---
_id: '8284'
abstract:
- lang: eng
text: Multiple resistance and pH adaptation (Mrp) antiporters are multi-subunit
Na+ (or K+)/H+ exchangers representing an ancestor of many essential redox-driven
proton pumps, such as respiratory complex I. The mechanism of coupling between
ion or electron transfer and proton translocation in this large protein family
is unknown. Here, we present the structure of the Mrp complex from Anoxybacillus
flavithermus solved by cryo-EM at 3.0 Å resolution. It is a dimer of seven-subunit
protomers with 50 trans-membrane helices each. Surface charge distribution within
each monomer is remarkably asymmetric, revealing probable proton and sodium translocation
pathways. On the basis of the structure we propose a mechanism where the coupling
between sodium and proton translocation is facilitated by a series of electrostatic
interactions between a cation and key charged residues. This mechanism is likely
to be applicable to the entire family of redox proton pumps, where electron transfer
to substrates replaces cation movements.
acknowledged_ssus:
- _id: EM-Fac
- _id: LifeSc
acknowledgement: This research was supported by the Scientific Service Units (SSU)
of IST Austria through resources provided by the Electron Microscopy Facility (EMF),
the Life Science Facility (LSF) and the IST high-performance computing cluster.
We thank Dr Victor-Valentin Hodirnau and Daniel Johann Gütl from IST Austria for
assistance with collecting cryo-EM data. We thank Prof. Masahiro Ito (Graduate School
of Life Sciences, Toyo University, Japan) for a kind provision of plasmid DNA encoding
Mrp from A. flavithermus WK1. JS is a recipient of a DOC Fellowship of the Austrian
Academy of Sciences at the Institute of Science and Technology, Austria.
article_number: e59407
article_processing_charge: No
article_type: original
author:
- first_name: Julia
full_name: Steiner, Julia
id: 3BB67EB0-F248-11E8-B48F-1D18A9856A87
last_name: Steiner
orcid: 0000-0003-0493-3775
- 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: Steiner J, Sazanov LA. Structure and mechanism of the Mrp complex, an ancient
cation/proton antiporter. eLife. 2020;9. doi:10.7554/eLife.59407
apa: Steiner, J., & Sazanov, L. A. (2020). Structure and mechanism of the Mrp
complex, an ancient cation/proton antiporter. ELife. eLife Sciences Publications.
https://doi.org/10.7554/eLife.59407
chicago: Steiner, Julia, and Leonid A Sazanov. “Structure and Mechanism of the Mrp
Complex, an Ancient Cation/Proton Antiporter.” ELife. eLife Sciences Publications,
2020. https://doi.org/10.7554/eLife.59407.
ieee: J. Steiner and L. A. Sazanov, “Structure and mechanism of the Mrp complex,
an ancient cation/proton antiporter,” eLife, vol. 9. eLife Sciences Publications,
2020.
ista: Steiner J, Sazanov LA. 2020. Structure and mechanism of the Mrp complex, an
ancient cation/proton antiporter. eLife. 9, e59407.
mla: Steiner, Julia, and Leonid A. Sazanov. “Structure and Mechanism of the Mrp
Complex, an Ancient Cation/Proton Antiporter.” ELife, vol. 9, e59407, eLife
Sciences Publications, 2020, doi:10.7554/eLife.59407.
short: J. Steiner, L.A. Sazanov, ELife 9 (2020).
date_created: 2020-08-24T06:24:04Z
date_published: 2020-07-31T00:00:00Z
date_updated: 2023-09-07T13:14:08Z
day: '31'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.7554/eLife.59407
external_id:
isi:
- '000562123600001'
pmid:
- '32735215'
file:
- access_level: open_access
checksum: b3656d14d5ddbb9d26e3074eea2d0c15
content_type: application/pdf
creator: cziletti
date_created: 2020-08-24T13:31:53Z
date_updated: 2020-08-24T13:31:53Z
file_id: '8289'
file_name: 2020_eLife_Steiner.pdf
file_size: 7320493
relation: main_file
success: 1
file_date_updated: 2020-08-24T13:31:53Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 26169496-B435-11E9-9278-68D0E5697425
grant_number: '24741'
name: Revealing the functional mechanism of Mrp antiporter, an ancestor of complex
I
publication: eLife
publication_identifier:
eissn:
- 2050084X
publication_status: published
publisher: eLife Sciences Publications
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/
record:
- id: '8353'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter
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: 9
year: '2020'
...
---
_id: '8285'
abstract:
- lang: eng
text: We demonstrate the utility of optical cavity generated spin-squeezed states
in free space atomic fountain clocks in ensembles of 390 000 87Rb atoms. Fluorescence
imaging, correlated to an initial quantum nondemolition measurement, is used for
population spectroscopy after the atoms are released from a confining lattice.
For a free fall time of 4 milliseconds, we resolve a single-shot phase sensitivity
of 814(61) microradians, which is 5.8(0.6) decibels (dB) below the quantum projection
limit. We observe that this squeezing is preserved as the cloud expands to a roughly
200 μm radius and falls roughly 300 μm in free space. Ramsey spectroscopy with
240 000 atoms at a 3.6 ms Ramsey time results in a single-shot fractional frequency
stability of 8.4(0.2)×10−12, 3.8(0.2) dB below the quantum projection limit. The
sensitivity and stability are limited by the technical noise in the fluorescence
detection protocol and the microwave system, respectively.
acknowledgement: This work is supported by the Office of Naval Research (N00014-16-1-2927-
A00003), Vannevar Bush Faculty Fellowship (N00014-16-1-2812- P00005), Department
of Energy (DE-SC0019174- 0001), and Defense Threat Reduction Agency (HDTRA1-15-1-0017-
P00005).
article_number: '043202'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Benjamin K.
full_name: Malia, Benjamin K.
last_name: Malia
- first_name: Julián
full_name: Martínez-Rincón, Julián
last_name: Martínez-Rincón
- first_name: Yunfan
full_name: Wu, Yunfan
last_name: Wu
- first_name: Onur
full_name: Hosten, Onur
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
- first_name: Mark A.
full_name: Kasevich, Mark A.
last_name: Kasevich
citation:
ama: Malia BK, Martínez-Rincón J, Wu Y, Hosten O, Kasevich MA. Free space Ramsey
spectroscopy in rubidium with noise below the quantum projection limit. Physical
Review Letters. 2020;125(4). doi:10.1103/PhysRevLett.125.043202
apa: Malia, B. K., Martínez-Rincón, J., Wu, Y., Hosten, O., & Kasevich, M. A.
(2020). Free space Ramsey spectroscopy in rubidium with noise below the quantum
projection limit. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.125.043202
chicago: Malia, Benjamin K., Julián Martínez-Rincón, Yunfan Wu, Onur Hosten, and
Mark A. Kasevich. “Free Space Ramsey Spectroscopy in Rubidium with Noise below
the Quantum Projection Limit.” Physical Review Letters. American Physical
Society, 2020. https://doi.org/10.1103/PhysRevLett.125.043202.
ieee: B. K. Malia, J. Martínez-Rincón, Y. Wu, O. Hosten, and M. A. Kasevich, “Free
space Ramsey spectroscopy in rubidium with noise below the quantum projection
limit,” Physical Review Letters, vol. 125, no. 4. American Physical Society,
2020.
ista: Malia BK, Martínez-Rincón J, Wu Y, Hosten O, Kasevich MA. 2020. Free space
Ramsey spectroscopy in rubidium with noise below the quantum projection limit.
