---
_id: '12667'
abstract:
- lang: eng
text: Unlike crystalline atomic and ionic solids, texture development due to crystallographically
preferred growth in colloidal crystals is less studied. Here we investigate the
underlying mechanisms of the texture evolution in an evaporation-induced colloidal
assembly process through experiments, modeling, and theoretical analysis. In this
widely used approach to obtain large-area colloidal crystals, the colloidal particles
are driven to the meniscus via the evaporation of a solvent or matrix precursor
solution where they close-pack to form a face-centered cubic colloidal assembly.
Via two-dimensional large-area crystallographic mapping, we show that the initial
crystal orientation is dominated by the interaction of particles with the meniscus,
resulting in the expected coalignment of the close-packed direction with the local
meniscus geometry. By combining with crystal structure analysis at a single-particle
level, we further reveal that, at the later stage of self-assembly, however, the
colloidal crystal undergoes a gradual rotation facilitated by geometrically necessary
dislocations (GNDs) and achieves a large-area uniform crystallographic orientation
with the close-packed direction perpendicular to the meniscus and parallel to
the growth direction. Classical slip analysis, finite element-based mechanical
simulation, computational colloidal assembly modeling, and continuum theory unequivocally
show that these GNDs result from the tensile stress field along the meniscus direction
due to the constrained shrinkage of the colloidal crystal during drying. The generation
of GNDs with specific slip systems within individual grains leads to crystallographic
rotation to accommodate the mechanical stress. The mechanistic understanding reported
here can be utilized to control crystallographic features of colloidal assemblies,
and may provide further insights into crystallographically preferred growth in
synthetic, biological, and geological crystals.
article_number: e2107588118
article_processing_charge: No
article_type: original
author:
- first_name: Ling
full_name: Li, Ling
last_name: Li
- 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: Haizhao
full_name: Yang, Haizhao
last_name: Yang
- first_name: Katherine R.
full_name: Phillips, Katherine R.
last_name: Phillips
- first_name: Zian
full_name: Jia, Zian
last_name: Jia
- first_name: Hongshun
full_name: Chen, Hongshun
last_name: Chen
- first_name: Lifeng
full_name: Wang, Lifeng
last_name: Wang
- first_name: Jinjin
full_name: Zhong, Jinjin
last_name: Zhong
- first_name: Anhua
full_name: Liu, Anhua
last_name: Liu
- first_name: Jianfeng
full_name: Lu, Jianfeng
last_name: Lu
- first_name: Jianwei
full_name: Shuai, Jianwei
last_name: Shuai
- first_name: Michael P.
full_name: Brenner, Michael P.
last_name: Brenner
- first_name: Frans
full_name: Spaepen, Frans
last_name: Spaepen
- first_name: Joanna
full_name: Aizenberg, Joanna
last_name: Aizenberg
citation:
ama: Li L, Goodrich CP, Yang H, et al. Microscopic origins of the crystallographically
preferred growth in evaporation-induced colloidal crystals. PNAS. 2021;118(32).
doi:10.1073/pnas.2107588118
apa: Li, L., Goodrich, C. P., Yang, H., Phillips, K. R., Jia, Z., Chen, H., … Aizenberg,
J. (2021). Microscopic origins of the crystallographically preferred growth in
evaporation-induced colloidal crystals. PNAS. Proceedings of the National
Academy of Sciences. https://doi.org/10.1073/pnas.2107588118
chicago: Li, Ling, Carl Peter Goodrich, Haizhao Yang, Katherine R. Phillips, Zian
Jia, Hongshun Chen, Lifeng Wang, et al. “Microscopic Origins of the Crystallographically
Preferred Growth in Evaporation-Induced Colloidal Crystals.” PNAS. Proceedings
of the National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2107588118.
ieee: L. Li et al., “Microscopic origins of the crystallographically preferred
growth in evaporation-induced colloidal crystals,” PNAS, vol. 118, no.
32. Proceedings of the National Academy of Sciences, 2021.
ista: Li L, Goodrich CP, Yang H, Phillips KR, Jia Z, Chen H, Wang L, Zhong J, Liu
A, Lu J, Shuai J, Brenner MP, Spaepen F, Aizenberg J. 2021. Microscopic origins
of the crystallographically preferred growth in evaporation-induced colloidal
crystals. PNAS. 118(32), e2107588118.
mla: Li, Ling, et al. “Microscopic Origins of the Crystallographically Preferred
Growth in Evaporation-Induced Colloidal Crystals.” PNAS, vol. 118, no.
32, e2107588118, Proceedings of the National Academy of Sciences, 2021, doi:10.1073/pnas.2107588118.
short: L. Li, C.P. Goodrich, H. Yang, K.R. Phillips, Z. Jia, H. Chen, L. Wang, J.
Zhong, A. Liu, J. Lu, J. Shuai, M.P. Brenner, F. Spaepen, J. Aizenberg, PNAS 118
(2021).
date_created: 2023-02-21T08:51:04Z
date_published: 2021-08-10T00:00:00Z
date_updated: 2023-02-23T10:45:44Z
day: '10'
ddc:
- '570'
doi: 10.1073/pnas.2107588118
extern: '1'
external_id:
pmid:
- '34341109'
file:
- access_level: open_access
checksum: 702f7ec60ce6f2815104ab649dc661a4
content_type: application/pdf
creator: dernst
date_created: 2023-02-23T10:42:07Z
date_updated: 2023-02-23T10:42:07Z
file_id: '12674'
file_name: 2021_PNAS_Li.pdf
file_size: 3275944
relation: main_file
success: 1
file_date_updated: 2023-02-23T10:42:07Z
has_accepted_license: '1'
intvolume: ' 118'
issue: '32'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: PNAS
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Microscopic origins of the crystallographically preferred growth in evaporation-induced
colloidal crystals
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: 118
year: '2021'
...
---
_id: '12767'
abstract:
- lang: eng
text: "Several problems in planning and reactive synthesis can be reduced to the
analysis of two-player quantitative graph games. Optimization is one form of analysis.
We argue that in many cases it may be better to replace the optimization problem
with the satisficing problem, where instead of searching for optimal solutions,
the goal is to search for solutions that adhere to a given threshold bound.\r\nThis
work defines and investigates the satisficing problem on a two-player graph game
with the discounted-sum cost model. We show that while the satisficing problem
can be solved using numerical methods just like the optimization problem, this
approach does not render compelling benefits over optimization. When the discount
factor is, however, an integer, we present another approach to satisficing, which
is purely based on automata methods. We show that this approach is algorithmically
more performant – both theoretically and empirically – and demonstrates the broader
applicability of satisficing over optimization."
acknowledgement: We thank anonymous reviewers for valuable inputs. This work is supported
in part by NSF grant 2030859 to the CRA for the CIFellows Project, NSF grants IIS-1527668,
CCF-1704883, IIS-1830549, the ERC CoG 863818 (ForM-SMArt), and an award from the
Maryland Procurement Office.
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Suguman
full_name: Bansal, Suguman
last_name: Bansal
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Moshe Y.
full_name: Vardi, Moshe Y.
last_name: Vardi
citation:
ama: 'Bansal S, Chatterjee K, Vardi MY. On satisficing in quantitative games. In:
27th International Conference on Tools and Algorithms for the Construction
and Analysis of Systems. Vol 12651. Springer Nature; 2021:20-37. doi:10.1007/978-3-030-72016-2_2'
apa: 'Bansal, S., Chatterjee, K., & Vardi, M. Y. (2021). On satisficing in quantitative
games. In 27th International Conference on Tools and Algorithms for the Construction
and Analysis of Systems (Vol. 12651, pp. 20–37). Luxembourg City, Luxembourg:
Springer Nature. https://doi.org/10.1007/978-3-030-72016-2_2'
chicago: Bansal, Suguman, Krishnendu Chatterjee, and Moshe Y. Vardi. “On Satisficing
in Quantitative Games.” In 27th International Conference on Tools and Algorithms
for the Construction and Analysis of Systems, 12651:20–37. Springer Nature,
2021. https://doi.org/10.1007/978-3-030-72016-2_2.
ieee: S. Bansal, K. Chatterjee, and M. Y. Vardi, “On satisficing in quantitative
games,” in 27th International Conference on Tools and Algorithms for the Construction
and Analysis of Systems, Luxembourg City, Luxembourg, 2021, vol. 12651, pp.
20–37.
ista: 'Bansal S, Chatterjee K, Vardi MY. 2021. On satisficing in quantitative games.
27th International Conference on Tools and Algorithms for the Construction and
Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis
of Systems, LNCS, vol. 12651, 20–37.'
mla: Bansal, Suguman, et al. “On Satisficing in Quantitative Games.” 27th International
Conference on Tools and Algorithms for the Construction and Analysis of Systems,
vol. 12651, Springer Nature, 2021, pp. 20–37, doi:10.1007/978-3-030-72016-2_2.
short: S. Bansal, K. Chatterjee, M.Y. Vardi, in:, 27th International Conference
on Tools and Algorithms for the Construction and Analysis of Systems, Springer
Nature, 2021, pp. 20–37.
conference:
end_date: 2021-04-01
location: Luxembourg City, Luxembourg
name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems'
start_date: 2021-03-27
date_created: 2023-03-26T22:01:09Z
date_published: 2021-03-21T00:00:00Z
date_updated: 2025-07-10T13:18:02Z
day: '21'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1007/978-3-030-72016-2_2
ec_funded: 1
external_id:
arxiv:
- '2101.02594'
file:
- access_level: open_access
checksum: b020b78b23587ce7610b1aafb4e63438
content_type: application/pdf
creator: dernst
date_created: 2023-03-28T11:00:33Z
date_updated: 2023-03-28T11:00:33Z
file_id: '12777'
file_name: 2021_LNCS_Bansal.pdf
file_size: 747418
relation: main_file
success: 1
file_date_updated: 2023-03-28T11:00:33Z
has_accepted_license: '1'
intvolume: ' 12651'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '03'
oa: 1
oa_version: Published Version
page: 20-37
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: 27th International Conference on Tools and Algorithms for the Construction
and Analysis of Systems
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783030720155'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: On satisficing in quantitative games
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: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12651
year: '2021'
...
