A contact map method to capture the features of knot conformations
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arXiv
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| Main Authors: | , , , |
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| Format: | Preprint |
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2024
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| _version_ | 1866910356033503232 |
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| author | Taklimi, Neda Abbasi Ferrari, Franco Piątek, Marcin Radosław Tubiana, Luca |
| author_facet | Taklimi, Neda Abbasi Ferrari, Franco Piątek, Marcin Radosław Tubiana, Luca |
| contents | 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. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2403_04060 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | A contact map method to capture the features of knot conformations Taklimi, Neda Abbasi Ferrari, Franco Piątek, Marcin Radosław Tubiana, Luca Soft Condensed Matter Statistical Mechanics 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. |
| title | A contact map method to capture the features of knot conformations |
| topic | Soft Condensed Matter Statistical Mechanics |
| url | https://arxiv.org/abs/2403.04060 |