---
_id: '8268'
abstract:
- lang: eng
text: 'Modern scientific instruments produce vast amounts of data, which can overwhelm
the processing ability of computer systems. Lossy compression of data is an intriguing
solution, but comes with its own drawbacks, such as potential signal loss, and
the need for careful optimization of the compression ratio. In this work, we focus
on a setting where this problem is especially acute: compressive sensing frameworks
for interferometry and medical imaging. We ask the following question: can the
precision of the data representation be lowered for all inputs, with recovery
guarantees and practical performance Our first contribution is a theoretical analysis
of the normalized Iterative Hard Thresholding (IHT) algorithm when all input data,
meaning both the measurement matrix and the observation vector are quantized aggressively.
We present a variant of low precision normalized IHT that, under mild conditions,
can still provide recovery guarantees. The second contribution is the application
of our quantization framework to radio astronomy and magnetic resonance imaging.
We show that lowering the precision of the data can significantly accelerate image
recovery. We evaluate our approach on telescope data and samples of brain images
using CPU and FPGA implementations achieving up to a 9x speedup with negligible
loss of recovery quality.'
acknowledgement: The authors would like to thank Dr. Michiel Brentjens at the Netherlands
Institute for Radio Astronomy (ASTRON) for providing radio interferometer data and
Dr. Josip Marjanovic and Dr. Franciszek Hennel at the Magnetic Resonance Technology
of ETH Zurich for providing their insights on the experiments. CZ and the DS3Lab
gratefully acknowledge the support from the Swiss Data Science Center, Alibaba,
Google Focused Research Awards, Huawei, MeteoSwiss, Oracle Labs, Swisscom, Zurich
Insurance, Chinese Scholarship Council, and the Department of Computer Science at
ETH Zurich.
article_processing_charge: No
article_type: original
author:
- first_name: Nezihe Merve
full_name: Gurel, Nezihe Merve
last_name: Gurel
- first_name: Kaan
full_name: Kara, Kaan
last_name: Kara
- first_name: Alen
full_name: Stojanov, Alen
last_name: Stojanov
- first_name: Tyler
full_name: Smith, Tyler
last_name: Smith
- first_name: Thomas
full_name: Lemmin, Thomas
last_name: Lemmin
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Markus
full_name: Puschel, Markus
last_name: Puschel
- first_name: Ce
full_name: Zhang, Ce
last_name: Zhang
citation:
ama: 'Gurel NM, Kara K, Stojanov A, et al. Compressive sensing using iterative hard
thresholding with low precision data representation: Theory and applications.
IEEE Transactions on Signal Processing. 2020;68:4268-4282. doi:10.1109/TSP.2020.3010355'
apa: 'Gurel, N. M., Kara, K., Stojanov, A., Smith, T., Lemmin, T., Alistarh, D.-A.,
… Zhang, C. (2020). Compressive sensing using iterative hard thresholding with
low precision data representation: Theory and applications. IEEE Transactions
on Signal Processing. IEEE. https://doi.org/10.1109/TSP.2020.3010355'
chicago: 'Gurel, Nezihe Merve, Kaan Kara, Alen Stojanov, Tyler Smith, Thomas Lemmin,
Dan-Adrian Alistarh, Markus Puschel, and Ce Zhang. “Compressive Sensing Using
Iterative Hard Thresholding with Low Precision Data Representation: Theory and
Applications.” IEEE Transactions on Signal Processing. IEEE, 2020. https://doi.org/10.1109/TSP.2020.3010355.'
ieee: 'N. M. Gurel et al., “Compressive sensing using iterative hard thresholding
with low precision data representation: Theory and applications,” IEEE Transactions
on Signal Processing, vol. 68. IEEE, pp. 4268–4282, 2020.'
ista: 'Gurel NM, Kara K, Stojanov A, Smith T, Lemmin T, Alistarh D-A, Puschel M,
Zhang C. 2020. Compressive sensing using iterative hard thresholding with low
precision data representation: Theory and applications. IEEE Transactions on Signal
Processing. 68, 4268–4282.'
mla: 'Gurel, Nezihe Merve, et al. “Compressive Sensing Using Iterative Hard Thresholding
with Low Precision Data Representation: Theory and Applications.” IEEE Transactions
on Signal Processing, vol. 68, IEEE, 2020, pp. 4268–82, doi:10.1109/TSP.2020.3010355.'
short: N.M. Gurel, K. Kara, A. Stojanov, T. Smith, T. Lemmin, D.-A. Alistarh, M.
Puschel, C. Zhang, IEEE Transactions on Signal Processing 68 (2020) 4268–4282.
date_created: 2020-08-16T22:00:56Z
date_published: 2020-07-20T00:00:00Z
date_updated: 2023-08-22T08:40:08Z
day: '20'
department:
- _id: DaAl
doi: 10.1109/TSP.2020.3010355
external_id:
arxiv:
- '1802.04907'
isi:
- '000562044500001'
intvolume: ' 68'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1802.04907
month: '07'
oa: 1
oa_version: Preprint
page: 4268-4282
publication: IEEE Transactions on Signal Processing
publication_identifier:
eissn:
- '19410476'
issn:
- 1053587X
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Compressive sensing using iterative hard thresholding with low precision data
representation: Theory and applications'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 68
year: '2020'
...
---
_id: '8271'
acknowledgement: We thank Dr. Gai Huang for his comments and help. We apologize to
authors whose work could not be cited due to space limitation. No conflict of interest
declared.
article_processing_charge: No
article_type: original
author:
- first_name: Peng
full_name: He, Peng
last_name: He
- first_name: Yuzhou
full_name: Zhang, Yuzhou
id: 3B6137F2-F248-11E8-B48F-1D18A9856A87
last_name: Zhang
orcid: 0000-0003-2627-6956
- first_name: Guanghui
full_name: Xiao, Guanghui
last_name: Xiao
citation:
ama: He P, Zhang Y, Xiao G. Origin of a subgenome and genome evolution of allotetraploid
cotton species. Molecular Plant. 2020;13(9):1238-1240. doi:10.1016/j.molp.2020.07.006
apa: He, P., Zhang, Y., & Xiao, G. (2020). Origin of a subgenome and genome
evolution of allotetraploid cotton species. Molecular Plant. Elsevier.
https://doi.org/10.1016/j.molp.2020.07.006
chicago: He, Peng, Yuzhou Zhang, and Guanghui Xiao. “Origin of a Subgenome and Genome
Evolution of Allotetraploid Cotton Species.” Molecular Plant. Elsevier,
2020. https://doi.org/10.1016/j.molp.2020.07.006.
ieee: P. He, Y. Zhang, and G. Xiao, “Origin of a subgenome and genome evolution
of allotetraploid cotton species,” Molecular Plant, vol. 13, no. 9. Elsevier,
pp. 1238–1240, 2020.
ista: He P, Zhang Y, Xiao G. 2020. Origin of a subgenome and genome evolution of
allotetraploid cotton species. Molecular Plant. 13(9), 1238–1240.
mla: He, Peng, et al. “Origin of a Subgenome and Genome Evolution of Allotetraploid
Cotton Species.” Molecular Plant, vol. 13, no. 9, Elsevier, 2020, pp. 1238–40,
doi:10.1016/j.molp.2020.07.006.
short: P. He, Y. Zhang, G. Xiao, Molecular Plant 13 (2020) 1238–1240.
date_created: 2020-08-16T22:00:57Z
date_published: 2020-09-07T00:00:00Z
date_updated: 2023-08-22T08:40:35Z
day: '07'
department:
- _id: JiFr
doi: 10.1016/j.molp.2020.07.006
external_id:
isi:
- '000566895400007'
pmid:
- '32688032'
intvolume: ' 13'
isi: 1
issue: '9'
language:
- iso: eng
month: '09'
oa_version: None
page: 1238-1240
pmid: 1
publication: Molecular Plant
publication_identifier:
eissn:
- '17529867'
issn:
- '16742052'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Origin of a subgenome and genome evolution of allotetraploid cotton species
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 13
year: '2020'
...
---
_id: '8101'
abstract:
- lang: eng
text: By rigorously accounting for mesoscale spatial correlations in donor/acceptor
surface properties, we develop a scale-spanning model for same-material tribocharging.
We find that mesoscale correlations affect not only the magnitude of charge transfer
but also the fluctuations—suppressing otherwise overwhelming charge-transfer variability
that is not observed experimentally. We furthermore propose a generic theoretical
mechanism by which the mesoscale features might emerge, which is qualitatively
consistent with other proposals in the literature.
acknowledgement: "We would like to thank Philip Born, Bartosz Grzybowski, Tarik Baytekin,
and Bilge Baytekin for helpful discussions.\r\nThis project has received funding
from the European Unions Horizon 2020 research and innovation programme under the
Marie Skłodowska-Curie Grant Agreement No. 754411."
article_number: '082602'
article_processing_charge: Yes
article_type: original
author:
- 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: Sebastian
full_name: Wald, Sebastian
id: 133F200A-B015-11E9-AD41-0EDAE5697425
last_name: Wald
- first_name: Juan Carlos A
full_name: Sobarzo Ponce, Juan Carlos A
id: 4B807D68-AE37-11E9-AC72-31CAE5697425
last_name: Sobarzo Ponce
- 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: Grosjean GM, Wald S, Sobarzo Ponce JCA, Waitukaitis SR. Quantitatively consistent
scale-spanning model for same-material tribocharging. Physical Review Materials.
2020;4(8). doi:10.1103/PhysRevMaterials.4.082602
apa: Grosjean, G. M., Wald, S., Sobarzo Ponce, J. C. A., & Waitukaitis, S. R.
(2020). Quantitatively consistent scale-spanning model for same-material tribocharging.
Physical Review Materials. American Physical Society. https://doi.org/10.1103/PhysRevMaterials.4.082602
chicago: Grosjean, Galien M, Sebastian Wald, Juan Carlos A Sobarzo Ponce, and Scott
R Waitukaitis. “Quantitatively Consistent Scale-Spanning Model for Same-Material
Tribocharging.” Physical Review Materials. American Physical Society, 2020.
https://doi.org/10.1103/PhysRevMaterials.4.082602.
ieee: G. M. Grosjean, S. Wald, J. C. A. Sobarzo Ponce, and S. R. Waitukaitis, “Quantitatively
consistent scale-spanning model for same-material tribocharging,” Physical
Review Materials, vol. 4, no. 8. American Physical Society, 2020.
ista: Grosjean GM, Wald S, Sobarzo Ponce JCA, Waitukaitis SR. 2020. Quantitatively
consistent scale-spanning model for same-material tribocharging. Physical Review
Materials. 4(8), 082602.
mla: Grosjean, Galien M., et al. “Quantitatively Consistent Scale-Spanning Model
for Same-Material Tribocharging.” Physical Review Materials, vol. 4, no.
