---
DOAJ_listed: '1'
_id: '15320'
abstract:
- lang: eng
text: Josephson diodes are superconducting elements that show an asymmetry in the
critical current depending on the direction of the current. Here, we theoretically
explore how an alternating current bias can tune the response of such a diode.
We show that for slow driving there is always a regime where the system can only
carry zero-voltage dc current in one direction, thus effectively behaving as an
ideal Josephson diode. Under fast driving, the diode efficiency is also tunable,
although the ideal regime cannot be reached in this case. We also investigate
the residual dissipation due to the time-dependent current bias and show that
it remains small. All our conclusions are solely based on the critical current
asymmetry of the junction, and are thus compatible with any Josephson diode.
acknowledgement: "We acknowledge support from research grants Spanish CM Talento Program
(Project No. 2022-T1/IND-24070), Spanish Ministry of Science, innovation, and Universities
through Grant No. PID2022-140552NA-I00, Swedish Research Council under Grant Agreement
No. 2020-03412, the European Research Council (ERC) under the European Union’s Horizon
2020 research and innovation programme under Grant Agreement No. 856526, Nanolund,
FWF Project with [82],\r\nand Microsoft Corporation. "
article_number: L022002
article_processing_charge: Yes
article_type: letter_note
author:
- first_name: Rubén
full_name: Seoane Souto, Rubén
last_name: Seoane Souto
- first_name: Martin
full_name: Leijnse, Martin
last_name: Leijnse
- first_name: Constantin
full_name: Schrade, Constantin
last_name: Schrade
- first_name: Marco
full_name: Valentini, Marco
id: C0BB2FAC-D767-11E9-B658-BC13E6697425
last_name: Valentini
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
- first_name: Jeroen
full_name: Danon, Jeroen
last_name: Danon
citation:
ama: Seoane Souto R, Leijnse M, Schrade C, Valentini M, Katsaros G, Danon J. Tuning
the Josephson diode response with an ac current. Physical Review Research.
2024;6(2). doi:10.1103/PhysRevResearch.6.L022002
apa: Seoane Souto, R., Leijnse, M., Schrade, C., Valentini, M., Katsaros, G., &
Danon, J. (2024). Tuning the Josephson diode response with an ac current. Physical
Review Research. American Physical Society. https://doi.org/10.1103/PhysRevResearch.6.L022002
chicago: Seoane Souto, Rubén, Martin Leijnse, Constantin Schrade, Marco Valentini,
Georgios Katsaros, and Jeroen Danon. “Tuning the Josephson Diode Response with
an Ac Current.” Physical Review Research. American Physical Society, 2024.
https://doi.org/10.1103/PhysRevResearch.6.L022002.
ieee: R. Seoane Souto, M. Leijnse, C. Schrade, M. Valentini, G. Katsaros, and J.
Danon, “Tuning the Josephson diode response with an ac current,” Physical Review
Research, vol. 6, no. 2. American Physical Society, 2024.
ista: Seoane Souto R, Leijnse M, Schrade C, Valentini M, Katsaros G, Danon J. 2024.
Tuning the Josephson diode response with an ac current. Physical Review Research.
6(2), L022002.
mla: Seoane Souto, Rubén, et al. “Tuning the Josephson Diode Response with an Ac
Current.” Physical Review Research, vol. 6, no. 2, L022002, American Physical
Society, 2024, doi:10.1103/PhysRevResearch.6.L022002.
short: R. Seoane Souto, M. Leijnse, C. Schrade, M. Valentini, G. Katsaros, J. Danon,
Physical Review Research 6 (2024).
date_created: 2024-04-14T22:01:02Z
date_published: 2024-04-01T00:00:00Z
date_updated: 2025-05-14T09:31:50Z
day: '01'
ddc:
- '530'
department:
- _id: GeKa
doi: 10.1103/PhysRevResearch.6.L022002
file:
- access_level: open_access
checksum: 7b9cb3b17d89f392bd582e30d7a72a29
content_type: application/pdf
creator: dernst
date_created: 2024-04-17T07:14:53Z
date_updated: 2024-04-17T07:14:53Z
file_id: '15327'
file_name: 2024_PhysReviewResearch_Souto.pdf
file_size: 1073544
relation: main_file
success: 1
file_date_updated: 2024-04-17T07:14:53Z
fulldoi: https://doi.org/10.1103/PhysRevResearch.6.L022002
has_accepted_license: '1'
intvolume: ' 6'
issue: '2'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '04'
oa: 1
oa_version: Published Version
publication: Physical Review Research
publication_identifier:
eissn:
- 2643-1564
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tuning the Josephson diode response with an ac current
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2024'
...
---
_id: '15321'
abstract:
- lang: eng
text: Boolean Networks (BNs) are widely used as a modeling formalism in several
domains, notably systems biology and computer science. A fundamental problem in
BN analysis is the enumeration of trap spaces, which are hypercubes in the state
space that cannot be escaped once entered. Several methods have been proposed
for enumerating trap spaces, however they often suffer from scalability and efficiency
issues, particularly for large and complex models. To our knowledge, the most
efficient and recent methods for the trap space enumeration all rely on Answer
Set Programming (ASP), which has been widely applied to the analysis of BNs. Motivated
by these considerations, our work proposes a new method for enumerating trap spaces
in BNs using ASP. We evaluate the method on a mix of 250+ real-world and 400+
randomly generated BNs, showing that it enables analysis of models beyond the
capabilities of existing tools (namely pyboolnet, mpbn, trappist, and trapmvn).
acknowledgement: This work was supported by Institut Carnot STAR, Marseille, France
and by the European Union’s Horizon 2020 research and innovation programme under
the Marie Skłodowska-Curie Grant Agreement No. 101034413.
article_processing_charge: No
author:
- first_name: Giang
full_name: Trinh, Giang
last_name: Trinh
- first_name: Belaid
full_name: Benhamou, Belaid
last_name: Benhamou
- first_name: Samuel
full_name: Pastva, Samuel
id: 07c5ea74-f61c-11ec-a664-aa7c5d957b2b
last_name: Pastva
orcid: 0000-0003-1993-0331
- first_name: Sylvain
full_name: Soliman, Sylvain
last_name: Soliman
citation:
ama: 'Trinh G, Benhamou B, Pastva S, Soliman S. Scalable enumeration of trap spaces
in boolean networks via answer set programming. In: Proceedings of the 38th
AAAI Conference on Artificial Intelligence. Vol 38. Association for the Advancement
of Artificial Intelligence; 2024:10714-10722. doi:10.1609/aaai.v38i9.28943'
apa: Trinh, G., Benhamou, B., Pastva, S., & Soliman, S. (2024). Scalable enumeration
of trap spaces in boolean networks via answer set programming. In Proceedings
of the 38th AAAI Conference on Artificial Intelligence (Vol. 38, pp. 10714–10722).
Association for the Advancement of Artificial Intelligence. https://doi.org/10.1609/aaai.v38i9.28943
chicago: Trinh, Giang, Belaid Benhamou, Samuel Pastva, and Sylvain Soliman. “Scalable
Enumeration of Trap Spaces in Boolean Networks via Answer Set Programming.” In
Proceedings of the 38th AAAI Conference on Artificial Intelligence, 38:10714–22.
Association for the Advancement of Artificial Intelligence, 2024. https://doi.org/10.1609/aaai.v38i9.28943.
ieee: G. Trinh, B. Benhamou, S. Pastva, and S. Soliman, “Scalable enumeration of
trap spaces in boolean networks via answer set programming,” in Proceedings
of the 38th AAAI Conference on Artificial Intelligence, 2024, vol. 38, no.
9, pp. 10714–10722.
ista: Trinh G, Benhamou B, Pastva S, Soliman S. 2024. Scalable enumeration of trap
spaces in boolean networks via answer set programming. Proceedings of the 38th
AAAI Conference on Artificial Intelligence. vol. 38, 10714–10722.
mla: Trinh, Giang, et al. “Scalable Enumeration of Trap Spaces in Boolean Networks
via Answer Set Programming.” Proceedings of the 38th AAAI Conference on Artificial
Intelligence, vol. 38, no. 9, Association for the Advancement of Artificial
Intelligence, 2024, pp. 10714–22, doi:10.1609/aaai.v38i9.28943.
short: G. Trinh, B. Benhamou, S. Pastva, S. Soliman, in:, Proceedings of the 38th
AAAI Conference on Artificial Intelligence, Association for the Advancement of
Artificial Intelligence, 2024, pp. 10714–10722.
date_created: 2024-04-14T22:01:02Z
date_published: 2024-03-25T00:00:00Z
date_updated: 2026-06-18T17:48:08Z
day: '25'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1609/aaai.v38i9.28943
ec_funded: 1
fulldoi: https://doi.org/10.1609/aaai.v38i9.28943
intvolume: ' 38'
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://amu.hal.science/hal-04523118/
month: '03'
oa: 1
oa_version: Published Version
page: 10714-10722
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Proceedings of the 38th AAAI Conference on Artificial Intelligence
publication_identifier:
eissn:
- 2374-3468
isbn:
- '1577358872'
issn:
- 2159-5399
publication_status: published
publisher: Association for the Advancement of Artificial Intelligence
quality_controlled: '1'
scopus_import: '1'
status: public
title: Scalable enumeration of trap spaces in boolean networks via answer set programming
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 38
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '15330'
abstract:
- lang: eng
text: Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth
and development by controlling plasma membrane protein composition and cargo uptake.
CME relies on the precise recruitment of regulators for vesicle maturation and
release. Homologues of components of mammalian vesicle scission are strong candidates
to be part of the scission machinery in plants, but the precise roles of these
proteins in this process are not fully understood. Here, we characterised the
roles of Plant Dynamin-Related Proteins 2 (DRP2s) and SH3-domain containing protein
2 (SH3P2), the plant homologue to Dynamins’ recruiters, like Endophilin and Amphiphysin,
in the CME by combining high-resolution imaging of endocytic events in vivo and
characterisation of the purified proteins in vitro. Although DRP2s and SH3P2 arrive
similarly late during CME and physically interact, genetic analysis of the sh3p123
triple-mutant and complementation assays with non-SH3P2-interacting DRP2 variants
suggests that SH3P2 does not directly recruit DRP2s to the site of endocytosis.
These observations imply that despite the presence of many well-conserved endocytic
components, plants have acquired a distinct mechanism for CME.
acknowledged_ssus:
- _id: EM-Fac
- _id: LifeSc
- _id: Bio
acknowledgement: "Nataliia Gnyliukh was partially funded by the European Union’s Horizon
2020 research and\r\ninnovation program (2018-2020) under the Marie Sklodowska-Curie
Grant (agreement no.\r\n665385). Taif University Researchers Supporting Project:
TURSP-HC2022/02. and Austrian\r\nScience Fund (FWF): I 6123-B.We thank Prof. Eileen
Lafer and Liping Wang for their suggestions regarding the optimisation of protein
expression and purification. We thank Prof. Sebastian Y. Bednarek for the useful
comments and constructive criticism of the project. We thank Maciek Adamowski for
providing genetic material. This research was supported by the Scientific Service
Units (SSU) of IST-Austria through resources provided by the Electron microscopy
(EMF), Lab Support Facility (LSF) (particularly Dorota Jaworska) and the Bioimaging
Facility (BIF)."
article_number: jcs.261720
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Nataliia
full_name: Gnyliukh, Nataliia
id: 390C1120-F248-11E8-B48F-1D18A9856A87
last_name: Gnyliukh
orcid: 0000-0002-2198-0509
- 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: MK
full_name: Nagel, MK
last_name: Nagel
- first_name: Aline
full_name: Monzer, Aline
id: 2DB5D88C-D7B3-11E9-B8FD-7907E6697425
last_name: Monzer
- first_name: David
full_name: Babic, David
id: db566d23-f6e0-11ea-865d-e6f270e968e7
last_name: Babic
- first_name: Annamaria
full_name: Hlavata, Annamaria
id: 36062FEC-F248-11E8-B48F-1D18A9856A87
last_name: Hlavata
- first_name: SS
full_name: Alotaibi, SS
last_name: Alotaibi
- first_name: E
full_name: Isono, E
last_name: Isono
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Gnyliukh N, Johnson AJ, Nagel M, et al. Role of dynamin-related proteins 2
and SH3P2 in clathrin-mediated endocytosis in Arabidopsis thaliana. Journal
of Cell Science. 2024;137(8). doi:10.1242/jcs.261720
apa: Gnyliukh, N., Johnson, A. J., Nagel, M., Monzer, A., Babic, D., Hlavata, A.,
… Friml, J. (2024). Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated
endocytosis in Arabidopsis thaliana. Journal of Cell Science. The Company
of Biologists. https://doi.org/10.1242/jcs.261720
chicago: Gnyliukh, Nataliia, Alexander J Johnson, MK Nagel, Aline Monzer, David
Babic, Annamaria Hlavata, SS Alotaibi, E Isono, Martin Loose, and Jiří Friml.
“Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis
in Arabidopsis Thaliana.” Journal of Cell Science. The Company of Biologists,
2024. https://doi.org/10.1242/jcs.261720.
ieee: N. Gnyliukh et al., “Role of dynamin-related proteins 2 and SH3P2 in
clathrin-mediated endocytosis in Arabidopsis thaliana,” Journal of Cell Science,
vol. 137, no. 8. The Company of Biologists, 2024.
ista: Gnyliukh N, Johnson AJ, Nagel M, Monzer A, Babic D, Hlavata A, Alotaibi S,
Isono E, Loose M, Friml J. 2024. Role of dynamin-related proteins 2 and SH3P2
in clathrin-mediated endocytosis in Arabidopsis thaliana. Journal of Cell Science.
137(8), jcs. 261720.
mla: Gnyliukh, Nataliia, et al. “Role of Dynamin-Related Proteins 2 and SH3P2 in
Clathrin-Mediated Endocytosis in Arabidopsis Thaliana.” Journal of Cell Science,
vol. 137, no. 8, jcs. 261720, The Company of Biologists, 2024, doi:10.1242/jcs.261720.
short: N. Gnyliukh, A.J. Johnson, M. Nagel, A. Monzer, D. Babic, A. Hlavata, S.
Alotaibi, E. Isono, M. Loose, J. Friml, Journal of Cell Science 137 (2024).
corr_author: '1'
date_created: 2024-04-19T09:54:59Z
date_published: 2024-04-01T00:00:00Z
date_updated: 2025-09-04T13:49:45Z
day: '01'
ddc:
- '570'
department:
- _id: MaLo
- _id: JiFr
- _id: CaBe
doi: 10.1242/jcs.261720
ec_funded: 1
external_id:
isi:
- '001266917100005'
pmid:
- '38506228'
file:
- access_level: open_access
checksum: 6dc023f0cc7052ad3cf0a42589d2e30f
content_type: application/pdf
creator: dernst
date_created: 2025-01-09T08:41:16Z
date_updated: 2025-01-09T08:41:16Z
file_id: '18792'
file_name: 2024_JourCellScience_Gnyliukh.pdf
file_size: 25845948
relation: main_file
success: 1
file_date_updated: 2025-01-09T08:41:16Z
fulldoi: https://doi.org/10.1242/jcs.261720
has_accepted_license: '1'
intvolume: ' 137'
isi: 1
issue: '8'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: bd76d395-d553-11ed-ba76-f678c14f9033
grant_number: I06123
name: Peptide receptors for auxin canalization in Arabidopsis
publication: Journal of Cell Science
publication_identifier:
eissn:
- 1477-9137
issn:
- 0021-9533
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
related_material:
record:
- id: '14591'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis
in Arabidopsis thaliana
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 137
year: '2024'
...
---
_id: '15333'
abstract:
- lang: eng
text: BUBAAK-SpLit is a tool for dynamically splitting verification tasks into parts
that can then be analyzed in parallel. It is built on top of BUBAAK, a tool designed
for running combinations of verifiers in parallel. In contrast to BUBAAK, that
directly invokes verifiers on the inputs, BUBAAK-SpLit first starts by splitting
the input program into multiple modified versions called program splits. During
the splitting process, BUBAAK-SpLit utilizes a weak verifier (in our case symbolic
execution with a short timelimit) to analyze each generated program split. If
the weak verifier fails on a program split, we split this program split again
and start the verification process again on the generated program splits. We run
the splitting process until a predefined number of hard-to-verify program splits
is generated or a splitting limit is reached. During the main verification phase,
we run a combination of BUBAAK-LEE and SLOWBEAST in parallel on the remaining
unsolved parts of the verification task.
acknowledgement: This work was partially supported by the ERC-2020-AdG 10102009 grant.
alternative_title:
- LNCS
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Marek
full_name: Chalupa, Marek
id: 87e34708-d6c6-11ec-9f5b-9391e7be2463
last_name: Chalupa
- first_name: Cedric
full_name: Richter, Cedric
last_name: Richter
citation:
ama: 'Chalupa M, Richter C. Bubaak-SpLit: Split what you cannot verify (Competition
contribution). In: 30th International Conference on Tools and Algorithms for
the Construction and Analysis of Systems. Vol 14572. Springer Nature; 2024:353–358.
doi:10.1007/978-3-031-57256-2_20'
apa: 'Chalupa, M., & Richter, C. (2024). Bubaak-SpLit: Split what you cannot
verify (Competition contribution). In 30th International Conference on Tools
and Algorithms for the Construction and Analysis of Systems (Vol. 14572, pp.
353–358). Luxembourg City, Luxembourg: Springer Nature. https://doi.org/10.1007/978-3-031-57256-2_20'
chicago: 'Chalupa, Marek, and Cedric Richter. “Bubaak-SpLit: Split What You Cannot
Verify (Competition Contribution).” In 30th International Conference on Tools
and Algorithms for the Construction and Analysis of Systems, 14572:353–358.
Springer Nature, 2024. https://doi.org/10.1007/978-3-031-57256-2_20.'
ieee: 'M. Chalupa and C. Richter, “Bubaak-SpLit: Split what you cannot verify (Competition
contribution),” in 30th International Conference on Tools and Algorithms for
the Construction and Analysis of Systems, Luxembourg City, Luxembourg, 2024,
vol. 14572, pp. 353–358.'
ista: 'Chalupa M, Richter C. 2024. Bubaak-SpLit: Split what you cannot verify (Competition
contribution). 30th International Conference on Tools and Algorithms for the Construction
and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and
Analysis of Systems, LNCS, vol. 14572, 353–358.'
mla: 'Chalupa, Marek, and Cedric Richter. “Bubaak-SpLit: Split What You Cannot Verify
(Competition Contribution).” 30th International Conference on Tools and Algorithms
for the Construction and Analysis of Systems, vol. 14572, Springer Nature,
2024, pp. 353–358, doi:10.1007/978-3-031-57256-2_20.'
short: M. Chalupa, C. Richter, in:, 30th International Conference on Tools and Algorithms
for the Construction and Analysis of Systems, Springer Nature, 2024, pp. 353–358.
conference:
end_date: 2024-04-11
location: Luxembourg City, Luxembourg
name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems'
start_date: 2024-04-06
corr_author: '1'
date_created: 2024-04-20T18:14:06Z
date_published: 2024-04-05T00:00:00Z
date_updated: 2025-09-04T13:48:25Z
day: '05'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-031-57256-2_20
ec_funded: 1
external_id:
isi:
- '001284187100020'
file:
- access_level: open_access
checksum: 208c855c60824bec936b8d01d0396474
content_type: application/pdf
creator: cchlebak
date_created: 2024-04-26T11:27:26Z
date_updated: 2024-04-26T11:27:26Z
file_id: '15347'
file_name: 2024_LNCS_Chalupa.pdf
file_size: 577128
relation: main_file
success: 1
file_date_updated: 2024-04-26T11:27:26Z
fulldoi: https://doi.org/10.1007/978-3-031-57256-2_20
has_accepted_license: '1'
intvolume: ' 14572'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 353–358
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: 30th International Conference on Tools and Algorithms for the Construction
and Analysis of Systems
publication_identifier:
eisbn:
- '9783031572562'
eissn:
- 1611-3349
isbn:
- '9783031572555'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Bubaak-SpLit: Split what you cannot verify (Competition contribution)'
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 14572
year: '2024'
...
---
_id: '15334'
abstract:
- lang: eng
text: We consider the sharp interface limit of a Navier-Stokes/Allen Cahn equation
in a bounded smooth domain in two space dimensions, in the case of vanishing mobility
mε=ε√, where the small parameter ε>0 related to the thickness of the diffuse interface
is sent to zero. For well-prepared initial data and sufficiently small times,
we rigorously prove convergence to the classical two-phase Navier-Stokes system
with surface tension. The idea of the proof is to use asymptotic expansions to
construct an approximate solution and to estimate the difference of the exact
and approximate solutions with a spectral estimate for the (at the approximate
solution) linearized Allen-Cahn operator. In the calculations we use a fractional
order ansatz and new ansatz terms in higher orders leading to a suitable ε-scaled
and coupled model problem. Moreover, we apply the novel idea of introducing ε-dependent
coordinates.
acknowledgement: "Open Access funding enabled and organized by Projekt DEAL.\r\nM.
Fei was partially supported by NSF of China under Grant No. 12271004 and Anhui Provincial
Funding Project under Grant Nos. gxbjZD2022009 and 2308085J10. Moreover, M. Moser
has received funding from the European Research Council (ERC) under the European
Union’s Horizon 2020 research and innovation programme (Grant Agreement No 948819)."
article_number: '94'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Helmut
full_name: Abels, Helmut
last_name: Abels
- first_name: Mingwen
full_name: Fei, Mingwen
last_name: Fei
- first_name: Maximilian
full_name: Moser, Maximilian
id: a60047a9-da77-11eb-85b4-c4dc385ebb8c
last_name: Moser
citation:
ama: Abels H, Fei M, Moser M. Sharp interface limit for a Navier–Stokes/Allen–Cahn
system in the case of a vanishing mobility. Calculus of Variations and Partial
Differential Equations. 2024;63(4). doi:10.1007/s00526-024-02715-7
apa: Abels, H., Fei, M., & Moser, M. (2024). Sharp interface limit for a Navier–Stokes/Allen–Cahn
system in the case of a vanishing mobility. Calculus of Variations and Partial
Differential Equations. Springer Nature. https://doi.org/10.1007/s00526-024-02715-7
chicago: Abels, Helmut, Mingwen Fei, and Maximilian Moser. “Sharp Interface Limit
for a Navier–Stokes/Allen–Cahn System in the Case of a Vanishing Mobility.” Calculus
of Variations and Partial Differential Equations. Springer Nature, 2024. https://doi.org/10.1007/s00526-024-02715-7.
ieee: H. Abels, M. Fei, and M. Moser, “Sharp interface limit for a Navier–Stokes/Allen–Cahn
system in the case of a vanishing mobility,” Calculus of Variations and Partial
Differential Equations, vol. 63, no. 4. Springer Nature, 2024.
ista: Abels H, Fei M, Moser M. 2024. Sharp interface limit for a Navier–Stokes/Allen–Cahn
system in the case of a vanishing mobility. Calculus of Variations and Partial
Differential Equations. 63(4), 94.
mla: Abels, Helmut, et al. “Sharp Interface Limit for a Navier–Stokes/Allen–Cahn
System in the Case of a Vanishing Mobility.” Calculus of Variations and Partial
Differential Equations, vol. 63, no. 4, 94, Springer Nature, 2024, doi:10.1007/s00526-024-02715-7.
short: H. Abels, M. Fei, M. Moser, Calculus of Variations and Partial Differential
Equations 63 (2024).
date_created: 2024-04-21T22:00:52Z
date_published: 2024-05-01T00:00:00Z
date_updated: 2025-09-04T13:45:40Z
day: '01'
ddc:
- '510'
department:
- _id: JuFi
doi: 10.1007/s00526-024-02715-7
ec_funded: 1
external_id:
arxiv:
- '2304.12096'
isi:
- '001199418100002'
file:
- access_level: open_access
checksum: b1095fad4cae596f52cc616a973bdde2
content_type: application/pdf
creator: dernst
date_created: 2024-04-23T07:30:48Z
date_updated: 2024-04-23T07:30:48Z
file_id: '15343'
file_name: 2024_CalculusEquations_Abels.pdf
file_size: 975186
relation: main_file
success: 1
file_date_updated: 2024-04-23T07:30:48Z
fulldoi: https://doi.org/10.1007/s00526-024-02715-7
has_accepted_license: '1'
intvolume: ' 63'
isi: 1
issue: '4'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 0aa76401-070f-11eb-9043-b5bb049fa26d
call_identifier: H2020
grant_number: '948819'
name: Bridging Scales in Random Materials
publication: Calculus of Variations and Partial Differential Equations
publication_identifier:
eissn:
- 1432-0835
issn:
- 0944-2669
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sharp interface limit for a Navier–Stokes/Allen–Cahn system in the case of
a vanishing mobility
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 63
year: '2024'
...