---
_id: '12909'
article_processing_charge: No
author:
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Stefano
full_name: Elefante, Stefano
id: 490F40CE-F248-11E8-B48F-1D18A9856A87
last_name: Elefante
- first_name: Andrei
full_name: Hornoiu, Andrei
id: 77129392-B450-11EA-8745-D4653DDC885E
last_name: Hornoiu
- first_name: Stephan
full_name: Stadlbauer, Stephan
id: 4D0BC184-F248-11E8-B48F-1D18A9856A87
last_name: Stadlbauer
citation:
ama: 'Schlögl A, Elefante S, Hornoiu A, Stadlbauer S. Managing software on a heterogenous
HPC cluster. In: ASHPC21 – Austrian-Slovenian HPC Meeting 2021. University
of Ljubljana; 2021:5. doi:10.3359/2021hpc'
apa: 'Schlögl, A., Elefante, S., Hornoiu, A., & Stadlbauer, S. (2021). Managing
software on a heterogenous HPC cluster. In ASHPC21 – Austrian-Slovenian HPC
Meeting 2021 (p. 5). Virtual: University of Ljubljana. https://doi.org/10.3359/2021hpc'
chicago: Schlögl, Alois, Stefano Elefante, Andrei Hornoiu, and Stephan Stadlbauer.
“Managing Software on a Heterogenous HPC Cluster.” In ASHPC21 – Austrian-Slovenian
HPC Meeting 2021, 5. University of Ljubljana, 2021. https://doi.org/10.3359/2021hpc.
ieee: A. Schlögl, S. Elefante, A. Hornoiu, and S. Stadlbauer, “Managing software
on a heterogenous HPC cluster,” in ASHPC21 – Austrian-Slovenian HPC Meeting
2021, Virtual, 2021, p. 5.
ista: 'Schlögl A, Elefante S, Hornoiu A, Stadlbauer S. 2021. Managing software on
a heterogenous HPC cluster. ASHPC21 – Austrian-Slovenian HPC Meeting 2021. ASHPC:
Austrian-Slovenian HPC Meeting, 5.'
mla: Schlögl, Alois, et al. “Managing Software on a Heterogenous HPC Cluster.” ASHPC21
– Austrian-Slovenian HPC Meeting 2021, University of Ljubljana, 2021, p. 5,
doi:10.3359/2021hpc.
short: A. Schlögl, S. Elefante, A. Hornoiu, S. Stadlbauer, in:, ASHPC21 – Austrian-Slovenian
HPC Meeting 2021, University of Ljubljana, 2021, p. 5.
conference:
end_date: 2021-06-02
location: Virtual
name: 'ASHPC: Austrian-Slovenian HPC Meeting'
start_date: 2021-05-31
corr_author: '1'
date_created: 2023-05-05T13:17:36Z
date_published: 2021-06-02T00:00:00Z
date_updated: 2026-04-16T10:19:31Z
day: '02'
ddc:
- '000'
department:
- _id: ScienComp
doi: 10.3359/2021hpc
file:
- access_level: open_access
checksum: ba73f85858fb9d5737ebc7724646dd45
content_type: application/pdf
creator: dernst
date_created: 2023-05-16T07:36:34Z
date_updated: 2023-05-16T07:36:34Z
file_id: '12971'
file_name: 2021_ASHPC_Schloegl.pdf
file_size: 422761
relation: main_file
success: 1
file_date_updated: 2023-05-16T07:36:34Z
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://vsc.ac.at/fileadmin/user_upload/vsc/conferences/ashpc21/BOOKLET_ASHPC21.pdf
month: '06'
oa: 1
oa_version: Published Version
page: '5'
publication: ASHPC21 – Austrian-Slovenian HPC Meeting 2021
publication_identifier:
isbn:
- 978-961-6980-77-7
- 978-961-6133-48-7
publication_status: published
publisher: University of Ljubljana
status: public
title: Managing software on a heterogenous HPC cluster
type: conference_abstract
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2021'
...
---
OA_place: publisher
_id: '12987'
abstract:
- lang: eng
text: Chromosomal inversion polymorphisms, segments of chromosomes that are flipped
in orientation and occur in reversed order in some individuals, have long been
recognized to play an important role in local adaptation. They can reduce recombination
in heterozygous individuals and thus help to maintain sets of locally adapted
alleles. In a wide range of organisms, populations adapted to different habitats
differ in frequency of inversion arrangements. However, getting a full understanding
of the importance of inversions for adaptation requires confirmation of their
influence on traits under divergent selection. Here, we studied a marine snail,
Littorina saxatilis, that has evolved ecotypes adapted to wave exposure or crab
predation. These two types occur in close proximity on different parts of the
shore. Gene flow between them exists in contact zones. However, they exhibit strong
phenotypic divergence in several traits under habitat-specific selection, including
size, shape and behaviour. We used crosses between these ecotypes to identify
genomic regions that explain variation in these traits by using QTL analysis and
variance partitioning across linkage groups. We could show that previously detected
inversion regions contribute to adaptive divergence. Some inversions influenced
multiple traits suggesting that they contain sets of locally adaptive alleles.
Our study also identified regions without known inversions that are important
for phenotypic divergence. Thus, we provide a more complete overview of the importance
of inversions in relation to the remaining genome.
article_processing_charge: No
author:
- first_name: Eva
full_name: Koch, Eva
last_name: Koch
- first_name: Hernán E.
full_name: Morales, Hernán E.
last_name: Morales
- first_name: Jenny
full_name: Larsson, Jenny
last_name: Larsson
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Alan R.
full_name: Lemmon, Alan R.
last_name: Lemmon
- first_name: E. Moriarty
full_name: Lemmon, E. Moriarty
last_name: Lemmon
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
citation:
ama: 'Koch E, Morales HE, Larsson J, et al. Data from: Genetic variation for adaptive
traits is associated with polymorphic inversions in Littorina saxatilis. 2021.
doi:10.5061/DRYAD.ZGMSBCCB4'
apa: 'Koch, E., Morales, H. E., Larsson, J., Westram, A. M., Faria, R., Lemmon,
A. R., … Butlin, R. K. (2021). Data from: Genetic variation for adaptive traits
is associated with polymorphic inversions in Littorina saxatilis. Dryad. https://doi.org/10.5061/DRYAD.ZGMSBCCB4'
chicago: 'Koch, Eva, Hernán E. Morales, Jenny Larsson, Anja M Westram, Rui Faria,
Alan R. Lemmon, E. Moriarty Lemmon, Kerstin Johannesson, and Roger K. Butlin.
“Data from: Genetic Variation for Adaptive Traits Is Associated with Polymorphic
Inversions in Littorina Saxatilis.” Dryad, 2021. https://doi.org/10.5061/DRYAD.ZGMSBCCB4.'
ieee: 'E. Koch et al., “Data from: Genetic variation for adaptive traits
is associated with polymorphic inversions in Littorina saxatilis.” Dryad, 2021.'
ista: 'Koch E, Morales HE, Larsson J, Westram AM, Faria R, Lemmon AR, Lemmon EM,
Johannesson K, Butlin RK. 2021. Data from: Genetic variation for adaptive traits
is associated with polymorphic inversions in Littorina saxatilis, Dryad, 10.5061/DRYAD.ZGMSBCCB4.'
mla: 'Koch, Eva, et al. Data from: Genetic Variation for Adaptive Traits Is Associated
with Polymorphic Inversions in Littorina Saxatilis. Dryad, 2021, doi:10.5061/DRYAD.ZGMSBCCB4.'
short: E. Koch, H.E. Morales, J. Larsson, A.M. Westram, R. Faria, A.R. Lemmon, E.M.
Lemmon, K. Johannesson, R.K. Butlin, (2021).
date_created: 2023-05-16T12:34:09Z
date_published: 2021-04-10T00:00:00Z
date_updated: 2026-04-07T14:01:30Z
day: '10'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.5061/DRYAD.ZGMSBCCB4
has_accepted_license: '1'
license: https://creativecommons.org/publicdomain/zero/1.0/
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.zgmsbccb4
month: '04'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '9394'
relation: used_in_publication
status: public
status: public
title: 'Data from: Genetic variation for adaptive traits is associated with polymorphic
inversions in Littorina saxatilis'
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data_reference
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2021'
...
---
_id: '13057'
abstract:
- lang: eng
text: 'This dataset comprises all data shown in the figures of the submitted article
"Geometric superinductance qubits: Controlling phase delocalization across a single
Josephson junction". Additional raw data are available from the corresponding
author on reasonable request.'
article_processing_charge: No
author:
- first_name: Matilda
full_name: Peruzzo, Matilda
id: 3F920B30-F248-11E8-B48F-1D18A9856A87
last_name: Peruzzo
orcid: 0000-0002-3415-4628
- first_name: Farid
full_name: Hassani, Farid
id: 2AED110C-F248-11E8-B48F-1D18A9856A87
last_name: Hassani
orcid: 0000-0001-6937-5773
- first_name: Grisha
full_name: Szep, Grisha
last_name: Szep
- first_name: Andrea
full_name: Trioni, Andrea
id: 42F71B44-F248-11E8-B48F-1D18A9856A87
last_name: Trioni
- first_name: Elena
full_name: Redchenko, Elena
id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87
last_name: Redchenko
- first_name: Martin
full_name: Zemlicka, Martin
id: 2DCF8DE6-F248-11E8-B48F-1D18A9856A87
last_name: Zemlicka
orcid: 0009-0005-0878-3032
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
citation:
ama: 'Peruzzo M, Hassani F, Szep G, et al. Geometric superinductance qubits: Controlling
phase delocalization across a single Josephson junction. 2021. doi:10.5281/ZENODO.5592103'
apa: 'Peruzzo, M., Hassani, F., Szep, G., Trioni, A., Redchenko, E., Zemlicka, M.,
& Fink, J. M. (2021). Geometric superinductance qubits: Controlling phase
delocalization across a single Josephson junction. Zenodo. https://doi.org/10.5281/ZENODO.5592103'
chicago: 'Peruzzo, Matilda, Farid Hassani, Grisha Szep, Andrea Trioni, Elena Redchenko,
Martin Zemlicka, and Johannes M Fink. “Geometric Superinductance Qubits: Controlling
Phase Delocalization across a Single Josephson Junction.” Zenodo, 2021. https://doi.org/10.5281/ZENODO.5592103.'
ieee: 'M. Peruzzo et al., “Geometric superinductance qubits: Controlling
phase delocalization across a single Josephson junction.” Zenodo, 2021.'
ista: 'Peruzzo M, Hassani F, Szep G, Trioni A, Redchenko E, Zemlicka M, Fink JM.
