Scattering properties of a single semiflexible polyelectrolyte

The structure factor of a single semiflexible polyelectrolyte has been calculated as a function of chain length, intrinsic backbone stiffness, and salt concentration. Because of the insignificant coupling of the intrinsic stiffness and electrostatic persistence length, we carry out our calculations in the flexible limit. Within the variational scheme adopted here, we obtain fractal dimensions consistent with our earlier calculations of the configurational properties. As the chain length is increased, the electrostatic interaction is progressively screened, leading to the crossover regions. In the first crossover, the effective fractal dimension, D_eff, is as low as 1, and in the second crossover D_eff is 5/3, although the radius of gyration exponent is 2/5. © 2001 John Wiley & Sons, Inc. J Polym Sci Part B: Polym Phys 39: 2644–2652, 2001     

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     

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.     

Directed motion of a polyelectrolyte micelle along tethered chains of oppositely charged polyelectrolyte brush

The complexation of different single polyelectrolyte (PE) micelles formed by linear diblock copolymers with oppositely charged brushes with varying grafting densities and charge content was studied by means of molecular dynamics simulations using the primitive model. We found that all micelles perform a directed motion along the vertical z axis on the grafted surface where they trapped while on the other axes the motion is restricted in a circle in which the diameter decreases with the increase of the hydrophilic length of the linear diblock copolymer. The motion of micelles is characterized as super diffusion inside brushes with low densities and low charge content. At high grafting densities and charge content the diffusion becomes Fickian or slightly subdiffusive. The number of the absorbed brush chains on the micelle corona increases almost monotonically with the increase of brush grafting density or with the decrease of charge content. The distance from the surface in which the micelle is trapped can be controlled by the charge density along the grafted PE chain. © 2019 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2019 , 57, 621–631     

Spatial blockage of ionic current for electrophoretic translocation of DNA through a graphene nanopore

Graphene nanopore has been promising the ultra‐high resolution for DNA sequencing due to the atomic thickness and excellent electronic properties of the graphene monolayer. The dynamical translocation phenomena and/or behaviors underneath the blocked ionic current, however, have not been well unveiled to date for the translocation of DNA electrophoretically through a graphene nanopore. In this report, the assessment on the sensitivity of ionic current to instantaneous statuses of DNA in a 2.4 nm graphene nanopore was carried out based on the all‐atom molecular dynamics simulations. By filtering out the thermal noise of ionic current, the instantaneous conformational variations of DNA in a graphene nanopore have been unveiled from the fluctuations of ionic current, because of the spatial blockage effect of DNA against ionic current. Interestingly, the neighborhood effect of DNA against ionic current was also observed within a distance of 1.5 nm nearby the graphene nanopore, suggesting the further precise control for DNA translocation through a graphene nanopore in gene sequencing. Moreover, the sensitivity of the blocked ionic current toward the instantaneous conformations of DNA in a graphene nanopore demonstrates the great potential of graphene nanopores in the dynamics analysis of single molecules.     

Theoretical study on the translocation of partially charged polymers through nanopore

The translocation time τ of partially charged polymers through a neutral nanopore is calculated using Fokker–Planck equation with adsorbing–adsorbing boundary conditions. For the polymer with one charged monomer, we find that τ is dependent on the position of the charged monomer and on the magnitude of the driving force f inside the nanopore. When the charge is located at the front half of the polymer chain, τ is larger than that of neutral polymer and increases with f. When the charge is located at the back half, it is smaller than that of the neutral polymer and decreases with increasing f. We have also studied the behavior of a symmetrical polymer with two like charges located symmetrically in the chain and that of an asymmetrical polymer with two unlike charges. Moreover, we have calculated the translocation time for a general condition of polymer with two randomly distributed charges. All results show that τ is dependent on the positions of charges in the polymer chain and on the magnitude of the driving force. The results can be explained qualitatively by the free‐energy landscape of polymer translocation. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2017 , 55, 1017–1025     

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     

Brownian dynamics simulation of polyelectrolyte dilute solutions: Relaxation time and elongational flow

The authors used the bead‐and‐spring model and the Brownian dynamics simulation technique including hydrodynamic interaction to study the behavior of dilute polyelectrolyte solutions under elongational flow. First they carried out simulations to determine the longest relaxation time of a polyelectrolyte, finding that the relaxation time depends on the ionic strength of the solution. Then, they studied the coil‐stretch transition of polyelectrolyte molecules in elongational flow and determined the critical value of the elongational rate necessary in order this transition to occur. In this way, they could compute the value of the Deborah number at which coil‐stretch transition sets in for polyelectrolyte dilute solutions. Finally, they studied the power law relationship that relates the critical elongational rate with the molecular weight of the polyelectrolyte. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 714–722, 2007     

Simulation Study of the Conformational Properties of Diblock Polyelectrolytes in Salt Solutions

