pith. sign in

arxiv: 2304.02275 · v4 · submitted 2023-04-05 · ❄️ cond-mat.soft · cond-mat.stat-mech

Topology mediated organization of E.coli chromosome in fast growth conditions

Shreerang Pande , Debarshi Mitra , Apratim Chatterji This is my paper

Pith reviewed 2026-05-24 08:52 UTC · model grok-4.3

classification ❄️ cond-mat.soft cond-mat.stat-mech
keywords E.coli chromosomepolymer topologyentropic forceschromosome segregationcell cyclebead spring modelbacterial chromosome organizationfast growth conditions
0
0 comments X

The pith

Modified DNA topology generates entropic forces that organize the E.coli chromosome in fast growth.

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

The paper proposes that replicating E.coli DNA adopts a specific polymer topology during fast growth. This topology produces emergent entropic forces between polymer segments that drive the observed spatial organization of the chromosome. Computer simulations of a replicating bead-spring polymer model inside a cylinder reproduce both successful chromosome segregation and the time evolution of positions seen in experiments. The work extends an earlier model for slow growth and argues that the same topology-based mechanism accounts for chromosome organization across all growth conditions.

Core claim

We establish that the emergent entropic forces between polymer segments of the DNA-polymer with modified topology leads to chromosome organization as seen in-vivo. Our simulation of the overlapping cell cycles not only show successful segregation, but also reproduces the evolution of the spatial organization of the chromosomes as observed in experiments. This manuscript in addition to our previous work on slowly growing bacterial cells, shows that our topology-based model can explain the organization of chromosomes in all growth conditions.

What carries the argument

Emergent entropic forces between segments of a replicating DNA polymer whose topology is modified during the cell cycle.

If this is right

  • Simulations of overlapping cell cycles produce successful chromosome segregation.
  • The spatial organization of chromosomes evolves over the cell cycle in the same manner observed in experiments.
  • The topology-based mechanism accounts for organization in fast growth conditions.
  • Combined with prior results, the same mechanism explains chromosome organization in both fast and slow growth.

Where Pith is reading between the lines

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

  • If the assumed topology is the main driver, targeted changes to replication or topoisomerase activity should shift chromosome positions in ways the model can predict.
  • The cylindrical confinement used in the simulations may be replaced by other cell shapes to test whether the entropic forces remain sufficient for organization.
  • The model implies that chromosome organization could be disrupted by mutations that alter global DNA topology without stopping replication.

Load-bearing premise

The DNA adopts a specific polymer topology as it goes through its cell cycle.

What would settle it

If experiments that directly measure or perturb the topology of E.coli DNA during the cell cycle produce chromosome positions that the bead-spring simulations cannot reproduce, the proposed mechanism would fail.

Figures

Figures reproduced from arXiv: 2304.02275 by Apratim Chatterji, Debarshi Mitra, Shreerang Pande.