2021. Geometric superinductance qubits: Controlling phase delocalization across
a single Josephson junction, Zenodo, 10.5281/ZENODO.5592103.'
mla: 'Peruzzo, Matilda, et al. Geometric Superinductance Qubits: Controlling
Phase Delocalization across a Single Josephson Junction. Zenodo, 2021, doi:10.5281/ZENODO.5592103.'
short: M. Peruzzo, F. Hassani, G. Szep, A. Trioni, E. Redchenko, M. Zemlicka, J.M.
Fink, (2021).
corr_author: '1'
date_created: 2023-05-23T13:42:27Z
date_published: 2021-10-22T00:00:00Z
date_updated: 2026-04-15T06:41:45Z
day: '22'
ddc:
- '530'
department:
- _id: JoFi
doi: 10.5281/ZENODO.5592103
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.5592104
month: '10'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '9928'
relation: used_in_publication
status: public
status: public
title: 'Geometric superinductance qubits: Controlling phase delocalization across
a single Josephson junction'
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: '2021'
...
---
_id: '13058'
abstract:
- lang: eng
text: The zip file includes source data used in the main text of the manuscript
"Theory of branching morphogenesis by local interactions and global guidance",
as well as a representative Jupyter notebook to reproduce the main figures. A
sample script for the simulations of branching and annihilating random walks is
also included (Sample_script_for_simulations_of_BARWs.ipynb) to generate exemplary
branched networks under external guidance. A detailed description of the simulation
setup is provided in the supplementary information of the manuscipt.
article_processing_charge: No
author:
- first_name: Mehmet C
full_name: Ucar, Mehmet C
id: 50B2A802-6007-11E9-A42B-EB23E6697425
last_name: Ucar
orcid: 0000-0003-0506-4217
citation:
ama: Ucar MC. Source data for the manuscript “Theory of branching morphogenesis
by local interactions and global guidance.” 2021. doi:10.5281/ZENODO.5257160
apa: Ucar, M. C. (2021). Source data for the manuscript “Theory of branching morphogenesis
by local interactions and global guidance.” Zenodo. https://doi.org/10.5281/ZENODO.5257160
chicago: Ucar, Mehmet C. “Source Data for the Manuscript ‘Theory of Branching Morphogenesis
by Local Interactions and Global Guidance.’” Zenodo, 2021. https://doi.org/10.5281/ZENODO.5257160.
ieee: M. C. Ucar, “Source data for the manuscript ‘Theory of branching morphogenesis
by local interactions and global guidance.’” Zenodo, 2021.
ista: Ucar MC. 2021. Source data for the manuscript ‘Theory of branching morphogenesis
by local interactions and global guidance’, Zenodo, 10.5281/ZENODO.5257160.
mla: Ucar, Mehmet C. Source Data for the Manuscript “Theory of Branching Morphogenesis
by Local Interactions and Global Guidance.” Zenodo, 2021, doi:10.5281/ZENODO.5257160.
short: M.C. Ucar, (2021).
corr_author: '1'
date_created: 2023-05-23T13:46:34Z
date_published: 2021-08-25T00:00:00Z
date_updated: 2025-04-15T06:54:54Z
day: '25'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.5281/ZENODO.5257160
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.5257161
month: '08'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '10402'
relation: used_in_publication
status: public
status: public
title: Source data for the manuscript "Theory of branching morphogenesis by local
interactions and global guidance"
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: '2021'
...
---
_id: '13061'
abstract:
- lang: eng
text: Infections early in life can have enduring effects on an organism’s development
and immunity. In this study, we show that this equally applies to developing “superorganisms”
– incipient social insect colonies. When we exposed newly mated Lasius niger ant
queens to a low pathogen dose, their colonies grew more slowly than controls before
winter, but reached similar sizes afterwards. Independent of exposure, queen hibernation
survival improved when the ratio of pupae to workers was small. Queens that reared
fewer pupae before worker emergence exhibited lower pathogen levels, indicating
that high brood rearing efforts interfere with the ability of the queen’s immune
system to suppress pathogen proliferation. Early-life queen pathogen-exposure
also improved the immunocompetence of her worker offspring, as demonstrated by
challenging the workers to the same pathogen a year later. Transgenerational transfer
of the queen’s pathogen experience to her workforce can hence durably reduce the
disease susceptibility of the whole superorganism.
article_processing_charge: No
author:
- first_name: Barbara E
full_name: Casillas Perez, Barbara E
id: 351ED2AA-F248-11E8-B48F-1D18A9856A87
last_name: Casillas Perez
- first_name: Christopher
full_name: Pull, Christopher
id: 3C7F4840-F248-11E8-B48F-1D18A9856A87
last_name: Pull
orcid: 0000-0003-1122-3982
- first_name: Filip
full_name: Naiser, Filip
last_name: Naiser
- first_name: Elisabeth
full_name: Naderlinger, Elisabeth
last_name: Naderlinger
- first_name: Jiri
full_name: Matas, Jiri
last_name: Matas
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Casillas Perez BE, Pull C, Naiser F, Naderlinger E, Matas J, Cremer S. Early
queen infection shapes developmental dynamics and induces long-term disease protection
in incipient ant colonies. 2021. doi:10.5061/DRYAD.7PVMCVDTJ
apa: Casillas Perez, B. E., Pull, C., Naiser, F., Naderlinger, E., Matas, J., &
Cremer, S. (2021). Early queen infection shapes developmental dynamics and induces
long-term disease protection in incipient ant colonies. Dryad. https://doi.org/10.5061/DRYAD.7PVMCVDTJ
chicago: Casillas Perez, Barbara E, Christopher Pull, Filip Naiser, Elisabeth Naderlinger,
Jiri Matas, and Sylvia Cremer. “Early Queen Infection Shapes Developmental Dynamics
and Induces Long-Term Disease Protection in Incipient Ant Colonies.” Dryad, 2021.
https://doi.org/10.5061/DRYAD.7PVMCVDTJ.
ieee: B. E. Casillas Perez, C. Pull, F. Naiser, E. Naderlinger, J. Matas, and S.
Cremer, “Early queen infection shapes developmental dynamics and induces long-term
disease protection in incipient ant colonies.” Dryad, 2021.
ista: Casillas Perez BE, Pull C, Naiser F, Naderlinger E, Matas J, Cremer S. 2021.
Early queen infection shapes developmental dynamics and induces long-term disease
protection in incipient ant colonies, Dryad, 10.5061/DRYAD.7PVMCVDTJ.
mla: Casillas Perez, Barbara E., et al. Early Queen Infection Shapes Developmental
Dynamics and Induces Long-Term Disease Protection in Incipient Ant Colonies.
Dryad, 2021, doi:10.5061/DRYAD.7PVMCVDTJ.
short: B.E. Casillas Perez, C. Pull, F. Naiser, E. Naderlinger, J. Matas, S. Cremer,
(2021).
corr_author: '1'
date_created: 2023-05-23T16:14:35Z
date_published: 2021-10-29T00:00:00Z
date_updated: 2025-04-14T13:55:31Z
day: '29'
ddc:
- '570'
department:
- _id: SyCr
doi: 10.5061/DRYAD.7PVMCVDTJ
ec_funded: 1
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.7pvmcvdtj
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 2649B4DE-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771402'
name: Epidemics in ant societies on a chip
publisher: Dryad
related_material:
record:
- id: '10284'
relation: used_in_publication
status: public
status: public
title: Early queen infection shapes developmental dynamics and induces long-term disease
protection in incipient ant colonies
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '13062'
abstract:
- lang: eng
text: 'This paper analyzes the conditions for local adaptation in a metapopulation
with infinitely many islands under a model of hard selection, where population
size depends on local fitness. Each island belongs to one of two distinct ecological
niches or habitats. Fitness is influenced by an additive trait which is under
habitat-dependent directional selection. Our analysis is based on the diffusion
approximation and accounts for both genetic drift and demographic stochasticity.
By neglecting linkage disequilibria, it yields the joint distribution of allele
frequencies and population size on each island. We find that under hard selection,
the conditions for local adaptation in a rare habitat are more restrictive for
more polygenic traits: even moderate migration load per locus at very many loci
is sufficient for population sizes to decline. This further reduces the efficacy
of selection at individual loci due to increased drift and because smaller populations
are more prone to swamping due to migration, causing a positive feedback between
increasing maladaptation and declining population sizes. Our analysis also highlights
the importance of demographic stochasticity, which exacerbates the decline in
numbers of maladapted populations, leading to population collapse in the rare
habitat at significantly lower migration than predicted by deterministic arguments.'
article_processing_charge: No
author:
- first_name: Eniko
full_name: Szep, Eniko
id: 485BB5A4-F248-11E8-B48F-1D18A9856A87
last_name: Szep
- first_name: Himani
full_name: Sachdeva, Himani
id: 42377A0A-F248-11E8-B48F-1D18A9856A87
last_name: Sachdeva
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Szep E, Sachdeva H, Barton NH. Supplementary code for: Polygenic local adaptation
in metapopulations: A stochastic eco-evolutionary model. 2021. doi:10.5061/DRYAD.8GTHT76P1'
apa: 'Szep, E., Sachdeva, H., & Barton, N. H. (2021). Supplementary code for:
Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model.
