---
OA_place: publisher
OA_type: hybrid
_id: '20318'
abstract:
- lang: eng
  text: Lipid membranes and membrane deformations are a long-standing area of research
    in soft matter and biophysics. Computer simulations have complemented analytical
    and experimental approaches as one of the pillars in the field. However, setting
    up and using membrane simulations can come with barriers due to the multidisciplinary
    effort involved and the vast choice of existing simulations models. In this review,
    we introduce the non-expert reader to coarse-grained membrane simulations at the
    mesoscale. Firstly, we give a concise overview of the modelling approaches to
    study fluid membranes, together with guidance to more specialized references.
    Secondly, we provide a conceptual guide on how to develop mesoscale membrane simulations.
    Lastly, we construct a hands-on tutorial on how to apply mesoscale membrane simulations,
    by providing a pedagogical examination of membrane tether pulling, shape and mechanics
    of membrane tubes, and membrane fluctuations with three different membrane models,
    and discussing them in terms of their scope and how resource-intensive they are.
    To ease the reader's venture into the field, we provide a repository with ready-to-run
    tutorials.
acknowledgement: We thank Oded Farago, Angelo Cacciuto, Jeriann Beiter and Pietro
  Sillano for helpful discussions and a critical reading of the manuscript. MMB and
  AP acknowledge funding by the European Unions Horizon 2020 research and innovation
  programme under Marie Skłodowska-Curie Grant Agreement No. 101034413. FF acknowledges
  financial support by the NOMIS foundation. BM and AŠ acknowledge funding by ERC
  Starting Grant “NEPA” 802960. MA and AŠ acknowledge funding by the Volkswagen Foundation
  Grant Az 96727.
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Maitane
  full_name: Muñoz Basagoiti, Maitane
  id: 1a8a7950-82cd-11ed-bd4f-9624c913a607
  last_name: Muñoz Basagoiti
  orcid: 0000-0003-1483-1457
- first_name: Felix F
  full_name: Frey, Felix F
  id: a0270b37-8f1a-11ec-95c7-8e710c59a4f3
  last_name: Frey
  orcid: 0000-0001-8501-6017
- first_name: Billie
  full_name: Meadowcroft, Billie
  id: a4725fd6-932b-11ed-81e2-c098c7f37ae1
  last_name: Meadowcroft
  orcid: 0000-0003-3441-1337
- first_name: Miguel
  full_name: Santana de Freitas Amaral, Miguel
  id: 4f2d02dd-47a9-11ec-ad10-82820ed3f501
  last_name: Santana de Freitas Amaral
- first_name: Adam
  full_name: Prada, Adam
  id: a43ed60a-dd22-11ed-9bf7-b34133792ea9
  last_name: Prada
- first_name: Anđela
  full_name: Šarić, Anđela
  id: bf63d406-f056-11eb-b41d-f263a6566d8b
  last_name: Šarić
  orcid: 0000-0002-7854-2139
citation:
  ama: 'Muñoz Basagoiti M, Frey FF, Meadowcroft B, Santana de Freitas Amaral M, Prada
    A, Šarić A. A tutorial for mesoscale computer simulations of lipid membranes:
    Tether pulling, tubulation and fluctuations. <i>Soft Matter</i>. 2025;21(40):7736-7756.
    doi:<a href="https://doi.org/10.1039/d5sm00148j">10.1039/d5sm00148j</a>'
  apa: 'Muñoz Basagoiti, M., Frey, F. F., Meadowcroft, B., Santana de Freitas Amaral,
    M., Prada, A., &#38; Šarić, A. (2025). A tutorial for mesoscale computer simulations
    of lipid membranes: Tether pulling, tubulation and fluctuations. <i>Soft Matter</i>.
    Royal Society of Chemistry. <a href="https://doi.org/10.1039/d5sm00148j">https://doi.org/10.1039/d5sm00148j</a>'
  chicago: 'Muñoz Basagoiti, Maitane, Felix F Frey, Billie Meadowcroft, Miguel Santana
    de Freitas Amaral, Adam Prada, and Anđela Šarić. “A Tutorial for Mesoscale Computer
    Simulations of Lipid Membranes: Tether Pulling, Tubulation and Fluctuations.”