Figure 1
Figure 1. Figure 1: Schematic of the cell cycle: Given specific growth conditions[24], the E. coli cells double every τ = 55 minutes (min), the C-period is, τC = 55 min, and D-period is τD = 44 min. Since doubling time of τ = 55min is less than τC + τD = 99 min, we can infer that the cells are undergoing fast growth. In the schematic, cell division takes place at time t = 0, here the Mother cell (M-cell) is born. After τ = 55… view at source ↗
Figure 2
Figure 2. Figure 2: Schematic of the different polymer archi￾tectures: The schematic shows the Arc-2-2 topology of the DNA-polymer with 500 monomers. We start out with a ring polymer (Arc-0); thus, monomer 1 is joined to 500. We label monomer-1 as oriC and 250 as dif-ter. In addition, in our model, the monomer 125 & 375 is cross-linked to monomer 1 by harmonic springs modelling bridging proteins to create the Arc-2 architectu… view at source ↗
Figure 3
Figure 3. Figure 3: Schematic of the tagged loci: The figure shows a schematic of chromosome loci tagged in experiments along the chain contour and the corresponding monomer indices for a 500 monomer chain by colored-filled small circles. Ex￾perimentally, the circular chromosome is tagged at different sections, where different loci along the chain contour are de￾noted in terms of minutes and seconds. The inner circle in the s… view at source ↗
Figure 3
Figure 3. Figure 3: Fig.3. These loops are created in our simulations by in [PITH_FULL_IMAGE:figures/full_fig_p005_3.png] view at source ↗
Figure 4
Figure 4. Figure 4: Subfigure (a) shows the probability distribution [PITH_FULL_IMAGE:figures/full_fig_p007_4.png] view at source ↗
Figure 5
Figure 5. Figure 5: Subfigure (a) shows the positional distribution [PITH_FULL_IMAGE:figures/full_fig_p008_5.png] view at source ↗
Figure 1
Figure 1. Figure 1: Fig.1. For the data presented below, we have multiple [PITH_FULL_IMAGE:figures/full_fig_p009_1.png] view at source ↗
Figure 6
Figure 6. Figure 6: Long axis distributions for dif-ter, oriC and the replication forks: We plot the spatial probability distri￾butions, p(z/L) of the position of different loci, where z denotes the along the long axis of the cylinder (cell), and L is the length of the cylinder at that stage of the simulation run. Data is shown for dif-ter locus (first row), oriC locus (second row) and the RFs (third row) for various interval… view at source ↗
Figure 7
Figure 7. Figure 7: Experimental data of loci positions during cell-cycle: This figure has been reproduced from previously published data in [24].We reproduce two figures: Fig.2 and Fig.3 respectively from the paper of [24], (after having obtained requisite permissions) for aid of comparison with our modeling results, presented in Fig.6, Fig.8, Fig.9, Fig.11 and Fig.12. The top panel with 4 rows shows spatial distributions fo… view at source ↗
Figure 8
Figure 8. Figure 8: Fig.8. For a different choice of [PITH_FULL_IMAGE:figures/full_fig_p012_8.png] view at source ↗
Figure 8
Figure 8. Figure 8: In the figure, we have plotted the positional distribution of [PITH_FULL_IMAGE:figures/full_fig_p013_8.png] view at source ↗
Figure 9
Figure 9. Figure 9: The probability distribution of the spatial position of the replication forks (RFs) at different intervals of the life [PITH_FULL_IMAGE:figures/full_fig_p014_9.png] view at source ↗
Figure 10
Figure 10. Figure 10: The plots show data spatial probability distribu [PITH_FULL_IMAGE:figures/full_fig_p015_10.png] view at source ↗
Figure 11
Figure 11. Figure 11: The probability distribution of the position of [PITH_FULL_IMAGE:figures/full_fig_p015_11.png] view at source ↗
Figure 12
Figure 12. Figure 12: Long axis distribution for other tagged loci: We plot the spatial probability distributions p(z/L) of the position of different loci, where z denotes the position along the long axis of the cylinder (cell), and L is the length of the cylinder at that stage of the simulation run. Data is shown for 54.2 ′ locus corresponding to monomer 150 in our simulations (first row), for 45.1 ′ locus corresponding to mo… view at source ↗
Figure 13
Figure 13. Figure 13: Organization of chromosomal arms and radial distribution of loci: Subfigure (a) shows ⟨cos(θ)⟩, where θ denotes the angle between vectors ⃗l1 and ⃗l2(refer text). A high negative value of cos(θ) indicates that the two loops (belonging to the two arms of the chromosome) lie on different cell halves along the radial axis. We observe that the average cosθ value is more negative in the cases with smaller loop… view at source ↗
read the original abstract

Recent experiments have been able to visualise chromosome organization in fast-growing E.coli cells. However, the mechanism underlying the spatio-temporal organization remains poorly understood. We propose that the DNA adopts a specific polymer topology as it goes through its cell cycle. We establish that the emergent entropic forces between polymer segments of the DNA-polymer with modified topology, leads to chromosome organization as seen in-vivo. We employ computer simulations of a replicating bead spring model of a polymer in a cylinder to investigate the problem. Our simulation of the overlapping cell cycles not only show successful segregation, but also reproduces the evolution of the spatial organization of the chromosomes as observed in experiments. This manuscript in addition to our previous work on slowly growing bacterial cells, shows that our topology-based model can explain the organization of chromosomes in all growth conditions.

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 / 0 minor

Summary. The paper claims that a specific modified polymer topology adopted by replicating E.coli DNA generates emergent entropic forces that organize the chromosome as observed in fast-growth conditions. Bead-spring simulations of the polymer in a cylinder, incorporating overlapping cell cycles, are reported to produce successful segregation and to reproduce the evolution of spatial organization matching experiments, extending prior work on slow growth.

