pith. sign in

arxiv: 2506.22842 · v2 · submitted 2025-06-28 · ❄️ cond-mat.soft · cond-mat.mes-hall· cond-mat.stat-mech· physics.bio-ph· q-bio.BM

Actively induced supercoiling can slow down plasmid solutions by trapping the threading entanglements

Roman Sta\v{n}o , Ren\'ata Ruskov\'a , Du\v{s}an Ra\v{c}ko , Jan Smrek This is my paper

Pith reviewed 2026-05-19 07:31 UTC · model grok-4.3

classification ❄️ cond-mat.soft cond-mat.mes-hallcond-mat.stat-mechphysics.bio-phq-bio.BM
keywords supercoilingplasmidsthreading entanglementsnon-equilibrium dynamicsring polymersmolecular simulationssupramolecular clusters
0
0 comments X

The pith

Active supercoiling traps threaded plasmid rings into slow-relaxing clusters.

A machine-rendered reading of the paper's core claim, the machinery that carries it, and where it could break.

The paper examines a non-equilibrium process in which a supercoiling agent rapidly adds twist to relaxed plasmid rings. This changes the rings from open conformations to branched supercoiled forms while also preventing the disentanglement of rings that thread through one another. The result is the formation of supramolecular clusters whose relaxation is much slower than in equilibrium solutions. A sympathetic reader would care because the finding indicates that ongoing activity can be used to control the dynamic properties of polymer solutions in ways that static topology alone cannot achieve.

Core claim

The activity of the agent not only alters the conformational topology from open to branched, but also locks-in threaded rings into supramolecular clusters, which relax very slowly.

What carries the argument

The supercoiling agent, which rapidly induces helical supercoiling and thereby traps threading entanglements into long-lived clusters.

If this is right

  • Plasmid solutions under active supercoiling exhibit slower overall relaxation than equilibrium counterparts.
  • Branched supercoiled conformations reduce the ability of rings to slide past threading entanglements.
  • Non-equilibrium activity provides a route to tune the dynamic behavior of ring-polymer systems.
  • The approach suggests a general method for creating driven materials whose glassy behavior arises from induced topology.

Where Pith is reading between the lines

These are editorial extensions of the paper, not claims the author makes directly.

  • Similar locking of entanglements might occur in cellular DNA environments where gyrase-like enzymes are active.
  • Varying the rate or specificity of the supercoiling agent could be used to test how sensitive cluster stability is to induction speed.
  • The mechanism may connect to other active-matter systems in which topology and threading control macroscopic flow or viscosity.

Load-bearing premise

The simulation model of the supercoiling agent accurately captures rapid and specific induction of supercoiling without introducing artifacts that artificially stabilize the clusters.

What would settle it

An experiment or simulation in which actively supercoiled plasmids are observed to relax at the same rate or faster than torsionally relaxed ones would contradict the central claim.

Figures

Figures reproduced from arXiv: 2506.22842 by Du\v{s}an Ra\v{c}ko, Jan Smrek, Ren\'ata Ruskov\'a, Roman Sta\v{n}o.

Figure 1
Figure 1. Figure 1: a Snapshot of the equilibrium system with fixed σ = 0 with different rings in shades of gray and gold beads representing the pair of monomers where the active torque is subsequently applied. b Scheme depicting the application of the active torque c Time evolution of conformations of a single ring of N = 400 in infinite dilution with βT Q = 3 applied. d Mean supercoiling density σ as a function of time for … view at source ↗
Figure 2
Figure 2. Figure 2: a Mean square displacement (1) divided by time since the onset of the activity in the units of mean square radius of gyration over monomer relaxation time for different torques. EQ stands for the equilibrium system with no driv￾ing. b Relaxation functions (2) for t ′ = 104 τ , probing the dynamics after saturation of supercoiling and after the sharp initial drop in threadings. The equilibrium system has ri… view at source ↗
Figure 3
Figure 3. Figure 3: a The mean number of threadings per ring as a function of time after the onset of the activity, shown for different torques. EQ stands for the equilibrium system with no driving. b Fraction fmax. of the rings belonging to the largest continuous networks of threadings present in the sys￾tem (solid, left axis) as a function of time. Fraction f0 of dangling rings (dashed, right axis), rings with no threading,… view at source ↗
Figure 4
Figure 4. Figure 4: a The mean square displacement (1) of all individual rings, with the point at time t colored black if the ring is threaded or orange if it is dangling. Three white dotted lines show means over three subpopulations of rings – over all dangling rings, over all threaded rings and over all of the rings, marked with orange, black and gray circular marker respectively. b Snapshot showing long-lived and deep lock… view at source ↗
read the original abstract

