---
_id: '11333'
abstract:
- lang: eng
text: Adenosine triphosphate (ATP) is the energy source for various biochemical
processes and biomolecular motors in living things. Development of ATP antagonists
and their stimuli-controlled actions offer a novel approach to regulate biological
processes. Herein, we developed azobenzene-based photoswitchable ATP antagonists
for controlling the activity of motor proteins; cytoplasmic and axonemal dyneins.
The new ATP antagonists showed reversible photoswitching of cytoplasmic dynein
activity in an in vitro dynein-microtubule system due to the trans and cis photoisomerization
of their azobenzene segment. Importantly, our ATP antagonists reversibly regulated
the axonemal dynein motor activity for the force generation in a demembranated
model of Chlamydomonas reinhardtii. We found that the trans and cis isomers of
ATP antagonists significantly differ in their affinity to the ATP binding site.
article_number: e202200807
article_processing_charge: No
article_type: original
author:
- first_name: Sampreeth
full_name: Thayyil, Sampreeth
last_name: Thayyil
- first_name: Yukinori
full_name: Nishigami, Yukinori
last_name: Nishigami
- first_name: Muhammad J
full_name: Islam, Muhammad J
id: C94881D2-008F-11EA-8E08-2637E6697425
last_name: Islam
- first_name: P. K.
full_name: Hashim, P. K.
last_name: Hashim
- first_name: Ken'Ya
full_name: Furuta, Ken'Ya
last_name: Furuta
- first_name: Kazuhiro
full_name: Oiwa, Kazuhiro
last_name: Oiwa
- first_name: Jian
full_name: Yu, Jian
last_name: Yu
- first_name: Min
full_name: Yao, Min
last_name: Yao
- first_name: Toshiyuki
full_name: Nakagaki, Toshiyuki
last_name: Nakagaki
- first_name: Nobuyuki
full_name: Tamaoki, Nobuyuki
last_name: Tamaoki
citation:
ama: Thayyil S, Nishigami Y, Islam MJ, et al. Dynamic control of microbial movement
by photoswitchable ATP antagonists. Chemistry - A European Journal. 2022;28(30).
doi:10.1002/chem.202200807
apa: Thayyil, S., Nishigami, Y., Islam, M. J., Hashim, P. K., Furuta, K., Oiwa,
K., … Tamaoki, N. (2022). Dynamic control of microbial movement by photoswitchable
ATP antagonists. Chemistry - A European Journal. Wiley. https://doi.org/10.1002/chem.202200807
chicago: Thayyil, Sampreeth, Yukinori Nishigami, Muhammad J Islam, P. K. Hashim,
Ken’Ya Furuta, Kazuhiro Oiwa, Jian Yu, Min Yao, Toshiyuki Nakagaki, and Nobuyuki
Tamaoki. “Dynamic Control of Microbial Movement by Photoswitchable ATP Antagonists.”
Chemistry - A European Journal. Wiley, 2022. https://doi.org/10.1002/chem.202200807.
ieee: S. Thayyil et al., “Dynamic control of microbial movement by photoswitchable
ATP antagonists,” Chemistry - A European Journal, vol. 28, no. 30. Wiley,
2022.
ista: Thayyil S, Nishigami Y, Islam MJ, Hashim PK, Furuta K, Oiwa K, Yu J, Yao M,
Nakagaki T, Tamaoki N. 2022. Dynamic control of microbial movement by photoswitchable
ATP antagonists. Chemistry - A European Journal. 28(30), e202200807.
mla: Thayyil, Sampreeth, et al. “Dynamic Control of Microbial Movement by Photoswitchable
ATP Antagonists.” Chemistry - A European Journal, vol. 28, no. 30, e202200807,
Wiley, 2022, doi:10.1002/chem.202200807.
short: S. Thayyil, Y. Nishigami, M.J. Islam, P.K. Hashim, K. Furuta, K. Oiwa, J.
Yu, M. Yao, T. Nakagaki, N. Tamaoki, Chemistry - A European Journal 28 (2022).
date_created: 2022-04-24T22:01:44Z
date_published: 2022-05-25T00:00:00Z
date_updated: 2026-04-02T11:59:00Z
day: '25'
department:
- _id: RySh
doi: 10.1002/chem.202200807
external_id:
isi:
- '000781658800001'
pmid:
- '35332959'
intvolume: ' 28'
isi: 1
issue: '30'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1002/chem.202200807
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
publication: Chemistry - A European Journal
publication_identifier:
eissn:
- 1521-3765
issn:
- 0947-6539
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamic control of microbial movement by photoswitchable ATP antagonists
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 28
year: '2022'
...
---
_id: '10766'
abstract:
- lang: eng
text: Tension of the actomyosin cell cortex plays a key role in determining cell–cell
contact growth and size. The level of cortical tension outside of the cell–cell
contact, when pulling at the contact edge, scales with the total size to which
a cell–cell contact can grow [J.-L. Maître et al., Science 338, 253–256 (2012)].
Here, we show in zebrafish primary germ-layer progenitor cells that this monotonic
relationship only applies to a narrow range of cortical tension increase and that
above a critical threshold, contact size inversely scales with cortical tension.
This switch from cortical tension increasing to decreasing progenitor cell–cell
contact size is caused by cortical tension promoting E-cadherin anchoring to the
actomyosin cytoskeleton, thereby increasing clustering and stability of E-cadherin
at the contact. After tension-mediated E-cadherin stabilization at the contact
exceeds a critical threshold level, the rate by which the contact expands in response
to pulling forces from the cortex sharply drops, leading to smaller contacts at
physiologically relevant timescales of contact formation. Thus, the activity of
cortical tension in expanding cell–cell contact size is limited by tension-stabilizing
E-cadherin–actin complexes at the contact.
acknowledged_ssus:
- _id: Bio
- _id: EM-Fac
- _id: PreCl
acknowledgement: 'We thank Guillaume Salbreaux, Silvia Grigolon, Edouard Hannezo,
and Vanessa Barone for discussions and comments on the manuscript and Shayan Shamipour
and Daniel Capek for help with data analysis. We also thank the Imaging & Optics,
Electron Microscopy, and Zebrafish Facility Scientific Service Units at the Institute
of Science and Technology Austria (ISTA)Nasser Darwish-Miranda for continuous support.
We acknowledge Hitoshi Morita for the gift of VinculinB-GFP plasmid. This research
was supported by an ISTA Fellow Marie-Curie Co-funding of regional, national, and
international programmes Grant P_IST_EU01 (to J.S.), European Molecular Biology
Organization Long-Term Fellowship Grant, ALTF reference number: 187-2013 (to M.S.),
Schroedinger Fellowship J4332-B28 (to M.S.), and European Research Council Advanced
Grant (MECSPEC; to C.-P.H.).'
article_number: e2122030119
article_processing_charge: No
article_type: original
author:
- first_name: Jana
full_name: Slovakova, Jana
id: 30F3F2F0-F248-11E8-B48F-1D18A9856A87
last_name: Slovakova
- first_name: Mateusz K
full_name: Sikora, Mateusz K
id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87
last_name: Sikora
- first_name: Feyza N
full_name: Arslan, Feyza N
id: 49DA7910-F248-11E8-B48F-1D18A9856A87
last_name: Arslan
orcid: 0000-0001-5809-9566
- first_name: Silvia
full_name: Caballero Mancebo, Silvia
id: 2F1E1758-F248-11E8-B48F-1D18A9856A87
last_name: Caballero Mancebo
orcid: 0000-0002-5223-3346
- first_name: Gabriel
full_name: Krens, Gabriel
id: 2B819732-F248-11E8-B48F-1D18A9856A87
last_name: Krens
orcid: 0000-0003-4761-5996
- first_name: Walter
full_name: Kaufmann, Walter
id: 3F99E422-F248-11E8-B48F-1D18A9856A87
last_name: Kaufmann
orcid: 0000-0001-9735-5315
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Slovakova J, Sikora MK, Arslan FN, et al. Tension-dependent stabilization of
E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor
cells. Proceedings of the National Academy of Sciences of the United States
of America. 2022;119(8). doi:10.1073/pnas.2122030119
apa: Slovakova, J., Sikora, M. K., Arslan, F. N., Caballero Mancebo, S., Krens,
G., Kaufmann, W., … Heisenberg, C.-P. J. (2022). Tension-dependent stabilization
of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor
cells. Proceedings of the National Academy of Sciences of the United States
of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2122030119
chicago: Slovakova, Jana, Mateusz K Sikora, Feyza N Arslan, Silvia Caballero Mancebo,
Gabriel Krens, Walter Kaufmann, Jack Merrin, and Carl-Philipp J Heisenberg. “Tension-Dependent
Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion in Zebrafish Germ-Layer
Progenitor Cells.” Proceedings of the National Academy of Sciences of the United
States of America. National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2122030119.
ieee: J. Slovakova et al., “Tension-dependent stabilization of E-cadherin
limits cell-cell contact expansion in zebrafish germ-layer progenitor cells,”
Proceedings of the National Academy of Sciences of the United States of America,
vol. 119, no. 8. National Academy of Sciences, 2022.
ista: Slovakova J, Sikora MK, Arslan FN, Caballero Mancebo S, Krens G, Kaufmann
W, Merrin J, Heisenberg C-PJ. 2022. Tension-dependent stabilization of E-cadherin
limits cell-cell contact expansion in zebrafish germ-layer progenitor cells. Proceedings
of the National Academy of Sciences of the United States of America. 119(8), e2122030119.
mla: Slovakova, Jana, et al. “Tension-Dependent Stabilization of E-Cadherin Limits
Cell-Cell Contact Expansion in Zebrafish Germ-Layer Progenitor Cells.” Proceedings
of the National Academy of Sciences of the United States of America, vol.
119, no. 8, e2122030119, National Academy of Sciences, 2022, doi:10.1073/pnas.2122030119.
short: J. Slovakova, M.K. Sikora, F.N. Arslan, S. Caballero Mancebo, G. Krens, W.
Kaufmann, J. Merrin, C.-P.J. Heisenberg, Proceedings of the National Academy of
Sciences of the United States of America 119 (2022).
corr_author: '1'
date_created: 2022-02-20T23:01:31Z
date_published: 2022-02-14T00:00:00Z
date_updated: 2026-04-02T12:54:56Z
day: '14'
ddc:
- '570'
department:
- _id: CaHe
- _id: EM-Fac
- _id: Bio
doi: 10.1073/pnas.2122030119
ec_funded: 1
external_id:
isi:
- '000766926900009'
pmid:
- '35165179'
file:
- access_level: open_access
checksum: d49f83c3580613966f71768ddb9a55a5
content_type: application/pdf
creator: dernst
date_created: 2022-02-21T08:45:11Z
date_updated: 2022-02-21T08:45:11Z
file_id: '10780'
file_name: 2022_PNAS_Slovakova.pdf
file_size: 1609678
relation: main_file
success: 1
file_date_updated: 2022-02-21T08:45:11Z
has_accepted_license: '1'
intvolume: ' 119'
isi: 1
issue: '8'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 260F1432-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742573'
name: Interaction and feedback between cell mechanics and fate specification in
vertebrate gastrulation
- _id: 2521E28E-B435-11E9-9278-68D0E5697425
grant_number: 187-2013
name: Modulation of adhesion function in cell-cell contact formation by cortical
tension
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'
related_material:
record:
- id: '9750'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion
in zebrafish germ-layer progenitor cells
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 119
year: '2022'
...
