---
OA_place: publisher
OA_type: hybrid
_id: '21408'
abstract:
- lang: eng
text: Rational design strategies for self-assembly require a detailed understanding
of both the equilibrium state and the assembly kinetics. While the former is starting
to be well understood, the latter remains a major theoretical challenge, especially
in programmable systems and the so-called semi-addressable regime, where binding
is often nondeterministic and the formation of off-target structures negatively
influences the assembly. Here, we show that it is possible to simultaneously sculpt
the assembly outcome and the assembly kinetics through the underexplored design
space of binding energies and particle concentrations. By formulating the assembly
process as a complex reaction network, we calculate and optimize the tradeoff
between assembly speed and quality and show that parameter optimization can speed
up assembly by many orders of magnitude without lowering the yield of the target
structure. Although the exact speedup varies from design to design, we find the
largest speedups for nondeterministic systems where unoptimized assembly is the
slowest, sometimes even making them assemble faster than optimized, fully addressable
designs. Therefore, these results not only solve a key challenge in semi-addressable
self-assembly but further emphasize the utility of semi-addressability, where
designs have the potential to be faster as well as cheaper (fewer particle species)
and better (higher yield). More broadly, our results highlight the importance
of parameter optimization in programmable self-assembly and provide practical
tools for simultaneous optimization of kinetics and yield in a wide range of systems.
acknowledgement: The research was supported by the Gesellschaft für Forschungsförderung
Niederösterreich under Project No. FTI23-G-011.
article_number: '084904'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Maximilian
full_name: Hübl, Maximilian
id: 5eb8629e-15b2-11ec-abd3-e6f3e5e01f32
last_name: Hübl
- 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: Hübl M, Goodrich CP. Simultaneous optimization of assembly time and yield in
programmable self-assembly. Journal of Chemical Physics. 2026;164(8). doi:10.1063/5.0304731
apa: Hübl, M., & Goodrich, C. P. (2026). Simultaneous optimization of assembly
time and yield in programmable self-assembly. Journal of Chemical Physics.
AIP Publishing. https://doi.org/10.1063/5.0304731
chicago: Hübl, Maximilian, and Carl Peter Goodrich. “Simultaneous Optimization of
Assembly Time and Yield in Programmable Self-Assembly.” Journal of Chemical
Physics. AIP Publishing, 2026. https://doi.org/10.1063/5.0304731.
ieee: M. Hübl and C. P. Goodrich, “Simultaneous optimization of assembly time and
yield in programmable self-assembly,” Journal of Chemical Physics, vol.
164, no. 8. AIP Publishing, 2026.
ista: Hübl M, Goodrich CP. 2026. Simultaneous optimization of assembly time and
yield in programmable self-assembly. Journal of Chemical Physics. 164(8), 084904.
mla: Hübl, Maximilian, and Carl Peter Goodrich. “Simultaneous Optimization of Assembly
Time and Yield in Programmable Self-Assembly.” Journal of Chemical Physics,
vol. 164, no. 8, 084904, AIP Publishing, 2026, doi:10.1063/5.0304731.
short: M. Hübl, C.P. Goodrich, Journal of Chemical Physics 164 (2026).
corr_author: '1'
date_created: 2026-03-08T23:01:45Z
date_published: 2026-02-28T00:00:00Z
date_updated: 2026-03-09T10:40:41Z
day: '28'
ddc:
- '540'
department:
- _id: CaGo
- _id: GradSch
doi: 10.1063/5.0304731
external_id:
arxiv:
- '2510.07876'
file:
- access_level: open_access
checksum: 9bdb8870930e83edb973408da3038559
content_type: application/pdf
creator: dernst
date_created: 2026-03-09T10:38:55Z
date_updated: 2026-03-09T10:38:55Z
file_id: '21415'
file_name: 2026_JourChemPhysics_Huebl.pdf
file_size: 6903766
relation: main_file
success: 1
file_date_updated: 2026-03-09T10:38:55Z
has_accepted_license: '1'
intvolume: ' 164'
issue: '8'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 8dd93da8-16d5-11f0-9cad-d2c70200d9a5
grant_number: FTI23-G-011
name: Dynamically reconfigurable self-assembly with triangular DNA-origami bricks
publication: Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Simultaneous optimization of assembly time and yield in programmable self-assembly
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 164
year: '2026'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '21482'
abstract:
- lang: eng
text: Controlling the size and shape of assembled structures is a fundamental challenge
in self-assembly and is highly relevant in material design and biology. Here,
we show that specific but promiscuous short-range binding interactions make it
possible to economically assemble linear filaments of user-defined length. Our
approach leads to independent control over the mean and width of the filament
size distribution and allows us to smoothly explore design trade-offs between
assembly quality (spread in size) and cost (number of particle species). We employ
a simple hierarchical assembly protocol to minimize assembly times and show that
multiple stages of hierarchy make it possible to extend our approach to the assembly
of higher-dimensional structures. Our work provides a conceptually simple solution
to size control that is applicable to a broad range of systems, from DNA nanoparticles
to supramolecular polymers and beyond.
acknowledgement: We thank Maitane Muñoz-Basagoiti for helpful discussions. The research
was supported by the Gesellschaft für Forschungsförderung Niederösterreich under
Project No. FTI23-G-011.
article_number: L012054
article_processing_charge: Yes
article_type: original
author:
- first_name: Maximilian
full_name: Hübl, Maximilian
id: 5eb8629e-15b2-11ec-abd3-e6f3e5e01f32
last_name: Hübl
- 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: Hübl M, Goodrich CP. Entropic size control of self-assembled filaments. Physical
Review Research. 2026;8. doi:10.1103/68rs-3qgn
apa: Hübl, M., & Goodrich, C. P. (2026). Entropic size control of self-assembled
filaments. Physical Review Research. American Physical Society. https://doi.org/10.1103/68rs-3qgn
chicago: Hübl, Maximilian, and Carl Peter Goodrich. “Entropic Size Control of Self-Assembled
Filaments.” Physical Review Research. American Physical Society, 2026.
https://doi.org/10.1103/68rs-3qgn.
ieee: M. Hübl and C. P. Goodrich, “Entropic size control of self-assembled filaments,”
Physical Review Research, vol. 8. American Physical Society, 2026.
ista: Hübl M, Goodrich CP. 2026. Entropic size control of self-assembled filaments.