Dryad. https://doi.org/10.5061/DRYAD.8GTHT76P1'
chicago: 'Szep, Eniko, Himani Sachdeva, and Nicholas H Barton. “Supplementary Code
for: Polygenic Local Adaptation in Metapopulations: A Stochastic Eco-Evolutionary
Model.” Dryad, 2021. https://doi.org/10.5061/DRYAD.8GTHT76P1.'
ieee: 'E. Szep, H. Sachdeva, and N. H. Barton, “Supplementary code for: Polygenic
local adaptation in metapopulations: A stochastic eco-evolutionary model.” Dryad,
2021.'
ista: 'Szep E, Sachdeva H, Barton NH. 2021. Supplementary code for: Polygenic local
adaptation in metapopulations: A stochastic eco-evolutionary model, Dryad, 10.5061/DRYAD.8GTHT76P1.'
mla: 'Szep, Eniko, et al. Supplementary Code for: Polygenic Local Adaptation
in Metapopulations: A Stochastic Eco-Evolutionary Model. Dryad, 2021, doi:10.5061/DRYAD.8GTHT76P1.'
short: E. Szep, H. Sachdeva, N.H. Barton, (2021).
corr_author: '1'
date_created: 2023-05-23T16:17:02Z
date_published: 2021-03-02T00:00:00Z
date_updated: 2025-06-12T06:35:39Z
day: '02'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.5061/DRYAD.8GTHT76P1
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.8gtht76p1
month: '03'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '9252'
relation: used_in_publication
status: public
status: public
title: 'Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic
eco-evolutionary model'
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '13063'
abstract:
- lang: eng
text: We develop a Bayesian model (BayesRR-RC) that provides robust SNP-heritability
estimation, an alternative to marker discovery, and accurate genomic prediction,
taking 22 seconds per iteration to estimate 8.4 million SNP-effects and 78 SNP-heritability
parameters in the UK Biobank. We find that only $\leq$ 10\% of the genetic variation
captured for height, body mass index, cardiovascular disease, and type 2 diabetes
is attributable to proximal regulatory regions within 10kb upstream of genes,
while 12-25% is attributed to coding regions, 32-44% to introns, and 22-28% to
distal 10-500kb upstream regions. Up to 24% of all cis and coding regions of each
chromosome are associated with each trait, with over 3,100 independent exonic
and intronic regions and over 5,400 independent regulatory regions having >95%
probability of contributing >0.001% to the genetic variance of these four traits.
Our open-source software (GMRM) provides a scalable alternative to current approaches
for biobank data.
article_processing_charge: No
author:
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
citation:
ama: Robinson MR. Probabilistic inference of the genetic architecture of functional
enrichment of complex traits. 2021. doi:10.5061/dryad.sqv9s4n51
apa: Robinson, M. R. (2021). Probabilistic inference of the genetic architecture
of functional enrichment of complex traits. Dryad. https://doi.org/10.5061/dryad.sqv9s4n51
chicago: Robinson, Matthew Richard. “Probabilistic Inference of the Genetic Architecture
of Functional Enrichment of Complex Traits.” Dryad, 2021. https://doi.org/10.5061/dryad.sqv9s4n51.
ieee: M. R. Robinson, “Probabilistic inference of the genetic architecture of functional
enrichment of complex traits.” Dryad, 2021.
ista: Robinson MR. 2021. Probabilistic inference of the genetic architecture of
functional enrichment of complex traits, Dryad, 10.5061/dryad.sqv9s4n51.
mla: Robinson, Matthew Richard. Probabilistic Inference of the Genetic Architecture
of Functional Enrichment of Complex Traits. Dryad, 2021, doi:10.5061/dryad.sqv9s4n51.
short: M.R. Robinson, (2021).
corr_author: '1'
date_created: 2023-05-23T16:20:16Z
date_published: 2021-11-04T00:00:00Z
date_updated: 2025-06-12T06:54:51Z
day: '04'
ddc:
- '570'
department:
- _id: MaRo
doi: 10.5061/dryad.sqv9s4n51
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.sqv9s4n51
month: '11'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
link:
- relation: software
url: https://github.com/medical-genomics-group/gmrm
record:
- id: '8429'
relation: used_in_publication
status: public
status: public
title: Probabilistic inference of the genetic architecture of functional enrichment
of complex traits
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '13068'
abstract:
- lang: eng
text: Source data and source code for the graphs in "Spatiotemporal dynamics of
self-organized branching pancreatic cancer-derived organoids".
article_processing_charge: No
author:
- first_name: Samuel
full_name: Randriamanantsoa, Samuel
last_name: Randriamanantsoa
- first_name: Aristeidis
full_name: Papargyriou, Aristeidis
last_name: Papargyriou
- first_name: Carlo
full_name: Maurer, Carlo
last_name: Maurer
- first_name: Katja
full_name: Peschke, Katja
last_name: Peschke
- first_name: Maximilian
full_name: Schuster, Maximilian
last_name: Schuster
- first_name: Giulia
full_name: Zecchin, Giulia
last_name: Zecchin
- first_name: Katja
full_name: Steiger, Katja
last_name: Steiger
- first_name: Rupert
full_name: Öllinger, Rupert
last_name: Öllinger
- first_name: Dieter
full_name: Saur, Dieter
last_name: Saur
- first_name: Christina
full_name: Scheel, Christina
last_name: Scheel
- first_name: Roland
full_name: Rad, Roland
last_name: Rad
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Maximilian
full_name: Reichert, Maximilian
last_name: Reichert
- first_name: Andreas R.
full_name: Bausch, Andreas R.
last_name: Bausch
citation:
ama: Randriamanantsoa S, Papargyriou A, Maurer C, et al. Spatiotemporal dynamics
of self-organized branching in pancreas-derived organoids. 2021. doi:10.5281/ZENODO.5148117
apa: Randriamanantsoa, S., Papargyriou, A., Maurer, C., Peschke, K., Schuster, M.,
Zecchin, G., … Bausch, A. R. (2021). Spatiotemporal dynamics of self-organized
branching in pancreas-derived organoids. Zenodo. https://doi.org/10.5281/ZENODO.5148117
chicago: Randriamanantsoa, Samuel, Aristeidis Papargyriou, Carlo Maurer, Katja Peschke,
Maximilian Schuster, Giulia Zecchin, Katja Steiger, et al. “Spatiotemporal Dynamics
of Self-Organized Branching in Pancreas-Derived Organoids.” Zenodo, 2021. https://doi.org/10.5281/ZENODO.5148117.
ieee: S. Randriamanantsoa et al., “Spatiotemporal dynamics of self-organized
branching in pancreas-derived organoids.” Zenodo, 2021.
ista: Randriamanantsoa S, Papargyriou A, Maurer C, Peschke K, Schuster M, Zecchin
G, Steiger K, Öllinger R, Saur D, Scheel C, Rad R, Hannezo EB, Reichert M, Bausch
AR. 2021. Spatiotemporal dynamics of self-organized branching in pancreas-derived
organoids, Zenodo, 10.5281/ZENODO.5148117.
mla: Randriamanantsoa, Samuel, et al. Spatiotemporal Dynamics of Self-Organized
Branching in Pancreas-Derived Organoids. Zenodo, 2021, doi:10.5281/ZENODO.5148117.
short: S. Randriamanantsoa, A. Papargyriou, C. Maurer, K. Peschke, M. Schuster,
G. Zecchin, K. Steiger, R. Öllinger, D. Saur, C. Scheel, R. Rad, E.B. Hannezo,
M. Reichert, A.R. Bausch, (2021).
date_created: 2023-05-23T16:39:24Z
date_published: 2021-07-30T00:00:00Z
date_updated: 2025-06-11T13:53:54Z
day: '30'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.5281/ZENODO.5148117
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.6577226
month: '07'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '12217'
relation: used_in_publication
status: public
status: public
title: Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids
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: '2021'
...
---
_id: '13069'
abstract:
- lang: eng
text: To survive elevated temperatures, ectotherms adjust the fluidity of membranes
by fine-tuning lipid desaturation levels in a process previously described to
be cell-autonomous. We have discovered that, in Caenorhabditis elegans, neuronal
Heat shock Factor 1 (HSF-1), the conserved master regulator of the heat shock
response (HSR)- causes extensive fat remodelling in peripheral tissues. These
changes include a decrease in fat desaturase and acid lipase expression in the
intestine, and a global shift in the saturation levels of plasma membrane’s phospholipids.
The observed remodelling of plasma membrane is in line with ectothermic adaptive
responses and gives worms a cumulative advantage to warm temperatures. We have
determined that at least six TAX-2/TAX-4 cGMP gated channel expressing sensory
neurons and TGF-β/BMP are required for signalling across tissues to modulate fat
desaturation. We also find neuronal hsf-1 is not only sufficient but also partially
necessary to control the fat remodelling response and for survival at warm temperatures.
This is the first study to show that a thermostat-based mechanism can cell non-autonomously
coordinate membrane saturation and composition across tissues in a multicellular
animal.
article_processing_charge: No
author:
- first_name: Laetitia
full_name: Chauve, Laetitia
last_name: Chauve
- first_name: Francesca
full_name: Hodge, Francesca
last_name: Hodge
- first_name: Sharlene
full_name: Murdoch, Sharlene
last_name: Murdoch
- first_name: Fatemah
full_name: Masoudzadeh, Fatemah
last_name: Masoudzadeh
- first_name: Harry-Jack
full_name: Mann, Harry-Jack
last_name: Mann
- first_name: Andrea
full_name: Lopez-Clavijo, Andrea
last_name: Lopez-Clavijo
- first_name: Hanneke
full_name: Okkenhaug, Hanneke
last_name: Okkenhaug
- first_name: Greg
full_name: West, Greg
last_name: West
- first_name: Bebiana C.
full_name: Sousa, Bebiana C.
last_name: Sousa
- first_name: Anne
full_name: Segonds-Pichon, Anne
last_name: Segonds-Pichon
- first_name: Cheryl
full_name: Li, Cheryl
last_name: Li
- first_name: Steven
full_name: Wingett, Steven
last_name: Wingett
- first_name: Hermine
full_name: Kienberger, Hermine
last_name: Kienberger
- first_name: Karin
full_name: Kleigrewe, Karin
last_name: Kleigrewe
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
- first_name: Michael
full_name: Wakelam, Michael
last_name: Wakelam
- first_name: Olivia
full_name: Casanueva, Olivia
last_name: Casanueva
citation:
ama: Chauve L, Hodge F, Murdoch S, et al. Neuronal HSF-1 coordinates the propagation
of fat desaturation across tissues to enable adaptation to high temperatures in
C. elegans. 2021. doi:10.5281/ZENODO.5519410
apa: Chauve, L., Hodge, F., Murdoch, S., Masoudzadeh, F., Mann, H.-J., Lopez-Clavijo,
A., … Casanueva, O. (2021). Neuronal HSF-1 coordinates the propagation of fat
desaturation across tissues to enable adaptation to high temperatures in C. elegans.