---
_id: '11353'
abstract:
- lang: eng
text: Micro- and nanoscale optical or microwave cavities are used in a wide range
of classical applications and quantum science experiments, ranging from precision
measurements, laser technologies to quantum control of mechanical motion. The
dissipative photon loss via absorption, present to some extent in any optical
cavity, is known to introduce thermo-optical effects and thereby impose fundamental
limits on precision measurements. Here, we theoretically and experimentally reveal
that such dissipative photon absorption can result in quantum feedback via in-loop
field detection of the absorbed optical field, leading to the intracavity field
fluctuations to be squashed or antisquashed. A closed-loop dissipative quantum
feedback to the cavity field arises. Strikingly, this modifies the optical cavity
susceptibility in coherent response measurements (capable of both increasing or
decreasing the bare cavity linewidth) and causes excess noise and correlations
in incoherent interferometric optomechanical measurements using a cavity, that
is parametrically coupled to a mechanical oscillator. We experimentally observe
such unanticipated dissipative dynamics in optomechanical spectroscopy of sideband-cooled
optomechanical crystal cavitiess at both cryogenic temperature (approximately
8 K) and ambient conditions. The dissipative feedback introduces effective modifications
to the optical cavity linewidth and the optomechanical scattering rate and gives
rise to excess imprecision noise in the interferometric quantum measurement of
mechanical motion. Such dissipative feedback differs fundamentally from a quantum
nondemolition feedback, e.g., optical Kerr squeezing. The dissipative feedback
itself always results in an antisqueezed out-of-loop optical field, while it can
enhance the coexisting Kerr squeezing under certain conditions. Our result applies
to cavity spectroscopy in both optical and superconducting microwave cavities,
and equally applies to any dissipative feedback mechanism of different bandwidth
inside the cavity. It has wide-ranging implications for future dissipation engineering,
such as dissipation enhanced sideband cooling and Kerr squeezing, quantum frequency
conversion, and nonreciprocity in photonic systems.
acknowledgement: "L.Q. acknowledges fruitful discussions with D. Vitali, R. Schnabel,
P.K. Lam, A. Nunnenkamp, and D. Malz. This work is supported by the EUH2020 research
and innovation programme under Grant No. 732894 (FET Proactive HOT), and the European
Research Council through \r\nGrant No. 835329 (ExCOM-cCEO). This work was further
supported by Swiss National Science Foundation under Grant Agreements No. 185870
(Ambizione) and No. 204927. Samples were fabricated at the Center of MicroNanoTechnology
(CMi) at EPFL and the Binnig and Rohrer Nanotechnology Center at IBM Research-Zurich."
article_number: '020309'
article_processing_charge: No
article_type: original
author:
- first_name: Liu
full_name: Qiu, Liu
id: 45e99c0d-1eb1-11eb-9b96-ed8ab2983cac
last_name: Qiu
orcid: 0000-0003-4345-4267
- first_name: Guanhao
full_name: Huang, Guanhao
last_name: Huang
- first_name: Itay
full_name: Shomroni, Itay
last_name: Shomroni
- first_name: Jiahe
full_name: Pan, Jiahe
last_name: Pan
- first_name: Paul
full_name: Seidler, Paul
last_name: Seidler
- first_name: Tobias J.
full_name: Kippenberg, Tobias J.
last_name: Kippenberg
citation:
ama: Qiu L, Huang G, Shomroni I, Pan J, Seidler P, Kippenberg TJ. Dissipative quantum
feedback in measurements using a parametrically coupled microcavity. PRX Quantum.
2022;3(2). doi:10.1103/PRXQuantum.3.020309
apa: Qiu, L., Huang, G., Shomroni, I., Pan, J., Seidler, P., & Kippenberg, T.
J. (2022). Dissipative quantum feedback in measurements using a parametrically
coupled microcavity. PRX Quantum. American Physical Society. https://doi.org/10.1103/PRXQuantum.3.020309
chicago: Qiu, Liu, Guanhao Huang, Itay Shomroni, Jiahe Pan, Paul Seidler, and Tobias
J. Kippenberg. “Dissipative Quantum Feedback in Measurements Using a Parametrically
Coupled Microcavity.” PRX Quantum. American Physical Society, 2022. https://doi.org/10.1103/PRXQuantum.3.020309.
ieee: L. Qiu, G. Huang, I. Shomroni, J. Pan, P. Seidler, and T. J. Kippenberg, “Dissipative
quantum feedback in measurements using a parametrically coupled microcavity,”
PRX Quantum, vol. 3, no. 2. American Physical Society, 2022.
ista: Qiu L, Huang G, Shomroni I, Pan J, Seidler P, Kippenberg TJ. 2022. Dissipative
quantum feedback in measurements using a parametrically coupled microcavity. PRX
Quantum. 3(2), 020309.
mla: Qiu, Liu, et al. “Dissipative Quantum Feedback in Measurements Using a Parametrically
Coupled Microcavity.” PRX Quantum, vol. 3, no. 2, 020309, American Physical
Society, 2022, doi:10.1103/PRXQuantum.3.020309.
short: L. Qiu, G. Huang, I. Shomroni, J. Pan, P. Seidler, T.J. Kippenberg, PRX Quantum
3 (2022).
date_created: 2022-05-08T22:01:43Z
date_published: 2022-04-13T00:00:00Z
date_updated: 2026-04-02T12:30:47Z
day: '13'
ddc:
- '530'
department:
- _id: JoFi
doi: 10.1103/PRXQuantum.3.020309
ec_funded: 1
external_id:
isi:
- '000789316700001'
file:
- access_level: open_access
checksum: 35ff9ddf1d54f64432e435b660edaeb6
content_type: application/pdf
creator: dernst
date_created: 2022-05-09T07:10:51Z
date_updated: 2022-05-09T07:10:51Z
file_id: '11358'
file_name: 2022_PRXQuantum_Qiu.pdf
file_size: 1657177
relation: main_file
success: 1
file_date_updated: 2022-05-09T07:10:51Z
has_accepted_license: '1'
intvolume: ' 3'
isi: 1
issue: '2'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '04'
oa: 1
oa_version: Published Version
project:
- _id: 257EB838-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '732894'
name: Hybrid Optomechanical Technologies
publication: PRX Quantum
publication_identifier:
eissn:
- 2691-3399
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dissipative quantum feedback in measurements using a parametrically coupled
microcavity
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 3
year: '2022'
...
---
_id: '10826'
abstract:
- lang: eng
text: Animals that lose one sensory modality often show augmented responses to other
sensory inputs. The mechanisms underpinning this cross-modal plasticity are poorly
understood. We probe such mechanisms by performing a forward genetic screen for
mutants with enhanced O2 perception in Caenorhabditis elegans. Multiple mutants
exhibiting increased O2 responsiveness concomitantly show defects in other sensory
responses. One mutant, qui-1, defective in a conserved NACHT/WD40 protein, abolishes
pheromone-evoked Ca2+ responses in the ADL pheromone-sensing neurons. At the same
time, ADL responsiveness to pre-synaptic input from O2-sensing neurons is heightened
in qui-1, and other sensory defective mutants, resulting in enhanced neurosecretion
although not increased Ca2+ responses. Expressing qui-1 selectively in ADL rescues
both the qui-1 ADL neurosecretory phenotype and enhanced escape from 21% O2. Profiling
ADL neurons in qui-1 mutants highlights extensive changes in gene expression,
notably of many neuropeptide receptors. We show that elevated ADL expression of
the conserved neuropeptide receptor NPR-22 is necessary for enhanced ADL neurosecretion
in qui-1 mutants, and is sufficient to confer increased ADL neurosecretion in
control animals. Sensory loss can thus confer cross-modal plasticity by changing
the peptidergic connectome.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: ScienComp
acknowledgement: "We would like to thank Gemma Chandratillake and Merav Cohen for
identifying mutants and José David Moñino Sánchez for his help on neurosecretion
assays. We are grateful to Kaveh Ashrafi (UCSF), Piali Sengupta (Brandeis), and
the Caenorhabditis Genetic Center (funded by National Institutes of Health Infrastructure
Program P40 OD010440) for strains and reagents ... and Rebecca Butcher (Univ. Florida)
for C9 pheromone. We thank Tim Stevens, Paula Freire-Pritchett, Alastair Crisp,
GurpreetGhattaoraya, and Fabian Amman for help with bioinformatic analysis, Ekaterina
Lashmanova for help with injections, Iris Hardege for strains, and Isabel Beets
(KU Leuven) and members of the de Bono Lab for comments on the manuscript. We thank
the CRUK Cambridge Research Institute Genomics Core for next generation sequencing
and the Flow Cytometry Facility at LMB for FACS. This research was supported by
the Scientific Service Units (SSU) of IST Austria through resources provided by
the Bioimaging Facility (BIF), the Life Science Facility (LSF) and Scientific Computing
(SciCo-p– Bioinformatics).\r\nThis work was supported by the Medical Research Council
UK (Studentship to GV), an\r\nAdvanced ERC grant (269,058 ACMO to MdB), and a Wellcome
Investigator Award (209504/Z/17/Z to MdB)."
article_number: e68040
article_processing_charge: No
article_type: original
author:
- first_name: Giulio
full_name: Valperga, Giulio
id: 67F289DE-0D8F-11EA-9BDD-54AE3DDC885E
last_name: Valperga
orcid: 0000-0001-6726-3890
- first_name: Mario
full_name: De Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: De Bono
orcid: 0000-0001-8347-0443
citation:
ama: Valperga G, de Bono M. Impairing one sensory modality enhances another by reconfiguring
peptidergic signalling in Caenorhabditis elegans. eLife. 2022;11. doi:10.7554/eLife.68040
apa: Valperga, G., & de Bono, M. (2022). Impairing one sensory modality enhances
another by reconfiguring peptidergic signalling in Caenorhabditis elegans. ELife.
eLife Sciences Publications. https://doi.org/10.7554/eLife.68040
chicago: Valperga, Giulio, and Mario de Bono. “Impairing One Sensory Modality Enhances
Another by Reconfiguring Peptidergic Signalling in Caenorhabditis Elegans.” ELife.
eLife Sciences Publications, 2022. https://doi.org/10.7554/eLife.68040.
ieee: G. Valperga and M. de Bono, “Impairing one sensory modality enhances another
by reconfiguring peptidergic signalling in Caenorhabditis elegans,” eLife,
vol. 11. eLife Sciences Publications, 2022.
ista: Valperga G, de Bono M. 2022. Impairing one sensory modality enhances another
by reconfiguring peptidergic signalling in Caenorhabditis elegans. eLife. 11,
e68040.
mla: Valperga, Giulio, and Mario de Bono. “Impairing One Sensory Modality Enhances
Another by Reconfiguring Peptidergic Signalling in Caenorhabditis Elegans.” ELife,
vol. 11, e68040, eLife Sciences Publications, 2022, doi:10.7554/eLife.68040.
short: G. Valperga, M. de Bono, ELife 11 (2022).
corr_author: '1'
date_created: 2022-03-06T23:01:52Z
date_published: 2022-02-24T00:00:00Z
date_updated: 2026-04-02T12:45:39Z
day: '24'
ddc:
- '570'
department:
- _id: MaDe
doi: 10.7554/eLife.68040
external_id:
isi:
- '000763432300001'
pmid:
- '35201977'
file:
- access_level: open_access
checksum: cc1b9bf866d0f61f965556e0dd03d3ac
content_type: application/pdf
creator: dernst
date_created: 2022-03-07T07:39:25Z
date_updated: 2022-03-07T07:39:25Z
file_id: '10830'
file_name: 2022_eLife_Valperga.pdf
file_size: 4095591
relation: main_file
success: 1
file_date_updated: 2022-03-07T07:39:25Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 23870BE8-32DE-11EA-91FC-C7463DDC885E
grant_number: 209504/A/17/Z
name: Molecular mechanisms of neural circuit function
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Impairing one sensory modality enhances another by reconfiguring peptidergic
signalling in Caenorhabditis elegans
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 11
year: '2022'
...
---
_id: '10829'
abstract:
- lang: eng
text: A novel multivariable system, combining a transistor with fiber optic-based
surface plasmon resonance spectroscopy with the gate electrode simultaneously
acting as the fiber optic sensor surface, is reported. The dual-mode sensor allows
for discrimination of mass and charge contributions for binding assays on the
same sensor surface. Furthermore, we optimize the sensor geometry by investigating
the influence of the fiber area to transistor channel area ratio and distance.
We show that larger fiber optic tip diameters are favorable for electronic and
optical signals and demonstrate the reversibility of plasmon resonance wavelength
shifts after electric field application. As a proof of principle, a layer-by-layer
assembly of polyelectrolytes is performed to benchmark the system against multivariable
sensing platforms with planar surface plasmon resonance configurations. Furthermore,
the biosensing performance is assessed using a thrombin binding assay with surface-immobilized
aptamers as receptors, allowing for the detection of medically relevant thrombin
concentrations.
acknowledgement: "This project has received funding from the European Union’s Horizon
2020 Research and Innovation Programme under the Marie Skłodowska-Curie grant agreement
No. 813863-\r\nBORGES. Additionally, we gratefully acknowledge the financial support
from the Austrian Research Promotion Agency (FFG; 870025 and 873541) for this research.
The data that support the findings of this study are openly available in Zenodo
(DOI: 10.5281/zenodo.5500360)"
article_processing_charge: No
article_type: original
author:
- first_name: Roger
full_name: Hasler, Roger
last_name: Hasler
- first_name: Ciril
full_name: Reiner-Rozman, Ciril
last_name: Reiner-Rozman
- first_name: Stefan
full_name: Fossati, Stefan
last_name: Fossati
- first_name: Patrik
full_name: Aspermair, Patrik
last_name: Aspermair
- first_name: Jakub
full_name: Dostalek, Jakub
last_name: Dostalek
- first_name: Seungho
full_name: Lee, Seungho
id: BB243B88-D767-11E9-B658-BC13E6697425
last_name: Lee
orcid: 0000-0002-6962-8598
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Johannes
full_name: Bintinger, Johannes
last_name: Bintinger
- first_name: Wolfgang
full_name: Knoll, Wolfgang
last_name: Knoll
citation:
ama: Hasler R, Reiner-Rozman C, Fossati S, et al. Field-effect transistor with a
plasmonic fiber optic gate electrode as a multivariable biosensor device. ACS
Sensors. 2022;7(2):504-512. doi:10.1021/acssensors.1c02313
apa: Hasler, R., Reiner-Rozman, C., Fossati, S., Aspermair, P., Dostalek, J., Lee,
S., … Knoll, W. (2022). Field-effect transistor with a plasmonic fiber optic gate
electrode as a multivariable biosensor device. ACS Sensors. American Chemical
Society. https://doi.org/10.1021/acssensors.1c02313
chicago: Hasler, Roger, Ciril Reiner-Rozman, Stefan Fossati, Patrik Aspermair, Jakub
Dostalek, Seungho Lee, Maria Ibáñez, Johannes Bintinger, and Wolfgang Knoll. “Field-Effect
Transistor with a Plasmonic Fiber Optic Gate Electrode as a Multivariable Biosensor
Device.” ACS Sensors. American Chemical Society, 2022. https://doi.org/10.1021/acssensors.1c02313.
ieee: R. Hasler et al., “Field-effect transistor with a plasmonic fiber optic
gate electrode as a multivariable biosensor device,” ACS Sensors, vol.