Harnessing the topology of ring polymers as a design motif in functional nanomaterials is becoming a promising direction in the field of soft matter. For example, the ring topology of DNA plasmids prevents the relaxation of excess twist introduced to the polymer, instead resulting in helical supercoiled structures. In equilibrium semi-dilute solutions, tightly supercoiled rings relax faster than their torsionally relaxed counterparts, since the looser conformations of the latter allow for rings to thread through each other and entrain through entanglements. Here we use molecular simulations to explore a non-equilibrium scenario, in which a supercoiling agent, akin to gyrase enzymes, rapidly induces supercoiling in the suspensions of relaxed plasmids. The activity of the agent not only alters the conformational topology from open to branched, but also locks-in threaded rings into supramolecular clusters, which relax very slowly. Ultimately, our work shows how the polymer topology under non-equilibrium conditions can be leveraged to tune dynamic behavior of macromolecular systems, suggesting a method to create a class of driven materials glassified by activity.

Editorial analysis

A structured set of objections, weighed in public.

Desk editor's note, referee report, simulated authors' rebuttal, and a circularity audit. Tearing a paper down is the easy half of reading it; the pith above is the substance, this is the friction.

Referee Report

2 major / 2 minor

Summary. The manuscript uses molecular simulations of semi-dilute plasmid solutions to explore a non-equilibrium scenario in which a supercoiling agent (modeled after gyrase) rapidly induces supercoiling in initially relaxed rings. The central claim is that this activity converts open conformations to branched ones while simultaneously locking threaded rings into supramolecular clusters whose relaxation is markedly slowed by trapped threading entanglements, in contrast to the faster relaxation of supercoiled rings seen in equilibrium. The work positions this as a route to activity-tuned glassy dynamics in topologically complex macromolecular systems.

Significance. If the simulation results are robust, the paper identifies a concrete mechanism by which non-equilibrium topological driving can stabilize entanglements that would otherwise relax, thereby providing a design principle for activity-controlled soft materials. It usefully extends equilibrium ring-polymer entanglement concepts into the driven regime and offers a plausible route toward glassification via topology rather than crowding or cross-linking.

major comments (2)
  1. [Simulation protocol] Simulation protocol section: No control simulation is reported in which the agent applies comparable local constraints or torques without net supercoiling induction (or in which the agent is removed after initial induction). Such a control is required to establish that the observed slow cluster relaxation arises from the induced branched topology and trapped threads rather than from the driving protocol itself altering unthreading moves or contact statistics.
  2. [Results] Results on relaxation times: The reported slowing is tied to the free parameter governing supercoiling induction rate, yet no systematic variation of this rate or comparison against equilibrium limits (e.g., known relaxation spectra of torsionally relaxed vs. supercoiled rings) is shown to confirm that the non-equilibrium dynamics are free of artifacts.
minor comments (2)
  1. [Introduction] The abstract and introduction would benefit from a brief citation to prior simulation or experimental work on gyrase-like supercoiling agents in polymer models to clarify how the present implementation differs from existing approaches.
  2. [Figures] Figure captions describing cluster identification should explicitly state the criteria used to define a 'supramolecular cluster' (e.g., threading number threshold or contact persistence time) so that the slow-relaxation claim can be reproduced.

Simulated Author's Rebuttal

2 responses · 0 unresolved

We thank the referee for their detailed and constructive comments on our manuscript. We have carefully considered each point and provide our responses below. We believe these revisions will strengthen the presentation of our results on activity-induced topological effects in plasmid solutions.

read point-by-point responses

  1. Referee: Simulation protocol section: No control simulation is reported in which the agent applies comparable local constraints or torques without net supercoiling induction (or in which the agent is removed after initial induction). Such a control is required to establish that the observed slow cluster relaxation arises from the induced branched topology and trapped threads rather than from the driving protocol itself altering unthreading moves or contact statistics.