Coarse-grained molecular dynamics simulations are performed to understand the behavior of diblock polyelectrolytes in solutions of divalent salt by studying the conformations of chains over a wide range of salt concentrations. The polymer molecules are modeled as bead spring chains with different charged fractions and the counterions and salt ions are incorporated explicitly. Upon addition of a divalent salt, the salt cations replace the monovalent counterions, and the condensation of divalent salt cations onto the polyelectrolyte increases, and the chains favor to collapse. The condensation of ions changes with the salt concentration and depends on the charged fraction. Also, the degree of collapse at a given salt concentration changes with the increasing valency of the counterion due to the bridging effect. As a quantitative measure of the distribution of counterions around the polyelectrolyte chain, we study the radial distribution function between monomers on different polyelectrolytes and the counterions inside the counterion worm surrounding a polymer chain at different concentrations of the divalent salt. Our simulation results show a strong dependence of salt concentration on the conformational properties of diblock copolymers and indicate that it can tune the self-assembly behaviors of such charged polyelectrolyte block copolymers.     

Mixed brushes consisting of oppositely charged Y-shaped polymers in salt free,monovalent, and divalent salt solutions

The conformation and the internal stratification of mixed brushes formed from oppositely charged Y(−) and Y(+)-shaped chains in salt free, monovalent, and divalent salt solutions were studied by means of molecular dynamics simulations using the primitive model. Scaling relations of mixed brush height with respect to the grafting surface per chain, the ratio of the total positive to the total negative charge of polyelectrolyte chains, and salt concentrations were obtained. The simulations predicted that mixed brushes show a unique response to divalent salt (1:2) solutions. For symmetric brushes having the same spacer lengths, number of chains and charged units fractions the increase of the salt concentration leads to the enrichment of the outer brush surface with Y(+) units and the lamella microphase separation. For asymmetric brushes in high salt concentration cylindrical domain microphases are formed.     

Chaperone-assisted translocation of a polymer through a nanopore

Using Langevin dynamics simulations, we investigate the dynamics of chaperone-assisted translocation of a flexible polymer through a nanopore. We find that increasing the binding energy ε between the chaperone and the chain and the chaperone concentration N(c) can greatly improve the translocation probability. Particularly, with increasing the chaperone concentration a maximum translocation probability is observed for weak binding. For a fixed chaperone concentration, the histogram of translocation time τ has a transition from a long-tailed distribution to a gaussian distribution with increasing ε. τ rapidly decreases and then almost saturates with increasing binding energy for a short chain; however, it has a minimum for longer chains at a lower chaperone concentration. We also show that τ has a minimum as a function of the chaperone concentration. For different ε, a nonuniversal dependence of τ on the chain length N is also observed. These results can be interpreted by characteristic entropic effects for flexible polymers induced by either the crowding effect from a high chaperone concentration or the intersegmental binding for the high binding energy.     

Evaluation of the adsorption trends of a low molecular-weight polyelectrolyte with a site-binding model

The site-binding model is very useful for describing the adsorption of ions and small ionized molecules. It has been slightly modified to include multi-site adsorption of larger molecules such as oligomers and low molecular weight polyelectrolytes. We describe alterations of the classical model and the results of calculations for adsorption of polyacrylic acid onto titanium dioxide as an example. The triple layer model is used to relate charge densities to interfacial potential profiles. Comparison between adsorption trends and the surface layer composition as a function of pH and ionic strength demonstrates the prominent influence of ions binding in the adsorption process. The site-binding model makes it easy to simulate the ions displacement associated with polyelectrolyte adsorption. Strongly bound electrolyte anions prevent polyacrylic acid from adsorbing, and, in contrast, electrostatic screening due to cation condensation makes it easier. Calculations of the pH change in the solution, due to adsorption, are also made by comparing ionization ratios of both the surface and polymer units in the adsorbed layer and before adsorption. Trends in electrokinetic potentials as a function of the solution's parameters are evaluated assuming the identity of the shearing surface and the inner boundary of the diffuse layer. All data compare well with experimental values. The very good agreement betwen the experiment and model calculations supports the fact that (small) polyelectrolyte molecules adsorb essentially flat on the surface.     

Superselective Adsorption of Multivalent Polymer Chains to a Surface with Receptors

Multivalent polymer chains exhibit excellent prospect in biomedical applications by serving as therapeutic agents. Using three-dimensional (3D) Langevin dynamics simulations, we investigate adsorption behaviors of multivalent polymer chains to a surface with receptors. Multivalent polymer chains display superselective adsorption. Furthermore, the range of density of surface receptors at which a multivalent polymer chain displays a superselective behavior, narrows down for chains with higher density of ligands. Meanwhile, the optimal density of surface receptors where the highest superselectivity is achieved, decreases with increasing the density of ligands. Then, the conformational properties of bound multivalent chains are studied systematically. Interestingly, we find that the equilibrium radius of gyration R_g and its horizontal component have a maximum as a function of the density of surface receptors. The scaling exponents of R_g with the length of chain suggest that with increasing the density of surface receptors., the conformations of a bound multivalent polymer chain first fall in between those of a two-dimensional (2D) and a 3D chain, while it is slightly collapsed subsequently.     

