520 results on '"Writhe"'
Search Results
2. Topological Methods for Polymeric Materials: Characterizing the Relationship Between Polymer Entanglement and Viscoelasticity.
- Author
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Panagiotou, Eleni, Millett, Kenneth C, and Atzberger, Paul J
- Subjects
entanglements ,knots ,linking number ,oscillatory shear ,topology ,viscoelasticity ,writhe ,cond-mat.soft ,Chemical Sciences ,Engineering - Abstract
We develop topological methods for characterizing the relationship between polymer chain entanglement and bulk viscoelastic responses. We introduce generalized Linking Number and Writhe characteristics that are applicable to open linear chains. We investigate the rheology of polymeric chains entangled into weaves with varying topologies and levels of chain density. To investigate viscoelastic responses, we perform non-equilibrium molecular simulations over a range of frequencies using sheared Lees⁻Edwards boundary conditions. We show how our topological characteristics can be used to capture key features of the polymer entanglements related to the viscoelastic responses. We find there is a linear relation over a significant range of frequencies between the mean absolute Writhe W r and the Loss Tangent tan ( δ ) . We also find an approximate inverse linear relationship between the mean absolute Periodic Linking Number L K P and the Loss Tangent tan ( δ ) . Our results show some of the ways topological methods can be used to characterize chain entanglements to better understand the origins of mechanical responses in polymeric materials.
- Published
- 2019
3. The Local Topological Free Energy of the SARS-CoV-2 Spike Protein.
- Author
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Baldwin, Quenisha, Sumpter, Bobby, and Panagiotou, Eleni
- Subjects
- *
SARS-CoV-2 , *PROTEINS , *DRUG development , *AMINO acids - Abstract
The novel coronavirus SARS-CoV-2 infects human cells using a mechanism that involves binding and structural rearrangement of its Spike protein. Understanding protein rearrangement and identifying specific amino acids where mutations affect protein rearrangement has attracted much attention for drug development. In this manuscript, we use a mathematical method to characterize the local topology/geometry of the SARS-CoV-2 Spike protein backbone. Our results show that local conformational changes in the FP, HR1, and CH domains are associated with global conformational changes in the RBD domain. The SARS-CoV-2 variants analyzed in this manuscript (alpha, beta, gamma, delta Mink, G614, N501) show differences in the local conformations of the FP, HR1, and CH domains as well. Finally, most mutations of concern are either in or in the vicinity of high local topological free energy conformations, suggesting that high local topological free energy conformations could be targets for mutations with significant impact of protein function. Namely, the residues 484, 570, 614, 796, and 969, which are present in variants of concern and are targeted as important in protein function, are predicted as such from our model. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
4. Topological Entanglement and Its Relation to Polymer Material Properties
- Author
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Panagiotou, Eleni, Adams, Colin C., editor, Gordon, Cameron McA., editor, Jones, Vaughan F.R., editor, Kauffman, Louis H., editor, Lambropoulou, Sofia, editor, Millett, Kenneth C., editor, Przytycki, Jozef H., editor, Ricca, Renzo, editor, and Sazdanovic, Radmila, editor
- Published
- 2019
- Full Text
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5. Writhe-like invariants of alternating links.
- Author
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Diao, Yuanan and Pham, Van
- Subjects
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CHARTS, diagrams, etc. , *KNOT theory , *POLYNOMIALS - Abstract
It is known that the writhe calculated from any reduced alternating link diagram of the same (alternating) link has the same value. That is, it is a link invariant if we restrict ourselves to reduced alternating link diagrams. This is due to the fact that reduced alternating link diagrams of the same link are obtainable from each other via flypes and flypes do not change writhe. In this paper, we introduce several quantities that are derived from Seifert graphs of reduced alternating link diagrams. We prove that they are "writhe-like" invariants, namely they are not general link invariants, but are invariants when restricted to reduced alternating link diagrams. The determination of these invariants are elementary and non-recursive so they are easy to calculate. We demonstrate that many different alternating links can be easily distinguished by these new invariants, even for large, complicated knots for which other invariants such as the Jones polynomial are hard to compute. As an application, we also derive an if and only if condition for a strongly invertible rational link. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
6. Global 3D parameter of the spine: application of Călugăreanu–White–Fuller theorem in classification of pediatric spinal deformity.
- Author
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Arginteanu, Toren, DeTurck, Dennis, and Pasha, Saba
- Subjects
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ADOLESCENT idiopathic scoliosis , *SPINAL curvatures , *MATHEMATICAL analysis , *THORACIC vertebrae , *SPONDYLOSIS - Abstract
Several classification systems of the spinal curves in adolescent idiopathic scoliosis (AIS) have been developed to guide surgical decision-making. The current classification systems are based on the spinal deformity patterns or deformity magnitudes in one or two anatomical planes. Considering the 3D nature of the spinal deformity in AIS, these classifications fail to capture the spine's curve in its entirety. We proposed a classification based on the axial plane and showed that mathematical analysis of the 3D spinal curve, using differential geometry, supports the differences between the subtypes in this classification system. We calculated the writhe and twist of the entire spinal centerline, elements of the Călugăreanu–White–Fuller theorem, in a cohort of 30 right thoracic AIS patients. We also classified this cohort manually based on the vertebral level at which the direction of vertebral rotation caudal to the thoracic curve changes: Lumbar in Group I (V-shaped axial projection) or thoracolumbar in Group II (S-shaped axial projection). The writhe and twist of the spinal curve were significantly different between these manual classification subgroups. Our manual classification distinguished the axial subgroups of right thoracic AIS supported by mathematical specifications of the entire curve in three dimensions. [ABSTRACT FROM AUTHOR]
- Published
- 2020
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7. Antinociceptive Effect of Ondansetron in Albino Mice Using Acetic Acid Induced Writhing Model
- Author
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Abhay Purohit, Sunil S. Gidamudi, Chitra C. Khanwelkar, Vandana M. Thorat, and Sujata A. Jadhav
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Ondansetron ,Diclofenac ,1% Acetic Acid ,Writhe ,Antinociceptive Effect ,Writhes ,Medicine ,Medicine (General) ,R5-920 - Abstract
Background: Pain is an unpleasant sensory and emotional experience. Pain is a protective mechanism. Pain occurs whenever any tissues are being damaged, and it causes the individual to react and to remove the pain stimulus. Aim and Objectives: To evaluate the antinociceptive effect of ondansetron in comparison with the standard diclofenac. Material and Methods: The antinociceptive effect was tested by using the acetic acid induced writhing model in Swiss Albino mice. Animals were divided into 4 groups of 6 animals each. Animals were received distilled water (control), diclofenac (standard), ondansetron 0.5mg/kg (test I) and ondansetron 1mg/kg (test II). After 30 minutes of drug administration, 0.1 ml of 1% acetic acid was injected. Mice were placed individually into glass beakers and five minutes were allowed to elapse. They were then observed for a period of ten minutes and the numbers of writhes were recorded in each animal. The results were expressed as mean ± SEM. One way ANOVA with post-test was used for statistical calculation. Results: The numbers of writhes were 1.33±0.494 for diclofenac; 6.33±1.872 and 9.33±1.706 for ondansetron 0.5 and 1mg/kg respectively. Conclusion: Ondansetron demonstrated statistical significant antinociceptive activity at both doses (0.5mg/kg and 1mg/kg) and statistically similar effect as diclofenac
- Published
- 2016
8. True 3D parameters of the spinal deformity in adolescent idiopathic scoliosis
- Author
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Pasha, Saba, Shen, Jesse, and Kadoury, Samuel
- Published
- 2021
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9. Average crossing number and writhe of knotted random polygons in confinement.
