---
_id: '14827'
abstract:
- lang: eng
  text: Understanding complex living systems, which are fundamentally constrained
    by physical phenomena, requires combining experimental data with theoretical physical
    and mathematical models. To develop such models, collaborations between experimental
    cell biologists and theoreticians are increasingly important but these two groups
    often face challenges achieving mutual understanding. To help navigate these challenges,
    this Perspective discusses different modelling approaches, including bottom-up
    hypothesis-driven and top-down data-driven models, and highlights their strengths
    and applications. Using cell mechanics as an example, we explore the integration
    of specific physical models with experimental data from the molecular, cellular
    and tissue level up to multiscale input. We also emphasize the importance of constraining
    model complexity and outline strategies for crosstalk between experimental design
    and model development. Furthermore, we highlight how physical models can provide
    conceptual insights and produce unifying and generalizable frameworks for biological
    phenomena. Overall, this Perspective aims to promote fruitful collaborations that
    advance our understanding of complex biological systems.
acknowledgement: "We thank Prisca Liberali and Edouard Hannezo for many inspiring
  discussions; Mehmet Can Uçar, Nicoletta I Petridou and Qiutan Yang for a critical
  reading of the manuscript, and Claudia Flandoli for the artwork in Figs 2 and 3.
  We would also like to thank The Company of Biologists for the opportunity to attend
  the 2023 workshop on Collective Cell Migration, and all workshop participants for
  discussions.\r\nC.S. was supported by a European Molecular Biology Organization
  (EMBO) Postdoctoral Fellowship (ALTF 660-2020) and Human Frontier Science Program
  (HFSP) Postdoctoral fellowship (LT000746/2021-L). D.B.B. was supported by the NOMIS
  Foundation as a NOMIS Fellow and by an EMBO Postdoctoral Fellowship (ALTF 343-2022)."
article_number: jcs.261515
article_processing_charge: No
article_type: original
author:
- first_name: Cornelia
  full_name: Schwayer, Cornelia
  id: 3436488C-F248-11E8-B48F-1D18A9856A87
  last_name: Schwayer
  orcid: 0000-0001-5130-2226
- first_name: David
  full_name: Brückner, David
  id: e1e86031-6537-11eb-953a-f7ab92be508d
  last_name: Brückner
  orcid: 0000-0001-7205-2975
citation:
  ama: Schwayer C, Brückner D. Connecting theory and experiment in cell and tissue
    mechanics. <i>Journal of Cell Science</i>. 2023;136(24). doi:<a href="https://doi.org/10.1242/jcs.261515">10.1242/jcs.261515</a>
  apa: Schwayer, C., &#38; Brückner, D. (2023). Connecting theory and experiment in
    cell and tissue mechanics. <i>Journal of Cell Science</i>. The Company of Biologists.
    <a href="https://doi.org/10.1242/jcs.261515">https://doi.org/10.1242/jcs.261515</a>
  chicago: Schwayer, Cornelia, and David Brückner. “Connecting Theory and Experiment
    in Cell and Tissue Mechanics.” <i>Journal of Cell Science</i>. The Company of
    Biologists, 2023. <a href="https://doi.org/10.1242/jcs.261515">https://doi.org/10.1242/jcs.261515</a>.
  ieee: C. Schwayer and D. Brückner, “Connecting theory and experiment in cell and
    tissue mechanics,” <i>Journal of Cell Science</i>, vol. 136, no. 24. The Company
    of Biologists, 2023.
  ista: Schwayer C, Brückner D. 2023. Connecting theory and experiment in cell and
    tissue mechanics. Journal of Cell Science. 136(24), jcs. 261515.
  mla: Schwayer, Cornelia, and David Brückner. “Connecting Theory and Experiment in
    Cell and Tissue Mechanics.” <i>Journal of Cell Science</i>, vol. 136, no. 24,
    jcs. 261515, The Company of Biologists, 2023, doi:<a href="https://doi.org/10.1242/jcs.261515">10.1242/jcs.261515</a>.
  short: C. Schwayer, D. Brückner, Journal of Cell Science 136 (2023).
date_created: 2024-01-17T12:46:55Z
date_published: 2023-12-27T00:00:00Z
date_updated: 2024-01-22T13:35:48Z
day: '27'
department:
- _id: EdHa
- _id: CaHe
doi: 10.1242/jcs.261515
external_id:
  pmid:
  - '38149871'
intvolume: '       136'
issue: '24'
keyword:
- Cell Biology
language:
- iso: eng
month: '12'
oa_version: None
pmid: 1
project:
- _id: 34e2a5b5-11ca-11ed-8bc3-b2265616ef0b
  grant_number: 343-2022
  name: A mechano-chemical theory for stem cell fate decisions in organoid development
publication: Journal of Cell Science
publication_identifier:
  eissn:
  - 1477-9137
  issn:
  - 0021-9533
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
scopus_import: '1'
status: public
title: Connecting theory and experiment in cell and tissue mechanics
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 136
year: '2023'
...
