxation of star polymers with stiff arms or branched semiflexible polymers moving in an array of obstacles.     

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.     

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 Angiotensin (1-7) Vasoactive Peptide in Aqueous Solution at the Density-Functional Based Tight-Binding Level

Summary : Structure and dynamics of heptapeptide Angiotensin (1-7) in aqueous solution have been investigated by means of density-functional based tight-binding molecular dynamics simulations. Solvent-solute interactions have been studied using a hybrid QM/MM method. The backbone of the heptapeptide remains relatively rigid in aqueous solution compared to gas phase. The solvent acts as a cushion, preventing the free motion of the molecule. Tyrosine is the residue which presents the smallest flexibility and the largest number of water molecules in its first solvation shell. This is in good agreement with the previously published NMR results. The intra– and intermolecular hydrogen bridges have been quantified and analyzed in terms of conformation and stability.     

The internal dynamic modes of charged self-assembled peptide fibrils

Photon correlation spectroscopy is used to study the internal dynamics of self-assembled charged peptide fibrils. Short neutral and charged polymeric aggregates have diffusive modes due to whole macromolecular motion. For long semiflexible fibrils the logarithm of the intermediate scattering function follows a q(2)t(3/4) scaling at long times consistent with a Kratky-Porod free energy and preaveraged Oseen hydrodynamics. Persistence lengths on the order of micrometers are calculated for the peptide fibrils consistent with estimates from the liquid-crystalline phase behavior. Fibril diameters (5-35 nm) calculated from the initial decay of the correlation functions are in agreement with transmission electron microscopy measurements.     

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.     

Dynamics of Biological Polyelectrolytes

Summary: Biological polymers and structures, including proteins and DNAs, can be made in essentially monodisperse form. Proteins usually have well-defined shapes. Duplex oligonucleotides are rigid and rodlike, and longer DNAs are semiflexible coils. The DNAs also constitute a homologous series. The dynamics of both proteins and DNAs can be studied by readily available techniques such as dynamic light scattering (DLS) and fluorescence correlation spectroscopy (FCS). These systems can thus be used as model systems to elucidate elusive charge effects on the dynamics of macromolecules in solution (polyelectrolyte effects) for both rigid and semiflexible polymers. We present here as examples the results of measurements of mutual and self-diffusion coefficients dynamics of a rodlike oligonucleotide as functions of polymer concentration and the concentration of added salt (which screens the charges).