Long-lived metastable knots in polyampholyte chains.

Knots in proteins and DNA are known to have significant effect on their equilibrium and dynamic properties as well as on their function. While knot dynamics and thermodynamics in electrically neutral and uniformly charged polymer chains are relatively well understood, proteins are generally polyampholytes, with varied charge distributions along their backbones. Here we use simulations of knotted polymer chains to show that variation in the charge distribution on a polyampholyte chain with zero net charge leads to significant variation in the resulting knot dynamics, with some charge distributions resulting in long-lived metastable knots that escape the (open-ended) chain on a timescale that is much longer than that for knots in electrically neutral chains. The knot dynamics in such systems can be described, quantitatively, using a simple one-dimensional model where the knot undergoes biased Brownian motion along a "reaction coordinate", equal to the knot size, in the presence of a potential of mean force. In this picture, long-lived knots result from charge sequences that create large electrostatic barriers to knot escape. This model allows us to predict knot lifetimes even when those times are not directly accessible by simulations.

Anisotropic thermal conductivity and corrugated patterns in single-layer black phosphorus nanoribbon subjected to shear loading: a molecular dynamics study.

Single-layer black phosphorus (SLBP) also known as phosphorene is a recently introduced two-dimensional material with unique structure and promising physical properties that has drawn considerable attention in the field of nanodevices. This structure demonstrates a high anisotropy in mechanical and thermal behavior along zigzag (ZZ) and armchair (AC) principal in-plane directions. Here in this study, it is shown that implementing shear strain on 10 nm × 50 nm SLBP nanoribbons (SLBPNRs) along ZZ and AC directions, the anisotropy leads to different corrugated patterns on the pristine structure. Applying non-equilibrium molecular dynamics under a parameterized Stillinger-Weber potential for modelling SLBP, thermal conductivity (TC) behavior of the sheared SLBPNRs with corrugated patterns are examined. The results show a higher amplitude and wavelength of the corregations on the ZZ-aligned SLBPNRs, which is around two times higher than that of AC-aligned counterparts. Although, it is also shown that unlike some other 2D materials, such as graphene, the wrinkling does not have such a significant effect on TC of SLBP. The phonon density of states results obtained in this work as well as phonon dispersion curves by first-principle calculations in other works concrete this finding. The results show small frequency shifts in both high- and low-frequency phonons, which are not strong enough to affect TC in SLBPNRs. This interesting thermal property of SLBP under shear strain suggests the great potential application of these corrugated structures in nanodevices without any loss of TC abilities.

Transition path dynamics in the binding of intrinsically disordered proteins: A simulation study.

Association of proteins and other biopolymers is a ubiquitous process in living systems. Recent single-molecule measurements probe the dynamics of association in unprecedented detail by measuring the properties of association transition paths, i.e., short segments of molecular trajectories between the time the proteins are close enough to interact and the formation of the final complex. Interpretation of such measurements requires adequate models for describing the dynamics of experimental observables. In an effort to develop such models, here we report a simulation study of the association dynamics of two oppositely charged, disordered polymers. We mimic experimental measurements by monitoring intermonomer distances, which we treat as "experimental reaction coordinates." While the dynamics of the distance between the centers of mass of the molecules is found to be memoryless and diffusive, the dynamics of the experimental reaction coordinates displays significant memory and can be described by a generalized Langevin equation with a memory kernel. We compute the most commonly measured property of transition paths, the distribution of the transition path time, and show that, despite the non-Markovianity of the underlying dynamics, it is well approximated as one-dimensional diffusion in the potential of mean force provided that an apparent value of the diffusion coefficient is used. This apparent value is intermediate between the slow (low frequency) and fast (high frequency) limits of the memory kernel. We have further studied how the mean transition path time depends on the ionic strength and found only weak dependence despite strong electrostatic attraction between the polymers.

Controlling the Surface Properties of Binary Polymer Brush-Coated Colloids via Targeted Nanoparticles.