---
_id: '15335'
abstract:
- lang: eng
text: Stable matching of neurotransmitters with their receptors is fundamental to
synapse function and reliable communication in neural circuits. Presynaptic neurotransmitters
regulate the stabilization of postsynaptic transmitter receptors. Whether postsynaptic
receptors regulate stabilization of presynaptic transmitters has received less
attention. Here, we show that blockade of endogenous postsynaptic acetylcholine
receptors (AChR) at the neuromuscular junction destabilizes the cholinergic phenotype
in motor neurons and stabilizes an earlier, developmentally transient glutamatergic
phenotype. Further, expression of exogenous postsynaptic gamma-aminobutyric acid
type A receptors (GABAA receptors) in muscle cells stabilizes an earlier, developmentally
transient GABAergic motor neuron phenotype. Both AChR and GABAA receptors are
linked to presynaptic neurons through transsynaptic bridges. Knockdown of specific
components of these transsynaptic bridges prevents stabilization of the cholinergic
or GABAergic phenotypes. Bidirectional communication can enforce a match between
transmitter and receptor and ensure the fidelity of synaptic transmission. Our
findings suggest a potential role of dysfunctional transmitter receptors in neurological
disorders that involve the loss of the presynaptic transmitter.
acknowledgement: We thank all members of the Spitzer laboratory for discussions and critical feedback; K. Marek for discussions of acknowledgment signals;
I. Gregor and R. Aricescu for discussions of receptor pharmacology and transsynaptic bridges; C. Kintner for advice on Xenopus blastomere lineage; A. Ray
and E. Park for guidance on miniature analysis; A. Glavis- Bloom, S.U. Choi, S.
Atkins, M. Gupta, and S. Malladi for technical assistance; and D. K. Berg and L.
R. Squire for comments on the manuscript. This work was supported by NSF 2051555
and the Overland Foundation. Microscopy for five- channel imaging utilized the UCSD
School of Medicine Microscopy Core, supported by NIH grant NS047101.
article_number: e2318041121
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Swetha K.
full_name: Godavarthi, Swetha K.
last_name: Godavarthi
- first_name: Masaki
full_name: Hiramoto, Masaki
last_name: Hiramoto
- first_name: Yuri
full_name: Ignatyev, Yuri
last_name: Ignatyev
- first_name: Jacqueline B.
full_name: Levin, Jacqueline B.
last_name: Levin
- first_name: Hui Quan
full_name: Li, Hui Quan
last_name: Li
- first_name: Marta
full_name: Pratelli, Marta
last_name: Pratelli
- first_name: Jennifer
full_name: Borchardt, Jennifer
last_name: Borchardt
- first_name: Cynthia
full_name: Czajkowski, Cynthia
last_name: Czajkowski
- first_name: Laura N.
full_name: Borodinsky, Laura N.
last_name: Borodinsky
- first_name: Lora Beatrice Jaeger
full_name: Sweeney, Lora Beatrice Jaeger
id: 56BE8254-C4F0-11E9-8E45-0B23E6697425
last_name: Sweeney
orcid: 0000-0001-9242-5601
- first_name: Hollis T.
full_name: Cline, Hollis T.
last_name: Cline
- first_name: Nicholas C.
full_name: Spitzer, Nicholas C.
last_name: Spitzer
citation:
ama: Godavarthi SK, Hiramoto M, Ignatyev Y, et al. Postsynaptic receptors regulate
presynaptic transmitter stability through transsynaptic bridges. Proceedings
of the National Academy of Sciences of the United States of America. 2024;121(15).
doi:10.1073/pnas.2318041121
apa: Godavarthi, S. K., Hiramoto, M., Ignatyev, Y., Levin, J. B., Li, H. Q., Pratelli,
M., … Spitzer, N. C. (2024). Postsynaptic receptors regulate presynaptic transmitter
stability through transsynaptic bridges. Proceedings of the National Academy
of Sciences of the United States of America. National Academy of Sciences.
https://doi.org/10.1073/pnas.2318041121
chicago: Godavarthi, Swetha K., Masaki Hiramoto, Yuri Ignatyev, Jacqueline B. Levin,
Hui Quan Li, Marta Pratelli, Jennifer Borchardt, et al. “Postsynaptic Receptors
Regulate Presynaptic Transmitter Stability through Transsynaptic Bridges.” Proceedings
of the National Academy of Sciences of the United States of America. National
Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2318041121.
ieee: S. K. Godavarthi et al., “Postsynaptic receptors regulate presynaptic
transmitter stability through transsynaptic bridges,” Proceedings of the National
Academy of Sciences of the United States of America, vol. 121, no. 15. National
Academy of Sciences, 2024.
ista: Godavarthi SK, Hiramoto M, Ignatyev Y, Levin JB, Li HQ, Pratelli M, Borchardt
J, Czajkowski C, Borodinsky LN, Sweeney LB, Cline HT, Spitzer NC. 2024. Postsynaptic
receptors regulate presynaptic transmitter stability through transsynaptic bridges.
Proceedings of the National Academy of Sciences of the United States of America.
121(15), e2318041121.
mla: Godavarthi, Swetha K., et al. “Postsynaptic Receptors Regulate Presynaptic
Transmitter Stability through Transsynaptic Bridges.” Proceedings of the National
Academy of Sciences of the United States of America, vol. 121, no. 15, e2318041121,
National Academy of Sciences, 2024, doi:10.1073/pnas.2318041121.
short: S.K. Godavarthi, M. Hiramoto, Y. Ignatyev, J.B. Levin, H.Q. Li, M. Pratelli,
J. Borchardt, C. Czajkowski, L.N. Borodinsky, L.B. Sweeney, H.T. Cline, N.C. Spitzer,
Proceedings of the National Academy of Sciences of the United States of America
121 (2024).
date_created: 2024-04-21T22:00:53Z
date_published: 2024-04-09T00:00:00Z
date_updated: 2025-09-04T13:42:01Z
day: '09'
ddc:
- '570'
department:
- _id: LoSw
doi: 10.1073/pnas.2318041121
external_id:
isi:
- '001243892800004'
pmid:
- '38568976'
file:
- access_level: open_access
checksum: f3b4ffad4ef3d1c443414edf0cd2392c
content_type: application/pdf
creator: dernst
date_created: 2024-04-23T06:53:14Z
date_updated: 2024-04-23T06:53:14Z
file_id: '15340'
file_name: 2024_PNAS_Godavarthi.pdf
file_size: 16187094
relation: main_file
success: 1
file_date_updated: 2024-04-23T06:53:14Z
fulldoi: https://doi.org/10.1073/pnas.2318041121
has_accepted_license: '1'
intvolume: ' 121'
isi: 1
issue: '15'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Postsynaptic receptors regulate presynaptic transmitter stability through transsynaptic
bridges
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 121
year: '2024'
...
---
_id: '15339'
abstract:
- lang: eng
text: We define even very stable Higgs bundles and study the Hitchin map restricted
to their upward flows. In the GLn case, we classify the type (1,…,1) examples,
and find that they are governed by a root system formed by the roots of even height.
We discuss how the spectrum of equivariant cohomology of real and quaternionic
Grassmannians, 4n-spheres and the real Cayley plane appear to describe the Hitchin
map on even cominuscule upward flows. The even upward flows in question are the
same as upward flows in Higgs bundle moduli spaces for quasi-split inner real
forms. The latter spaces have been pioneered by Oscar García-Prada and his collaborators.
acknowledgement: Most of the research for this paper was done when the first author
visited the second author's group at IST Austria as a summer intern in 2022. The
second author was supported by an FWF grant "Geometry of the top of the nilpotent
cone" number P35847.
article_number: '2441009'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Miguel
full_name: González, Miguel
last_name: González
- first_name: Tamás
full_name: Hausel, Tamás
id: 4A0666D8-F248-11E8-B48F-1D18A9856A87
last_name: Hausel
orcid: 0000-0002-9582-2634
citation:
ama: González M, Hausel T. Hitchin map on even very stable upward flows. International
Journal of Mathematics. 2024;35(09). doi:10.1142/S0129167X2441009X
apa: González, M., & Hausel, T. (2024). Hitchin map on even very stable upward
flows. International Journal of Mathematics. World Scientific Publishing.
https://doi.org/10.1142/S0129167X2441009X
chicago: González, Miguel, and Tamás Hausel. “Hitchin Map on Even Very Stable Upward
Flows.” International Journal of Mathematics. World Scientific Publishing,
2024. https://doi.org/10.1142/S0129167X2441009X.
ieee: M. González and T. Hausel, “Hitchin map on even very stable upward flows,”
International Journal of Mathematics, vol. 35, no. 09. World Scientific
Publishing, 2024.
ista: González M, Hausel T. 2024. Hitchin map on even very stable upward flows.
International Journal of Mathematics. 35(09), 2441009.
mla: González, Miguel, and Tamás Hausel. “Hitchin Map on Even Very Stable Upward
Flows.” International Journal of Mathematics, vol. 35, no. 09, 2441009,
World Scientific Publishing, 2024, doi:10.1142/S0129167X2441009X.
short: M. González, T. Hausel, International Journal of Mathematics 35 (2024).
date_created: 2024-04-21T22:00:54Z
date_published: 2024-04-04T00:00:00Z
date_updated: 2025-09-04T13:40:37Z
day: '04'
department:
- _id: TaHa
doi: 10.1142/S0129167X2441009X
external_id:
arxiv:
- '2303.01404'
isi:
- '001251179200003'
fulldoi: https://doi.org/10.1142/S0129167X2441009X
intvolume: ' 35'
isi: 1
issue: '09'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2303.01404
month: '04'
oa: 1
oa_version: Preprint
project:
- _id: 34b2c9cb-11ca-11ed-8bc3-a50ba74ca4a3
grant_number: P35847
name: Geometry of the tip of the global nilpotent cone
publication: International Journal of Mathematics
publication_identifier:
eissn:
- 1793-6519
issn:
- 0129-167X
publication_status: published
publisher: World Scientific Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Hitchin map on even very stable upward flows
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 35
year: '2024'
...
---
OA_type: closed access
_id: '15348'
abstract:
- lang: eng
text: We report on synthesis of highly crystalline polythiophene and its application
in supercapacitor electrodes. The material exhibits a remarkably stable electrochemical
behavior and an excellent device performance. The device delivers an electrode
specific capacitance (Csp) of 129.13F g−1, Cell Csp of 32.28F g−1 at 0.5 A/g;
energy, and power densities of ∼ 3 Wh kg−1 and 250 W kg -1, respectively at 0.5
A/g. Also, it exhibits an excellent retention of Cell Csp and coulombic efficiency
up to ∼ 95 % over 10,000 continuous galvanostatic charge discharge (GCD) cycles
indicating a remarkable performance by a standalone, pristine and undoped polythiophene.
Electrochemical impedance spectroscopy (EIS) studies further suggest material’s
stable capacitive behavior. The material’s enhanced electrochemical properties,
stable behavior and outstanding performance in device application are attributed
to the crystalline phases present in the polymer matrix achievable via a slow
rate of synthesis; overall, an edge over other conventional synthesis methods.
acknowledgement: This research was supported by the Korea Evaluation Institute of
Industrial Technology (No. 200116167, Development of Battery Safety Diagnosis System
(BDS) SoC that predicts the internal state, explosion risk, remaining useful life,
and replacement timing of electric vehicle batteries).
article_number: '136483'
article_processing_charge: No
article_type: original
author:
- first_name: Neelima
full_name: Mahato, Neelima
last_name: Mahato
- first_name: Saurabh
full_name: Singh, Saurabh
id: 12d625da-9cb3-11ed-9667-af09d37d3f0a
last_name: Singh
orcid: 0000-0003-2209-5269
- first_name: T. V.M.
full_name: Sreekanth, T. V.M.
last_name: Sreekanth
- first_name: Kisoo
full_name: Yoo, Kisoo
last_name: Yoo
- first_name: Jonghoon
full_name: Kim, Jonghoon
last_name: Kim
citation:
ama: 'Mahato N, Singh S, Sreekanth TVM, Yoo K, Kim J. In-situ engineered highly
crystalline polythiophene empowered electrochemical capacitor-I: Synthesis, characterization,
and electrochemical charge storage. Materials Letters. 2024;365. doi:10.1016/j.matlet.2024.136483'
apa: 'Mahato, N., Singh, S., Sreekanth, T. V. M., Yoo, K., & Kim, J. (2024).
In-situ engineered highly crystalline polythiophene empowered electrochemical
capacitor-I: Synthesis, characterization, and electrochemical charge storage.
Materials Letters. Elsevier. https://doi.org/10.1016/j.matlet.2024.136483'
chicago: 'Mahato, Neelima, Saurabh Singh, T. V.M. Sreekanth, Kisoo Yoo, and Jonghoon
Kim. “In-Situ Engineered Highly Crystalline Polythiophene Empowered Electrochemical
Capacitor-I: Synthesis, Characterization, and Electrochemical Charge Storage.”