Physical Review Research. 8, L012054.
mla: Hübl, Maximilian, and Carl Peter Goodrich. “Entropic Size Control of Self-Assembled
Filaments.” Physical Review Research, vol. 8, L012054, American Physical
Society, 2026, doi:10.1103/68rs-3qgn.
short: M. Hübl, C.P. Goodrich, Physical Review Research 8 (2026).
corr_author: '1'
date_created: 2026-03-23T14:58:31Z
date_published: 2026-03-05T00:00:00Z
date_updated: 2026-03-23T15:59:11Z
day: '05'
ddc:
- '530'
department:
- _id: CaGo
- _id: GradSch
doi: 10.1103/68rs-3qgn
file:
- access_level: open_access
checksum: 6d8a68e4a19f8dad5abdf75f72316f3d
content_type: application/pdf
creator: dernst
date_created: 2026-03-23T15:53:29Z
date_updated: 2026-03-23T15:53:29Z
file_id: '21493'
file_name: 2026_PhysicalReviewResearch_Huebl.pdf
file_size: 2680924
relation: main_file
success: 1
file_date_updated: 2026-03-23T15:53:29Z
has_accepted_license: '1'
intvolume: ' 8'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 8dd93da8-16d5-11f0-9cad-d2c70200d9a5
grant_number: FTI23-G-011
name: Dynamically reconfigurable self-assembly with triangular DNA-origami bricks
publication: Physical Review Research
publication_identifier:
eissn:
- 2643-1564
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Entropic size control of self-assembled filaments
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '21006'
abstract:
- lang: eng
text: Modern experimental methods in programmable self-assembly make it possible
to precisely design particle concentrations, shapes and interactions. However,
more physical insight is needed before we can take full advantage of this vast
design space to assemble nanostructures with complex form and function. Here we
show how a substantial part of this design space can be quickly and comprehensively
understood by identifying a class of thermodynamic constraints that act on it.
These thermodynamic constraints form a high-dimensional convex polyhedron that
determines which nanostructures can be assembled at high equilibrium yield and
reveals limitations that govern the coexistence of structures. We validate our
predictions through detailed, quantitative assembly experiments of nanoscale particles
synthesized using DNA origami. Our results uncover physical relationships underpinning
many-component programmable self-assembly in equilibrium and form the basis for
robust inverse design, applicable to various systems from biological protein complexes
to synthetic nanomachines.
acknowledgement: We thank B. Isaac and A. Tiano for their technical support with the
electron microscopy and S. Waitukaitis for helpful comments on the manuscript. The
TEM images were prepared and imaged at the Brandeis Electron Microscopy facility.
This work was supported by the Gesellschaft für Forschungsförderung Niederösterreich
under project FTI23-G-011 (M.C.H. and C.P.G.), the Brandeis University Materials
Research Science and Engineering Center (MRSEC) under grant number NSF DMR-2011846
(T.E.V., D.H. and W.B.R.) and the Smith Family Foundation (W.B.R.). Open access
funding provided by Institute of Science and Technology (IST Austria).
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Maximilian
full_name: Hübl, Maximilian
id: 5eb8629e-15b2-11ec-abd3-e6f3e5e01f32
last_name: Hübl
- first_name: Thomas E.
full_name: Videbæk, Thomas E.
last_name: Videbæk
- first_name: Daichi
full_name: Hayakawa, Daichi
last_name: Hayakawa
- first_name: W. Benjamin
full_name: Rogers, W. Benjamin
last_name: Rogers
- 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: Hübl M, Videbæk TE, Hayakawa D, Rogers WB, Goodrich CP. A polyhedral structure
controls programmable self-assembly. Nature Physics. 2026. doi:10.1038/s41567-025-03120-3
apa: Hübl, M., Videbæk, T. E., Hayakawa, D., Rogers, W. B., & Goodrich, C. P.
(2026). A polyhedral structure controls programmable self-assembly. Nature
Physics. Springer Nature. https://doi.org/10.1038/s41567-025-03120-3
chicago: Hübl, Maximilian, Thomas E. Videbæk, Daichi Hayakawa, W. Benjamin Rogers,
and Carl Peter Goodrich. “A Polyhedral Structure Controls Programmable Self-Assembly.”
Nature Physics. Springer Nature, 2026. https://doi.org/10.1038/s41567-025-03120-3.
ieee: M. Hübl, T. E. Videbæk, D. Hayakawa, W. B. Rogers, and C. P. Goodrich, “A
polyhedral structure controls programmable self-assembly,” Nature Physics.
Springer Nature, 2026.
ista: Hübl M, Videbæk TE, Hayakawa D, Rogers WB, Goodrich CP. 2026. A polyhedral
structure controls programmable self-assembly. Nature Physics.
mla: Hübl, Maximilian, et al. “A Polyhedral Structure Controls Programmable Self-Assembly.”
Nature Physics, Springer Nature, 2026, doi:10.1038/s41567-025-03120-3.
short: M. Hübl, T.E. Videbæk, D. Hayakawa, W.B. Rogers, C.P. Goodrich, Nature Physics
(2026).
corr_author: '1'
date_created: 2026-01-20T10:02:19Z
date_published: 2026-01-08T00:00:00Z
date_updated: 2026-04-28T11:56:45Z
day: '08'
ddc:
- '570'
- '540'
department:
- _id: CaGo
- _id: GradSch
doi: 10.1038/s41567-025-03120-3
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41567-025-03120-3
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 8dd93da8-16d5-11f0-9cad-d2c70200d9a5
grant_number: FTI23-G-011
name: Dynamically reconfigurable self-assembly with triangular DNA-origami bricks
publication: Nature Physics
publication_identifier:
eissn:
- 1745-2481
issn:
- 1745-2473
publication_status: epub_ahead
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on ISTA website
relation: press_release
url: https://ista.ac.at/en/news/behind-natures-blueprints/
scopus_import: '1'
status: public
title: A polyhedral structure controls programmable self-assembly
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2026'
...
