arXiv subjects

Neda Abbasi Taklimi

Publications and source records attributed to Neda Abbasi Taklimi.

4 recordsLinked to original sources

arXiv2026

On the thermal properties of knotted block copolymer rings

We investigate the thermal and structural properties of knotted diblock copolymer rings using a coarse-grained lattice model in an implicit solvent. The system is studied by means of the Wang--Landau Monte Carlo algorithm, allowing us to analyze thermodynamic and conformational responses over a wide temperature range. Different knot topologies, including the unknot, trefoil, figure-eight, and pentafoil knots, are considered for both symmetric and asymmetric monomer compositions. In the AB model employed here, A-type monomers are self-repulsive, B-type monomers are self-attractive, and A-B interactions are neutral, such that the solvent is effectively good for A-type monomers and poor for B-type monomers at low temperatures. We analyze several key observables, including the heat capacity, the radius of gyration, and its temperature derivative for both the entire copolymer ring and the individual blocks, and the probability that a monomer belongs to the knotted region. Our results show that the interplay between knot topology, monomer composition, and temperature strongly influences polymer conformations. Small variations in the B-block length induce nonmonotonic, reentrant-like conformational behavior as a function of temperature, including transitions between knot localization and delocalization at low temperatures. These effects arise from the competition between energetic and entropic contributions imposed by topological constraints.

cond-mat.soft↗

arXiv2024

A contact map method to capture the features of knot conformations

Inspired by recent advances in the chromosome capture techniques, a method is proposed to study the structural organization of systems of polymers rings with topological constraints.To this purpose, the system is divided into compartments and a simple condition is provided in order to determine if two compartments are in contact or not. Next, a set of contact matrices $\bar T_{ab}$ is defined that count how many times during a simulation a compartment $a$ was found in contact with a non-contiguous compartment $b$ in conformations with a given energy or temperature. Similar strategies based on correlation maps have been applied to the study of knotted polymers in the recent past. The advantage of the present approach is that is coupled with the Wang-Landau algorithm. Once the density of states is computed, it is possible to generate the contact matrices at any temperature. This gives an immediate overview over the changes of phases that polymer systems undergo. The information on the structure of knotted polymers and links stored in the contact matrices is the result of averaging hundred of billions of conformations and visualized by means of colormaps. The obtained color patterns allow to identify the main properties of the structure of the system under investigation at any temperature. The method is applied to detect the structural rearrangements following the phase transitions of a knotted polymer ring and a circular polycatenane composed by four rings in a solution. It is shown that the colormaps have a finite number of patterns that can be clearly associated with the different phases of these systems. Colormaps also bring new knowledge, for instance predicting the average number of tails appearing in the conformations of the considered polymers at a given temperature.

cond-mat.soft↗

arXiv2023

Self-dual solutions of a field theory model of two linked rings

In this work the connection established in [7, 8] between a model of two linked polymers rings with fixed Gaussian linking number forming a 4-plat and the statistical mechanics of non-relativistic anyon particles is explored. The excluded volume interactions have been switched off and only the interactions of entropic origin arising from the topological constraints are considered. An interpretation from the polymer point of view of the field equations that minimize the energy of the model in the limit in which one of the spatial dimensions of the 4-plat becomes very large is provided. It is shown that the self-dual contributions are responsible for the long-range interactions that are necessary for preserving the global topological properties of the system during the thermal fluctuations. The non self-dual part is also related to the topological constraints, and takes into account the local interactions acting on the monomers in order to prevent the breaking of the polymer lines. It turns out that the energy landscape of the two linked rings is quite complex. Assuming as a rough approximation that the monomer densities of half of the 4-plat are constant, at least two points of energy minimum are found. Classes of non-trivial self-dual solutions of the self-dual field equations are derived. ... .

hep-th↗

arXiv2022

On the thermal properties of knotted block copolymer rings

The thermal properties of coarse grained knotted polymers containing two kinds of monomers $A$ and $B$ fluctuating in a solution are investigated on a simple cubic lattice using the Wang-Landau MC algorithm. These knots have a more complex phase diagram than knots formed by homopolymers, including the possible presence of metastable states. Two different setups are considered: i) charged block copolymers in a ion solution and ii) neutral copolymers with the $A$ monomers above and the $B$ monomers below the theta point. A precise interpretation of the peaks observed in the plots of the specific heat capacity is provided. In view of possible applications in medicine and the construction of intelligent materials, it is also shown that the behavior of copolymer rings can be tuned by changing both their monomer configuration and topology. We find that the most stable compact states are formed by charged copolymers in which very short segments with $A$ monomers are alternated by short segments with $B$ monomers. In such knots the transition from the compact to the expanded state is very fast, leading to a narrow and high peak in the specific heat capacity which appears at very high temperatures. The effects of topology allow to tune the radius of gyration of the knotted polymer ring and to increase or decrease the temperatures at which the observed phase transitions or rearrangements of the system occur. While we observe a general fading out of the influence of topology in longer polymers, our simulations have captured a few exceptions to this rule.

cond-mat.soft↗