---
OA_place: repository
_id: '22852'
abstract:
- lang: eng
  text: "This Research Data contains supplemental videos for Chapter 4 \"Designing
    bistable nanostructures for target behavior\" of my PhD Thesis \"Biological functionality
    without biochemistry: designing nanomachines for target behavior\".\r\nSupplemental
    video 1: Video showing the transition pathway of a bistable nanostructure with
    sphere-based arms, corresponding to the Machine in Scenario 4.\r\nSupplemental
    video 2: Video showing the transition pathway of the Source in Scenario 1. The
    arm tips change sides during the transition, demonstrating that the arms pass
    through each other.\r\nSupplemental video 3: Video showing the transition pathway
    of a fully polyhedral hinge structure with unconstrained arms. Note that we only
    show the ends of the arms.\r\nSupplemental video 4: Video showing the transition
    pathway of the coupled energy-delivery reaction of a Machine (gray) and a Source
    (blue) nanostructure for the optimized parameters in Scenario 3. Note that we
    only show the ends of the arms."
acknowledged_ssus:
- _id: ScienComp
article_processing_charge: No
author:
- first_name: Andreas
  full_name: Ehrmann, Andreas
  id: eaa689ed-f6e0-11ea-865d-bd98cbcf83c2
  last_name: Ehrmann
  orcid: 0000-0002-0997-5678
citation:
  ama: Ehrmann A. Supplemental videos for Designing bistable nanostructures for target
    behavior. 2026. doi:<a href="https://doi.org/10.15479/AT-ISTA-22852">10.15479/AT-ISTA-22852</a>
  apa: Ehrmann, A. (2026). Supplemental videos for Designing bistable nanostructures
    for target behavior. Institute of Science and Technology Austria. <a href="https://doi.org/10.15479/AT-ISTA-22852">https://doi.org/10.15479/AT-ISTA-22852</a>
  chicago: Ehrmann, Andreas. “Supplemental Videos for Designing Bistable Nanostructures
    for Target Behavior.” Institute of Science and Technology Austria, 2026. <a href="https://doi.org/10.15479/AT-ISTA-22852">https://doi.org/10.15479/AT-ISTA-22852</a>.
  ieee: A. Ehrmann, “Supplemental videos for Designing bistable nanostructures for
    target behavior.” Institute of Science and Technology Austria, 2026.
  ista: Ehrmann A. 2026. Supplemental videos for Designing bistable nanostructures
    for target behavior, Institute of Science and Technology Austria, <a href="https://doi.org/10.15479/AT-ISTA-22852">10.15479/AT-ISTA-22852</a>.
  mla: Ehrmann, Andreas. <i>Supplemental Videos for Designing Bistable Nanostructures
    for Target Behavior</i>. Institute of Science and Technology Austria, 2026, doi:<a
    href="https://doi.org/10.15479/AT-ISTA-22852">10.15479/AT-ISTA-22852</a>.
  short: A. Ehrmann, (2026).
contributor:
- contributor_type: data_collector
  first_name: Andreas
  id: eaa689ed-f6e0-11ea-865d-bd98cbcf83c2
  last_name: Ehrmann
  orcid: 0000-0002-0997-5678
corr_author: '1'
date_created: 2026-09-08T11:32:53Z
date_published: 2026-09-09T00:00:00Z
date_updated: 2026-09-09T07:24:10Z
day: '09'
department:
- _id: GradSch
- _id: CaGo
- _id: EdHa
doi: 10.15479/AT-ISTA-22852
doi_confirm: '1'
file:
- access_level: open_access
  checksum: 966417b3eab49523068bb0dfba4ecc07
  content_type: video/mp4
  creator: aehrmann
  date_created: 2026-09-08T11:31:32Z
  date_updated: 2026-09-08T11:31:32Z
  file_id: '22853'
  file_name: Supplemental video 1.mp4
  file_size: 1513964
  relation: main_file
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  checksum: deddcae30875bff8e59d5dc9ee3c196f
  content_type: video/mp4
  creator: aehrmann
  date_created: 2026-09-08T11:31:37Z
  date_updated: 2026-09-08T11:31:37Z
  file_id: '22854'
  file_name: Supplemental video 2.mp4
  file_size: 2634179
  relation: main_file
  success: 1