7, no. 2. American Chemical Society, pp. 504–512, 2022.
ista: Hasler R, Reiner-Rozman C, Fossati S, Aspermair P, Dostalek J, Lee S, Ibáñez
M, Bintinger J, Knoll W. 2022. Field-effect transistor with a plasmonic fiber
optic gate electrode as a multivariable biosensor device. ACS Sensors. 7(2), 504–512.
mla: Hasler, Roger, et al. “Field-Effect Transistor with a Plasmonic Fiber Optic
Gate Electrode as a Multivariable Biosensor Device.” ACS Sensors, vol.
7, no. 2, American Chemical Society, 2022, pp. 504–12, doi:10.1021/acssensors.1c02313.
short: R. Hasler, C. Reiner-Rozman, S. Fossati, P. Aspermair, J. Dostalek, S. Lee,
M. Ibáñez, J. Bintinger, W. Knoll, ACS Sensors 7 (2022) 504–512.
date_created: 2022-03-06T23:01:54Z
date_published: 2022-02-08T00:00:00Z
date_updated: 2026-04-02T12:33:46Z
day: '08'
ddc:
- '540'
department:
- _id: MaIb
doi: 10.1021/acssensors.1c02313
external_id:
isi:
- '000765113000016'
pmid:
- '35134289'
file:
- access_level: open_access
checksum: d704af7262cd484da9bb84b7d84e2b09
content_type: application/pdf
creator: dernst
date_created: 2022-03-07T08:15:01Z
date_updated: 2022-03-07T08:15:01Z
file_id: '10832'
file_name: 2022_ACSSensors_Hasler.pdf
file_size: 2969415
relation: main_file
success: 1
file_date_updated: 2022-03-07T08:15:01Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
issue: '2'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 504-512
pmid: 1
publication: ACS Sensors
publication_identifier:
eissn:
- 2379-3694
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
related_material:
record:
- id: '10833'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable
biosensor device
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 7
year: '2022'
...
---
_id: '10827'
abstract:
- lang: eng
text: Titanium dioxide has been extensively studied in the rutile or anatase phase,
while its high-pressure phases are less well-understood, despite that many are
thought to have interesting optical, mechanical, and electrochemical properties.
First-principles methods, such as density functional theory (DFT), are often used
to compute the enthalpies of TiO2 phases at 0 K, but they are expensive and, thus,
impractical for long time scale and large system-size simulations at finite temperatures.
On the other hand, cheap empirical potentials fail to capture the relative stabilities
of various polymorphs. To model the thermodynamic behaviors of ambient and high-pressure
phases of TiO2, we design an empirical model as a baseline and then train a machine
learning potential based on the difference between the DFT data and the empirical
model. This so-called Δ-learning potential contains long-range electrostatic interactions
and predicts the 0 K enthalpies of stable TiO2 phases that are in good agreement
with DFT. We construct a pressure–temperature phase diagram of TiO2 in the range
0 < P < 70 GPa and 100 < T < 1500 K. We then simulate dynamic phase transition
processes by compressing anatase at different temperatures. At 300 K, we predominantly
observe an anatase-to-baddeleyite transformation at about 20 GPa via a martensitic
two-step mechanism with a highly ordered and collective atomic motion. At 2000
K, anatase can transform into cotunnite around 45–55 GPa in a thermally activated
and probabilistic manner, accompanied by diffusive movement of oxygen atoms. The
pressures computed for these transitions show good agreement with experiments.
Our results shed light on how to synthesize and stabilize high-pressure TiO2 phases,
and our method is generally applicable to other functional materials with multiple
polymorphs.
acknowledgement: J.G.L. and B.C. acknowledge the resources provided by the Cambridge
Tier-2 system operated by the University of Cambridge Research Computing Service
funded by the EPSRC Tier-2 capital (Grant No. EP/P020259/1).
article_number: '074106'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Jacob G.
full_name: Lee, Jacob G.
last_name: Lee
- first_name: Chris J.
full_name: Pickard, Chris J.
last_name: Pickard
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
citation:
ama: Lee JG, Pickard CJ, Cheng B. High-pressure phase behaviors of titanium dioxide
revealed by a Δ-learning potential. The Journal of chemical physics. 2022;156(7).
doi:10.1063/5.0079844
apa: Lee, J. G., Pickard, C. J., & Cheng, B. (2022). High-pressure phase behaviors
of titanium dioxide revealed by a Δ-learning potential. The Journal of Chemical
Physics. AIP Publishing. https://doi.org/10.1063/5.0079844
chicago: Lee, Jacob G., Chris J. Pickard, and Bingqing Cheng. “High-Pressure Phase
Behaviors of Titanium Dioxide Revealed by a Δ-Learning Potential.” The Journal
of Chemical Physics. AIP Publishing, 2022. https://doi.org/10.1063/5.0079844.
ieee: J. G. Lee, C. J. Pickard, and B. Cheng, “High-pressure phase behaviors of
titanium dioxide revealed by a Δ-learning potential,” The Journal of chemical
physics, vol. 156, no. 7. AIP Publishing, 2022.
ista: Lee JG, Pickard CJ, Cheng B. 2022. High-pressure phase behaviors of titanium
dioxide revealed by a Δ-learning potential. The Journal of chemical physics. 156(7),
074106.
mla: Lee, Jacob G., et al. “High-Pressure Phase Behaviors of Titanium Dioxide Revealed
by a Δ-Learning Potential.” The Journal of Chemical Physics, vol. 156,
no. 7, 074106, AIP Publishing, 2022, doi:10.1063/5.0079844.
short: J.G. Lee, C.J. Pickard, B. Cheng, The Journal of Chemical Physics 156 (2022).
corr_author: '1'
date_created: 2022-03-06T23:01:53Z
date_published: 2022-02-16T00:00:00Z
date_updated: 2026-04-02T12:37:16Z
day: '16'
department:
- _id: BiCh
doi: 10.1063/5.0079844
external_id:
arxiv:
- '2111.12968'
isi:
- '000796704500014'
pmid:
- '35183078'
intvolume: ' 156'
isi: 1
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2111.12968
month: '02'
oa: 1
oa_version: Preprint
pmid: 1
publication: The Journal of chemical physics
publication_identifier:
eissn:
- 1089-7690
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: High-pressure phase behaviors of titanium dioxide revealed by a Δ-learning
potential
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 156
year: '2022'
...
---
_id: '10771'
abstract:
- lang: eng
text: A critical overview of the theory of the chirality-induced spin selectivity
(CISS) effect, that is, phenomena in which the chirality of molecular species
imparts significant spin selectivity to various electron processes, is provided.
Based on discussions in a recently held workshop, and further work published since,
the status of CISS effects—in electron transmission, electron transport, and chemical
reactions—is reviewed. For each, a detailed discussion of the state-of-the-art
in theoretical understanding is provided and remaining challenges and research
opportunities are identified.
article_number: '2106629'
article_processing_charge: No
article_type: review
arxiv: 1
author:
- first_name: Ferdinand
full_name: Evers, Ferdinand
last_name: Evers
- first_name: Amnon
full_name: Aharony, Amnon
last_name: Aharony
- first_name: Nir
full_name: Bar-Gill, Nir
last_name: Bar-Gill
- first_name: Ora
full_name: Entin-Wohlman, Ora
last_name: Entin-Wohlman
- first_name: Per
full_name: Hedegård, Per
last_name: Hedegård
- first_name: Oded
full_name: Hod, Oded
last_name: Hod
- first_name: Pavel
full_name: Jelinek, Pavel
last_name: Jelinek
- first_name: Grzegorz
full_name: Kamieniarz, Grzegorz
last_name: Kamieniarz
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Karen
full_name: Michaeli, Karen
last_name: Michaeli
- first_name: Vladimiro
full_name: Mujica, Vladimiro
last_name: Mujica
- first_name: Ron
full_name: Naaman, Ron
last_name: Naaman
- first_name: Yossi
full_name: Paltiel, Yossi
last_name: Paltiel
- first_name: Sivan
full_name: Refaely-Abramson, Sivan
last_name: Refaely-Abramson
- first_name: Oren
full_name: Tal, Oren
last_name: Tal
- first_name: Jos
full_name: Thijssen, Jos
last_name: Thijssen
- first_name: Michael
full_name: Thoss, Michael
last_name: Thoss
- first_name: Jan M.
full_name: Van Ruitenbeek, Jan M.
last_name: Van Ruitenbeek
- first_name: Latha
full_name: Venkataraman, Latha
last_name: Venkataraman
- first_name: David H.
full_name: Waldeck, David H.
last_name: Waldeck
- first_name: Binghai
full_name: Yan, Binghai
last_name: Yan
- first_name: Leeor
full_name: Kronik, Leeor
last_name: Kronik
citation:
ama: 'Evers F, Aharony A, Bar-Gill N, et al. Theory of chirality induced spin selectivity:
Progress and challenges. Advanced Materials. 2022;34(13). doi:10.1002/adma.202106629'
apa: 'Evers, F., Aharony, A., Bar-Gill, N., Entin-Wohlman, O., Hedegård, P., Hod,
O., … Kronik, L. (2022). Theory of chirality induced spin selectivity: Progress
and challenges. Advanced Materials. Wiley. https://doi.org/10.1002/adma.202106629'
chicago: 'Evers, Ferdinand, Amnon Aharony, Nir Bar-Gill, Ora Entin-Wohlman, Per
Hedegård, Oded Hod, Pavel Jelinek, et al. “Theory of Chirality Induced Spin Selectivity:
Progress and Challenges.” Advanced Materials. Wiley, 2022. https://doi.org/10.1002/adma.202106629.'
ieee: 'F. Evers et al., “Theory of chirality induced spin selectivity: Progress
and challenges,” Advanced Materials, vol. 34, no. 13. Wiley, 2022.'
ista: 'Evers F, Aharony A, Bar-Gill N, Entin-Wohlman O, Hedegård P, Hod O, Jelinek
P, Kamieniarz G, Lemeshko M, Michaeli K, Mujica V, Naaman R, Paltiel Y, Refaely-Abramson
S, Tal O, Thijssen J, Thoss M, Van Ruitenbeek JM, Venkataraman L, Waldeck DH,
Yan B, Kronik L. 2022. Theory of chirality induced spin selectivity: Progress
and challenges. Advanced Materials. 34(13), 2106629.'
mla: 'Evers, Ferdinand, et al. “Theory of Chirality Induced Spin Selectivity: Progress
and Challenges.” Advanced Materials, vol. 34, no. 13, 2106629, Wiley, 2022,
doi:10.1002/adma.202106629.'
short: F. Evers, A. Aharony, N. Bar-Gill, O. Entin-Wohlman, P. Hedegård, O. Hod,
P. Jelinek, G. Kamieniarz, M. Lemeshko, K. Michaeli, V. Mujica, R. Naaman, Y.
Paltiel, S. Refaely-Abramson, O. Tal, J. Thijssen, M. Thoss, J.M. Van Ruitenbeek,
L. Venkataraman, D.H. Waldeck, B. Yan, L. Kronik, Advanced Materials 34 (2022).
date_created: 2022-02-20T23:01:33Z
date_published: 2022-04-01T00:00:00Z
date_updated: 2026-04-02T12:45:15Z
day: '01'
department:
- _id: MiLe
doi: 10.1002/adma.202106629
external_id:
arxiv:
- '2108.09998'
isi:
- '000753795900001'
pmid:
- '35064943'
intvolume: ' 34'
isi: 1
issue: '13'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2108.09998
month: '04'
oa: 1
oa_version: Preprint
pmid: 1
publication: Advanced Materials
publication_identifier:
eissn:
- 1521-4095
issn:
- 0935-9648
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Theory of chirality induced spin selectivity: Progress and challenges'
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 34
year: '2022'
...