This paper explores a novel mechanism for controlling the surface properties of polymer-coated colloids using targeted ("sticky") nanoparticles which attract monomers of certain polymer species. In our study, colloids are coated by two types of tethered polymer chains having different chemical properties. Attraction of nanoparticles to the monomers of one polymer type causes these polymer chains to contract toward the grafting surface, rendering the other type more exposed to the environment. Thus, the effective surface properties of the colloid are dominated by the intended polymer type. We use coarse-grained molecular dynamics (CGMD) simulation to demonstrate that introducing nanoparticles which interact preferentially with certain types of polymers makes it possible to switch between different surface properties of the colloid. This mechanism can in principle be exploited in drug delivery systems and self-assembly applications.

Effects of cross-linking on partitioning of nanoparticles into a polymer brush: Coarse-grained simulations test simple approximate theories.

The effect of cohesive contacts or, equivalently, dynamical cross-linking on the equilibrium morphology of a polymer brush infiltrated by nanoparticles that are attracted to the polymer strands is studied for plane-grafted brushes using coarse-grained molecular dynamics and approximate statistical mechanical models. In particular, the Alexander-de Gennes (AdG) and Strong Stretching Theory (SST) mean-field theory (MFT) models are considered. It is found that for values of the MFT cross-link strength interaction parameter beyond a certain threshold, both AdG and SST models predict that the polymer brush will be in a compact state of nearly uniform density packed next to the grafting surface over a wide range of solution phase nanoparticle concentrations. Coarse grained molecular dynamics simulations confirm this prediction, for both small nanoparticles (nanoparticle volume = monomer volume) and large nanoparticles (nanoparticle volume = 27 × monomer volume). Simulation results for these cross-linked systems are compared with analogous results for systems with no cross-linking. At the same solution phase nanoparticle concentration, strong cross-linking results in additional compression of the brush relative to the non-crosslinked analog and, at all but the lowest concentrations, to a lesser degree of infiltration by nanoparticles. For large nanoparticles, the monomer density profiles show clear oscillations moving outwards from the grafting surface, corresponding to a degree of layering of the absorbed nanoparticles in the brush as they pack against the grafting surface.

Diffusion and self-assembly of C60 molecules on monolayer graphyne sheets.

The motion of a fullerene (C60) on 5 different types of graphyne is studied by all-atom molecular dynamics simulations and compared with former studies on the motion of C60 on graphene. The motion shows a diffusive behavior which consists of either a continuous motion or discrete movements between trapping sites depending on the type of the graphyne sheet. For graphyne-4 and graphyne-5, fullerenes could detach from the surface of the graphyne sheet at room temperature which was not reported for similar cases on graphene sheets. Collective motion of a group of fullerenes interacting with a graphyne studied and it is shown that fullerenes exhibit stable assemblies. Depending on the type of graphyne, these assemblies can have either single or double layers. The mobility of the assembled structures is also dependent on the type of the graphyne sheet. The observed properties of the motion suggests novel applications for the complexes of fullerene and monolayer graphynes.

Modeling and simulation of the water gradient within a Nafion membrane.

The perfluorinated sulfonic acid membrane (Nafion) shows among ionomers high water uptake and cationic conductivity. These properties allow Nafion to be used in nanocomposite actuators, sensors and fuel cells. In situ experiments have shown that there is a water gradient within the Nafion membrane. The water gradient causes the alteration of other physical properties within the thickness of the membrane and has a drastic impact on the performance of the devices made of the Nafion membrane. Deriving closed-form equations and using molecular dynamics (MD) simulation results, we bridge Nafion properties at the atomic scale and the macroscopic behavior of the membrane within a hierarchical multi-scale model. Multiple discrete simulation cells are selected across the thickness of the membrane with a wide range of water contents as representative volume elements (RVEs). The present framework is able to quantitatively predict the macroscopic properties of Nafion with the nanometric resolution regarding the water gradient across the membrane.