    Authors: We agree that additional control simulations would help to more rigorously isolate the role of the induced supercoiling. In the revised version of the manuscript, we have included new control simulations in which the agent applies local torques without resulting in a net increase in supercoiling (by balancing positive and negative twists or allowing periodic relaxation). These controls demonstrate that the slow relaxation of clusters is indeed tied to the branched conformations and trapped threading entanglements rather than the driving mechanism itself. We have also added a simulation where the agent is deactivated after initial supercoiling induction, showing that the slow dynamics persist due to the locked-in topology. revision: yes

  2. Referee: Results on relaxation times: The reported slowing is tied to the free parameter governing supercoiling induction rate, yet no systematic variation of this rate or comparison against equilibrium limits (e.g., known relaxation spectra of torsionally relaxed vs. supercoiled rings) is shown to confirm that the non-equilibrium dynamics are free of artifacts.

    Authors: The referee correctly notes that the induction rate is a key parameter. While the manuscript does include comparisons to equilibrium cases of relaxed and supercoiled rings, showing faster relaxation in the latter, we acknowledge the benefit of a more systematic exploration. In the revision, we now present results for a range of supercoiling induction rates and explicitly compare the relaxation spectra to established equilibrium data for ring polymers. This analysis confirms that the non-equilibrium slowing arises from the activity-induced trapping of entanglements and is not an artifact of the simulation protocol. revision: yes

Circularity Check

0 steps flagged

No significant circularity detected in the derivation chain

full rationale

The paper reports results from direct molecular dynamics simulations of non-equilibrium plasmid suspensions under active supercoiling. The observed slowing of relaxation emerges from the explicit time evolution of threaded entanglements and cluster formation in the simulated trajectories, without any fitted parameters being repurposed as predictions or any self-referential definitions of relaxation times. No load-bearing steps reduce by construction to inputs, and the central claim is grounded in the simulation protocol rather than self-citation chains or ansatzes.

Axiom & Free-Parameter Ledger

1 free parameters · 1 axioms · 0 invented entities

The claim depends on the fidelity of the active-agent model and on standard assumptions of the underlying polymer simulation force field; no new physical constants or entities are introduced.

free parameters (1)
  • supercoiling induction rate
    The speed and strength with which the agent adds supercoils is a tunable simulation parameter that controls the non-equilibrium drive.
axioms (1)
  • domain assumption The coarse-grained model of the supercoiling agent faithfully reproduces enzymatic action without side effects on threading or cluster stability.
    Invoked when the agent is introduced to drive the system out of equilibrium.

pith-pipeline@v0.9.0 · 5756 in / 1053 out tokens · 33593 ms · 2026-05-19T07:31:18.055480+00:00 · methodology

discussion (0)

Sign in with ORCID, Apple, or X to comment. Anyone can read and Pith papers without signing in.

Lean theorems connected to this paper

Citations machine-checked in the Pith Canon. Every link opens the source theorem in the public Lean library.

What do these tags mean?
matches
The paper's claim is directly supported by a theorem in the formal canon.
supports
The theorem supports part of the paper's argument, but the paper may add assumptions or extra steps.
extends
The paper goes beyond the formal theorem; the theorem is a base layer rather than the whole result.
uses
The paper appears to rely on the theorem as machinery.
contradicts
The paper's claim conflicts with a theorem or certificate in the canon.
unclear
Pith found a possible connection, but the passage is too broad, indirect, or ambiguous to say the theorem truly supports the claim.

Reference graph

Works this paper leans on

91 extracted references · 91 canonical work pages

  1. [1]

    Tubiana, G

    L. Tubiana, G. P. Alexander, A. Barbensi, D. Buck, J. H. Cartwright, M. Chwastyk, M. Cieplak, I. Coluzza, S. Čopar, D. J. Craik, M. Di Stefano, R. Everaers, P. F. Faísca, F. Ferrari, A. Giacometti, D. Goundaroulis, E. Haglund, Y.-M. Hou, N. Ilieva, S. E. Jackson, A. Japaridze, N. Kaplan, A. R. Klotz, H. Li, C. N. Likos, E. Locatelli, T. López-León, T. Mac...

    work page 2024

  2. [2]

    Z.Qu, S.Z.D.Cheng,andW.-B.Zhang,Macromolecular topology engineering, Trends in Chemistry 3, 402–415 (2021)

    work page 2021

  3. [3]

    L. F. Hart, J. E. Hertzog, P. M. Rauscher, B. W. Rawe, M. M. Tranquilli, and S. J. Rowan, Material properties and applications of mechanically interlocked polymers, Nat. Rev. Mater.6, 508 (2021)

    work page 2021

  4. [4]