---
OA_place: repository
OA_type: green
_id: '19067'
abstract:
- lang: eng
text: Modern experimental methods enable the creation of self-assembly building
blocks with tunable interactions, but optimally exploiting this tunability for
the self-assembly of desired structures remains an important challenge. Many studies
of this inverse problem start with the so-called fully addressable limit, where
every particle in a target structure is different. This leads to clear design
principles that often result in high assembly yield, but it is not a scalable
approach—at some point, one must grapple with “reusing” building blocks, which
lowers the degree of addressability and may cause a multitude of off-target structures
to form, complicating the design process. Here, we solve a key obstacle preventing
robust inverse design in the “semiaddressable regime” by developing a highly efficient
algorithm that enumerates all structures that can be formed from a given set of
building blocks. By combining this with established partition-function-based yield
calculations, we show that it is almost always possible to find economical semiaddressable
designs where the entropic gain from reusing building blocks outweighs the presence
of off-target structures and even increases the yield of the target. Thus, not
only does our enumeration algorithm enable robust and scalable inverse design
in the semiaddressable regime, our results demonstrate that it is possible to
operate in this regime while maintaining the level of control often associated
with full addressability.
acknowledgement: We thank Daichi Hayakawa, Thomas E. Videbæk, and W. Benjamin Rogers
for important discussions and Jérémie Palacci, Anđela Šarić, and Scott Waitukaitis
for helpful comments on the manuscript. The research was supported by the Gesellschaft
für Forschungsförderung Niederösterreich under Project No. FTI23-G-011.
article_number: '058204'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Maximilian
full_name: Hübl, Maximilian
id: 5eb8629e-15b2-11ec-abd3-e6f3e5e01f32
last_name: Hübl
- 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: Hübl M, Goodrich CP. Accessing semiaddressable self-assembly with efficient
structure enumeration. Physical Review Letters. 2025;134(5). doi:10.1103/PhysRevLett.134.058204
apa: Hübl, M., & Goodrich, C. P. (2025). Accessing semiaddressable self-assembly
with efficient structure enumeration. Physical Review Letters. American
Physical Society. https://doi.org/10.1103/PhysRevLett.134.058204
chicago: Hübl, Maximilian, and Carl Peter Goodrich. “Accessing Semiaddressable Self-Assembly
with Efficient Structure Enumeration.” Physical Review Letters. American
Physical Society, 2025. https://doi.org/10.1103/PhysRevLett.134.058204.
ieee: M. Hübl and C. P. Goodrich, “Accessing semiaddressable self-assembly with
efficient structure enumeration,” Physical Review Letters, vol. 134, no.
5. American Physical Society, 2025.
ista: Hübl M, Goodrich CP. 2025. Accessing semiaddressable self-assembly with efficient
structure enumeration. Physical Review Letters. 134(5), 058204.
mla: Hübl, Maximilian, and Carl Peter Goodrich. “Accessing Semiaddressable Self-Assembly
with Efficient Structure Enumeration.” Physical Review Letters, vol. 134,
no. 5, 058204, American Physical Society, 2025, doi:10.1103/PhysRevLett.134.058204.
short: M. Hübl, C.P. Goodrich, Physical Review Letters 134 (2025).
corr_author: '1'
date_created: 2025-02-23T23:01:55Z
date_published: 2025-02-07T00:00:00Z
date_updated: 2025-09-30T10:35:47Z
day: '07'
department:
- _id: CaGo
- _id: GradSch
doi: 10.1103/PhysRevLett.134.058204
external_id:
arxiv:
- '2405.13567'
isi:
- '001454696800003'
pmid:
- '39983190'
intvolume: ' 134'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2405.13567
month: '02'
oa: 1
oa_version: Preprint
pmid: 1
project:
- _id: 8dd93da8-16d5-11f0-9cad-d2c70200d9a5
grant_number: FTI23-G-011
name: Dynamically reconfigurable self-assembly with triangular DNA-origami bricks
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/mxhbl/Roly.jl
scopus_import: '1'
status: public
title: Accessing semiaddressable self-assembly with efficient structure enumeration
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 134
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '21237'
abstract:
- lang: eng
text: Intelligent soft matter lies at the intersection of materials science, physics,
and cognitive science, promising to change how we design and interact with materials.
This transformative field aims to create materials with life-like capabilities,
such as perception, learning, memory, and adaptive behavior. Unlike traditional
materials, which typically perform static or predefined functions, intelligent
soft matter can dynamically interact with its environment, integrating multiple
sensory inputs, retaining past experiences, and making decisions to optimize its
responses. Inspired by biological systems, these materials leverage the inherent
properties of soft matter such as flexibility, adaptability, and responsiveness
to perform functions that mimic cognitive processes. By synthesizing current research
trends and projecting their evolution, we present a forward-looking perspective
on how intelligent soft matter could be constructed, with the aim of inspiring
innovations in areas such as biomedical devices, adaptive robotics, and beyond.
We highlight new pathways for integrating sensing, memory and actuation with low-power
internal operations, and we discuss key challenges in realizing materials that
exhibit truly “intelligent behavior”. These approaches outline a path toward more
robust, versatile, and scalable materials that can potentially act, compute, and
“think” through their inherent intrinsic material properties—moving beyond traditional
smart technologies that rely on external control.
acknowledgement: 'The work is the result of the SoftComp Topical workshop on Intelligent
Soft Matter, Salou 2025 (https://softmat.net/intelligent-soft-matter/) financed
by SoftComp Network of Excellence (https://eu-softcomp.net/). Various AI tools were
used for preparation of the manuscript: language models Google Gemini 2.0 series
and Discovery Engine (https://explore-the-unknown.vercel.app) for literature processing,
structuring contributions, finding concept overlaps and summarizing according to
procedure explained in https://github.com/vbaulin/IntelliDE/.'
article_processing_charge: No
article_type: review
author:
- first_name: Vladimir A.
full_name: Baulin, Vladimir A.
last_name: Baulin
- first_name: Achille
full_name: Giacometti, Achille
last_name: Giacometti
- first_name: Dmitry A.
full_name: Fedosov, Dmitry A.
last_name: Fedosov
- first_name: Stephen
full_name: Ebbens, Stephen
last_name: Ebbens
- first_name: Nydia R.
full_name: Varela-Rosales, Nydia R.