Materials Letters. Elsevier, 2024. https://doi.org/10.1016/j.matlet.2024.136483.'
ieee: 'N. Mahato, S. Singh, T. V. M. Sreekanth, K. Yoo, and J. Kim, “In-situ engineered
highly crystalline polythiophene empowered electrochemical capacitor-I: Synthesis,
characterization, and electrochemical charge storage,” Materials Letters,
vol. 365. Elsevier, 2024.'
ista: 'Mahato N, Singh S, Sreekanth TVM, Yoo K, Kim J. 2024. In-situ engineered
highly crystalline polythiophene empowered electrochemical capacitor-I: Synthesis,
characterization, and electrochemical charge storage. Materials Letters. 365,
136483.'
mla: 'Mahato, Neelima, et al. “In-Situ Engineered Highly Crystalline Polythiophene
Empowered Electrochemical Capacitor-I: Synthesis, Characterization, and Electrochemical
Charge Storage.” Materials Letters, vol. 365, 136483, Elsevier, 2024, doi:10.1016/j.matlet.2024.136483.'
short: N. Mahato, S. Singh, T.V.M. Sreekanth, K. Yoo, J. Kim, Materials Letters
365 (2024).
corr_author: '1'
date_created: 2024-04-28T22:00:56Z
date_published: 2024-06-15T00:00:00Z
date_updated: 2025-09-04T13:49:05Z
day: '15'
department:
- _id: MaIb
doi: 10.1016/j.matlet.2024.136483
external_id:
isi:
- '001300025600001'
fulldoi: https://doi.org/10.1016/j.matlet.2024.136483
intvolume: ' 365'
isi: 1
language:
- iso: eng
month: '06'
oa_version: None
publication: Materials Letters
publication_identifier:
eissn:
- 1873-4979
issn:
- 0167-577X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'In-situ engineered highly crystalline polythiophene empowered electrochemical
capacitor-I: Synthesis, characterization, and electrochemical charge storage'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 365
year: '2024'
...
---
_id: '15350'
abstract:
- lang: eng
text: We extend three related results from the analysis of influences of Boolean
functions to the quantum setting, namely the KKL theorem, Friedgut’s Junta theorem
and Talagrand’s variance inequality for geometric influences. Our results are
derived by a joint use of recently studied hypercontractivity and gradient estimates.
These generic tools also allow us to derive generalizations of these results in
a general von Neumann algebraic setting beyond the case of the quantum hypercube,
including examples in infinite dimensions relevant to quantum information theory
such as continuous variables quantum systems. Finally, we comment on the implications
of our results as regards to noncommutative extensions of isoperimetric type inequalities,
quantum circuit complexity lower bounds and the learnability of quantum observables.
acknowledgement: "Open access funding provided by the Carolinas Consortium.\r\nH.Z.
is supported by the Lise Meitner fellowship, Austrian Science Fund (FWF) M3337.
H.Z. would like to thank the American Institute of Mathematics and the AIM workshop
Analysis on the hypercube with applications to quantum computing. He is also grateful
to the organizers and other participants for creating an active atmosphere. The
research of C.R. has been supported by ANR project QTraj (ANR-20-CE40-0024-01) of
the French National Research Agency (ANR). C.R. acknowledges the support of the
Munich Center for Quantum Sciences and Technology, as well as the Humboldt Foundation.
C.R. would like to thank Amanda Young for fruitful discussion on the applications
of Friedgut’s Junta theorem to learning quantum dynamics. The research of M.W. was
funded by the Austrian Science Fund (FWF) under the Esprit Programme [ESP 156].
For the purpose of Open Access, the authors have applied a CC BY public copyright
licence to any Author Accepted Manuscript (AAM) version arising from this submission.
The authors want to thank Francisco Escudero Gutierrez and Hsin-Yuan Huang for helpful
comments on an earlier version of the paper. They are grateful to the referees for
the careful reading and helpful comments."
article_number: '95'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Cambyse
full_name: Rouzé, Cambyse
last_name: Rouzé
- first_name: Melchior
full_name: Wirth, Melchior
id: 88644358-0A0E-11EA-8FA5-49A33DDC885E
last_name: Wirth
orcid: 0000-0002-0519-4241
- first_name: Haonan
full_name: Zhang, Haonan
id: D8F41E38-9E66-11E9-A9E2-65C2E5697425
last_name: Zhang
citation:
ama: Rouzé C, Wirth M, Zhang H. Quantum Talagrand, KKL and Friedgut’s theorems and
the learnability of quantum boolean functions. Communications in Mathematical
Physics. 2024;405(4). doi:10.1007/s00220-024-04981-0
apa: Rouzé, C., Wirth, M., & Zhang, H. (2024). Quantum Talagrand, KKL and Friedgut’s
theorems and the learnability of quantum boolean functions. Communications
in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-024-04981-0
chicago: Rouzé, Cambyse, Melchior Wirth, and Haonan Zhang. “Quantum Talagrand, KKL
and Friedgut’s Theorems and the Learnability of Quantum Boolean Functions.” Communications
in Mathematical Physics. Springer Nature, 2024. https://doi.org/10.1007/s00220-024-04981-0.
ieee: C. Rouzé, M. Wirth, and H. Zhang, “Quantum Talagrand, KKL and Friedgut’s theorems
and the learnability of quantum boolean functions,” Communications in Mathematical
Physics, vol. 405, no. 4. Springer Nature, 2024.
ista: Rouzé C, Wirth M, Zhang H. 2024. Quantum Talagrand, KKL and Friedgut’s theorems
and the learnability of quantum boolean functions. Communications in Mathematical
Physics. 405(4), 95.
mla: Rouzé, Cambyse, et al. “Quantum Talagrand, KKL and Friedgut’s Theorems and
the Learnability of Quantum Boolean Functions.” Communications in Mathematical
Physics, vol. 405, no. 4, 95, Springer Nature, 2024, doi:10.1007/s00220-024-04981-0.
short: C. Rouzé, M. Wirth, H. Zhang, Communications in Mathematical Physics 405
(2024).
corr_author: '1'
date_created: 2024-04-29T08:47:28Z
date_published: 2024-04-09T00:00:00Z
date_updated: 2025-09-04T13:50:22Z
day: '09'
ddc:
- '510'
department:
- _id: JaMa
doi: 10.1007/s00220-024-04981-0
external_id:
arxiv:
- '2209.07279'
isi:
- '001199509500004'
pmid:
- '38606337'
file:
- access_level: open_access
checksum: 8ecd168755f0d40ebd7cd0b71063acfc
content_type: application/pdf
creator: dernst
date_created: 2024-05-06T06:18:45Z
date_updated: 2024-05-06T06:18:45Z
file_id: '15365'
file_name: 2024_CommMathPhysics_Rouze.pdf
file_size: 653676
relation: main_file
success: 1
file_date_updated: 2024-05-06T06:18:45Z
fulldoi: https://doi.org/10.1007/s00220-024-04981-0
has_accepted_license: '1'
intvolume: ' 405'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: eb958bca-77a9-11ec-83b8-c565cb50d8d6
grant_number: M03337
name: Curvature-dimension in noncommutative analysis
- _id: 34c6ea2d-11ca-11ed-8bc3-c04f3c502833
grant_number: ESP156_N
name: Gradient flow techniques for quantum Markov semigroups
publication: Communications in Mathematical Physics
publication_identifier:
eissn:
- 1432-0916
issn:
- 0010-3616
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantum Talagrand, KKL and Friedgut’s theorems and the learnability of quantum
boolean functions
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 405
year: '2024'
...
---
OA_type: free access
_id: '15356'
abstract:
- lang: eng
text: Identifying efficient active sites for the direct synthesis of hydrogen peroxide
over Pd-based catalysts has been a subject of considerable debate. In this study,
we employ particle swarm optimization method and density functional theory to
explore the H2O2 synthesis mechanism on Pd, PdO, and the partially oxidized surface
(Pd9OX). A comprehensive mechanism for Pd9OX is elucidated, and subsequent coverage-dependent
kinetic analysis allows for a quantitative assessment of catalytic performance
at the interphase. Our findings conclusively establish that the interphase between
Pd and PdO represents the optimal active site. Phase diagram analysis further
aids in determining stable structures under reaction conditions. At 298.15 K and
under oxygen balance, the Pd9O6 surface remains stable throughout the reaction,
demonstrating high activity and selectivity. This work underscores the significance
of the interphase in comprehending catalytic performance and unveils promising
avenues for optimizing catalyst performance by controlling reaction conditions
and surface composition.
acknowledgement: The authors acknowledge the financial support from the National Key
Research and Development Project of China (2021YFA1500900, 2022YFE0113800), the
National Natural Science Foundation of China (22141001, U21A20298), Zhejiang Innovation
Team (2017R5203).
article_number: '120199'
article_processing_charge: No
article_type: original
author:
- first_name: Jinyan
full_name: Zhao, Jinyan
last_name: Zhao
- first_name: Zihao
full_name: Yao, Zihao
last_name: Yao
- first_name: Rhys
full_name: Bunting, Rhys
id: 91deeae8-1207-11ec-b130-c194ad5b50c6
last_name: Bunting
orcid: 0000-0001-6928-074X
- first_name: Yaqiu
full_name: Wang, Yaqiu
last_name: Wang
- first_name: Jianguo
full_name: Wang, Jianguo
last_name: Wang
citation:
ama: Zhao J, Yao Z, Bunting R, Wang Y, Wang J. Identifying Pd9OX as the optimum
catalyst for the direct synthesis of H2O2 through microkinetic modeling with coverage
effects. Chemical Engineering Science. 2024;295. doi:10.1016/j.ces.2024.120199
apa: Zhao, J., Yao, Z., Bunting, R., Wang, Y., & Wang, J. (2024). Identifying
Pd9OX as the optimum catalyst for the direct synthesis of H2O2 through microkinetic
modeling with coverage effects. Chemical Engineering Science. Elsevier.
https://doi.org/10.1016/j.ces.2024.120199
chicago: Zhao, Jinyan, Zihao Yao, Rhys Bunting, Yaqiu Wang, and Jianguo Wang. “Identifying
Pd9OX as the Optimum Catalyst for the Direct Synthesis of H2O2 through Microkinetic
Modeling with Coverage Effects.” Chemical Engineering Science. Elsevier,
2024. https://doi.org/10.1016/j.ces.2024.120199.
ieee: J. Zhao, Z. Yao, R. Bunting, Y. Wang, and J. Wang, “Identifying Pd9OX as the
optimum catalyst for the direct synthesis of H2O2 through microkinetic modeling
with coverage effects,” Chemical Engineering Science, vol. 295. Elsevier,
2024.
ista: Zhao J, Yao Z, Bunting R, Wang Y, Wang J. 2024. Identifying Pd9OX as the optimum
catalyst for the direct synthesis of H2O2 through microkinetic modeling with coverage
effects. Chemical Engineering Science. 295, 120199.
mla: Zhao, Jinyan, et al. “Identifying Pd9OX as the Optimum Catalyst for the Direct
Synthesis of H2O2 through Microkinetic Modeling with Coverage Effects.” Chemical
Engineering Science, vol. 295, 120199, Elsevier, 2024, doi:10.1016/j.ces.2024.120199.
short: J. Zhao, Z. Yao, R. Bunting, Y. Wang, J. Wang, Chemical Engineering Science
295 (2024).
date_created: 2024-05-05T22:01:02Z
date_published: 2024-08-05T00:00:00Z
date_updated: 2025-09-04T13:54:17Z
day: '05'
department:
- _id: MaIb
doi: 10.1016/j.ces.2024.120199
external_id:
isi:
- '001236643300001'
fulldoi: https://doi.org/10.1016/j.ces.2024.120199
intvolume: ' 295'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.ces.2024.120199
month: '08'
oa: 1
oa_version: None
publication: Chemical Engineering Science
publication_identifier:
issn:
- 0009-2509
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Identifying Pd9OX as the optimum catalyst for the direct synthesis of H2O2
through microkinetic modeling with coverage effects
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 295
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '15357'
abstract:
- lang: eng
text: 'There is a growing interest in cost-effective polycrystalline SnSe-based
thermoelectric (TE) materials, which are able to replace the high performance
but mechanically fragile and costly single-crystalline SnSe. In this study, we
present a low-temperature solution-based approach to produce SnSe-PbSe nanocomposites
with outstanding TE performance. Our method involves combining surfactant-free
SnSe particles with oleate-capped PbSe nanocrystals in specific ratios, followed
by thermal annealing and consolidation using spark plasma sintering. These nanocomposites
are characterized by distinct compositional and structural properties that significantly
impact their transport properties. In particular, the addition of oleate-capped
PbSe nanocrystals results in: i) a reduction in the electrostatically adsorbed
Na at the surface of the SnSe particles; ii) a reduction of Sn vacancies due to
alloying with Pb; iii) an increase in grain boundary density; and iv) the formation
of PbSnSe secondary phases. Notably, the SnSe-2.5 %PbSe nanocomposites demonstrate
a 30 % decrease in thermal conductivity compared to that of the SnSe matrix. This
reduction contributes to a maximum figure of merit (zT) of 1.75 at 788 K with
a high average zT value of ca. 1.2 in the medium temperature range of 573–773
K. These values represent one of the highest reported in polycrystalline SnSe
materials, showcasing the potential of our fabricated SnSe-PbSe nanocomposites
for cost-effective TE applications.'
acknowledged_ssus:
- _id: EM-Fac
- _id: NMR
- _id: LifeSc
acknowledgement: 'The Scientific Service Units (SSU) of ISTA supported this research
through resources provided by the Electron Microscopy Facility (EMF), NMR Facility,
and the Lab Support Facility (LSF). Y.L., S.L., C.F., C.C. and M.I. acknowledge
financial support from ISTA and the Werner Siemens Foundation. Y.L. acknowledges
funding from the National Natural Science Foundation of China (NSFC) (Grants No.