- Author
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Diao, Yuanan, Ernst, Claus, Rawdon, Eric J., and Ziegler, Uta
- Subjects
- *
CROSSING numbers (Graph theory) , *POLYGONS , *STANDARD deviations , *KNOTS & splices , *PROBABILITY density function - Abstract
Abstract In this paper we study the average crossing number and writhe of random freely-jointed polygons in spherical confinement. Specifically, we use numerical studies to investigate how these geometric quantities are affected by confinement and by knot complexity within random polygons. We report and compare our results with previously published results on knotted random polygons that are unconfined. While some of the results fall in line with what have been observed in studies of unconfined random polygons, some surprising results have emerged from our study, showing properties that are unique due to the effect of confinement. For example, under tight confinement, the average crossing number and the squared writhe grow proportional to the polygon length squared. However, the squared writhe of polygons with a fixed knot type (such as the trefoil) grows much slower than the squared writhe of all polygons. We also observe that while the writhe values at a given length and confinement radius are normally distributed, the distribution of the average crossing number values around their mean are not normal, but rather log-normal. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
10. A Hi–C data-integrated model elucidatesE. colichromosome’s multiscale organization at various replication stages
- Author
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Jagannath Mondal, Ankit Gupta, and Abdul Wasim
- Subjects
DNA Replication ,Recombination, Genetic ,Models, Genetic ,AcademicSubjects/SCI00010 ,Operon ,DNA replication ,Computational Biology ,Chromosome ,Computational biology ,Chromosomes, Bacterial ,Biology ,medicine.disease_cause ,Genome ,Chromosome conformation capture ,Microscopy, Fluorescence ,Escherichia coli ,Genetics ,medicine ,Recombination ,Writhe - Abstract
The chromosome of Escherichia coli is riddled with multi-faceted complexity. The emergence of chromosome conformation capture techniques are providing newer ways to explore chromosome organization. Here we combine a beads-on-a-spring polymer-based framework with recently reported Hi–C data for E. coli chromosome, in rich growth condition, to develop a comprehensive model of its chromosome at 5 kb resolution. The investigation focuses on a range of diverse chromosome architectures of E. coli at various replication states corresponding to a collection of cells, individually present in different stages of cell cycle. The Hi–C data-integrated model captures the self-organization of E. coli chromosome into multiple macrodomains within a ring-like architecture. The model demonstrates that the position of oriC is dependent on architecture and replication state of chromosomes. The distance profiles extracted from the model reconcile fluorescence microscopy and DNA-recombination assay experiments. Investigations into writhe of the chromosome model reveal that it adopts helix-like conformation with no net chirality, earlier hypothesized in experiments. A genome-wide radius of gyration map captures multiple chromosomal interaction domains and identifies the precise locations of rrn operons in the chromosome. We show that a model devoid of Hi–C encoded information would fail to recapitulate most genomic features unique to E. coli.
- Published
- 2021
- Full Text
- View/download PDF
11. The Local Topological Free Energy of the SARS-CoV-2 Spike Protein
- Author
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Sumpter Bg, Eleni Panagiotou, and Quenisha Baldwin
- Subjects
2019-20 coronavirus outbreak ,Polymers and Plastics ,Coronavirus disease 2019 (COVID-19) ,Chemistry ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Protein domain ,Spike Protein ,SARS-CoV-2 ,Spike protein ,topology ,mutations ,writhe ,Density functional theory ,General Chemistry ,Solvent effects ,Topology ,Energy (signal processing) - Abstract
The novel coronavirus SARS-CoV-2 infects human cells using a mechanism that involves binding and structural rearrangement of its Spike protein. Understanding protein rearrangement and identifying specific amino acids where mutations affect protein rearrangement has attracted much attention for drug development. In this manuscript, we use a mathematical method to characterize the local topology/geometry of the SARS-CoV-2 Spike protein backbone. Our results show that local conformational changes in the FP, HR1, and CH domains are associated with global conformational changes in the RBD domain. The SARS-CoV-2 variants analyzed in this manuscript (alpha, beta, gamma, delta Mink, G614, N501) show differences in the local conformations of the FP, HR1, and CH domains as well. Finally, most mutations of concern are either in or in the vicinity of high local topological free energy conformations, suggesting that high local topological free energy conformations could be targets for mutations with significant impact of protein function. Namely, the residues 484, 570, 614, 796, and 969, which are present in variants of concern and are targeted as important in protein function, are predicted as such from our model.
- Published
- 2022
12. The writhe of permutations and random framed knots.
- Author
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Even‐Zohar, Chaim
- Subjects
PERMUTATIONS ,RANDOM measures ,RANK correlation (Statistics) ,MOMENTS method (Statistics) ,GAUSSIAN processes - Abstract
ABSTRACT We introduce and study the writhe of a permutation, a circular variant of the well-known inversion number. This simple permutation statistics has several interpretations, which lead to some interesting properties. For a permutation sampled uniformly at random, we study the asymptotics of the writhe, and obtain a non-Gaussian limit distribution. This work is motivated by the study of random knots. A model for random framed knots is described, which refines the Petaluma model, studied with Hass, Linial, and Nowik (Discrete Comput Geom, 2016). The distribution of the framing in this model is equivalent to the writhe of random permutations. © 2016 Wiley Periodicals, Inc. Random Struct. Alg., 51, 121-142, 2017 [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
13. Helicity conservation and twisted Seifert surfaces for superfluid vortices.
- Author
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Salman, Hayder
- Subjects
- *
GEOMETRIC surfaces , *SUPERFLUIDITY , *CONTINUUM mechanics , *PHYSICAL constants , *KNOT theory - Abstract
Starting from the continuum definition of helicity, we derive from first principles its different contributions for superfluid vortices. Our analysis shows that an internal twist contribution emerges naturally from the mathematical derivation. This reveals that the spanwise vector that is used to characterize the twist contribution must point in the direction of a surface of constant velocity potential. An immediate consequence of the Seifert framing is that the continuum definition of helicity for a superfluid is trivially zero at all times. It follows that the Gauss-linking number is a more appropriate definition of helicity for superfluids. Despite this, we explain how a quasi-classical limit can arise in a superfluid in which the continuum definition for helicity can be used. This provides a clear connection between a microscopic and a macroscopic description of a superfluid as provided by the Hall–Vinen–Bekarevich–Khalatnikov equations. This leads to consistency with the definition of helicity used for classical vortices. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
14. Tying different knots in a molecular strand
- Author
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David P. August, David A. Leigh, Joakim Halldin Stenlid, Lucian Pirvu, Julien Segard, and Fredrik Schaufelberger
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chemistry.chemical_classification ,Physics ,Lanthanide ,Quantitative Biology::Biomolecules ,Multidisciplinary ,010405 organic chemistry ,Metal ions in aqueous solution ,Polymer ,010402 general chemistry ,Mathematics::Geometric Topology ,01 natural sciences ,0104 chemical sciences ,Crystallography ,Knot (unit) ,chemistry ,Molecule ,Unknot ,Writhe - Abstract
The properties of knots are exploited in a range of applications, from shoelaces to the knots used for climbing, fishing and sailing1. Although knots are found in DNA and proteins2, and form randomly in other long polymer chains3,4, methods for tying5 different sorts of knots in a synthetic nanoscale strand are lacking. Molecular knots of high symmetry have previously been synthesized by using non-covalent interactions to assemble and entangle molecular chains6-15, but in such instances the template and/or strand structure intrinsically determines topology, which means that only one type of knot is usually possible. Here we show that interspersing coordination sites for different metal ions within an artificial molecular strand enables it to be tied into multiple knots. Three topoisomers-an unknot (01) macrocycle, a trefoil (31) knot6-15, and a three-twist (52) knot-were each selectively prepared from the same molecular strand by using transition-metal and lanthanide ions to guide chain folding in a manner reminiscent of the action of protein chaperones16. We find that the metal-ion-induced folding can proceed with stereoinduction: in the case of one knot, a lanthanide(III)-coordinated crossing pattern formed only with a copper(I)-coordinated crossing of particular handedness. In an unanticipated finding, metal-ion coordination was also found to translocate an entanglement from one region of a knotted molecular structure to another, resulting in an increase in writhe (topological strain) in the new knotted conformation. The knot topology affects the chemical properties of the strand: whereas the tighter 52 knot can bind two different metal ions simultaneously, the looser 31 isomer can bind only either one copper(I) ion or one lutetium(III) ion. The ability to tie nanoscale chains into different knots offers opportunities to explore the modification of the structure and properties of synthetic oligomers, polymers and supramolecules.