Physical Review Letters. 125(4), 043202.
mla: Malia, Benjamin K., et al. “Free Space Ramsey Spectroscopy in Rubidium with
Noise below the Quantum Projection Limit.” Physical Review Letters, vol.
125, no. 4, 043202, American Physical Society, 2020, doi:10.1103/PhysRevLett.125.043202.
short: B.K. Malia, J. Martínez-Rincón, Y. Wu, O. Hosten, M.A. Kasevich, Physical
Review Letters 125 (2020).
date_created: 2020-08-24T06:24:04Z
date_published: 2020-07-24T00:00:00Z
date_updated: 2023-10-18T08:38:35Z
day: '24'
department:
- _id: OnHo
doi: 10.1103/PhysRevLett.125.043202
external_id:
arxiv:
- '1912.10218'
isi:
- '000552227400008'
pmid:
- '32794788'
intvolume: ' 125'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1912.10218
month: '07'
oa: 1
oa_version: Preprint
pmid: 1
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Free space Ramsey spectroscopy in rubidium with noise below the quantum projection
limit
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 125
year: '2020'
...
---
_id: '8287'
abstract:
- lang: eng
text: Reachability analysis aims at identifying states reachable by a system within
a given time horizon. This task is known to be computationally expensive for linear
hybrid systems. Reachability analysis works by iteratively applying continuous
and discrete post operators to compute states reachable according to continuous
and discrete dynamics, respectively. In this paper, we enhance both of these operators
and make sure that most of the involved computations are performed in low-dimensional
state space. In particular, we improve the continuous-post operator by performing
computations in high-dimensional state space only for time intervals relevant
for the subsequent application of the discrete-post operator. Furthermore, the
new discrete-post operator performs low-dimensional computations by leveraging
the structure of the guard and assignment of a considered transition. We illustrate
the potential of our approach on a number of challenging benchmarks.
article_processing_charge: No
arxiv: 1
author:
- first_name: Sergiy
full_name: Bogomolov, Sergiy
last_name: Bogomolov
- first_name: Marcelo
full_name: Forets, Marcelo
last_name: Forets
- first_name: Goran
full_name: Frehse, Goran
last_name: Frehse
- first_name: Kostiantyn
full_name: Potomkin, Kostiantyn
last_name: Potomkin
- first_name: Christian
full_name: Schilling, Christian
id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87
last_name: Schilling
orcid: 0000-0003-3658-1065
citation:
ama: 'Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. Reachability analysis
of linear hybrid systems via block decomposition. In: Proceedings of the International
Conference on Embedded Software. ; 2020.'
apa: Bogomolov, S., Forets, M., Frehse, G., Potomkin, K., & Schilling, C. (2020).
Reachability analysis of linear hybrid systems via block decomposition. In Proceedings
of the International Conference on Embedded Software. Virtual .
chicago: Bogomolov, Sergiy, Marcelo Forets, Goran Frehse, Kostiantyn Potomkin, and
Christian Schilling. “Reachability Analysis of Linear Hybrid Systems via Block
Decomposition.” In Proceedings of the International Conference on Embedded
Software, 2020.
ieee: S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, and C. Schilling, “Reachability
analysis of linear hybrid systems via block decomposition,” in Proceedings
of the International Conference on Embedded Software, Virtual , 2020.
ista: 'Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. 2020. Reachability
analysis of linear hybrid systems via block decomposition. Proceedings of the
International Conference on Embedded Software. EMSOFT: International Conference
on Embedded Software.'
mla: Bogomolov, Sergiy, et al. “Reachability Analysis of Linear Hybrid Systems via
Block Decomposition.” Proceedings of the International Conference on Embedded
Software, 2020.
short: S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, C. Schilling, in:, Proceedings
of the International Conference on Embedded Software, 2020.
conference:
end_date: 2020-09-25
location: 'Virtual '
name: 'EMSOFT: International Conference on Embedded Software'
start_date: 2020-09-20
date_created: 2020-08-24T12:56:20Z
date_published: 2020-01-01T00:00:00Z
date_updated: 2023-08-22T13:27:32Z
ddc:
- '000'
department:
- _id: ToHe
ec_funded: 1
external_id:
arxiv:
- '1905.02458'
file:
- access_level: open_access
checksum: d19e97d0f8a3a441dc078ec812297d75
content_type: application/pdf
creator: cschilli
date_created: 2020-08-24T12:53:15Z
date_updated: 2020-08-24T12:53:15Z
file_id: '8288'
file_name: 2020EMSOFT.pdf
file_size: 696384
relation: main_file
success: 1
file_date_updated: 2020-08-24T12:53:15Z
has_accepted_license: '1'
keyword:
- reachability
- hybrid systems
- decomposition
language:
- iso: eng
oa: 1
oa_version: Preprint
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: The Wittgenstein Prize
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Proceedings of the International Conference on Embedded Software
publication_status: published
quality_controlled: '1'
related_material:
record:
- id: '8790'
relation: later_version
status: public
status: public
title: Reachability analysis of linear hybrid systems via block decomposition
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: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2020'
...
---
_id: '8294'
abstract:
- lang: eng
text: 'Automated root growth analysis and tracking of root tips. '
author:
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
citation:
ama: Hauschild R. RGtracker. 2020. doi:10.15479/AT:ISTA:8294
apa: Hauschild, R. (2020). RGtracker. IST Austria. https://doi.org/10.15479/AT:ISTA:8294
chicago: Hauschild, Robert. “RGtracker.” IST Austria, 2020. https://doi.org/10.15479/AT:ISTA:8294.
ieee: R. Hauschild, “RGtracker.” IST Austria, 2020.
ista: Hauschild R. 2020. RGtracker, IST Austria, 10.15479/AT:ISTA:8294.
mla: Hauschild, Robert. RGtracker. IST Austria, 2020, doi:10.15479/AT:ISTA:8294.
short: R. Hauschild, (2020).
date_created: 2020-08-25T12:52:48Z
date_published: 2020-09-10T00:00:00Z
date_updated: 2021-01-12T08:17:56Z
day: '10'
ddc:
- '570'
department:
- _id: Bio
doi: 10.15479/AT:ISTA:8294
file:
- access_level: open_access
checksum: 108352149987ac6f066e4925bd56e35e
content_type: text/plain
creator: rhauschild
date_created: 2020-09-08T14:26:31Z
date_updated: 2020-09-08T14:26:31Z
file_id: '8346'
file_name: readme.txt
file_size: 882
relation: main_file
success: 1
- access_level: open_access
checksum: ffd6c643b28e0cc7c6d0060a18a7e8ea
content_type: application/octet-stream
creator: rhauschild
date_created: 2020-09-08T14:26:33Z
date_updated: 2020-09-08T14:26:33Z
file_id: '8347'
file_name: RGtracker.mlappinstall
file_size: 246121
relation: main_file
success: 1
file_date_updated: 2020-09-08T14:26:33Z
has_accepted_license: '1'
license: https://opensource.org/licenses/BSD-3-Clause
month: '09'
oa: 1
publisher: IST Austria
status: public
title: RGtracker
tmp:
legal_code_url: https://opensource.org/licenses/BSD-3-Clause
name: The 3-Clause BSD License
short: 3-Clause BSD
type: software
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '8308'
abstract:
- lang: eng
text: 'Many-body localization provides a mechanism to avoid thermalization in isolated
interacting quantum systems. The breakdown of thermalization may be complete,
when all eigenstates in the many-body spectrum become localized, or partial, when
the so-called many-body mobility edge separates localized and delocalized parts
of the spectrum. Previously, De Roeck et al. [Phys. Rev. B 93, 014203 (2016)]
suggested a possible instability of the many-body mobility edge in energy density.