    Shankar, A

    S. Shankar, A. Souslov, M. J. Bowick, M. C. Marchetti, andV.Vitelli,Topologicalactivematter,NatureReviews Physics 4, 380–398 (2022)

    work page 2022

  5. [5]

    Martinez, and R

    D.Michieletto, P.Neill, S.Weir, D.Evans, N.Crist, V.A. Martinez, and R. M. Robertson-Anderson, Topological digestion drives time-varying rheology of entangled DNA fluids, Nat. Commun. 13, 10.1038/s41467-022-31828-w (2022)

    work page doi:10.1038/s41467-022-31828-w 2022

  6. [6]

    D. Kong, S. Banik, M. J. San Francisco, M. Lee, R. M. Robertson Anderson, C. M. Schroeder, and G. B. McKenna, Rheology of entangled solutions of ring–linear DNA blends, Macromolecules55, 1205 (2022)

    work page 2022

  7. [7]

    K. R. Peddireddy, M. Lee, Y. Zhou, S. Adalbert, S. An- derson, C.M.Schroeder,andR.M.Robertson-Anderson, Unexpected entanglement dynamics in semidilute blends of supercoiled and ring DNA, Soft Matter16, 152 (2020)

    work page 2020

  8. [8]

    A. Rosa, J. Smrek, M. S. Turner, and D. Michieletto, Threading-Induced Dynamical Transition in Tadpole- Shaped Polymers, ACS Macro Lett.9, 743 (2020)

    work page 2020

  9. [9]

    Kapnistos, M

    M. Kapnistos, M. Lang, D. Vlassopoulos, W. Pyckhout- Hintzen, D. Richter, D. Cho, T. Chang, and M. Rubin- stein, Unexpected power-law stress relaxation of entan- gled ring polymers, Nat. Mater.7, 997 (2008)

    work page 2008

  10. [10]

    Neill, N

    P. Neill, N. Crist, R. McGorty, and R. Robertson- Anderson, Enzymatic cleaving of entangled dna rings drives scale-dependent rheological trajectories, Soft Mat- ter 20, 2750–2766 (2024)

    work page 2024

  11. [11]

    G. Liu, P. M. Rauscher, B. W. Rawe, M. M. Tranquilli, and S. J. Rowan, Polycatenanes: synthesis, characteriza- tion, and physical understanding, Chem. Soc. Rev.51, 4928 (2022)

    work page 2022

  12. [12]

    Ito, Novel entropic elasticity of polymeric materials: why is slide-ring gel so soft?, Polymer Journal44, 38–41 (2011)

    K. Ito, Novel entropic elasticity of polymeric materials: why is slide-ring gel so soft?, Polymer Journal44, 38–41 (2011)

    work page 2011

  13. [13]

    J.-X. Li, S. Wu, L.-L. Hao, Q.-L. Lei, and Y.-Q. Ma, Activity-driven polymer knotting for macromolecular topology engineering, Science Advances10, 10.1126/sci- adv.adr0716 (2024)

    work page doi:10.1126/sci- 2024

  14. [14]

    Zhang, B

    Z.-H. Zhang, B. J. Andreassen, D. P. August, D. A. Leigh, and L. Zhang, Molecular weaving, Nature Materi- als 21, 275–283 (2022)

    work page 2022

  15. [15]

    Deblais, S

    A. Deblais, S. Woutersen, and D. Bonn, Rheology of en- tangled active polymer-like t. tubifex worms, Phys. Rev. Lett. 124, 188002 (2020)

    work page 2020

  16. [16]

    V. P. Patil, H. Tuazon, E. Kaufman, T. Chakrabortty, D. Qin, J. Dunkel, and M. S. Bhamla, Ultrafast re- versible self-assembly of living tangled matter, Science 380, 392–398 (2023)

    work page 2023

  17. [17]

    Ozkan-Aydin, D

    Y. Ozkan-Aydin, D. I. Goldman, and M. S. Bhamla, Col- lective dynamics in entangled worm and robot blobs, Proceedings of the National Academy of Sciences118, 10.1073/pnas.2010542118 (2021)

    work page doi:10.1073/pnas.2010542118 2021

  18. [18]

    V. P. Patil, J. D. Sandt, M. Kolle, and J. Dunkel, Topo- logical mechanics of knots and tangles, Science 367, 71–75 (2020)

    work page 2020

  19. [19]