Zenodo. https://doi.org/10.5281/ZENODO.5519410
chicago: Chauve, Laetitia, Francesca Hodge, Sharlene Murdoch, Fatemah Masoudzadeh,
Harry-Jack Mann, Andrea Lopez-Clavijo, Hanneke Okkenhaug, et al. “Neuronal HSF-1
Coordinates the Propagation of Fat Desaturation across Tissues to Enable Adaptation
to High Temperatures in C. Elegans.” Zenodo, 2021. https://doi.org/10.5281/ZENODO.5519410.
ieee: L. Chauve et al., “Neuronal HSF-1 coordinates the propagation of fat
desaturation across tissues to enable adaptation to high temperatures in C. elegans.”
Zenodo, 2021.
ista: Chauve L, Hodge F, Murdoch S, Masoudzadeh F, Mann H-J, Lopez-Clavijo A, Okkenhaug
H, West G, Sousa BC, Segonds-Pichon A, Li C, Wingett S, Kienberger H, Kleigrewe
K, de Bono M, Wakelam M, Casanueva O. 2021. Neuronal HSF-1 coordinates the propagation
of fat desaturation across tissues to enable adaptation to high temperatures in
C. elegans, Zenodo, 10.5281/ZENODO.5519410.
mla: Chauve, Laetitia, et al. Neuronal HSF-1 Coordinates the Propagation of Fat
Desaturation across Tissues to Enable Adaptation to High Temperatures in C. Elegans.
Zenodo, 2021, doi:10.5281/ZENODO.5519410.
short: L. Chauve, F. Hodge, S. Murdoch, F. Masoudzadeh, H.-J. Mann, A. Lopez-Clavijo,
H. Okkenhaug, G. West, B.C. Sousa, A. Segonds-Pichon, C. Li, S. Wingett, H. Kienberger,
K. Kleigrewe, M. de Bono, M. Wakelam, O. Casanueva, (2021).
date_created: 2023-05-23T16:40:56Z
date_published: 2021-12-25T00:00:00Z
date_updated: 2023-08-14T11:53:26Z
day: '25'
ddc:
- '570'
department:
- _id: MaDe
doi: 10.5281/ZENODO.5519410
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.5547464
month: '12'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '10322'
relation: used_in_publication
status: public
status: public
title: Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues
to enable adaptation to high temperatures in C. elegans
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: '2021'
...
---
_id: '13072'
abstract:
- lang: eng
text: CpGs and corresponding mean weights for DNAm-based prediction of cognitive
abilities (6 traits)
article_processing_charge: No
author:
- first_name: Daniel L
full_name: McCartney, Daniel L
last_name: McCartney
- first_name: Robert F
full_name: Hillary, Robert F
last_name: Hillary
- first_name: Eleanor LS
full_name: Conole, Eleanor LS
last_name: Conole
- first_name: Daniel
full_name: Trejo Banos, Daniel
last_name: Trejo Banos
- first_name: Danni A
full_name: Gadd, Danni A
last_name: Gadd
- first_name: Rosie M
full_name: Walker, Rosie M
last_name: Walker
- first_name: Cliff
full_name: Nangle, Cliff
last_name: Nangle
- first_name: Robin
full_name: Flaig, Robin
last_name: Flaig
- first_name: Archie
full_name: Campbell, Archie
last_name: Campbell
- first_name: Alison D
full_name: Murray, Alison D
last_name: Murray
- first_name: Susana
full_name: Munoz Maniega, Susana
last_name: Munoz Maniega
- first_name: Maria
full_name: del C Valdes-Hernandez, Maria
last_name: del C Valdes-Hernandez
- first_name: Mathew A
full_name: Harris, Mathew A
last_name: Harris
- first_name: Mark E
full_name: Bastin, Mark E
last_name: Bastin
- first_name: Joanna M
full_name: Wardlaw, Joanna M
last_name: Wardlaw
- first_name: Sarah E
full_name: Harris, Sarah E
last_name: Harris
- first_name: David J
full_name: Porteous, David J
last_name: Porteous
- first_name: Elliot M
full_name: Tucker-Drob, Elliot M
last_name: Tucker-Drob
- first_name: Andrew M
full_name: McIntosh, Andrew M
last_name: McIntosh
- first_name: Kathryn L
full_name: Evans, Kathryn L
last_name: Evans
- first_name: Ian J
full_name: Deary, Ian J
last_name: Deary
- first_name: Simon R
full_name: Cox, Simon R
last_name: Cox
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: Riccardo E
full_name: Marioni, Riccardo E
last_name: Marioni
citation:
ama: McCartney DL, Hillary RF, Conole EL, et al. Blood-based epigenome-wide analyses
of cognitive abilities. 2021. doi:10.5281/ZENODO.5794028
apa: McCartney, D. L., Hillary, R. F., Conole, E. L., Trejo Banos, D., Gadd, D.
A., Walker, R. M., … Marioni, R. E. (2021). Blood-based epigenome-wide analyses
of cognitive abilities. Zenodo. https://doi.org/10.5281/ZENODO.5794028
chicago: McCartney, Daniel L, Robert F Hillary, Eleanor LS Conole, Daniel Trejo
Banos, Danni A Gadd, Rosie M Walker, Cliff Nangle, et al. “Blood-Based Epigenome-Wide
Analyses of Cognitive Abilities.” Zenodo, 2021. https://doi.org/10.5281/ZENODO.5794028.
ieee: D. L. McCartney et al., “Blood-based epigenome-wide analyses of cognitive
abilities.” Zenodo, 2021.
ista: McCartney DL, Hillary RF, Conole EL, Trejo Banos D, Gadd DA, Walker RM, Nangle
C, Flaig R, Campbell A, Murray AD, Munoz Maniega S, del C Valdes-Hernandez M,
Harris MA, Bastin ME, Wardlaw JM, Harris SE, Porteous DJ, Tucker-Drob EM, McIntosh
AM, Evans KL, Deary IJ, Cox SR, Robinson MR, Marioni RE. 2021. Blood-based epigenome-wide
analyses of cognitive abilities, Zenodo, 10.5281/ZENODO.5794028.
mla: McCartney, Daniel L., et al. Blood-Based Epigenome-Wide Analyses of Cognitive
Abilities. Zenodo, 2021, doi:10.5281/ZENODO.5794028.
short: D.L. McCartney, R.F. Hillary, E.L. Conole, D. Trejo Banos, D.A. Gadd, R.M.
Walker, C. Nangle, R. Flaig, A. Campbell, A.D. Murray, S. Munoz Maniega, M. del
C Valdes-Hernandez, M.A. Harris, M.E. Bastin, J.M. Wardlaw, S.E. Harris, D.J.
Porteous, E.M. Tucker-Drob, A.M. McIntosh, K.L. Evans, I.J. Deary, S.R. Cox, M.R.
Robinson, R.E. Marioni, (2021).
date_created: 2023-05-23T16:46:20Z
date_published: 2021-12-20T00:00:00Z
date_updated: 2025-06-11T13:54:53Z
day: '20'
ddc:
- '570'
department:
- _id: MaRo
doi: 10.5281/ZENODO.5794028
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.5794029
month: '12'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '10702'
relation: used_in_publication
status: public
status: public
title: Blood-based epigenome-wide analyses of cognitive abilities
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: '2021'
...
---
_id: '13080'
abstract:
- lang: eng
text: "Data for the manuscript 'Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor
Nanowire' ([2006.01275] Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor
Nanowire (arxiv.org))\r\n\r\nWe upload a pdf with extended data sets, and the
raw data for these extended datasets as well."
article_processing_charge: No
author:
- first_name: Denise
full_name: Puglia, Denise
id: 4D495994-AE37-11E9-AC72-31CAE5697425
last_name: Puglia
orcid: 0000-0003-1144-2763
- first_name: Esteban
full_name: Martinez, Esteban
last_name: Martinez
- first_name: Gerbold
full_name: Menard, Gerbold
last_name: Menard
- first_name: Andreas
full_name: Pöschl, Andreas
last_name: Pöschl
- first_name: Sergei
full_name: Gronin, Sergei
last_name: Gronin
- first_name: Geoffrey
full_name: Gardner, Geoffrey
last_name: Gardner
- first_name: Ray
full_name: Kallaher, Ray
last_name: Kallaher
- first_name: Michael
full_name: Manfra, Michael
last_name: Manfra
- first_name: Charles
full_name: Marcus, Charles
last_name: Marcus
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
- first_name: Lucas
full_name: Casparis, Lucas
last_name: Casparis
citation:
ama: Puglia D, Martinez E, Menard G, et al. Data for ’Closing of the Induced Gap
in a Hybrid Superconductor-Semiconductor Nanowire. 2021. doi:10.5281/ZENODO.4592435
apa: Puglia, D., Martinez, E., Menard, G., Pöschl, A., Gronin, S., Gardner, G.,
… Casparis, L. (2021). Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor
Nanowire. Zenodo. https://doi.org/10.5281/ZENODO.4592435
chicago: Puglia, Denise, Esteban Martinez, Gerbold Menard, Andreas Pöschl, Sergei
Gronin, Geoffrey Gardner, Ray Kallaher, et al. “Data for ’Closing of the Induced
Gap in a Hybrid Superconductor-Semiconductor Nanowire.” Zenodo, 2021. https://doi.org/10.5281/ZENODO.4592435.
