Heirarchical and synergistic self-assembly in composites of model Wormlike micellar-polymers and nanoparticles results in nanostructures with diverse morphologies

Using Monte Carlo simulations, we investigate the self-assembly of model nanoparticles inside a matrix of model equilibrium polymers (or matrix of Wormlike micelles) as a function of the polymeric matrix density and the excluded volume parameter between polymers and nanoparticles. In this paper, we show morphological transitions in the system architecture via synergistic self-assembly of nanoparticles and the equilibrium polymers. In a synergistic self-assembly, the resulting morphology of the system is a result of the interaction between both nanoparticles and the polymers, unlike the polymer templating method. We report the morphological transition of nanoparticle aggregates from percolating network-like structures to non-percolating clusters as a result of the change in the excluded volume parameter between nanoparticles and polymeric chains. In parallel with the change in the self-assembled structures of nanoparticles, the matrix of equilibrium polymers also shows a transition from a dispersed state to a percolating network-like structure formed by the clusters of polymeric chains. We show that the shape anisotropy of the nanoparticle clusters formed is governed by the polymeric density resulting in rod-like, sheet-like or other anisotropic nanoclusters. It is also shown that the pore shape and the pore size of the porous network of nanoparticles can be changed by changing the minimum approaching distance between nanoparticles and polymers. We provide a theoretical understanding of why various nanostructures with very different morphologies are obtained.Comment: 24 pages, 23 figure

Origin of spatial organization of DNA-polymer in bacterial chromosomes

In-vivo DNA organization at large length scales ($\sim 100nm$) is highly debated and polymer models have proved useful to understand the principle of DNA-organization. Here, we show that $<2$% cross-links at specific points in a ring polymer can lead to a distinct spatial organization of the polymer. The specific pairs of cross-linked monomers were extracted from contact maps of bacterial DNA. We are able to predict the structure of 2 DNAs using Monte Carlo simulations of the bead-spring polymer with cross-links at these special positions. Simulations with cross-links at random positions along the chain show that the organization of the polymer is different in nature from the previous case.Comment: arXiv admin note: text overlap with arXiv:1701.0506

Entropy mediated organization of E.coli chromosome in fast growth conditions

Recent experiments have been able to visualise chromosome organization in fast-growing E.coli cells. However, the mechanism underlying the spatio-temporal organization remains poorly understood. We propose that the DNA adopts a specific polymer topology as it goes through its cell cycle. We establish that the emergent entropic forces between polymer segments of the DNA-polymer with modified topology, leads to chromosome organization as seen in-vivo. We employ computer simulations of a replicating bead spring model of a polymer in a cylinder to investigate the problem. Our simulation of the overlapping cell cycles not only show successful segregation, but also reproduces the evolution of the spatial organization of the chromosomes as observed in experiments. This manuscript in addition to our previous work on slowly growing bacterial cells, shows that our topology-based model can explain the organization of chromosomes in all growth conditions

Combining Molecular Dynamics with Lattice-Boltzmann: A Hybrid Method for the Simulation of (Charged) Colloidal Systems

We present a hybrid method for the simulation of colloidal systems, that combines molecular dynamics (MD) with the Lattice-Boltzmann (LB) scheme. The LB method is used as a model for the solvent in order to take into account the hydrodynamic mass and momentum transport through the solvent. The colloidal particles are propagated via MD and they are coupled to the LB fluid by viscous forces. With respect to the LB fluid, the colloids are represented by uniformly distributed points on a sphere. Each such point (with a velocity V(r) at any off-lattice position r is interacting with the neighboring eight LB nodes by a frictional force F=\xi_0(V(r)-u(r)) with \xi_0 being a friction force and u(r) being the velocity of the fluid at the position r. Thermal fluctuations are introduced in the framework of fluctuating hydrodynamics. This coupling scheme has been proposed recently for polymer systems by Ahlrichs and D"unweg [J. Chem. Phys. 111, 8225 (1999)]. We investigate several properties of a single colloidal particle in a LB fluid, namely the effective Stokes friction and long time tails in the autocorrelation functions for the translational and rotational velocity. Moreover, a charged colloidal system is considered consisting of a macroion, counterions and coions that are coupled to a LB fluid. We study the behavior of the ions in a constant electric field. In particular, an estimate of the effective charge of the macroion is yielded from the number of counterions that move with the macroion in the direction of the electric field.Comment: 37 pages, 12 figure

Electrophoretic Properties of Highly Charged Colloids: A Hybrid MD/LB Simulation Study

Using computer simulations, the electrophoretic motion of a positively charged colloid (macroion) in an electrolyte solution is studied in the framework of the primitive model. Hydrodynamic interactions are fully taken into account by applying a hybrid simulation scheme, where the charged ions (i.e. macroion and electrolyte), propagated via molecular dynamics (MD), are coupled to a Lattice Boltzmann (LB) fluid. In a recent experiment it was shown that, for multivalent salt ions, the mobility $\mu$ initially increases with charge density $\sigma$, reaches a maximum and then decreases with further increase of $\sigma$. The aim of the present work is to elucidate the behaviour of $\mu$ at high values of $\sigma$. Even for the case of monovalent microions, we find a decrease of $\mu$ with $\sigma$. A dynamic Stern layer is defined that includes all the counterions that move with the macroion while subject to an external electrical field. The number of counterions in the Stern layer, $q_0$, is a crucial parameter for the behavior of $\mu$ at high values of $\sigma$. In this case, the mobility $\mu$ depends primarily on the ratio $q_0/Q$ (with $Q$ the valency of the macroion). The previous contention that the increase in the distortion of the electric double layer (EDL) with increasing $\sigma$ leads to the lowering of $\mu$ does not hold for high $\sigma$. In fact, we show that the deformation of the EDL decreases with increase of $\sigma$. The role of hydrodynamic interactions is inferred from direct comparisons to Langevin simulations where the coupling to the LB fluid is switched off. Moreover, systems with divalent counterions are considered. In this case, at high values of $\sigma$ the phenomenon of charge inversion is found.Comment: accepted in J. Chem Phys., 10 pages, 9 figure