last_name: Varela-Rosales
- first_name: Neus
full_name: Feliu, Neus
last_name: Feliu
- first_name: Mithun
full_name: Chowdhury, Mithun
last_name: Chowdhury
- first_name: Minghan
full_name: Hu, Minghan
last_name: Hu
- first_name: Rudolf
full_name: Füchslin, Rudolf
last_name: Füchslin
- first_name: Marjolein
full_name: Dijkstra, Marjolein
last_name: Dijkstra
- first_name: Matan
full_name: Mussel, Matan
last_name: Mussel
- first_name: René
full_name: van Roij, René
last_name: van Roij
- first_name: Dong
full_name: Xie, Dong
last_name: Xie
- first_name: Vassil
full_name: Tzanov, Vassil
last_name: Tzanov
- first_name: Mengjie
full_name: Zu, Mengjie
id: 26dd9e7c-e86a-11eb-a854-82ac731c9ae2
last_name: Zu
- first_name: Samuel
full_name: Hidalgo-Caballero, Samuel
last_name: Hidalgo-Caballero
- first_name: Ye
full_name: Yuan, Ye
last_name: Yuan
- first_name: Luca
full_name: Cocconi, Luca
last_name: Cocconi
- first_name: Cheol-Min
full_name: Ghim, Cheol-Min
last_name: Ghim
- first_name: Cécile
full_name: Cottin-Bizonne, Cécile
last_name: Cottin-Bizonne
- first_name: M. Carmen
full_name: Miguel, M. Carmen
last_name: Miguel
- first_name: Maria Jose
full_name: Esplandiu, Maria Jose
last_name: Esplandiu
- first_name: Juliane
full_name: Simmchen, Juliane
last_name: Simmchen
- first_name: Wolfgang J.
full_name: Parak, Wolfgang J.
last_name: Parak
- first_name: Marco
full_name: Werner, Marco
last_name: Werner
- first_name: Gerhard
full_name: Gompper, Gerhard
last_name: Gompper
- first_name: Martin M.
full_name: Hanczyc, Martin M.
last_name: Hanczyc
citation:
ama: 'Baulin VA, Giacometti A, Fedosov DA, et al. Intelligent soft matter: Towards
embodied intelligence. Soft Matter. 2025;(21):4129-4145. doi:10.1039/d5sm00174a'
apa: 'Baulin, V. A., Giacometti, A., Fedosov, D. A., Ebbens, S., Varela-Rosales,
N. R., Feliu, N., … Hanczyc, M. M. (2025). Intelligent soft matter: Towards embodied
intelligence. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/d5sm00174a'
chicago: 'Baulin, Vladimir A., Achille Giacometti, Dmitry A. Fedosov, Stephen Ebbens,
Nydia R. Varela-Rosales, Neus Feliu, Mithun Chowdhury, et al. “Intelligent Soft
Matter: Towards Embodied Intelligence.” Soft Matter. Royal Society of Chemistry,
2025. https://doi.org/10.1039/d5sm00174a.'
ieee: 'V. A. Baulin et al., “Intelligent soft matter: Towards embodied intelligence,”
Soft Matter, no. 21. Royal Society of Chemistry, pp. 4129–4145, 2025.'
ista: 'Baulin VA, Giacometti A, Fedosov DA, Ebbens S, Varela-Rosales NR, Feliu N,
Chowdhury M, Hu M, Füchslin R, Dijkstra M, Mussel M, van Roij R, Xie D, Tzanov
V, Zu M, Hidalgo-Caballero S, Yuan Y, Cocconi L, Ghim C-M, Cottin-Bizonne C, Miguel
MC, Esplandiu MJ, Simmchen J, Parak WJ, Werner M, Gompper G, Hanczyc MM. 2025.
Intelligent soft matter: Towards embodied intelligence. Soft Matter. (21), 4129–4145.'
mla: 'Baulin, Vladimir A., et al. “Intelligent Soft Matter: Towards Embodied Intelligence.”
Soft Matter, no. 21, Royal Society of Chemistry, 2025, pp. 4129–45, doi:10.1039/d5sm00174a.'
short: V.A. Baulin, A. Giacometti, D.A. Fedosov, S. Ebbens, N.R. Varela-Rosales,
N. Feliu, M. Chowdhury, M. Hu, R. Füchslin, M. Dijkstra, M. Mussel, R. van Roij,
D. Xie, V. Tzanov, M. Zu, S. Hidalgo-Caballero, Y. Yuan, L. Cocconi, C.-M. Ghim,
C. Cottin-Bizonne, M.C. Miguel, M.J. Esplandiu, J. Simmchen, W.J. Parak, M. Werner,
G. Gompper, M.M. Hanczyc, Soft Matter (2025) 4129–4145.
date_created: 2026-02-16T15:03:08Z
date_published: 2025-06-07T00:00:00Z
date_updated: 2026-02-17T11:27:48Z
day: '07'
department:
- _id: CaGo
doi: 10.1039/d5sm00174a
external_id:
pmid:
- '40358970'
issue: '21'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprints.whiterose.ac.uk/id/eprint/226553/4/Perspective_v6_clean.pdf
month: '06'
oa: 1
oa_version: Submitted Version
page: 4129-4145
pmid: 1
publication: Soft Matter
publication_identifier:
eissn:
- 1744-6848
issn:
- 1744-683X
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
status: public
title: 'Intelligent soft matter: Towards embodied intelligence'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '19856'
abstract:
- lang: eng
text: Unlike in crystals, it is difficult to trace emergent material properties
of amorphous solids to their underlying structure. Nevertheless, one can tune
features of a disordered spring network, ranging from bulk elastic constants to
specific allosteric responses, through highly precise alterations of the structure.
This has been understood through the notion of independent bond-level response—the
observation that, in many cases, different springs have different effects on different
properties. While this idea has motivated inverse design in numerous contexts,
it has not been formalized and quantified in a general context that not just informs
but enables and predicts inverse design. Here, we show how to quantify independent
response by linearizing the simultaneous change in multiple emergent features,
and introduce the much stronger notion of fully independent response. Remarkably,
we find that the mechanical properties of disordered solids are always fully independent
across a wide array of scenarios, regardless of the target features, tunable parameters,
system size, dimensionality, and class of interactions. Furthermore, our formulation
quantifies the susceptibility of features to parameter changes, which is correlated
with the maximum linear tunability. We also demonstrate the implications for multifeature
inverse design beyond the linear regime. These results formalize our understanding
of a key fundamental difference between ordered and disordered solids while also
creating a practical tool to both understand and perform inverse design.
acknowledgement: We gratefully acknowledge Edouard Hannezo for helpful comments on
the manuscript. The work was funded by the Institute of Science and Technology Austria.
article_number: '238201'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Mengjie
full_name: Zu, Mengjie
id: 26dd9e7c-e86a-11eb-a854-82ac731c9ae2
last_name: Zu
- first_name: Aayush A
full_name: Desai, Aayush A
id: 502cfd30-32c1-11ee-a9a4-d8dad5c6739e
last_name: Desai
- 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: Zu M, Desai AA, Goodrich CP. Fully independent response in disordered solids.