8, 082602, American Physical Society, 2020, doi:10.1103/PhysRevMaterials.4.082602.
short: G.M. Grosjean, S. Wald, J.C.A. Sobarzo Ponce, S.R. Waitukaitis, Physical
Review Materials 4 (2020).
date_created: 2020-07-07T11:33:54Z
date_published: 2020-08-17T00:00:00Z
date_updated: 2023-08-22T08:41:32Z
day: '17'
ddc:
- '530'
department:
- _id: ScWa
doi: 10.1103/PhysRevMaterials.4.082602
ec_funded: 1
external_id:
arxiv:
- '2006.07120'
isi:
- '000561897000001'
file:
- access_level: open_access
checksum: 288fef1eeb6540c6344bb8f7c8159dc9
content_type: application/pdf
creator: ggrosjea
date_created: 2020-08-17T15:54:20Z
date_updated: 2020-08-17T15:54:20Z
file_id: '8277'
file_name: Grosjean2020.pdf
file_size: 853753
relation: main_file
success: 1
file_date_updated: 2020-08-17T15:54:20Z
has_accepted_license: '1'
intvolume: ' 4'
isi: 1
issue: '8'
keyword:
- electric charge
- tribocharging
- soft matter
- granular materials
- polymers
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Physical Review Materials
publication_identifier:
issn:
- 2475-9953
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
record:
- id: '12697'
relation: popular_science
status: public
scopus_import: '1'
status: public
title: Quantitatively consistent scale-spanning model for same-material tribocharging
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 4
year: '2020'
...
---
_id: '8325'
abstract:
- lang: eng
text: "Let \U0001D439:ℤ2→ℤ be the pointwise minimum of several linear functions.
The theory of smoothing allows us to prove that under certain conditions there
exists the pointwise minimal function among all integer-valued superharmonic functions
coinciding with F “at infinity”. We develop such a theory to prove existence of
so-called solitons (or strings) in a sandpile model, studied by S. Caracciolo,
G. Paoletti, and A. Sportiello. Thus we made a step towards understanding the
phenomena of the identity in the sandpile group for planar domains where solitons
appear according to experiments. We prove that sandpile states, defined using
our smoothing procedure, move changeless when we apply the wave operator (that
is why we call them solitons), and can interact, forming triads and nodes. "
acknowledgement: We thank Andrea Sportiello for sharing his insights on perturbative
regimes of the Abelian sandpile model which was the starting point of our work.
We also thank Grigory Mikhalkin, who encouraged us to approach this problem. We
thank an anonymous referee. Also we thank Misha Khristoforov and Sergey Lanzat who
participated on the initial state of this project, when we had nothing except the
computer simulation and pictures. We thank Mikhail Raskin for providing us the code
on Golly for faster simulations. Ilia Zharkov, Ilia Itenberg, Kristin Shaw, Max
Karev, Lionel Levine, Ernesto Lupercio, Pavol Ševera, Yulieth Prieto, Michael Polyak,
Danila Cherkashin asked us a lot of questions and listened to us; not all of their
questions found answers here, but we are going to treat them in subsequent papers.
article_processing_charge: No
article_type: original
author:
- first_name: Nikita
full_name: Kalinin, Nikita
last_name: Kalinin
- first_name: Mikhail
full_name: Shkolnikov, Mikhail
id: 35084A62-F248-11E8-B48F-1D18A9856A87
last_name: Shkolnikov
orcid: 0000-0002-4310-178X
citation:
ama: Kalinin N, Shkolnikov M. Sandpile solitons via smoothing of superharmonic functions.
Communications in Mathematical Physics. 2020;378(9):1649-1675. doi:10.1007/s00220-020-03828-8
apa: Kalinin, N., & Shkolnikov, M. (2020). Sandpile solitons via smoothing of
superharmonic functions. Communications in Mathematical Physics. Springer
Nature. https://doi.org/10.1007/s00220-020-03828-8
chicago: Kalinin, Nikita, and Mikhail Shkolnikov. “Sandpile Solitons via Smoothing
of Superharmonic Functions.” Communications in Mathematical Physics. Springer
Nature, 2020. https://doi.org/10.1007/s00220-020-03828-8.
ieee: N. Kalinin and M. Shkolnikov, “Sandpile solitons via smoothing of superharmonic
functions,” Communications in Mathematical Physics, vol. 378, no. 9. Springer
Nature, pp. 1649–1675, 2020.
ista: Kalinin N, Shkolnikov M. 2020. Sandpile solitons via smoothing of superharmonic
functions. Communications in Mathematical Physics. 378(9), 1649–1675.
mla: Kalinin, Nikita, and Mikhail Shkolnikov. “Sandpile Solitons via Smoothing of
Superharmonic Functions.” Communications in Mathematical Physics, vol.
378, no. 9, Springer Nature, 2020, pp. 1649–75, doi:10.1007/s00220-020-03828-8.
short: N. Kalinin, M. Shkolnikov, Communications in Mathematical Physics 378 (2020)
1649–1675.
date_created: 2020-08-30T22:01:13Z
date_published: 2020-09-01T00:00:00Z
date_updated: 2023-08-22T09:00:03Z
day: '01'
department:
- _id: TaHa
doi: 10.1007/s00220-020-03828-8
ec_funded: 1
external_id:
arxiv:
- '1711.04285'
isi:
- '000560620600001'
intvolume: ' 378'
isi: 1
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1711.04285
month: '09'
oa: 1
oa_version: Preprint
page: 1649-1675
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Communications in Mathematical Physics
publication_identifier:
eissn:
- '14320916'
issn:
- '00103616'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sandpile solitons via smoothing of superharmonic functions
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 378
year: '2020'
...
---
_id: '8318'
abstract:
- lang: eng
text: Complex I is the first and the largest enzyme of respiratory chains in bacteria
and mitochondria. The mechanism which couples spatially separated transfer of
electrons to proton translocation in complex I is not known. Here we report five
crystal structures of T. thermophilus enzyme in complex with NADH or quinone-like
compounds. We also determined cryo-EM structures of major and minor native states
of the complex, differing in the position of the peripheral arm. Crystal structures
show that binding of quinone-like compounds (but not of NADH) leads to a related
global conformational change, accompanied by local re-arrangements propagating
from the quinone site to the nearest proton channel. Normal mode and molecular
dynamics analyses indicate that these are likely to represent the first steps
in the proton translocation mechanism. Our results suggest that quinone binding
and chemistry play a key role in the coupling mechanism of complex I.
acknowledgement: This work was funded by the Medical Research Council, UK and IST
Austria. We thank the European Synchrotron Radiation Facility and the Diamond Light
Source for provision of synchrotron radiation facilities. We are grateful to the
staff of beamlines ID29, ID23-2 (ESRF, Grenoble, France) and I03 (Diamond Light
Source, Didcot, UK) for assistance. Data processing was performed at the IST high-performance
computing cluster.
article_number: '4135'
article_processing_charge: No
article_type: original
author:
- first_name: Javier
full_name: Gutierrez-Fernandez, Javier
id: 3D9511BA-F248-11E8-B48F-1D18A9856A87
last_name: Gutierrez-Fernandez
- first_name: Karol
full_name: Kaszuba, Karol
id: 3FDF9472-F248-11E8-B48F-1D18A9856A87
last_name: Kaszuba
- first_name: Gurdeep S.
full_name: Minhas, Gurdeep S.
last_name: Minhas
- first_name: Rozbeh
full_name: Baradaran, Rozbeh
last_name: Baradaran
- first_name: Margherita
full_name: Tambalo, Margherita
id: 4187dfe4-ec23-11ea-ae46-f08ab378313a
last_name: Tambalo
- first_name: David T.
full_name: Gallagher, David T.
last_name: Gallagher
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Gutierrez-Fernandez J, Kaszuba K, Minhas GS, et al. Key role of quinone in
the mechanism of respiratory complex I. Nature Communications. 2020;11(1).
doi:10.1038/s41467-020-17957-0
apa: Gutierrez-Fernandez, J., Kaszuba, K., Minhas, G. S., Baradaran, R., Tambalo,
M., Gallagher, D. T., & Sazanov, L. A. (2020). Key role of quinone in the
mechanism of respiratory complex I. Nature Communications. Springer Nature.
https://doi.org/10.1038/s41467-020-17957-0
chicago: Gutierrez-Fernandez, Javier, Karol Kaszuba, Gurdeep S. Minhas, Rozbeh Baradaran,
Margherita Tambalo, David T. Gallagher, and Leonid A Sazanov. “Key Role of Quinone
in the Mechanism of Respiratory Complex I.” Nature Communications. Springer
Nature, 2020. https://doi.org/10.1038/s41467-020-17957-0.
ieee: J. Gutierrez-Fernandez et al., “Key role of quinone in the mechanism
of respiratory complex I,” Nature Communications, vol. 11, no. 1. Springer
Nature, 2020.
ista: Gutierrez-Fernandez J, Kaszuba K, Minhas GS, Baradaran R, Tambalo M, Gallagher
DT, Sazanov LA. 2020. Key role of quinone in the mechanism of respiratory complex
I. Nature Communications. 11(1), 4135.
mla: Gutierrez-Fernandez, Javier, et al. “Key Role of Quinone in the Mechanism of
Respiratory Complex I.” Nature Communications, vol. 11, no. 1, 4135, Springer
Nature, 2020, doi:10.1038/s41467-020-17957-0.
short: J. Gutierrez-Fernandez, K. Kaszuba, G.S. Minhas, R. Baradaran, M. Tambalo,
D.T. Gallagher, L.A. Sazanov, Nature Communications 11 (2020).
date_created: 2020-08-30T22:01:10Z
date_published: 2020-08-18T00:00:00Z
date_updated: 2023-08-22T09:03:00Z
day: '18'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.1038/s41467-020-17957-0
external_id:
isi:
- '000607072900001'
pmid:
- '32811817'
file:
- access_level: open_access
checksum: 52b96f41d7d0db9728064c08da00d030
content_type: application/pdf
creator: cziletti
date_created: 2020-08-31T13:40:00Z
date_updated: 2020-08-31T13:40:00Z
file_id: '8326'
file_name: 2020_NatComm_Gutierrez-Fernandez.pdf
file_size: 7527373
relation: main_file
success: 1
file_date_updated: 2020-08-31T13:40:00Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
issue: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- '20411723'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/mystery-of-giant-proton-pump-solved/
scopus_import: '1'
status: public
title: Key role of quinone in the mechanism of respiratory complex I
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2020'
...
---
_id: '8320'
abstract:
- lang: eng
text: The genetic code is considered to use five nucleic bases (adenine, guanine,
cytosine, thymine and uracil), which form two pairs for encoding information in
DNA and two pairs for encoding information in RNA. Nevertheless, in recent years
several artificial base pairs have been developed in attempts to expand the genetic
code. Employment of these additional base pairs increases the information capacity
and variety of DNA sequences, and provides a platform for the site-specific, enzymatic
incorporation of extra functional components into DNA and RNA. As a result, of
the development of such expanded systems, many artificial base pairs have been
synthesized and tested under various conditions. Following many stages of enhancement,
unnatural base pairs have been modified to eliminate their weak points, qualifying
them for specific research needs. Moreover, the first attempts to create a semi-synthetic
organism containing DNA with unnatural base pairs seem to have been successful.
This further extends the possible applications of these kinds of pairs. Herein,
we describe the most significant qualities of unnatural base pairs and their actual
applications.
acknowledgement: We would like to thank our co-workers and members of the Alkalaeva
lab for participating in discussions about the topics covered in this essay.
article_processing_charge: No
article_type: original
author:
- first_name: S. A.
full_name: Mukba, S. A.
last_name: Mukba
- first_name: Petr
full_name: Vlasov, Petr
id: 38BB9AC4-F248-11E8-B48F-1D18A9856A87
last_name: Vlasov
- first_name: P. M.
full_name: Kolosov, P. M.
last_name: Kolosov
- first_name: E. Y.
full_name: Shuvalova, E. Y.
last_name: Shuvalova
- first_name: T. V.
full_name: Egorova, T. V.
last_name: Egorova
- first_name: E. Z.
full_name: Alkalaeva, E. Z.
last_name: Alkalaeva
citation:
ama: 'Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. Expanding
the genetic code: Unnatural base pairs in biological systems. Molecular Biology.