- Published
- 2020
- Full Text
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15. Quantitative Study of the Chiral Organization of the Phage Genome Induced by the Packaging Motor
- Author
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Zihao Zhu, Javier Arsuaga, Carme Calderer, Brian Cruz, and Mariel Vazquez
- Subjects
Biophysics ,Genome, Viral ,Rotation ,Genome ,Quantitative Biology::Subcellular Processes ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Capsid ,DNA Packaging ,Molecular motor ,Genetics ,Bacteriophages ,Kinetic Monte Carlo ,Viral ,030304 developmental biology ,Writhe ,Physics ,0303 health sciences ,Quantitative Biology::Biomolecules ,Human Genome ,DNA ,Articles ,Biological Sciences ,Quantitative Biology::Genomics ,chemistry ,Physical Sciences ,Chemical Sciences ,DNA, Viral ,Brownian dynamics ,Generic health relevance ,Biological system ,030217 neurology & neurosurgery - Abstract
Molecular motors that translocate DNA are ubiquitous in nature. During morphogenesis of double-stranded DNA bacteriophages, a molecular motor drives the viral genome inside a protein capsid. Several models have been proposed for the three-dimensional geometry of the packaged genome, but very little is known of the signature of the molecular packaging motor. For instance, biophysical experiments show that in some systems, DNA rotates during the packaging reaction, but most current biophysical models fail to incorporate this property. Furthermore, studies including rotation mechanisms have reached contradictory conclusions. In this study, we compare the geometrical signatures imposed by different possible mechanisms for the packaging motors: rotation, revolution, and rotation with revolution. We used a previously proposed kinetic Monte Carlo model of the motor, combined with Brownian dynamics simulations of DNA to simulate deterministic and stochastic motor models. We find that rotation is necessary for the accumulation of DNA writhe and for the chiral organization of the genome. We observe that although in the initial steps of the packaging reaction, the torsional strain of the genome is released by rotation of the molecule, in the later stages, it is released by the accumulation of writhe. We suggest that the molecular motor plays a key role in determining the final structure of the encapsidated genome in bacteriophages.
- Published
- 2020
16. A Symmetry Motivated Link Table
- Author
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Shawn Witte, Michelle Flanner, and Mariel Vazquez
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writhe ,chirality ,nomenclature ,link symmetries ,link table ,knot table ,lattice polygons ,DNA topology ,Mathematics ,QA1-939 - Abstract
Proper identification of oriented knots and 2-component links requires a precise link nomenclature. Motivated by questions arising in DNA topology, this study aims to produce a nomenclature unambiguous with respect to link symmetries. For knots, this involves distinguishing a knot type from its mirror image. In the case of 2-component links, there are up to sixteen possible symmetry types for each link type. The study revisits the methods previously used to disambiguate chiral knots and extends them to oriented 2-component links with up to nine crossings. Monte Carlo simulations are used to report on writhe, a geometric indicator of chirality. There are ninety-two prime 2-component links with up to nine crossings. Guided by geometrical data, linking number, and the symmetry groups of 2-component links, canonical link diagrams for all but five link types (9 5 2, 9 34 2, 9 35 2, 9 39 2, and 9 41 2) are proposed. We include complete tables for prime knots with up to ten crossings and prime links with up to nine crossings. We also prove a result on the behavior of the writhe under local lattice moves.
- Published
- 2018
- Full Text
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17. On torus knots and unknots.
- Author
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Oberti, Chiara and Ricca, Renzo L.
- Subjects
- *
TORUS , *KNOT theory , *GEOMETRIC analysis , *TOPOLOGY , *MATHEMATICAL symmetry - Abstract
A comprehensive study of geometric and topological properties of torus knots and unknots is presented. Torus knots/unknots are particularly symmetric, closed, space curves, that wrap the surface of a mathematical torus a number of times in the longitudinal and meridian direction. By using a standard parametrization, new results on local and global properties are found. In particular, we demonstrate the existence of inflection points for a given critical aspect ratio, determine the location and prescribe the regularization condition to remove the local singularity associated with torsion. Since to first approximation total length grows linearly with the number of coils, its nondimensional counterpart is proportional to the topological crossing number of the knot type. We analyze several global geometric quantities, such as total curvature, writhing number, total torsion, and geometric 'energies' given by total squared curvature and torsion, in relation to knot complexity measured by the winding number. We conclude with a brief presentation of research topics, where geometric and topological information on torus knots/unknots finds useful application. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
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18. Topological mechanics of knots and tangles
- Author
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Mathias Kolle, Joseph D. Sandt, Vishal P. Patil, and Jörn Dunkel
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Physics ,Multidisciplinary ,Physical system ,02 engineering and technology ,Mechanics ,021001 nanoscience & nanotechnology ,Topology ,01 natural sciences ,Simple (abstract algebra) ,Mechanical stability ,0103 physical sciences ,Twist ,010306 general physics ,0210 nano-technology ,Weaving ,Topology (chemistry) ,Writhe ,Spin-½ - Abstract
It's knot what you know Why is it that some knots seem to hold tight while others readily slip apart? Patil et al. develop a theoretical analysis of the stability of knots and find links between topological parameters (twist charge, crossing numbers, handedness) and mechanical stability. The theory is confirmed using simulations and experiments on color-changing fibers that optically show localized stress differences in different parts of the knot as the two strands are pulled apart. The authors show why some common knots slip easily and untie, whereas others hold tight. Science , this issue p. 71
- Published
- 2020
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19. Braiding topology and the energy landscape of chromosome organization proteins
- Author
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Nicholas P. Schafer, José N. Onuchic, Aram Davtyan, Peter G. Wolynes, and Dana Krepel
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Physics ,Multidisciplinary ,Cohesin ,biology ,Condensin ,Energy landscape ,Topology ,Force field (chemistry) ,Molecular dynamics ,chemistry.chemical_compound ,chemistry ,biology.protein ,Protein topology ,DNA ,Writhe - Abstract
Assemblies of structural maintenance of chromosomes (SMC) proteins and kleisin subunits are essential to chromosome organization and segregation across all kingdoms of life. While structural data exist for parts of the SMC−kleisin complexes, complete structures of the entire complexes have yet to be determined, making mechanistic studies difficult. Using an integrative approach that combines crystallographic structural information about the globular subdomains, along with coevolutionary information and an energy landscape optimized force field (AWSEM), we predict atomic-scale structures for several tripartite SMC−kleisin complexes, including prokaryotic condensin, eukaryotic cohesin, and eukaryotic condensin. The molecular dynamics simulations of the SMC−kleisin protein complexes suggest that these complexes exist as a broad conformational ensemble that is made up of different topological isomers. The simulations suggest a critical role for the SMC coiled-coil regions, where the coils intertwine with various linking numbers. The twist and writhe of these braided coils are coupled with the motion of the SMC head domains, suggesting that the complexes may function as topological motors. Opening, closing, and translation along the DNA of the SMC−kleisin protein complexes would allow these motors to couple to the topology of DNA when DNA is entwined with the braided coils.
- Published
- 2019
- Full Text
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20. Influence of Nucleoid-Associated Proteins on DNA Supercoiling
- Author
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Katelyn Dahlke and Charles E. Sing
- Subjects
DNA, Bacterial ,Plasma protein binding ,Molecular Dynamics Simulation ,010402 general chemistry ,01 natural sciences ,chemistry.chemical_compound ,Factor For Inversion Stimulation Protein ,mental disorders ,0103 physical sciences ,Escherichia coli ,Materials Chemistry ,Nucleoid ,Physical and Theoretical Chemistry ,Binding site ,Writhe ,Binding Sites ,010304 chemical physics ,DNA, Superhelical ,Extramural ,Chemistry ,Escherichia coli Proteins ,musculoskeletal, neural, and ocular physiology ,fungi ,0104 chemical sciences ,Surfaces, Coatings and Films ,Kinetics ,Torque ,Dna compaction ,Biophysics ,Thermodynamics ,DNA supercoil ,psychological phenomena and processes ,DNA ,Protein Binding - Abstract
DNA supercoiling, where the DNA strand forms a writhe to relieve torsional stress, plays a vital role in packaging the genetic material in cells. Experiment, simulation, and theory have all demonstrated how supercoiling emerges due to the over- or underwinding of the DNA strand. Nucleoid-associated proteins (NAPs) help structure DNA in prokaryotes, yet the role that they play in the supercoiling process has not been as thoroughly investigated. We develop a coarse-grained simulation to model DNA supercoiling in the presence of proteins, providing a rigorous physical understanding of how NAPs affect supercoiling behavior. Specifically, we demonstrate how the force and torque necessary to form supercoils are affected by the presence of NAPs. NAPs that bend DNA stabilize the supercoil, thus shifting the transition between extended and supercoiled DNAs. We develop a theory to explain how NAP binding affects DNA supercoiling. This provides insight into how NAPs modulate DNA compaction via a combination of supercoiling and local protein-dependent deformations.
- Published
- 2019
- Full Text
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21. On Osculating Framing of Real Algebraic Links
- Author
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Grigory Mikhalkin and Stepan Yu Orevkov
- Subjects
Combinatorics ,General Mathematics ,Algebraic link ,Algebraic number ,Mathematics::Geometric Topology ,Mathematics ,Writhe ,Osculating circle - Abstract
For a real algebraic link in $${{\mathbb {RP}}}^3$$, we prove that its encomplexed writhe (an invariant introduced by Viro) is maximal for a given degree and genus if and only if its self-linking number with respect to the framing by the osculating planes is maximal for a given degree.