The local ergodic regions—so-called “bubbles”—resonantly spread throughout the
system, leading to delocalization. In order to study such instability mechanism,
in this work we design a model featuring many-body mobility edge in particle density:
the states at small particle density are localized, while increasing the density
of particles leads to delocalization. Using numerical simulations with matrix
product states, we demonstrate the stability of many-body localization with respect
to small bubbles in large dilute systems for experimentally relevant timescales.
In addition, we demonstrate that processes where the bubble spreads are favored
over processes that lead to resonant tunneling, suggesting a possible mechanism
behind the observed stability of many-body mobility edge. We conclude by proposing
experiments to probe particle density mobility edge in the Bose-Hubbard model.'
acknowledgement: 'Acknowledgments. We acknowledge useful discussions with W. De Roeck
and A. Michailidis. P.B. was supported by the European Union''s Horizon 2020 research
and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 665385.
D.A. was supported by the Swiss National Science Foundation. M.S. was supported
by European Research Council (ERC) under the European Union''s Horizon 2020 research
and innovation program (Grant Agreement No. 850899). This work benefited from visits
to KITP, supported by the National Science Foundation under Grant No. NSF PHY-1748958
and from the program “Thermalization, Many Body Localization and Hydrodynamics”
at International Centre for Theoretical Sciences (Code: ICTS/hydrodynamics2019/11).'
article_number: 060202(R)
article_processing_charge: No
article_type: original
author:
- first_name: Pietro
full_name: Brighi, Pietro
id: 4115AF5C-F248-11E8-B48F-1D18A9856A87
last_name: Brighi
orcid: 0000-0002-7969-2729
- first_name: Dmitry A.
full_name: Abanin, Dmitry A.
last_name: Abanin
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: Brighi P, Abanin DA, Serbyn M. Stability of mobility edges in disordered interacting
systems. Physical Review B. 2020;102(6). doi:10.1103/physrevb.102.060202
apa: Brighi, P., Abanin, D. A., & Serbyn, M. (2020). Stability of mobility edges
in disordered interacting systems. Physical Review B. American Physical
Society. https://doi.org/10.1103/physrevb.102.060202
chicago: Brighi, Pietro, Dmitry A. Abanin, and Maksym Serbyn. “Stability of Mobility
Edges in Disordered Interacting Systems.” Physical Review B. American Physical
Society, 2020. https://doi.org/10.1103/physrevb.102.060202.
ieee: P. Brighi, D. A. Abanin, and M. Serbyn, “Stability of mobility edges in disordered
interacting systems,” Physical Review B, vol. 102, no. 6. American Physical
Society, 2020.
ista: Brighi P, Abanin DA, Serbyn M. 2020. Stability of mobility edges in disordered
interacting systems. Physical Review B. 102(6), 060202(R).
mla: Brighi, Pietro, et al. “Stability of Mobility Edges in Disordered Interacting
Systems.” Physical Review B, vol. 102, no. 6, 060202(R), American Physical
Society, 2020, doi:10.1103/physrevb.102.060202.
short: P. Brighi, D.A. Abanin, M. Serbyn, Physical Review B 102 (2020).
date_created: 2020-08-26T19:27:42Z
date_published: 2020-08-26T00:00:00Z
date_updated: 2023-08-24T14:20:21Z
day: '26'
ddc:
- '530'
department:
- _id: MaSe
doi: 10.1103/physrevb.102.060202
ec_funded: 1
external_id:
isi:
- '000562628300001'
file:
- access_level: open_access
checksum: 716442fa7861323fcc80b93718ca009c
content_type: application/pdf
creator: mserbyn
date_created: 2020-08-26T19:28:55Z
date_updated: 2020-08-26T19:28:55Z
file_id: '8309'
file_name: PhysRevB.102.060202.pdf
file_size: 488825
relation: main_file
success: 1
- access_level: open_access
checksum: be0abdc8f60fe065ea6dc92e08487122
content_type: application/pdf
creator: mserbyn
date_created: 2020-08-26T19:29:00Z
date_updated: 2020-08-26T19:29:00Z
file_id: '8310'
file_name: Supplementary-mbme.pdf
file_size: 711405
relation: main_file
success: 1
file_date_updated: 2020-08-26T19:29:00Z
has_accepted_license: '1'
intvolume: ' 102'
isi: 1
issue: '6'
language:
- iso: eng
month: '08'
oa: 1
oa_version: None
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
record:
- id: '12732'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Stability of mobility edges in disordered interacting systems
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 102
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: '8319'
abstract:
- lang: eng
text: We demonstrate that releasing atoms into free space from an optical lattice
does not deteriorate cavity-generated spin squeezing for metrological purposes.
In this work, an ensemble of 500000 spin-squeezed atoms in a high-finesse optical
cavity with near-uniform atom-cavity coupling is prepared, released into free
space, recaptured in the cavity, and probed. Up to ∼10 dB of metrologically relevant
squeezing is retrieved for 700μs free-fall times, and decaying levels of squeezing
are realized for up to 3 ms free-fall times. The degradation of squeezing results
from loss of atom-cavity coupling homogeneity between the initial squeezed state
generation and final collective state readout. A theoretical model is developed
to quantify this degradation and this model is experimentally validated.
acknowledgement: We thank N. Engelsen for comments on the manuscript. This work was
supported by the Office of Naval Research, Vannevar Bush Faculty Fellowship, Department
of Energy, and Defense Threat Reduction Agency. R.K. was partly supported by the
AQT/INQNET program at Caltech.
article_number: '012224'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Yunfan
full_name: Wu, Yunfan
last_name: Wu
- first_name: Rajiv
full_name: Krishnakumar, Rajiv
last_name: Krishnakumar
- first_name: Julián
full_name: Martínez-Rincón, Julián
last_name: Martínez-Rincón
- first_name: Benjamin K.
full_name: Malia, Benjamin K.
last_name: Malia
- first_name: Onur
full_name: Hosten, Onur
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
- first_name: Mark A.
full_name: Kasevich, Mark A.
last_name: Kasevich
citation:
ama: Wu Y, Krishnakumar R, Martínez-Rincón J, Malia BK, Hosten O, Kasevich MA. Retrieval
of cavity-generated atomic spin squeezing after free-space release. Physical
Review A. 2020;102(1). doi:10.1103/PhysRevA.102.012224
apa: Wu, Y., Krishnakumar, R., Martínez-Rincón, J., Malia, B. K., Hosten, O., &
Kasevich, M. A. (2020). Retrieval of cavity-generated atomic spin squeezing after
free-space release. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.102.012224
chicago: Wu, Yunfan, Rajiv Krishnakumar, Julián Martínez-Rincón, Benjamin K. Malia,
Onur Hosten, and Mark A. Kasevich. “Retrieval of Cavity-Generated Atomic Spin
Squeezing after Free-Space Release.” Physical Review A. American Physical
Society, 2020. https://doi.org/10.1103/PhysRevA.102.012224.
ieee: Y. Wu, R. Krishnakumar, J. Martínez-Rincón, B. K. Malia, O. Hosten, and M.