    Becker, C

    K. Becker, C. Teeple, N. Charles, Y. Jung, D. Baum, J. C. Weaver, L. Mahadevan, and R. Wood, Active entanglement enables stochastic, topological grasping, Proceedings of the National Academy of Sciences119, 10.1073/pnas.2209819119 (2022)

    work page doi:10.1073/pnas.2209819119 2022

  20. [20]

    Huang, J

    Q. Huang, J. Ahn, D. Parisi, T. Chang, O. Hassager, S. Panyukov, M. Rubinstein, and D. Vlassopoulos, Un- expected stretching of entangled ring macromolecules, Phys. Rev. Lett.122, 208001 (2019)

    work page 2019

  21. [21]

    Parisi, S

    D. Parisi, S. Costanzo, Y. Jeong, J. Ahn, T. Chang, D. Vlassopoulos, J. D. Halverson, K. Kremer, T. Ge, M. Rubinstein, G. S. Grest, W. Srinin, and A. Y. Gros- berg, Nonlinear shear rheology of entangled polymer rings, Macromolecules , 2811

    work page

  22. [22]

    Breoni, C

    D. Breoni, C. Kurzthaler, B. Liebchen, H. Löwen, and S. Mandal, Giant activity-induced elasticity in entan- gled polymer solutions, Nature Communications 16, 10.1038/s41467-025-60210-9 (2025)

    work page doi:10.1038/s41467-025-60210-9 2025

  23. [23]

    Kruteva, J

    M. Kruteva, J. Allgaier, and D. Richter, Topology mat- ters: Conformation and microscopic dynamics of ring polymers, Macromolecules56, 7203 (2023)

    work page 2023

  24. [24]

    Wang and T

    J. Wang and T. Ge, Crazing reveals an entanglement net- work in glassy ring polymers, Macromolecules54, 7500 (2021)

    work page 2021

  25. [25]

    Smrek and A

    J. Smrek and A. Y. Grosberg, Understanding the dy- namics of rings in the melt in terms of the annealed tree model, J. Phys. Condens. Matter27, 064117 (2015)

    work page 2015

  26. [26]

    T. Ge, S. Panyukov, and M. Rubinstein, Self- similar conformations and dynamics in entangled melts and solutions of nonconcatenated ring poly- 8 mers, Macromolecules49, 708 (2016), pMID: 27057066, https://doi.org/10.1021/acs.macromol.5b02319

    work page doi:10.1021/acs.macromol.5b02319 2016

  27. [27]

    Ghobadpour, M

    E. Ghobadpour, M. Kolb, M. R. Ejtehadi, and R. Ev- eraers, Monte carlo simulation of a lattice model for the dynamics of randomly branching double-folded ring poly- mers, Phys. Rev. E 104, 10.1103/physreve.104.014501 (2021)

    work page doi:10.1103/physreve.104.014501 2021

  28. [28]

    Ghobadpour, M

    E. Ghobadpour, M. Kolb, I. Junier, and R. Everaers, The emergent dynamics of double-folded randomly branching ring polymers (2025), arXiv:2503.01446 [cond-mat.soft]

    work page arXiv 2025

  29. [29]

    Rosa and R

    A. Rosa and R. Everaers, Ring polymers in the melt state: The physics of crumpling, Phys. Rev. Lett.112, 118302 (2014)

    work page 2014

  30. [30]

    Smrek and A

    J. Smrek and A. Y. Grosberg, Minimal Surfaces on Un- concatenated Polymer Rings in Melt, ACS Macro Lett. 5, 750 (2016)

    work page 2016

  31. [31]

    M. A. Ubertini, J. Smrek, and A. Rosa, Entanglement length scale separates threading from branching of un- knotted and non-concatenated ring polymers in melts, Macromolecules 55, 10723 (2022)

    work page 2022

  32. [32]

    A. Y. Grosberg, Annealed lattice animal model and flory theory for the melt of non-concatenated rings: towards the physics of crumpling, Soft Matter10, 560 (2014)

    work page 2014

  33. [33]

    J. D. Halverson, W. B. Lee, G. S. Grest, A. Y. Grosberg, and K. Kremer, Molecular dynamics simulation study of nonconcatenated ring polymers in a melt. II. Dynamics, J. Chem. Phys.134, 204905 (2011)

    work page 2011

  34. [34]

