Coarse-grained simulations of the salt dependence of the radius of gyration of polyelectrolytes as models for biomolecules in aqueous solution

Conformational Transition of Semiflexible Ring Polyelectrolyte in Tetravalent Salt Solutions: A Simple Numerical Modeling without the Effect of Twisting

In this work, the conformational behaviors of ring polyelectrolyte in tetravalent salt solutions are discussed in detail through molecular dynamics simulation. For simplification, here we have neglected the effect of the twisting interaction, although it has been well known that both bending and twisting interactions play a deterministic in the steric conformation of a semiflexible ring polymer. The salt concentration CS and the bending energy b take a decisive role in the conformation of the ring polyelectrolyte (PE). Throughout our calculations, the b varies from b = 0 (freely joint chain) to b = 120. The salt concentration CS changes in the range of 3.56 × 10-4 M ≤ CS ≤ 2.49 × 10-1 M. Upon the addition of salt, ring PE contracts at first, subsequently re-expands. More abundant conformations are observed for a semiflexible ring PE. For b = 10, the conformation of semiflexible ring PE shifts from the loop to two-racquet-head spindle, then it condenses into toroid, finally arranges into coil with the increase of CS. As b increases further, four phase transitions are observed. The latter two phase transitions are different. The semiflexible ring PE experiences transformation from toroid to two racquet head spindle, finally to loop in the latter two phase transitions. Its conformation is determined by the competition among the bending energy, cation-bridge, and entropy. Combined, our findings indicate that the conformations of semiflexible ring PE can be controlled by changing the salt concentration and chain stiffness.

The viscosity of polyelectrolyte solutions and its dependence on their persistence length, concentration and solvent quality

In this work, a comprehensive study of the influence on shear viscosity of polyelectrolyte concentration, persistence length, salt concentration and solvent quality is reported, using numerical simulations of confined solutions under stationary Poiseuille flow. Various scaling regimes for the viscosity are reproduced, both under good solvent and theta solvent conditions. The key role played by the electrostatic interactions in the viscosity is borne out when the ionic strength is varied. It is argued that these results are helpful for the understanding of viscosity scaling in entangled polyelectrolyte solutions for both rigid and flexible polyelectrolytes in different solvents, which is needed to perform intelligent design of new polyelectrolytes capable of fine tuning the viscosity in complex fluids.

DNA Coil Dynamics and Hydrodynamic Gating of Pressure-Biased Nanopores

Nanopores are ideally suited for the analysis of long DNA fragments including chromosomal DNA and synthetic DNA with applications in genome sequencing and DNA data storage, respectively. Hydrodynamic fluid flow has been shown to slow down DNA transit time within the pore, however other influences of hydrodynamic forces have yet to be explored. In this report, a broad analysis of pressure-biased nanopores and the impact of hydrodynamics on DNA transit time, capture rate, current blockade depth, and DNA folding are conducted. Using a 10 nm pore, it is shown that hydrodynamic flow inhibits the early stages of linearization of DNA and produces predominately folded events which are initiated by folded DNA (2-strands) entering the pore. Furthermore, utilizing larger pores (30 nm) leads to unique DNA gating behavior in which DNA events can be switched on and off with the application of pressure. A computational model, based on combining electrophoretic drift velocities with fluid velocities, accurately predicts the pore size required to observe DNA gating. Hydrodynamic fluid flow generated by a pressure bias, or potentially more generally by other mechanisms like electroosmotic flow, is shown to have significant effects on DNA sensing and can be useful for DNA sensing technologies.

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.

Coarse-Grained Molecular Dynamics (CG-MD) Simulation of the Encapsulation of Dexamethasone in PSS/PDDA Layer-by-Layer Assembled Polyelectrolyte Nanocapsules

Experimental studies have reported the fundamental and applied science aspects of polyelectrolyte (PE) layer-by-layer (LbL) self-assembly. LbL nanocoating is a simple and robust technique that can be used to modify the surface properties of nearly any material. These modifications take place by adsorption of mere nanometers of PE to impart previously absent properties to the nanocoated substrate. Paper manufacturing, drug delivery, and antimicrobial applications have since been developed. LbL self-assembly has become a very lucrative field of research. Computational modeling of LbL nanocoating has received limited attention. PE simulations often require significant computational resources and make computational modeling studies challenging. In this study, atomic-level PE and dexamethasone models are developed and then converted into coarse-grained (CG) models. This modeling study is based on experimental results that were previously reported. The CG models showed the effect of salt concentration and the number of PE layers on the LbL drug nanocapsule. The suitability of the model was evaluated and showed that this model can serve as a predictive tool for an LbL-nanocoated drug delivery system. It is suggested that this model can be used to simulate LbL drug delivery systems before the experimental evaluation of the real systems take place.