A. Kasevich, “Retrieval of cavity-generated atomic spin squeezing after free-space
release,” Physical Review A, vol. 102, no. 1. American Physical Society,
2020.
ista: Wu Y, Krishnakumar R, Martínez-Rincón J, Malia BK, Hosten O, Kasevich MA.
2020. Retrieval of cavity-generated atomic spin squeezing after free-space release.
Physical Review A. 102(1), 012224.
mla: Wu, Yunfan, et al. “Retrieval of Cavity-Generated Atomic Spin Squeezing after
Free-Space Release.” Physical Review A, vol. 102, no. 1, 012224, American
Physical Society, 2020, doi:10.1103/PhysRevA.102.012224.
short: Y. Wu, R. Krishnakumar, J. Martínez-Rincón, B.K. Malia, O. Hosten, M.A. Kasevich,
Physical Review A 102 (2020).
date_created: 2020-08-30T22:01:10Z
date_published: 2020-07-30T00:00:00Z
date_updated: 2024-02-28T13:11:28Z
day: '30'
department:
- _id: OnHo
doi: 10.1103/PhysRevA.102.012224
external_id:
arxiv:
- '1912.08334'
isi:
- '000555104200011'
intvolume: ' 102'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1912.08334
month: '07'
oa: 1
oa_version: Preprint
publication: Physical Review A
publication_identifier:
eissn:
- '24699934'
issn:
- '24699926'
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Retrieval of cavity-generated atomic spin squeezing after free-space release
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 102
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: '8322'
abstract:
- lang: eng
text: "Reverse firewalls were introduced at Eurocrypt 2015 by Miro-nov and Stephens-Davidowitz,
as a method for protecting cryptographic protocols against attacks on the devices
of the honest parties. In a nutshell: a reverse firewall is placed outside of
a device and its goal is to “sanitize” the messages sent by it, in such a way
that a malicious device cannot leak its secrets to the outside world. It is typically
assumed that the cryptographic devices are attacked in a “functionality-preserving
way” (i.e. informally speaking, the functionality of the protocol remains unchanged
under this attacks). In their paper, Mironov and Stephens-Davidowitz construct
a protocol for passively-secure two-party computations with firewalls, leaving
extension of this result to stronger models as an open question.\r\nIn this paper,
we address this problem by constructing a protocol for secure computation with
firewalls that has two main advantages over the original protocol from Eurocrypt
2015. Firstly, it is a multiparty computation protocol (i.e. it works for an arbitrary
number n of the parties, and not just for 2). Secondly, it is secure in much stronger
corruption settings, namely in the active corruption model. More precisely: we
consider an adversary that can fully corrupt up to \U0001D45B−1 parties, while
the remaining parties are corrupt in a functionality-preserving way.\r\nOur core
techniques are: malleable commitments and malleable non-interactive zero-knowledge,
which in particular allow us to create a novel protocol for multiparty augmented
coin-tossing into the well with reverse firewalls (that is based on a protocol
of Lindell from Crypto 2001)."
acknowledgement: We would like to thank the anonymous reviewers for their helpful
comments and suggestions. The work was initiated while the first author was in IIT
Madras, India. Part of this work was done while the author was visiting the University
of Warsaw. This project has received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme
(682815 - TOCNeT) and from the Foundation for Polish Science under grant TEAM/2016-1/4
founded within the UE 2014–2020 Smart Growth Operational Program. The last author
was supported by the Independent Research Fund Denmark project BETHE and the Concordium
Blockchain Research Center, Aarhus University, Denmark.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Suvradip
full_name: Chakraborty, Suvradip
id: B9CD0494-D033-11E9-B219-A439E6697425
last_name: Chakraborty
- first_name: Stefan
full_name: Dziembowski, Stefan
last_name: Dziembowski
- first_name: Jesper Buus
full_name: Nielsen, Jesper Buus
last_name: Nielsen
citation:
ama: 'Chakraborty S, Dziembowski S, Nielsen JB. Reverse firewalls for actively secure MPCs.
In: Advances in Cryptology – CRYPTO 2020. Vol 12171. Springer Nature; 2020:732-762.
doi:10.1007/978-3-030-56880-1_26'
apa: 'Chakraborty, S., Dziembowski, S., & Nielsen, J. B. (2020). Reverse firewalls for actively secure MPCs.
In Advances in Cryptology – CRYPTO 2020 (Vol. 12171, pp. 732–762). Santa
Barbara, CA, United States: Springer Nature. https://doi.org/10.1007/978-3-030-56880-1_26'
chicago: Chakraborty, Suvradip, Stefan Dziembowski, and Jesper Buus Nielsen. “Reverse Firewalls for Actively Secure MPCs.”
In Advances in Cryptology – CRYPTO 2020, 12171:732–62. Springer Nature,
2020. https://doi.org/10.1007/978-3-030-56880-1_26.
ieee: S. Chakraborty, S. Dziembowski, and J. B. Nielsen, “Reverse firewalls for actively secure MPCs,”
in Advances in Cryptology – CRYPTO 2020, Santa Barbara, CA, United States,
2020, vol. 12171, pp. 732–762.
ista: 'Chakraborty S, Dziembowski S, Nielsen JB. 2020. Reverse firewalls for actively secure MPCs.
Advances in Cryptology – CRYPTO 2020. CRYPTO: Annual International Cryptology
Conference, LNCS, vol. 12171, 732–762.'
mla: Chakraborty, Suvradip, et al. “Reverse Firewalls for Actively Secure MPCs.”
Advances in Cryptology – CRYPTO 2020, vol. 12171, Springer Nature, 2020,
pp. 732–62, doi:10.1007/978-3-030-56880-1_26.
short: S. Chakraborty, S. Dziembowski, J.B. Nielsen, in:, Advances in Cryptology
– CRYPTO 2020, Springer Nature, 2020, pp. 732–762.
conference:
end_date: 2020-08-21
location: Santa Barbara, CA, United States
name: 'CRYPTO: Annual International Cryptology Conference'
start_date: 2020-08-17
date_created: 2020-08-30T22:01:12Z
date_published: 2020-08-10T00:00:00Z
date_updated: 2021-01-12T08:18:08Z
day: '10'
department:
- _id: KrPi
doi: 10.1007/978-3-030-56880-1_26
ec_funded: 1
intvolume: ' 12171'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2019/1317
month: '08'
oa: 1
oa_version: Preprint
page: 732-762
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication: Advances in Cryptology – CRYPTO 2020
publication_identifier:
eissn:
- '16113349'
isbn:
- '9783030568795'
issn:
- '03029743'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Reverse firewalls for actively secure MPCs
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12171
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: '8324'
abstract:
- lang: eng
text: The notion of program sensitivity (aka Lipschitz continuity) specifies that
changes in the program input result in proportional changes to the program output.