    E. Lee, S. Kim, and Y. Jung, Slowing down of ring poly- mer diffusion caused by inter-ring threading, Macromol. Rapid Commun.36, 1115 (2015)

    work page 2015

  35. [35]

    D. G. Tsalikis, V. G. Mavrantzas, and D. Vlassopoulos, Analysis of slow modes in ring polymers: Threading of rings controls long-time relaxation, ACS Macro Lett.5, 755 (2016)

    work page 2016

  36. [36]

    Lee and Y

    E. Lee and Y. Jung, Slow dynamics of ring polymer melts by asymmetric interaction of threading configura- tion: Monte carlo study of a dynamically constrained lattice model, Polymers11, 516 (2019)

    work page 2019

  37. [37]

    Michieletto, N

    D. Michieletto, N. Nahali, and A. Rosa, Glassiness and heterogeneous dynamics in dense solutions of ring poly- mers, Phys. Rev. Lett.119, 197801 (2017)

    work page 2017

  38. [38]

    S. Goto, K. Kim, and N. Matubayasi, Unraveling the glass-like dynamic heterogeneity in ring polymer melts: From semiflexible to stiff chain, ACS Polymers Au3, 437 (2023), https://doi.org/10.1021/acspolymersau.3c00013

    work page doi:10.1021/acspolymersau.3c00013 2023

  39. [39]

    M. Q. Tu, O. Davydovich, B. Mei, P. K. Singh, G. S. Grest, K. S. Schweizer, T. C. O’Connor, and C. M. Schroeder, Unexpected slow relaxation dynamics in pure ring polymers arise from intermolecular interactions, ACS Polym. Au3, 307 (2023)

    work page 2023

  40. [40]

    P. K. Roy, P. Chaudhuri, and S. Vemparala, Bidisperse ring polymers: Topological glass to stacking, Phys. Rev. Mater. 8, 045601 (2024)

    work page 2024

  41. [41]

    Staňo, J

    R. Staňo, J. Smrek, and C. N. Likos, Cluster formation in solutions of polyelectrolyte rings, ACS Nano17, 21369 (2023), pMID: 37729077

    work page 2023

  42. [42]

    T. C. O’Connor, T. Ge, M. Rubinstein, and G. S. Grest, Topological linking drives anomalous thickening of ring polymersinweakextensionalflows,Phys.Rev.Lett. 124, 027801 (2020)

    work page 2020

  43. [43]

    Smrek, I

    J. Smrek, I. Chubak, C. N. Likos, and K. Kremer, Active topological glass, Nat. Commun.11, 26 (2020)

    work page 2020

  44. [44]

    Micheletti, I

    C. Micheletti, I. Chubak, E. Orlandini, and J. Sm- rek, Topology-based detection and tracking of deadlocks reveal aging of active ring melts, ACS Macro Letters 13, 124 (2024), pMID: 38198592, https://doi.org/10.1021/acsmacrolett.3c00567

    work page doi:10.1021/acsmacrolett.3c00567 2024

  45. [45]

    Fathizadeh, H

    A. Fathizadeh, H. Schiessel, and M. R. Ejtehadi, Molec- ular dynamics simulation of supercoiled DNA rings, Macromolecules 48, 164 (2015)

    work page 2015

  46. [46]

    J.111, 1339–1349 (2016)

    B.A.KrajinaandA.J.Spakowitz,Large-scaleconforma- tional transitions in supercoiled DNA revealed by coarse- grained simulation, Biophys. J.111, 1339–1349 (2016)

    work page 2016

  47. [47]

    Segers, E

    M. Segers, E. Skoruppa, H. Schiessel, and E. Carlon, Statistical mechanics of multiplectoneme phases in dna, Physical Review E 111, 10.1103/physreve.111.044408 (2025)

    work page doi:10.1103/physreve.111.044408 2025

  48. [48]

    Smrek, J

    J. Smrek, J. Garamella, R. Robertson-Anderson, and D. Michieletto, Topological tuning of DNA mobility in entangled solutions of supercoiled plasmids, Sci. Adv.7, eabf9260 (2021)

    work page 2021

  49. [49]

    Gellert, K

    M. Gellert, K. Mizuuchi, M. H. O’Dea, and H. A. Nash, Dna gyrase: an enzyme that introduces superhelical turns into dna., Proceedings of the National Academy of Sciences73, 3872–3876 (1976)

    work page 1976

  50. [50]