---
_id: '10833'
abstract:
- lang: eng
text: Detailed information about the data set see "dataset description.txt" file.
article_processing_charge: No
author:
- first_name: Roger
full_name: Hasler, Roger
last_name: Hasler
- first_name: Ciril
full_name: Reiner-Rozman, Ciril
last_name: Reiner-Rozman
- first_name: Stefan
full_name: Fossati, Stefan
last_name: Fossati
- first_name: Patrik
full_name: Aspermair, Patrik
last_name: Aspermair
- first_name: Jakub
full_name: Dostalek, Jakub
last_name: Dostalek
- first_name: Seungho
full_name: Lee, Seungho
id: BB243B88-D767-11E9-B658-BC13E6697425
last_name: Lee
orcid: 0000-0002-6962-8598
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Johannes
full_name: Bintinger, Johannes
last_name: Bintinger
- first_name: Wolfgang
full_name: Knoll, Wolfgang
last_name: Knoll
citation:
ama: Hasler R, Reiner-Rozman C, Fossati S, et al. Field-effect transistor with a
plasmonic fiber optic gate electrode as a multivariable biosensor device. 2022.
doi:10.5281/ZENODO.5500360
apa: Hasler, R., Reiner-Rozman, C., Fossati, S., Aspermair, P., Dostalek, J., Lee,
S., … Knoll, W. (2022). Field-effect transistor with a plasmonic fiber optic gate
electrode as a multivariable biosensor device. Zenodo. https://doi.org/10.5281/ZENODO.5500360
chicago: Hasler, Roger, Ciril Reiner-Rozman, Stefan Fossati, Patrik Aspermair, Jakub
Dostalek, Seungho Lee, Maria Ibáñez, Johannes Bintinger, and Wolfgang Knoll. “Field-Effect
Transistor with a Plasmonic Fiber Optic Gate Electrode as a Multivariable Biosensor
Device.” Zenodo, 2022. https://doi.org/10.5281/ZENODO.5500360.
ieee: R. Hasler et al., “Field-effect transistor with a plasmonic fiber optic
gate electrode as a multivariable biosensor device.” Zenodo, 2022.
ista: Hasler R, Reiner-Rozman C, Fossati S, Aspermair P, Dostalek J, Lee S, Ibáñez
M, Bintinger J, Knoll W. 2022. Field-effect transistor with a plasmonic fiber
optic gate electrode as a multivariable biosensor device, Zenodo, 10.5281/ZENODO.5500360.
mla: Hasler, Roger, et al. Field-Effect Transistor with a Plasmonic Fiber Optic
Gate Electrode as a Multivariable Biosensor Device. Zenodo, 2022, doi:10.5281/ZENODO.5500360.
short: R. Hasler, C. Reiner-Rozman, S. Fossati, P. Aspermair, J. Dostalek, S. Lee,
M. Ibáñez, J. Bintinger, W. Knoll, (2022).
date_created: 2022-03-07T08:19:11Z
date_published: 2022-02-08T00:00:00Z
date_updated: 2026-04-02T12:33:44Z
day: '08'
ddc:
- '540'
department:
- _id: MaIb
doi: 10.5281/ZENODO.5500360
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.5500360
month: '02'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '10829'
relation: used_in_publication
status: public
status: public
title: Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable
biosensor device
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2022'
...
---
_id: '11551'
abstract:
- lang: eng
text: Imbalanced mitochondrial dNTP pools are known players in the pathogenesis
of multiple human diseases. Here we show that, even under physiological conditions,
dGTP is largely overrepresented among other dNTPs in mitochondria of mouse tissues
and human cultured cells. In addition, a vast majority of mitochondrial dGTP is
tightly bound to NDUFA10, an accessory subunit of complex I of the mitochondrial
respiratory chain. NDUFA10 shares a deoxyribonucleoside kinase (dNK) domain with
deoxyribonucleoside kinases in the nucleotide salvage pathway, though no specific
function beyond stabilizing the complex I holoenzyme has been described for this
subunit. We mutated the dNK domain of NDUFA10 in human HEK-293T cells while preserving
complex I assembly and activity. The NDUFA10E160A/R161A shows reduced dGTP binding
capacity in vitro and leads to a 50% reduction in mitochondrial dGTP content,
proving that most dGTP is directly bound to the dNK domain of NDUFA10. This interaction
may represent a hitherto unknown mechanism regulating mitochondrial dNTP availability
and linking oxidative metabolism to DNA maintenance.
acknowledgement: "We thank Dr, Luke Formosa (Department of Biochemistry and Molecular
Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia)
for his valuable advice and assistance on NDUFA10 molecular studies and Dr. Francesc
Canals and his team (Proteomics Laboratory, Vall d’Hebron Institute of Oncology
[VHIO], Universitat Autònoma de Barcelona, Barcelona, Spain) for their assistance
with LC-MS/MS analyses. This work was supported by the Spanish Ministry of Industry,
Economy and Competitiveness [grants BFU2014-52618-R, SAF2017-87506, and PID2020-112929RB-I00
to Y.C.], by the Spanish Instituto de Salud Carlos III [grants PI21/00554 and PMP15/00025
to R.M.], co-financed by the European Regional Development Fund (ERDF), and by an
NHMRC Project grant to M.R. (GNT1164459).\r\n"
article_number: '620'
article_processing_charge: No
author:
- first_name: David
full_name: Molina-Granada, David
last_name: Molina-Granada
- first_name: Emiliano
full_name: González-Vioque, Emiliano
last_name: González-Vioque
- first_name: Marris G.
full_name: Dibley, Marris G.
last_name: Dibley
- first_name: Raquel
full_name: Cabrera-Pérez, Raquel
last_name: Cabrera-Pérez
- first_name: Antoni
full_name: Vallbona-Garcia, Antoni
last_name: Vallbona-Garcia
- first_name: Javier
full_name: Torres-Torronteras, Javier
last_name: Torres-Torronteras
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
- first_name: Michael T.
full_name: Ryan, Michael T.
last_name: Ryan
- first_name: Yolanda
full_name: Cámara, Yolanda
last_name: Cámara
- first_name: Ramon
full_name: Martí, Ramon
last_name: Martí
citation:
ama: Molina-Granada D, González-Vioque E, Dibley MG, et al. Most mitochondrial dGTP
is tightly bound to respiratory complex I through the NDUFA10 subunit. Communications
Biology. 2022;5(1). doi:10.1038/s42003-022-03568-6
apa: Molina-Granada, D., González-Vioque, E., Dibley, M. G., Cabrera-Pérez, R.,
Vallbona-Garcia, A., Torres-Torronteras, J., … Martí, R. (2022). Most mitochondrial
dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit. Communications
Biology. Springer Nature. https://doi.org/10.1038/s42003-022-03568-6
chicago: Molina-Granada, David, Emiliano González-Vioque, Marris G. Dibley, Raquel
Cabrera-Pérez, Antoni Vallbona-Garcia, Javier Torres-Torronteras, Leonid A Sazanov,
Michael T. Ryan, Yolanda Cámara, and Ramon Martí. “Most Mitochondrial DGTP Is
Tightly Bound to Respiratory Complex I through the NDUFA10 Subunit.” Communications
Biology. Springer Nature, 2022. https://doi.org/10.1038/s42003-022-03568-6.
ieee: D. Molina-Granada et al., “Most mitochondrial dGTP is tightly bound
to respiratory complex I through the NDUFA10 subunit,” Communications Biology,
vol. 5, no. 1. Springer Nature, 2022.
ista: Molina-Granada D, González-Vioque E, Dibley MG, Cabrera-Pérez R, Vallbona-Garcia
A, Torres-Torronteras J, Sazanov LA, Ryan MT, Cámara Y, Martí R. 2022. Most mitochondrial
dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit. Communications
Biology. 5(1), 620.
mla: Molina-Granada, David, et al. “Most Mitochondrial DGTP Is Tightly Bound to
Respiratory Complex I through the NDUFA10 Subunit.” Communications Biology,
vol. 5, no. 1, 620, Springer Nature, 2022, doi:10.1038/s42003-022-03568-6.
short: D. Molina-Granada, E. González-Vioque, M.G. Dibley, R. Cabrera-Pérez, A.
Vallbona-Garcia, J. Torres-Torronteras, L.A. Sazanov, M.T. Ryan, Y. Cámara, R.
Martí, Communications Biology 5 (2022).
date_created: 2022-07-10T22:01:52Z
date_published: 2022-06-23T00:00:00Z
date_updated: 2026-04-02T13:22:53Z
day: '23'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.1038/s42003-022-03568-6
external_id:
isi:
- '000815098500002'
pmid:
- ' 35739187'
file:
- access_level: open_access
checksum: 965f88bbcef3fd0c3e121340555c4467
content_type: application/pdf
creator: kschuh
date_created: 2022-07-13T07:44:58Z
date_updated: 2022-07-13T07:44:58Z
file_id: '11571'
file_name: 2022_communicationsbiology_Molina-Granada.pdf
file_size: 2335369
relation: main_file
success: 1
file_date_updated: 2022-07-13T07:44:58Z
has_accepted_license: '1'
intvolume: ' 5'
isi: 1
issue: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: Communications Biology
publication_identifier:
eissn:
- 2399-3642
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Most mitochondrial dGTP is tightly bound to respiratory complex I through the
NDUFA10 subunit
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 5
year: '2022'
...
---
_id: '12101'
abstract:
- lang: eng
text: 'Spatial games form a widely-studied class of games from biology and physics
modeling the evolution of social behavior. Formally, such a game is defined by
a square (d by d) payoff matrix M and an undirected graph G. Each vertex of G
represents an individual, that initially follows some strategy i ∈ {1,2,…,d}.
In each round of the game, every individual plays the matrix game with each of
its neighbors: An individual following strategy i meeting a neighbor following
strategy j receives a payoff equal to the entry (i,j) of M. Then, each individual
updates its strategy to its neighbors'' strategy with the highest sum of payoffs,
and the next round starts. The basic computational problems consist of reachability
between configurations and the average frequency of a strategy. For general spatial
games and graphs, these problems are in PSPACE. In this paper, we examine restricted
setting: the game is a prisoner’s dilemma; and G is a subgraph of grid. We prove
that basic computational problems for spatial games with prisoner’s dilemma on
a subgraph of a grid are PSPACE-hard.'
acknowledgement: "Krishnendu Chatterjee: The research was partially supported by the
ERC CoG 863818\r\n(ForM-SMArt).\r\nIsmaël Jecker: The research was partially supported
by the ERC grant 950398 (INFSYS).\r\nJakub Svoboda: The research was partially supported
by the ERC CoG 863818 (ForM-SMArt)"
article_number: 11:1-11:14
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Ismael R
full_name: Jecker, Ismael R
id: 85D7C63E-7D5D-11E9-9C0F-98C4E5697425
last_name: Jecker
- first_name: Jakub
full_name: Svoboda, Jakub
id: 130759D2-D7DD-11E9-87D2-DE0DE6697425
last_name: Svoboda
orcid: 0000-0002-1419-3267
citation:
ama: 'Chatterjee K, Ibsen-Jensen R, Jecker IR, Svoboda J. Complexity of spatial
games. In: 42nd IARCS Annual Conference on Foundations of Software Technology
and Theoretical Computer Science. Vol 250. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik; 2022. doi:10.4230/LIPIcs.FSTTCS.2022.11'
apa: 'Chatterjee, K., Ibsen-Jensen, R., Jecker, I. R., & Svoboda, J. (2022).
Complexity of spatial games. In 42nd IARCS Annual Conference on Foundations
of Software Technology and Theoretical Computer Science (Vol. 250). Madras,
India: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.FSTTCS.2022.11'
chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, Ismael R Jecker, and Jakub
Svoboda. “Complexity of Spatial Games.” In 42nd IARCS Annual Conference on
Foundations of Software Technology and Theoretical Computer Science, Vol.
250. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022. https://doi.org/10.4230/LIPIcs.FSTTCS.2022.11.
ieee: K. Chatterjee, R. Ibsen-Jensen, I. R. Jecker, and J. Svoboda, “Complexity
of spatial games,” in 42nd IARCS Annual Conference on Foundations of Software
Technology and Theoretical Computer Science, Madras, India, 2022, vol. 250.
ista: 'Chatterjee K, Ibsen-Jensen R, Jecker IR, Svoboda J. 2022. Complexity of spatial
games. 42nd IARCS Annual Conference on Foundations of Software Technology and
Theoretical Computer Science. FSTTCS: Foundations of Software Technology and Theoretical
Computer Science vol. 250, 11:1-11:14.'
mla: Chatterjee, Krishnendu, et al. “Complexity of Spatial Games.” 42nd IARCS
Annual Conference on Foundations of Software Technology and Theoretical Computer
Science, vol. 250, 11:1-11:14, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2022, doi:10.4230/LIPIcs.FSTTCS.2022.11.
short: K. Chatterjee, R. Ibsen-Jensen, I.R. Jecker, J. Svoboda, in:, 42nd IARCS
Annual Conference on Foundations of Software Technology and Theoretical Computer
Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022.
conference:
end_date: 2022-12-20
location: Madras, India
name: 'FSTTCS: Foundations of Software Technology and Theoretical Computer Science'
start_date: 2022-12-18
corr_author: '1'
date_created: 2023-01-01T23:00:50Z
date_published: 2022-12-14T00:00:00Z
date_updated: 2026-04-07T11:49:11Z
day: '14'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.4230/LIPIcs.FSTTCS.2022.11
ec_funded: 1
file:
- access_level: open_access
checksum: a21e3ba2421e2c4a06aa2cb6d530ede1
content_type: application/pdf
creator: dernst
date_created: 2023-01-20T10:19:19Z
date_updated: 2023-01-20T10:19:19Z
file_id: '12323'
file_name: 2022_LIPICs_Chatterjee.pdf
file_size: 657396
relation: main_file
success: 1
file_date_updated: 2023-01-20T10:19:19Z
has_accepted_license: '1'
intvolume: ' 250'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: 42nd IARCS Annual Conference on Foundations of Software Technology and
Theoretical Computer Science
publication_identifier:
isbn:
- '9783959772617'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
related_material:
record:
- id: '20138'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Complexity of spatial games
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 250
year: '2022'
...
---
_id: '12257'
abstract:
- lang: eng
text: Structural balance theory is an established framework for studying social
relationships of friendship and enmity. These relationships are modeled by a signed
network whose energy potential measures the level of imbalance, while stochastic
dynamics drives the network toward a state of minimum energy that captures social
balance. It is known that this energy landscape has local minima that can trap
socially aware dynamics, preventing it from reaching balance. Here we first study
the robustness and attractor properties of these local minima. We show that a
stochastic process can reach them from an abundance of initial states and that
some local minima cannot be escaped by mild perturbations of the network. Motivated
by these anomalies, we introduce best-edge dynamics (BED), a new plausible stochastic
process. We prove that BED always reaches balance and that it does so fast in
various interesting settings.
acknowledgement: "K.C. acknowledges support from ERC Start Grant No. (279307: Graph
Games), ERC Consolidator Grant No. (863818: ForM-SMart), and Austrian Science Fund
(FWF)\r\nGrants No. P23499-N23 and No. S11407-N23 (RiSE). This project has received
funding from the European Union’s Horizon 2020 research and innovation programme
under the Marie\r\nSkłodowska-Curie Grant Agreement No. 665385."
article_number: '034321'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Jakub
full_name: Svoboda, Jakub
id: 130759D2-D7DD-11E9-87D2-DE0DE6697425
last_name: Svoboda
orcid: 0000-0002-1419-3267
- first_name: Dorde
full_name: Zikelic, Dorde
id: 294AA7A6-F248-11E8-B48F-1D18A9856A87
last_name: Zikelic
orcid: 0000-0002-4681-1699
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
citation:
ama: 'Chatterjee K, Svoboda J, Zikelic D, Pavlogiannis A, Tkadlec J. Social balance
on networks: Local minima and best-edge dynamics. Physical Review E. 2022;106(3).
doi:10.1103/physreve.106.034321'
apa: 'Chatterjee, K., Svoboda, J., Zikelic, D., Pavlogiannis, A., & Tkadlec,
J. (2022). Social balance on networks: Local minima and best-edge dynamics. Physical
Review E. American Physical Society. https://doi.org/10.1103/physreve.106.034321'
chicago: 'Chatterjee, Krishnendu, Jakub Svoboda, Dorde Zikelic, Andreas Pavlogiannis,
and Josef Tkadlec. “Social Balance on Networks: Local Minima and Best-Edge Dynamics.”
Physical Review E. American Physical Society, 2022. https://doi.org/10.1103/physreve.106.034321.'
ieee: 'K. Chatterjee, J. Svoboda, D. Zikelic, A. Pavlogiannis, and J. Tkadlec, “Social
balance on networks: Local minima and best-edge dynamics,” Physical Review
E, vol. 106, no. 3. American Physical Society, 2022.'
ista: 'Chatterjee K, Svoboda J, Zikelic D, Pavlogiannis A, Tkadlec J. 2022. Social
balance on networks: Local minima and best-edge dynamics. Physical Review E. 106(3),
034321.'
mla: 'Chatterjee, Krishnendu, et al. “Social Balance on Networks: Local Minima and
Best-Edge Dynamics.” Physical Review E, vol. 106, no. 3, 034321, American
Physical Society, 2022, doi:10.1103/physreve.106.034321.'
short: K. Chatterjee, J. Svoboda, D. Zikelic, A. Pavlogiannis, J. Tkadlec, Physical
Review E 106 (2022).
date_created: 2023-01-16T09:57:57Z
date_published: 2022-09-29T00:00:00Z
date_updated: 2026-04-07T11:49:11Z
day: '29'
department:
- _id: KrCh
doi: 10.1103/physreve.106.034321
ec_funded: 1
external_id:
arxiv:
- '2210.02394'
isi:
- '000870243100001'
intvolume: ' 106'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2210.02394
month: '09'
oa: 1
oa_version: Preprint
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Physical Review E
publication_identifier:
eissn:
- 2470-0053
issn:
- 2470-0045
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
record:
- id: '20138'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'Social balance on networks: Local minima and best-edge dynamics'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 106
year: '2022'
...
---
_id: '11839'
abstract:
- lang: eng
text: "It is a highly desirable property for deep networks to be robust against\r\nsmall
input changes. One popular way to achieve this property is by designing\r\nnetworks
with a small Lipschitz constant. In this work, we propose a new\r\ntechnique for
constructing such Lipschitz networks that has a number of\r\ndesirable properties:
it can be applied to any linear network layer\r\n(fully-connected or convolutional),
it provides formal guarantees on the\r\nLipschitz constant, it is easy to implement
and efficient to run, and it can be\r\ncombined with any training objective and
optimization method. In fact, our\r\ntechnique is the first one in the literature
that achieves all of these\r\nproperties simultaneously. Our main contribution
is a rescaling-based weight\r\nmatrix parametrization that guarantees each network
layer to have a Lipschitz\r\nconstant of at most 1 and results in the learned
weight matrices to be close to\r\northogonal. Hence we call such layers almost-orthogonal
Lipschitz (AOL).\r\nExperiments and ablation studies in the context of image classification
with\r\ncertified robust accuracy confirm that AOL layers achieve results that
are on\r\npar with most existing methods. Yet, they are simpler to implement and
more\r\nbroadly applicable, because they do not require computationally expensive\r\nmatrix
orthogonalization or inversion steps as part of the network\r\narchitecture. We
provide code at https://github.com/berndprach/AOL."
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Bernd
full_name: Prach, Bernd
id: 2D561D42-C427-11E9-89B4-9C1AE6697425
last_name: Prach
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Prach B, Lampert C. Almost-orthogonal layers for efficient general-purpose
Lipschitz networks. In: Computer Vision – ECCV 2022. Vol 13681. Springer
Nature; 2022:350-365. doi:10.1007/978-3-031-19803-8_21'
apa: 'Prach, B., & Lampert, C. (2022). Almost-orthogonal layers for efficient
general-purpose Lipschitz networks. In Computer Vision – ECCV 2022 (Vol.
13681, pp. 350–365). Tel Aviv, Israel: Springer Nature. https://doi.org/10.1007/978-3-031-19803-8_21'
chicago: Prach, Bernd, and Christoph Lampert. “Almost-Orthogonal Layers for Efficient
General-Purpose Lipschitz Networks.” In Computer Vision – ECCV 2022, 13681:350–65.
Springer Nature, 2022. https://doi.org/10.1007/978-3-031-19803-8_21.
ieee: B. Prach and C. Lampert, “Almost-orthogonal layers for efficient general-purpose
Lipschitz networks,” in Computer Vision – ECCV 2022, Tel Aviv, Israel,
2022, vol. 13681, pp. 350–365.
ista: 'Prach B, Lampert C. 2022. Almost-orthogonal layers for efficient general-purpose
Lipschitz networks. Computer Vision – ECCV 2022. ECCV: European Conference on
Computer Vision, LNCS, vol. 13681, 350–365.'
mla: Prach, Bernd, and Christoph Lampert. “Almost-Orthogonal Layers for Efficient
General-Purpose Lipschitz Networks.” Computer Vision – ECCV 2022, vol.
13681, Springer Nature, 2022, pp. 350–65, doi:10.1007/978-3-031-19803-8_21.
short: B. Prach, C. Lampert, in:, Computer Vision – ECCV 2022, Springer Nature,
2022, pp. 350–365.
conference:
end_date: 2022-10-27
location: Tel Aviv, Israel
name: 'ECCV: European Conference on Computer Vision'
start_date: 2022-10-23
corr_author: '1'
date_created: 2022-08-12T15:09:47Z
date_published: 2022-10-23T00:00:00Z
date_updated: 2026-04-07T11:49:51Z
day: '23'
department:
- _id: GradSch
- _id: ChLa
doi: 10.1007/978-3-031-19803-8_21
external_id:
arxiv:
- '2208.03160'
isi:
- '000904104000021'
intvolume: ' 13681'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2208.03160'
month: '10'
oa: 1
oa_version: Preprint
page: 350-365
publication: Computer Vision – ECCV 2022
publication_identifier:
eisbn:
- '9783031198038'
isbn:
- '9783031198021'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '19759'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Almost-orthogonal layers for efficient general-purpose Lipschitz networks
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 13681
year: '2022'
...
---
_id: '12109'
abstract:
- lang: eng
text: Kelvin probe force microscopy (KPFM) is a powerful tool for studying contact
electrification (CE) at the nanoscale, but converting KPFM voltage maps to charge
density maps is nontrivial due to long-range forces and complex system geometry.
Here we present a strategy using finite-element method (FEM) simulations to determine
the Green's function of the KPFM probe/insulator/ground system, which allows us
to quantitatively extract surface charge. Testing our approach with synthetic
data, we find that accounting for the atomic force microscope (AFM) tip, cone,
and cantilever is necessary to recover a known input and that existing methods
lead to gross miscalculation or even the incorrect sign of the underlying charge.
Applying it to experimental data, we demonstrate its capacity to extract realistic
surface charge densities and fine details from contact-charged surfaces. Our method
gives a straightforward recipe to convert qualitative KPFM voltage data into quantitative
charge data over a range of experimental conditions, enabling quantitative CE
at the nanoscale.
acknowledged_ssus:
- _id: M-Shop
- _id: NanoFab
- _id: ScienComp
acknowledgement: "This project has received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme
(Grant Agreement\r\nNo. 949120). This research was supported by the Scientific Service
Units of the Institute of Science and Technology Austria (ISTA) through resources
provided by the Miba Machine\r\nShop, the Nanofabrication Facility, and the Scientific
Computing Facility. We thank F. Stumpf from Park Systems for useful discussions
and support with scanning probe microscopy.\r\nF.P. and J.C.S. contributed equally
to this work."
article_number: '125605'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Felix
full_name: Pertl, Felix
id: 6313aec0-15b2-11ec-abd3-ed67d16139af
last_name: Pertl
orcid: 0000-0003-0463-5794
- first_name: Juan Carlos A
full_name: Sobarzo Ponce, Juan Carlos A
id: 4B807D68-AE37-11E9-AC72-31CAE5697425
last_name: Sobarzo Ponce
- first_name: Lubuna B
full_name: Shafeek, Lubuna B
id: 3CD37A82-F248-11E8-B48F-1D18A9856A87
last_name: Shafeek
orcid: 0000-0001-7180-6050
- first_name: Tobias
full_name: Cramer, Tobias
last_name: Cramer
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
citation:
ama: Pertl F, Sobarzo Ponce JCA, Shafeek LB, Cramer T, Waitukaitis SR. Quantifying
nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid
approach. Physical Review Materials. 2022;6(12). doi:10.1103/PhysRevMaterials.6.125605
apa: Pertl, F., Sobarzo Ponce, J. C. A., Shafeek, L. B., Cramer, T., & Waitukaitis,
S. R. (2022). Quantifying nanoscale charge density features of contact-charged
surfaces with an FEM/KPFM-hybrid approach. Physical Review Materials. American
Physical Society. https://doi.org/10.1103/PhysRevMaterials.6.125605
chicago: Pertl, Felix, Juan Carlos A Sobarzo Ponce, Lubuna B Shafeek, Tobias Cramer,
and Scott R Waitukaitis. “Quantifying Nanoscale Charge Density Features of Contact-Charged
Surfaces with an FEM/KPFM-Hybrid Approach.” Physical Review Materials.
American Physical Society, 2022. https://doi.org/10.1103/PhysRevMaterials.6.125605.
ieee: F. Pertl, J. C. A. Sobarzo Ponce, L. B. Shafeek, T. Cramer, and S. R. Waitukaitis,
“Quantifying nanoscale charge density features of contact-charged surfaces with
an FEM/KPFM-hybrid approach,” Physical Review Materials, vol. 6, no. 12.