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  checksum: 721446b7595edc670d877185637cf15c
  content_type: video/mp4
  creator: aehrmann
  date_created: 2026-09-08T11:31:42Z
  date_updated: 2026-09-08T11:31:42Z
  file_id: '22855'
  file_name: Supplemental video 3.mp4
  file_size: 2080684
  relation: main_file
  success: 1
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  checksum: da44153821aa4f8f3cbc2860ef6d1bad
  content_type: video/mp4
  creator: aehrmann
  date_created: 2026-09-08T11:31:48Z
  date_updated: 2026-09-08T11:31:48Z
  file_id: '22856'
  file_name: Supplemental video 4.mp4
  file_size: 4047831
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 1e94cd067809e1a93e21676181b4c102
  content_type: text/plain
  creator: aehrmann
  date_created: 2026-09-08T18:36:14Z
  date_updated: 2026-09-08T18:36:14Z
  file_id: '22860'
  file_name: README.txt
  file_size: 1122
  relation: main_file
  success: 1
file_date_updated: 2026-09-08T18:36:14Z
fulldoi: https://doi.org/10.15479/AT-ISTA-22852
has_accepted_license: '1'
keyword:
- functional nanostructures
- bistability
- target behavior
- transition pathway
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '09'
oa: 1
oa_version: None
project:
- _id: 90a98bb5-16d5-11f0-9cad-9675f3f8015d
  grant_number: PAT 8537123
  name: Functional bio-inspired nanomachines from sticky colloids
publisher: Institute of Science and Technology Austria
status: public
title: Supplemental videos for Designing bistable nanostructures for target behavior
tmp:
  image: /images/cc_by_nc_sa.png
  legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
  name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
    BY-NC-SA 4.0)
  short: CC BY-NC-SA (4.0)
type: research_data
user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d
year: '2026'
...
---
OA_place: publisher
_id: '22873'
acknowledged_ssus:
- _id: ScienComp
- _id: CampIT
acknowledgement: I acknowledge funding by the Austrian Science Fund (FWF) [10.55776/PAT8537123].
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Andreas
  full_name: Ehrmann, Andreas
  id: eaa689ed-f6e0-11ea-865d-bd98cbcf83c2
  last_name: Ehrmann
  orcid: 0000-0002-0997-5678
citation:
  ama: 'Ehrmann A. Biological functionality without biochemistry: Designing nanomachines
    for target behavior. 2026. doi:<a href="https://doi.org/10.15479/AT-ISTA-22873">10.15479/AT-ISTA-22873</a>'
  apa: 'Ehrmann, A. (2026). <i>Biological functionality without biochemistry: Designing
    nanomachines for target behavior</i>. Institute of Science and Technology Austria.
    <a href="https://doi.org/10.15479/AT-ISTA-22873">https://doi.org/10.15479/AT-ISTA-22873</a>'
  chicago: 'Ehrmann, Andreas. “Biological Functionality without Biochemistry: Designing
    Nanomachines for Target Behavior.” Institute of Science and Technology Austria,
    2026. <a href="https://doi.org/10.15479/AT-ISTA-22873">https://doi.org/10.15479/AT-ISTA-22873</a>.'
  ieee: 'A. Ehrmann, “Biological functionality without biochemistry: Designing nanomachines
    for target behavior,” Institute of Science and Technology Austria, 2026.'
  ista: 'Ehrmann A. 2026. Biological functionality without biochemistry: Designing
    nanomachines for target behavior. Institute of Science and Technology Austria.'
  mla: 'Ehrmann, Andreas. <i>Biological Functionality without Biochemistry: Designing
    Nanomachines for Target Behavior</i>. Institute of Science and Technology Austria,
    2026, doi:<a href="https://doi.org/10.15479/AT-ISTA-22873">10.15479/AT-ISTA-22873</a>.'
  short: 'A. Ehrmann, Biological Functionality without Biochemistry: Designing Nanomachines
    for Target Behavior, Institute of Science and Technology Austria, 2026.'