22209034), the Innovation and Entrepreneurship Project of Overseas Returnees in
Anhui Province (Grant No. 2022LCX002). C.C. acknowledges funding from the National
Natural Science Foundation of China (NSFC) (Grants No. 12374023). ICN2 acknowledges
funding from Generalitat de Catalunya 2021SGR00457. The authors thank support from
the project NANOGEN(PID2020-116093RB-C43), funded by MCIN/ AEI/10.13039/501100011033/
and by “ERDF Away of making Europe”, by the “European Union”. ICN2 is supported
by the Severo Ochoaprogram from Spanish MCIN / AEI (Grant No.: CEX2021-001214-S)
and is funded by the CERCA Programme / Generalitat de Catalunya. ICN2 is founding
member of e-DREAM [70].'
article_number: '151405'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Yu
full_name: Liu, Yu
id: 2A70014E-F248-11E8-B48F-1D18A9856A87
last_name: Liu
orcid: 0000-0001-7313-6740
- first_name: Seungho
full_name: Lee, Seungho
id: BB243B88-D767-11E9-B658-BC13E6697425
last_name: Lee
orcid: 0000-0002-6962-8598
- first_name: Christine
full_name: Fiedler, Christine
id: bd3fceba-dc74-11ea-a0a7-c17f71817366
last_name: Fiedler
- first_name: Maria Chiara
full_name: ' Spadaro, Maria Chiara'
last_name: ' Spadaro'
- first_name: Cheng
full_name: Chang, Cheng
id: 9E331C2E-9F27-11E9-AE48-5033E6697425
last_name: Chang
orcid: 0000-0002-9515-4277
- first_name: Mingquan
full_name: Li, Mingquan
last_name: Li
- first_name: Min
full_name: Hong, Min
last_name: Hong
- first_name: Jordi
full_name: Arbiol, Jordi
last_name: Arbiol
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
citation:
ama: Liu Y, Lee S, Fiedler C, et al. Enhancing thermoelectric performance of solutionpProcessed
polycrystalline SnSe with PbSe nanocrystals. Chemical Engineering Journal.
2024;490. doi:10.1016/j.cej.2024.151405
apa: Liu, Y., Lee, S., Fiedler, C., Spadaro, M. C., Chang, C., Li, M., … Ibáñez,
M. (2024). Enhancing thermoelectric performance of solutionpProcessed polycrystalline
SnSe with PbSe nanocrystals. Chemical Engineering Journal. Elsevier. https://doi.org/10.1016/j.cej.2024.151405
chicago: Liu, Yu, Seungho Lee, Christine Fiedler, Maria Chiara Spadaro, Cheng Chang,
Mingquan Li, Min Hong, Jordi Arbiol, and Maria Ibáñez. “Enhancing Thermoelectric
Performance of SolutionpProcessed Polycrystalline SnSe with PbSe Nanocrystals.”
Chemical Engineering Journal. Elsevier, 2024. https://doi.org/10.1016/j.cej.2024.151405.
ieee: Y. Liu et al., “Enhancing thermoelectric performance of solutionpProcessed
polycrystalline SnSe with PbSe nanocrystals,” Chemical Engineering Journal,
vol. 490. Elsevier, 2024.
ista: Liu Y, Lee S, Fiedler C, Spadaro MC, Chang C, Li M, Hong M, Arbiol J, Ibáñez
M. 2024. Enhancing thermoelectric performance of solutionpProcessed polycrystalline
SnSe with PbSe nanocrystals. Chemical Engineering Journal. 490, 151405.
mla: Liu, Yu, et al. “Enhancing Thermoelectric Performance of SolutionpProcessed
Polycrystalline SnSe with PbSe Nanocrystals.” Chemical Engineering Journal,
vol. 490, 151405, Elsevier, 2024, doi:10.1016/j.cej.2024.151405.
short: Y. Liu, S. Lee, C. Fiedler, M.C. Spadaro, C. Chang, M. Li, M. Hong, J. Arbiol,
M. Ibáñez, Chemical Engineering Journal 490 (2024).
corr_author: '1'
date_created: 2024-05-05T22:01:03Z
date_published: 2024-06-15T00:00:00Z
date_updated: 2026-04-07T11:52:31Z
day: '15'
ddc:
- '540'
department:
- _id: MaIb
doi: 10.1016/j.cej.2024.151405
external_id:
isi:
- '001234835500001'
file:
- access_level: open_access
checksum: 6609232a208b9a89d055a270ef0af1fe
content_type: application/pdf
creator: dernst
date_created: 2025-01-09T09:24:29Z
date_updated: 2025-01-09T09:24:29Z
file_id: '18800'
file_name: 2024_ChemEngineeringJour_Liu.pdf
file_size: 12233704
relation: main_file
success: 1
file_date_updated: 2025-01-09T09:24:29Z
fulldoi: https://doi.org/10.1016/j.cej.2024.151405
has_accepted_license: '1'
intvolume: ' 490'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 9B8F7476-BA93-11EA-9121-9846C619BF3A
name: 'HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of
Semiconductors for Waste Heat Recovery'
publication: Chemical Engineering Journal
publication_identifier:
issn:
- 1385-8947
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '20415'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Enhancing thermoelectric performance of solutionpProcessed polycrystalline
SnSe with PbSe nanocrystals
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 490
year: '2024'
...
---
_id: '15358'
abstract:
- lang: eng
text: 'We consider how a population of N haploid individuals responds to directional
selection on standing variation, with no new variation from recombination or mutation.
Individuals have trait values z1,…,zN, which are drawn from a distribution ψ;
the fitness of individual i is proportional to [Formula: see text] . For illustration,
we consider the Laplace and Gaussian distributions, which are parametrised only
by the variance V0, and show that for large N, there is a scaling limit which
depends on a single parameter NV0. When selection is weak relative to drift (NV0≪1),
the variance decreases exponentially at rate 1/N, and the expected ultimate gain
in log fitness (scaled by V0), is just NV0, which is the same as Robertson''s
(1960) prediction for a sexual population. In contrast, when selection is strong
relative to drift (NV0≫1), the ultimate gain can be found by approximating the
establishment of alleles by a branching process in which each allele competes
independently with the population mean and the fittest allele to establish is
certain to fix. Then, if the probability of survival to time t∼1/V0 of an allele
with value z is P(z), with mean P¯, the winning allele is the fittest of NP¯ survivors
drawn from a distribution ψP/P¯. The expected ultimate change is ∼2log(1.15NV0)
for a Gaussian distribution, and ∼-12log0.36NV0-log-log0.36NV0 for a Laplace distribution.
This approach also predicts the variability of the process, and its dynamics;
we show that in the strong selection regime, the expected genetic variance decreases
as ∼t-3 at large times. We discuss how these results may be related to selection
on standing variation that is spread along a linear chromosome.'
acknowledgement: We thank Emmanuel Schertzer and two reviewers for comments on this
manuscript. NB thanks the European Research Council for support via the grant “HaplotypeStructure”
101055327. We would also like to give our sincere thanks to Alison Etheridge for
her insight, inspiration and support over the years.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Himani
full_name: Sachdeva, Himani
id: 42377A0A-F248-11E8-B48F-1D18A9856A87
last_name: Sachdeva
citation:
ama: Barton NH, Sachdeva H. Limits to selection on standing variation in an asexual
population. Theoretical Population Biology. 2024;157:129-137. doi:10.1016/j.tpb.2024.04.001
apa: Barton, N. H., & Sachdeva, H. (2024). Limits to selection on standing variation
in an asexual population. Theoretical Population Biology. Elsevier. https://doi.org/10.1016/j.tpb.2024.04.001
chicago: Barton, Nicholas H, and Himani Sachdeva. “Limits to Selection on Standing
Variation in an Asexual Population.” Theoretical Population Biology. Elsevier,
2024. https://doi.org/10.1016/j.tpb.2024.04.001.
ieee: N. H. Barton and H. Sachdeva, “Limits to selection on standing variation in
an asexual population,” Theoretical Population Biology, vol. 157. Elsevier,
pp. 129–137, 2024.
ista: Barton NH, Sachdeva H. 2024. Limits to selection on standing variation in
an asexual population. Theoretical Population Biology. 157, 129–137.
mla: Barton, Nicholas H., and Himani Sachdeva. “Limits to Selection on Standing
Variation in an Asexual Population.” Theoretical Population Biology, vol.
157, Elsevier, 2024, pp. 129–37, doi:10.1016/j.tpb.2024.04.001.
short: N.H. Barton, H. Sachdeva, Theoretical Population Biology 157 (2024) 129–137.
corr_author: '1'
date_created: 2024-05-05T22:01:03Z
date_published: 2024-06-01T00:00:00Z
date_updated: 2025-09-04T13:56:11Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1016/j.tpb.2024.04.001
external_id:
isi:
- '001237016800001'
pmid:
- '38643838'
file:
- access_level: open_access
checksum: 78f36488d24f868d5913624e9c8d88bf
content_type: application/pdf
creator: dernst
date_created: 2024-05-13T08:22:21Z
date_updated: 2024-05-13T08:22:21Z
file_id: '15383'
file_name: 2024_TheorPopulationBiology_Barton.pdf
file_size: 1098292
relation: main_file
success: 1
file_date_updated: 2024-05-13T08:22:21Z
fulldoi: https://doi.org/10.1016/j.tpb.2024.04.001
has_accepted_license: '1'
intvolume: ' 157'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 129-137
pmid: 1
project:
- _id: bd6958e0-d553-11ed-ba76-86eba6a76c00
grant_number: '101055327'
name: Understanding the evolution of continuous genomes
publication: Theoretical Population Biology
publication_identifier:
eissn:
- 1096-0325
issn:
- 0040-5809
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Limits to selection on standing variation in an asexual population
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 157
year: '2024'
...
---
_id: '15360'
abstract:
- lang: eng
text: We investigate superradiant enhancements in the refrigeration performance
of a set of N three-level systems that are collectively coupled to a hot and a
cold thermal reservoir and are additionally subject to collective periodic (circular)
driving. Assuming the system-reservoir coupling to be weak, we explore the regime
of stronger periodic driving strengths by comparing collective weak driving, Floquet-Lindblad,
and Floquet-Redfield master equations. We identify regimes where the power injected
by the periodic driving is used to pump heat from the cold to the hot reservoir
and derive analytic sufficient conditions for them based on a cycle analysis of
the Floquet-Lindblad master equation. In those regimes, we also argue for which
parameters collective enhancements like a quadratic scaling of the cooling current
with N can be expected and support our arguments by numerical simulations.
acknowledgement: "Financial support by the DFG (project ID 278162697 – SFB 1242) is
gratefully acknowledged.\r\n"
article_number: '044050'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Dmytro
full_name: Kolisnyk, Dmytro
id: 530a7320-5355-11ee-ae5a-82a46997aaa7
last_name: Kolisnyk
- first_name: Friedemann
full_name: Queißer, Friedemann
last_name: Queißer
- first_name: Gernot
full_name: Schaller, Gernot
last_name: Schaller
- first_name: Ralf
full_name: Schützhold, Ralf
last_name: Schützhold
citation:
ama: Kolisnyk D, Queißer F, Schaller G, Schützhold R. Floquet analysis of a superradiant
many-qutrit refrigerator. Physical Review Applied. 2024;21(4). doi:10.1103/PhysRevApplied.21.044050
apa: Kolisnyk, D., Queißer, F., Schaller, G., & Schützhold, R. (2024). Floquet
analysis of a superradiant many-qutrit refrigerator. Physical Review Applied.
American Physical Society. https://doi.org/10.1103/PhysRevApplied.21.044050
chicago: Kolisnyk, Dmytro, Friedemann Queißer, Gernot Schaller, and Ralf Schützhold.
“Floquet Analysis of a Superradiant Many-Qutrit Refrigerator.” Physical Review
Applied. American Physical Society, 2024. https://doi.org/10.1103/PhysRevApplied.21.044050.
ieee: D. Kolisnyk, F. Queißer, G. Schaller, and R. Schützhold, “Floquet analysis
of a superradiant many-qutrit refrigerator,” Physical Review Applied, vol.
