---
_id: '12702'
abstract:
- lang: eng
text: Hydrocarbon mixtures are extremely abundant in the Universe, and diamond formation
from them can play a crucial role in shaping the interior structure and evolution
of planets. With first-principles accuracy, we first estimate the melting line
of diamond, and then reveal the nature of chemical bonding in hydrocarbons at
extreme conditions. We finally establish the pressure-temperature phase boundary
where it is thermodynamically possible for diamond to form from hydrocarbon mixtures
with different atomic fractions of carbon. Notably, here we show a depletion zone
at pressures above 200 GPa and temperatures below 3000 K-3500 K where diamond
formation is thermodynamically favorable regardless of the carbon atomic fraction,
due to a phase separation mechanism. The cooler condition of the interior of Neptune
compared to Uranus means that the former is much more likely to contain the depletion
zone. Our findings can help explain the dichotomy of the two ice giants manifested
by the low luminosity of Uranus, and lead to a better understanding of (exo-)planetary
formation and evolution.
acknowledgement: BC thanks Daan Frenkel for stimulating discussions. We thank Aleks
Reinhardt, Daan Frenkel, Marius Millot, Federica Coppari, Rhys Bunting, and Chris
J. Pickard for critically reading the manuscript and providing useful suggestions.
BC acknowledges resources provided by the Cambridge Tier-2 system operated by the
University of Cambridge Research Computing Service funded by EPSRC Tier-2 capital
grant EP/P020259/1. SH acknowledges support from LDRD 19-ERD-031 and computing support
from the Lawrence Livermore National Laboratory (LLNL) Institutional Computing Grand
Challenge program. Lawrence Livermore National Laboratory is operated by Lawrence
Livermore National Security, LLC, for the U.S. Department of Energy, National Nuclear
Security Administration under Contract DE-AC52-07NA27344. MB acknowledges support
by the European Horizon 2020 program within the Marie Skłodowska-Curie actions (xICE
grant number 894725), funding from the NOMIS foundation and computational resources
at the North-German Supercomputing Alliance (HLRN) facilities.
article_number: '1104'
article_processing_charge: No
article_type: original
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Sebastien
full_name: Hamel, Sebastien
last_name: Hamel
- first_name: Mandy
full_name: Bethkenhagen, Mandy
id: 201939f4-803f-11ed-ab7e-d8da4bd1517f
last_name: Bethkenhagen
orcid: 0000-0002-1838-2129
citation:
ama: Cheng B, Hamel S, Bethkenhagen M. Thermodynamics of diamond formation from
hydrocarbon mixtures in planets. Nature Communications. 2023;14. doi:10.1038/s41467-023-36841-1
apa: Cheng, B., Hamel, S., & Bethkenhagen, M. (2023). Thermodynamics of diamond
formation from hydrocarbon mixtures in planets. Nature Communications.
Springer Nature. https://doi.org/10.1038/s41467-023-36841-1
chicago: Cheng, Bingqing, Sebastien Hamel, and Mandy Bethkenhagen. “Thermodynamics
of Diamond Formation from Hydrocarbon Mixtures in Planets.” Nature Communications.
Springer Nature, 2023. https://doi.org/10.1038/s41467-023-36841-1.
ieee: B. Cheng, S. Hamel, and M. Bethkenhagen, “Thermodynamics of diamond formation
from hydrocarbon mixtures in planets,” Nature Communications, vol. 14.
Springer Nature, 2023.
ista: Cheng B, Hamel S, Bethkenhagen M. 2023. Thermodynamics of diamond formation
from hydrocarbon mixtures in planets. Nature Communications. 14, 1104.
mla: Cheng, Bingqing, et al. “Thermodynamics of Diamond Formation from Hydrocarbon
Mixtures in Planets.” Nature Communications, vol. 14, 1104, Springer Nature,
2023, doi:10.1038/s41467-023-36841-1.
short: B. Cheng, S. Hamel, M. Bethkenhagen, Nature Communications 14 (2023).
date_created: 2023-03-05T23:01:04Z
date_published: 2023-02-27T00:00:00Z
date_updated: 2023-08-01T13:36:11Z
day: '27'
ddc:
- '540'
department:
- _id: BiCh
doi: 10.1038/s41467-023-36841-1
external_id:
isi:
- '000939678300002'
pmid:
- '36843123'
file:
- access_level: open_access
checksum: 5ff61ad21511950c15abb73b18613883
content_type: application/pdf
creator: cchlebak
date_created: 2023-03-07T10:58:00Z
date_updated: 2023-03-07T10:58:00Z
file_id: '12713'
file_name: 2023_NatComm_Cheng.pdf
file_size: 1946443
relation: main_file
success: 1
file_date_updated: 2023-03-07T10:58:00Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 9B861AAC-BA93-11EA-9121-9846C619BF3A
name: NOMIS Fellowship Program
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Thermodynamics of diamond formation from hydrocarbon mixtures in planets
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: 14
year: '2023'
...