corr_author: '1'
das_tickbox: '0'
date_created: 2026-09-09T12:18:24Z
date_published: 2026-09-04T00:00:00Z
date_updated: 2026-09-18T11:28:29Z
day: '04'
ddc:
- '530'
- '600'
- '621'
- '004'
- '005'
degree_awarded: PhD
department:
- _id: GradSch
- _id: CaGo
- _id: EdHa
doi: 10.15479/AT-ISTA-22873
doi_confirm: '1'
file:
- access_level: closed
  checksum: a5e3d79e0e5f3f4fb3c414e48116dc9e
  content_type: application/pdf
  creator: aehrmann
  date_created: 2026-09-11T07:23:57Z
  date_updated: 2026-09-17T08:59:39Z
  embargo: 2027-01-15
  embargo_to: open_access
  file_id: '22901'
  file_name: 2026_Ehrmann_Andreas_Thesis.pdf
  file_size: 14782662
  relation: main_file
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  checksum: 0235b9c52fee0c97f402f1c3d4efc1eb
  content_type: application/zip
  creator: aehrmann
  date_created: 2026-09-11T07:24:14Z
  date_updated: 2026-09-11T07:24:14Z
  description: All LaTeX files to compile my PhD Thesis.
  file_id: '22902'
  file_name: thesis_latex_files.zip
  file_size: 155228
  relation: source_file
file_date_updated: 2026-09-17T08:59:39Z
fulldoi: https://doi.org/10.15479/AT-ISTA-22873
has_accepted_license: '1'
keyword:
- PhD Thesis
- functional nanomachines
- biological functionality
- nanotechnology
- energy delivery
- target behavior
- dynamics
- design principles
- optimization
- differentiable statistical physics
- machine learning
language:
- iso: eng
month: '09'
oa_version: Published Version
page: '168'
project:
- _id: 90a98bb5-16d5-11f0-9cad-9675f3f8015d
  grant_number: PAT 8537123
  name: Functional bio-inspired nanomachines from sticky colloids
publication_identifier:
  isbn:
  - 978-3-99078-092-3
  issn:
  - 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
  record:
  - id: '22893'
    relation: part_of_dissertation
    status: public
  - id: '22892'
    relation: part_of_dissertation
    status: public
researchdata_availability: upon request
status: public
supervisor:
- first_name: Carl Peter
  full_name: Goodrich, Carl Peter
  id: EB352CD2-F68A-11E9-89C5-A432E6697425
  last_name: Goodrich
  orcid: 0000-0002-1307-5074
- first_name: Edouard B
  full_name: Hannezo, Edouard B
  id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
  last_name: Hannezo
  orcid: 0000-0001-6005-1561
supplementarymaterial: not applicable
title: 'Biological functionality without biochemistry: Designing nanomachines for
  target behavior'
tmp:
  image: /images/cc_by_nc_sa.png
  legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
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    BY-NC-SA 4.0)
  short: CC BY-NC-SA (4.0)
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2026'
...
---
OA_place: repository
OA_type: green
_id: '22893'
abstract:
- lang: eng
  text: Many biological machines function through controlled conformational transitions,
    yet designing synthetic nanostructures with prescribed dynamical behavior remains
    a major challenge. Here, we develop a modular inverse-design framework for bistable
    nanostructures whose function is controlled by an energy profile along a geometric
    reaction coordinate. Inspired by proteins with rigid domains connected by flexible
    hinges, we introduce a hinge-arm paradigm in which a small bistable hinge controls
    the energetics of a conformational transition, while rigid arms map this transition
    onto the separation between external binding sites. Specifically, we ask which
    features of a target energy profile can be programmed under different design constraints.
    We find that the energy barriers and the binding-site separations in the two metastable
    states can be readily designed, while controlling the location of the transition
    state or the full shape of the energy profile requires additional design freedom.
    Using a differentiable design framework, we find that some optimized solutions
    are numerically inexact but still display the functional behavior for which the
    target profile was selected, emphasizing the importance of function-based evaluation
    criteria. These results establish a practical hierarchy of designability for bistable
    nanostructures and provide a route toward synthetic nanomachines that couple conformational
    transitions to target behavior.
acknowledgement: "We thank Maitane Muñoz-Basagoiti for stimulating\r\ndiscussions.