21, no. 4. American Physical Society, 2024.
ista: Kolisnyk D, Queißer F, Schaller G, Schützhold R. 2024. Floquet analysis of
a superradiant many-qutrit refrigerator. Physical Review Applied. 21(4), 044050.
mla: Kolisnyk, Dmytro, et al. “Floquet Analysis of a Superradiant Many-Qutrit Refrigerator.”
Physical Review Applied, vol. 21, no. 4, 044050, American Physical Society,
2024, doi:10.1103/PhysRevApplied.21.044050.
short: D. Kolisnyk, F. Queißer, G. Schaller, R. Schützhold, Physical Review Applied
21 (2024).
date_created: 2024-05-05T22:01:04Z
date_published: 2024-04-26T00:00:00Z
date_updated: 2025-09-04T13:51:06Z
day: '26'
department:
- _id: GradSch
doi: 10.1103/PhysRevApplied.21.044050
external_id:
arxiv:
- '2310.18126'
isi:
- '001226579400001'
fulldoi: https://doi.org/10.1103/PhysRevApplied.21.044050
intvolume: ' 21'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2310.18126
month: '04'
oa: 1
oa_version: Preprint
publication: Physical Review Applied
publication_identifier:
eissn:
- 2331-7019
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Floquet analysis of a superradiant many-qutrit refrigerator
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 21
year: '2024'
...
---
_id: '15361'
abstract:
- lang: eng
text: Bimolecular fluorescence complementation (BiFC) is a powerful tool for studying
protein-protein interactions in living cells. By fusing interacting proteins to
fluorescent protein fragments, BiFC allows visualization of spatial localization
patterns of protein complexes. This method has been adapted to a variety of expression
systems in different organisms and is widely used to study protein interactions
in plant cells. The Agrobacterium-mediated transient expression protocol for BiFC
assays in Nicotiana benthamiana (N. benthamiana) leaf cells is widely used, but
in this chapter, a method for BiFC assay using Arabidopsis thaliana protoplasts
is presented.
acknowledgement: Special thanks to Dr. Marta Zwiewka for the support. Thanks to the
Czech Science Foundation GA 20-20860Y for financial aid and support of A.S.S., respectively.
Thanks go to Core Facility Cellular Imaging (CELLIM), and Plant Sciences Core Facility
of CEITEC Masaryk University is acknowledged for the technical support.
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
author:
- first_name: Aswathy
full_name: Jayasree, Aswathy
last_name: Jayasree
- first_name: Hymavathi
full_name: Salava, Hymavathi
last_name: Salava
- first_name: Tomasz
full_name: Nodzynski, Tomasz
last_name: Nodzynski
- first_name: Thula
full_name: Sravankumar, Thula
id: 055b7938-0b72-11ef-94eb-d14136011bb5
last_name: Sravankumar
orcid: 0000-0001-6925-6950
citation:
ama: 'Jayasree A, Salava H, Nodzynski T, Sravankumar T. Protein-Protein Interactions
Visualized by Bimolecular Fluorescence Complementation in Arabidopsis thaliana
Protoplasts from Leaf. In: Maghuly F, ed. Plant Functional Genomics. Vol
2787. MIMB. Springer Nature; 2024:305-313. doi:10.1007/978-1-0716-3778-4_21'
apa: Jayasree, A., Salava, H., Nodzynski, T., & Sravankumar, T. (2024). Protein-Protein
Interactions Visualized by Bimolecular Fluorescence Complementation in Arabidopsis
thaliana Protoplasts from Leaf. In F. Maghuly (Ed.), Plant Functional Genomics
(Vol. 2787, pp. 305–313). Springer Nature. https://doi.org/10.1007/978-1-0716-3778-4_21
chicago: Jayasree, Aswathy, Hymavathi Salava, Tomasz Nodzynski, and Thula Sravankumar.
“Protein-Protein Interactions Visualized by Bimolecular Fluorescence Complementation
in Arabidopsis Thaliana Protoplasts from Leaf.” In Plant Functional Genomics,
edited by Fatemeh Maghuly, 2787:305–13. MIMB. Springer Nature, 2024. https://doi.org/10.1007/978-1-0716-3778-4_21.
ieee: A. Jayasree, H. Salava, T. Nodzynski, and T. Sravankumar, “Protein-Protein
Interactions Visualized by Bimolecular Fluorescence Complementation in Arabidopsis
thaliana Protoplasts from Leaf,” in Plant Functional Genomics, vol. 2787,
F. Maghuly, Ed. Springer Nature, 2024, pp. 305–313.
ista: 'Jayasree A, Salava H, Nodzynski T, Sravankumar T. 2024.Protein-Protein Interactions
Visualized by Bimolecular Fluorescence Complementation in Arabidopsis thaliana
Protoplasts from Leaf. In: Plant Functional Genomics. Methods in Molecular Biology,
vol. 2787, 305–313.'
mla: Jayasree, Aswathy, et al. “Protein-Protein Interactions Visualized by Bimolecular
Fluorescence Complementation in Arabidopsis Thaliana Protoplasts from Leaf.” Plant
Functional Genomics, edited by Fatemeh Maghuly, vol. 2787, Springer Nature,
2024, pp. 305–13, doi:10.1007/978-1-0716-3778-4_21.
short: A. Jayasree, H. Salava, T. Nodzynski, T. Sravankumar, in:, F. Maghuly (Ed.),
Plant Functional Genomics, Springer Nature, 2024, pp. 305–313.
date_created: 2024-05-05T22:01:04Z
date_published: 2024-04-25T00:00:00Z
date_updated: 2024-05-06T06:39:10Z
day: '25'
department:
- _id: JiFr
doi: 10.1007/978-1-0716-3778-4_21
editor:
- first_name: Fatemeh
full_name: Maghuly, Fatemeh
last_name: Maghuly
external_id:
pmid:
- '38656499'
fulldoi: https://doi.org/10.1007/978-1-0716-3778-4_21
intvolume: ' 2787'
language:
- iso: eng
month: '04'
oa_version: None
page: 305-313
pmid: 1
publication: Plant Functional Genomics
publication_identifier:
eissn:
- 1940-6029
isbn:
- '9781071637777'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: MIMB
status: public
title: Protein-Protein Interactions Visualized by Bimolecular Fluorescence Complementation
in Arabidopsis thaliana Protoplasts from Leaf
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2787
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '15362'
abstract:
- lang: eng
text: Constitutional heterozygous pathogenic variants in the exonuclease domain
of POLE and POLD1, which affect the proofreading activity of the corresponding
polymerases, cause a cancer predisposition syndrome characterized by increased
risk of gastrointestinal polyposis, colorectal cancer, endometrial cancer and
other tumor types. The generally accepted explanation for the connection between
the disruption of the proofreading activity of polymerases epsilon and delta and
cancer development is through an increase in the somatic mutation rate. Here we
studied an extended family with multiple members heterozygous for the pathogenic
POLD1 variant c.1421T>C p.(Leu474Pro), which segregates with the polyposis and
cancer phenotypes. Through the analysis of mutational patterns of patient-derived
fibroblasts colonies and de novo mutations obtained by parent-offspring comparisons,
we concluded that heterozygous POLD1 L474P just subtly increases the somatic and
germline mutation burden. In contrast, tumors developed in individuals with a
heterozygous mutation in the exonuclease domain of POLD1, including L474P, have
an extremely high mutation rate (>100 mut/Mb) associated with signature SBS10d.
We solved this contradiction through the observation that tumorigenesis involves
somatic inactivation of the wildtype POLD1 allele. These results imply that exonuclease
deficiency of polymerase delta has a recessive effect on mutation rate.
acknowledgement: 'This study was funded by the Spanish Ministry of Science and Innovation
(Agencia Estatal de Investigación), co-funded by FEDER funds a way to build Europe
[PID2020-112595RB-I00 (LV)], Instituto de Salud Carlos III [CIBERONC CB16/12/00234
(LV); ISCIII-AES-2017 PI17/01082 (JLS), PMP22/00064], Government of Catalonia [AGAUR
2021SGR01112, CERCA Program for institutional support (LV)], Scientific Foundation
Asociación Española Contra el Cáncer [AECC Investigador (MT)], Austrian Science
Fund FWF [Grant Agreement # I5127-B (FK)], German Research Foundation DFG [Grant
Agreement # 429960716 (FK)], and ERC Consolidator [Grant Agreement # 771209 ChrFL
(FK)].'
article_processing_charge: No
article_type: original
author:
- first_name: Maria A.
full_name: Andrianova, Maria A.
last_name: Andrianova
- first_name: Vladimir B.
full_name: Seplyarskiy, Vladimir B.
last_name: Seplyarskiy
- first_name: Mariona
full_name: Terradas, Mariona
last_name: Terradas
- first_name: Ana Beatriz
full_name: Sánchez-Heras, Ana Beatriz
last_name: Sánchez-Heras
- first_name: Pilar
full_name: Mur, Pilar
last_name: Mur
- first_name: José Luis
full_name: Soto, José Luis
last_name: Soto
- first_name: Gemma
full_name: Aiza, Gemma
last_name: Aiza
- first_name: Emma
full_name: Borràs, Emma
last_name: Borràs
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Alexey S.
full_name: Kondrashov, Alexey S.
last_name: Kondrashov
- first_name: Georgii A.
full_name: Bazykin, Georgii A.
last_name: Bazykin
- first_name: Laura
full_name: Valle, Laura
last_name: Valle
citation:
ama: Andrianova MA, Seplyarskiy VB, Terradas M, et al. Discovery of recessive effect
of human polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated
normal and cancer cells. European Journal of Human Genetics. 2024;32:837-845.
doi:10.1038/s41431-024-01598-8
apa: Andrianova, M. A., Seplyarskiy, V. B., Terradas, M., Sánchez-Heras, A. B.,
Mur, P., Soto, J. L., … Valle, L. (2024). Discovery of recessive effect of human
polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated
normal and cancer cells. European Journal of Human Genetics. Springer Nature.
https://doi.org/10.1038/s41431-024-01598-8
chicago: Andrianova, Maria A., Vladimir B. Seplyarskiy, Mariona Terradas, Ana Beatriz
Sánchez-Heras, Pilar Mur, José Luis Soto, Gemma Aiza, et al. “Discovery of Recessive
Effect of Human Polymerase δ Proofreading Deficiency through Mutational Analysis
of POLD1-Mutated Normal and Cancer Cells.” European Journal of Human Genetics.
Springer Nature, 2024. https://doi.org/10.1038/s41431-024-01598-8.
ieee: M. A. Andrianova et al., “Discovery of recessive effect of human polymerase
δ proofreading deficiency through mutational analysis of POLD1-mutated normal
and cancer cells,” European Journal of Human Genetics, vol. 32. Springer
Nature, pp. 837–845, 2024.
ista: Andrianova MA, Seplyarskiy VB, Terradas M, Sánchez-Heras AB, Mur P, Soto JL,
Aiza G, Borràs E, Kondrashov F, Kondrashov AS, Bazykin GA, Valle L. 2024. Discovery
of recessive effect of human polymerase δ proofreading deficiency through mutational
analysis of POLD1-mutated normal and cancer cells. European Journal of Human Genetics.
32, 837–845.
mla: Andrianova, Maria A., et al. “Discovery of Recessive Effect of Human Polymerase
δ Proofreading Deficiency through Mutational Analysis of POLD1-Mutated Normal
and Cancer Cells.” European Journal of Human Genetics, vol. 32, Springer
Nature, 2024, pp. 837–45, doi:10.1038/s41431-024-01598-8.
short: M.A. Andrianova, V.B. Seplyarskiy, M. Terradas, A.B. Sánchez-Heras, P. Mur,
J.L. Soto, G. Aiza, E. Borràs, F. Kondrashov, A.S. Kondrashov, G.A. Bazykin, L.
Valle, European Journal of Human Genetics 32 (2024) 837–845.
date_created: 2024-05-05T22:01:04Z
date_published: 2024-07-01T00:00:00Z
date_updated: 2026-04-15T08:51:09Z
day: '01'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.1038/s41431-024-01598-8
ec_funded: 1
external_id:
isi:
- '001207703200001'
pmid:
- '38658779'
file:
- access_level: open_access
checksum: e45fc987f4e9ebafdd0ec4f0e9027de4
content_type: application/pdf
creator: dernst
date_created: 2025-01-09T09:21:25Z
date_updated: 2025-01-09T09:21:25Z
file_id: '18799'
file_name: 2024_EJHG_Andrianova.pdf
file_size: 3060724
relation: main_file
success: 1
file_date_updated: 2025-01-09T09:21:25Z
fulldoi: https://doi.org/10.1038/s41431-024-01598-8
has_accepted_license: '1'
intvolume: ' 32'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 837-845
pmid: 1
project:
- _id: 9B767A34-BA93-11EA-9121-9846C619BF3A
grant_number: '429960716'
name: Evolution of Sensorimotor Transformation Across Diptera
- _id: 26580278-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771209'
name: Characterizing the fitness landscape on population and global scales
- _id: 34e076d6-11ca-11ed-8bc3-aec76c41a181
grant_number: I05127
name: Evolutionary analysis of gene regulation
publication: European Journal of Human Genetics
publication_identifier:
eissn:
- 1476-5438
issn:
- 1018-4813
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Discovery of recessive effect of human polymerase δ proofreading deficiency
through mutational analysis of POLD1-mutated normal and cancer cells
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2024'
...