American Physical Society, 2022.
ista: Pertl F, Sobarzo Ponce JCA, Shafeek LB, Cramer T, Waitukaitis SR. 2022. Quantifying
nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid
approach. Physical Review Materials. 6(12), 125605.
mla: Pertl, Felix, et al. “Quantifying Nanoscale Charge Density Features of Contact-Charged
Surfaces with an FEM/KPFM-Hybrid Approach.” Physical Review Materials,
vol. 6, no. 12, 125605, American Physical Society, 2022, doi:10.1103/PhysRevMaterials.6.125605.
short: F. Pertl, J.C.A. Sobarzo Ponce, L.B. Shafeek, T. Cramer, S.R. Waitukaitis,
Physical Review Materials 6 (2022).
corr_author: '1'
date_created: 2023-01-08T23:00:53Z
date_published: 2022-12-29T00:00:00Z
date_updated: 2026-04-07T11:50:54Z
day: '29'
department:
- _id: ScWa
- _id: NanoFab
doi: 10.1103/PhysRevMaterials.6.125605
ec_funded: 1
external_id:
arxiv:
- '2209.01889'
isi:
- '000908384800001'
intvolume: ' 6'
isi: 1
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2209.01889'
month: '12'
oa: 1
oa_version: Preprint
project:
- _id: 0aa60e99-070f-11eb-9043-a6de6bdc3afa
call_identifier: H2020
grant_number: '949120'
name: 'Tribocharge: a multi-scale approach to an enduring problem in physics'
publication: Physical Review Materials
publication_identifier:
eissn:
- 2475-9953
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
record:
- id: '20203'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Quantifying nanoscale charge density features of contact-charged surfaces with
an FEM/KPFM-hybrid approach
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 6
year: '2022'
...
---
_id: '11478'
abstract:
- lang: eng
text: Cerebral organoids differentiated from human-induced pluripotent stem cells
(hiPSC) provide a unique opportunity to investigate brain development. However,
organoids usually lack microglia, brain-resident immune cells, which are present
in the early embryonic brain and participate in neuronal circuit development.
Here, we find IBA1+ microglia-like cells alongside retinal cups between week 3
and 4 in 2.5D culture with an unguided retinal organoid differentiation protocol.
Microglia do not infiltrate the neuroectoderm and instead enrich within non-pigmented,
3D-cystic compartments that develop in parallel to the 3D-retinal organoids. When
we guide the retinal organoid differentiation with low-dosed BMP4, we prevent
cup development and enhance microglia and 3D-cysts formation. Mass spectrometry
identifies these 3D-cysts to express mesenchymal and epithelial markers. We confirmed
this microglia-preferred environment also within the unguided protocol, providing
insight into microglial behavior and migration and offer a model to study how
they enter and distribute within the human brain.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: We thank the scientific service units at ISTA, specifically the lab
support facility and imaging & optics facility for their support; Nicolas Armel
for performing the Mass Spectrometry. We thank Alexandra Lang and Tanja Peilnsteiner
for their help in human brain tissue collection, Rouven Schulz for his insights
into the functional assays We thank all members of the Siegert group for constant
feedback on the project and Margaret Maes, Rouven Schulz, and Marco Benevento for
feedback on the manuscript. This project has received funding from the European
Research Council (ERC) under the European Union’s Horizon 2020 research and innovation
program (grant No. 715571 to S.S.) and from the Gesellschaft für Forschungsförderung
Niederösterreich (grant No. Sc19-017 to V.H.).
article_number: '104580'
article_processing_charge: Yes
article_type: original
author:
- first_name: Katarina
full_name: Bartalska, Katarina
id: 4D883232-F248-11E8-B48F-1D18A9856A87
last_name: Bartalska
- first_name: Verena
full_name: Hübschmann, Verena
id: 32B7C918-F248-11E8-B48F-1D18A9856A87
last_name: Hübschmann
- first_name: Medina
full_name: Korkut, Medina
id: 4B51CE74-F248-11E8-B48F-1D18A9856A87
last_name: Korkut
orcid: 0000-0003-4309-2251
- first_name: Ryan J
full_name: Cubero, Ryan J
id: 850B2E12-9CD4-11E9-837F-E719E6697425
last_name: Cubero
orcid: 0000-0003-0002-1867
- first_name: Alessandro
full_name: Venturino, Alessandro
id: 41CB84B2-F248-11E8-B48F-1D18A9856A87
last_name: Venturino
orcid: 0000-0003-2356-9403
- first_name: Karl
full_name: Rössler, Karl
last_name: Rössler
- first_name: Thomas
full_name: Czech, Thomas
last_name: Czech
- first_name: Sandra
full_name: Siegert, Sandra
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
citation:
ama: Bartalska K, Hübschmann V, Korkut M, et al. A systematic characterization of
microglia-like cell occurrence during retinal organoid differentiation. iScience.
2022;25(7). doi:10.1016/j.isci.2022.104580
apa: Bartalska, K., Hübschmann, V., Korkut, M., Cubero, R. J., Venturino, A., Rössler,
K., … Siegert, S. (2022). A systematic characterization of microglia-like cell
occurrence during retinal organoid differentiation. IScience. Elsevier.
https://doi.org/10.1016/j.isci.2022.104580
chicago: Bartalska, Katarina, Verena Hübschmann, Medina Korkut, Ryan J Cubero, Alessandro
Venturino, Karl Rössler, Thomas Czech, and Sandra Siegert. “A Systematic Characterization
of Microglia-like Cell Occurrence during Retinal Organoid Differentiation.” IScience.
Elsevier, 2022. https://doi.org/10.1016/j.isci.2022.104580.
ieee: K. Bartalska et al., “A systematic characterization of microglia-like
cell occurrence during retinal organoid differentiation,” iScience, vol.
25, no. 7. Elsevier, 2022.
ista: Bartalska K, Hübschmann V, Korkut M, Cubero RJ, Venturino A, Rössler K, Czech
T, Siegert S. 2022. A systematic characterization of microglia-like cell occurrence
during retinal organoid differentiation. iScience. 25(7), 104580.
mla: Bartalska, Katarina, et al. “A Systematic Characterization of Microglia-like
Cell Occurrence during Retinal Organoid Differentiation.” IScience, vol.
25, no. 7, 104580, Elsevier, 2022, doi:10.1016/j.isci.2022.104580.
short: K. Bartalska, V. Hübschmann, M. Korkut, R.J. Cubero, A. Venturino, K. Rössler,
T. Czech, S. Siegert, IScience 25 (2022).
corr_author: '1'
date_created: 2022-07-03T22:01:33Z
date_published: 2022-07-15T00:00:00Z
date_updated: 2026-04-07T11:51:43Z
day: '15'
ddc:
- '610'
department:
- _id: SaSi
doi: 10.1016/j.isci.2022.104580
ec_funded: 1
external_id:
isi:
- '000830428500005'
pmid:
- '35789843'
file:
- access_level: open_access
checksum: a470b74e1b3796c710189c81a4cd4329
content_type: application/pdf
creator: cchlebak
date_created: 2022-07-04T08:19:25Z
date_updated: 2022-07-04T08:19:25Z
file_id: '11480'
file_name: 2022_iScience_Bartalska.pdf
file_size: 19400048
relation: main_file
success: 1
file_date_updated: 2022-07-04T08:19:25Z
has_accepted_license: '1'
intvolume: ' 25'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25D4A630-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715571'
name: Microglia action towards neuronal circuit formation and function in health
and disease
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
- _id: 9B99D380-BA93-11EA-9121-9846C619BF3A
grant_number: SC19-017
name: How human microglia shape developing neurons during health and inflammation
publication: iScience
publication_identifier:
eissn:
- 2589-0042
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '12117'
relation: other
status: public
- id: '20074'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: A systematic characterization of microglia-like cell occurrence during retinal
organoid differentiation
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2022'
...
---
_id: '12291'
abstract:
- lang: eng
text: The phytohormone auxin triggers transcriptional reprogramming through a well-characterized
perception machinery in the nucleus. By contrast, mechanisms that underlie fast
effects of auxin, such as the regulation of ion fluxes, rapid phosphorylation
of proteins or auxin feedback on its transport, remain unclear1,2,3. Whether auxin-binding
protein 1 (ABP1) is an auxin receptor has been a source of debate for decades1,4.
Here we show that a fraction of Arabidopsis thaliana ABP1 is secreted and binds
auxin specifically at an acidic pH that is typical of the apoplast. ABP1 and its
plasma-membrane-localized partner, transmembrane kinase 1 (TMK1), are required
for the auxin-induced ultrafast global phospho-response and for downstream processes
that include the activation of H+-ATPase and accelerated cytoplasmic streaming.
abp1 and tmk mutants cannot establish auxin-transporting channels and show defective
auxin-induced vasculature formation and regeneration. An ABP1(M2X) variant that
lacks the capacity to bind auxin is unable to complement these defects in abp1
mutants. These data indicate that ABP1 is the auxin receptor for TMK1-based cell-surface
signalling, which mediates the global phospho-response and auxin canalization.
acknowledged_ssus:
- _id: Bio
- _id: EM-Fac
- _id: LifeSc
acknowledgement: We acknowledge K. Kubiasová for excellent technical assistance, J.
Neuhold, A. Lehner and A. Sedivy for technical assistance with protein production
and purification at Vienna Biocenter Core Facilities; Creoptix for performing GCI;
and the Bioimaging, Electron Microscopy and Life Science Facilities at ISTA, the
Plant Sciences Core Facility of CEITEC Masaryk University, the Core Facility CELLIM
(MEYS CR, LM2018129 Czech-BioImaging) and J. Sprakel for their assistance. J.F.
is grateful to R. Napier for many insightful suggestions and support. We thank all
past and present members of the Friml group for their support and for other contributions
to this effort to clarify the controversial role of ABP1 over the past seven years.
The project received funding from the European Research Council (ERC) under the
European Union’s Horizon 2020 research and innovation program (grant agreement no.
742985 to J.F. and 833867 to D.W.); the Austrian Science Fund (FWF; P29988 to J.F.);
the Netherlands Organization for Scientific Research (NWO; VICI grant 865.14.001
to D.W. and VENI grant VI.Veni.212.003 to A.K.); the Ministry of Education, Science
and Technological Development of the Republic of Serbia (contract no. 451-03-68/2022-14/200053
to B.D.Ž.); and the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and
20H05910).
article_processing_charge: No
article_type: original
author:
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Michelle C
full_name: Gallei, Michelle C
id: 35A03822-F248-11E8-B48F-1D18A9856A87
last_name: Gallei
orcid: 0000-0003-1286-7368
- first_name: Zuzana
full_name: Gelová, Zuzana
id: 0AE74790-0E0B-11E9-ABC7-1ACFE5697425
last_name: Gelová
orcid: 0000-0003-4783-1752
- first_name: Alexander J
full_name: Johnson, Alexander J
id: 46A62C3A-F248-11E8-B48F-1D18A9856A87
last_name: Johnson
orcid: 0000-0002-2739-8843
- first_name: Ewa
full_name: Mazur, Ewa
last_name: Mazur
- first_name: Aline
full_name: Monzer, Aline
id: 2DB5D88C-D7B3-11E9-B8FD-7907E6697425
last_name: Monzer
- first_name: Lesia
full_name: Rodriguez Solovey, Lesia
id: 3922B506-F248-11E8-B48F-1D18A9856A87
last_name: Rodriguez Solovey
orcid: 0000-0002-7244-7237
- first_name: Mark
full_name: Roosjen, Mark
last_name: Roosjen
- first_name: Inge
full_name: Verstraeten, Inge
id: 362BF7FE-F248-11E8-B48F-1D18A9856A87
last_name: Verstraeten
orcid: 0000-0001-7241-2328
- first_name: Branka D.
full_name: Živanović, Branka D.