2020;54(4):475-484. doi:10.1134/S0026893320040111'
apa: 'Mukba, S. A., Vlasov, P., Kolosov, P. M., Shuvalova, E. Y., Egorova, T. V.,
& Alkalaeva, E. Z. (2020). Expanding the genetic code: Unnatural base pairs
in biological systems. Molecular Biology. Springer Nature. https://doi.org/10.1134/S0026893320040111'
chicago: 'Mukba, S. A., Petr Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova,
and E. Z. Alkalaeva. “Expanding the Genetic Code: Unnatural Base Pairs in Biological
Systems.” Molecular Biology. Springer Nature, 2020. https://doi.org/10.1134/S0026893320040111.'
ieee: 'S. A. Mukba, P. Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and
E. Z. Alkalaeva, “Expanding the genetic code: Unnatural base pairs in biological
systems,” Molecular Biology, vol. 54, no. 4. Springer Nature, pp. 475–484,
2020.'
ista: 'Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. 2020.
Expanding the genetic code: Unnatural base pairs in biological systems. Molecular
Biology. 54(4), 475–484.'
mla: 'Mukba, S. A., et al. “Expanding the Genetic Code: Unnatural Base Pairs in
Biological Systems.” Molecular Biology, vol. 54, no. 4, Springer Nature,
2020, pp. 475–84, doi:10.1134/S0026893320040111.'
short: S.A. Mukba, P. Vlasov, P.M. Kolosov, E.Y. Shuvalova, T.V. Egorova, E.Z. Alkalaeva,
Molecular Biology 54 (2020) 475–484.
date_created: 2020-08-30T22:01:11Z
date_published: 2020-08-19T00:00:00Z
date_updated: 2023-08-22T09:01:03Z
day: '19'
department:
- _id: FyKo
doi: 10.1134/S0026893320040111
external_id:
isi:
- '000562110300001'
intvolume: ' 54'
isi: 1
issue: '4'
language:
- iso: eng
month: '08'
oa_version: None
page: 475-484
publication: Molecular Biology
publication_identifier:
eissn:
- '16083245'
issn:
- '00268933'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '8321'
relation: original
status: public
scopus_import: '1'
status: public
title: 'Expanding the genetic code: Unnatural base pairs in biological systems'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 54
year: '2020'
...
---
_id: '8321'
abstract:
- lang: eng
text: The genetic code is considered to use five nucleic bases (adenine, guanine,
cytosine, thymine and uracil), which form two pairs for encoding information in
DNA and two pairs for encoding information in RNA. Nevertheless, in recent years
several artificial base pairs have been developed in attempts to expand the genetic
code. Employment of these additional base pairs increases the information capacity
and variety of DNA sequences, and provides a platform for the site-specific, enzymatic
incorporation of extra functional components into DNA and RNA. As a result, of
the development of such expanded systems, many artificial base pairs have been
synthesized and tested under various conditions. Following many stages of enhancement,
unnatural base pairs have been modified to eliminate their weak points, qualifying
them for specific research needs. Moreover, the first attempts to create a semi-synthetic
organism containing DNA with unnatural base pairs seem to have been successful.
This further extends the possible applications of these kinds of pairs. Herein,
we describe the most significant qualities of unnatural base pairs and their actual
applications.
article_processing_charge: No
article_type: original
author:
- first_name: S. A.
full_name: Mukba, S. A.
last_name: Mukba
- first_name: Petr
full_name: Vlasov, Petr
id: 38BB9AC4-F248-11E8-B48F-1D18A9856A87
last_name: Vlasov
- first_name: P. M.
full_name: Kolosov, P. M.
last_name: Kolosov
- first_name: E. Y.
full_name: Shuvalova, E. Y.
last_name: Shuvalova
- first_name: T. V.
full_name: Egorova, T. V.
last_name: Egorova
- first_name: E. Z.
full_name: Alkalaeva, E. Z.
last_name: Alkalaeva
citation:
ama: 'Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. Expanding
the genetic code: Unnatural base pairs in biological systems. Molekuliarnaia
biologiia. 2020;54(4):531-541. doi:10.31857/S0026898420040126'
apa: 'Mukba, S. A., Vlasov, P., Kolosov, P. M., Shuvalova, E. Y., Egorova, T. V.,
& Alkalaeva, E. Z. (2020). Expanding the genetic code: Unnatural base pairs
in biological systems. Molekuliarnaia biologiia. Russian Academy of Sciences.
https://doi.org/10.31857/S0026898420040126'
chicago: 'Mukba, S. A., Petr Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova,
and E. Z. Alkalaeva. “Expanding the genetic code: Unnatural base pairs in biological
systems.” Molekuliarnaia biologiia. Russian Academy of Sciences, 2020.
https://doi.org/10.31857/S0026898420040126.'
ieee: 'S. A. Mukba, P. Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and
E. Z. Alkalaeva, “Expanding the genetic code: Unnatural base pairs in biological
systems,” Molekuliarnaia biologiia, vol. 54, no. 4. Russian Academy of
Sciences, pp. 531–541, 2020.'
ista: 'Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. 2020.
Expanding the genetic code: Unnatural base pairs in biological systems. Molekuliarnaia
biologiia. 54(4), 531–541.'
mla: 'Mukba, S. A., et al. “Expanding the genetic code: Unnatural base pairs in
biological systems.” Molekuliarnaia biologiia, vol. 54, no. 4, Russian
Academy of Sciences, 2020, pp. 531–41, doi:10.31857/S0026898420040126.'
short: S.A. Mukba, P. Vlasov, P.M. Kolosov, E.Y. Shuvalova, T.V. Egorova, E.Z. Alkalaeva,
Molekuliarnaia biologiia 54 (2020) 531–541.
date_created: 2020-08-30T22:01:11Z
date_published: 2020-07-01T00:00:00Z
date_updated: 2023-08-22T09:01:02Z
day: '01'
department:
- _id: FyKo
doi: 10.31857/S0026898420040126
external_id:
pmid:
- '32799218'
intvolume: ' 54'
issue: '4'
language:
- iso: rus
month: '07'
oa_version: None
page: 531-541
pmid: 1
publication: Molekuliarnaia biologiia
publication_identifier:
issn:
- '00268984'
publication_status: published
publisher: Russian Academy of Sciences
quality_controlled: '1'
related_material:
record:
- id: '8320'
relation: translation
status: public
scopus_import: '1'
status: public
title: 'Expanding the genetic code: Unnatural base pairs in biological systems'
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 54
year: '2020'
...
---
_id: '8323'
article_processing_charge: No
article_type: letter_note
author:
- first_name: János
full_name: Pach, János
id: E62E3130-B088-11EA-B919-BF823C25FEA4
last_name: Pach
citation:
ama: Pach J. A farewell to Ricky Pollack. Discrete and Computational Geometry.
2020;64:571-574. doi:10.1007/s00454-020-00237-5
apa: Pach, J. (2020). A farewell to Ricky Pollack. Discrete and Computational
Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00237-5
chicago: Pach, János. “A Farewell to Ricky Pollack.” Discrete and Computational
Geometry. Springer Nature, 2020. https://doi.org/10.1007/s00454-020-00237-5.
ieee: J. Pach, “A farewell to Ricky Pollack,” Discrete and Computational Geometry,
vol. 64. Springer Nature, pp. 571–574, 2020.
ista: Pach J. 2020. A farewell to Ricky Pollack. Discrete and Computational Geometry.
64, 571–574.
mla: Pach, János. “A Farewell to Ricky Pollack.” Discrete and Computational Geometry,
vol. 64, Springer Nature, 2020, pp. 571–74, doi:10.1007/s00454-020-00237-5.
short: J. Pach, Discrete and Computational Geometry 64 (2020) 571–574.
date_created: 2020-08-30T22:01:12Z
date_published: 2020-10-01T00:00:00Z
date_updated: 2023-08-22T09:05:04Z
day: '01'
department:
- _id: HeEd
doi: 10.1007/s00454-020-00237-5
external_id:
isi:
- '000561483500001'
intvolume: ' 64'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1007/s00454-020-00237-5
month: '10'
oa: 1
oa_version: None
page: 571-574
publication: Discrete and Computational Geometry
publication_identifier:
eissn:
- '14320444'
issn:
- '01795376'
publication_status: published
publisher: Springer Nature
scopus_import: '1'
status: public
title: A farewell to Ricky Pollack
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 64
year: '2020'
...
---
_id: '8336'
abstract:
- lang: eng
text: Plant hormone cytokinins are perceived by a subfamily of sensor histidine
kinases (HKs), which via a two-component phosphorelay cascade activate transcriptional
responses in the nucleus. Subcellular localization of the receptors proposed the
endoplasmic reticulum (ER) membrane as a principal cytokinin perception site,
while study of cytokinin transport pointed to the plasma membrane (PM)-mediated
cytokinin signalling. Here, by detailed monitoring of subcellular localizations
of the fluorescently labelled natural cytokinin probe and the receptor ARABIDOPSIS
HISTIDINE KINASE 4 (CRE1/AHK4) fused to GFP reporter, we show that pools of the
ER-located cytokinin receptors can enter the secretory pathway and reach the PM
in cells of the root apical meristem, and the cell plate of dividing meristematic
cells. Brefeldin A (BFA) experiments revealed vesicular recycling of the receptor
and its accumulation in BFA compartments. We provide a revised view on cytokinin
signalling and the possibility of multiple sites of perception at PM and ER.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: This paper is dedicated to deceased P. Galuszka for his support and
contribution to the project. This research was supported by the Scientific Service
Units (SSU) of IST-Austria through resources provided by the Bioimaging Facility
(BIF), the Life Science Facility (LSF) and by Centre of the Region Haná (CRH), Palacký
University. We thank Lucia Hlusková, Zuzana Pěkná and Martin Hönig for technical
assistance, and Fernando Aniento, Rashed Abualia and Andrej Hurný for sharing material.