ieee: D. Puglia et al., “Data for ’Closing of the Induced Gap in a Hybrid
Superconductor-Semiconductor Nanowire.” Zenodo, 2021.
ista: Puglia D, Martinez E, Menard G, Pöschl A, Gronin S, Gardner G, Kallaher R,
Manfra M, Marcus C, Higginbotham AP, Casparis L. 2021. Data for ’Closing of the
Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire, Zenodo, 10.5281/ZENODO.4592435.
mla: Puglia, Denise, et al. Data for ’Closing of the Induced Gap in a Hybrid
Superconductor-Semiconductor Nanowire. Zenodo, 2021, doi:10.5281/ZENODO.4592435.
short: D. Puglia, E. Martinez, G. Menard, A. Pöschl, S. Gronin, G. Gardner, R. Kallaher,
M. Manfra, C. Marcus, A.P. Higginbotham, L. Casparis, (2021).
corr_author: '1'
date_created: 2023-05-23T17:11:28Z
date_published: 2021-03-09T00:00:00Z
date_updated: 2025-07-10T12:01:53Z
day: '09'
ddc:
- '530'
department:
- _id: AnHi
doi: 10.5281/ZENODO.4592435
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.4592460
month: '03'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
link:
- relation: software
url: https://github.com/caslu85/Induced-Gap-Closing-Shared/tree/1.1.3
record:
- id: '9570'
relation: used_in_publication
status: public
status: public
title: Data for 'Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor
Nanowire
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '13146'
abstract:
- lang: eng
text: 'A recent line of work has analyzed the theoretical properties of deep neural
networks via the Neural Tangent Kernel (NTK). In particular, the smallest eigenvalue
of the NTK has been related to the memorization capacity, the global convergence
of gradient descent algorithms and the generalization of deep nets. However, existing
results either provide bounds in the two-layer setting or assume that the spectrum
of the NTK matrices is bounded away from 0 for multi-layer networks. In this paper,
we provide tight bounds on the smallest eigenvalue of NTK matrices for deep ReLU
nets, both in the limiting case of infinite widths and for finite widths. In the
finite-width setting, the network architectures we consider are fairly general:
we require the existence of a wide layer with roughly order of N neurons, N being
the number of data samples; and the scaling of the remaining layer widths is arbitrary
(up to logarithmic factors). To obtain our results, we analyze various quantities
of independent interest: we give lower bounds on the smallest singular value of
hidden feature matrices, and upper bounds on the Lipschitz constant of input-output
feature maps.'
acknowledgement: The authors would like to thank the anonymous reviewers for their
helpful comments. MM was partially supported by the 2019 Lopez-Loreta Prize. QN
and GM acknowledge support from the European Research Council (ERC) under the European
Union’s Horizon 2020 research and innovation programme (grant agreement no 757983).
article_processing_charge: No
arxiv: 1
author:
- first_name: Quynh
full_name: Nguyen, Quynh
last_name: Nguyen
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: Guido
full_name: Montufar, Guido
last_name: Montufar
citation:
ama: 'Nguyen Q, Mondelli M, Montufar G. Tight bounds on the smallest Eigenvalue
of the neural tangent kernel for deep ReLU networks. In: Proceedings of the
38th International Conference on Machine Learning. Vol 139. ML Research Press;
2021:8119-8129.'
apa: 'Nguyen, Q., Mondelli, M., & Montufar, G. (2021). Tight bounds on the smallest
Eigenvalue of the neural tangent kernel for deep ReLU networks. In Proceedings
of the 38th International Conference on Machine Learning (Vol. 139, pp. 8119–8129).
Virtual: ML Research Press.'
chicago: Nguyen, Quynh, Marco Mondelli, and Guido Montufar. “Tight Bounds on the
Smallest Eigenvalue of the Neural Tangent Kernel for Deep ReLU Networks.” In Proceedings
of the 38th International Conference on Machine Learning, 139:8119–29. ML
Research Press, 2021.
ieee: Q. Nguyen, M. Mondelli, and G. Montufar, “Tight bounds on the smallest Eigenvalue
of the neural tangent kernel for deep ReLU networks,” in Proceedings of the
38th International Conference on Machine Learning, Virtual, 2021, vol. 139,
pp. 8119–8129.
ista: 'Nguyen Q, Mondelli M, Montufar G. 2021. Tight bounds on the smallest Eigenvalue
of the neural tangent kernel for deep ReLU networks. Proceedings of the 38th International
Conference on Machine Learning. ICML: International Conference on Machine Learning
vol. 139, 8119–8129.'
mla: Nguyen, Quynh, et al. “Tight Bounds on the Smallest Eigenvalue of the Neural
Tangent Kernel for Deep ReLU Networks.” Proceedings of the 38th International
Conference on Machine Learning, vol. 139, ML Research Press, 2021, pp. 8119–29.
short: Q. Nguyen, M. Mondelli, G. Montufar, in:, Proceedings of the 38th International
Conference on Machine Learning, ML Research Press, 2021, pp. 8119–8129.
conference:
end_date: 2021-07-24
location: Virtual
name: 'ICML: International Conference on Machine Learning'
start_date: 2021-07-18
date_created: 2023-06-18T22:00:48Z
date_published: 2021-07-01T00:00:00Z
date_updated: 2025-07-10T11:50:36Z
day: '01'
ddc:
- '000'
department:
- _id: MaMo
external_id:
arxiv:
- '2012.11654'
file:
- access_level: open_access
checksum: 19489cf5e16a0596b1f92e317d97c9b0
content_type: application/pdf
creator: dernst
date_created: 2023-06-19T10:49:12Z
date_updated: 2023-06-19T10:49:12Z
file_id: '13155'
file_name: 2021_PMLR_Nguyen.pdf
file_size: 591332
relation: main_file
success: 1
file_date_updated: 2023-06-19T10:49:12Z
has_accepted_license: '1'
intvolume: ' 139'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 8119-8129
project:
- _id: 059876FA-7A3F-11EA-A408-12923DDC885E
name: Prix Lopez-Loretta 2019 - Marco Mondelli
publication: Proceedings of the 38th International Conference on Machine Learning
publication_identifier:
eissn:
- 2640-3498
isbn:
- '9781713845065'
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tight bounds on the smallest Eigenvalue of the neural tangent kernel for deep
ReLU networks
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: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 139
year: '2021'
...
---
_id: '13147'
abstract:
- lang: eng
text: "We investigate fast and communication-efficient algorithms for the classic
problem of minimizing a sum of strongly convex and smooth functions that are distributed
among n\r\n different nodes, which can communicate using a limited number of bits.
Most previous communication-efficient approaches for this problem are limited
to first-order optimization, and therefore have \\emph{linear} dependence on the
condition number in their communication complexity. We show that this dependence
is not inherent: communication-efficient methods can in fact have sublinear dependence
on the condition number. For this, we design and analyze the first communication-efficient
distributed variants of preconditioned gradient descent for Generalized Linear
Models, and for Newton’s method. Our results rely on a new technique for quantizing
both the preconditioner and the descent direction at each step of the algorithms,
while controlling their convergence rate. We also validate our findings experimentally,
showing faster convergence and reduced communication relative to previous methods."
acknowledgement: The authors would like to thank Janne Korhonen, Aurelien Lucchi,
Celestine MendlerDunner and Antonio Orvieto for helpful discussions. FA ¨and DA
were supported during this work by the European Research Council (ERC) under the
European Union’s Horizon 2020 research and innovation programme (grant agreement
No 805223 ScaleML). PD was supported by the European Union’s Horizon 2020 programme
under the Marie Skłodowska-Curie grant agreement No. 754411.
article_processing_charge: No
arxiv: 1
author:
- first_name: Foivos
full_name: Alimisis, Foivos
last_name: Alimisis
- first_name: Peter
full_name: Davies, Peter
id: 11396234-BB50-11E9-B24C-90FCE5697425
last_name: Davies
orcid: 0000-0002-5646-9524
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
citation:
ama: 'Alimisis F, Davies P, Alistarh D-A. Communication-efficient distributed optimization
with quantized preconditioners. In: Proceedings of the 38th International Conference
on Machine Learning. Vol 139. ML Research Press; 2021:196-206.'
apa: 'Alimisis, F., Davies, P., & Alistarh, D.-A. (2021). Communication-efficient
distributed optimization with quantized preconditioners. In Proceedings of
the 38th International Conference on Machine Learning (Vol. 139, pp. 196–206).
Virtual: ML Research Press.'
chicago: Alimisis, Foivos, Peter Davies, and Dan-Adrian Alistarh. “Communication-Efficient
Distributed Optimization with Quantized Preconditioners.” In Proceedings of
the 38th International Conference on Machine Learning, 139:196–206. ML Research
Press, 2021.
ieee: F. Alimisis, P. Davies, and D.-A. Alistarh, “Communication-efficient distributed
optimization with quantized preconditioners,” in Proceedings of the 38th International
Conference on Machine Learning, Virtual, 2021, vol. 139, pp. 196–206.
ista: 'Alimisis F, Davies P, Alistarh D-A. 2021. Communication-efficient distributed
optimization with quantized preconditioners. Proceedings of the 38th International
Conference on Machine Learning. ICML: International Conference on Machine Learning
vol. 139, 196–206.'
mla: Alimisis, Foivos, et al. “Communication-Efficient Distributed Optimization
with Quantized Preconditioners.” Proceedings of the 38th International Conference
on Machine Learning, vol. 139, ML Research Press, 2021, pp. 196–206.
short: F. Alimisis, P. Davies, D.-A. Alistarh, in:, Proceedings of the 38th International
Conference on Machine Learning, ML Research Press, 2021, pp. 196–206.
conference:
end_date: 2021-07-24
location: Virtual
name: 'ICML: International Conference on Machine Learning'
start_date: 2021-07-18
corr_author: '1'
date_created: 2023-06-18T22:00:48Z
date_published: 2021-07-01T00:00:00Z
date_updated: 2025-07-10T11:50:37Z
day: '01'
ddc:
- '000'
department:
- _id: DaAl
ec_funded: 1
external_id:
arxiv:
- '2102.07214'
file:
- access_level: open_access
checksum: 7ec0d59bac268b49c76bf2e036dedd7a
content_type: application/pdf
creator: dernst
date_created: 2023-06-19T10:41:05Z
date_updated: 2023-06-19T10:41:05Z
file_id: '13154'
file_name: 2021_PMLR_Alimisis.pdf
file_size: 429087
relation: main_file
success: 1
file_date_updated: 2023-06-19T10:41:05Z
has_accepted_license: '1'
intvolume: ' 139'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 196-206
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Proceedings of the 38th International Conference on Machine Learning
publication_identifier:
eissn:
- 2640-3498
isbn:
- '9781713845065'
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Communication-efficient distributed optimization with quantized preconditioners
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: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 139
year: '2021'
...