last_name: Živanović
- first_name: Minxia
full_name: Zou, Minxia
id: 5c243f41-03f3-11ec-841c-96faf48a7ef9
last_name: Zou
- first_name: Lukas
full_name: Fiedler, Lukas
id: 7c417475-8972-11ed-ae7b-8b674ca26986
last_name: Fiedler
- first_name: Caterina
full_name: Giannini, Caterina
id: e3fdddd5-f6e0-11ea-865d-ca99ee6367f4
last_name: Giannini
- first_name: Peter
full_name: Grones, Peter
last_name: Grones
- first_name: Mónika
full_name: Hrtyan, Mónika
id: 45A71A74-F248-11E8-B48F-1D18A9856A87
last_name: Hrtyan
- first_name: Walter
full_name: Kaufmann, Walter
id: 3F99E422-F248-11E8-B48F-1D18A9856A87
last_name: Kaufmann
orcid: 0000-0001-9735-5315
- first_name: Andre
full_name: Kuhn, Andre
last_name: Kuhn
- first_name: Madhumitha
full_name: Narasimhan, Madhumitha
id: 44BF24D0-F248-11E8-B48F-1D18A9856A87
last_name: Narasimhan
orcid: 0000-0002-8600-0671
- first_name: Marek
full_name: Randuch, Marek
id: 6ac4636d-15b2-11ec-abd3-fb8df79972ae
last_name: Randuch
- first_name: Nikola
full_name: Rýdza, Nikola
last_name: Rýdza
- first_name: Koji
full_name: Takahashi, Koji
last_name: Takahashi
- first_name: Shutang
full_name: Tan, Shutang
id: 2DE75584-F248-11E8-B48F-1D18A9856A87
last_name: Tan
orcid: 0000-0002-0471-8285
- first_name: Anastasiia
full_name: Teplova, Anastasiia
id: e3736151-106c-11ec-b916-c2558e2762c6
last_name: Teplova
- first_name: Toshinori
full_name: Kinoshita, Toshinori
last_name: Kinoshita
- first_name: Dolf
full_name: Weijers, Dolf
last_name: Weijers
- first_name: Hana
full_name: Rakusová, Hana
last_name: Rakusová
citation:
ama: Friml J, Gallei MC, Gelová Z, et al. ABP1–TMK auxin perception for global phosphorylation
and auxin canalization. Nature. 2022;609(7927):575-581. doi:10.1038/s41586-022-05187-x
apa: Friml, J., Gallei, M. C., Gelová, Z., Johnson, A. J., Mazur, E., Monzer, A.,
… Rakusová, H. (2022). ABP1–TMK auxin perception for global phosphorylation and
auxin canalization. Nature. Springer Nature. https://doi.org/10.1038/s41586-022-05187-x
chicago: Friml, Jiří, Michelle C Gallei, Zuzana Gelová, Alexander J Johnson, Ewa
Mazur, Aline Monzer, Lesia Rodriguez Solovey, et al. “ABP1–TMK Auxin Perception
for Global Phosphorylation and Auxin Canalization.” Nature. Springer Nature,
2022. https://doi.org/10.1038/s41586-022-05187-x.
ieee: J. Friml et al., “ABP1–TMK auxin perception for global phosphorylation
and auxin canalization,” Nature, vol. 609, no. 7927. Springer Nature, pp.
575–581, 2022.
ista: Friml J, Gallei MC, Gelová Z, Johnson AJ, Mazur E, Monzer A, Rodriguez Solovey
L, Roosjen M, Verstraeten I, Živanović BD, Zou M, Fiedler L, Giannini C, Grones
P, Hrtyan M, Kaufmann W, Kuhn A, Narasimhan M, Randuch M, Rýdza N, Takahashi K,
Tan S, Teplova A, Kinoshita T, Weijers D, Rakusová H. 2022. ABP1–TMK auxin perception
for global phosphorylation and auxin canalization. Nature. 609(7927), 575–581.
mla: Friml, Jiří, et al. “ABP1–TMK Auxin Perception for Global Phosphorylation and
Auxin Canalization.” Nature, vol. 609, no. 7927, Springer Nature, 2022,
pp. 575–81, doi:10.1038/s41586-022-05187-x.
short: J. Friml, M.C. Gallei, Z. Gelová, A.J. Johnson, E. Mazur, A. Monzer, L. Rodriguez
Solovey, M. Roosjen, I. Verstraeten, B.D. Živanović, M. Zou, L. Fiedler, C. Giannini,
P. Grones, M. Hrtyan, W. Kaufmann, A. Kuhn, M. Narasimhan, M. Randuch, N. Rýdza,
K. Takahashi, S. Tan, A. Teplova, T. Kinoshita, D. Weijers, H. Rakusová, Nature
609 (2022) 575–581.
corr_author: '1'
date_created: 2023-01-16T10:04:48Z
date_published: 2022-09-15T00:00:00Z
date_updated: 2026-04-07T11:52:15Z
day: '15'
ddc:
- '580'
department:
- _id: JiFr
- _id: GradSch
- _id: EvBe
- _id: EM-Fac
doi: 10.1038/s41586-022-05187-x
ec_funded: 1
external_id:
isi:
- '000851357500002'
pmid:
- '36071161'
file:
- access_level: open_access
checksum: a6055c606aefb900bf62ae3e7d15f921
content_type: application/pdf
creator: amally
date_created: 2023-11-02T17:12:37Z
date_updated: 2023-11-02T17:12:37Z
file_id: '14483'
file_name: Friml Nature 2022_merged.pdf
file_size: 79774945
relation: main_file
success: 1
file_date_updated: 2023-11-02T17:12:37Z
has_accepted_license: '1'
intvolume: ' 609'
isi: 1
issue: '7927'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 575-581
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
- _id: 262EF96E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29988
name: RNA-directed DNA methylation in plant development
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
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relation: dissertation_contains
status: public
- id: '20364'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: ABP1–TMK auxin perception for global phosphorylation and auxin canalization
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 609
year: '2022'
...
---
_id: '10845'
abstract:
- lang: eng
text: We study an impurity with a resonance level whose position coincides with
the Fermi energy of the surrounding Fermi gas. An impurity causes a rapid variation
of the scattering phase shift for fermions at the Fermi surface, introducing a
new characteristic length scale into the problem. We investigate manifestations
of this length scale in the self-energy of the impurity and in the density of
the bath. Our calculations reveal a model-independent deformation of the density
of the Fermi gas, which is determined by the width of the resonance. To provide
a broader picture, we investigate time evolution of the density in quench dynamics,
and study the behavior of the system at finite temperatures. Finally, we briefly
discuss implications of our findings for the Fermi-polaron problem.
acknowledgement: M.L. acknowledges support by the Austrian Science Fund (FWF), under
Project No. P29902-N27, and by the European Research Council (ERC) starting Grant
No. 801770 (ANGULON). A.G.V. acknowledges support by European Union’s Horizon 2020
research and innovation programme under the Marie Skłodowska-Curie Grant Agreement
No. 754411.
article_number: '013160'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Mikhail
full_name: Maslov, Mikhail
id: 2E65BB0E-F248-11E8-B48F-1D18A9856A87
last_name: Maslov
orcid: 0000-0003-4074-2570
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
citation:
ama: Maslov M, Lemeshko M, Volosniev A. Impurity with a resonance in the vicinity
of the Fermi energy. Physical Review Research. 2022;4. doi:10.1103/PhysRevResearch.4.013160
apa: Maslov, M., Lemeshko, M., & Volosniev, A. (2022). Impurity with a resonance
in the vicinity of the Fermi energy. Physical Review Research. American
Physical Society. https://doi.org/10.1103/PhysRevResearch.4.013160
chicago: Maslov, Mikhail, Mikhail Lemeshko, and Artem Volosniev. “Impurity with
a Resonance in the Vicinity of the Fermi Energy.” Physical Review Research.
American Physical Society, 2022. https://doi.org/10.1103/PhysRevResearch.4.013160.
ieee: M. Maslov, M. Lemeshko, and A. Volosniev, “Impurity with a resonance in the
vicinity of the Fermi energy,” Physical Review Research, vol. 4. American
Physical Society, 2022.
ista: Maslov M, Lemeshko M, Volosniev A. 2022. Impurity with a resonance in the
vicinity of the Fermi energy. Physical Review Research. 4, 013160.
mla: Maslov, Mikhail, et al. “Impurity with a Resonance in the Vicinity of the Fermi
Energy.” Physical Review Research, vol. 4, 013160, American Physical Society,
2022, doi:10.1103/PhysRevResearch.4.013160.
short: M. Maslov, M. Lemeshko, A. Volosniev, Physical Review Research 4 (2022).
corr_author: '1'
date_created: 2022-03-13T23:01:46Z
date_published: 2022-03-01T00:00:00Z
date_updated: 2026-04-07T11:52:53Z
day: '01'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1103/PhysRevResearch.4.013160
ec_funded: 1
external_id:
arxiv:
- '2111.13570'
file:
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checksum: 62f64b3421a969656ebf52467fa7b6e8
content_type: application/pdf
creator: dernst
date_created: 2022-03-14T08:38:49Z
date_updated: 2022-03-14T08:38:49Z
file_id: '10848'
file_name: 2022_PhysicalReviewResearch_Maslov.pdf
file_size: 1258324
relation: main_file
success: 1
file_date_updated: 2022-03-14T08:38:49Z
has_accepted_license: '1'
intvolume: ' 4'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Physical Review Research
publication_identifier:
issn:
- 2643-1564
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
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- id: '19048'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Impurity with a resonance in the vicinity of the Fermi energy
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: 4
year: '2022'
...
---
_id: '12431'
abstract:
- lang: eng
text: This paper presents a new representation of curve dynamics, with applications
to vortex filaments in fluid dynamics. Instead of representing these filaments
with explicit curve geometry and Lagrangian equations of motion, we represent
curves implicitly with a new co-dimensional 2 level set description. Our implicit
representation admits several redundant mathematical degrees of freedom in both
the configuration and the dynamics of the curves, which can be tailored specifically
to improve numerical robustness, in contrast to naive approaches for implicit
curve dynamics that suffer from overwhelming numerical stability problems. Furthermore,
we note how these hidden degrees of freedom perfectly map to a Clebsch representation
in fluid dynamics. Motivated by these observations, we introduce untwisted level
set functions and non-swirling dynamics which successfully regularize sources
of numerical instability, particularly in the twisting modes around curve filaments.
A consequence is a novel simulation method which produces stable dynamics for
large numbers of interacting vortex filaments and effortlessly handles topological
changes and re-connection events.
acknowledgement: We thank the visual computing group at IST Austria for their valuable
discussions and feedback. Houdini Education licenses were provided by SideFX software.
This project was funded in part by the European Research Council (ERC Consolidator
Grant 101045083 CoDiNA).
article_number: '241'
article_processing_charge: No
article_type: original
author:
- first_name: Sadashige
full_name: Ishida, Sadashige
id: 6F7C4B96-A8E9-11E9-A7CA-09ECE5697425
last_name: Ishida
orcid: 0000-0002-3121-3100
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
- first_name: Albert
full_name: Chern, Albert
last_name: Chern
citation:
ama: Ishida S, Wojtan C, Chern A. Hidden degrees of freedom in implicit vortex filaments.
ACM Transactions on Graphics. 2022;41(6). doi:10.1145/3550454.3555459
apa: Ishida, S., Wojtan, C., & Chern, A. (2022). Hidden degrees of freedom in
implicit vortex filaments. ACM Transactions on Graphics. Association for
Computing Machinery. https://doi.org/10.1145/3550454.3555459
chicago: Ishida, Sadashige, Chris Wojtan, and Albert Chern. “Hidden Degrees of Freedom
in Implicit Vortex Filaments.” ACM Transactions on Graphics. Association
for Computing Machinery, 2022. https://doi.org/10.1145/3550454.3555459.
ieee: S. Ishida, C. Wojtan, and A. Chern, “Hidden degrees of freedom in implicit
vortex filaments,” ACM Transactions on Graphics, vol. 41, no. 6. Association
for Computing Machinery, 2022.
ista: Ishida S, Wojtan C, Chern A. 2022. Hidden degrees of freedom in implicit vortex
filaments. ACM Transactions on Graphics. 41(6), 241.
mla: Ishida, Sadashige, et al. “Hidden Degrees of Freedom in Implicit Vortex Filaments.”
ACM Transactions on Graphics, vol. 41, no. 6, 241, Association for Computing
Machinery, 2022, doi:10.1145/3550454.3555459.
short: S. Ishida, C. Wojtan, A. Chern, ACM Transactions on Graphics 41 (2022).
date_created: 2023-01-29T23:00:59Z
date_published: 2022-12-01T00:00:00Z
date_updated: 2026-04-07T12:02:23Z
day: '01'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/3550454.3555459
external_id:
isi:
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file:
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creator: dernst
date_created: 2023-01-30T07:15:48Z
date_updated: 2023-01-30T07:15:48Z
file_id: '12433'
file_name: 2022_ACM_Ishida.pdf
file_size: 15551202
relation: main_file
success: 1
file_date_updated: 2023-01-30T07:15:48Z
has_accepted_license: '1'
intvolume: ' 41'
isi: 1
issue: '6'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 34bc2376-11ca-11ed-8bc3-9a3b3961a088
grant_number: '101045083'
name: Computational Discovery of Numerical Algorithms for Animation and Simulation
of Natural Phenomena
publication: ACM Transactions on Graphics
publication_identifier:
eissn:
- 1557-7368
issn:
- 0730-0301
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
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- id: '20551'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Hidden degrees of freedom in implicit vortex filaments
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 41
year: '2022'
...