- Published
- 2019
- Full Text
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22. Modelling and DNA topology of compact 2-start and 1-start chromatin fibres
- Author
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Chenyi Wu and Andrew Travers
- Subjects
Models, Molecular ,Histones ,Turn (biochemistry) ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Structural Biology ,Genetics ,Animals ,Humans ,Nucleosome ,030304 developmental biology ,Writhe ,0303 health sciences ,biology ,DNA ,Linker DNA ,Chromatin ,Nucleosomes ,Rats ,Histone ,chemistry ,biology.protein ,Biophysics ,Nucleic Acid Conformation ,Thermodynamics ,K562 Cells ,Linker ,030217 neurology & neurosurgery - Abstract
We have investigated the structure of the most compact 30-nm chromatin fibres by modelling those with 2-start or 1-start crossed-linker organisations. Using an iterative procedure we obtained possible structural solutions for fibres of the highest possible compaction permitted by physical constraints, including the helical repeat of linker DNA. We find that this procedure predicts a quantized nucleosome repeat length (NRL) and that only fibres with longer NRLs (≥197 bp) can more likely adopt the 1-start organisation. The transition from 2-start to 1-start fibres is consistent with reported differing binding modes of the linker histone. We also calculate that in 1-start fibres the DNA constrains more torsion (as writhe) than 2-start fibres with the same NRL and that the maximum constraint obtained is in accord with previous experimental results. We posit that the coiling of the fibre is driven by overtwisting of linker DNA which, in the most compact forms - for example, in echinoderm sperm and avian erythrocytes - could adopt a helical repeat of ∼10 bp/turn. We argue that in vivo the total twist of linker DNA could be modulated by interaction with other abundant chromatin-associated proteins and by epigenetic modifications of the C-terminal tail of linker histones.
- Published
- 2019
- Full Text
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23. Helicity spectra and topological dynamics of vortex links at high Reynolds numbers
- Author
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Anthony Leonard and Demosthenes Kivotides
- Subjects
Physics ,Quantitative Biology::Biomolecules ,Vortex tube ,Turbulence ,Mechanical Engineering ,Reynolds number ,Condensed Matter Physics ,01 natural sciences ,Helicity ,010305 fluids & plasmas ,Vortex ,Physics::Fluid Dynamics ,symbols.namesake ,Classical mechanics ,Mechanics of Materials ,Condensed Matter::Superconductivity ,Vortex stretching ,0103 physical sciences ,symbols ,Potential flow ,TJ ,010306 general physics ,Writhe - Abstract
We employ reconnection-capable, vortex filament methods and finite-volume, Navier–Stokes flow solvers to investigate the topological and helicity dynamics of vortex links for medium and high Reynolds numbers. Our vortex-dynamical model is based on discretization of vortex tubes into bundles of numerical analogues of vortex lines. Due to their nearly singular nature, the numerical vortex lines have topological writhe but not twist. By means of our reconnecting vortex tube model, it is shown that the helicity of a vortex link is conserved during the unknotting process. The dynamics of linking and writhe topological measures indicate that most of the initial linking becomes writhe during the post-reconnection evolution. The helicity spectra of the vortex link present alternating-sign helicity fluctuations at all (potential flow) scales up to the vortex core. At pre-reconnection times, these fluctuations are damped by Biot–Savart vortex stretching and helicity becomes single signed. The post-reconnection spectra indicate an inverse helicity cascade corresponding to the creation of a homogenized vortex blob, a process reminiscent of coherent structure formation in turbulence. An accompanying Navier–Stokes calculation of vortex link dynamics at Reynolds numbers Re=1500 confirms the post-reconnection transformation of linking into different topological measures, the pre-reconnection damping of helicity spectra fluctuations and the spectral shift to low wavenumbers at post-reconnection times. Due to viscous dissipation action, however, this shift is accompanied by progressive reduction of helicity peak values.
- Published
- 2021
24. Twisting or untwisting graphene twisted nanoribbons without rotation
- Author
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Alexandre F. Fonseca
- Subjects
Physics ,Condensed Matter - Mesoscale and Nanoscale Physics ,Graphene ,FOS: Physical sciences ,Linking number ,Rotation ,Space (mathematics) ,law.invention ,symbols.namesake ,Molecular dynamics ,Classical mechanics ,law ,Mesoscale and Nanoscale Physics (cond-mat.mes-hall) ,Ribbon ,symbols ,Twist ,Writhe - Abstract
The common sense regarding twisting or untwisting a ribbon is that it requires the application of an external rotation to happen. However, at nanoscale, the application of precise amounts of rotation on a nanoribbon is not a trivial task. Here, the concept of an alternative method to add twist to or remove twist from a twisted graphene nanoribbon (TGNR) without rotation is presented. The method consists of suspending a TGNR on two separate substrates and by changing only their distance, the total amount of twist of the TGNR is shown to change. The possibility to fine-tuning the amount of twist of a TGNR is also shown. The concept is demonstrated through fully atomistic molecular dynamics simulations and numerical calculations of the topological parameters twist and writhe of a TGNR. It is shown that the above process satisfies the so-called linking number theorem of space curves. Besides being experimentally feasible, this concept reveals a new kind of twist to writhe transition phenomenon that is tension-free and does not require controlling neither the nanoribbon end-to-end distance nor its critical twist density., This is the submitted version of the paper, that was published in PRB
- Published
- 2021
25. Nonequilibrium dynamics and action at a distance in transcriptionally driven DNA supercoiling
- Author
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Davide Michieletto, Chris A. Brackley, Yair Augusto Gutierrez Fosado, and Davide Marenduzzo
- Subjects
DNA, Bacterial ,Transcription, Genetic ,Molecular Dynamics Simulation ,Quantitative Biology::Subcellular Processes ,chemistry.chemical_compound ,Bacterial Proteins ,RNA polymerase ,nonequilibrium physics ,supercoiling ,Nucleosome ,Histone octamer ,Twist ,Writhe ,Physics ,Physics::Biological Physics ,Quantitative Biology::Biomolecules ,Multidisciplinary ,DNA, Superhelical ,Quantitative Biology::Molecular Networks ,DNA-Directed RNA Polymerases ,Quantitative Biology::Genomics ,DNA topology ,DNA-Binding Proteins ,chemistry ,Physical Sciences ,Biophysics ,Brownian dynamics ,DNA supercoil ,transcription ,DNA - Abstract
We study the effect of transcription on the kinetics of DNA supercoiling in three dimensions by means of Brownian dynamics simulations of a single-nucleotide–resolution coarse-grained model for double-stranded DNA. By explicitly accounting for the action of a transcribing RNA polymerase (RNAP), we characterize the geometry and nonequilibrium dynamics of the ensuing twin supercoiling domains. Contrary to the typical textbook picture, we find that the generation of twist by RNAP results in the formation of plectonemes (writhed DNA) some distance away. We further demonstrate that this translates into an “action at a distance” on DNA-binding proteins; for instance, positive supercoils downstream of an elongating RNAP destabilize nucleosomes long before the transcriptional machinery reaches the histone octamer. We also analyze the relaxation dynamics of supercoiled double-stranded DNA, and characterize the widely different timescales of twist diffusion, which is a simple and fast process, and writhe relaxation, which is much slower and entails multiple steps.
- Published
- 2021
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26. Topoisomerase VI is a chirally-selective, preferential DNA decatenase
- Author
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Parth Rakesh Desai, Anthony Maxwell, Keir C. Neuman, Yeonee Seol, and Shannon J. Mckie
- Subjects
Magnetic tweezers ,biology ,Chemistry ,Topoisomerase ,biology.organism_classification ,chemistry.chemical_compound ,biology.protein ,Biophysics ,DNA supercoil ,A-DNA ,Bacteria ,DNA ,Writhe ,Archaea - Abstract
DNA topoisomerase VI (topo VI) is a type IIB DNA topoisomerase found predominantly in archaea and some bacteria, but also in plants and algae. Since its discovery, topo VI has been proposed to be a DNA decatenase, however robust evidence and a mechanism for its preferential decatenation activity was lacking. Using single-molecule magnetic tweezers measurements and supporting ensemble biochemistry, we demonstrate that Methanosarcina mazei topo VI preferentially unlinks, or decatenates, DNA crossings, in comparison to relaxing supercoils, through a preference for certain DNA crossing geometries. In addition, topo VI demonstrates a dramatic increase in ATPase activity, DNA binding and rate of strand passage, with increasing DNA writhe, providing further evidence that topo VI is a DNA crossing sensor. Our study strongly suggests that topo VI has evolved an intrinsic preference for the unknotting and decatenation of interlinked chromosomes by sensing and preferentially unlinking DNA crossings with geometries close to 90°.