---
_id: '13356'
abstract:
- lang: eng
text: 'Self-assembly of nanoparticles can be mediated by polymers, but has so far
led almost exclusively to nanoparticle aggregates that are amorphous. Here, we
employed Coulombic interactions to generate a range of composite materials from
mixtures of charged nanoparticles and oppositely charged polymers. The assembly
behavior of these nanoparticle/polymer composites depends on their order of addition:
polymers added to nanoparticles give rise to stable aggregates, but nanoparticles
added to polymers disassemble the initially formed aggregates. The amorphous aggregates
were transformed into crystalline ones by transiently increasing the ionic strength
of the solution. The morphology of the resulting crystals depended on the length
of the polymer: short polymer chains mediated the self-assembly of nanoparticles
into strongly faceted crystals, whereas long chains led to pseudospherical nanoparticle/polymer
assemblies, within which the crystalline order of nanoparticles was retained.'
article_processing_charge: No
article_type: original
author:
- first_name: Tong
full_name: Bian, Tong
last_name: Bian
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Bian T, Klajn R. Morphology control in crystalline nanoparticle–polymer aggregates.
Annals of the New York Academy of Sciences. 2021;1505(1):191-201. doi:10.1111/nyas.14674
apa: Bian, T., & Klajn, R. (2021). Morphology control in crystalline nanoparticle–polymer
aggregates. Annals of the New York Academy of Sciences. Wiley. https://doi.org/10.1111/nyas.14674
chicago: Bian, Tong, and Rafal Klajn. “Morphology Control in Crystalline Nanoparticle–Polymer
Aggregates.” Annals of the New York Academy of Sciences. Wiley, 2021. https://doi.org/10.1111/nyas.14674.
ieee: T. Bian and R. Klajn, “Morphology control in crystalline nanoparticle–polymer
aggregates,” Annals of the New York Academy of Sciences, vol. 1505, no.
1. Wiley, pp. 191–201, 2021.
ista: Bian T, Klajn R. 2021. Morphology control in crystalline nanoparticle–polymer
aggregates. Annals of the New York Academy of Sciences. 1505(1), 191–201.
mla: Bian, Tong, and Rafal Klajn. “Morphology Control in Crystalline Nanoparticle–Polymer
Aggregates.” Annals of the New York Academy of Sciences, vol. 1505, no.
1, Wiley, 2021, pp. 191–201, doi:10.1111/nyas.14674.
short: T. Bian, R. Klajn, Annals of the New York Academy of Sciences 1505 (2021)
191–201.
date_created: 2023-08-01T09:33:39Z
date_published: 2021-12-01T00:00:00Z
date_updated: 2024-10-14T12:12:06Z
day: '01'
ddc:
- '540'
doi: 10.1111/nyas.14674
extern: '1'
external_id:
pmid:
- '34427923'
intvolume: ' 1505'
issue: '1'
keyword:
- History and Philosophy of Science
- General Biochemistry
- Genetics and Molecular Biology
- General Neuroscience
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/nyas.14674
month: '12'
oa: 1
oa_version: Published Version
page: 191-201
pmid: 1
publication: Annals of the New York Academy of Sciences
publication_identifier:
eissn:
- 1749-6632
issn:
- 0077-8923
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Morphology control in crystalline nanoparticle–polymer aggregates
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1505
year: '2021'
...
---
OA_place: publisher
OA_type: gold
_id: '21081'
abstract:
- lang: eng
text: Macrocyclic peptides are an important class of bioactive substances. When
inserting an aromatic foldamer segment in a macrocyclic peptide, the strong folding
propensity of the former may influence the conformation and alter the properties
of the latter. Such an insertion is relevant because some foldamer–peptide hybrids
have recently been shown to be tolerated by the ribosome, prior to forming macrocycles,
and can thus be produced using an in vitro translation system. We have investigated
the interplay of peptide and foldamer conformations in such hybrid macrocycles.
We show that foldamer helical folding always prevails and stands as a viable means
to stretch, i.e. unfold, peptides in a solvent dependent manner. Conversely, the
peptide systematically has a reciprocal influence and gives rise to strong foldamer
helix handedness bias as well as foldamer helix stabilisation. The hybrid macrocycles
also show resistance towards proteolytic degradation.
article_processing_charge: Yes
article_type: original
author:
- first_name: Sebastian
full_name: Dengler, Sebastian
last_name: Dengler
- first_name: Pradeep K
full_name: Mandal, Pradeep K
id: 6a3def15-d4b4-11ef-9fa9-a24c1f545ec3
last_name: Mandal
orcid: 0000-0001-5996-956X
- first_name: Lars
full_name: Allmendinger, Lars
last_name: Allmendinger
- first_name: Céline
full_name: Douat, Céline
last_name: Douat
- first_name: Ivan
full_name: Huc, Ivan
last_name: Huc
citation:
ama: Dengler S, Mandal PK, Allmendinger L, Douat C, Huc I. Conformational interplay
in hybrid peptide–helical aromatic foldamer macrocycles. Chemical Science.
2021;12(33):11004-11012. doi:10.1039/d1sc03640h
apa: Dengler, S., Mandal, P. K., Allmendinger, L., Douat, C., & Huc, I. (2021).
Conformational interplay in hybrid peptide–helical aromatic foldamer macrocycles.
Chemical Science. Royal Society of Chemistry. https://doi.org/10.1039/d1sc03640h
chicago: Dengler, Sebastian, Pradeep K Mandal, Lars Allmendinger, Céline Douat,
and Ivan Huc. “Conformational Interplay in Hybrid Peptide–Helical Aromatic Foldamer
Macrocycles.” Chemical Science. Royal Society of Chemistry, 2021. https://doi.org/10.1039/d1sc03640h.
ieee: S. Dengler, P. K. Mandal, L. Allmendinger, C. Douat, and I. Huc, “Conformational
interplay in hybrid peptide–helical aromatic foldamer macrocycles,” Chemical
Science, vol. 12, no. 33. Royal Society of Chemistry, pp. 11004–11012, 2021.
ista: Dengler S, Mandal PK, Allmendinger L, Douat C, Huc I. 2021. Conformational
interplay in hybrid peptide–helical aromatic foldamer macrocycles. Chemical Science.
12(33), 11004–11012.
mla: Dengler, Sebastian, et al. “Conformational Interplay in Hybrid Peptide–Helical
Aromatic Foldamer Macrocycles.” Chemical Science, vol. 12, no. 33, Royal
Society of Chemistry, 2021, pp. 11004–12, doi:10.1039/d1sc03640h.
short: S. Dengler, P.K. Mandal, L. Allmendinger, C. Douat, I. Huc, Chemical Science
12 (2021) 11004–11012.
date_created: 2026-01-29T15:15:12Z
date_published: 2021-07-27T00:00:00Z
date_updated: 2026-02-20T06:57:41Z
day: '27'
ddc:
- '540'
doi: 10.1039/d1sc03640h
extern: '1'
has_accepted_license: '1'
intvolume: ' 12'
issue: '33'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/3.0/
main_file_link:
- open_access: '1'
url: https://doi.org/10.1039/D1SC03640H
month: '07'
oa: 1
oa_version: Published Version
page: 11004-11012
publication: Chemical Science
publication_identifier:
eissn:
- 2041-6539
issn:
- 2041-6520
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
status: public
title: Conformational interplay in hybrid peptide–helical aromatic foldamer macrocycles
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/3.0/legalcode
name: Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0)
short: CC BY-NC (3.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2021'
...
---
OA_type: closed access
_id: '21082'
abstract:
- lang: eng
text: A novel chiral aromatic δ-amino acid building block was shown to fully induce
handedness in quinoline oligoamide foldamers with the possibility of further increasing
the bias by combining multiples of these units in the same sequence. Through its
incorporation within the helix, both N- and C-termini are still accessible for
further functionalisation.
article_processing_charge: No
article_type: original
author:
- first_name: Daniel
full_name: Bindl, Daniel
last_name: Bindl
- first_name: Elisabeth
full_name: Heinemann, Elisabeth
last_name: Heinemann
- first_name: Pradeep K
full_name: Mandal, Pradeep K
id: 6a3def15-d4b4-11ef-9fa9-a24c1f545ec3
last_name: Mandal
orcid: 0000-0001-5996-956X
- first_name: Ivan
full_name: Huc, Ivan
last_name: Huc
citation:
ama: Bindl D, Heinemann E, Mandal PK, Huc I. Quantitative helix handedness bias
through a single H vs. CH3 stereochemical differentiation. Chemical Communications.
2021;57(46):5662-5665. doi:10.1039/d1cc01452h
apa: Bindl, D., Heinemann, E., Mandal, P. K., & Huc, I. (2021). Quantitative
helix handedness bias through a single H vs. CH3 stereochemical differentiation.
Chemical Communications. Royal Society of Chemistry. https://doi.org/10.1039/d1cc01452h
chicago: Bindl, Daniel, Elisabeth Heinemann, Pradeep K Mandal, and Ivan Huc. “Quantitative
Helix Handedness Bias through a Single H vs. CH3 Stereochemical Differentiation.”