The work was supported from ERDF project “Plants as a tool for sustainable global
development” (No. CZ.02.1.01/0.0/0.0/16_019/0000827), from Czech Science Foundation
via projects 16-04184S (O.P., K.K. and K.D.), 18-23972Y (D.Z., K.K.), 17-21122S
(K.B.), Erasmus+ (K.K.), Endowment Fund of Palacký University (K.K.) and EMBO Long-Term
Fellowship, ALTF number 710-2016 (J.C.M.); People Programme (Marie Curie Actions)
of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant
agreement no. [291734] (N.C.); DOC Fellowship of the Austrian Academy of Sciences
at the Institute of Science and Technology, Austria (H.S.).
article_number: '4285'
article_processing_charge: No
article_type: original
author:
- first_name: Karolina
full_name: Kubiasova, Karolina
id: 946011F4-3E71-11EA-860B-C7A73DDC885E
last_name: Kubiasova
orcid: 0000-0001-5630-9419
- first_name: Juan C
full_name: Montesinos López, Juan C
id: 310A8E3E-F248-11E8-B48F-1D18A9856A87
last_name: Montesinos López
orcid: 0000-0001-9179-6099
- first_name: Olga
full_name: Šamajová, Olga
last_name: Šamajová
- first_name: Jaroslav
full_name: Nisler, Jaroslav
last_name: Nisler
- first_name: Václav
full_name: Mik, Václav
last_name: Mik
- first_name: Hana
full_name: Semeradova, Hana
id: 42FE702E-F248-11E8-B48F-1D18A9856A87
last_name: Semeradova
- first_name: Lucie
full_name: Plíhalová, Lucie
last_name: Plíhalová
- first_name: Ondřej
full_name: Novák, Ondřej
last_name: Novák
- first_name: Peter
full_name: Marhavý, Peter
id: 3F45B078-F248-11E8-B48F-1D18A9856A87
last_name: Marhavý
orcid: 0000-0001-5227-5741
- first_name: Nicola
full_name: Cavallari, Nicola
id: 457160E6-F248-11E8-B48F-1D18A9856A87
last_name: Cavallari
- first_name: David
full_name: Zalabák, David
last_name: Zalabák
- first_name: Karel
full_name: Berka, Karel
last_name: Berka
- first_name: Karel
full_name: Doležal, Karel
last_name: Doležal
- first_name: Petr
full_name: Galuszka, Petr
last_name: Galuszka
- first_name: Jozef
full_name: Šamaj, Jozef
last_name: Šamaj
- first_name: Miroslav
full_name: Strnad, Miroslav
last_name: Strnad
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Ondřej
full_name: Plíhal, Ondřej
last_name: Plíhal
- first_name: Lukáš
full_name: Spíchal, Lukáš
last_name: Spíchal
citation:
ama: Kubiasova K, Montesinos López JC, Šamajová O, et al. Cytokinin fluoroprobe
reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic
reticulum. Nature Communications. 2020;11. doi:10.1038/s41467-020-17949-0
apa: Kubiasova, K., Montesinos López, J. C., Šamajová, O., Nisler, J., Mik, V.,
Semerádová, H., … Spíchal, L. (2020). Cytokinin fluoroprobe reveals multiple sites
of cytokinin perception at plasma membrane and endoplasmic reticulum. Nature
Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17949-0
chicago: Kubiasova, Karolina, Juan C Montesinos López, Olga Šamajová, Jaroslav Nisler,
Václav Mik, Hana Semerádová, Lucie Plíhalová, et al. “Cytokinin Fluoroprobe Reveals
Multiple Sites of Cytokinin Perception at Plasma Membrane and Endoplasmic Reticulum.”
Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17949-0.
ieee: K. Kubiasova et al., “Cytokinin fluoroprobe reveals multiple sites
of cytokinin perception at plasma membrane and endoplasmic reticulum,” Nature
Communications, vol. 11. Springer Nature, 2020.
ista: Kubiasova K, Montesinos López JC, Šamajová O, Nisler J, Mik V, Semerádová
H, Plíhalová L, Novák O, Marhavý P, Cavallari N, Zalabák D, Berka K, Doležal K,
Galuszka P, Šamaj J, Strnad M, Benková E, Plíhal O, Spíchal L. 2020. Cytokinin
fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane
and endoplasmic reticulum. Nature Communications. 11, 4285.
mla: Kubiasova, Karolina, et al. “Cytokinin Fluoroprobe Reveals Multiple Sites of
Cytokinin Perception at Plasma Membrane and Endoplasmic Reticulum.” Nature
Communications, vol. 11, 4285, Springer Nature, 2020, doi:10.1038/s41467-020-17949-0.
short: K. Kubiasova, J.C. Montesinos López, O. Šamajová, J. Nisler, V. Mik, H. Semerádová,
L. Plíhalová, O. Novák, P. Marhavý, N. Cavallari, D. Zalabák, K. Berka, K. Doležal,
P. Galuszka, J. Šamaj, M. Strnad, E. Benková, O. Plíhal, L. Spíchal, Nature Communications
11 (2020).
date_created: 2020-09-06T22:01:12Z
date_published: 2020-08-27T00:00:00Z
date_updated: 2023-08-22T09:09:06Z
day: '27'
ddc:
- '580'
department:
- _id: EvBe
doi: 10.1038/s41467-020-17949-0
ec_funded: 1
external_id:
isi:
- '000567931000002'
pmid:
- '32855390'
file:
- access_level: open_access
checksum: 7494b7665b3d2bf2d8edb13e4f12b92d
content_type: application/pdf
creator: dernst
date_created: 2020-09-10T08:05:19Z
date_updated: 2020-09-10T08:05:19Z
file_id: '8357'
file_name: 2020_NatureComm_Kubiasova.pdf
file_size: 3455704
relation: main_file
success: 1
file_date_updated: 2020-09-10T08:05:19Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 261821BC-B435-11E9-9278-68D0E5697425
grant_number: '24746'
name: Molecular mechanisms of the cytokinin regulated endomembrane trafficking to
coordinate plant organogenesis.
- _id: 253E54C8-B435-11E9-9278-68D0E5697425
grant_number: ALTF710-2016
name: Molecular mechanism of auxindriven formative divisions delineating lateral
root organogenesis in plants
publication: Nature Communications
publication_identifier:
eissn:
- '20411723'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma
membrane and endoplasmic reticulum
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2020'
...
---
_id: '8337'
abstract:
- lang: eng
text: Cytokinins are mobile multifunctional plant hormones with roles in development
and stress resilience. Although their Histidine Kinase receptors are substantially
localised to the endoplasmic reticulum, cellular sites of cytokinin perception
and importance of spatially heterogeneous cytokinin distribution continue to be
debated. Here we show that cytokinin perception by plasma membrane receptors is
an effective additional path for cytokinin response. Readout from a Two Component
Signalling cytokinin-specific reporter (TCSn::GFP) closely matches intracellular
cytokinin content in roots, yet we also find cytokinins in extracellular fluid,
potentially enabling action at the cell surface. Cytokinins covalently linked
to beads that could not pass the plasma membrane increased expression of both
TCSn::GFP and Cytokinin Response Factors. Super-resolution microscopy of GFP-labelled
receptors and diminished TCSn::GFP response to immobilised cytokinins in cytokinin
receptor mutants, further indicate that receptors can function at the cell surface.
We argue that dual intracellular and surface locations may augment flexibility
of cytokinin responses.
acknowledged_ssus:
- _id: Bio
acknowledgement: 'We thank Bruno Müller and Aaron Rashotte for critical discussions
and provision of plant lines used in this work, Roger Granbom and Tamara Hernández
Verdeja (UPSC, Umeå, Sweden) for technical assistance and providing materials, Zuzana
Pěkná and Karolina Wojewodová (CRH, Palacký University, Olomouc, Czech Republic)
for help with cytokinin receptor binding assays, and David Zalabák (CRH, Palacký
University, Olomouc, Czech Republic) for provision of vector pINIIIΔEH expressing
CRE1/AHK4. The bioimaging facility of IST Austria, the Swedish Metabolomics Centre
and the IST Austria Bio-Imaging facility are acknowledged for support. The work
was funded by the European Molecular Biology Organization (EMBO ASTF 297-2013) (I.A.),
Development—The Company of Biologists (DEVTF2012) (I.A.; C.T.), Plant Fellows (the
International Post doc Fellowship Programme in Plant Sciences, 267423) (I.A.; K.L.),
the Swedish Research Council (621-2014-4514) (K.L.), UPSC Berzelii Center for Forest
Biotechnology (Vinnova 2012-01560), Kempestiftelserna (JCK-2711) (K.L.) and (JCK-1811)
(E.-M.B., K.L.). The Ministry of Education, Youth and Sports of the Czech Republic
via the European Regional Development Fund-Project “Plants as a tool for sustainable
global development” (CZ.02.1.01/0.0/0.0/16_019/0000827) (O.N., O.P., R.S., V.M.,
L.P., K.D.) and project CEITEC 2020 (LQ1601) (M.P., J.H.) provided support, as did
the Czech Science Foundation via projects GP14-30004P (M.P.) and 16-04184S (O.P.,
K.D., O.N.), Vetenskapsrådet and Vinnova (Verket för Innovationssystem) (T.V., S.R.),
Knut och Alice Wallenbergs Stiftelse via “Shapesystem” grant number 2012.0050. A.J.
was supported by the Austria Science Fund (FWF): I03630 to J.F. The research leading
to these results received funding from European Union’s Horizon 2020 programme (ERC
grant no. 742985) and FWO-FWF joint project G0E5718N to J.F.'
article_number: '4284'
article_processing_charge: No
article_type: original
author:
- first_name: Ioanna
full_name: Antoniadi, Ioanna
last_name: Antoniadi
- first_name: Ondřej
full_name: Novák, Ondřej
last_name: Novák
- first_name: Zuzana
full_name: Gelová, Zuzana
id: 0AE74790-0E0B-11E9-ABC7-1ACFE5697425
last_name: Gelová
orcid: 0000-0003-4783-1752
- first_name: Alexander J
full_name: Johnson, Alexander J
id: 46A62C3A-F248-11E8-B48F-1D18A9856A87
last_name: Johnson
orcid: 0000-0002-2739-8843
- first_name: Ondřej
full_name: Plíhal, Ondřej
last_name: Plíhal
- first_name: Radim
full_name: Simerský, Radim
last_name: Simerský
- first_name: Václav
full_name: Mik, Václav
last_name: Mik
- first_name: Thomas
full_name: Vain, Thomas
last_name: Vain
- first_name: Eduardo
full_name: Mateo-Bonmatí, Eduardo
last_name: Mateo-Bonmatí
- first_name: Michal
full_name: Karady, Michal
last_name: Karady
- first_name: Markéta
full_name: Pernisová, Markéta
last_name: Pernisová
- first_name: Lenka
full_name: Plačková, Lenka
last_name: Plačková
- first_name: Korawit
full_name: Opassathian, Korawit
last_name: Opassathian
- first_name: Jan
full_name: Hejátko, Jan
last_name: Hejátko
- first_name: Stéphanie
full_name: Robert, Stéphanie
last_name: Robert
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Karel
full_name: Doležal, Karel
last_name: Doležal
- first_name: Karin
full_name: Ljung, Karin
last_name: Ljung
- first_name: Colin
full_name: Turnbull, Colin
last_name: Turnbull
citation:
ama: Antoniadi I, Novák O, Gelová Z, et al. Cell-surface receptors enable perception
of extracellular cytokinins. Nature Communications. 2020;11. doi:10.1038/s41467-020-17700-9
apa: Antoniadi, I., Novák, O., Gelová, Z., Johnson, A. J., Plíhal, O., Simerský,
R., … Turnbull, C. (2020). Cell-surface receptors enable perception of extracellular
cytokinins. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17700-9
chicago: Antoniadi, Ioanna, Ondřej Novák, Zuzana Gelová, Alexander J Johnson, Ondřej
Plíhal, Radim Simerský, Václav Mik, et al. “Cell-Surface Receptors Enable Perception
of Extracellular Cytokinins.” Nature Communications. Springer Nature, 2020.
https://doi.org/10.1038/s41467-020-17700-9.
ieee: I. Antoniadi et al., “Cell-surface receptors enable perception of extracellular
cytokinins,” Nature Communications, vol. 11. Springer Nature, 2020.