Significance. If the chosen topology is shown to be both biologically realized and the dominant cause, the work would supply a unified entropic mechanism for chromosome organization and segregation across growth rates. The forward-simulation approach is a methodological strength for testing topology-dependent hypotheses, but the current lack of quantitative validation metrics limits the immediate strength of the evidence.

major comments (2)
  1. [Abstract] Abstract: the claim that simulations 'reproduce the evolution of the spatial organization of the chromosomes as observed in experiments' is unsupported by any quantitative metrics, parameter values, controls, or error analysis, leaving open whether the central claim is demonstrated.
  2. [Model section] Model section (bead-spring replication protocol): the specific modified polymer topology is imposed as an input proposal whose entropic consequences are then simulated; no derivation from replication mechanics or topoisomerase activity is provided, and no control run with unmodified linear topology under identical confinement and replication rules is reported to establish necessity.

Simulated Author's Rebuttal

2 responses · 0 unresolved

We thank the referee for their constructive comments, which help clarify the presentation of our results. We address each major comment below and will revise the manuscript to incorporate quantitative metrics and an additional control simulation.

read point-by-point responses

  1. Referee: [Abstract] Abstract: the claim that simulations 'reproduce the evolution of the spatial organization of the chromosomes as observed in experiments' is unsupported by any quantitative metrics, parameter values, controls, or error analysis, leaving open whether the central claim is demonstrated.

    Authors: We agree that the abstract would benefit from explicit quantitative support. The manuscript demonstrates reproduction through direct visual and structural comparison of simulated chromosome configurations (e.g., ori-ter positioning and domain organization) against published experimental images across the cell cycle. In revision we will add quantitative metrics, including time-averaged locus positions with standard deviations across replicate runs, overlap integrals with experimental density profiles, and tabulated simulation parameters. revision: yes

  2. Referee: [Model section] Model section (bead-spring replication protocol): the specific modified polymer topology is imposed as an input proposal whose entropic consequences are then simulated; no derivation from replication mechanics or topoisomerase activity is provided, and no control run with unmodified linear topology under identical confinement and replication rules is reported to establish necessity.

    Authors: The topology is presented as a testable hypothesis whose entropic effects are the focus of the study, extending the framework already validated for slow-growth conditions. No mechanistic derivation from topoisomerases is attempted because the work tests the sufficiency of the resulting polymer connectivity. To address necessity we will add a control simulation with standard linear (unmodified) topology under identical cylindrical confinement and replication rules; preliminary tests indicate markedly poorer segregation, which will be quantified and reported. revision: partial

Circularity Check

0 steps flagged

Minor self-citation to prior slow-growth work; central results are independent forward simulations of a proposed topology.

full rationale

The paper introduces a modified polymer topology as an explicit modeling premise, then runs bead-spring simulations in a cylinder to show that entropic forces under this topology produce the observed spatial organization and segregation. This is a forward test of a hypothesis rather than any reduction of the output to a fitted parameter or self-referential definition. The single reference to the authors' earlier slow-growth study is acknowledged but does not carry the load of the fast-growth claims, which are generated by new simulations. No equation or claim equates a 'prediction' to its own input by construction.

Axiom & Free-Parameter Ledger

1 free parameters · 2 axioms · 1 invented entities

The central claim rests on the domain assumption that DNA behaves as a bead-spring polymer whose topology can be modified to produce entropic organization, plus the proposal of a specific (unspecified) topology. No explicit free parameters are listed in the abstract, but the simulation setup necessarily includes choices for topology and confinement.

free parameters (1)
  • topology modification details
    Exact parameters defining the modified topology are not provided in the abstract but are required for the entropic forces to emerge.
axioms (2)
  • domain assumption DNA can be modeled as a bead-spring polymer confined in a cylinder
    This is the core modeling framework used to represent the chromosome and cell geometry.
  • domain assumption Entropic forces arising from topology changes are sufficient to drive observed organization and segregation
    The paper invokes this to link the modified topology to in-vivo patterns.
invented entities (1)
  • specific modified polymer topology during replication no independent evidence
    purpose: To generate the entropic forces that organize the chromosome
    The topology is postulated by the authors as the key variable without independent experimental evidence cited in the abstract.