Polarity of Cationic Lignin Polymers: Physicochemical Behavior in Aqueous Solutions and Suspensions

The structure of cationic monomers can significantly impact the polarity of lignin after polymerization. Cationic hydrolysis lignin (CHL) polymers were produced by polymerizing hydrolysis lignin (HL) with [3-(methacryloylamino)propyl] trimethylammonium chloride (MAPTAC) or [2-(methacryloyloxy)ethyl] trimethyl ammonium chloride (METAC). The METAC monomer has an oxygen atom, with larger electronegativity, in its molecular structure, whereas the MAPTAC monomer contains a nitrogen atom, as well as an extra nonpolar CH₂ group, facilitating investigation into the effects of the polarity of CHLs on their physicochemical performance in an aqueous system. CHL polymers are analyzed and their interactions with clay particles are determined in colloidal systems. CHLs are designed to have similar charge densities (2.1-2.2 mmol g^-1) and molecular weights (55000-60000 g mol^-1 ). The hydrodynamic radius (H_y) and radius of gyration, (R_g) of HL-METAC are larger than those of HL-MAPTAC, implying a more 3-dimensional structure of HL-METAC in aqueous solution. The stability ratio of kaolin particles affirms the better performance of HL-METAC in comparison to HL-MAPTAC, which reflects the better flocculation efficiency of HL-METAC. The results also reveal that salt and urea aqueous solutions affect the H_y, R_g, and configuration of CHL polymers, which alters the flocculation efficiency of HL-METAC and HL-MAPTAC polymers in kaolin suspensions.

Surfactant chain length and concentration influence on the interfacial tension of two immiscible model liquids: a coarse-grained approach

The interfacial tension between immiscible liquids is studied as a function of a model linear surfactant length and concentration using coarse-grained, dissipative particle dynamics numerical simulations. The adsorption isotherms obtained from the simulations are found to be in agreement with Langmuir's model. The reduction of the interfacial tension with increasing surfactant concentration is found to display some common characteristics for all the values of chain length modeled, with our predictions being in agreement with Szyszkowski's equation. Lastly, the critical micelle concentration is predicted for all surfactant lengths, finding exponentially decaying behavior, in agreement with Kleven's model. It is argued that these findings can be helpful guiding tools in the interpretation of available experiments and in the design of new ones with new surfactants and polymers.

Electrostatics in dissipative particle dynamics using Ewald sums with point charges

A proper treatment of electrostatic interactions is crucial for the accurate calculation of forces in computer simulations. Electrostatic interactions are typically modeled using Ewald-based methods, which have become some of the cornerstones upon which many other methods for the numerical computation of electrostatic interactions are based. However, their use with charge distributions rather than point charges requires the inclusion of ansatz for the solutions of the Poisson equation, since there is no exact solution known for smeared out charges. The interest in incorporating electrostatic interactions at the scales of length and time that are relevant for the study the physics of soft condensed matter has increased considerably. Using mesoscale simulation techniques, such as dissipative particle dynamics (DPD), allows us to reach longer time scales in numerical simulations, without abandoning the particulate description of the problem. The main problem with incorporating electrostatics into DPD simulations is that DPD particles are soft and those particles with opposite charge can form artificial clusters of ions. Here we show that one can incorporate the electrostatic interactions through Ewald sums with point charges in DPD if larger values of coarse-graining degree are used, where DPD is truly mesoscopic. Using point charges with larger excluded volume interactions, the artificial formation of ionic pairs with point charges can be avoided and one obtains correct predictions. We establish ranges of parameters useful for detecting boundaries where artificial formation of ionic pairs occurs. Lastly, using point charges we predict the scaling properties of polyelectrolytes in solvents of varying quality, and obtain predictions that are in agreement with calculations that use other methods and with recent experimental results.

Nanotribology of biopolymer brushes in aqueous solution using dissipative particle dynamics simulations: an application to PEG covered liposomes in a theta solvent

We undertake the investigation of sheared polymer chains grafted onto flat surfaces to model liposomes covered with polyethylene glycol brushes as a case study for the mechanisms of efficient drug delivery in biologically relevant situations, for example, as carriers for topical treatments of illnesses in the human vasculature. For these applications, specific rheological properties are required, such as low viscosity at high shear rates, to improve the transport of the liposomes. Therefore, extensive non-equilibrium, coarse-grained dissipative particle dynamics simulations of polymer brushes of various lengths and shear rates are performed to obtain the average viscosity and the friction coefficient of the system as functions of the shear rate and polymerization degree under theta-solvent conditions, and we find that the brushes experience considerable shear thinning at large shear rates. The viscosity (η) and the friction coefficient (μ) are shown to obey the scaling laws η ∼ γ dot above (-0.31) and μ ∼ γ dot above (0.69) at high shear rates (γ dot above) in a theta solvent, irrespective of the degree of polymerization of brushes. These results confirm recent scaling predictions and reproduce very well trends in measurements of the viscosity at a high shear rate (γ dot above) of red blood cells in a liposome containing medium.