Simulation of Chain Organization in Encapsulated Polymers

Journal of Chemical Physics, 2000

The behavior of a grafted polymer chain confined in a tube is investigated within a scaling theory substantiated with biased Monte Carlo simulations of a self-avoiding walk ͑SAW͒ on a cubic lattice. All the statistical and thermodynamic properties of the chain follow from the knowledge of the joint distribution P(z,m) giving the probability to observe a length z and a number of contacts m, in a model where the energy of the chain in a given configuration is proportional to m. The analysis is based on the factorization of P(z,m) into the a priori distribution P(z) and the conditional probability P(m͉z) of finding m contacts given that the chain length is z. P(m͉z) is well-approximated by a Gaussian distribution. Taking the variance ͗m 2 ͘Ϫm 2 of this distribution into account, we obtain a nonmean-field expression for the free energy of the confined chain. We show that the coil-globule transition of the confined chain is independent of its size but depends on the pore diameter. Contrary to free, unconfined chains, it is always a continuous transition.

Aiche Journal, 2017

The properties of macromolecules in presence of an interface could be considerably modified due to confinement effects. When phase separations are performed in nanoconfined domains, the concurrent presence of high-energy interfaces and conformational entropy constraints of the macromolecules causes profound differences in polymer aggregation behavior. Here, thermodynamics of a polymer chain in solution, confined by a three-dimensional cubic interface, is studied by means of Monte Carlo method, focusing on the chain conformational entropy penalty arising from the excluded volume effects. The presented method might become a general tool for a preliminary evaluation of the thermodynamic effects due to the confinement of a polymer system. Further, the interface effects on Thermally Induced Phase Separation (TIPS) of polymer solutions, confined by High-Pressure Homogenization, are experimentally studied, regarding final morphologies. It is confirmed how peculiar polymer morphologies are obtained only when the TIPS develops under nanoconfinement degrees above a threshold one.

The Journal of Chemical Physics, 2005

A single semiflexible polymer chain folds into a toroidal object under poor solvent conditions. In this study, we examined the morphological change in such a toroidal state as a function of the width and stiffness of the chain together with the surface energy, which characterizes the segmental interaction parameter. Change s in the thickness and outer/inner radius are interpreted in terms of these parameters. Our theoretical expectation corresponds to the actual morphological changes i n a single giant DNA molecule as observed by electron microscopy.

The Journal of Physical Chemistry B, 2008

The behavior of semiflexible chains modeling wormlike polymers such as DNA and actin in confined spaces was explored by coarse-grained Monte Carlo simulations. The persistence length P, mean end-to-end distance 〈R 2 〉, mean radius of gyration 〈R g 2 〉, and the size ratio 〈R 2 〉/〈R g 2 〉 were computed for chains in slits, cylinders, and spheres. It was found that the intrinsic persistence length of a free chain undergoes on confinement substantial alteration into the apparent persistence length. The qualitative differences were found in trends of the apparent persistence lengths between slits and cylinders on one side and spheres on the other side. The quantities P, 〈R 2 〉, 〈R g 2 〉, and 〈R 2 〉/〈R g 2 〉 display similar dependences upon squeezing the chains in nanopores. The above quantities change nonmonotonically with confinement in slits and cylinders, whereas they drop smoothly with decreasing radius of a sphere. For elongation of a chain in a cylinder, two regimes corresponding to strong and moderate confinements were found and compared to experiments and predictions of the blob and Odijk theories. In a spherical cavity, the toroidal chain structure with a hole in the center was detected under strong confinements. The scattering form factor S(q) computed for semiflexible confined chains revealed three regimes of behavior in a slit and a cylinder that matched up well with the scaling theory. The complex form of the function S(q) computed for a sphere was interpreted as a sign of the toroidal structure. A reasonable agreement was found between the simulations and measurements of DNA and actin filaments, confined in nano-and microfluidic channels and spherical droplets, pertaining to the changes of the persistence lengths, chain elongation, and toroidal structure formation.

The Journal of Chemical Physics, 2014

The competition between toroidal and rod-like conformations as possible ground states for DNA condensation is studied as a function of the stiffness, the length of the DNA and the form of the long-range interactions between neighboring molecules, using analytical theory supported by Monte Carlo simulations. Both conformations considered are characterized by a local nematic order with hexagonal packing symmetry of neighboring DNA molecules, but differ in global configuration of the chain and the distribution of its curvature as it wraps around to form a condensate. The long-range interactions driving the DNA condensation are assumed to be of the form pertaining to the attractive depletion potential as well as the attractive counterion induced soft potential. In the stiffness-length plane we find a transition between rod-like to toroid condensate for increasing stiffness at a fixed chain length L. Strikingly, the transition line is found to have a L 1/3 dependence irrespective of the details of the long-range interactions between neighboring molecules. When realistic DNA parameters are used, our description reproduces rather well some of the experimental features observed in DNA condensates. arXiv:1401.4300v1 [cond-mat.soft]

Journal of Polymer …, 2006

Chemical Physics Letters, 2000

Lattice-field calculations are performed on a Gaussian polymer chain confined to move within the region defined by two fused spheres. The results of the calculations are in accord with recent experimental measurements and computer simulations, and suggest that current theoretical understanding of polymer partitioning phenomena is not adequate when excluded volume interactions between the monomers are present. It is also shown that the notion of ground state dominance can fail even in the large monomer limit.

Macromolecules, 2013

We approach the problem of coil−globule transition dynamics numerically by Brownian dynamics simulations. This method allows us to study the behavior of polymer chains of varying stiffness and the effects of bending stiffness on chain morphology during the process of coil− globule collapse, imitating globule formation in poor solvent conditions. We record and analyze a three-stage process of globule formation for flexible chains: (1) nucleation, (2) coalescence of nuclei, and (3) collapsed globule formation. Stiffer chains undergo similar formation stages; however, the "raindrops" formed by these chains are elongated (unlike spherical structures formed by flexible chains) and exhibit regular packing of chains into antiparallel hairpin structures. In order to assess the transition dynamics quantitatively, polymer chain configurations were analyzed by generating contact maps and contact frequency histograms for all given configurations. These clusters are initial-configuration-dependent, and their growth and intercluster contacts have direct analogy with the process of raindrop coalescence.

1990

ABSTRACT: We present results of a detailed Monte Carlo simulation study of a system of a large number of polymer chains terminally anchored or end-grafted on a flat surface. We study this system on a three-dimensional lattice for several different values of the surface coverage and the chain length. We also consider several different distributions for the chain lengths.

1999

ABSTRACT Molecular dynamics simulations of single chains in vacuo have been used to investigate the role of flexible branches on the dimensions and in particular the backbone rigidity of flexible polymers. A series of isotactic poly-α-olefin chains was chosen as a model system to study because of their simplicity of structure. Θ-conditions were simulated for each branched chain by careful adjustment of the Van der Waals parameters, and properties such as end-to-end length, radius of gyration and persistence length were measured. As expected the backbone rigidity of the polymers was found to be determined by a balance between the coiling of the backbone induced by a gauche state at the branch point and the size of the side chain. Trends in persistence length with branch content compared favourably to the previous Rotational Isomeric State and experimental measurements of the characteristic ratio. The stiffening of the backbone under good solvent conditions was also investigated and it was found that the persistence length could be systematically increased by increasing the size of the side group, with the shape of the side group also making a small difference to the sampled backbone conformations.