  This research was funded in part by the\r\nAustrian Science Fund (FWF) [10.55776/PAT8537123].\r\n"
article_processing_charge: No
arxiv: 1
author:
- first_name: Andreas
  full_name: Ehrmann, Andreas
  id: eaa689ed-f6e0-11ea-865d-bd98cbcf83c2
  last_name: Ehrmann
  orcid: 0000-0002-0997-5678
- first_name: Marija
  full_name: Krstić, Marija
  id: a8f6d1c6-3200-11ee-973b-dab948eace26
  last_name: Krstić
- first_name: Sahar
  full_name: Samadzadeh, Sahar
  id: 0099896b-5fb8-11ef-8420-b30b14627e93
  last_name: Samadzadeh
- first_name: Carl Peter
  full_name: Goodrich, Carl Peter
  id: EB352CD2-F68A-11E9-89C5-A432E6697425
  last_name: Goodrich
  orcid: 0000-0002-1307-5074
citation:
  ama: Ehrmann A, Krstić M, Samadzadeh S, Goodrich CP. Designing bistable nanostructures
    for target behavior. <i>arXiv</i>. doi:<a href="https://doi.org/10.48550/arXiv.2606.31620">10.48550/arXiv.2606.31620</a>
  apa: Ehrmann, A., Krstić, M., Samadzadeh, S., &#38; Goodrich, C. P. (n.d.). Designing
    bistable nanostructures for target behavior. <i>arXiv</i>. <a href="https://doi.org/10.48550/arXiv.2606.31620">https://doi.org/10.48550/arXiv.2606.31620</a>
  chicago: Ehrmann, Andreas, Marija Krstić, Sahar Samadzadeh, and Carl Peter Goodrich.
    “Designing Bistable Nanostructures for Target Behavior.” <i>ArXiv</i>, n.d. <a
    href="https://doi.org/10.48550/arXiv.2606.31620">https://doi.org/10.48550/arXiv.2606.31620</a>.
  ieee: A. Ehrmann, M. Krstić, S. Samadzadeh, and C. P. Goodrich, “Designing bistable
    nanostructures for target behavior,” <i>arXiv</i>. .
  ista: Ehrmann A, Krstić M, Samadzadeh S, Goodrich CP. Designing bistable nanostructures
    for target behavior. arXiv, <a href="https://doi.org/10.48550/arXiv.2606.31620">10.48550/arXiv.2606.31620</a>.
  mla: Ehrmann, Andreas, et al. “Designing Bistable Nanostructures for Target Behavior.”
    <i>ArXiv</i>, doi:<a href="https://doi.org/10.48550/arXiv.2606.31620">10.48550/arXiv.2606.31620</a>.
  short: A. Ehrmann, M. Krstić, S. Samadzadeh, C.P. Goodrich, ArXiv (n.d.).
corr_author: '1'
date_created: 2026-09-09T13:19:13Z
date_published: 2026-06-30T00:00:00Z
date_updated: 2026-09-18T11:28:28Z
day: '30'
department:
- _id: CaGo
- _id: EdHa
- _id: AnSa
doi: 10.48550/arXiv.2606.31620
external_id:
  arxiv:
  - '2606.31620'
fulldoi: https://doi.org/10.48550/arXiv.2606.31620
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
main_file_link:
- open_access: '1'
  url: https://doi.org/10.48550/arXiv.2606.31620
month: '06'
oa: 1
oa_version: Preprint
project:
- _id: 90a98bb5-16d5-11f0-9cad-9675f3f8015d
  grant_number: PAT 8537123
  name: Functional bio-inspired nanomachines from sticky colloids
publication: arXiv
publication_status: draft
related_material:
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    relation: dissertation_contains
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status: public
title: Designing bistable nanostructures for target behavior
tmp:
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  short: CC BY-NC-ND (4.0)
type: preprint
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2026'
...