Physical Review Letters. 2025;134(23). doi:10.1103/PhysRevLett.134.238201
apa: Zu, M., Desai, A. A., & Goodrich, C. P. (2025). Fully independent response
in disordered solids. Physical Review Letters. American Physical Society.
https://doi.org/10.1103/PhysRevLett.134.238201
chicago: Zu, Mengjie, Aayush A Desai, and Carl Peter Goodrich. “Fully Independent
Response in Disordered Solids.” Physical Review Letters. American Physical
Society, 2025. https://doi.org/10.1103/PhysRevLett.134.238201.
ieee: M. Zu, A. A. Desai, and C. P. Goodrich, “Fully independent response in disordered
solids,” Physical Review Letters, vol. 134, no. 23. American Physical Society,
2025.
ista: Zu M, Desai AA, Goodrich CP. 2025. Fully independent response in disordered
solids. Physical Review Letters. 134(23), 238201.
mla: Zu, Mengjie, et al. “Fully Independent Response in Disordered Solids.” Physical
Review Letters, vol. 134, no. 23, 238201, American Physical Society, 2025,
doi:10.1103/PhysRevLett.134.238201.
short: M. Zu, A.A. Desai, C.P. Goodrich, Physical Review Letters 134 (2025).
corr_author: '1'
date_created: 2025-06-22T22:02:06Z
date_published: 2025-06-13T00:00:00Z
date_updated: 2026-04-28T13:28:02Z
day: '13'
ddc:
- '530'
department:
- _id: CaGo
- _id: IlCa
doi: 10.1103/PhysRevLett.134.238201
external_id:
arxiv:
- '2412.05031'
isi:
- '001509005900006'
file:
- access_level: open_access
checksum: 040b6779c91aac62c15a9b2cc417b360
content_type: application/pdf
creator: dernst
date_created: 2025-06-23T11:41:08Z
date_updated: 2025-06-23T11:41:08Z
file_id: '19874'
file_name: 2025_PhysReviewLetters_Zu.pdf
file_size: 1132625
relation: main_file
success: 1
file_date_updated: 2025-06-23T11:41:08Z
has_accepted_license: '1'
intvolume: ' 134'
isi: 1
issue: '23'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
link:
- description: News on ISTA website
relation: press_release
url: https://ista.ac.at/en/news/infinite-diversity-in-infinite-combinations/
scopus_import: '1'
status: public
title: Fully independent response in disordered solids
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 134
year: '2025'
...
---
APC_amount: 5599.52 EUR
OA_place: publisher
OA_type: hybrid
_id: '20727'
abstract:
- lang: eng
text: Acoustic levitation provides a unique method for manipulating small particles
as it completely evades effects from gravity, container walls, or physical handling.
These advantages make it a tantalizing platform for studying complex phenomena
in many-particle systems. In most standing-wave traps, however, particles interact
via acoustic scattering forces that cause them to merge into a single dense object.
Here, we introduce a complementary approach that combines acoustic levitation
with electrostatic charging to assemble, adapt, and activate complex, separated
many-particle systems. The key idea is to superimpose electrostatic repulsion
on the intrinsic acoustic attraction, rendering a so-called “mermaid” potential
where interactions are attractive at short range and repulsive at long range.
By controlling the attraction–repulsion balance, we can levitate expanded structures
where all particles are separated, collapsed structures where they are in contact,
and hybrid ones consisting of both expanded and collapsed components. We find
that collapsed and expanded structures are inherently stable, whereas hybrid ones
exhibit transient stability governed by acoustically unstable dimers. Furthermore,
we show how electrostatics allow us to adapt between configurations on the fly,
either by quasistatic discharge or discrete up/down charge steps. Finally, we
demonstrate how large structures experience selective energy pumping from the
acoustic field—thrusting some particles into motion while others remain stationary—leading
to complex dynamics including coupled rotations and oscillations. Our approach
establishes a design space beyond acoustic collapse, offering possibilities to
study many-particle systems with complex interactions, while suggesting pathways
toward scalable integration into materials processing and other applications.
acknowledged_ssus:
- _id: M-Shop
acknowledgement: We thank Dustin Kleckner, Jack-William Barotta, and Daniel M. Harris
for insightful discussions. We acknowledge the Miba machine shop at the Institute
of Science and Technology Austria for instrumentation support. M.C.H. and C.P.G.
acknowledge funding by the Gesellschaft für Forschungsförderung Niederösterreich
under project FTI23-G-011.
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: Sue
full_name: Shi, Sue
id: 5c5b9247-15b2-11ec-abd3-fd958715639c
last_name: Shi
- first_name: Maximilian
full_name: Hübl, Maximilian
id: 5eb8629e-15b2-11ec-abd3-e6f3e5e01f32
last_name: Hübl
- first_name: Galien M
full_name: Grosjean, Galien M
id: 0C5FDA4A-9CF6-11E9-8939-FF05E6697425
last_name: Grosjean
orcid: 0000-0001-5154-417X
- 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: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
citation:
ama: Shi S, Hübl M, Grosjean GM, Goodrich CP, Waitukaitis SR. Electrostatics overcome
acoustic collapse to assemble, adapt, and activate levitated matter. Proceedings
of the National Academy of Sciences. 2025;122(50):e2516865122. doi:10.1073/pnas.2516865122
apa: Shi, S., Hübl, M., Grosjean, G. M., Goodrich, C. P., & Waitukaitis, S.
R. (2025). Electrostatics overcome acoustic collapse to assemble, adapt, and activate
levitated matter. Proceedings of the National Academy of Sciences. National
Academy of Sciences. https://doi.org/10.1073/pnas.2516865122
chicago: Shi, Sue, Maximilian Hübl, Galien M Grosjean, Carl Peter Goodrich, and
Scott R Waitukaitis. “Electrostatics Overcome Acoustic Collapse to Assemble, Adapt,
and Activate Levitated Matter.” Proceedings of the National Academy of Sciences.