- Published
- 2021
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27. The local topological free energy of proteins
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Quenisha Baldwin and Eleni Panagiotou
- Subjects
Statistics and Probability ,Sequence ,Protein Folding ,General Immunology and Microbiology ,Protein Conformation ,Applied Mathematics ,Entropy ,Protein Data Bank (RCSB PDB) ,Proteins ,General Medicine ,Function (mathematics) ,Topology ,General Biochemistry, Genetics and Molecular Biology ,Folding (chemistry) ,Protein structure ,Modeling and Simulation ,Torsion (algebra) ,Peptide bond ,Protein folding ,Amino Acids ,General Agricultural and Biological Sciences ,Topology (chemistry) ,Writhe - Abstract
Protein folding, the process by which proteins attain a 3-dimensional conformation necessary for their function, remains an important unsolved problem in biology. A major gap in our understanding is how local properties of proteins relate to their global properties. In this manuscript, we use the Writhe and Torsion to introduce a new local topological/geometrical free energy that can be associated to 4 consecutive amino acids along the protein backbone. By analyzing a culled protein dataset from the PDB, our results show that high local topological free energy conformations are independent of sequence and may be involved in the rate limiting step in protein folding. By analyzing a set of 2-state single domain proteins, we find that the total local topological free energy of these proteins correlates with the experimentally observed folding rates reported in Plaxco et al. (2000).
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- 2021
28. A topological extension of movement primitives for curvature modulation and sampling of robot motion
- Author
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Carme Torras, Adrià Colomé, European Research Council, European Commission, Ministerio de Economía y Competitividad (España), Institut de Robòtica i Informàtica Industrial, and Universitat Politècnica de Catalunya. ROBiri - Grup de Robòtica de l'IRI
- Subjects
0209 industrial biotechnology ,Computer science ,02 engineering and technology ,Intelligent robots ,Topology ,Curvature ,Adaptive systems ,Curling ,Automation::Robots [Classificació INSPEC] ,symbols.namesake ,020901 industrial engineering & automation ,Artificial Intelligence ,0202 electrical engineering, electronic engineering, information engineering ,Humanoid robots ,Robot motion ,Writhe ,Imitation learning ,Linking number ,Manipulators ,Generative model ,Feature (computer vision) ,Line (geometry) ,symbols ,Trajectory ,020201 artificial intelligence & image processing ,Informàtica::Robòtica [Àrees temàtiques de la UPC] ,Robots ,Topological methods - Abstract
This paper proposes to enrich robot motion data with trajectory curvature information. To do so, we use an approximate implementation of a topological feature named writhe, which measures the curling of a closed curve around itself, and its analog feature for two closed curves, namely the linking number. Despite these features have been established for closed curves, their definition allows for a discrete calculation that is well-defined for non-closed curves and can thus provide information about how much a robot trajectory is curling around a line in space. Such lines can be predefined by a user, observed by vision or, in our case, inferred as virtual lines in space around which the robot motion is curling. We use these topological features to augment the data of a trajectory encapsulated as a Movement Primitive (MP). We propose a method to determine how many virtual segments best characterize a trajectory and then find such segments. This results in a generative model that permits modulating curvature to generate new samples, while still staying within the dataset distribution and being able to adapt to contextual variables., Thiswork has been carried out within the projectCLOTHILDE (“CLOTH manIpulation Learning from DEmonstrations”) funded by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Advanced Grant agreementNo 741930).Research at IRI is also supported by the Spanish State Research Agency through theMaría de Maeztu Seal of Excellence to IRI MDM-2016-0656.
- Published
- 2021
29. Global 3D Parameter of the Spine: Application of Călugăreanu–White–Fuller Theorem in Classification of Pediatric Spinal Deformity
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Dennis DeTurck, Saba Pasha, and Toren Arginteanu
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Adolescent ,Rotation ,Vertebral level ,0206 medical engineering ,Biomedical Engineering ,02 engineering and technology ,Article ,Thoracic Vertebrae ,030218 nuclear medicine & medical imaging ,03 medical and health sciences ,0302 clinical medicine ,Lumbar ,Vertebral rotation ,Deformity ,medicine ,Humans ,Kyphosis ,Twist ,Child ,Writhe ,Mathematics ,Axial projection ,Anatomy ,020601 biomedical engineering ,Computer Science Applications ,Radiography ,Scoliosis ,Spinal deformity ,medicine.symptom - Abstract
Several classification systems of the spinal curves in adolescent idiopathic scoliosis (AIS) have been developed to guide surgical decision-making. The current classification systems are based on the spinal deformity patterns or deformity magnitudes in one or two anatomical planes. Considering the 3D nature of the spinal deformity in AIS, these classifications fail to capture the spine's curve in its entirety. We proposed a classification based on the axial plane and showed that mathematical analysis of the 3D spinal curve, using differential geometry, supports the differences between the subtypes in this classification system. We calculated the writhe and twist of the entire spinal centerline, elements of the Calugareanu-White-Fuller theorem, in a cohort of 30 right thoracic AIS patients. We also classified this cohort manually based on the vertebral level at which the direction of vertebral rotation caudal to the thoracic curve changes: Lumbar in Group I (V-shaped axial projection) or thoracolumbar in Group II (S-shaped axial projection). The writhe and twist of the spinal curve were significantly different between these manual classification subgroups. Our manual classification distinguished the axial subgroups of right thoracic AIS supported by mathematical specifications of the entire curve in three dimensions. Graphical abstract.
- Published
- 2020
30. Writhe-like invariants of alternating links
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Yuanan Diao and Van Pham
- Subjects
Pure mathematics ,Algebra and Number Theory ,Link diagram ,General Topology (math.GN) ,Value (computer science) ,Geometric Topology (math.GT) ,57K10 ,Mathematics::Geometric Topology ,Flype ,Mathematics - Geometric Topology ,FOS: Mathematics ,Invariant (mathematics) ,Link (knot theory) ,Mathematics ,Writhe ,Mathematics - General Topology - Abstract
It is known that the writhe calculated from any reduced alternating link diagram of the same (alternating) link has the same value. That is, it is a link invariant if we restrict ourselves to reduced alternating link diagrams. This is due to the fact that reduced alternating link diagrams of the same link are obtainable from each other via flypes and flypes do not change writhe. In this paper, we introduce several quantities that are derived from Seifert graphs of reduced alternating link diagrams. We prove that they are "writhe-like" invariants in the sense that they are also link invariants among reduced alternating link diagrams. The determination of these invariants are elementary and non-recursive so they are easy to calculate. We demonstrate that many different alternating links can be easily distinguished by these new invariants, even for large, complicated knots for which other invariants such as the Jones polynomial are hard to compute. As an application, we also derive an if and only if condition for a strongly invertible rational link., 16 pages, 18 figures
- Published
- 2020
31. WASP: A software package for correctly characterizing the topological development of ribbon structures
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Jeff Wereszczynski, Zachary Sierzega, and Christopher Prior
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Science ,Closure (topology) ,Topology ,01 natural sciences ,Measure (mathematics) ,Article ,Computational biophysics ,Biopolymers ,Development (topology) ,Single-molecule biophysics ,0103 physical sciences ,Ribbon ,010306 general physics ,Condensed-matter physics ,010303 astronomy & astrophysics ,Topology (chemistry) ,Writhe ,Physics ,Physics::Biological Physics ,Quantitative Biology::Biomolecules ,Multidisciplinary ,DNA, Superhelical ,DNA ,Models, Theoretical ,Applied mathematics ,Molecular biophysics ,Mathematics::Geometric Topology ,Magnetic flux ,Models, Chemical ,Medicine ,Nucleic Acid Conformation ,Polar ,Software - Abstract
We introduce the Writhe Application Software Package (WASP) which can be used to characterisze the topology of ribbon structures, the underlying mathematical model of DNA, Biopolymers, superfluid vorticies, elastic ropes and magnetic flux ropes. This characterization is achieved by the general twist–writhe decomposition of both open and closed ribbons, in particular through a quantity termed the polar writhe. We demonstrate how this decomposition is far more natural and straightforward than artificial closure methods commonly utilized in DNA modelling. In particular, we demonstrate how the decomposition of the polar writhe into local and non-local components distinctly characterizes the local helical structure and knotting/linking of the ribbon. This decomposition provides additional information not given by alternative approaches. As example applications, the WASP routines are used to characterise the evolving topology (writhe) of DNA minicircle and open ended plectoneme formation magnetic/optical tweezer simulations, and it is shown that the decomponsition into local and non-local components is particularly important for the detection of plectonemes. Finally it is demonstrated that a number of well known alternative writhe expressions are actually simplifications of the polar writhe measure.