---
_id: '15367'
abstract:
- lang: eng
text: Two-dimensional semiconductor-superconductor heterostructures form the foundation
of numerous nanoscale physical systems. However, measuring the properties of such
heterostructures, and characterizing the semiconductor in-situ is challenging.
A recent experimental study by [Phys. Rev. Lett. 128, 107701 (2022)] was able
to probe the semiconductor within the heterostructure using microwave measurements
of the superfluid density. This work revealed a rapid depletion of superfluid
density in semiconductor, caused by the in-plane magnetic field which in presence
of spin-orbit coupling creates so-called Bogoliubov Fermi surfaces. The experimental
work used a simplified theoretical model that neglected the presence of non-magnetic
disorder in the semiconductor, hence describing the data only qualitatively. Motivated
by experiments, we introduce a theoretical model describing a disordered semiconductor
with strong spin-orbit coupling that is proximitized by a superconductor. Our
model provides specific predictions for the density of states and superfluid density.
Presence of disorder leads to the emergence of a gapless superconducting phase,
that may be viewed as a manifestation of Bogoliubov Fermi surface. When applied
to real experimental data, our model showcases excellent quantitative agreement,
enabling the extraction of material parameters such as mean free path and mobility,
and estimating g-tensor after taking into account the orbital contribution of
magnetic field. Our model can be used to probe in-situ parameters of other superconductor-semiconductor
heterostructures and can be further extended to give access to transport properties.
acknowledgement: "We acknowledge useful discussions with M. Geier, A. Levchenko, B.
Ramshaw, T. Scaffidi, and\r\nJ. Shabani. This research was funded by the Austrian
Science Fund (FWF) F 86.\r\nFor the purpose of open access, authors have applied
a CC BY public copyright licence to any\r\nAuthor Accepted Manuscript version arising
from this submission. MS acknowledges hospitality of KITP supported in part by the
National Science Foundation under Grants No. NSF\r\nPHY-1748958 and PHY-2309135.
APH acknowledges the support of the NOMIS foundation."
article_number: '115'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Serafim
full_name: Babkin, Serafim
id: 41e64307-6672-11ee-b9ad-cc7a0075a479
last_name: Babkin
orcid: 0009-0003-7382-8036
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: Babkin S, Higginbotham AP, Serbyn M. Proximity-induced gapless superconductivity
in two-dimensional Rashba semiconductor in magnetic field. SciPost Physics.
2024;16(5). doi:10.21468/scipostphys.16.5.115
apa: Babkin, S., Higginbotham, A. P., & Serbyn, M. (2024). Proximity-induced
gapless superconductivity in two-dimensional Rashba semiconductor in magnetic
field. SciPost Physics. SciPost Foundation. https://doi.org/10.21468/scipostphys.16.5.115
chicago: Babkin, Serafim, Andrew P Higginbotham, and Maksym Serbyn. “Proximity-Induced
Gapless Superconductivity in Two-Dimensional Rashba Semiconductor in Magnetic
Field.” SciPost Physics. SciPost Foundation, 2024. https://doi.org/10.21468/scipostphys.16.5.115.
ieee: S. Babkin, A. P. Higginbotham, and M. Serbyn, “Proximity-induced gapless superconductivity
in two-dimensional Rashba semiconductor in magnetic field,” SciPost Physics,
vol. 16, no. 5. SciPost Foundation, 2024.
ista: Babkin S, Higginbotham AP, Serbyn M. 2024. Proximity-induced gapless superconductivity
in two-dimensional Rashba semiconductor in magnetic field. SciPost Physics. 16(5),
115.
mla: Babkin, Serafim, et al. “Proximity-Induced Gapless Superconductivity in Two-Dimensional
Rashba Semiconductor in Magnetic Field.” SciPost Physics, vol. 16, no.
5, 115, SciPost Foundation, 2024, doi:10.21468/scipostphys.16.5.115.
short: S. Babkin, A.P. Higginbotham, M. Serbyn, SciPost Physics 16 (2024).
corr_author: '1'
date_created: 2024-05-06T09:02:18Z
date_published: 2024-05-01T00:00:00Z
date_updated: 2026-06-03T07:16:00Z
day: '01'
ddc:
- '530'
department:
- _id: MaSe
- _id: AnHi
doi: 10.21468/scipostphys.16.5.115
external_id:
arxiv:
- '2311.09347'
isi:
- '001215855200002'
file:
- access_level: open_access
checksum: f999204856417dcf5a736ac8df432b96
content_type: application/pdf
creator: dernst
date_created: 2024-05-07T12:58:47Z
date_updated: 2024-05-07T12:58:47Z
file_id: '15369'
file_name: 2024_SciPostPhys_Babkin.pdf
file_size: 2733685
relation: main_file
success: 1
file_date_updated: 2024-05-07T12:58:47Z
fulldoi: https://doi.org/10.21468/scipostphys.16.5.115
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: eb9b30ac-77a9-11ec-83b8-871f581d53d2
name: Protected states of quantum matter
- _id: 34a7f947-11ca-11ed-8bc3-c5dc2bbaae25
grant_number: F8609
name: 'Center for Correlated Quantum Materials and Solid State Quantum Systems: Probing
topology in circuits and quantum materials'
publication: SciPost Physics
publication_identifier:
issn:
- 2542-4653
publication_status: published
publisher: SciPost Foundation
quality_controlled: '1'
scopus_import: '1'
status: public
title: Proximity-induced gapless superconductivity in two-dimensional Rashba semiconductor
in magnetic field
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 16
year: '2024'
...
---
DOAJ_listed: '1'
_id: '15372'
abstract:
- lang: eng
text: CRISPR-Cas9 is a powerful tool for genome editing, but the strict requirement
for an NGG protospacer-adjacent motif (PAM) sequence immediately next to the DNA
target limits the number of editable genes. Recently developed Cas9 variants have
been engineered with relaxed PAM requirements, including SpG-Cas9 (SpG) and the
nearly PAM-less SpRY-Cas9 (SpRY). However, the molecular mechanisms of how SpRY
recognizes all potential PAM sequences remains unclear. Here, we combine structural
and biochemical approaches to determine how SpRY interrogates DNA and recognizes
target sites. Divergent PAM sequences can be accommodated through conformational
flexibility within the PAM-interacting region, which facilitates tight binding
to off-target DNA sequences. Nuclease activation occurs ~1000-fold slower than
for Streptococcus pyogenes Cas9, enabling us to directly visualize multiple on-pathway
intermediate states. Experiments with SpG position it as an intermediate enzyme
between Cas9 and SpRY. Our findings shed light on the molecular mechanisms of
PAMless genome editing.
acknowledgement: We thank I. Stohkendl in the Taylor group for insightful discussions.
This work was supported in part by Welch Foundation grants F-1808 (to I.J.F.), and
F-1938 (to D.W.T.), the National Institutes of Health R01GM124141 (to I.J.F.), R01AI110577
(to K.A.J.), and R35GM138348 (to D.W.T.), and a Robert J. Kleberg, Jr. and Helen
C. Kleberg Foundation Medical Research Grant (to D.W.T.). The content is solely
the responsibility of the authors and does not necessarily represent the official
views of the National Institutes of Health.
article_number: '3663'
article_processing_charge: Yes
article_type: original
author:
- first_name: Grace N.
full_name: Hibshman, Grace N.
last_name: Hibshman
- first_name: Jack Peter Kelly
full_name: Bravo, Jack Peter Kelly
id: 96aecfa5-8931-11ee-af30-aa6a5d6eee0e
last_name: Bravo
orcid: 0000-0003-0456-0753
- first_name: Matthew M.
full_name: Hooper, Matthew M.
last_name: Hooper
- first_name: Tyler L.
full_name: Dangerfield, Tyler L.
last_name: Dangerfield
- first_name: Hongshan
full_name: Zhang, Hongshan
last_name: Zhang
- first_name: Ilya J.
full_name: Finkelstein, Ilya J.
last_name: Finkelstein
- first_name: Kenneth A.
full_name: Johnson, Kenneth A.
last_name: Johnson
- first_name: David W.
full_name: Taylor, David W.
last_name: Taylor
citation:
ama: Hibshman GN, Bravo JPK, Hooper MM, et al. Unraveling the mechanisms of PAMless
DNA interrogation by SpRY-Cas9. Nature Communications. 2024;15. doi:10.1038/s41467-024-47830-3
apa: Hibshman, G. N., Bravo, J. P. K., Hooper, M. M., Dangerfield, T. L., Zhang,
H., Finkelstein, I. J., … Taylor, D. W. (2024). Unraveling the mechanisms of PAMless
DNA interrogation by SpRY-Cas9. Nature Communications. Springer Nature.
https://doi.org/10.1038/s41467-024-47830-3
chicago: Hibshman, Grace N., Jack Peter Kelly Bravo, Matthew M. Hooper, Tyler L.
Dangerfield, Hongshan Zhang, Ilya J. Finkelstein, Kenneth A. Johnson, and David
W. Taylor. “Unraveling the Mechanisms of PAMless DNA Interrogation by SpRY-Cas9.”
Nature Communications. Springer Nature, 2024. https://doi.org/10.1038/s41467-024-47830-3.
ieee: G. N. Hibshman et al., “Unraveling the mechanisms of PAMless DNA interrogation
by SpRY-Cas9,” Nature Communications, vol. 15. Springer Nature, 2024.
ista: Hibshman GN, Bravo JPK, Hooper MM, Dangerfield TL, Zhang H, Finkelstein IJ,
Johnson KA, Taylor DW. 2024. Unraveling the mechanisms of PAMless DNA interrogation
by SpRY-Cas9. Nature Communications. 15, 3663.
mla: Hibshman, Grace N., et al. “Unraveling the Mechanisms of PAMless DNA Interrogation
by SpRY-Cas9.” Nature Communications, vol. 15, 3663, Springer Nature, 2024,
doi:10.1038/s41467-024-47830-3.
short: G.N. Hibshman, J.P.K. Bravo, M.M. Hooper, T.L. Dangerfield, H. Zhang, I.J.
Finkelstein, K.A. Johnson, D.W. Taylor, Nature Communications 15 (2024).
corr_author: '1'
date_created: 2024-05-12T22:01:00Z
date_published: 2024-04-30T00:00:00Z
date_updated: 2025-05-14T09:33:21Z
day: '30'
ddc:
- '570'
department:
- _id: JaBr
doi: 10.1038/s41467-024-47830-3
external_id:
pmid:
- '38688943'
file:
- access_level: open_access
checksum: 509c65919067a03ef8ad65c7192cd860
content_type: application/pdf
creator: dernst
date_created: 2024-05-13T11:46:19Z
date_updated: 2024-05-13T11:46:19Z
file_id: '15386'
file_name: 2024_NatureComm_Hibshman.pdf
file_size: 7477013
relation: main_file
success: 1
file_date_updated: 2024-05-13T11:46:19Z
fulldoi: https://doi.org/10.1038/s41467-024-47830-3
has_accepted_license: '1'
intvolume: ' 15'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '15373'
abstract:
- lang: eng
text: In this article we prove a refined version of the Christensen–Evans theorem
for generators of uniformly continuous GNS-symmetric quantum Markov semigroups.
We use this result to show the existence of GNS-symmetric extensions of GNS-symmetric
quantum Markov semigroups. In particular, this implies that the generators of
GNS-symmetric quantum Markov semigroups on finite-dimensional von Neumann algebra
can be written in the form specified by Alicki's theorem.
article_number: '110475'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Melchior
full_name: Wirth, Melchior
id: 88644358-0A0E-11EA-8FA5-49A33DDC885E
last_name: Wirth
orcid: 0000-0002-0519-4241
citation:
ama: Wirth M. Christensen–Evans theorem and extensions of GNS-symmetric quantum
Markov semigroups. Journal of Functional Analysis. 2024;287(3). doi:10.1016/j.jfa.2024.110475
apa: Wirth, M. (2024). Christensen–Evans theorem and extensions of GNS-symmetric
quantum Markov semigroups. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2024.110475
chicago: Wirth, Melchior. “Christensen–Evans Theorem and Extensions of GNS-Symmetric
Quantum Markov Semigroups.” Journal of Functional Analysis. Elsevier, 2024.
https://doi.org/10.1016/j.jfa.2024.110475.
ieee: M. Wirth, “Christensen–Evans theorem and extensions of GNS-symmetric quantum
Markov semigroups,” Journal of Functional Analysis, vol. 287, no. 3. Elsevier,
2024.
ista: Wirth M. 2024. Christensen–Evans theorem and extensions of GNS-symmetric quantum
Markov semigroups. Journal of Functional Analysis. 287(3), 110475.
mla: Wirth, Melchior. “Christensen–Evans Theorem and Extensions of GNS-Symmetric
Quantum Markov Semigroups.” Journal of Functional Analysis, vol. 287, no.