For probabilistic programs the notion is naturally extended to expected sensitivity.
A previous approach develops a relational program logic framework for proving
expected sensitivity of probabilistic while loops, where the number of iterations
is fixed and bounded. In this work, we consider probabilistic while loops where
the number of iterations is not fixed, but randomized and depends on the initial
input values. We present a sound approach for proving expected sensitivity of
such programs. Our sound approach is martingale-based and can be automated through
existing martingale-synthesis algorithms. Furthermore, our approach is compositional
for sequential composition of while loops under a mild side condition. We demonstrate
the effectiveness of our approach on several classical examples from Gambler's
Ruin, stochastic hybrid systems and stochastic gradient descent. We also present
experimental results showing that our automated approach can handle various probabilistic
programs in the literature.
acknowledgement: We thank anonymous reviewers for helpful comments, especially for
pointing to us a scenario of piecewise-linear approximation (Remark5). The research
was partially supported by the National Natural Science Foundation of China (NSFC)
under Grant No. 61802254, 61672229, 61832015,61772336,11871221 and Austrian Science
Fund (FWF) NFN under Grant No. S11407-N23 (RiSE/SHiNE). We thank Prof. Yuxi Fu,
director of the BASICS Lab at Shanghai Jiao Tong University, for his support.
article_number: '25'
article_processing_charge: No
arxiv: 1
author:
- first_name: Peixin
full_name: Wang, Peixin
last_name: Wang
- first_name: Hongfei
full_name: Fu, Hongfei
last_name: Fu
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Yuxin
full_name: Deng, Yuxin
last_name: Deng
- first_name: Ming
full_name: Xu, Ming
last_name: Xu
citation:
ama: 'Wang P, Fu H, Chatterjee K, Deng Y, Xu M. Proving expected sensitivity of
probabilistic programs with randomized variable-dependent termination time. In:
Proceedings of the ACM on Programming Languages. Vol 4. ACM; 2020. doi:10.1145/3371093'
apa: Wang, P., Fu, H., Chatterjee, K., Deng, Y., & Xu, M. (2020). Proving expected
sensitivity of probabilistic programs with randomized variable-dependent termination
time. In Proceedings of the ACM on Programming Languages (Vol. 4). ACM.
https://doi.org/10.1145/3371093
chicago: Wang, Peixin, Hongfei Fu, Krishnendu Chatterjee, Yuxin Deng, and Ming Xu.
“Proving Expected Sensitivity of Probabilistic Programs with Randomized Variable-Dependent
Termination Time.” In Proceedings of the ACM on Programming Languages,
Vol. 4. ACM, 2020. https://doi.org/10.1145/3371093.
ieee: P. Wang, H. Fu, K. Chatterjee, Y. Deng, and M. Xu, “Proving expected sensitivity
of probabilistic programs with randomized variable-dependent termination time,”
in Proceedings of the ACM on Programming Languages, 2020, vol. 4, no. POPL.
ista: Wang P, Fu H, Chatterjee K, Deng Y, Xu M. 2020. Proving expected sensitivity
of probabilistic programs with randomized variable-dependent termination time.
Proceedings of the ACM on Programming Languages. vol. 4, 25.
mla: Wang, Peixin, et al. “Proving Expected Sensitivity of Probabilistic Programs
with Randomized Variable-Dependent Termination Time.” Proceedings of the ACM
on Programming Languages, vol. 4, no. POPL, 25, ACM, 2020, doi:10.1145/3371093.
short: P. Wang, H. Fu, K. Chatterjee, Y. Deng, M. Xu, in:, Proceedings of the ACM
on Programming Languages, ACM, 2020.
date_created: 2020-08-30T22:01:12Z
date_published: 2020-01-01T00:00:00Z
date_updated: 2024-02-22T15:16:45Z
day: '01'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.1145/3371093
external_id:
arxiv:
- '1902.04744'
file:
- access_level: open_access
checksum: c6193d109ff4ecb17e7a6513d8eb34c0
content_type: application/pdf
creator: cziletti
date_created: 2020-09-01T11:12:58Z
date_updated: 2020-09-01T11:12:58Z
file_id: '8328'
file_name: 2019_ACM_POPL_Wang.pdf
file_size: 564151
relation: main_file
success: 1
file_date_updated: 2020-09-01T11:12:58Z
has_accepted_license: '1'
intvolume: ' 4'
issue: POPL
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
publication: Proceedings of the ACM on Programming Languages
publication_identifier:
eissn:
- 2475-1421
publication_status: published
publisher: ACM
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://doi.org/10.5281/zenodo.3533633
scopus_import: '1'
status: public
title: Proving expected sensitivity of probabilistic programs with randomized variable-dependent
termination time
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
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
arxiv: 1
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: '8329'
abstract:
- lang: eng
text: We show the synthesis of a redox‐active quinone, 2‐methoxy‐1,4‐hydroquinone
(MHQ), from a bio‐based feedstock and its suitability as electrolyte in aqueous
redox flow batteries. We identified semiquinone intermediates at insufficiently
low pH and quinoid radicals as responsible for decomposition of MHQ under electrochemical
conditions. Both can be avoided and/or stabilized, respectively, using H 3 PO
4 electrolyte, allowing for reversible cycling in a redox flow battery for hundreds
of cycles.
acknowledgement: The Austrian Research Promotion Agency (FFG) is gratefully acknowledged
for financial support of the project LignoBatt (860429).
article_processing_charge: No
article_type: original
author:
- first_name: Werner
full_name: Schlemmer, Werner
last_name: Schlemmer
- first_name: Philipp
full_name: Nothdurft, Philipp
last_name: Nothdurft
- first_name: Alina
full_name: Petzold, Alina
last_name: Petzold
- first_name: Philipp
full_name: Frühwirt, Philipp
last_name: Frühwirt
- first_name: Max
full_name: Schmallegger, Max
last_name: Schmallegger
- first_name: Georg
full_name: Gescheidt-Demner, Georg
last_name: Gescheidt-Demner
- first_name: Roland
full_name: Fischer, Roland
last_name: Fischer
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: Wolfgang
full_name: Kern, Wolfgang
last_name: Kern
- first_name: Stefan
full_name: Spirk, Stefan
last_name: Spirk
citation:
ama: Schlemmer W, Nothdurft P, Petzold A, et al. 2‐methoxyhydroquinone from vanillin
for aqueous redox‐flow batteries. Angewandte Chemie International Edition.
2020;59(51):22943-22946. doi:10.1002/anie.202008253
apa: Schlemmer, W., Nothdurft, P., Petzold, A., Frühwirt, P., Schmallegger, M.,
Gescheidt-Demner, G., … Spirk, S. (2020). 2‐methoxyhydroquinone from vanillin
for aqueous redox‐flow batteries. Angewandte Chemie International Edition.