- Published
- 2020
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32. True 3D parameters of the spinal deformity in adolescent idiopathic scoliosis
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Saba Pasha, Samuel Kadoury, and Jesse Shen
- Subjects
Orthodontics ,030222 orthopedics ,medicine.medical_specialty ,Adolescent ,business.industry ,Radiography ,Torsion (mechanics) ,Idiopathic scoliosis ,Thoracic Vertebrae ,03 medical and health sciences ,0302 clinical medicine ,Lumbar ,Imaging, Three-Dimensional ,Scoliosis ,Orthopedic surgery ,medicine ,Spinal deformity ,Humans ,Orthopedics and Sports Medicine ,Kyphosis ,Twist ,business ,030217 neurology & neurosurgery ,Writhe - Abstract
Spinal deformities in adolescent idiopathic scoliosis (AIS) are measured on 2D radiographs. Due to the 3D nature of the curve in AIS, such 2D measurements fail to differentiate between the true curve patterns, which in turn may adversly impact the clinical care and surgical planning. The use of 3D models of the spinal radiographs largely remains limited to the 3D measurements of the 2D parameters. The use of the true 3D variables of the spinal curves in describing the differences between the AIS patients is not fully explored. A cohort of 141 Lenke 1 AIS with two-view spinal stereoradiographs and 3D models of the spines were included. The 3D model of the spine was used to determine the spinal centerlines. The writhe and torsion of the 3D centerlines, which, respectively, quantify the coiling and twist of the curve, were calculated using differential geometry. Patients were clustered based on the writhe and torsion values to determine the patient groups with significantly different 3D curve characteristics. The relationship between the writhe and torsion was statistically determined. The distribution of the writhe and torsion groups between the lumbar modifier types was determined. Two writhe and two torsion clusters were determined. Lumbar orientation of plane of maximum curvature (PMC) was significantly different between the torsion clusters and thoracic and lumbar PMC and thoracic Cobb angles were significantly different between the writhe groups, p
- Published
- 2020
33. Bosonization in 2+1 dimensions via Chern-Simons bosonic particle-vortex duality
- Author
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Flavio S. Nogueira, Jeroen van den Brink, Oguz Turker, and Tobias Meng
- Subjects
High Energy Physics - Theory ,Condensed Matter::Quantum Gases ,Bosonization ,Physics ,Particle statistics ,Statistical Mechanics (cond-mat.stat-mech) ,010308 nuclear & particles physics ,High Energy Physics::Lattice ,Chern–Simons theory ,FOS: Physical sciences ,Fermion ,01 natural sciences ,Scaling limit ,High Energy Physics - Theory (hep-th) ,0103 physical sciences ,Higgs boson ,010306 general physics ,Condensed Matter - Statistical Mechanics ,Mathematical physics ,Writhe ,Boson - Abstract
Dualities provide deep insight into physics by relating two seemingly distinct theories. Here we consider a duality between lattice fermions and bosons in (2+1) spacetime dimensions, relating free massive Dirac fermions to Abelian Chern-Simons Higgs (ACSH) bosons. To establish the duality we represent the exact partition function of the lattice fermions in terms of the writhe of fermionic worldlines. On the bosonic side the partition function is expressed in the writhe of the vortex loops of the particle-vortex dual of the ACSH Lagrangian. In the continuum and scaling limit we show these to be identical. This result can be understood from the closed fermionic worldlines being direct mappings of the ACSH vortex loops, with the writhe keeping track of particle statistics., Comment: 13 pages, 4 figures; v2 matches published version
- Published
- 2020
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34. Effects of twist on the evolution of knotted magnetic flux tubes
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Shiying Xiong and Yue Yang
- Subjects
Hopf bifurcation ,Physics ,Flux tube ,Phase portrait ,Mechanical Engineering ,Applied Mathematics ,Topological fluid dynamics ,Mechanics ,Condensed Matter Physics ,01 natural sciences ,Magnetic flux ,010305 fluids & plasmas ,symbols.namesake ,Mechanics of Materials ,0103 physical sciences ,symbols ,Twist ,010306 general physics ,Lorentz force ,Writhe - Abstract
We develop a general method for constructing knotted flux tubes with finite thickness, arbitrary shape and tunable twist. The central axis of the knotted tube is specified by a smooth and non-degenerate parametric equation. The helicity of the corresponding solenoidal knotted field can be explicitly decomposed into writhe, normalized total torsion and intrinsic twist. We construct several knotted magnetic flux tubes with various twisting degrees, and investigate the effect of twist on their evolution in resistive magnetohydrodynamic flows using direct numerical simulation. For large twist, the magnetic knot gradually shrinks to a tight stable state, similar to the relaxation process in ideal magnetohydrodynamic flows. For small twist, the knotted flux tube splits at early times, accompanied by a rising magnetic dissipation rate. We elucidate the mechanism of the tube splitting using the phase portrait of the Lorentz force projected onto divergence-free space. For finite twist, the Hopf bifurcation from an unstable spiral point to a limit cycle occurs on the phase plane. In the evolution, field lines inside the limit cycle form invariant tori, whereas they become chaotic outside the limit cycle.
- Published
- 2020
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35. The creation of twist by reconnection of flux tubes
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Dana Longcope, Eric Priest, and University of St Andrews. Applied Mathematics
- Subjects
T-NDAS ,01 natural sciences ,solar flares [Sun] ,010305 fluids & plasmas ,Helicity ,Magnetic helicity ,Physics::Plasma Physics ,0103 physical sciences ,Coronal mass ejection ,Astrophysics::Solar and Stellar Astrophysics ,QA Mathematics ,Twist ,QA ,010303 astronomy & astrophysics ,QC ,Writhe ,Physics ,Solar flare ,Astronomy and Astrophysics ,Magnetic reconnection ,Coronal loop ,Mechanics ,magnetic topology [Sun] ,QC Physics ,Space and Planetary Science ,Physics::Space Physics ,Coronal mass ejections ,Erupting prominences - Abstract
A fundamental process in a plasma is the magnetic reconnection of one pair of flux tubes (such as solar coronal loops) to produce a new pair. During this process magnetic helicity is conserved, but mutual helicity can be transformed to self-helicity, so that the new tubes acquire twist. However, until recently, when Wright (Astrophys. J.878, 102, 2019) supplied a solution, the partition of self-helicity between the two tubes was an outstanding puzzle. Here we examine Wright’s result in detail and apply it to a variety of cases. The simplest case, which Wright himself used to illustrate the result, is that of thin ribbons or flux sheets. We first explicitly apply his method to the usually expected standard case (when the tubes approach one another without twisting before reconnection) and confirm his result is valid for flux sheaths and tubes as well as sheets.For the reconnection of sheets, it is shown that the orientation of the sheets needs to be chosen carefully. For flux sheaths and tubes, Wright’s results are demonstrated to hold for the standard case. There is both a local and a global aspect to the effect of reconnection. The local effect of reconnection is to produce an equipartition of the added self-helicity (and therefore of twist), but the extra global effect of the location and orientation of the feet of the sheet, shell or tube in general adds different amounts of magnetic helicity to the two structures.It is important, as Wright realized, to account for any twist or writhe already existing in the fluxes prior to reconnection. Here we show explicitly that, if a section of a flux sheet is twisted by a multiple of $\pi $π with its ends held fixed and is then reconnected with another sheet, then the effect of the reconnection is to add that multiple of $\pi $π to one sheet and subtract it from the other, while conserving the total helicity. If, on the other hand, the central part of a flux sheath is twisted before reconnection by any angle, then the effect of reconnection is to add that amount of twist to one sheath and subtract it from the other, while conserving the total helicity. Thus, for the local part of the process in both sheets and sheaths, there is no longer helicity equipartition.Finally, we apply Wright’s results explicitly to flux tubes, and in particular to determine the twist that is acquired by an erupting flux rope due to reconnection during an eruptive solar flare or coronal mass ejection.