3, 110475, Elsevier, 2024, doi:10.1016/j.jfa.2024.110475.
short: M. Wirth, Journal of Functional Analysis 287 (2024).
corr_author: '1'
date_created: 2024-05-12T22:01:01Z
date_published: 2024-08-01T00:00:00Z
date_updated: 2025-09-08T07:24:07Z
day: '01'
ddc:
- '510'
department:
- _id: JaMa
doi: 10.1016/j.jfa.2024.110475
external_id:
isi:
- '001237916800001'
file:
- access_level: open_access
checksum: 657c9f77dd30bb31ce43a591f58126a2
content_type: application/pdf
creator: dernst
date_created: 2025-01-09T09:33:56Z
date_updated: 2025-01-09T09:33:56Z
file_id: '18802'
file_name: 2024_JourFunctAnalysis_Wirth.pdf
file_size: 503148
relation: main_file
success: 1
file_date_updated: 2025-01-09T09:33:56Z
fulldoi: https://doi.org/10.1016/j.jfa.2024.110475
has_accepted_license: '1'
intvolume: ' 287'
isi: 1
issue: '3'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication: Journal of Functional Analysis
publication_identifier:
eissn:
- 1096-0783
issn:
- 0022-1236
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Christensen–Evans theorem and extensions of GNS-symmetric quantum Markov semigroups
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 287
year: '2024'
...
---
_id: '15374'
abstract:
- lang: eng
text: Clathrin-mediated endocytosis (CME) is an essential process of cargo uptake
operating in all eukaryotes. In animals and yeast, BAR-SH3 domain proteins, endophilins
and amphiphysins, function at the conclusion of CME to recruit factors for vesicle
scission and uncoating. Arabidopsis thaliana contains the BAR-SH3 domain proteins
SH3P1–SH3P3, but their role is poorly understood. Here, we identify SH3Ps as functional
homologs of endophilin/amphiphysin. SH3P1–SH3P3 bind to discrete foci at the plasma
membrane (PM), and SH3P2 recruits late to a subset of clathrin-coated pits. The
SH3P2 PM recruitment pattern is nearly identical to its interactor, a putative
uncoating factor, AUXILIN-LIKE1. Notably, SH3P1–SH3P3 are required for most of
AUXILIN-LIKE1 recruitment to the PM. This indicates a plant-specific modification
of CME, where BAR-SH3 proteins recruit auxilin-like uncoating factors rather than
the uncoating phosphatases, synaptojanins. SH3P1–SH3P3 act redundantly in overall
CME with the plant-specific endocytic adaptor TPLATE complex but not due to an
SH3 domain in its TASH3 subunit.
acknowledgement: 'The authors wish to acknowledge Dr. Daniel van Damme for mRuby3/pDONRP2rP3
and Prof. Qi-Jun Chen for sharing plasmids used for CRISPR-Cas9 mutagenesis. This
work was supported by the Austrian Science Fund (FWF): I 3630-B25.'
article_number: '114195'
article_processing_charge: Yes
article_type: original
author:
- first_name: Maciek
full_name: Adamowski, Maciek
id: 45F536D2-F248-11E8-B48F-1D18A9856A87
last_name: Adamowski
orcid: 0000-0001-6463-5257
- first_name: Marek
full_name: Randuch, Marek
id: 6ac4636d-15b2-11ec-abd3-fb8df79972ae
last_name: Randuch
- first_name: Ivana
full_name: Matijevic, Ivana
id: 83c17ce3-15b2-11ec-abd3-f486545870bd
last_name: Matijevic
- first_name: Madhumitha
full_name: Narasimhan, Madhumitha
id: 44BF24D0-F248-11E8-B48F-1D18A9856A87
last_name: Narasimhan
orcid: 0000-0002-8600-0671
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Adamowski M, Randuch M, Matijevic I, Narasimhan M, Friml J. SH3Ps recruit auxilin-like
vesicle uncoating factors for clathrin-mediated endocytosis. Cell Reports.
2024;43(5). doi:10.1016/j.celrep.2024.114195
apa: Adamowski, M., Randuch, M., Matijevic, I., Narasimhan, M., & Friml, J.
(2024). SH3Ps recruit auxilin-like vesicle uncoating factors for clathrin-mediated
endocytosis. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2024.114195
chicago: Adamowski, Maciek, Marek Randuch, Ivana Matijevic, Madhumitha Narasimhan,
and Jiří Friml. “SH3Ps Recruit Auxilin-like Vesicle Uncoating Factors for Clathrin-Mediated
Endocytosis.” Cell Reports. Cell Press, 2024. https://doi.org/10.1016/j.celrep.2024.114195.
ieee: M. Adamowski, M. Randuch, I. Matijevic, M. Narasimhan, and J. Friml, “SH3Ps
recruit auxilin-like vesicle uncoating factors for clathrin-mediated endocytosis,”
Cell Reports, vol. 43, no. 5. Cell Press, 2024.
ista: Adamowski M, Randuch M, Matijevic I, Narasimhan M, Friml J. 2024. SH3Ps recruit
auxilin-like vesicle uncoating factors for clathrin-mediated endocytosis. Cell
Reports. 43(5), 114195.
mla: Adamowski, Maciek, et al. “SH3Ps Recruit Auxilin-like Vesicle Uncoating Factors
for Clathrin-Mediated Endocytosis.” Cell Reports, vol. 43, no. 5, 114195,
Cell Press, 2024, doi:10.1016/j.celrep.2024.114195.
short: M. Adamowski, M. Randuch, I. Matijevic, M. Narasimhan, J. Friml, Cell Reports
43 (2024).
corr_author: '1'
date_created: 2024-05-12T22:01:01Z
date_published: 2024-05-28T00:00:00Z
date_updated: 2025-09-08T07:23:07Z
day: '28'
ddc:
- '580'
department:
- _id: JiFr
- _id: MaLo
doi: 10.1016/j.celrep.2024.114195
external_id:
isi:
- '001240362800001'
pmid:
- '38717900'
file:
- access_level: open_access
checksum: a06bb85be4fc765c51554d27ee2da802
content_type: application/pdf
creator: dernst
date_created: 2024-05-13T12:11:22Z
date_updated: 2024-05-13T12:11:22Z
file_id: '15387'
file_name: 2024_CellReports_Adamowski.pdf
file_size: 5698598
relation: main_file
success: 1
file_date_updated: 2024-05-13T12:11:22Z
fulldoi: https://doi.org/10.1016/j.celrep.2024.114195
has_accepted_license: '1'
intvolume: ' 43'
isi: 1
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 26538374-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03630
name: Molecular mechanisms of endocytic cargo recognition in plants
publication: Cell Reports
publication_identifier:
eissn:
- 2211-1247
publication_status: published
publisher: Cell Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: SH3Ps recruit auxilin-like vesicle uncoating factors for clathrin-mediated
endocytosis
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 43
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '15375'
abstract:
- lang: eng
text: In the eukaryotic nucleus, heterochromatin forms highly condensed, visible
foci known as heterochromatin foci (HF). These HF are enriched with linker histone
H1, a key player in heterochromatin condensation and silencing. However, it is
unknown how H1 aggregates HF and condenses heterochromatin. In this study, we
established that H1 facilitates heterochromatin condensation by enhancing inter-
and intrachromosomal interactions between and within heterochromatic regions of
the Arabidopsis (Arabidopsis thaliana) genome. We demonstrated that H1 drives
HF formation via phase separation, which requires its C-terminal intrinsically
disordered region (C-IDR). A truncated H1 lacking the C-IDR fails to form foci
or recover HF in the h1 mutant background, whereas C-IDR with a short stretch
of the globular domain (18 out of 71 amino acids) is sufficient to rescue both
defects. In addition, C-IDR is essential for H1's roles in regulating nucleosome
repeat length and DNA methylation in Arabidopsis, indicating that phase separation
capability is required for chromatin functions of H1. Our data suggest that bacterial
H1-like proteins, which have been shown to condense DNA, are intrinsically disordered
and capable of mediating phase separation. Therefore, we propose that phase separation
mediated by H1 or H1-like proteins may represent an ancient mechanism for condensing
chromatin and DNA.
acknowledged_ssus:
- _id: Bio
- _id: ScienComp
acknowledgement: "This work was funded by ISTA core support (Y.Y. and X.F.) and grants
from the National Natural Science Foundation of China (31871443 to L.W. and P.L.;
32100417 to L.W.).\r\nWe thank the ISTA Imaging and Optics Facility for assistance
with microscopy and the ISTA Scientific Computing Facility for high-performance
computing resources."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Shengbo
full_name: He, Shengbo
last_name: He
- first_name: Yiming
full_name: Yu, Yiming
id: 318e643b-8b61-11ed-b69e-aafa103ec8dd
last_name: Yu
- first_name: Liang
full_name: Wang, Liang
last_name: Wang
- first_name: Jingyi
full_name: Zhang, Jingyi
last_name: Zhang
- first_name: Zhengyong
full_name: Bai, Zhengyong
last_name: Bai
- first_name: Guohong
full_name: Li, Guohong
last_name: Li
- first_name: Pilong
full_name: Li, Pilong
last_name: Li
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
citation:
ama: He S, Yu Y, Wang L, et al. Linker histone H1 drives heterochromatin condensation
via phase separation in Arabidopsis. The Plant Cell. 2024;36(5):1829-1843.
doi:10.1093/plcell/koae034
apa: He, S., Yu, Y., Wang, L., Zhang, J., Bai, Z., Li, G., … Feng, X. (2024). Linker
histone H1 drives heterochromatin condensation via phase separation in Arabidopsis.
The Plant Cell. Oxford University Press. https://doi.org/10.1093/plcell/koae034
chicago: He, Shengbo, Yiming Yu, Liang Wang, Jingyi Zhang, Zhengyong Bai, Guohong
Li, Pilong Li, and Xiaoqi Feng. “Linker Histone H1 Drives Heterochromatin Condensation
via Phase Separation in Arabidopsis.” The Plant Cell. Oxford University
Press, 2024. https://doi.org/10.1093/plcell/koae034.
ieee: S. He et al., “Linker histone H1 drives heterochromatin condensation
via phase separation in Arabidopsis,” The Plant Cell, vol. 36, no. 5. Oxford
University Press, pp. 1829–1843, 2024.
ista: He S, Yu Y, Wang L, Zhang J, Bai Z, Li G, Li P, Feng X. 2024. Linker histone
H1 drives heterochromatin condensation via phase separation in Arabidopsis. The
Plant Cell. 36(5), 1829–1843.
mla: He, Shengbo, et al. “Linker Histone H1 Drives Heterochromatin Condensation
via Phase Separation in Arabidopsis.” The Plant Cell, vol. 36, no. 5, Oxford
University Press, 2024, pp. 1829–43, doi:10.1093/plcell/koae034.
short: S. He, Y. Yu, L. Wang, J. Zhang, Z. Bai, G. Li, P. Li, X. Feng, The Plant
Cell 36 (2024) 1829–1843.
corr_author: '1'
date_created: 2024-05-12T22:01:01Z
date_published: 2024-05-01T00:00:00Z
date_updated: 2025-09-08T07:21:17Z
day: '01'
ddc:
- '580'
department:
- _id: XiFe
doi: 10.1093/plcell/koae034
external_id:
isi:
- '001180817000001'
pmid:
- '38309957'
file:
- access_level: open_access
checksum: eed76c848fe3d8fe9a53943181aaa53c
content_type: application/pdf
creator: dernst
date_created: 2025-04-23T07:43:12Z
date_updated: 2025-04-23T07:43:12Z
file_id: '19611'
file_name: 2024_PlantCell_He.pdf
file_size: 50791962
relation: main_file
success: 1
file_date_updated: 2025-04-23T07:43:12Z
fulldoi: https://doi.org/10.1093/plcell/koae034
has_accepted_license: '1'
intvolume: ' 36'
isi: 1
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 1829-1843
pmid: 1
publication: The Plant Cell
publication_identifier:
eissn:
- 1532-298X
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Linker histone H1 drives heterochromatin condensation via phase separation
in Arabidopsis
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 36
year: '2024'
...