---
_id: '13261'
abstract:
- lang: eng
  text: Chromosomes in the eukaryotic nucleus are highly compacted. However, for many
    functional processes, including transcription initiation, the pairwise motion
    of distal chromosomal elements such as enhancers and promoters is essential and
    necessitates dynamic fluidity. Here, we used a live-imaging assay to simultaneously
    measure the positions of pairs of enhancers and promoters and their transcriptional
    output while systematically varying the genomic separation between these two DNA
    loci. Our analysis reveals the coexistence of a compact globular organization
    and fast subdiffusive dynamics. These combined features cause an anomalous scaling
    of polymer relaxation times with genomic separation leading to long-ranged correlations.
    Thus, encounter times of DNA loci are much less dependent on genomic distance
    than predicted by existing polymer models, with potential consequences for eukaryotic
    gene expression.
acknowledgement: This work was supported in part by the U.S. National Science Foundation,
  the Center for the Physics of Biological Function (grant PHY-1734030), and the National
  Institutes of Health (grants R01GM097275, U01DA047730, and U01DK127429). D.B.B.
  was supported by the NOMIS Foundation as a fellow and by an EMBO postdoctoral fellowship
  (ALTF 343-2022). H.C. was supported by a Charles H. Revson Biomedical Science Fellowship.
article_processing_charge: No
article_type: original
author:
- first_name: David
  full_name: Brückner, David
  id: e1e86031-6537-11eb-953a-f7ab92be508d
  last_name: Brückner
  orcid: 0000-0001-7205-2975
- first_name: Hongtao
  full_name: Chen, Hongtao
  last_name: Chen
- first_name: Lev
  full_name: Barinov, Lev
  last_name: Barinov
- first_name: Benjamin
  full_name: Zoller, Benjamin
  last_name: Zoller
- first_name: Thomas
  full_name: Gregor, Thomas
  last_name: Gregor
citation:
  ama: Brückner D, Chen H, Barinov L, Zoller B, Gregor T. Stochastic motion and transcriptional
    dynamics of pairs of distal DNA loci on a compacted chromosome. <i>Science</i>.
    2023;380(6652):1357-1362. doi:<a href="https://doi.org/10.1126/science.adf5568">10.1126/science.adf5568</a>
  apa: Brückner, D., Chen, H., Barinov, L., Zoller, B., &#38; Gregor, T. (2023). Stochastic
    motion and transcriptional dynamics of pairs of distal DNA loci on a compacted
    chromosome. <i>Science</i>. American Association for the Advancement of Science.
    <a href="https://doi.org/10.1126/science.adf5568">https://doi.org/10.1126/science.adf5568</a>
  chicago: Brückner, David, Hongtao Chen, Lev Barinov, Benjamin Zoller, and Thomas
    Gregor. “Stochastic Motion and Transcriptional Dynamics of Pairs of Distal DNA
    Loci on a Compacted Chromosome.” <i>Science</i>. American Association for the
    Advancement of Science, 2023. <a href="https://doi.org/10.1126/science.adf5568">https://doi.org/10.1126/science.adf5568</a>.
  ieee: D. Brückner, H. Chen, L. Barinov, B. Zoller, and T. Gregor, “Stochastic motion
    and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome,”
    <i>Science</i>, vol. 380, no. 6652. American Association for the Advancement of
    Science, pp. 1357–1362, 2023.
  ista: Brückner D, Chen H, Barinov L, Zoller B, Gregor T. 2023. Stochastic motion
    and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome.
    Science. 380(6652), 1357–1362.
  mla: Brückner, David, et al. “Stochastic Motion and Transcriptional Dynamics of
    Pairs of Distal DNA Loci on a Compacted Chromosome.” <i>Science</i>, vol. 380,
    no. 6652, American Association for the Advancement of Science, 2023, pp. 1357–62,
    doi:<a href="https://doi.org/10.1126/science.adf5568">10.1126/science.adf5568</a>.
  short: D. Brückner, H. Chen, L. Barinov, B. Zoller, T. Gregor, Science 380 (2023)
    1357–1362.
date_created: 2023-07-23T22:01:12Z
date_published: 2023-06-29T00:00:00Z
date_updated: 2023-12-13T11:41:07Z
day: '29'
department:
- _id: EdHa
doi: 10.1126/science.adf5568
external_id:
  isi:
  - '001106405600028'
intvolume: '       380'
isi: 1
issue: '6652'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1126/science.adf5568
month: '06'
oa: 1
oa_version: Preprint
page: 1357-1362
project:
- _id: 34e2a5b5-11ca-11ed-8bc3-b2265616ef0b
  grant_number: 343-2022
  name: A mechano-chemical theory for stem cell fate decisions in organoid development
publication: Science
publication_identifier:
  eissn:
  - 1095-9203
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Stochastic motion and transcriptional dynamics of pairs of distal DNA loci
  on a compacted chromosome
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 380
year: '2023'
...