---
_id: '12719'
abstract:
- lang: eng
text: "Background\r\nEpigenetic clocks can track both chronological age (cAge) and
biological age (bAge). The latter is typically defined by physiological biomarkers
and risk of adverse health outcomes, including all-cause mortality. As cohort
sample sizes increase, estimates of cAge and bAge become more precise. Here, we
aim to develop accurate epigenetic predictors of cAge and bAge, whilst improving
our understanding of their epigenomic architecture.\r\n\r\nMethods\r\nFirst, we
perform large-scale (N = 18,413) epigenome-wide association studies (EWAS) of
chronological age and all-cause mortality. Next, to create a cAge predictor, we
use methylation data from 24,674 participants from the Generation Scotland study,
the Lothian Birth Cohorts (LBC) of 1921 and 1936, and 8 other cohorts with publicly
available data. In addition, we train a predictor of time to all-cause mortality
as a proxy for bAge using the Generation Scotland cohort (1214 observed deaths).
For this purpose, we use epigenetic surrogates (EpiScores) for 109 plasma proteins
and the 8 component parts of GrimAge, one of the current best epigenetic predictors
of survival. We test this bAge predictor in four external cohorts (LBC1921, LBC1936,
the Framingham Heart Study and the Women’s Health Initiative study).\r\n\r\nResults\r\nThrough
the inclusion of linear and non-linear age-CpG associations from the EWAS, feature
pre-selection in advance of elastic net regression, and a leave-one-cohort-out
(LOCO) cross-validation framework, we obtain cAge prediction with a median absolute
error equal to 2.3 years. Our bAge predictor was found to slightly outperform
GrimAge in terms of the strength of its association to survival (HRGrimAge = 1.47
[1.40, 1.54] with p = 1.08 × 10−52, and HRbAge = 1.52 [1.44, 1.59] with p = 2.20 × 10−60).
Finally, we introduce MethylBrowsR, an online tool to visualise epigenome-wide
CpG-age associations.\r\n\r\nConclusions\r\nThe integration of multiple large
datasets, EpiScores, non-linear DNAm effects, and new approaches to feature selection
has facilitated improvements to the blood-based epigenetic prediction of biological
and chronological age."
acknowledgement: We are grateful to all the families who took part, the general practitioners,
and the Scottish School of Primary Care for their help in recruiting them and the
whole GS team that includes interviewers, computer and laboratory technicians, clerical
workers, research scientists, volunteers, managers, receptionists, healthcare assistants,
and nurses.
article_number: '12'
article_processing_charge: No
article_type: original
author:
- first_name: Elena
full_name: Bernabeu, Elena
last_name: Bernabeu
- first_name: Daniel L.
full_name: Mccartney, Daniel L.
last_name: Mccartney
- first_name: Danni A.
full_name: Gadd, Danni A.
last_name: Gadd
- first_name: Robert F.
full_name: Hillary, Robert F.
last_name: Hillary
- first_name: Ake T.
full_name: Lu, Ake T.
last_name: Lu
- first_name: Lee
full_name: Murphy, Lee
last_name: Murphy
- first_name: Nicola
full_name: Wrobel, Nicola
last_name: Wrobel
- first_name: Archie
full_name: Campbell, Archie
last_name: Campbell
- first_name: Sarah E.
full_name: Harris, Sarah E.
last_name: Harris
- first_name: David
full_name: Liewald, David
last_name: Liewald
- first_name: Caroline
full_name: Hayward, Caroline
last_name: Hayward
- first_name: Cathie
full_name: Sudlow, Cathie
last_name: Sudlow
- first_name: Simon R.
full_name: Cox, Simon R.
last_name: Cox
- first_name: Kathryn L.
full_name: Evans, Kathryn L.
last_name: Evans
- first_name: Steve
full_name: Horvath, Steve
last_name: Horvath
- first_name: Andrew M.
full_name: Mcintosh, Andrew M.
last_name: Mcintosh
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: Catalina A.
full_name: Vallejos, Catalina A.
last_name: Vallejos
- first_name: Riccardo E.
full_name: Marioni, Riccardo E.