    <i>Soft Matter</i>. Royal Society of Chemistry, 2025. <a href="https://doi.org/10.1039/d5sm00148j">https://doi.org/10.1039/d5sm00148j</a>.'
  ieee: 'M. Muñoz Basagoiti, F. F. Frey, B. Meadowcroft, M. Santana de Freitas Amaral,
    A. Prada, and A. Šarić, “A tutorial for mesoscale computer simulations of lipid
    membranes: Tether pulling, tubulation and fluctuations,” <i>Soft Matter</i>, vol.
    21, no. 40. Royal Society of Chemistry, pp. 7736–7756, 2025.'
  ista: 'Muñoz Basagoiti M, Frey FF, Meadowcroft B, Santana de Freitas Amaral M, Prada
    A, Šarić A. 2025. A tutorial for mesoscale computer simulations of lipid membranes:
    Tether pulling, tubulation and fluctuations. Soft Matter. 21(40), 7736–7756.'
  mla: 'Muñoz Basagoiti, Maitane, et al. “A Tutorial for Mesoscale Computer Simulations
    of Lipid Membranes: Tether Pulling, Tubulation and Fluctuations.” <i>Soft Matter</i>,
    vol. 21, no. 40, Royal Society of Chemistry, 2025, pp. 7736–56, doi:<a href="https://doi.org/10.1039/d5sm00148j">10.1039/d5sm00148j</a>.'
  short: M. Muñoz Basagoiti, F.F. Frey, B. Meadowcroft, M. Santana de Freitas Amaral,
    A. Prada, A. Šarić, Soft Matter 21 (2025) 7736–7756.
corr_author: '1'
date_created: 2025-09-10T05:34:36Z
date_published: 2025-07-28T00:00:00Z
date_updated: 2025-12-30T10:16:52Z
day: '28'
ddc:
- '540'
department:
- _id: AnSa
doi: 10.1039/d5sm00148j
ec_funded: 1
external_id:
  arxiv:
  - '2502.09798'
  isi:
  - '001562846800001'
file:
- access_level: open_access
  checksum: 590bedad19b6f6d40a7ee036a056a6d9
  content_type: application/pdf
  creator: dernst
  date_created: 2025-12-30T10:16:40Z
  date_updated: 2025-12-30T10:16:40Z
  file_id: '20912'
  file_name: 2025_SoftMatter_MunozBasagoiti.pdf
  file_size: 4841140
  relation: main_file
  success: 1
file_date_updated: 2025-12-30T10:16:40Z
has_accepted_license: '1'
intvolume: '        21'
isi: 1
issue: '40'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '07'
oa: 1
oa_version: Published Version
page: 7736-7756
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
  call_identifier: H2020
  grant_number: '101034413'
  name: 'IST-BRIDGE: International postdoctoral program'
- _id: eba2549b-77a9-11ec-83b8-a81e493eae4e
  call_identifier: H2020
  grant_number: '802960'
  name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines'
- _id: 9B861AAC-BA93-11EA-9121-9846C619BF3A
  name: NOMIS Fellowship Program
- _id: eba0f67c-77a9-11ec-83b8-cc8501b3e222
  grant_number: '96752'
  name: 'The evolution of trafficking: from archaea to eukaryotes'
publication: Soft Matter
publication_identifier:
  eissn:
  - 1744-6848
  issn:
  - 1744-683X
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'A tutorial for mesoscale computer simulations of lipid membranes: Tether pulling,
  tubulation and fluctuations'
tmp:
  image: /images/cc_by_nc.png
  legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
  name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
  short: CC BY-NC (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 21
year: '2025'
...
---
_id: '14831'
abstract:
- lang: eng
  text: Catalysis, the acceleration of product formation by a substance that is left
    unchanged, typically results from multiple elementary processes, including diffusion
    of the reactants toward the catalyst, chemical steps, and release of the products.