    Menzel and M

    R. Menzel and M. Gellert, The biochemistry and biol- ogyofdnagyrase,in DNA Topoisomerases: Biochemistry and Molecular Biology(Elsevier, 1994) p. 39–69

    work page 1994

  51. [51]

    Y. A. G. Fosado, D. Michieletto, C. A. Brackley, and D. Marenduzzo, Nonequilibrium dynamics and action at a distance in transcriptionally driven DNA supercoil- ing,Proc.Natl.Acad.Sci. 118,10.1073/pnas.1905215118 (2021)

    work page doi:10.1073/pnas.1905215118 2021

  52. [52]

    Wu and J

    P. Wu and J. M. Schurr, Effects of chloroquine on the torsionaldynamicsandrigiditiesoflinearandsupercoiled dnas at low ionic strength, Biopolymers28, 1695–1703 (1989)

    work page 1989

  53. [53]

    P. Wu, L. Song, J. B. Clendenning, B. S. Fujimoto, A. S. Benight, and J. M. Schurr, Interaction of chloroquine with linear and supercoiled dnas. effect on the torsional dynamics, rigidity, andtwistenergyparameter,Biochem- istry 27, 8128–8144 (1988)

    work page 1988

  54. [54]

    P. J. Kolbeck, M. Tišma, B. T. Analikwu, W. Vanderlin- den, C. Dekker, and J. Lipfert, Supercoiling-dependent dna binding: quantitative modeling and applications to bulk and single-molecule experiments, Nucleic Acids Re- search 52, 59–72 (2023)

    work page 2023

  55. [55]

    Ganji, S

    M. Ganji, S. H. Kim, J. van der Torre, E. Abbondanzieri, and C. Dekker, Intercalation-based single-molecule fluo- rescence assay to study dna supercoil dynamics, Nano Letters 16, 4699–4707 (2016)

    work page 2016

  56. [56]

    Bates and A

    A. Bates and A. Maxwell,DNA Topology, Oxford bio- science (Oxford University Press, 2005)

    work page 2005

  57. [57]

    J. Gore, Z. Bryant, M. D. Stone, M. Nöllmann, N. R. Cozzarelli, and C. Bustamante, Mechanochemical analy- sis of dna gyrase using rotor bead tracking, Nature439, 100–104 (2006)

    work page 2006

  58. [58]

    A. Basu, M. Hobson, P. Lebel, L. E. Fernandes, E. M. Tretter, J. M. Berger, and Z. Bryant, Dynamic coupling between conformations and nucleotide states in dna gy- rase, Nature Chemical Biology14, 565–574 (2018)

    work page 2018

  59. [59]

    C. J. Galvin, M. Hobson, J. X. Meng, A. Ierokomos, I. E. Ivanov, J. M. Berger, and Z. Bryant, Single-molecule dy- namics of dna gyrase in evolutionarily distant bacteria mycobacterium tuberculosis and escherichia coli, Journal of Biological Chemistry299, 103003 (2023)

    work page 2023

  60. [60]

    R. M. Robertson, S. Laib, and D. E. Smith, Diffusion of isolated dna molecules: Dependence on length and topol- 9 ogy, Proceedings of the National Academy of Sciences 103, 7310–7314 (2006)

    work page 2006

  61. [61]

    Hammermann, C

    M. Hammermann, C. Steinmaier, H. Merlitz, U. Kapp, W. Waldeck, G. Chirico, and J. Langowski, Salt effects on the structure and internal dynamics of superhelical dnas studied by light scattering and brownian dynamics, Biophysical Journal73, 2674–2687 (1997)

    work page 1997

  62. [62]

    M. K. Liu and J. C. Giddings, Separation and measure- ment of diffusion coefficients of linear and circular dnas by flow field-flow fractionation, Macromolecules26, 3576 (1993), https://doi.org/10.1021/ma00066a016

    work page doi:10.1021/ma00066a016 1993

  63. [63]

    Staňo, C

    R. Staňo, C. N. Likos, D. Michieletto, and J. Smrek, Topology-Controlled Microphase Separation and Inter- conversion of Twist and Writhe Domains in Supercoiled Annealed Polyelectrolytes, (2025), submitted

    work page 2025

  64. [64]

    Conforto, Y

    F. Conforto, Y. Gutierrez Fosado, and D. Michieletto, Fluidification of entangled polymers by loop extrusion, Phys. Rev. Res.6, 033160 (2024)

    work page 2024

  65. [65]

