The second Vassiliev measure of uniform random walks and polygons in confined space

Biopolymers, like chromatin, are often confined in small volumes. Confinement has a great effect on polymer conformations, including polymer entanglement. Polymer chains and other filamentous structures can be represented by polygonal curves in 3-space. In this manuscript, we examine the topological complexity of polygonal chains in 3-space and in confinement as a function of their length. We model polygonal chains by equilateral random walks in 3-space and by uniform random walks in confinement. For the topological characterization, we use the second Vassiliev measure. This is an integer topological invariant for polygons and a continuous functions over the real numbers, as a function of the chain coordinates for open polygonal chains. For uniform random walks in confined space, we prove that the average value of the Vassiliev measure in the space of configurations increases as $O(n^2)$ with the length of the walks or polygons. We verify this result numerically and our numerical results also show that the mean value of the second Vassiliev measure of equilateral random walks in 3-space increases as $O(n)$. These results reveal the rate at which knotting of open curves and not simply entanglement are affected by confinement.

Computing Correlation among the Graphs under Lexicographic Product via Zagreb Indices

A topological index (TI) is a numerical descriptor of a molecule structure or graph that predicts its different physical, biological, and chemical properties in a theoretical way avoiding the difficult and costly procedures of chemical labs. In this paper, for two connected (molecular) graphs G 1 and G 2 , we define the generalized total-sum graph consisting of various (molecular) polygonal chains by the lexicographic product of the graphs T k G 1 and G 2 , where T k G 1 is obtained by applying the generalized total operation T k on G 1 with k ≥ 1 as some integral value. Moreover, we compute the different degree-based TIs such as first Zagreb, second Zagreb, forgotten Zagreb, and hyper-Zagreb. In the end, a comparison among all the aforesaid TIs is also conducted with the help of certain statistical tools for some particular families of generalized total-sum graphs under lexicographic product.

How Can Biomechanical Multibody Models of Scoliosis Be Accurate in Simulating Spine Movement Behavior While Neglecting the Changes of Spinal Length?

This paper studies how biomechanical multibody models of scoliosis can neglect the changes of spinal length and yet be accurate in reconstructing spinal columns. As these models with fixed length comprise rigid links interconnected by rotary joints, they resemble polygonal chains that approximate spine curves with a finite number of line segments. In mathematics, using more segments with shorter length can result in more accurate curve approximations. This raises the question of whether more accurate spine curve approximations by increasing the number of links/joints can yield more accurate spinal column reconstructions. For this, the accuracy of spine curve approximation was improved consistently by increasing the number of links/joints, and its effects on the accuracy of spinal column reconstruction were assessed. Positive correlation was found between the accuracy of spine reconstruction and curve approximation. It was shown that while increasing the accuracy of curve approximations, the representation of scoliosis concavity and its side-to-side deviations were improved. Moreover, reconstruction errors of the spine regions separated by the inflection vertebrae had minimal impacts on each other. Overall, multibody scoliosis models with fixed spinal length can benefit from the extra rotational joints that contribute towards the accuracy of spine curve approximation. The outcome of this study leads to concurrent accuracy improvement and simplification of multibody models; joint-link configurations can be independently defined for the regions separated by the inflection vertebrae, enabling local optimization of the models for higher accuracy without unnecessary added complexity to the whole model.

Nets of Lines with the Combinatorics of the Square Grid and with Touching Inscribed Conics

In the projective plane, we consider congruences of straight lines with the combinatorics of the square grid and with all elementary quadrilaterals possessing touching inscribed conics. The inscribed conics of two combinatorially neighbouring quadrilaterals have the same touching point on their common edge-line. We suggest that these nets are a natural projective generalisation of incircular nets. It is shown that these nets are planar Koenigs nets. Moreover, we show that general Koenigs nets are characterised by the existence of a 1-parameter family of touching inscribed conics. It is shown that the lines of any grid of quadrilaterals with touching inscribed conics are tangent to a common conic. These grids can be constructed via polygonal chains that are inscribed in conics. The special case of billiards in conics corresponds to incircular nets.

Topological Indices of Proteins

Protein molecules can be approximated by discrete polygonal chains of amino acids. Standard topological tools can be applied to the smoothening of the polygons to introduce a topological classification of folded states of proteins, for example, using the self-linking number of the corresponding framed curves. In this paper we extend this classification to the discrete version, taking advantage of the “randomness” of such curves. Known definitions of the self-linking number apply to non-singular framings: for example, the Frenet framing cannot be used if the curve has inflection points. However, in the discrete proteins the special points are naturally resolved. Consequently, a separate integer topological characteristics can be introduced, which takes into account the intrinsic features of the special points. This works well for the proteins in our analysis, for which we compute integer topological indices associated with the singularities of the Frenet framing. We show how a version of the Calugareanu’s theorem is satisfied for the associated self-linking number of a discrete curve. Since the singularities of the Frenet framing correspond to the structural motifs of proteins, we propose topological indices as a technical tool for the description of the folding dynamics of proteins.