    While efforts to design catalysts are often focused on accelerating the chemical
    reaction on the catalyst, catalysis is a global property of the catalytic cycle
    that involves all processes. These are controlled by both intrinsic parameters
    such as the composition and shape of the catalyst and extrinsic parameters such
    as the concentration of the chemical species at play. We examine here the conditions
    that catalysis imposes on the different steps of a reaction cycle and the respective
    role of intrinsic and extrinsic parameters of the system on the emergence of catalysis
    by using an approach based on first-passage times. We illustrate this approach
    for various decompositions of a catalytic cycle into elementary steps, including
    non-Markovian decompositions, which are useful when the presence and nature of
    intermediate states are a priori unknown. Our examples cover different types of
    reactions and clarify the constraints on elementary steps and the impact of species
    concentrations on catalysis.
acknowledgement: We acknowledge funding from ANR-22-CE06-0037-02. This work has received
  funding from the European Unions Horizon 2020 research and innovation program under
  the Marie Sklodowska-Curie grant agreement No. 754387.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Yann
  full_name: Sakref, Yann
  last_name: Sakref
- first_name: Maitane
  full_name: Muñoz Basagoiti, Maitane
  id: 1a8a7950-82cd-11ed-bd4f-9624c913a607
  last_name: Muñoz Basagoiti
  orcid: 0000-0003-1483-1457
- first_name: Zorana
  full_name: Zeravcic, Zorana
  last_name: Zeravcic
- first_name: Olivier
  full_name: Rivoire, Olivier
  last_name: Rivoire
citation:
  ama: Sakref Y, Muñoz Basagoiti M, Zeravcic Z, Rivoire O. On kinetic constraints
    that catalysis imposes on elementary processes. <i>The Journal of Physical Chemistry
    B</i>. 2023;127(51):10950-10959. doi:<a href="https://doi.org/10.1021/acs.jpcb.3c04627">10.1021/acs.jpcb.3c04627</a>
  apa: Sakref, Y., Muñoz Basagoiti, M., Zeravcic, Z., &#38; Rivoire, O. (2023). On
    kinetic constraints that catalysis imposes on elementary processes. <i>The Journal
    of Physical Chemistry B</i>. American Chemical Society. <a href="https://doi.org/10.1021/acs.jpcb.3c04627">https://doi.org/10.1021/acs.jpcb.3c04627</a>
  chicago: Sakref, Yann, Maitane Muñoz Basagoiti, Zorana Zeravcic, and Olivier Rivoire.
    “On Kinetic Constraints That Catalysis Imposes on Elementary Processes.” <i>The
    Journal of Physical Chemistry B</i>. American Chemical Society, 2023. <a href="https://doi.org/10.1021/acs.jpcb.3c04627">https://doi.org/10.1021/acs.jpcb.3c04627</a>.
  ieee: Y. Sakref, M. Muñoz Basagoiti, Z. Zeravcic, and O. Rivoire, “On kinetic constraints
    that catalysis imposes on elementary processes,” <i>The Journal of Physical Chemistry
    B</i>, vol. 127, no. 51. American Chemical Society, pp. 10950–10959, 2023.
  ista: Sakref Y, Muñoz Basagoiti M, Zeravcic Z, Rivoire O. 2023. On kinetic constraints
    that catalysis imposes on elementary processes. The Journal of Physical Chemistry
    B. 127(51), 10950–10959.
  mla: Sakref, Yann, et al. “On Kinetic Constraints That Catalysis Imposes on Elementary
    Processes.” <i>The Journal of Physical Chemistry B</i>, vol. 127, no. 51, American
    Chemical Society, 2023, pp. 10950–59, doi:<a href="https://doi.org/10.1021/acs.jpcb.3c04627">10.1021/acs.jpcb.3c04627</a>.
  short: Y. Sakref, M. Muñoz Basagoiti, Z. Zeravcic, O. Rivoire, The Journal of Physical
    Chemistry B 127 (2023) 10950–10959.
date_created: 2024-01-18T07:47:11Z
date_published: 2023-12-13T00:00:00Z
date_updated: 2025-04-23T13:15:17Z
day: '13'
department:
- _id: AnSa
doi: 10.1021/acs.jpcb.3c04627
external_id:
  arxiv:
  - '2312.15940'
  isi:
  - '001134068000001'
  pmid:
  - '38091487'
intvolume: '       127'
isi: 1
issue: '51'
keyword:
- Materials Chemistry
- Surfaces
- Coatings and Films
- Physical and Theoretical Chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.48550/arXiv.2312.15940
month: '12'
oa: 1
oa_version: Preprint
page: 10950-10959
pmid: 1
publication: The Journal of Physical Chemistry B
publication_identifier:
  eissn:
  - 1520-5207
  issn:
  - 1520-6106
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: On kinetic constraints that catalysis imposes on elementary processes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 127
year: '2023'
...