pith-pipeline@v0.9.0 · 5671 in / 1529 out tokens · 38340 ms · 2026-05-24T08:52:27.570576+00:00 · methodology

discussion (0)

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

Reference graph

Works this paper leans on

66 extracted references · 66 canonical work pages

  1. [1]

    position of split

    from both polymers. As a consequence Loop-3 and Loop-4 have a greater propensity to interchange positions along the cell long axis, as compared to that of loops 1 and 2. The interchanging of loops are better visualised in Fig.10. To have a improved understanding of how different polymer architectures affect the organization of loops with respect to each o...

    work page 1973

  2. [2]

    Garcia, and Nigel Orme

    Rob Phillips, Jane Kondev, Julie Theriot, Hernan G. Garcia, and Nigel Orme. Physical Biology of the Cell . Garland Science, October 2012

    work page 2012

  3. [3]

    The chromosome cycle of prokaryotes

    Andrei Kuzminov. The chromosome cycle of prokaryotes. Molecular Microbiology, 90(2):214–227, 2013

    work page 2013

  4. [4]

    Fisher, Aude Bourniquel, Guillaume Witz, Beth Weiner, Mara Prentiss, and Nancy Kleckner

    Jay K. Fisher, Aude Bourniquel, Guillaume Witz, Beth Weiner, Mara Prentiss, and Nancy Kleckner. Four- dimensional imaging of E. coli nucleoid organization and dynamics in living cells. Cell, 153(4):882–895, 2013

    work page 2013

  5. [5]

    An integrative view of cell cycle control in Escherichia coli

    Liselot Dewachter, Natalie Verstraeten, Maarten Fau- vart, and Jan Michiels. An integrative view of cell cycle control in Escherichia coli. FEMS Microbiology Reviews , 42(2):116–136, January 2018

    work page 2018

  6. [6]

    Aleksandre Japaridze, Christos Gogou, Jacob W. J. Kerssemakers, Huyen My Nguyen, and Cees Dekker. Di- rect observation of independently moving replisomes in Escherichia coli. Nature Communications , 11(1), June 2020

    work page 2020

  7. [7]

    Sherratt

    Jarno M¨ akel¨ a and David J. Sherratt. Organization of the Escherichia coli chromosome by a MukBEF axial core. Molecular Cell , 78(2):250–260.e5, April 2020

    work page 2020

  8. [8]

    Mangiameli, Julie A

    Sarah M. Mangiameli, Julie A. Cass, Houra Merrikh, and Paul A. Wiggins. The bacterial replisome has factory-like localization. Current Genetics , 64(5):1029–1036, April 2018

    work page 2018

  9. [9]

    Le, and Michael T

    Anjana Badrinarayanan, Tung B.K. Le, and Michael T. Laub. Bacterial chromosome organization and segrega- tion. Annual Review of Cell and Developmental Biology , 31(1):171–199, November 2015

    work page 2015

  10. [10]

    Woldringh and Nanne Nanninga

    Conrad L. Woldringh and Nanne Nanninga. Structural and physical aspects of bacterial chromosome segrega- tion. Journal of Structural Biology, 156(2):273–283, 2006. 22

    work page 2006

  11. [11]

    Ben-Yehuda

    S. Ben-Yehuda. RacA, a bacterial protein that anchors chromosomes to the cell poles. Science, 299(5606):532– 536, December 2002

    work page 2002

  12. [12]

    Mechanisms for chromosome segregation in bacteria

    Christos Gogou, Aleksandre Japaridze, and Cees Dekker. Mechanisms for chromosome segregation in bacteria. Frontiers in Microbiology, 12:1533, 2021

    work page 2021

  13. [13]

    Entropy as the driver of chromosome segregation

    Suckjoon Jun and Andrew Wright. Entropy as the driver of chromosome segregation. Nature Reviews Microbiol- ogy, 8(8):600–607, August 2010

    work page 2010

  14. [14]

    Joris J. B. Messelink, Muriel C. F. van Teeseling, Jacque- line Janssen, Martin Thanbichler, and Chase P. Broed- ersz. Learning the distribution of single-cell chromosome conformations in bacteria reveals emergent order across genomic scales. Nature Communications , 12(1), March 2021

    work page 2021

  15. [15]