ista: Antoniadi I, Novák O, Gelová Z, Johnson AJ, Plíhal O, Simerský R, Mik V, Vain
T, Mateo-Bonmatí E, Karady M, Pernisová M, Plačková L, Opassathian K, Hejátko
J, Robert S, Friml J, Doležal K, Ljung K, Turnbull C. 2020. Cell-surface receptors
enable perception of extracellular cytokinins. Nature Communications. 11, 4284.
mla: Antoniadi, Ioanna, et al. “Cell-Surface Receptors Enable Perception of Extracellular
Cytokinins.” Nature Communications, vol. 11, 4284, Springer Nature, 2020,
doi:10.1038/s41467-020-17700-9.
short: I. Antoniadi, O. Novák, Z. Gelová, A.J. Johnson, O. Plíhal, R. Simerský,
V. Mik, T. Vain, E. Mateo-Bonmatí, M. Karady, M. Pernisová, L. Plačková, K. Opassathian,
J. Hejátko, S. Robert, J. Friml, K. Doležal, K. Ljung, C. Turnbull, Nature Communications
11 (2020).
date_created: 2020-09-06T22:01:13Z
date_published: 2020-08-27T00:00:00Z
date_updated: 2023-08-22T09:10:32Z
day: '27'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1038/s41467-020-17700-9
ec_funded: 1
external_id:
isi:
- '000567931000001'
file:
- access_level: open_access
checksum: 5b96f39b598de7510cfefefb819b9a6d
content_type: application/pdf
creator: dernst
date_created: 2020-12-10T12:23:56Z
date_updated: 2020-12-10T12:23:56Z
file_id: '8936'
file_name: 2020_NatureComm_Antoniadi.pdf
file_size: 3526415
relation: main_file
success: 1
file_date_updated: 2020-12-10T12:23:56Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 26538374-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03630
name: Molecular mechanisms of endocytic cargo recognition in plants
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication: Nature Communications
publication_identifier:
eissn:
- '20411723'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cell-surface receptors enable perception of extracellular cytokinins
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2020'
...
---
_id: '8067'
abstract:
- lang: eng
text: "With the lithium-ion technology approaching its intrinsic limit with graphite-based
anodes, lithium metal is recently receiving renewed interest from the battery
community as potential high capacity anode for next-generation rechargeable batteries.
In this focus paper, we review the main advances in this field since the first
attempts in the\r\nmid-1970s. Strategies for enabling reversible cycling and avoiding
dendrite growth are thoroughly discussed, including specific applications in all-solid-state
(polymeric and inorganic), Lithium-sulphur and Li-O2 (air) batteries. A particular
attention is paid to review recent developments in regard of prototype manufacturing
and current state-ofthe-art of these battery technologies with respect to the
2030 targets of the EU Integrated Strategic Energy Technology Plan (SET-Plan)
Action 7."
alternative_title:
- IST Austria Technical Report
article_processing_charge: No
author:
- first_name: Alberto
full_name: Varzi, Alberto
last_name: Varzi
- first_name: Katharina
full_name: Thanner, Katharina
last_name: Thanner
- first_name: Roberto
full_name: Scipioni, Roberto
last_name: Scipioni
- first_name: Daniele
full_name: Di Lecce, Daniele
last_name: Di Lecce
- first_name: Jusef
full_name: Hassoun, Jusef
last_name: Hassoun
- first_name: Susanne
full_name: Dörfler, Susanne
last_name: Dörfler
- first_name: Holger
full_name: Altheus, Holger
last_name: Altheus
- first_name: Stefan
full_name: Kaskel, Stefan
last_name: Kaskel
- first_name: Christian
full_name: Prehal, Christian
last_name: Prehal
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
citation:
ama: Varzi A, Thanner K, Scipioni R, et al. Current Status and Future Perspectives
of Lithium Metal Batteries. IST Austria doi:10.15479/AT:ISTA:8067
apa: Varzi, A., Thanner, K., Scipioni, R., Di Lecce, D., Hassoun, J., Dörfler, S.,
… Freunberger, S. A. (n.d.). Current status and future perspectives of Lithium
metal batteries. IST Austria. https://doi.org/10.15479/AT:ISTA:8067
chicago: Varzi, Alberto, Katharina Thanner, Roberto Scipioni, Daniele Di Lecce,
Jusef Hassoun, Susanne Dörfler, Holger Altheus, Stefan Kaskel, Christian Prehal,
and Stefan Alexander Freunberger. Current Status and Future Perspectives of
Lithium Metal Batteries. IST Austria, n.d. https://doi.org/10.15479/AT:ISTA:8067.
ieee: A. Varzi et al., Current status and future perspectives of Lithium
metal batteries. IST Austria.
ista: Varzi A, Thanner K, Scipioni R, Di Lecce D, Hassoun J, Dörfler S, Altheus
H, Kaskel S, Prehal C, Freunberger SA. Current status and future perspectives
of Lithium metal batteries, IST Austria, 63p.
mla: Varzi, Alberto, et al. Current Status and Future Perspectives of Lithium
Metal Batteries. IST Austria, doi:10.15479/AT:ISTA:8067.
short: A. Varzi, K. Thanner, R. Scipioni, D. Di Lecce, J. Hassoun, S. Dörfler, H.
Altheus, S. Kaskel, C. Prehal, S.A. Freunberger, Current Status and Future Perspectives
of Lithium Metal Batteries, IST Austria, n.d.
date_created: 2020-06-30T07:37:39Z
date_published: 2020-07-01T00:00:00Z
date_updated: 2023-08-22T09:20:36Z
day: '01'
ddc:
- '540'
department:
- _id: StFr
doi: 10.15479/AT:ISTA:8067
file:
- access_level: open_access
checksum: d183ca1465a1cbb4f8db27875cd156f7
content_type: application/pdf
creator: dernst
date_created: 2020-07-02T07:36:04Z
date_updated: 2020-07-14T12:48:08Z
file_id: '8076'
file_name: 20200612_JPS_review_Li_metal_submitted.pdf
file_size: 2612498
relation: main_file
file_date_updated: 2020-07-14T12:48:08Z
has_accepted_license: '1'
keyword:
- Battery
- Lithium metal
- Lithium-sulphur
- Lithium-air
- All-solid-state
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '63'
publication_identifier:
issn:
- 2664-1690
publication_status: submitted
publisher: IST Austria
related_material:
record:
- id: '8361'
relation: later_version
status: public
status: public
title: Current status and future perspectives of Lithium metal batteries
type: technical_report
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2020'
...
---
_id: '8361'
abstract:
- lang: eng
text: With the lithium-ion technology approaching its intrinsic limit with graphite-based
anodes, Li metal is recently receiving renewed interest from the battery community
as potential high capacity anode for next-generation rechargeable batteries. In
this focus paper, we review the main advances in this field since the first attempts
in the mid-1970s. Strategies for enabling reversible cycling and avoiding dendrite
growth are thoroughly discussed, including specific applications in all-solid-state
(inorganic and polymeric), Lithium–Sulfur (Li–S) and Lithium-O2 (air) batteries.
A particular attention is paid to recent developments of these battery technologies
and their current state with respect to the 2030 targets of the EU Integrated
Strategic Energy Technology Plan (SET-Plan) Action 7.
acknowledgement: A.V. and K.T. acknowledge, respectively, the financial support of
the Helmholtz Association and BMW AG. J.H. acknowledges the collabo-ration project
“Accordo di Collaborazione Quadro 2015” between Uni-versity of Ferrara (Department
of Chemical and Pharmaceutical Sciences) and Sapienza University of Rome (Department
of Chemistry). S.D., H.A. and S.K. thank the Fraunhofer Gesellschaft, Technische
Uni-versit ̈at Dresden and would like to acknowledge European Union’s Horizon
2020 research and innovation programme under grant agree-ment No 814471. S.A.F.
and C.P. are indebted to the European Research Council (ERC) under the European
Union’s Horizon 2020 research and innovation program (grant agreement no. 636069)
and IST Austria.
article_number: '228803'
article_processing_charge: No
article_type: original
author:
- first_name: Alberto
full_name: Varzi, Alberto
last_name: Varzi
orcid: 0000-0001-5069-0589
- first_name: Katharina
full_name: Thanner, Katharina
last_name: Thanner
orcid: 0000-0001-5394-2323
- first_name: Roberto
full_name: Scipioni, Roberto
last_name: Scipioni
orcid: 0000-0003-1926-421X
- first_name: Daniele
full_name: Di Lecce, Daniele
last_name: Di Lecce
- first_name: Jusef
full_name: Hassoun, Jusef
last_name: Hassoun
- first_name: Susanne
full_name: Dörfler, Susanne
last_name: Dörfler
- first_name: Holger
full_name: Altheus, Holger
last_name: Altheus
- first_name: Stefan
full_name: Kaskel, Stefan
last_name: Kaskel
- first_name: Christian
full_name: Prehal, Christian
last_name: Prehal
orcid: 0000-0003-0654-0940
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
citation:
ama: Varzi A, Thanner K, Scipioni R, et al. Current status and future perspectives
of lithium metal batteries. Journal of Power Sources. 2020;480(12). doi:10.1016/j.jpowsour.2020.228803
apa: Varzi, A., Thanner, K., Scipioni, R., Di Lecce, D., Hassoun, J., Dörfler, S.,
… Freunberger, S. A. (2020). Current status and future perspectives of lithium
metal batteries. Journal of Power Sources. Elsevier. https://doi.org/10.1016/j.jpowsour.2020.228803
chicago: Varzi, Alberto, Katharina Thanner, Roberto Scipioni, Daniele Di Lecce,
Jusef Hassoun, Susanne Dörfler, Holger Altheus, Stefan Kaskel, Christian Prehal,
and Stefan Alexander Freunberger. “Current Status and Future Perspectives of Lithium
Metal Batteries.” Journal of Power Sources. Elsevier, 2020. https://doi.org/10.1016/j.jpowsour.2020.228803.
ieee: A. Varzi et al., “Current status and future perspectives of lithium
metal batteries,” Journal of Power Sources, vol. 480, no. 12. Elsevier,
2020.
ista: Varzi A, Thanner K, Scipioni R, Di Lecce D, Hassoun J, Dörfler S, Altheus
H, Kaskel S, Prehal C, Freunberger SA. 2020. Current status and future perspectives
of lithium metal batteries. Journal of Power Sources. 480(12), 228803.
mla: Varzi, Alberto, et al. “Current Status and Future Perspectives of Lithium Metal
Batteries.” Journal of Power Sources, vol. 480, no. 12, 228803, Elsevier,
2020, doi:10.1016/j.jpowsour.2020.228803.
short: A. Varzi, K. Thanner, R. Scipioni, D. Di Lecce, J. Hassoun, S. Dörfler, H.
Altheus, S. Kaskel, C. Prehal, S.A. Freunberger, Journal of Power Sources 480
(2020).
date_created: 2020-09-10T10:48:40Z
date_published: 2020-12-31T00:00:00Z
date_updated: 2023-08-22T09:20:37Z
day: '31'
department:
- _id: StFr
doi: 10.1016/j.jpowsour.2020.228803
external_id:
isi:
- '000593857300001'
intvolume: ' 480'
isi: 1
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.jpowsour.2020.228803
month: '12'
oa: 1
oa_version: Published Version
publication: Journal of Power Sources
publication_identifier:
issn:
- 0378-7753
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '8067'
relation: earlier_version
status: public
status: public
title: Current status and future perspectives of lithium metal batteries
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 480
year: '2020'
...