Wiley. https://doi.org/10.1002/anie.202008253
chicago: Schlemmer, Werner, Philipp Nothdurft, Alina Petzold, Philipp Frühwirt,
Max Schmallegger, Georg Gescheidt-Demner, Roland Fischer, Stefan Alexander Freunberger,
Wolfgang Kern, and Stefan Spirk. “2‐methoxyhydroquinone from Vanillin for Aqueous
Redox‐flow Batteries.” Angewandte Chemie International Edition. Wiley,
2020. https://doi.org/10.1002/anie.202008253.
ieee: W. Schlemmer et al., “2‐methoxyhydroquinone from vanillin for aqueous
redox‐flow batteries,” Angewandte Chemie International Edition, vol. 59,
no. 51. Wiley, pp. 22943–22946, 2020.
ista: Schlemmer W, Nothdurft P, Petzold A, Frühwirt P, Schmallegger M, Gescheidt-Demner
G, Fischer R, Freunberger SA, Kern W, Spirk S. 2020. 2‐methoxyhydroquinone from
vanillin for aqueous redox‐flow batteries. Angewandte Chemie International Edition.
59(51), 22943–22946.
mla: Schlemmer, Werner, et al. “2‐methoxyhydroquinone from Vanillin for Aqueous
Redox‐flow Batteries.” Angewandte Chemie International Edition, vol. 59,
no. 51, Wiley, 2020, pp. 22943–46, doi:10.1002/anie.202008253.
short: W. Schlemmer, P. Nothdurft, A. Petzold, P. Frühwirt, M. Schmallegger, G.
Gescheidt-Demner, R. Fischer, S.A. Freunberger, W. Kern, S. Spirk, Angewandte
Chemie International Edition 59 (2020) 22943–22946.
date_created: 2020-09-03T16:10:56Z
date_published: 2020-12-14T00:00:00Z
date_updated: 2023-09-05T16:03:47Z
day: '14'
department:
- _id: StFr
doi: 10.1002/anie.202008253
external_id:
isi:
- '000576148700001'
intvolume: ' 59'
isi: 1
issue: '51'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1002/anie.202008253
month: '12'
oa: 1
oa_version: Published Version
page: 22943-22946
publication: Angewandte Chemie International Edition
publication_identifier:
eissn:
- 1521-3773
issn:
- 1433-7851
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '9780'
relation: research_data
status: public
scopus_import: '1'
status: public
title: 2‐methoxyhydroquinone from vanillin for aqueous redox‐flow batteries
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 59
year: '2020'
...
---
_id: '8332'
abstract:
- lang: eng
text: "Designing and verifying concurrent programs is a notoriously challenging,
time consuming, and error prone task, even for experts. This is due to the sheer
number of possible interleavings of a concurrent program, all of which have to
be tracked and accounted for in a formal proof. Inventing an inductive invariant
that captures all interleavings of a low-level implementation is theoretically
possible, but practically intractable. We develop a refinement-based verification
framework that provides mechanisms to simplify proof construction by decomposing
the verification task into smaller subtasks.\r\n\r\nIn a first line of work, we
present a foundation for refinement reasoning over structured concurrent programs.
We introduce layered concurrent programs as a compact notation to represent multi-layer
refinement proofs. A layered concurrent program specifies a sequence of connected
concurrent programs, from most concrete to most abstract, such that common parts
of different programs are written exactly once. Each program in this sequence
is expressed as structured concurrent program, i.e., a program over (potentially
recursive) procedures, imperative control flow, gated atomic actions, structured
parallelism, and asynchronous concurrency. This is in contrast to existing refinement-based
verifiers, which represent concurrent systems as flat transition relations. We
present a powerful refinement proof rule that decomposes refinement checking over
structured programs into modular verification conditions. Refinement checking
is supported by a new form of modular, parameterized invariants, called yield
invariants, and a linear permission system to enhance local reasoning.\r\n\r\nIn
a second line of work, we present two new reduction-based program transformations
that target asynchronous programs. These transformations reduce the number of
interleavings that need to be considered, thus reducing the complexity of invariants.
Synchronization simplifies the verification of asynchronous programs by introducing
the fiction, for proof purposes, that asynchronous operations complete synchronously.
Synchronization summarizes an asynchronous computation as immediate atomic effect.
Inductive sequentialization establishes sequential reductions that captures every
behavior of the original program up to reordering of coarse-grained commutative
actions. A sequential reduction of a concurrent program is easy to reason about
since it corresponds to a simple execution of the program in an idealized synchronous
environment, where processes act in a fixed order and at the same speed.\r\n\r\nOur
approach is implemented the CIVL verifier, which has been successfully used for
the verification of several complex concurrent programs. In our methodology, the
overall correctness of a program is established piecemeal by focusing on the invariant
required for each refinement step separately. While the programmer does the creative
work of specifying the chain of programs and the inductive invariant justifying
each link in the chain, the tool automatically constructs the verification conditions
underlying each refinement step."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Bernhard
full_name: Kragl, Bernhard
id: 320FC952-F248-11E8-B48F-1D18A9856A87
last_name: Kragl
orcid: 0000-0001-7745-9117
citation:
ama: 'Kragl B. Verifying concurrent programs: Refinement, synchronization, sequentialization.
2020. doi:10.15479/AT:ISTA:8332'
apa: 'Kragl, B. (2020). Verifying concurrent programs: Refinement, synchronization,
sequentialization. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8332'
chicago: 'Kragl, Bernhard. “Verifying Concurrent Programs: Refinement, Synchronization,
Sequentialization.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8332.'
ieee: 'B. Kragl, “Verifying concurrent programs: Refinement, synchronization, sequentialization,”
Institute of Science and Technology Austria, 2020.'
ista: 'Kragl B. 2020. Verifying concurrent programs: Refinement, synchronization,
sequentialization. Institute of Science and Technology Austria.'
mla: 'Kragl, Bernhard. Verifying Concurrent Programs: Refinement, Synchronization,
Sequentialization. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8332.'
short: 'B. Kragl, Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization,
Institute of Science and Technology Austria, 2020.'
date_created: 2020-09-04T12:24:12Z
date_published: 2020-09-03T00:00:00Z
date_updated: 2023-09-13T08:45:08Z
day: '03'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: ToHe
doi: 10.15479/AT:ISTA:8332
file:
- access_level: open_access
checksum: 26fe261550f691280bda4c454bf015c7
content_type: application/pdf
creator: bkragl
date_created: 2020-09-04T12:17:47Z
date_updated: 2020-09-04T12:17:47Z
file_id: '8333'
file_name: kragl-thesis.pdf
file_size: 1348815
relation: main_file
- access_level: closed
checksum: b9694ce092b7c55557122adba8337ebc
content_type: application/zip
creator: bkragl
date_created: 2020-09-04T13:00:17Z
date_updated: 2020-09-04T13:00:17Z
file_id: '8335'
file_name: kragl-thesis.zip
file_size: 372312
relation: source_file
file_date_updated: 2020-09-04T13:00:17Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '120'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '133'
relation: part_of_dissertation
status: public
- id: '8012'
relation: part_of_dissertation
status: public
- id: '8195'
relation: part_of_dissertation
status: public
- id: '160'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
title: 'Verifying concurrent programs: Refinement, synchronization, sequentialization'
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
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: '8339'
abstract:
- lang: eng
text: "Discrete Gaussian distributions over lattices are central to lattice-based
cryptography, and to the computational and mathematical aspects of lattices more
broadly. The literature contains a wealth of useful theorems about the behavior
of discrete Gaussians under convolutions and related operations. Yet despite their
structural similarities, most of these theorems are formally incomparable, and
their proofs tend to be monolithic and written nearly “from scratch,” making them
unnecessarily hard to verify, understand, and extend.\r\nIn this work we present
a modular framework for analyzing linear operations on discrete Gaussian distributions.