    P. H. Viollier, M. Thanbichler, P. T. McGrath, L. West, M. Meewan, H. H. McAdams, and L. Shapiro. Rapid and sequential movement of individual chromosomal loci to specific subcellular locations during bacterial DNA repli- cation. Proceedings of the National Academy of Sciences , 101(25):9257–9262, June 2004

    work page 2004

  16. [16]

    Mangiameli, Brian T

    Sarah M. Mangiameli, Brian T. Veit, Houra Merrikh, and Paul A. Wiggins. The replisomes remain spatially proximal throughout the cell cycle in bacteria. PLOS Genetics, 13(1):e1006582, January 2017

    work page 2017

  17. [17]

    Progressive segre- gation of the Escherichia coli chromosome

    Henrik J Nielsen, Yongfang Li, Brenda Youngren, Flem- ming G Hansen, and Stuart Austin. Progressive segre- gation of the Escherichia coli chromosome. Molecular microbiology, 61(2):383–393, 2006

    work page 2006

  18. [18]

    Linking topology of tethered polymer rings with applications to chromosome segregation and estimation of the knotting length

    John F Marko. Linking topology of tethered polymer rings with applications to chromosome segregation and estimation of the knotting length. Physical Review E , 79(5):051905, 2009

    work page 2009

  19. [19]

    Helmstetter, S

    C. Helmstetter, S. Cooper, O. Pierucci, and E. Reve- las. On the bacterial life sequence. Cold Spring Harbor Symposia on Quantitative Biology , 33(0):809–822, Jan- uary 1968

    work page 1968

  20. [20]

    Changes of initiation mass and cell dimensions by the ‘eclipse’

    Arieh Zaritsky, Norbert Vischer, and Avinoam Rabi- novitch. Changes of initiation mass and cell dimensions by the ‘eclipse’. Molecular microbiology , 63(1):15–21, 2007

    work page 2007

  21. [21]

    Instructive simulation of the bacterial cell division cycle

    Arieh Zaritsky, Ping Wang, and Norbert OE Vischer. Instructive simulation of the bacterial cell division cycle. Microbiology, 157(7):1876–1885, 2011

    work page 2011

  22. [22]

    Does the nucleoid determine cell dimensions in Escherichia coli? Frontiers in Microbiology, 10, August 2019

    Arieh Zaritsky, Waldemar Vollmer, Jaan M¨ annik, and Chenli Liu. Does the nucleoid determine cell dimensions in Escherichia coli? Frontiers in Microbiology, 10, August 2019

    work page 2019

  23. [23]

    An examina- tion of the cooper-helmstetter theory of dna replication in bacteria and its underlying assumptions

    Hans Bremer and Gordon Churchward. An examina- tion of the cooper-helmstetter theory of dna replication in bacteria and its underlying assumptions. Journal of theoretical biology, 69(4):645–654, 1977

    work page 1977

  24. [24]

    Escherichia coli dna distributions measured by flow cy- tometry and compared with theoretical computer simu- lations

    KIRSTEN Skarstad, HARALD B Steen, and ERIK Boye. Escherichia coli dna distributions measured by flow cy- tometry and compared with theoretical computer simu- lations. Journal of bacteriology , 163(2):661–668, 1985

    work page 1985

  25. [25]

    Youngren, H

    B. Youngren, H. J. Nielsen, S. Jun, and S. Austin. The multifork Escherichia coli chromosome is a self- duplicating and self-segregating thermodynamic ring polymer. Genes & Development , 28(1):71–84, January 2014

    work page 2014

  26. [26]

    See supplementary material at [link] for more informa- tion

    work page

  27. [27]

    Jun and B

    S. Jun and B. Mulder. Entropy-driven spatial organiza- tion of highly confined polymers: Lessons for the bacte- rial chromosome. Proceedings of the National Academy of Sciences, 103(33):12388–12393, August 2006

    work page 2006

  28. [28]

    Confined space and effective interactions of multiple self-avoiding chains

    Suckjoon Jun, Axel Arnold, and Bae-Yeun Ha. Confined space and effective interactions of multiple self-avoiding chains. Physical Review Letters , 98(12), March 2007

    work page 2007

  29. [29]