- Published
- 2020
36. On arrow polynomials of checkerboard colorable virtual links
- Author
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Xian'an Jin, Louis H. Kauffman, and Qingying Deng
- Subjects
Condensed Matter::Quantum Gases ,Polynomial ,Algebra and Number Theory ,Geometric Topology (math.GT) ,Mathematics::Geometric Topology ,Combinatorics ,Mathematics - Geometric Topology ,Checkerboard ,57M25 ,Arrow ,FOS: Mathematics ,Condensed Matter::Strongly Correlated Electrons ,Virtual link ,Writhe ,Mathematics - Abstract
In this paper we give two new criteria of detecting the checkerboard colorability of virtual links by using odd writhe and arrow polynomial of virtual links, respectively. By applying new criteria, we prove that 6 virtual knots are not checkerboard colorable, leaving only one virtual knot whose checkerboard colorability is unknown among all virtual knots up to four classical crossings., 16 pages, 17 figures
- Published
- 2020
37. Twist–coil coupling fibres for high stroke tensile artificial muscles
- Author
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Javad Foroughi, Geoffrey M. Spinks, Sina Naficy, Shazed Aziz, and Hugh R. Brown
- Subjects
Materials science ,Metals and Alloys ,02 engineering and technology ,010402 general chemistry ,021001 nanoscience & nanotechnology ,Condensed Matter Physics ,Rotation ,Elastomer ,01 natural sciences ,0104 chemical sciences ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials ,Electromagnetic coil ,Ultimate tensile strength ,Coupling (piping) ,Artificial muscle ,Electrical and Electronic Engineering ,Composite material ,Twist ,0210 nano-technology ,Instrumentation ,Writhe - Abstract
A new concept for tensile artificial muscles is introduced in which the torsional actuation of a twisted polymer fibre drives a twist to writhe conversion in a serially attached elastomeric fibre. Thermally induced torsional rotation of the twisted fibre caused formation of coils in the elastomeric fibre which resulted in overall muscle length contraction. Theoretical predictions of the muscle strain were developed by means of a modified single-helix theory. Experimental tests were conducted to measure the isotonic contraction strains for elastomeric fibres of different diameters and lengths. A good agreement between the measured and calculated results was found. Practical applicability of this muscle is evaluated by using different mechanical loading conditions. Actuation contraction strains as high as 10% were observed with excellent reversibility. Unlike original coiled fibre tensile actuators, these twist-coil artificial muscles did not require any pre-conditioning cycles. (C) 2018 Elsevier B.V. All rights reserved.
- Published
- 2018
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38. Knotting and linking in macromolecules
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Kenneth C. Millett
- Subjects
0301 basic medicine ,Quantitative Biology::Biomolecules ,Polymers and Plastics ,Polymer science ,Computer science ,General Chemical Engineering ,010102 general mathematics ,General Chemistry ,Mathematics::Geometric Topology ,01 natural sciences ,Biochemistry ,03 medical and health sciences ,030104 developmental biology ,Materials Chemistry ,Environmental Chemistry ,0101 mathematics ,Writhe - Abstract
In the 1980’s, knotting in DNA became a fundamental research dimension in the study of the mechanisms by which enzymes act on it. Later, the first compelling identification of knotting in proteins, in 2000, launched the study of knotting in protein structures, and linear macromolecules more generally, following on theoretical efforts of the 1960’s. The linking occurring in structures such as DNA, with the articulation of the relationship between linking, twisting, and writhe, and, more directly, linking in Olympic gels has been of interest to geometers, molecular biologists, and polymer physicists since the 1960’s. More recently, a new mathematical analysis of both global and local facets of knotting and linking is providing promising discoveries. Following a discussion of the topological structures of knotting and linking, we will consider some of their applications, and close with a consideration of new questions that suggest attractive directions for future research.
- Published
- 2018
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39. Protein-mediated loops in supercoiled DNA create large topological domains
- Author
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Fenfei Leng, Laura Finzi, David Dunlap, Yue Ding, and Yan Yan
- Subjects
Regulation of gene expression ,0301 basic medicine ,0303 health sciences ,Base pair ,DNA, Superhelical ,Gene regulation, Chromatin and Epigenetics ,Biophysics ,Torsion, Mechanical ,Biology ,Topology ,Chromatin ,chemistry.chemical_compound ,03 medical and health sciences ,0302 clinical medicine ,030104 developmental biology ,chemistry ,Helix ,Lac Repressors ,Genetics ,DNA supercoil ,Binding site ,030217 neurology & neurosurgery ,DNA ,030304 developmental biology ,Writhe - Abstract
Supercoiling can alter the form and base pairing of the double helix and directly impact protein binding. More indirectly, changes in protein binding and the stress of supercoiling also influence the thermodynamic stability of regulatory, protein-mediated loops and shift the equilibria of fundamental DNA/chromatin transactions. For example, supercoiling affects the hierarchical organization and function of chromatin in topologically associating domains (TADs) in both eukaryotes and bacteria. On the other hand, a protein-mediated loop in DNA can constrain supercoiling within a plectonemic structure. To characterize the extent of constrained supercoiling, 400 bp, lac repressor-secured loops were formed in extensively over- or under-wound DNA under gentle tension in a magnetic tweezer. The protein-mediated loops constrained variable amounts of supercoiling that often exceeded the maximum writhe expected for a 400 bp plectoneme. Loops with such high levels of supercoiling appear to be entangled with flanking domains. Thus, loop-mediating proteins operating on supercoiled substrates can establish topological domains that may coordinate gene regulation and other DNA transactions across spans in the genome that are larger than the separation between the binding sites.
- Published
- 2018
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40. Kink-induced full and failed eruptions of two coupled flux tubes of the same filament
- Author
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P. Duchlev, M. Dechev, and K. Koleva
- Subjects
Physics ,010504 meteorology & atmospheric sciences ,Solar dynamics observatory ,Flux ,Astronomy ,Astronomy and Astrophysics ,Astrophysics ,Kink instability ,01 natural sciences ,Helicity ,Solar prominence ,Protein filament ,Space and Planetary Science ,Observatory ,0103 physical sciences ,010303 astronomy & astrophysics ,Instrumentation ,0105 earth and related environmental sciences ,Writhe - Abstract
In this work, we report results from the study of a filament/prominence eruption on 2014 May 4. This eruption belongs to the class of rarely reported causally linked eruptions of two coupled flux tubes (FTs) of a quiet region filament. We made a comparative analysis based on multiwave observations from Solar Dynamics Observatory (SDO) and Solar Terrestrial Relations Observatory (STEREO) A and B combining the high temporal and spatial data taken from three different viewpoints. The main results of the study are as follows: (1) The source of the eruptive prominence consists of two coupled FTs located near the eastern limb: top-located one (FT1) and bottom-located one (FT2). (2) FT1 and FT2 had the same helicity, i.e. left-handed twist and writhe. Their untwisting motion during eruption suggests that kink instability seems to act. (3) The kinematic evolution of the FT1 suggests a slow successful eruption that was associated with a slow CME. (4) The FT2 exhibited failed kinked eruption with a non-radial propagation followed by its reformation. This eruption was accompanied of apparent mass draining in the legs, flare-ribbons and post-flare EUV arcade.
- Published
- 2018
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41. AN AFFINE INDEX POLYNOMIAL INVARIANT OF VIRTUAL KNOTS.
- Author
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KAUFFMAN, LOUIS H.
- Subjects
- *
KNOT theory , *POLYNOMIALS , *INVARIANTS (Mathematics) , *DATA analysis , *GEOMETRIC topology , *LOW-dimensional topology - Abstract
This paper describes a polynomial invariant of virtual knots that is defined in terms of an integer labeling of the virtual knot diagram. This labeling is seen to derive from an essentially unique structure of affine flat biquandle for flat virtual diagrams. The invariant is discussed in detail with many examples, including its relation to previous invariants of this type and we show how to construct Vassiliev invariants from the same data. [ABSTRACT FROM AUTHOR]
- Published
- 2013
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42. Framed curves and knotted DNA.
- Author
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Chirikjian, Gregory S.
- Subjects
- *
DNA analysis , *GEOMETRY , *COMPUTATIONAL biology , *DNA structure , *MATHEMATICAL inequalities - Abstract
The present mini-review covers the local and global geometry of framed curves and the computation of twist and writhe in knotted DNA circles. Classical inequalities relating the total amount of bending of a closed space curve and associated knot parameters are also explained. [ABSTRACT FROM AUTHOR]
- Published
- 2013
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43. New biologically motivated knot table.