The framework abstracts away the particulars of Gaussians, and usually reduces
proofs to the choice of appropriate linear transformations and elementary linear
algebra. To showcase the approach, we establish several general properties of
discrete Gaussians, and show how to obtain all prior convolution theorems (along
with some new ones) as straightforward corollaries. As another application, we
describe a self-reduction for Learning With Errors (LWE) that uses a fixed number
of samples to generate an unlimited number of additional ones (having somewhat
larger error). The distinguishing features of our reduction are its simple analysis
in our framework, and its exclusive use of discrete Gaussians without any loss
in parameters relative to a prior mixed discrete-and-continuous approach.\r\nAs
a contribution of independent interest, for subgaussian random matrices we prove
a singular value concentration bound with explicitly stated constants, and we
give tighter heuristics for specific distributions that are commonly used for
generating lattice trapdoors. These bounds yield improvements in the concrete
bit-security estimates for trapdoor lattice cryptosystems."
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Nicholas
full_name: Genise, Nicholas
last_name: Genise
- first_name: Daniele
full_name: Micciancio, Daniele
last_name: Micciancio
- first_name: Chris
full_name: Peikert, Chris
last_name: Peikert
- first_name: Michael
full_name: Walter, Michael
id: 488F98B0-F248-11E8-B48F-1D18A9856A87
last_name: Walter
orcid: 0000-0003-3186-2482
citation:
ama: 'Genise N, Micciancio D, Peikert C, Walter M. Improved discrete Gaussian and
subgaussian analysis for lattice cryptography. In: 23rd IACR International
Conference on the Practice and Theory of Public-Key Cryptography. Vol 12110.
Springer Nature; 2020:623-651. doi:10.1007/978-3-030-45374-9_21'
apa: 'Genise, N., Micciancio, D., Peikert, C., & Walter, M. (2020). Improved
discrete Gaussian and subgaussian analysis for lattice cryptography. In 23rd
IACR International Conference on the Practice and Theory of Public-Key Cryptography
(Vol. 12110, pp. 623–651). Edinburgh, United Kingdom: Springer Nature. https://doi.org/10.1007/978-3-030-45374-9_21'
chicago: Genise, Nicholas, Daniele Micciancio, Chris Peikert, and Michael Walter.
“Improved Discrete Gaussian and Subgaussian Analysis for Lattice Cryptography.”
In 23rd IACR International Conference on the Practice and Theory of Public-Key
Cryptography, 12110:623–51. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-45374-9_21.
ieee: N. Genise, D. Micciancio, C. Peikert, and M. Walter, “Improved discrete Gaussian
and subgaussian analysis for lattice cryptography,” in 23rd IACR International
Conference on the Practice and Theory of Public-Key Cryptography, Edinburgh,
United Kingdom, 2020, vol. 12110, pp. 623–651.
ista: 'Genise N, Micciancio D, Peikert C, Walter M. 2020. Improved discrete Gaussian
and subgaussian analysis for lattice cryptography. 23rd IACR International Conference
on the Practice and Theory of Public-Key Cryptography. PKC: Public-Key Cryptography,
LNCS, vol. 12110, 623–651.'
mla: Genise, Nicholas, et al. “Improved Discrete Gaussian and Subgaussian Analysis
for Lattice Cryptography.” 23rd IACR International Conference on the Practice
and Theory of Public-Key Cryptography, vol. 12110, Springer Nature, 2020,
pp. 623–51, doi:10.1007/978-3-030-45374-9_21.
short: N. Genise, D. Micciancio, C. Peikert, M. Walter, in:, 23rd IACR International
Conference on the Practice and Theory of Public-Key Cryptography, Springer Nature,
2020, pp. 623–651.
conference:
end_date: 2020-05-07
location: Edinburgh, United Kingdom
name: 'PKC: Public-Key Cryptography'
start_date: 2020-05-04
date_created: 2020-09-06T22:01:13Z
date_published: 2020-05-15T00:00:00Z
date_updated: 2023-02-23T13:31:06Z
day: '15'
department:
- _id: KrPi
doi: 10.1007/978-3-030-45374-9_21
ec_funded: 1
intvolume: ' 12110'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2020/337
month: '05'
oa: 1
oa_version: Preprint
page: 623-651
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication: 23rd IACR International Conference on the Practice and Theory of Public-Key
Cryptography
publication_identifier:
eissn:
- '16113349'
isbn:
- '9783030453732'
issn:
- '03029743'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Improved discrete Gaussian and subgaussian analysis for lattice cryptography
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12110
year: '2020'
...
---
_id: '8340'
abstract:
- lang: eng
text: Mitochondria are sites of oxidative phosphorylation in eukaryotic cells. Oxidative
phosphorylation operates by a chemiosmotic mechanism made possible by redox-driven
proton pumping machines which establish a proton motive force across the inner
mitochondrial membrane. This electrochemical proton gradient is used to drive
ATP synthesis, which powers the majority of cellular processes such as protein
synthesis, locomotion and signalling. In this thesis I investigate the structures
and molecular mechanisms of two inner mitochondrial proton pumping enzymes, respiratory
complex I and transhydrogenase. I present the first high-resolution structure
of the full transhydrogenase from any species, and a significantly improved structure
of complex I. Improving the resolution from 3.3 Å available previously to up to
2.3 Å in this thesis allowed us to model bound water molecules, crucial in the
proton pumping mechanism. For both enzymes, up to five cryo-EM datasets with different
substrates and inhibitors bound were solved to delineate the catalytic cycle and
understand the proton pumping mechanism. In transhydrogenase, the proton channel
is gated by reversible detachment of the NADP(H)-binding domain which opens the
proton channel to the opposite sites of the membrane. In complex I, the proton
channels are gated by reversible protonation of key glutamate and lysine residues
and breaking of the water wire connecting the proton pumps with the quinone reduction
site. The tight coupling between the redox and the proton pumping reactions in
transhydrogenase is achieved by controlling the NADP(H) exchange which can only
happen when the NADP(H)-binding domain interacts with the membrane domain. In
complex I, coupling is achieved by cycling of the whole complex between the closed
state, in which quinone can get reduced, and the open state, in which NADH can
induce quinol ejection from the binding pocket. On the basis of these results
I propose detailed mechanisms for catalytic cycles of transhydrogenase and complex
I that are consistent with a large amount of previous work. In both enzymes, conformational
and electrostatic mechanisms contribute to the overall catalytic process. Results
presented here could be used for better understanding of the human pathologies
arising from deficiencies of complex I or transhydrogenase and could be used to
develop novel therapies.