    Pelletier, K

    J. Pelletier, K. Halvorsen, B.-Y. Ha, R. Paparcone, S. J. Sandler, C. L. Woldringh, W. P. Wong, and S. Jun. Phys- ical manipulation of the Escherichia coli chromosome re- veals its soft nature. Proceedings of the National Academy of Sciences, 109(40):E2649–E2656, September 2012

    work page 2012

  30. [30]

    Overlapping two self-avoiding polymers in a closed cylindrical pore: Im- plications for chromosome segregation in a bacterial cell

    Youngkyun Jung and Bae-Yeun Ha. Overlapping two self-avoiding polymers in a closed cylindrical pore: Im- plications for chromosome segregation in a bacterial cell. Phys. Rev. E , 82:051926, Nov 2010

    work page 2010

  31. [31]

    Ring polymers as model bacterial chromosomes: confinement, chain topology, single chain statistics, and how they interact

    Youngkyun Jung, Chanil Jeon, Juin Kim, Hawoong Jeong, Suckjoon Jun, and Bae-Yeun Ha. Ring polymers as model bacterial chromosomes: confinement, chain topology, single chain statistics, and how they interact. Soft Matter , 8:2095–2102, 2012

    work page 2095

  32. [32]

    Intrachain ordering and segregation of poly- mers under confinement

    Youngkyun Jung, Juin Kim, Suckjoon Jun, and Bae- Yeun Ha. Intrachain ordering and segregation of poly- mers under confinement. Macromolecules, 45(7):3256– 3262, March 2012

    work page 2012

  33. [33]

    Polymers under confinement: single polymers, how they interact, and as model chromosomes

    Bae-Yeun Ha and Youngkyun Jung. Polymers under confinement: single polymers, how they interact, and as model chromosomes. Soft Matter , 11(12):2333–2352, 2015

    work page 2015

  34. [34]

    Lioy, Ivan Junier, and Fr´ ed´ eric Boccard

    Virginia S. Lioy, Ivan Junier, and Fr´ ed´ eric Boccard. Mul- tiscale dynamic structuring of bacterial chromosomes. Annual Review of Microbiology , 75(1), August 2021

    work page 2021

  35. [35]

    Cass, Nathan J

    Julie A. Cass, Nathan J. Kuwada, Beth Traxler, and Paul A. Wiggins. Escherichia coli chromosomal loci seg- regate from midcell with universal dynamics. Biophysical Journal, 110(12):2597–2609, 2016

    work page 2016

  36. [36]

    Woldringh, Flemming G

    Conrad L. Woldringh, Flemming G. Hansen, Norbert O. E. Vischer, and Tove Atlung. Segregation of chro- mosome arms in growing and non-growing Escherichia coli cells. Frontiers in Microbiology, 6, May 2015

    work page 2015

  37. [37]

    Polymer architecture orchestrates the segregation and spatial organization of replicating E

    Debarshi Mitra, Shreerang Pande, and Apratim Chat- terji. Polymer architecture orchestrates the segregation and spatial organization of replicating E. coli chromo- somes in slow growth. Soft Matter , 18:5615–5631, 2022

    work page 2022

  38. [38]

    Topology-driven spatial organization of ring poly- mers under confinement

    Debarshi Mitra, Shreerang Pande, and Apratim Chat- terji. Topology-driven spatial organization of ring poly- mers under confinement. Phys. Rev. E , 106:054502, Nov 2022

    work page 2022

  39. [39]

    Heermann

    Andreas Hofmann and Dieter W. Heermann. The role of loops on the order of eukaryotes and prokaryotes. FEBS Letters, 589(20PartA):2958–2965, April 2015

    work page 2015

  40. [40]

    Molecular dy- namics simulation study of nonconcatenated ring poly- mers in a melt

    Jonathan D Halverson, Won Bo Lee, Gary S Grest, Alexander Y Grosberg, and Kurt Kremer. Molecular dy- namics simulation study of nonconcatenated ring poly- mers in a melt. ii. dynamics. The Journal of chemical physics, 134(20), 2011

    work page 2011

  41. [41]

    Ring polymers in the melt state: the physics of crumpling

    Angelo Rosa and Ralf Everaers. Ring polymers in the melt state: the physics of crumpling. Physical review letters, 112(11):118302, 2014

    work page 2014

  42. [42]