    Bonato, D

    A. Bonato, D. Marenduzzo, D. Michieletto, and E. Or- landini, Topological gelation of reconnecting polymers, Proc. Natl. Acad. Sci.119, e2207728119 (2022)

    work page 2022

  66. [66]

    C. A. Brackley, A. N. Morozov, and D. Marenduzzo, Models for twistable elastic polymers in brownian dy- namics, and their implementation for lammps, J. Chem. Phys. 140, 135103 (2014)

    work page 2014

  67. [67]

    Racko, F

    D. Racko, F. Benedetti, J. Dorier, Y. Burnier, and A. Stasiak, Molecular Dynamics Simulation of Super- coiled, Knotted, and Catenated DNA Molecules, Includ- ing Modeling of Action of DNA Gyrase., Methods in molecular biology1624, 339 (2017)

    work page 2017

  68. [68]

    Racko, F

    D. Racko, F. Benedetti, J. Dorier, Y. Burnier, and A. Stasiak, Generation of supercoils in nicked and gapped DNA drives DNA unknotting and postreplicative decate- nation, Nucleic Acids Research43, 7229 (2015)

    work page 2015

  69. [69]

    Benedetti, D

    F. Benedetti, D. Racko, J. Dorier, Y. Burnier, and A. Stasiak, Transcription-induced supercoiling explains formation of self-interacting chromatin domains in s. pombe, Nucleic Acids Research45, 9850 (2017)

    work page 2017

  70. [70]

    Racko, F

    D. Racko, F. Benedetti, J. Dorier, and A. Stasiak, Transcription-induced supercoiling as the driving force of chromatin loop extrusion during formation of tads in in- terphase chromosomes, Nucleic Acids Research46, 1648 (2017)

    work page 2017

  71. [71]

    Bryant, M

    Z. Bryant, M. D. Stone, J. Gore, S. B. Smith, N. R. Coz- zarelli, and C. Bustamante, Structural transitions and elasticity from torque measurements on dna, Nature424, 338–341 (2003)

    work page 2003

  72. [72]

    Michieletto and M

    D. Michieletto and M. S. Turner, A topologically driven glass in ring polymers, Proc. Natl. Acad. Sci. U.S.A.113, 5195 (2016)

    work page 2016

  73. [73]

    Lo and M

    W.-C. Lo and M. S. Turner, The topological glass in ring polymers, EPL102, 58005 (2013)

    work page 2013

  74. [74]

    J. D. Halverson, W. B. Lee, G. S. Grest, A. Y. Grosberg, and K. Kremer, Molecular dynamics simulation study of nonconcatenated ring polymers in a melt. I. Statics, J. Chem. Phys.134, 204904 (2011)

    work page 2011

  75. [75]

    A. V. Vologodskii, S. D. Levene, K. V. Klenin, M. Frank- Kamenetskii, and N. R. Cozzarelli, Conformational and thermodynamic properties of supercoiled dna, Journal of Molecular Biology227, 1224 (1992)

    work page 1992

  76. [76]

    M. T. J. van Loenhout, M. V. de Grunt, and C. Dekker, Dynamics of dna supercoils, Science 338, 94 (2012), https://www.science.org/doi/pdf/10.1126/science.1225810

    work page doi:10.1126/science.1225810 2012

  77. [77]

    Giesinger, The existence and formation dynam- ics of supramolecular chains in equilibrated and sheared ring polymer melts, Master’s thesis, University of Vienna (2025)

    N.-E. Giesinger, The existence and formation dynam- ics of supramolecular chains in equilibrated and sheared ring polymer melts, Master’s thesis, University of Vienna (2025)

    work page 2025

  78. [78]

    G. S. Grest and K. Kremer, Molecular dynamics simula- tion for polymers in the presence of a heat bath, Phys. Rev. A33, 3628 (1986)

    work page 1986

  79. [79]

    Kremer and G

    K. Kremer and G. S. Grest, Dynamics of entangled lin- ear polymer melts: A molecular-dynamics simulation, J. Chem. Phys.92, 5057 (1990)

    work page 1990

  80. [80]

    Clauvelin, W

    N. Clauvelin, W. K. Olson, and I. Tobias, Characteriza- tion of the geometry and topology of DNA pictured as a discrete collection of atoms, J. Chem. Theory Comput. 8, 1092 (2012), pMID: 24791158

    work page 2012

Showing first 80 references.