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: 'I acknowledge the support of IST facilities, especially the Electron
Miscroscopy facility for providing training and resources. Special thanks also go
to cryo-EM specialists who helped me to collect the data present here: Dr Valentin
Hodirnau (IST Austria), Dr Tom Heuser (IMBA, Vienna), Dr Rebecca Thompson (Uni.
of Leeds) and Dr Jirka Nováček (CEITEC). This work has been supported by iNEXT,
project number 653706, funded by the Horizon 2020 programme of the European Union.
This project has received funding from the European Union’s Horizon 2020 research
and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.'
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Domen
full_name: Kampjut, Domen
id: 37233050-F248-11E8-B48F-1D18A9856A87
last_name: Kampjut
citation:
ama: Kampjut D. Molecular mechanisms of mitochondrial redox-coupled proton pumping
enzymes. 2020. doi:10.15479/AT:ISTA:8340
apa: Kampjut, D. (2020). Molecular mechanisms of mitochondrial redox-coupled
proton pumping enzymes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8340
chicago: Kampjut, Domen. “Molecular Mechanisms of Mitochondrial Redox-Coupled Proton
Pumping Enzymes.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8340.
ieee: D. Kampjut, “Molecular mechanisms of mitochondrial redox-coupled proton pumping
enzymes,” Institute of Science and Technology Austria, 2020.
ista: Kampjut D. 2020. Molecular mechanisms of mitochondrial redox-coupled proton
pumping enzymes. Institute of Science and Technology Austria.
mla: Kampjut, Domen. Molecular Mechanisms of Mitochondrial Redox-Coupled Proton
Pumping Enzymes. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8340.
short: D. Kampjut, Molecular Mechanisms of Mitochondrial Redox-Coupled Proton Pumping
Enzymes, Institute of Science and Technology Austria, 2020.
date_created: 2020-09-07T18:42:23Z
date_published: 2020-09-09T00:00:00Z
date_updated: 2023-09-07T13:26:17Z
day: '09'
ddc:
- '572'
degree_awarded: PhD
department:
- _id: LeSa
doi: 10.15479/AT:ISTA:8340
ec_funded: 1
file:
- access_level: closed
checksum: dd270baf82121eb4472ad19d77bf227c
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: dkampjut
date_created: 2020-09-08T13:32:06Z
date_updated: 2021-09-11T22:30:04Z
embargo_to: open_access
file_id: '8345'
file_name: ThesisFull20200908.docx
file_size: 166146359
relation: source_file
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checksum: 82fce6f95ffa47ecc4ebca67ea2cc38c
content_type: application/pdf
creator: dernst
date_created: 2020-09-14T15:02:20Z
date_updated: 2021-09-11T22:30:04Z
embargo: 2021-09-10
file_id: '8393'
file_name: 2020_Thesis_Kampjut.pdf
file_size: 13873769
relation: main_file
file_date_updated: 2021-09-11T22:30:04Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: None
page: '242'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
isbn:
- 978-3-99078-008-4
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '6848'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
title: Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '8341'
abstract:
- lang: eng
text: "One of the most striking hallmarks of the eukaryotic cell is the presence
of intracellular vesicles and organelles. Each of these membrane-enclosed compartments
has a distinct composition of lipids and proteins, which is essential for accurate
membrane traffic and homeostasis. Interestingly, their biochemical identities
are achieved with the help\r\nof small GTPases of the Rab family, which cycle
between GDP- and GTP-bound forms on the selected membrane surface. While this
activity switch is well understood for an individual protein, how Rab GTPases
collectively transition between states to generate decisive signal propagation
in space and time is unclear. In my PhD thesis, I present\r\nin vitro reconstitution
experiments with theoretical modeling to systematically study a minimal Rab5 activation
network from bottom-up. We find that positive feedback based on known molecular
interactions gives rise to bistable GTPase activity switching on system’s scale.
Furthermore, we determine that collective transition near the critical\r\npoint
is intrinsically stochastic and provide evidence that the inactive Rab5 abundance
on the membrane can shape the network response. Finally, we demonstrate that collective
switching can spread on the lipid bilayer as a traveling activation wave, representing
a possible emergent activity pattern in endosomal maturation. Together, our\r\nfindings
reveal new insights into the self-organization properties of signaling networks
away from chemical equilibrium. Our work highlights the importance of systematic
characterization of biochemical systems in well-defined physiological conditions.
This way, we were able to answer long-standing open questions in the field and
close the gap between regulatory processes on a molecular scale and emergent responses
on system’s level."
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: NanoFab
acknowledgement: My thanks goes to the Loose lab members, BioImaging, Life Science
and Nanofabrication Facilities and the wonderful international community at IST
for sharing this experience with me.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Urban
full_name: Bezeljak, Urban
id: 2A58201A-F248-11E8-B48F-1D18A9856A87
last_name: Bezeljak
orcid: 0000-0003-1365-5631
citation:
ama: Bezeljak U. In vitro reconstitution of a Rab activation switch. 2020. doi:10.15479/AT:ISTA:8341
apa: Bezeljak, U. (2020). In vitro reconstitution of a Rab activation switch.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8341
chicago: Bezeljak, Urban. “In Vitro Reconstitution of a Rab Activation Switch.”
Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8341.
ieee: U. Bezeljak, “In vitro reconstitution of a Rab activation switch,” Institute
of Science and Technology Austria, 2020.
ista: Bezeljak U. 2020. In vitro reconstitution of a Rab activation switch. Institute
of Science and Technology Austria.
mla: Bezeljak, Urban. In Vitro Reconstitution of a Rab Activation Switch.
Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8341.
short: U. Bezeljak, In Vitro Reconstitution of a Rab Activation Switch, Institute
of Science and Technology Austria, 2020.
date_created: 2020-09-08T08:53:53Z
date_published: 2020-09-08T00:00:00Z
date_updated: 2023-09-07T13:17:06Z
day: '08'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: MaLo
doi: 10.15479/AT:ISTA:8341
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checksum: 70871b335a595252a66c6bbf0824fb02
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creator: dernst
date_created: 2020-09-08T09:00:29Z
date_updated: 2021-09-16T12:49:12Z
file_id: '8342'
file_name: 2020_Urban_Bezeljak_Thesis_TeX.zip
file_size: 65246782
relation: source_file
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checksum: 59a62275088b00b7241e6ff4136434c7
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creator: dernst
date_created: 2020-09-08T09:00:27Z
date_updated: 2021-09-16T12:49:12Z
file_id: '8343'
file_name: 2020_Urban_Bezeljak_Thesis.pdf
file_size: 31259058
relation: main_file
file_date_updated: 2021-09-16T12:49:12Z
has_accepted_license: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '09'
oa: 1
oa_version: Published Version
page: '215'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7580'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
title: In vitro reconstitution of a Rab activation switch
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...