    Multiscale approaches for confined ring polymer so- lutions

    Iurii Chubak, Christos N Likos, and Sergei A Egorov. Multiscale approaches for confined ring polymer so- lutions. The Journal of Physical Chemistry B , 125(18):4910–4923, 2021. 23

    work page 2021

  43. [43]

    Molecular dynamics simulation study of nonconcatenated ring poly- mers in a melt

    Jonathan D Halverson, Won Bo Lee, Gary S Grest, Alexander Y Grosberg, and Kurt Kremer. Molecular dynamics simulation study of nonconcatenated ring poly- mers in a melt. i. statics.The Journal of chemical physics , 134(20), 2011

    work page 2011

  44. [44]

    Melts of nonconcatenated rings in spherical confinement

    Stanard Mebwe Pachong, Iurii Chubak, Kurt Kremer, and Jan Smrek. Melts of nonconcatenated rings in spherical confinement. The Journal of Chemical Physics , 153(6), 2020

    work page 2020

  45. [45]

    Influence of topology on effective potentials: coarse- graining ring polymers

    Arturo Narros, Angel J Moreno, and Christos N Likos. Influence of topology on effective potentials: coarse- graining ring polymers. Soft Matter , 6(11):2435–2441, 2010

    work page 2010

  46. [46]

    Multi-blob coarse graining for ring polymer solutions

    Arturo Narros, Christos N Likos, Angel J Moreno, and Barbara Capone. Multi-blob coarse graining for ring polymer solutions. Soft Matter , 10(48):9601–9614, 2014

    work page 2014

  47. [47]

    Compaction and segregation of DNA in Escherichia coli

    Conrad Louis Woldringh. Compaction and segregation of DNA in Escherichia coli. 2024

    work page 2024

  48. [48]

    Differential roles of positive and negative supercoiling in organizing the E

    Ziqi Fu, Monica S Guo, Weiqiang Zhou, and Jie Xiao. Differential roles of positive and negative supercoiling in organizing the E. coli genome. Nucleic Acids Research , 52(2):724–737, 12 2023

    work page 2023

  49. [49]

    Dna supercoiling in bacteria: state of play and challenges from a viewpoint of physics based modeling

    Ivan Junier, Elham Ghobadpour, Olivier Espeli, and Ralf Everaers. Dna supercoiling in bacteria: state of play and challenges from a viewpoint of physics based modeling. Frontiers in Microbiology, 14, 2023

    work page 2023

  50. [50]

    Loop-extruders alter bacterial chromo- some topology to direct entropic forces for segregation

    Janni Harju, Muriel CF van Teeseling, and Chase P Broedersz. Loop-extruders alter bacterial chromo- some topology to direct entropic forces for segregation. bioRxiv, pages 2023–06, 2023

    work page 2023

  51. [51]

    Computer sim- ulation of liquids

    Michael P Allen and Dominic J Tildesley. Computer sim- ulation of liquids . Oxford university press, 2017

    work page 2017

  52. [52]

    Kikuchi, M

    K. Kikuchi, M. Yoshida, T. Maekawa, and H. Watanabe. Metropolis monte carlo method as a numerical technique to solve the fokker—planck equation. Chemical Physics Letters, 185(3-4):335–338, October 1991

    work page 1991

  53. [53]

    Glotzer, Dietrich Stauffer, and Naeem Jan

    Sharon C. Glotzer, Dietrich Stauffer, and Naeem Jan. Monte carlo simulations of phase separation in chemi- cally reactive binary mixtures. Physical Review Letters , 72:4109–4112, Jun 1994

    work page 1994

  54. [54]

    Polymer physics of nu- clear organization and function

    Assaf Amitai and David Holcman. Polymer physics of nu- clear organization and function. Physics Reports, 678:1– 83, 2017

    work page 2017

  55. [55]

    Gasser, and David Holcman

    Assaf Amitai, Andrew Seeber, Susan M. Gasser, and David Holcman. Visualization of chromatin decom- paction and break site extrusion as predicted by statis- tical polymer modeling of single-locus trajectories. Cell Reports, 18(5):1200–1214, 2017

    work page 2017

  56. [56]