National Academy of Sciences, 2025. https://doi.org/10.1073/pnas.2516865122.
ieee: S. Shi, M. Hübl, G. M. Grosjean, C. P. Goodrich, and S. R. Waitukaitis, “Electrostatics
overcome acoustic collapse to assemble, adapt, and activate levitated matter,”
Proceedings of the National Academy of Sciences, vol. 122, no. 50. National
Academy of Sciences, p. e2516865122, 2025.
ista: Shi S, Hübl M, Grosjean GM, Goodrich CP, Waitukaitis SR. 2025. Electrostatics
overcome acoustic collapse to assemble, adapt, and activate levitated matter.
Proceedings of the National Academy of Sciences. 122(50), e2516865122.
mla: Shi, Sue, et al. “Electrostatics Overcome Acoustic Collapse to Assemble, Adapt,
and Activate Levitated Matter.” Proceedings of the National Academy of Sciences,
vol. 122, no. 50, National Academy of Sciences, 2025, p. e2516865122, doi:10.1073/pnas.2516865122.
short: S. Shi, M. Hübl, G.M. Grosjean, C.P. Goodrich, S.R. Waitukaitis, Proceedings
of the National Academy of Sciences 122 (2025) e2516865122.
corr_author: '1'
date_created: 2025-12-07T23:02:00Z
date_published: 2025-12-16T00:00:00Z
date_updated: 2026-05-20T08:41:15Z
day: '16'
ddc:
- '530'
department:
- _id: ScWa
- _id: CaGo
doi: 10.1073/pnas.2516865122
external_id:
arxiv:
- '2507.01739'
file:
- access_level: open_access
checksum: c40dc4c909724b9d1146636612e8821a
content_type: application/pdf
creator: dernst
date_created: 2025-12-09T12:45:53Z
date_updated: 2025-12-09T12:45:53Z
file_id: '20744'
file_name: 2025_PNAS_Shi.pdf
file_size: 10621381
relation: main_file
success: 1
file_date_updated: 2025-12-09T12:45:53Z
has_accepted_license: '1'
intvolume: ' 122'
issue: '50'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '12'
oa: 1
oa_version: Published Version
page: e2516865122
project:
- _id: 8dd93da8-16d5-11f0-9cad-d2c70200d9a5
grant_number: FTI23-G-011
name: Dynamically reconfigurable self-assembly with triangular DNA-origami bricks
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- description: News on ISTA website
relation: press_release
url: https://ista.ac.at/en/news/science-is-like-magic-just-real/
record:
- id: '20749'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Electrostatics overcome acoustic collapse to assemble, adapt, and activate
levitated matter
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 122
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '20749'
abstract:
- lang: eng
text: Datasets and code for publication "Electrostatics overcome acoustic collapse
to assemble, adapt, and activate levitated matter"
article_processing_charge: No
author:
- first_name: Sue
full_name: Shi, Sue
id: 5c5b9247-15b2-11ec-abd3-fd958715639c
last_name: Shi
citation:
ama: Shi S. Datasets and code for manuscript “Electrostatics overcome acoustic collapse
to assemble, adapt, and activate levitated matter.” 2025. doi:10.5281/ZENODO.15752991
apa: Shi, S. (2025). Datasets and code for manuscript “Electrostatics overcome acoustic
collapse to assemble, adapt, and activate levitated matter.” Zenodo. https://doi.org/10.5281/ZENODO.15752991
chicago: Shi, Sue. “Datasets and Code for Manuscript ‘Electrostatics Overcome Acoustic
Collapse to Assemble, Adapt, and Activate Levitated Matter.’” Zenodo, 2025. https://doi.org/10.5281/ZENODO.15752991.
ieee: S. Shi, “Datasets and code for manuscript ‘Electrostatics overcome acoustic
collapse to assemble, adapt, and activate levitated matter.’” Zenodo, 2025.
ista: Shi S. 2025. Datasets and code for manuscript ‘Electrostatics overcome acoustic
collapse to assemble, adapt, and activate levitated matter’, Zenodo, 10.5281/ZENODO.15752991.
mla: Shi, Sue. Datasets and Code for Manuscript “Electrostatics Overcome Acoustic
Collapse to Assemble, Adapt, and Activate Levitated Matter.” Zenodo, 2025,
doi:10.5281/ZENODO.15752991.
short: S. Shi, (2025).
contributor:
- first_name: Maximilian
id: 5eb8629e-15b2-11ec-abd3-e6f3e5e01f32
last_name: Hübl
- first_name: Galien M
id: 0C5FDA4A-9CF6-11E9-8939-FF05E6697425
last_name: Grosjean
orcid: 0000-0001-5154-417X
corr_author: '1'
date_created: 2025-12-09T13:36:16Z
date_published: 2025-11-10T00:00:00Z
date_updated: 2026-05-20T08:41:14Z
day: '10'
ddc:
- '530'
department:
- _id: ScWa
- _id: CaGo
doi: 10.5281/ZENODO.15752991
has_accepted_license: '1'
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/ZENODO.15752991
month: '11'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '20727'
relation: used_in_publication
status: public
status: public
title: Datasets and code for manuscript "Electrostatics overcome acoustic collapse
to assemble, adapt, and activate levitated matter"
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
APC_amount: 3534 EUR
OA_place: publisher
OA_type: gold
_id: '17407'
abstract:
- lang: eng
text: The ability to control forces between sub-micron-scale building blocks offers
significant potential for designing new materials through self-assembly. Traditionally,
this involves identifying a crystal structure with a desired property and then
designing building-block interactions so that it assembles spontaneously. However,
this paradigm fails for structurally disordered solids, which lack a well-defined
structure. Here, we show that disordered solids can still be treated from an inverse
self-assembly perspective by bypassing structure and directly targeting material
properties. Using the Poisson’s ratio as a primary example, we demonstrate how
differentiable programming links interaction parameters with emergent behavior,
enabling iterative training to achieve the desired Poisson’s ratio. We also tune
other properties, including pressure and local 8-fold structural order, and can
even control multiple properties simultaneously. This robust, transferable, and
scalable approach can handle a wide variety of systems and properties, demonstrating
the utility of disordered solids as a practical avenue for self-assembly platforms.
acknowledgement: We thank M. Lechner for helpful discussions.
article_number: '141'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Mengjie
full_name: Zu, Mengjie
id: 26dd9e7c-e86a-11eb-a854-82ac731c9ae2
last_name: Zu
- 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: Zu M, Goodrich CP. Designing athermal disordered solids with automatic differentiation.