---
_id: '14028'
abstract:
- lang: eng
text: 'The present review addresses the technical advances and the theoretical developments
to realize and rationalize attosecond-science experiments that reveal a new dynamical
time scale (10−15-10−18 s), with a particular emphasis on molecular systems and
the implications of attosecond processes for chemical dynamics. After a brief
outline of the theoretical framework for treating non-perturbative phenomena in
Section 2, we introduce the physical mechanisms underlying high-harmonic generation
and attosecond technology. The relevant technological developments and experimental
schemes are covered in Section 3. Throughout the remainder of the chapter, we
report on selected applications in molecular attosecond physics, thereby addressing
specific phenomena mediated by purely electronic dynamics: charge localization
in molecular hydrogen, charge migration in biorelevant molecules, high-harmonic
spectroscopy, and delays in molecular photoionization.'
article_processing_charge: No
author:
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: Hans Jakob
full_name: Wörner, Hans Jakob
last_name: Wörner
citation:
ama: Baykusheva DR, Wörner HJ. Attosecond molecular spectroscopy and dynamics. doi:10.48550/arXiv.2002.02111
apa: Baykusheva, D. R., & Wörner, H. J. (n.d.). Attosecond molecular spectroscopy
and dynamics. https://doi.org/10.48550/arXiv.2002.02111
chicago: Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. “Attosecond Molecular
Spectroscopy and Dynamics,” n.d. https://doi.org/10.48550/arXiv.2002.02111.
ieee: D. R. Baykusheva and H. J. Wörner, “Attosecond molecular spectroscopy and
dynamics.” .
ista: Baykusheva DR, Wörner HJ. Attosecond molecular spectroscopy and dynamics.
10.48550/arXiv.2002.02111.
mla: Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. Attosecond Molecular
Spectroscopy and Dynamics. doi:10.48550/arXiv.2002.02111.
short: D.R. Baykusheva, H.J. Wörner, (n.d.).
date_created: 2023-08-10T06:47:45Z
date_published: 2020-02-01T00:00:00Z
date_updated: 2023-08-22T09:17:34Z
day: '01'
doi: 10.48550/arXiv.2002.02111
extern: '1'
external_id:
arxiv:
- '2002.02111'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2002.02111
month: '02'
oa: 1
oa_version: Preprint
page: '2002.02111'
publication_status: submitted
status: public
title: Attosecond molecular spectroscopy and dynamics
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '8529'
abstract:
- lang: eng
text: Practical quantum networks require low-loss and noise-resilient optical interconnects
as well as non-Gaussian resources for entanglement distillation and distributed
quantum computation. The latter could be provided by superconducting circuits
but existing solutions to interface the microwave and optical domains lack either
scalability or efficiency, and in most cases the conversion noise is not known.
In this work we utilize the unique opportunities of silicon photonics, cavity
optomechanics and superconducting circuits to demonstrate a fully integrated,
coherent transducer interfacing the microwave X and the telecom S bands with a
total (internal) bidirectional transduction efficiency of 1.2% (135%) at millikelvin
temperatures. The coupling relies solely on the radiation pressure interaction
mediated by the femtometer-scale motion of two silicon nanobeams reaching a Vπ
as low as 16 μV for sub-nanowatt pump powers. Without the associated optomechanical
gain, we achieve a total (internal) pure conversion efficiency of up to 0.019%
(1.6%), relevant for future noise-free operation on this qubit-compatible platform.
acknowledged_ssus:
- _id: NanoFab
acknowledgement: We thank Yuan Chen for performing supplementary FEM simulations and
Andrew Higginbotham, Ralf Riedinger, Sungkun Hong, and Lorenzo Magrini for valuable
discussions. This work was supported by IST Austria, the IST nanofabrication facility
(NFF), the European Union’s Horizon 2020 research and innovation program under grant
agreement no. 732894 (FET Proactive HOT) and the European Research Council under
grant agreement no. 758053 (ERC StG QUNNECT). G.A. is the recipient of a DOC fellowship
of the Austrian Academy of Sciences at IST Austria. W.H. is the recipient of an
ISTplus postdoctoral fellowship with funding from the European Union’s Horizon 2020
research and innovation program under the Marie Sklodowska-Curie grant agreement
no. 754411. J.M.F. acknowledges support from the Austrian Science Fund (FWF) through
BeyondC (F71), a NOMIS foundation research grant, and the EU’s Horizon 2020 research
and innovation program under grant agreement no. 862644 (FET Open QUARTET).
article_number: '4460'
article_processing_charge: No
article_type: original
author:
- first_name: Georg M
full_name: Arnold, Georg M
id: 3770C838-F248-11E8-B48F-1D18A9856A87
last_name: Arnold
orcid: 0000-0003-1397-7876
- first_name: Matthias
full_name: Wulf, Matthias
id: 45598606-F248-11E8-B48F-1D18A9856A87
last_name: Wulf
orcid: 0000-0001-6613-1378
- first_name: Shabir
full_name: Barzanjeh, Shabir
id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87
last_name: Barzanjeh
orcid: 0000-0003-0415-1423
- first_name: Elena
full_name: Redchenko, Elena
id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87
last_name: Redchenko
- first_name: Alfredo R
full_name: Rueda Sanchez, Alfredo R
id: 3B82B0F8-F248-11E8-B48F-1D18A9856A87
last_name: Rueda Sanchez
orcid: 0000-0001-6249-5860
- first_name: William J
full_name: Hease, William J
id: 29705398-F248-11E8-B48F-1D18A9856A87
last_name: Hease
orcid: 0000-0001-9868-2166
- first_name: Farid
full_name: Hassani, Farid
id: 2AED110C-F248-11E8-B48F-1D18A9856A87
last_name: Hassani
orcid: 0000-0001-6937-5773
- 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: Arnold GM, Wulf M, Barzanjeh S, et al. Converting microwave and telecom photons
with a silicon photonic nanomechanical interface. Nature Communications.
2020;11. doi:10.1038/s41467-020-18269-z
apa: Arnold, G. M., Wulf, M., Barzanjeh, S., Redchenko, E., Rueda Sanchez, A. R.,
Hease, W. J., … Fink, J. M. (2020). Converting microwave and telecom photons with
a silicon photonic nanomechanical interface. Nature Communications. Springer
Nature. https://doi.org/10.1038/s41467-020-18269-z
chicago: Arnold, Georg M, Matthias Wulf, Shabir Barzanjeh, Elena Redchenko, Alfredo
R Rueda Sanchez, William J Hease, Farid Hassani, and Johannes M Fink. “Converting
Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.”
Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-18269-z.
ieee: G. M. Arnold et al., “Converting microwave and telecom photons with
a silicon photonic nanomechanical interface,” Nature Communications, vol.
11. Springer Nature, 2020.
ista: Arnold GM, Wulf M, Barzanjeh S, Redchenko E, Rueda Sanchez AR, Hease WJ, Hassani
F, Fink JM. 2020. Converting microwave and telecom photons with a silicon photonic
nanomechanical interface. Nature Communications. 11, 4460.
mla: Arnold, Georg M., et al. “Converting Microwave and Telecom Photons with a Silicon
Photonic Nanomechanical Interface.” Nature Communications, vol. 11, 4460,
Springer Nature, 2020, doi:10.1038/s41467-020-18269-z.
short: G.M. Arnold, M. Wulf, S. Barzanjeh, E. Redchenko, A.R. Rueda Sanchez, W.J.
Hease, F. Hassani, J.M. Fink, Nature Communications 11 (2020).
date_created: 2020-09-18T10:56:20Z
date_published: 2020-09-08T00:00:00Z
date_updated: 2023-08-22T09:27:12Z
day: '08'
ddc:
- '530'
department:
- _id: JoFi
doi: 10.1038/s41467-020-18269-z
ec_funded: 1
external_id:
isi:
- '000577280200001'
file:
- access_level: open_access
checksum: 88f92544889eb18bb38e25629a422a86
content_type: application/pdf
creator: dernst
date_created: 2020-09-18T13:02:37Z
date_updated: 2020-09-18T13:02:37Z
file_id: '8530'
file_name: 2020_NatureComm_Arnold.pdf
file_size: 1002818
relation: main_file
success: 1
file_date_updated: 2020-09-18T13:02:37Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
keyword:
- General Biochemistry
- Genetics and Molecular Biology
- General Physics and Astronomy
- General Chemistry
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 257EB838-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '732894'
name: Hybrid Optomechanical Technologies
- _id: 26336814-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '758053'
name: A Fiber Optic Transceiver for Superconducting Qubits
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 237CBA6C-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '862644'
name: Quantum readout techniques and technologies
- _id: 2671EB66-B435-11E9-9278-68D0E5697425
name: Coherent on-chip conversion of superconducting qubit signals from microwaves
to optical frequencies
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41467-020-18912-9
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/how-to-transport-microwave-quantum-information-via-optical-fiber/
record:
- id: '13056'
relation: research_data
status: public
status: public
title: Converting microwave and telecom photons with a silicon photonic nanomechanical
interface
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2020'
...
---
_id: '8535'
abstract:
- lang: eng
text: We propose a method to enhance the visual detail of a water surface simulation.
Our method works as a post-processing step which takes a simulation as input and
increases its apparent resolution by simulating many detailed Lagrangian water
waves on top of it. We extend linear water wave theory to work in non-planar domains
which deform over time, and we discretize the theory using Lagrangian wave packets
attached to spline curves. The method is numerically stable and trivially parallelizable,
and it produces high frequency ripples with dispersive wave-like behaviors customized
to the underlying fluid simulation.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: We wish to thank the anonymous reviewers and the members of the Visual
Computing Group at IST Austria for their valuable feedback. This research was supported
by the Scientific Service Units (SSU) of IST Austria through resources provided
by Scientific Computing. This project has received funding from the European Research
Council (ERC) under the European Union’s Horizon 2020 research and innovation programme
under grant agreement No. 638176 and Marie SkłodowskaCurie Grant Agreement No. 665385.
article_number: '65'
article_processing_charge: No
article_type: original
author:
- first_name: Tomas
full_name: Skrivan, Tomas
id: 486A5A46-F248-11E8-B48F-1D18A9856A87
last_name: Skrivan
- first_name: Andreas
full_name: Soderstrom, Andreas
last_name: Soderstrom
- first_name: John
full_name: Johansson, John
last_name: Johansson
- first_name: Christoph
full_name: Sprenger, Christoph
last_name: Sprenger
- first_name: Ken
full_name: Museth, Ken
last_name: Museth
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: 'Skrivan T, Soderstrom A, Johansson J, Sprenger C, Museth K, Wojtan C. Wave
curves: Simulating Lagrangian water waves on dynamically deforming surfaces. ACM
Transactions on Graphics. 2020;39(4). doi:10.1145/3386569.3392466'
apa: 'Skrivan, T., Soderstrom, A., Johansson, J., Sprenger, C., Museth, K., &
Wojtan, C. (2020). Wave curves: Simulating Lagrangian water waves on dynamically
deforming surfaces. ACM Transactions on Graphics. Association for Computing
Machinery. https://doi.org/10.1145/3386569.3392466'
chicago: 'Skrivan, Tomas, Andreas Soderstrom, John Johansson, Christoph Sprenger,
Ken Museth, and Chris Wojtan. “Wave Curves: Simulating Lagrangian Water Waves
on Dynamically Deforming Surfaces.” ACM Transactions on Graphics. Association
for Computing Machinery, 2020. https://doi.org/10.1145/3386569.3392466.'
ieee: 'T. Skrivan, A. Soderstrom, J. Johansson, C. Sprenger, K. Museth, and C. Wojtan,
“Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces,”
ACM Transactions on Graphics, vol. 39, no. 4. Association for Computing
Machinery, 2020.'
ista: 'Skrivan T, Soderstrom A, Johansson J, Sprenger C, Museth K, Wojtan C. 2020.
Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces.
ACM Transactions on Graphics. 39(4), 65.'
mla: 'Skrivan, Tomas, et al. “Wave Curves: Simulating Lagrangian Water Waves on
Dynamically Deforming Surfaces.” ACM Transactions on Graphics, vol. 39,
no. 4, 65, Association for Computing Machinery, 2020, doi:10.1145/3386569.3392466.'
short: T. Skrivan, A. Soderstrom, J. Johansson, C. Sprenger, K. Museth, C. Wojtan,
ACM Transactions on Graphics 39 (2020).
date_created: 2020-09-20T22:01:37Z
date_published: 2020-07-08T00:00:00Z
date_updated: 2023-08-22T09:28:27Z
day: '08'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/3386569.3392466
ec_funded: 1
external_id:
isi:
- '000583700300038'
file:
- access_level: open_access
checksum: c3a680893f01cc4a9e961ff0a4cfa12f
content_type: application/pdf
creator: dernst
date_created: 2020-09-21T07:51:44Z
date_updated: 2020-09-21T07:51:44Z
file_id: '8541'
file_name: 2020_ACM_Skrivan.pdf
file_size: 20223953
relation: main_file
success: 1
file_date_updated: 2020-09-21T07:51:44Z
has_accepted_license: '1'
intvolume: ' 39'
isi: 1
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: Efficient Simulation of Natural Phenomena at Extremely Large Scales
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: ACM Transactions on Graphics
publication_identifier:
eissn:
- '15577368'
issn:
- '07300301'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 39
year: '2020'
...
---
_id: '8539'
abstract:
- lang: eng
text: Cohomological and K-theoretic stable bases originated from the study of quantum
cohomology and quantum K-theory. Restriction formula for cohomological stable
bases played an important role in computing the quantum connection of cotangent
bundle of partial flag varieties. In this paper we study the K-theoretic stable
bases of cotangent bundles of flag varieties. We describe these bases in terms
of the action of the affine Hecke algebra and the twisted group algebra of KostantKumar.
Using this algebraic description and the method of root polynomials, we give a
restriction formula of the stable bases. We apply it to obtain the restriction
formula for partial flag varieties. We also build a relation between the stable
basis and the Casselman basis in the principal series representations of the Langlands
dual group. As an application, we give a closed formula for the transition matrix
between Casselman basis and the characteristic functions.
- lang: fre
text: "Les bases stables cohomologiques et K-théoriques proviennent de l’étude de
la cohomologie quantique et de la K-théorie quantique. La formule de restriction
pour les bases stables cohomologiques a joué un rôle important dans le calcul
de la connexion quantique du fibré cotangent de variétés de drapeaux partielles.
Dans cet article, nous étudions les bases stables K-théoriques de fibré cotangents
des variétés de drapeaux. Nous décrivons ces bases en fonction de l’action de
l’algèbre de Hecke affine et de l’algèbre de Kostant-Kumar. En utilisant cette
description algébrique et la méthode des polynômes de racine, nous donnons une
formule de restriction des bases stables. Nous l’appliquons\r\npour obtenir la
formule de restriction pour les variétés de drapeaux partielles. Nous construisons
également une relation entre la base stable et la base de Casselman dans les représentations
de la série principale du groupe dual de Langlands p-adique. Comme une application,
nous donnons une formule close pour la matrice de transition entre la base de
Casselman et les fonctions caractéristiques. "
article_processing_charge: No
article_type: original
author:
- first_name: C.
full_name: Su, C.
last_name: Su
- first_name: Gufang
full_name: Zhao, Gufang
id: 2BC2AC5E-F248-11E8-B48F-1D18A9856A87
last_name: Zhao
- first_name: C.
full_name: Zhong, C.
last_name: Zhong
citation:
ama: Su C, Zhao G, Zhong C. On the K-theory stable bases of the springer resolution.
Annales Scientifiques de l’Ecole Normale Superieure. 2020;53(3):663-671.
doi:10.24033/asens.2431
apa: Su, C., Zhao, G., & Zhong, C. (2020). On the K-theory stable bases of the
springer resolution. Annales Scientifiques de l’Ecole Normale Superieure.
Société Mathématique de France. https://doi.org/10.24033/asens.2431
chicago: Su, C., Gufang Zhao, and C. Zhong. “On the K-Theory Stable Bases of the
Springer Resolution.” Annales Scientifiques de l’Ecole Normale Superieure.
Société Mathématique de France, 2020. https://doi.org/10.24033/asens.2431.
ieee: C. Su, G. Zhao, and C. Zhong, “On the K-theory stable bases of the springer
resolution,” Annales Scientifiques de l’Ecole Normale Superieure, vol.
53, no. 3. Société Mathématique de France, pp. 663–671, 2020.
ista: Su C, Zhao G, Zhong C. 2020. On the K-theory stable bases of the springer
resolution. Annales Scientifiques de l’Ecole Normale Superieure. 53(3), 663–671.
mla: Su, C., et al. “On the K-Theory Stable Bases of the Springer Resolution.” Annales
Scientifiques de l’Ecole Normale Superieure, vol. 53, no. 3, Société Mathématique
de France, 2020, pp. 663–71, doi:10.24033/asens.2431.
short: C. Su, G. Zhao, C. Zhong, Annales Scientifiques de l’Ecole Normale Superieure
53 (2020) 663–671.
date_created: 2020-09-20T22:01:38Z
date_published: 2020-06-01T00:00:00Z
date_updated: 2023-08-22T09:27:57Z
day: '01'
department:
- _id: TaHa
doi: 10.24033/asens.2431
external_id:
arxiv:
- '1708.08013'
isi:
- '000592182600004'
intvolume: ' 53'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1708.08013
month: '06'
oa: 1
oa_version: Preprint
page: 663-671
publication: Annales Scientifiques de l'Ecole Normale Superieure
publication_identifier:
issn:
- 0012-9593
publication_status: published
publisher: Société Mathématique de France
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the K-theory stable bases of the springer resolution
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 53
year: '2020'
...
---
_id: '14000'
abstract:
- lang: eng
text: This chapter presents an overview of the state of the art in attosecond time-resolved
spectroscopy. The theoretical foundations of strong-field light–matter interaction
and attosecond pulse generation are described. The enabling laser technologies
are reviewed from chirped-pulse amplification and carrier-envelope-phase stabilization
to the generation and characterization of attosecond pulses. The applications
of attosecond pulses and pulse trains in electron- or ion-imaging experiments
are presented, followed by attosecond electron spectroscopy in larger molecules.
After this, high-harmonic spectroscopy and its applications to probing charge
migration on attosecond time scales is reviewed. The rapidly evolving field of
molecular photoionization delays is discussed. Finally, the applications of attosecond
transient absorption to probing molecular dynamics are presented.
article_processing_charge: No
author:
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: Hans Jakob
full_name: Wörner, Hans Jakob
last_name: Wörner
citation:
ama: 'Baykusheva DR, Wörner HJ. Attosecond Molecular Dynamics and Spectroscopy.
In: Marquardt R, Quack M, eds. Molecular Spectroscopy and Quantum Dynamics.
1st ed. Elsevier; 2020:113-161. doi:10.1016/b978-0-12-817234-6.00009-x'
apa: Baykusheva, D. R., & Wörner, H. J. (2020). Attosecond Molecular Dynamics
and Spectroscopy. In R. Marquardt & M. Quack (Eds.), Molecular Spectroscopy
and Quantum Dynamics (1st ed., pp. 113–161). Elsevier. https://doi.org/10.1016/b978-0-12-817234-6.00009-x
chicago: Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. “Attosecond Molecular
Dynamics and Spectroscopy.” In Molecular Spectroscopy and Quantum Dynamics,
edited by Roberto Marquardt and Martin Quack, 1st ed., 113–61. Elsevier, 2020.
https://doi.org/10.1016/b978-0-12-817234-6.00009-x.
ieee: D. R. Baykusheva and H. J. Wörner, “Attosecond Molecular Dynamics and Spectroscopy,”
in Molecular Spectroscopy and Quantum Dynamics, 1st ed., R. Marquardt and
M. Quack, Eds. Elsevier, 2020, pp. 113–161.
ista: 'Baykusheva DR, Wörner HJ. 2020.Attosecond Molecular Dynamics and Spectroscopy.
In: Molecular Spectroscopy and Quantum Dynamics. , 113–161.'
mla: Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. “Attosecond Molecular
Dynamics and Spectroscopy.” Molecular Spectroscopy and Quantum Dynamics,
edited by Roberto Marquardt and Martin Quack, 1st ed., Elsevier, 2020, pp. 113–61,
doi:10.1016/b978-0-12-817234-6.00009-x.
short: D.R. Baykusheva, H.J. Wörner, in:, R. Marquardt, M. Quack (Eds.), Molecular
Spectroscopy and Quantum Dynamics, 1st ed., Elsevier, 2020, pp. 113–161.
date_created: 2023-08-09T13:10:23Z
date_published: 2020-09-25T00:00:00Z
date_updated: 2023-08-22T09:25:07Z
day: '25'
doi: 10.1016/b978-0-12-817234-6.00009-x
edition: '1'
editor:
- first_name: Roberto
full_name: Marquardt, Roberto
last_name: Marquardt
- first_name: Martin
full_name: Quack, Martin
last_name: Quack
extern: '1'
language:
- iso: eng
month: '09'
oa_version: None
page: 113-161
publication: Molecular Spectroscopy and Quantum Dynamics
publication_identifier:
eisbn:
- '0128172355'
isbn:
- '9780128172353'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Attosecond Molecular Dynamics and Spectroscopy
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '13056'
abstract:
- lang: eng
text: This datasets comprises all data shown in plots of the submitted article "Converting
microwave and telecom photons with a silicon photonic nanomechanical interface".