---
_id: '11775'
abstract:
- lang: eng
text: 'Quantitative monitoring can be universal and approximate: For every finite
sequence of observations, the specification provides a value and the monitor outputs
a best-effort approximation of it. The quality of the approximation may depend
on the resources that are available to the monitor. By taking to the limit the
sequences of specification values and monitor outputs, we obtain precision-resource
trade-offs also for limit monitoring. This paper provides a formal framework for
studying such trade-offs using an abstract interpretation for monitors: For each
natural number n, the aggregate semantics of a monitor at time n is an equivalence
relation over all sequences of at most n observations so that two equivalent sequences
are indistinguishable to the monitor and thus mapped to the same output. This
abstract interpretation of quantitative monitors allows us to measure the number
of equivalence classes (or “resource use”) that is necessary for a certain precision
up to a certain time, or at any time. Our framework offers several insights. For
example, we identify a family of specifications for which any resource-optimal
exact limit monitor is independent of any error permitted over finite traces.
Moreover, we present a specification for which any resource-optimal approximate
limit monitor does not minimize its resource use at any time. '
acknowledgement: We thank the anonymous reviewers for their helpful comments. This
work was supported in part by the ERC-2020-AdG 101020093.
alternative_title:
- LNCS
article_processing_charge: Yes
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Nicolas Adrien
full_name: Mazzocchi, Nicolas Adrien
id: b26baa86-3308-11ec-87b0-8990f34baa85
last_name: Mazzocchi
- first_name: Naci E
full_name: Sarac, Naci E
id: 8C6B42F8-C8E6-11E9-A03A-F2DCE5697425
last_name: Sarac
citation:
ama: 'Henzinger TA, Mazzocchi NA, Sarac NE. Abstract monitors for quantitative specifications.
In: 22nd International Conference on Runtime Verification. Vol 13498. Springer
Nature; 2022:200-220. doi:10.1007/978-3-031-17196-3_11'
apa: 'Henzinger, T. A., Mazzocchi, N. A., & Sarac, N. E. (2022). Abstract monitors
for quantitative specifications. In 22nd International Conference on Runtime
Verification (Vol. 13498, pp. 200–220). Tbilisi, Georgia: Springer Nature.
https://doi.org/10.1007/978-3-031-17196-3_11'
chicago: Henzinger, Thomas A, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Abstract
Monitors for Quantitative Specifications.” In 22nd International Conference
on Runtime Verification, 13498:200–220. Springer Nature, 2022. https://doi.org/10.1007/978-3-031-17196-3_11.
ieee: T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “Abstract monitors for
quantitative specifications,” in 22nd International Conference on Runtime Verification,
Tbilisi, Georgia, 2022, vol. 13498, pp. 200–220.
ista: 'Henzinger TA, Mazzocchi NA, Sarac NE. 2022. Abstract monitors for quantitative
specifications. 22nd International Conference on Runtime Verification. RV: Runtime
Verification, LNCS, vol. 13498, 200–220.'
mla: Henzinger, Thomas A., et al. “Abstract Monitors for Quantitative Specifications.”
22nd International Conference on Runtime Verification, vol. 13498, Springer
Nature, 2022, pp. 200–20, doi:10.1007/978-3-031-17196-3_11.
short: T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, in:, 22nd International Conference
on Runtime Verification, Springer Nature, 2022, pp. 200–220.
conference:
end_date: 2022-09-30
location: Tbilisi, Georgia
name: 'RV: Runtime Verification'
start_date: 2022-09-28
corr_author: '1'
date_created: 2022-08-08T17:09:09Z
date_published: 2022-09-23T00:00:00Z
date_updated: 2026-04-07T12:02:56Z
day: '23'
ddc:
- '000'
department:
- _id: GradSch
- _id: ToHe
doi: 10.1007/978-3-031-17196-3_11
ec_funded: 1
external_id:
isi:
- '000866539700011'
file:
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checksum: 05c7dcfbb9053a98f46441fb2eccb213
content_type: application/pdf
creator: dernst
date_created: 2023-01-20T07:34:50Z
date_updated: 2023-01-20T07:34:50Z
file_id: '12317'
file_name: 2022_LNCS_RV_Henzinger.pdf
file_size: 477110
relation: main_file
success: 1
file_date_updated: 2023-01-20T07:34:50Z
has_accepted_license: '1'
intvolume: ' 13498'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 200-220
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: 22nd International Conference on Runtime Verification
publication_identifier:
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
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- id: '20147'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Abstract monitors for quantitative specifications
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 13498
year: '2022'
...
---
_id: '12065'
abstract:
- lang: eng
text: Capacity, rate performance, and cycle life of aprotic Li–O2 batteries critically
depend on reversible electrodeposition of Li2O2. Current understanding states
surface-adsorbed versus solvated LiO2 controls Li2O2 growth as surface film or
as large particles. Herein, we show that Li2O2 forms across a wide range of electrolytes,
carbons, and current densities as particles via solution-mediated LiO2 disproportionation,
bringing into question the prevalence of any surface growth under practical conditions.
We describe a unified O2 reduction mechanism, which can explain all found capacity
relations and Li2O2 morphologies with exclusive solution discharge. Determining
particle morphology and achievable capacities are species mobilities, true areal
rate, and the degree of LiO2 association in solution. Capacity is conclusively
limited by mass transport through the tortuous Li2O2 rather than electron transport
through a passivating Li2O2 film. Provided that species mobilities and surface
growth are high, high capacities are also achieved with weakly solvating electrolytes,
which were previously considered prototypical for low capacity via surface growth.
acknowledged_ssus:
- _id: EM-Fac
- _id: M-Shop
acknowledgement: S.A.F. and C.P. are indebted to the European Research Council (ERC)
under the European Union’s Horizon 2020 research and innovation program (Grant Agreement
No. 636069). This project has received funding from the European Union’s Horizon
2020 research and innovation program under the Marie Skłodowska-Curie Grant NanoEvolution,
Grant Agreement No. 894042. S.A.F. and S.M. are indebted to Institute of Science
and Technology Austria (ISTA) for support. This research was supported by the Scientific
Service Units of ISTA through resources provided by the Electron Microscopy Facility
and the Miba Machine Shop. C.P. thanks Vanessa Wood (ETH Zürich) for her continuing
support.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Christian
full_name: Prehal, Christian
last_name: Prehal
- first_name: Soumyadip
full_name: Mondal, Soumyadip
id: d25d21ef-dc8d-11ea-abe3-ec4576307f48
last_name: Mondal
- first_name: Ludek
full_name: Lovicar, Ludek
id: 36DB3A20-F248-11E8-B48F-1D18A9856A87
last_name: Lovicar
orcid: 0000-0001-6206-4200
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
citation:
ama: Prehal C, Mondal S, Lovicar L, Freunberger SA. Exclusive solution discharge
in Li-O₂ batteries? ACS Energy Letters. 2022;7(9):3112-3119. doi:10.1021/acsenergylett.2c01711
apa: Prehal, C., Mondal, S., Lovicar, L., & Freunberger, S. A. (2022). Exclusive
solution discharge in Li-O₂ batteries? ACS Energy Letters. American Chemical
Society. https://doi.org/10.1021/acsenergylett.2c01711
chicago: Prehal, Christian, Soumyadip Mondal, Ludek Lovicar, and Stefan Alexander
Freunberger. “Exclusive Solution Discharge in Li-O₂ Batteries?” ACS Energy
Letters. American Chemical Society, 2022. https://doi.org/10.1021/acsenergylett.2c01711.
ieee: C. Prehal, S. Mondal, L. Lovicar, and S. A. Freunberger, “Exclusive solution
discharge in Li-O₂ batteries?,” ACS Energy Letters, vol. 7, no. 9. American
Chemical Society, pp. 3112–3119, 2022.
ista: Prehal C, Mondal S, Lovicar L, Freunberger SA. 2022. Exclusive solution discharge
in Li-O₂ batteries? ACS Energy Letters. 7(9), 3112–3119.
mla: Prehal, Christian, et al. “Exclusive Solution Discharge in Li-O₂ Batteries?”
ACS Energy Letters, vol. 7, no. 9, American Chemical Society, 2022, pp.
3112–19, doi:10.1021/acsenergylett.2c01711.
short: C. Prehal, S. Mondal, L. Lovicar, S.A. Freunberger, ACS Energy Letters 7
(2022) 3112–3119.
corr_author: '1'
date_created: 2022-09-08T09:51:09Z
date_published: 2022-08-29T00:00:00Z
date_updated: 2026-04-07T12:27:23Z
day: '29'
ddc:
- '540'
department:
- _id: StFr
- _id: EM-Fac
doi: 10.1021/acsenergylett.2c01711
external_id:
isi:
- '000860787000001'
pmid:
- '36120663'
file:
- access_level: open_access
checksum: cf0bed3a2535c11d27244cd029dbc1d0
content_type: application/pdf
creator: dernst
date_created: 2023-01-20T08:43:51Z
date_updated: 2023-01-20T08:43:51Z
file_id: '12319'
file_name: 2022_ACSEnergyLetters_Prehal.pdf
file_size: 3827583
relation: main_file
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file_date_updated: 2023-01-20T08:43:51Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
issue: '9'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 3112-3119
pmid: 1
publication: ACS Energy Letters
publication_identifier:
eissn:
- 2380-8195
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
related_material:
record:
- id: '20607'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Exclusive solution discharge in Li-O₂ batteries?
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: 7
year: '2022'
...
---
_id: '9311'
abstract:
- lang: eng
text: 'Partially observable Markov decision processes (POMDPs) are standard models
for dynamic systems with probabilistic and nondeterministic behaviour in uncertain
environments. We prove that in POMDPs with long-run average objective, the decision
maker has approximately optimal strategies with finite memory. This implies notably
that approximating the long-run value is recursively enumerable, as well as a
weak continuity property of the value with respect to the transition function. '
acknowledgement: "Partially supported by Austrian Science Fund (FWF) NFN Grant No
RiSE/SHiNE S11407, by CONICYT Chile through grant PII 20150140, and by ECOS-CONICYT
through grant C15E03.\r\n"
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Raimundo J
full_name: Saona Urmeneta, Raimundo J
id: BD1DF4C4-D767-11E9-B658-BC13E6697425
last_name: Saona Urmeneta
orcid: 0000-0001-5103-038X
- first_name: Bruno
full_name: Ziliotto, Bruno
last_name: Ziliotto
citation:
ama: Chatterjee K, Saona Urmeneta RJ, Ziliotto B. Finite-memory strategies in POMDPs
with long-run average objectives. Mathematics of Operations Research. 2022;47(1):100-119.
doi:10.1287/moor.2020.1116
apa: Chatterjee, K., Saona Urmeneta, R. J., & Ziliotto, B. (2022). Finite-memory
strategies in POMDPs with long-run average objectives. Mathematics of Operations
Research. Institute for Operations Research and the Management Sciences. https://doi.org/10.1287/moor.2020.1116
chicago: Chatterjee, Krishnendu, Raimundo J Saona Urmeneta, and Bruno Ziliotto.
“Finite-Memory Strategies in POMDPs with Long-Run Average Objectives.” Mathematics
of Operations Research. Institute for Operations Research and the Management
Sciences, 2022. https://doi.org/10.1287/moor.2020.1116.
ieee: K. Chatterjee, R. J. Saona Urmeneta, and B. Ziliotto, “Finite-memory strategies
in POMDPs with long-run average objectives,” Mathematics of Operations Research,
vol. 47, no. 1. Institute for Operations Research and the Management Sciences,
pp. 100–119, 2022.
ista: Chatterjee K, Saona Urmeneta RJ, Ziliotto B. 2022. Finite-memory strategies
in POMDPs with long-run average objectives. Mathematics of Operations Research.
47(1), 100–119.
mla: Chatterjee, Krishnendu, et al. “Finite-Memory Strategies in POMDPs with Long-Run
Average Objectives.” Mathematics of Operations Research, vol. 47, no. 1,
Institute for Operations Research and the Management Sciences, 2022, pp. 100–19,
doi:10.1287/moor.2020.1116.
short: K. Chatterjee, R.J. Saona Urmeneta, B. Ziliotto, Mathematics of Operations
Research 47 (2022) 100–119.
date_created: 2021-04-08T09:33:31Z
date_published: 2022-02-01T00:00:00Z
date_updated: 2026-04-07T12:31:21Z
day: '01'
department:
- _id: GradSch
- _id: KrCh
doi: 10.1287/moor.2020.1116
external_id:
arxiv:
- '1904.13360'
isi:
- '000731918100001'
intvolume: ' 47'
isi: 1
issue: '1'
keyword:
- Management Science and Operations Research
- General Mathematics
- Computer Science Applications
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1904.13360
month: '02'
oa: 1
oa_version: Preprint
page: 100-119
project:
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
publication: Mathematics of Operations Research
publication_identifier:
eissn:
- 1526-5471
issn:
- 0364-765X
publication_status: published
publisher: Institute for Operations Research and the Management Sciences
quality_controlled: '1'
related_material:
record:
- id: '20234'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Finite-memory strategies in POMDPs with long-run average objectives
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 47
year: '2022'
...