Communications Materials. 2024;5. doi:10.1038/s43246-024-00583-4
apa: Zu, M., & Goodrich, C. P. (2024). Designing athermal disordered solids
with automatic differentiation. Communications Materials. Springer Nature.
https://doi.org/10.1038/s43246-024-00583-4
chicago: Zu, Mengjie, and Carl Peter Goodrich. “Designing Athermal Disordered Solids
with Automatic Differentiation.” Communications Materials. Springer Nature,
2024. https://doi.org/10.1038/s43246-024-00583-4.
ieee: M. Zu and C. P. Goodrich, “Designing athermal disordered solids with automatic
differentiation,” Communications Materials, vol. 5. Springer Nature, 2024.
ista: Zu M, Goodrich CP. 2024. Designing athermal disordered solids with automatic
differentiation. Communications Materials. 5, 141.
mla: Zu, Mengjie, and Carl Peter Goodrich. “Designing Athermal Disordered Solids
with Automatic Differentiation.” Communications Materials, vol. 5, 141,
Springer Nature, 2024, doi:10.1038/s43246-024-00583-4.
short: M. Zu, C.P. Goodrich, Communications Materials 5 (2024).
corr_author: '1'
date_created: 2024-08-11T22:01:11Z
date_published: 2024-08-01T00:00:00Z
date_updated: 2025-05-08T09:45:35Z
day: '01'
ddc:
- '530'
department:
- _id: CaGo
doi: 10.1038/s43246-024-00583-4
external_id:
arxiv:
- '2404.15101'
file:
- access_level: open_access
checksum: d6f74e242db5f46bb0e380ee23a268af
content_type: application/pdf
creator: dernst
date_created: 2024-08-12T07:56:38Z
date_updated: 2024-08-12T07:56:38Z
file_id: '17416'
file_name: 2024_CommMaterials_Zu.pdf
file_size: 9824134
relation: main_file
success: 1
file_date_updated: 2024-08-12T07:56:38Z
has_accepted_license: '1'
intvolume: ' 5'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Communications Materials
publication_identifier:
eissn:
- 2662-4443
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Designing athermal disordered solids with automatic differentiation
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2024'
...
---
_id: '14710'
abstract:
- lang: eng
text: The self-assembly of complex structures from a set of non-identical building
blocks is a hallmark of soft matter and biological systems, including protein
complexes, colloidal clusters, and DNA-based assemblies. Predicting the dependence
of the equilibrium assembly yield on the concentrations and interaction energies
of building blocks is highly challenging, owing to the difficulty of computing
the entropic contributions to the free energy of the many structures that compete
with the ground state configuration. While these calculations yield well known
results for spherically symmetric building blocks, they do not hold when the building
blocks have internal rotational degrees of freedom. Here we present an approach
for solving this problem that works with arbitrary building blocks, including
proteins with known structure and complex colloidal building blocks. Our algorithm
combines classical statistical mechanics with recently developed computational
tools for automatic differentiation. Automatic differentiation allows efficient
evaluation of equilibrium averages over configurations that would otherwise be
intractable. We demonstrate the validity of our framework by comparison to molecular
dynamics simulations of simple examples, and apply it to calculate the yield curves
for known protein complexes and for the assembly of colloidal shells.
acknowledgement: 'We thank Lucy Colwell for suggesting that we use covariance based
methods to predict contacts and Yang Hsia, Scott Boyken, Zibo Chen, and David Baker
for collaborations on designed protein complexes. We also thank Ned Wingreen for
suggesting the alternative derivation of (11). This research was supported by the
Office of Naval Research through ONR N00014-17-1-3029, the Simons Foundation the
NSF-Simons Center for Mathematical and Statistical Analysis of Biology at Harvard
(award number #1764269), the Peter B. Lewis ’55 Lewis-Sigler Institute/Genomics
Fund through the Lewis-Sigler Institute of Integrative Genomics at Princeton University,
and the National Science Foundation through the Center for the Physics of Biological
Function (PHY-1734030).'
article_number: '8328'
article_processing_charge: Yes
article_type: original
author:
- first_name: Agnese I.
full_name: Curatolo, Agnese I.
last_name: Curatolo
- first_name: Ofer
full_name: Kimchi, Ofer
last_name: Kimchi
- 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: Ryan K.
full_name: Krueger, Ryan K.
last_name: Krueger
- first_name: Michael P.
full_name: Brenner, Michael P.
last_name: Brenner
citation:
ama: Curatolo AI, Kimchi O, Goodrich CP, Krueger RK, Brenner MP. A computational
toolbox for the assembly yield of complex and heterogeneous structures. Nature
Communications. 2023;14. doi:10.1038/s41467-023-43168-4
apa: Curatolo, A. I., Kimchi, O., Goodrich, C. P., Krueger, R. K., & Brenner,
M. P. (2023). A computational toolbox for the assembly yield of complex and heterogeneous
structures. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-43168-4
chicago: Curatolo, Agnese I., Ofer Kimchi, Carl Peter Goodrich, Ryan K. Krueger,
and Michael P. Brenner. “A Computational Toolbox for the Assembly Yield of Complex
and Heterogeneous Structures.” Nature Communications. Springer Nature,
2023. https://doi.org/10.1038/s41467-023-43168-4.
ieee: A. I. Curatolo, O. Kimchi, C. P. Goodrich, R. K. Krueger, and M. P. Brenner,
“A computational toolbox for the assembly yield of complex and heterogeneous structures,”
Nature Communications, vol. 14. Springer Nature, 2023.
ista: Curatolo AI, Kimchi O, Goodrich CP, Krueger RK, Brenner MP. 2023. A computational
toolbox for the assembly yield of complex and heterogeneous structures. Nature
Communications. 14, 8328.
mla: Curatolo, Agnese I., et al. “A Computational Toolbox for the Assembly Yield
of Complex and Heterogeneous Structures.” Nature Communications, vol. 14,
8328, Springer Nature, 2023, doi:10.1038/s41467-023-43168-4.
short: A.I. Curatolo, O. Kimchi, C.P. Goodrich, R.K. Krueger, M.P. Brenner, Nature
Communications 14 (2023).
date_created: 2023-12-24T23:00:53Z
date_published: 2023-12-01T00:00:00Z
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title: A computational toolbox for the assembly yield of complex and heterogeneous
structures
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abstract:
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text: 'The inverse problem of designing component interactions to target emergent
structure is fundamental to numerous applications in biotechnology, materials
science, and statistical physics. Equally important is the inverse problem of
designing emergent kinetics, but this has received considerably less attention.