Additional raw data are available from the corresponding author on reasonable
request.
article_processing_charge: No
author:
- first_name: Georg M
full_name: Arnold, Georg M
id: 3770C838-F248-11E8-B48F-1D18A9856A87
last_name: Arnold
orcid: 0000-0003-1397-7876
- first_name: Matthias
full_name: Wulf, Matthias
id: 45598606-F248-11E8-B48F-1D18A9856A87
last_name: Wulf
orcid: 0000-0001-6613-1378
- first_name: Shabir
full_name: Barzanjeh, Shabir
id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87
last_name: Barzanjeh
orcid: 0000-0003-0415-1423
- first_name: Elena
full_name: Redchenko, Elena
id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87
last_name: Redchenko
- first_name: Alfredo R
full_name: Rueda Sanchez, Alfredo R
id: 3B82B0F8-F248-11E8-B48F-1D18A9856A87
last_name: Rueda Sanchez
orcid: 0000-0001-6249-5860
- first_name: William J
full_name: Hease, William J
id: 29705398-F248-11E8-B48F-1D18A9856A87
last_name: Hease
orcid: 0000-0001-9868-2166
- first_name: Farid
full_name: Hassani, Farid
id: 2AED110C-F248-11E8-B48F-1D18A9856A87
last_name: Hassani
orcid: 0000-0001-6937-5773
- 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: Arnold GM, Wulf M, Barzanjeh S, et al. Converting microwave and telecom photons
with a silicon photonic nanomechanical interface. 2020. doi:10.5281/ZENODO.3961561
apa: Arnold, G. M., Wulf, M., Barzanjeh, S., Redchenko, E., Rueda Sanchez, A. R.,
Hease, W. J., … Fink, J. M. (2020). Converting microwave and telecom photons with
a silicon photonic nanomechanical interface. Zenodo. https://doi.org/10.5281/ZENODO.3961561
chicago: Arnold, Georg M, Matthias Wulf, Shabir Barzanjeh, Elena Redchenko, Alfredo
R Rueda Sanchez, William J Hease, Farid Hassani, and Johannes M Fink. “Converting
Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.”
Zenodo, 2020. https://doi.org/10.5281/ZENODO.3961561.
ieee: G. M. Arnold et al., “Converting microwave and telecom photons with
a silicon photonic nanomechanical interface.” Zenodo, 2020.
ista: Arnold GM, Wulf M, Barzanjeh S, Redchenko E, Rueda Sanchez AR, Hease WJ, Hassani
F, Fink JM. 2020. Converting microwave and telecom photons with a silicon photonic
nanomechanical interface, Zenodo, 10.5281/ZENODO.3961561.
mla: Arnold, Georg M., et al. Converting Microwave and Telecom Photons with a
Silicon Photonic Nanomechanical Interface. Zenodo, 2020, doi:10.5281/ZENODO.3961561.
short: G.M. Arnold, M. Wulf, S. Barzanjeh, E. Redchenko, A.R. Rueda Sanchez, W.J.
Hease, F. Hassani, J.M. Fink, (2020).
date_created: 2023-05-23T13:37:41Z
date_published: 2020-07-27T00:00:00Z
date_updated: 2023-08-22T09:27:11Z
day: '27'
ddc:
- '530'
department:
- _id: JoFi
doi: 10.5281/ZENODO.3961561
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.3961562
month: '07'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '8529'
relation: used_in_publication
status: public
status: public
title: Converting microwave and telecom photons with a silicon photonic nanomechanical
interface
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: '2020'
...
---
_id: '8579'
abstract:
- lang: eng
text: Copper (Cu) is an essential trace element for all living organisms and used
as cofactor in key enzymes of important biological processes, such as aerobic
respiration or superoxide dismutation. However, due to its toxicity, cells have
developed elaborate mechanisms for Cu homeostasis, which balance Cu supply for
cuproprotein biogenesis with the need to remove excess Cu. This review summarizes
our current knowledge on bacterial Cu homeostasis with a focus on Gram-negative
bacteria and describes the multiple strategies that bacteria use for uptake, storage
and export of Cu. We furthermore describe general mechanistic principles that
aid the bacterial response to toxic Cu concentrations and illustrate dedicated
Cu relay systems that facilitate Cu delivery for cuproenzyme biogenesis. Progress
in understanding how bacteria avoid Cu poisoning while maintaining a certain Cu
quota for cell proliferation is of particular importance for microbial pathogens
because Cu is utilized by the host immune system for attenuating pathogen survival
in host cells.
article_number: '242'
article_processing_charge: No
article_type: original
author:
- first_name: Andreea
full_name: Andrei, Andreea
last_name: Andrei
- first_name: Yavuz
full_name: Öztürk, Yavuz
last_name: Öztürk
- first_name: Bahia
full_name: Khalfaoui-Hassani, Bahia
last_name: Khalfaoui-Hassani
- first_name: Juna
full_name: Rauch, Juna
last_name: Rauch
- first_name: Dorian
full_name: Marckmann, Dorian
last_name: Marckmann
- first_name: Petru Iulian
full_name: Trasnea, Petru Iulian
id: D560034C-10C4-11EA-ABF4-A4B43DDC885E
last_name: Trasnea
- first_name: Fevzi
full_name: Daldal, Fevzi
last_name: Daldal
- first_name: Hans-Georg
full_name: Koch, Hans-Georg
last_name: Koch
citation:
ama: 'Andrei A, Öztürk Y, Khalfaoui-Hassani B, et al. Cu homeostasis in bacteria:
The ins and outs. Membranes. 2020;10(9). doi:10.3390/membranes10090242'
apa: 'Andrei, A., Öztürk, Y., Khalfaoui-Hassani, B., Rauch, J., Marckmann, D., Trasnea,
P. I., … Koch, H.-G. (2020). Cu homeostasis in bacteria: The ins and outs. Membranes.
MDPI. https://doi.org/10.3390/membranes10090242'
chicago: 'Andrei, Andreea, Yavuz Öztürk, Bahia Khalfaoui-Hassani, Juna Rauch, Dorian
Marckmann, Petru Iulian Trasnea, Fevzi Daldal, and Hans-Georg Koch. “Cu Homeostasis
in Bacteria: The Ins and Outs.” Membranes. MDPI, 2020. https://doi.org/10.3390/membranes10090242.'
ieee: 'A. Andrei et al., “Cu homeostasis in bacteria: The ins and outs,”
Membranes, vol. 10, no. 9. MDPI, 2020.'
ista: 'Andrei A, Öztürk Y, Khalfaoui-Hassani B, Rauch J, Marckmann D, Trasnea PI,
Daldal F, Koch H-G. 2020. Cu homeostasis in bacteria: The ins and outs. Membranes.
10(9), 242.'
mla: 'Andrei, Andreea, et al. “Cu Homeostasis in Bacteria: The Ins and Outs.” Membranes,
vol. 10, no. 9, 242, MDPI, 2020, doi:10.3390/membranes10090242.'
short: A. Andrei, Y. Öztürk, B. Khalfaoui-Hassani, J. Rauch, D. Marckmann, P.I.
Trasnea, F. Daldal, H.-G. Koch, Membranes 10 (2020).
date_created: 2020-09-28T08:59:26Z
date_published: 2020-09-01T00:00:00Z
date_updated: 2023-08-22T09:34:06Z
day: '01'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.3390/membranes10090242
external_id:
isi:
- '000581446000001'
file:
- access_level: open_access
checksum: ceb43d7554e712dea6f36f9287271737
content_type: application/pdf
creator: dernst
date_created: 2020-09-28T11:36:50Z
date_updated: 2020-09-28T11:36:50Z
file_id: '8583'
file_name: 2020_Membranes_Andrei.pdf
file_size: 4612258
relation: main_file
success: 1
file_date_updated: 2020-09-28T11:36:50Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: Membranes
publication_identifier:
eissn:
- '20770375'
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Cu homeostasis in bacteria: The ins and outs'
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 10
year: '2020'
...
---
_id: '8581'
abstract:
- lang: eng
text: The majority of adenosine triphosphate (ATP) powering cellular processes in
eukaryotes is produced by the mitochondrial F1Fo ATP synthase. Here, we present
the atomic models of the membrane Fo domain and the entire mammalian (ovine) F1Fo,
determined by cryo-electron microscopy. Subunits in the membrane domain are arranged
in the ‘proton translocation cluster’ attached to the c-ring and a more distant
‘hook apparatus’ holding subunit e. Unexpectedly, this subunit is anchored to
a lipid ‘plug’ capping the c-ring. We present a detailed proton translocation
pathway in mammalian Fo and key inter-monomer contacts in F1Fo multimers. Cryo-EM
maps of F1Fo exposed to calcium reveal a retracted subunit e and a disassembled
c-ring, suggesting permeability transition pore opening. We propose a model for
the permeability transition pore opening, whereby subunit e pulls the lipid plug
out of the c-ring. Our structure will allow the design of drugs for many emerging
applications in medicine.
acknowledged_ssus:
- _id: EM-Fac
- _id: ScienComp
acknowledgement: We thank J. Novacek from CEITEC (Brno, Czech Republic) for assistance
with collecting the FEI Krios dataset and iNEXT for providing access to CEITEC.
We thank the IST Austria EM facility for access and assistance with collecting the
FEI Glacios dataset. Data processing was performed at the IST high-performance computing
cluster. This work has been supported by iNEXT EM HEDC (proposal 4506), funded by
the Horizon 2020 Programme of the European Commission.
article_processing_charge: No
article_type: original
author:
- first_name: Gergely
full_name: Pinke, Gergely
id: 4D5303E6-F248-11E8-B48F-1D18A9856A87
last_name: Pinke
- first_name: Long
full_name: Zhou, Long
id: 3E751364-F248-11E8-B48F-1D18A9856A87
last_name: Zhou
orcid: 0000-0002-1864-8951
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Pinke G, Zhou L, Sazanov LA. Cryo-EM structure of the entire mammalian F-type
ATP synthase. Nature Structural and Molecular Biology. 2020;27(11):1077-1085.
doi:10.1038/s41594-020-0503-8
apa: Pinke, G., Zhou, L., & Sazanov, L. A. (2020). Cryo-EM structure of the
entire mammalian F-type ATP synthase. Nature Structural and Molecular Biology.
Springer Nature. https://doi.org/10.1038/s41594-020-0503-8
chicago: Pinke, Gergely, Long Zhou, and Leonid A Sazanov. “Cryo-EM Structure of
the Entire Mammalian F-Type ATP Synthase.” Nature Structural and Molecular
Biology. Springer Nature, 2020. https://doi.org/10.1038/s41594-020-0503-8.
ieee: G. Pinke, L. Zhou, and L. A. Sazanov, “Cryo-EM structure of the entire mammalian
F-type ATP synthase,” Nature Structural and Molecular Biology, vol. 27,
no. 11. Springer Nature, pp. 1077–1085, 2020.
ista: Pinke G, Zhou L, Sazanov LA. 2020. Cryo-EM structure of the entire mammalian
F-type ATP synthase. Nature Structural and Molecular Biology. 27(11), 1077–1085.
mla: Pinke, Gergely, et al. “Cryo-EM Structure of the Entire Mammalian F-Type ATP
Synthase.” Nature Structural and Molecular Biology, vol. 27, no. 11, Springer
Nature, 2020, pp. 1077–85, doi:10.1038/s41594-020-0503-8.
short: G. Pinke, L. Zhou, L.A. Sazanov, Nature Structural and Molecular Biology
27 (2020) 1077–1085.
date_created: 2020-09-28T08:59:27Z
date_published: 2020-11-01T00:00:00Z
date_updated: 2023-08-22T09:33:09Z
day: '01'
department:
- _id: LeSa
doi: 10.1038/s41594-020-0503-8
external_id:
isi:
- '000569299400004'
pmid:
- '32929284'
intvolume: ' 27'
isi: 1
issue: '11'
language:
- iso: eng
month: '11'
oa_version: None
page: 1077-1085
pmid: 1
publication: Nature Structural and Molecular Biology
publication_identifier:
eissn:
- '15459985'
issn:
- '15459993'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/structure-of-atpase-solved/
scopus_import: '1'
status: public
title: Cryo-EM structure of the entire mammalian F-type ATP synthase
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 27
year: '2020'
...