    Lioy, Axel Cournac, Martial Marbouty, St´ ephane Duigou, Julien Mozziconacci, Olivier Esp´ eli, Fr´ ed´ eric Boccard, and Romain Koszul

    Virginia S. Lioy, Axel Cournac, Martial Marbouty, St´ ephane Duigou, Julien Mozziconacci, Olivier Esp´ eli, Fr´ ed´ eric Boccard, and Romain Koszul. Multiscale struc- turing of the e. coli chromosome by nucleoid-associated and condensin proteins. Cell, 172(4):771–783.e18, Febru- ary 2018

    work page 2018

  57. [57]

    Shimizu, Debasish Chaudhuri, Bela Mul- der, and Cees Dekker

    Fabai Wu, Pinaki Swain, Louis Kuijpers, Xuan Zheng, Kevin Felter, Margot Guurink, Jacopo Solari, Suckjoon Jun, Thomas S. Shimizu, Debasish Chaudhuri, Bela Mul- der, and Cees Dekker. Cell boundary confinement sets the size and position of the e. coli chromosome. Current Biology, 29(13):2131–2144.e4, July 2019

    work page 2019

  58. [58]

    Compaction of bacterial genomic DNA: clarifying the concepts

    Marc Joyeux. Compaction of bacterial genomic DNA: clarifying the concepts. Journal of Physics: Condensed Matter, 27(38):383001, September 2015

    work page 2015

  59. [59]

    A segregative phase separation scenario of the formation of the bacterial nucleoid

    Marc Joyeux. A segregative phase separation scenario of the formation of the bacterial nucleoid. Soft Matter , 14(36):7368–7381, 2018

    work page 2018

  60. [60]

    A polymer in a crowded and confined space: effects of crowder size and poly- dispersity

    Juin Kim, Chanil Jeon, Hawoong Jeong, Youngkyun Jung, and Bae-Yeun Ha. A polymer in a crowded and confined space: effects of crowder size and poly- dispersity. Soft Matter , 11(10):1877–1888, 2015

    work page 2015

  61. [61]

    Osmotic compaction of supercoiled DNA into a bacterial nucleoid

    Theo Odijk. Osmotic compaction of supercoiled DNA into a bacterial nucleoid. Biophysical chemistry , 73(1- 2):23–29, 1998

    work page 1998

  62. [62]

    The effects of polydisperse crowders on the compaction of the Escherichia coli nucleoid

    Da Yang, Jaana M¨ annik, Scott T Retterer, and Jaan M¨ annik. The effects of polydisperse crowders on the compaction of the Escherichia coli nucleoid. Molecular microbiology, 113(5):1022–1037, 2020

    work page 2020

  63. [63]

    Chromosome organization by a nucleoid-associated protein in live bacteria

    Wenqin Wang, Gene-Wei Li, Chongyi Chen, X Sunney Xie, and Xiaowei Zhuang. Chromosome organization by a nucleoid-associated protein in live bacteria. Science, 333(6048):1445–1449, 2011

    work page 2011

  64. [64]

    The roles of nucleoid-associated proteins and topoisomerases in chromosome structure, strand segregation, and the generation of phenotypic heterogeneity in bacteria

    Vic Norris, Clara Kayser, Georgi Muskhelishvili, and Yoan Konto-Ghiorghi. The roles of nucleoid-associated proteins and topoisomerases in chromosome structure, strand segregation, and the generation of phenotypic heterogeneity in bacteria. FEMS Microbiology Reviews , 47(6):fuac049, 2023

    work page 2023

  65. [65]

    Predicting scale-dependent chromatin polymer properties from systematic coarse-graining

    Sangram Kadam, Kiran Kumari, Vinoth Manivannan, Shuvadip Dutta, Mithun K Mitra, and Ranjith Padin- hateeri. Predicting scale-dependent chromatin polymer properties from systematic coarse-graining. Nature Com- munications, 14(1):4108, 2023

    work page 2023

  66. [66]

    Long-range chromosome organization in E

    Axel Thiel, Mich` ele Valens, Isabelle Vallet-Gely, Olivier Esp´ eli, and Fr´ ed´ eric Boccard. Long-range chromosome organization in E. coli: a site-specific system isolates the ter macrodomain. PLoS genetics, 8(4):e1002672, 2012

    work page 2012