Using recent advances in automatic differentiation, we show how kinetic pathways
can be precisely designed by directly differentiating through statistical physics
models, namely free energy calculations and molecular dynamics simulations. We
consider two systems that are crucial to our understanding of structural self-assembly:
bulk crystallization and small nanoclusters. In each case, we are able to assemble
precise dynamical features. Using gradient information, we manipulate interactions
among constituent particles to tune the rate at which these systems yield specific
structures of interest. Moreover, we use this approach to learn nontrivial features
about the high-dimensional design space, allowing us to accurately predict when
multiple kinetic features can be simultaneously and independently controlled.
These results provide a concrete and generalizable foundation for studying nonstructural
self-assembly, including kinetic properties as well as other complex emergent
properties, in a vast array of systems.'
acknowledgement: We thank Agnese Curatolo, Megan Engel, Ofer Kimchi, Seong Ho Pahng,
and Roy Frostig for helpful discussions. This material is based on work supported
by NSF Graduate Research Fellowship Grant DGE1745303. This research was funded by
NSF Grant DMS-1715477, Materials Research Science and Engineering Centers Grant
DMR-1420570, and Office of Naval Research Grant N00014-17-1-3029. M.P.B. is an investigator
of the Simons Foundation.
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full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Ella M.
full_name: King, Ella M.
last_name: King
- first_name: Samuel S.
full_name: Schoenholz, Samuel S.
last_name: Schoenholz
- first_name: Ekin D.
full_name: Cubuk, Ekin D.
last_name: Cubuk
- first_name: Michael P.
full_name: Brenner, Michael P.
last_name: Brenner
citation:
ama: Goodrich CP, King EM, Schoenholz SS, Cubuk ED, Brenner MP. Designing self-assembling
kinetics with differentiable statistical physics models. Proceedings of the
National Academy of Sciences of the United States of America. 2021;118(10).
doi:10.1073/pnas.2024083118
apa: Goodrich, C. P., King, E. M., Schoenholz, S. S., Cubuk, E. D., & Brenner,
M. P. (2021). Designing self-assembling kinetics with differentiable statistical
physics models. Proceedings of the National Academy of Sciences of the United
States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2024083118
chicago: Goodrich, Carl Peter, Ella M. King, Samuel S. Schoenholz, Ekin D. Cubuk,
and Michael P. Brenner. “Designing Self-Assembling Kinetics with Differentiable
Statistical Physics Models.” Proceedings of the National Academy of Sciences
of the United States of America. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2024083118.
ieee: C. P. Goodrich, E. M. King, S. S. Schoenholz, E. D. Cubuk, and M. P. Brenner,
“Designing self-assembling kinetics with differentiable statistical physics models,”
Proceedings of the National Academy of Sciences of the United States of America,
vol. 118, no. 10. National Academy of Sciences, 2021.
ista: Goodrich CP, King EM, Schoenholz SS, Cubuk ED, Brenner MP. 2021. Designing
self-assembling kinetics with differentiable statistical physics models. Proceedings
of the National Academy of Sciences of the United States of America. 118(10),
e2024083118.
mla: Goodrich, Carl Peter, et al. “Designing Self-Assembling Kinetics with Differentiable
Statistical Physics Models.” Proceedings of the National Academy of Sciences
of the United States of America, vol. 118, no. 10, e2024083118, National Academy
of Sciences, 2021, doi:10.1073/pnas.2024083118.
short: C.P. Goodrich, E.M. King, S.S. Schoenholz, E.D. Cubuk, M.P. Brenner, Proceedings
of the National Academy of Sciences of the United States of America 118 (2021).
date_created: 2021-03-21T23:01:20Z
date_published: 2021-03-09T00:00:00Z
date_updated: 2025-05-14T10:58:42Z
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ddc:
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doi: 10.1073/pnas.2024083118
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publication: Proceedings of the National Academy of Sciences of the United States
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title: Designing self-assembling kinetics with differentiable statistical physics
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abstract:
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text: Those who aim to devise new materials with desirable properties usually examine
present methods first. However, they will find out that some approaches can exist
only conceptually without high chances to become practically useful. It seems
that a numerical technique called automatic differentiation together with increasing
supply of computational accelerators will soon shift many methods of the material
design from the category ”unimaginable” to the category ”expensive but possible”.
Approach we suggest is not an exception. Our overall goal is to have an efficient
and generalizable approach allowing to solve inverse design problems. In this
thesis we scratch its surface. We consider jammed systems of identical particles.
And ask ourselves how the shape of those particles (or the parameters codifying
it) may affect mechanical properties of the system. An indispensable part of reaching
the answer is an appropriate particle parametrization. We come up with a simple,
yet generalizable and purposeful scheme for it. Using our generalizable shape
parameterization, we simulate the formation of a solid composed of pentagonal-like
particles and measure anisotropy in the resulting elastic response. Through automatic
differentiation techniques, we directly connect the shape parameters with the
elastic response. Interestingly, for our system we find that less isotropic particles
lead to a more isotropic elastic response. Together with other results known about
our method it seems that it can be successfully generalized for different inverse
design problems.
alternative_title:
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apa: Piankov, A. (2021). Towards designer materials using customizable particle
shape. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10422
chicago: Piankov, Anton. “Towards Designer Materials Using Customizable Particle
Shape.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10422.
ieee: A. Piankov, “Towards designer materials using customizable particle shape,”
Institute of Science and Technology Austria, 2021.
ista: Piankov A. 2021. Towards designer materials using customizable particle shape.
Institute of Science and Technology Austria.
mla: Piankov, Anton. Towards Designer Materials Using Customizable Particle Shape.
Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10422.
short: A. Piankov, Towards Designer Materials Using Customizable Particle Shape,
Institute of Science and Technology Austria, 2021.
corr_author: '1'
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status: public
supervisor:
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full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
title: Towards designer materials using customizable particle shape
type: dissertation
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...