- Author
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Brasher, Reuben, Scharein, Rob G., and Vazquez, Mariel
- Subjects
- *
BIOPOLYMERS , *NUMERICAL analysis , *CONFORMATIONAL analysis , *DNA structure , *CHIRALITY , *PROTEIN analysis - Abstract
The knot nomenclature in common use, summarized in Rolfsen's knot table [Rolfsen (1990) Knots and Links, American Mathematical Society], was not originally designed to distinguish between mirror images. This ambiguity is particularly inconvenient when studying knotted biopolymers such as DNA and proteins, since their chirality is often significant. In the present article, we propose a biologically meaningful knot table where a representative of a chiral pair is chosen on the basis of its mean writhe. There is numerical evidence that the sign of the mean writhe is invariant for each knot in a chiral pair. We review numerical evidence where, for each knot type K, the mean writhe is taken over a large ensemble of randomly chosen realizations of K. It has also been proposed that a chiral pair can be distinguished by assessing the writhe of a minimal or ideal conformation of the knot. In all cases examined to date, the two methods produce the same results. [ABSTRACT FROM AUTHOR]
- Published
- 2013
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44. Seifert graphs and the braid index of classical and singular links
- Author
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Plachta, Leonid, Przybyło, Jakub, and Woźniak, Mariusz
- Subjects
- *
GRAPH theory , *BRAID theory , *MATHEMATICAL singularities , *KNOT theory , *LOGICAL prediction , *COMBINATORICS - Abstract
Abstract: We discuss two well known conjectures in knot theory on the relationship between the number of Seifert circles in a link diagram and the writhe of this diagram. One of them, the Malešič and Traczyk conjecture, is formulated in terms of link diagrams and Seifert graphs. By using combinatorial methods, we obtain some new results which confirm partially the Malešič and Traczyk conjecture and disprove its variations formulated in terms of -graphs. We also indicate the connection of -graphs with singular link diagrams. [Copyright &y& Elsevier]
- Published
- 2012
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45. MINIMAL UNKNOTTING SEQUENCES OF REIDEMEISTER MOVES CONTAINING UNMATCHED RII MOVES.
- Author
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HAYASHI, CHUICHIRO, HAYASHI, MIWA, SAWADA, MINORI, and YAMADA, SAYAKA
- Subjects
- *
KNOT theory , *MATHEMATICAL sequences , *REIDEMEISTER moves , *INVARIANTS (Mathematics) , *CURVES , *ESTIMATION theory , *MATHEMATICAL analysis , *CHARTS, diagrams, etc. - Abstract
Arnold introduced invariants J+, J- and St for generic planar curves. It is known that both J+/2 + St and J-/2 + St are invariants for generic spherical curves. Applying these invariants to underlying curves of knot diagrams, we can obtain lower bounds for the number of Reidemeister moves required for unknotting. J- /2 + St works well to count the minimum number of unmatched RII moves. However, it works only up to a factor of two for RI moves. Let w denote the writhe for a knot diagram. We show that J-/2 + St ± w/2 also gives sharp counts for the number of required RI moves, and demonstrate that it gives a precise estimate for a certain family of diagrams of the unknot with the underlying curve r = 2 + cos(nθ/(n + 1)), (0 ≤ θ ≤ 2(n + 1)π). [ABSTRACT FROM AUTHOR]
- Published
- 2012
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46. Unraveling the Tangled Complexity of DNA: Combining Mathematical Modeling and Experimental Biology to Understand Replication, Recombination and Repair.
- Author
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Robic, S. and Jungck, J. R.
- Subjects
- *
MATHEMATICAL models , *EXPERIMENTAL biology , *MOLECULAR biology , *MATHEMATICS students , *DNA topoisomerases - Abstract
How does DNA, the molecule containing genetic information, change its three-dimensional shape during the complex cellular processes of replication, recombination and repair? This is one of the core questions in molecular biology which cannot be answered without help from mathematical modeling. Basic concepts of topology and geometry can be introduced in undergraduate teaching to help students understand counterintuitive complex structural transformations that occur in every living cell. Topoisomerases, a fascinating class of enzymes involved in replication, recombination and repair, catalyze a change in DNA topology through a series of highly coordinated mechanistic steps. Undergraduate biology and mathematics students can visualize and explore the principles of topoisomerase action by using easily available materials such as Velcro, ribbons, telephone cords, zippers and tubing. These simple toys can be used as powerful teaching tools to engage students in hands-on exploration with the goal of learning about both the mathematics and the biology of DNA structure. [ABSTRACT FROM PUBLISHER]
- Published
- 2011
- Full Text
- View/download PDF
47. Three dimensional dynamics of ferromagnetic swimmer
- Author
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Ērglis, K., Livanovičs, R., and Cēbers, A.
- Subjects
- *
FERROMAGNETIC materials , *METAL fibers , *MAGNETIC fields , *TRANSITION metals , *PERTURBATION theory , *OSCILLATIONS , *PROPULSION systems - Abstract
Abstract: It is shown that a flexible ferromagnetic filament self-propels perpendicularly to the AC magnetic field during a limited period of time due to the instability of the planar motion with respect to three dimensional perturbations. The transition from the oscillating U-like shapes to the oscillating S-like shapes is characterized by the calculated Wr number. [Copyright &y& Elsevier]
- Published
- 2011
- Full Text
- View/download PDF
48. Tops and Writhing DNA.
- Author
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Samuel, Joseph and Sinha, Supurna
- Subjects
- *
POLYMERS , *DNA , *COMPUTER simulation , *PROPERTIES of matter , *ANALYTICAL mechanics - Abstract
The torsional elasticity of semiflexible polymers like DNA is of biological significance. A mathematical treatment of this problem was begun by Fuller using the relation between link, twist and writhe, but progress has been hindered by the non-local nature of the writhe. This stands in the way of an analytic statistical mechanical treatment, which takes into account thermal fluctuations, in computing the partition function. In this paper we use the well known analogy with the dynamics of tops to show that when subjected to stretch and twist, the polymer configurations which dominate the partition function admit a local writhe formulation in the spirit of Fuller and thus provide an underlying justification for the use of Fuller's 'local writhe expression' which leads to considerable mathematical simplification in solving theoretical models of DNA and elucidating their predictions. Our result facilitates comparison of the theoretical models with single molecule micromanipulation experiments and computer simulations. [ABSTRACT FROM AUTHOR]
- Published
- 2011
- Full Text
- View/download PDF
49. CONFORMAL INVARIANCE OF THE WRITHE OF A KNOT.
- Author
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LANGEVIN, R. and O'HARA, J.
- Subjects
- *
BRAID theory , *NUMBER theory , *ALGEBRA , *KNOT theory , *GEOMETRY - Abstract
We give a new proof of the conformal invariance of the writhe of a knot from a conformal geometric vewpoint. [ABSTRACT FROM AUTHOR]
- Published
- 2010
- Full Text
- View/download PDF
50. Action at Hooked or Twisted–Hooked DNA Juxtapositions Rationalizes Unlinking Preference of Type-2 Topoisomerases
- Author
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Liu, Zhirong, Zechiedrich, Lynn, and Chan, Hue Sun
- Subjects
- *
DNA topoisomerases , *DNA , *LATTICE theory , *VARIANCES , *ALGORITHMS , *POLYGONS - Abstract
Abstract: The mathematical basis of the hypothesis that type-2 topoisomerases recognize and act at specific DNA juxtapositions has been investigated by coarse-grained lattice polymer models, showing that selective segment passages at hooked juxtapositions can result in dramatic reductions in catenane and knot populations. The lattice modeling approach is here extended to account for the narrowing of variance of linking number (Lk) of DNA circles by type-2 topoisomerases. In general, the steady-state variance of Lk resulting from selective segment passages at a specific juxtaposition geometry j is inversely proportional to the average linking number, 〈Lk〉 j , of circles with the given juxtaposition. Based on this formulation, we demonstrate that selective segment passages at hooked juxtapositions reduce the variance of Lk. The dependence of this effect on model DNA circle size is remarkably similar to that observed experimentally for type-2 topoisomerases, which appear to be less capable in narrowing Lk variance for small DNA circles than for larger DNA circles. This behavior is rationalized by a substantial cancellation of writhe in small circles with hook-like juxtapositions. During our simulations, we uncovered a twisted variation of the hooked juxtaposition that has an even more dramatic effect on Lk variance narrowing than the hooked juxtaposition. For an extended set of juxtapositions, we detected a significant correlation between the Lk narrowing potential and the logarithmic decatenating and unknotting potentials for a given juxtaposition, a trend reminiscent of scaling relations observed with experimental measurements on type-2 topoisomerases from a variety of organisms. The consistent agreement between theory and experiment argues for type-2 topoisomerase action at hooked or twisted–hooked DNA juxtapositions. [Copyright &y& Elsevier]
- Published
- 2010
- Full Text
- View/download PDF
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