Electrokinetic particle translocation through a nanopore containing a floating electrode

Electrokinetic particle translocation through a nanopore containing a floating electrode is investigated by solving a continuum model, composed of the coupled Poisson-Nernst-Planck (PNP) equations for the ionic mass transport and the modified Stokes equations for the flow field. Two effects due to the presence of the floating electrode, the induced-charge electroosmosis (ICEO) and the particle-floating electrode electrostatic interaction, could significantly affect the electrokinetic mobility of DNA nanoparticles. When the electrical double layers (EDLs) of the DNA nanoparticle and the floating electrode are not overlapped, the particle-floating electrode electrostatic interaction becomes negligible. As a result, the DNA nanoparticle could be trapped near the floating electrode arising from the induced-charge electroosmosis when the applied electric field is relatively high. The presence of the floating electrode attracts more ions inside the nanopore resulting in an increase in the ionic current flowing through the nanopore; however, it has a limited effect on the deviation of the current from its base current when the particle is far from the pore.     

Dynamics of polymer translocation into a circular nanocontainer through a nanopore

Using Langevin dynamics simulations, we investigate the dynamics of polymer translocation into a circular nanocontainer through a nanopore under a driving force F. We observe that the translocation probability initially increases and then saturates with increasing F, independent of φ, which is the average density of the whole chain in the nanocontainer. The translocation time distribution undergoes a transition from a Gaussian distribution to an asymmetric distribution with increasing φ. Moreover, we find a nonuniversal scaling exponent of the translocation time as chain length, depending on φ and F. These results are interpreted by the conformation of the translocated chain in the nanocontainer and the time of an individual segment passing through the pore during translocation.     

Diffusive dynamics of DNA unzipping in a nanopore

When an electric field is applied to an insulating membrane, movement of charged particles through a nanopore is induced. The measured ionic current reports on biomolecules passing through the nanopore. In this work, we explored the kinetics of DNA unzipping in a nanopore using our coarse‐grained model (Stachiewicz and Molski, J. Comput. Chem. 2015, 36, 947). Coarse graining allowed a more detailed analysis for a wider range of parameters than all‐atom simulations. Dependence of the translocation mode (unzipping or distortion) on the pore diameter was examined, and the threshold voltages were estimated. We determined the potential of mean force, position‐dependent diffusion coefficient, and position‐dependent effective charge for the DNA unzipping. The three molecular profiles were correlated with the ionic current and molecular events. On the unzipping/translocation force profile, two energy maxima were found, one of them corresponding to the unzipping, and the other to the translocation barriers. The unzipping kinetics were further explored using Brownian dynamics. © 2015 Wiley Periodicals, Inc.     

Folding transition of a single semiflexible polyelectrolyte chain through toroidal bundling of loop structures

We consider how the DNA coil-globule transition progresses via the formation of a toroidal ring structure. We formulate a theoretical model of this transition as a phenomenon in which an unstable single loop generated as a result of thermal fluctuation is stabilized through association with other loops along a polyelectrolyte chain. An essential property of the chain under consideration is that it follows a wormlike chain model. A toroidal bundle of loop structures is characterized by a radius and a winding number. The statistical properties of such a chain are discussed in terms of the free energy as a function of the fraction of unfolded segments. We also present an actual experimental observation of the coil-globule transition of single giant DNA molecules, T4 DNA (165.5 kbp), with spermidine (3+), where intrachain phase segregation appears at a NaCl concentration of more than 10 mM. Both the theory and experiments lead to two important points. First, the transition from a partially folded state to a completely folded state has the characteristics of a continuous transition, while the transition from an unfolded state to a folded state has the characteristics of a first-order phase transition. Second, the appearance of a partially folded structure requires a folded structure to be less densely packed than in the fully folded compact state.     

Memory effects during the unbiased translocation of a polymer through a nanopore

Through a detailed Langevin dynamics simulation study, the role of memory effects during unbiased translocation is explored. Tests are devised to uncover the presence of memory effects by directly measuring forward/backward-correlated motion as well as the associated change in the dynamics. Conducting these tests at low and high viscosities, a range of behaviours across different time scales is revealed: short-time forward correlations at all viscosities, quasi-static behaviour at low viscosity, and long-time backward correlations at high viscosity. By applying these tests at different portions of the translocation process, these memory effects are also shown to vary as translocation proceeds. Combining this information with standard measurements, a physical picture of unbiased translocation as the diffusion of a local minimum is proposed.