Chemical Communications. Royal Society of Chemistry, 2021. https://doi.org/10.1039/d1cc01452h.
ieee: D. Bindl, E. Heinemann, P. K. Mandal, and I. Huc, “Quantitative helix handedness
bias through a single H vs. CH3 stereochemical differentiation,” Chemical Communications,
vol. 57, no. 46. Royal Society of Chemistry, pp. 5662–5665, 2021.
ista: Bindl D, Heinemann E, Mandal PK, Huc I. 2021. Quantitative helix handedness
bias through a single H vs. CH3 stereochemical differentiation. Chemical Communications.
57(46), 5662–5665.
mla: Bindl, Daniel, et al. “Quantitative Helix Handedness Bias through a Single
H vs. CH3 Stereochemical Differentiation.” Chemical Communications, vol.
57, no. 46, Royal Society of Chemistry, 2021, pp. 5662–65, doi:10.1039/d1cc01452h.
short: D. Bindl, E. Heinemann, P.K. Mandal, I. Huc, Chemical Communications 57 (2021)
5662–5665.
date_created: 2026-01-29T15:18:02Z
date_published: 2021-04-29T00:00:00Z
date_updated: 2026-02-20T07:01:01Z
day: '29'
doi: 10.1039/d1cc01452h
extern: '1'
external_id:
pmid:
- '33972976 '
has_accepted_license: '1'
intvolume: ' 57'
issue: '46'
language:
- iso: eng
month: '04'
oa_version: None
page: 5662-5665
pmid: 1
publication: Chemical Communications
publication_identifier:
eissn:
- 1364-548X
issn:
- 1359-7345
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
status: public
title: Quantitative helix handedness bias through a single H vs. CH3 stereochemical
differentiation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 57
year: '2021'
...
---
OA_place: publisher
OA_type: hybrid
_id: '21552'
abstract:
- lang: eng
text: We present full-Maxwell topology-optimization design of a single-piece multilayer
metalens, about 10 wavelengths λ in thickness, which simultaneously focuses over
a 60° angular range and a 23% spectral bandwidth without suffering chromatic or
angular aberration, a “plan-achromat.” At all angles and frequencies, it achieves
diffraction-limited focusing (Strehl ratio >0.8) and an absolute focusing
efficiency of >50%. Both 2D and 3D axisymmetric designs are presented,
optimized over ∼105 degrees of freedom. We also demonstrate shortening the lens-to-sensor
distance while producing the same image as for a longer “virtual” focal length
and maintaining plan-achromaticity. These proof-of-concept designs demonstrate
the ultra-compact multifunctionality that can be achieved by exploiting the full
wave physics of subwavelength designs and motivate future work on design and fabrication
of multilayer metaoptics.
article_number: '041104'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Zin
full_name: Lin, Zin
last_name: Lin
- first_name: Charles
full_name: Roques-Carmes, Charles
id: e2e68fc9-6505-11ef-a541-eb4e72cc3e82
last_name: Roques-Carmes
- first_name: Rasmus E.
full_name: Christiansen, Rasmus E.
last_name: Christiansen
- first_name: Marin
full_name: Soljačić, Marin
last_name: Soljačić
- first_name: Steven G.
full_name: Johnson, Steven G.
last_name: Johnson
citation:
ama: Lin Z, Roques-Carmes C, Christiansen RE, Soljačić M, Johnson SG. Computational
inverse design for ultra-compact single-piece metalenses free of chromatic and
angular aberration. Applied Physics Letters. 2021;118(4). doi:10.1063/5.0035419
apa: Lin, Z., Roques-Carmes, C., Christiansen, R. E., Soljačić, M., & Johnson,
S. G. (2021). Computational inverse design for ultra-compact single-piece metalenses
free of chromatic and angular aberration. Applied Physics Letters. AIP
Publishing. https://doi.org/10.1063/5.0035419
chicago: Lin, Zin, Charles Roques-Carmes, Rasmus E. Christiansen, Marin Soljačić,
and Steven G. Johnson. “Computational Inverse Design for Ultra-Compact Single-Piece
Metalenses Free of Chromatic and Angular Aberration.” Applied Physics Letters.
AIP Publishing, 2021. https://doi.org/10.1063/5.0035419.
ieee: Z. Lin, C. Roques-Carmes, R. E. Christiansen, M. Soljačić, and S. G. Johnson,
“Computational inverse design for ultra-compact single-piece metalenses free of
chromatic and angular aberration,” Applied Physics Letters, vol. 118, no.
4. AIP Publishing, 2021.
ista: Lin Z, Roques-Carmes C, Christiansen RE, Soljačić M, Johnson SG. 2021. Computational
inverse design for ultra-compact single-piece metalenses free of chromatic and
angular aberration. Applied Physics Letters. 118(4), 041104.
mla: Lin, Zin, et al. “Computational Inverse Design for Ultra-Compact Single-Piece
Metalenses Free of Chromatic and Angular Aberration.” Applied Physics Letters,
vol. 118, no. 4, 041104, AIP Publishing, 2021, doi:10.1063/5.0035419.
short: Z. Lin, C. Roques-Carmes, R.E. Christiansen, M. Soljačić, S.G. Johnson, Applied
Physics Letters 118 (2021).
date_created: 2026-03-30T12:22:47Z
date_published: 2021-01-27T00:00:00Z
date_updated: 2026-04-27T09:56:01Z
day: '27'
ddc:
- '530'
doi: 10.1063/5.0035419
extern: '1'
external_id:
arxiv:
- '2011.10467'
intvolume: ' 118'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1063/5.0035419
month: '01'
oa: 1
oa_version: Published Version
publication: Applied Physics Letters
publication_identifier:
eissn:
- 1077-3118
issn:
- 0003-6951
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Computational inverse design for ultra-compact single-piece metalenses free
of chromatic and angular aberration
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: 118
year: '2021'
...
---
OA_type: green
_id: '21559'
abstract:
- lang: eng
text: Being a general wave phenomenon, bound states in the continuum (BICs) appear
in acoustic, hydrodynamic, and photonic systems of various dimensionalities. Here,
we report the first experimental observation of an accidental electromagnetic
BIC in a one-dimensional periodic chain of coaxial ceramic disks. We show that
the accidental BIC manifests itself as a narrow peak in the transmission spectra
of the chain placed between two loop antennas. We demonstrate a linear growth
of the radiative quality factor of the BICs with the number of disks that is well
described with the developed tight-binding model. We estimate the number of disks
when the radiation losses become negligible in comparison to material absorption
and, therefore, the chain can be considered as practically infinite. The presented
analysis is supported by near-field measurements of the BIC profile. The obtained
results provide useful guidelines for practical implementations of structures
with BICs opening up horizons for the development of radio-frequency and optical
metadevices.
article_number: '034041'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: M.S.
full_name: Sidorenko, M.S.
last_name: Sidorenko
- first_name: O.N.
full_name: Sergaeva, O.N.
last_name: Sergaeva
- first_name: Z.F.
full_name: Sadrieva, Z.F.
last_name: Sadrieva
- first_name: Charles
full_name: Roques-Carmes, Charles
id: e2e68fc9-6505-11ef-a541-eb4e72cc3e82
last_name: Roques-Carmes
- first_name: P.S.
full_name: Muraev, P.S.
last_name: Muraev
- first_name: D.N.
full_name: Maksimov, D.N.
last_name: Maksimov
- first_name: A.A.
full_name: Bogdanov, A.A.
last_name: Bogdanov
citation:
ama: Sidorenko MS, Sergaeva ON, Sadrieva ZF, et al. Observation of an accidental
bound state in the continuum in a chain of dielectric disks. Physical Review
Applied. 2021;15(3). doi:10.1103/physrevapplied.15.034041
apa: Sidorenko, M. S., Sergaeva, O. N., Sadrieva, Z. F., Roques-Carmes, C., Muraev,
P. S., Maksimov, D. N., & Bogdanov, A. A. (2021). Observation of an accidental
bound state in the continuum in a chain of dielectric disks. Physical Review
Applied. American Physical Society . https://doi.org/10.1103/physrevapplied.15.034041
chicago: Sidorenko, M.S., O.N. Sergaeva, Z.F. Sadrieva, Charles Roques-Carmes, P.S.
Muraev, D.N. Maksimov, and A.A. Bogdanov. “Observation of an Accidental Bound
State in the Continuum in a Chain of Dielectric Disks.” Physical Review Applied.
American Physical Society , 2021. https://doi.org/10.1103/physrevapplied.15.034041.
ieee: M. S. Sidorenko et al., “Observation of an accidental bound state in
the continuum in a chain of dielectric disks,” Physical Review Applied,
vol. 15, no. 3. American Physical Society , 2021.
ista: Sidorenko MS, Sergaeva ON, Sadrieva ZF, Roques-Carmes C, Muraev PS, Maksimov
DN, Bogdanov AA. 2021. Observation of an accidental bound state in the continuum
in a chain of dielectric disks. Physical Review Applied. 15(3), 034041.
mla: Sidorenko, M. S., et al. “Observation of an Accidental Bound State in the Continuum
in a Chain of Dielectric Disks.” Physical Review Applied, vol. 15, no.
3, 034041, American Physical Society , 2021, doi:10.1103/physrevapplied.15.034041.
short: M.S. Sidorenko, O.N. Sergaeva, Z.F. Sadrieva, C. Roques-Carmes, P.S. Muraev,
D.N. Maksimov, A.A. Bogdanov, Physical Review Applied 15 (2021).
date_created: 2026-03-30T12:22:47Z
date_published: 2021-03-15T00:00:00Z
date_updated: 2026-04-15T11:47:34Z
day: '15'
ddc:
- '530'
doi: 10.1103/physrevapplied.15.034041
extern: '1'
external_id:
arxiv:
- '2010.15167'
intvolume: ' 15'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2010.15167
month: '03'
oa: 1
oa_version: Preprint
publication: Physical Review Applied
publication_identifier:
eissn:
- 2331-7019
publication_status: published
publisher: 'American Physical Society '
quality_controlled: '1'
scopus_import: '1'
status: public
title: Observation of an accidental bound state in the continuum in a chain of dielectric
disks
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2021'
...