---
OA_place: repository
_id: '22892'
abstract:
- lang: eng
  text: 'Countless biological processes are fueled by energy-rich molecules like ATP
    and GTP that supply energy with extreme efficiency. However, designing similar
    energy-delivery schemes from the bottom up, essential for the development of powered
    nanostructures and other \emph{de novo} machinery, presents a significant challenge:
    how can an energy-rich structure be stable in solution yet still deliver this
    energy at precisely the right time? In this paper, we present a purely physical
    mechanism that solves this challenge, facilitating energy transfer akin to ATP
    hydrolysis, yet occurring between synthetic nanostructures without any biochemical
    interactions. This targeted energy delivery is achieved by exploiting a differentiable
    state-based model to balance the energy profiles that govern the structural transitions
    in the two nanostructures, creating a coupled relaxation pathway with minimal
    barriers that facilitates energy delivery. We verify the effectiveness and robustness
    of this mechanism through Langevin Dynamics simulations, demonstrating that a
    bath of the high-energy structures can systematically and repeatedly drive the
    target structure out of equilibrium, enabling it to perform tasks. As the mechanism
    operates only through explicit physical forces without any biochemistry or internal
    state variables, our results present generic and far-reaching design principles,
    setting the stage for the next generation of synthetic nanomachines.'
acknowledgement: "We thank Edouard Hannezo, Ella King, Maximilian Lechner, and Jérémie
  Palacci for stimulating discussions, and Edouard Hannezo, Maximilian Hübl, and\r\nMaitane
  Muñoz-Basagoiti for helpful comments on the manuscript. This research was funded
  in part by the\r\nAustrian Science Fund (FWF) [10.55776/PAT8537123]."
article_processing_charge: No
arxiv: 1
author:
- first_name: Andreas
  full_name: Ehrmann, Andreas
  id: eaa689ed-f6e0-11ea-865d-bd98cbcf83c2
  last_name: Ehrmann
  orcid: 0000-0002-0997-5678
- first_name: Carl Peter
  full_name: Goodrich, Carl Peter
  id: EB352CD2-F68A-11E9-89C5-A432E6697425
  last_name: Goodrich
  orcid: 0000-0002-1307-5074
citation:
  ama: Ehrmann A, Goodrich CP. Controlling energy delivery with bistable nanostructures.
    <i>arXiv</i>. doi:<a href="https://doi.org/10.48550/arXiv.2506.14266">10.48550/arXiv.2506.14266</a>
  apa: Ehrmann, A., &#38; Goodrich, C. P. (n.d.). Controlling energy delivery with
    bistable nanostructures. <i>arXiv</i>. <a href="https://doi.org/10.48550/arXiv.2506.14266">https://doi.org/10.48550/arXiv.2506.14266</a>
  chicago: Ehrmann, Andreas, and Carl Peter Goodrich. “Controlling Energy Delivery
    with Bistable Nanostructures.” <i>ArXiv</i>, n.d. <a href="https://doi.org/10.48550/arXiv.2506.14266">https://doi.org/10.48550/arXiv.2506.14266</a>.
  ieee: A. Ehrmann and C. P. Goodrich, “Controlling energy delivery with bistable
    nanostructures,” <i>arXiv</i>. .
  ista: Ehrmann A, Goodrich CP. Controlling energy delivery with bistable nanostructures.
    arXiv, <a href="https://doi.org/10.48550/arXiv.2506.14266">10.48550/arXiv.2506.14266</a>.
  mla: Ehrmann, Andreas, and Carl Peter Goodrich. “Controlling Energy Delivery with
    Bistable Nanostructures.” <i>ArXiv</i>, doi:<a href="https://doi.org/10.48550/arXiv.2506.14266">10.48550/arXiv.2506.14266</a>.
  short: A. Ehrmann, C.P. Goodrich, ArXiv (n.d.).
corr_author: '1'
date_created: 2026-09-09T13:16:54Z
date_published: 2026-06-07T00:00:00Z
date_updated: 2026-09-18T11:28:29Z
day: '07'
department:
- _id: CaGo
- _id: EdHa
doi: 10.48550/arXiv.2506.14266
external_id:
  arxiv:
  - '2506.14266'
fulldoi: https://doi.org/10.48550/arXiv.2506.14266
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.48550/arXiv.2506.14266
month: '06'
oa: 1
oa_version: Preprint
project:
- _id: 90a98bb5-16d5-11f0-9cad-9675f3f8015d
  grant_number: PAT 8537123
  name: Functional bio-inspired nanomachines from sticky colloids
publication: arXiv
publication_status: draft
related_material:
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  - id: '22873'
    relation: dissertation_contains
    status: public
status: public
title: Controlling energy delivery with bistable nanostructures
tmp:
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  legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
  name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
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  short: CC BY-NC-ND (4.0)
type: preprint
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2026'
...