last_name: Marioni
citation:
ama: Bernabeu E, Mccartney DL, Gadd DA, et al. Refining epigenetic prediction of
chronological and biological age. Genome Medicine. 2023;15. doi:10.1186/s13073-023-01161-y
apa: Bernabeu, E., Mccartney, D. L., Gadd, D. A., Hillary, R. F., Lu, A. T., Murphy,
L., … Marioni, R. E. (2023). Refining epigenetic prediction of chronological and
biological age. Genome Medicine. Springer Nature. https://doi.org/10.1186/s13073-023-01161-y
chicago: Bernabeu, Elena, Daniel L. Mccartney, Danni A. Gadd, Robert F. Hillary,
Ake T. Lu, Lee Murphy, Nicola Wrobel, et al. “Refining Epigenetic Prediction of
Chronological and Biological Age.” Genome Medicine. Springer Nature, 2023.
https://doi.org/10.1186/s13073-023-01161-y.
ieee: E. Bernabeu et al., “Refining epigenetic prediction of chronological
and biological age,” Genome Medicine, vol. 15. Springer Nature, 2023.
ista: Bernabeu E, Mccartney DL, Gadd DA, Hillary RF, Lu AT, Murphy L, Wrobel N,
Campbell A, Harris SE, Liewald D, Hayward C, Sudlow C, Cox SR, Evans KL, Horvath
S, Mcintosh AM, Robinson MR, Vallejos CA, Marioni RE. 2023. Refining epigenetic
prediction of chronological and biological age. Genome Medicine. 15, 12.
mla: Bernabeu, Elena, et al. “Refining Epigenetic Prediction of Chronological and
Biological Age.” Genome Medicine, vol. 15, 12, Springer Nature, 2023, doi:10.1186/s13073-023-01161-y.
short: E. Bernabeu, D.L. Mccartney, D.A. Gadd, R.F. Hillary, A.T. Lu, L. Murphy,
N. Wrobel, A. Campbell, S.E. Harris, D. Liewald, C. Hayward, C. Sudlow, S.R. Cox,
K.L. Evans, S. Horvath, A.M. Mcintosh, M.R. Robinson, C.A. Vallejos, R.E. Marioni,
Genome Medicine 15 (2023).
date_created: 2023-03-12T23:01:02Z
date_published: 2023-02-28T00:00:00Z
date_updated: 2023-08-01T13:38:12Z
day: '28'
ddc:
- '570'
department:
- _id: MaRo
doi: 10.1186/s13073-023-01161-y
external_id:
isi:
- '000940286600001'
file:
- access_level: open_access
checksum: 833b837910c4db42fb5f0f34125f77a7
content_type: application/pdf
creator: cchlebak
date_created: 2023-03-14T10:29:47Z
date_updated: 2023-03-14T10:29:47Z
file_id: '12722'
file_name: 2023_GenomeMed_Bernabeu.pdf
file_size: 4275987
relation: main_file
success: 1
file_date_updated: 2023-03-14T10:29:47Z
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
publication: Genome Medicine
publication_identifier:
eissn:
- 1756-994X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Refining epigenetic prediction of chronological and biological age
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: 15
year: '2023'
...
---
_id: '12704'
abstract:
- lang: eng
text: Adversarial training (i.e., training on adversarially perturbed input data)
is a well-studied method for making neural networks robust to potential adversarial
attacks during inference. However, the improved robustness does not come for free
but rather is accompanied by a decrease in overall model accuracy and performance.
Recent work has shown that, in practical robot learning applications, the effects
of adversarial training do not pose a fair trade-off but inflict a net loss when
measured in holistic robot performance. This work revisits the robustness-accuracy
trade-off in robot learning by systematically analyzing if recent advances in
robust training methods and theory in conjunction with adversarial robot learning,
are capable of making adversarial training suitable for real-world robot applications.
We evaluate three different robot learning tasks ranging from autonomous driving
in a high-fidelity environment amenable to sim-to-real deployment to mobile robot
navigation and gesture recognition. Our results demonstrate that, while these
techniques make incremental improvements on the trade-off on a relative scale,
the negative impact on the nominal accuracy caused by adversarial training still
outweighs the improved robustness by an order of magnitude. We conclude that although
progress is happening, further advances in robust learning methods are necessary
before they can benefit robot learning tasks in practice.
acknowledgement: "We thank Christoph Lampert for inspiring this work. The\r\nviews
and conclusions contained in this document are those of\r\nthe authors and should
not be interpreted as representing the\r\nofficial policies, either expressed or
implied, of the United States\r\nAir Force or the U.S. Government. The U.S. Government
is\r\nauthorized to reproduce and distribute reprints for Government\r\npurposes
notwithstanding any copyright notation herein."
article_processing_charge: No
article_type: original
author:
- first_name: Mathias
full_name: Lechner, Mathias
id: 3DC22916-F248-11E8-B48F-1D18A9856A87
last_name: Lechner
- first_name: Alexander
full_name: Amini, Alexander
last_name: Amini
- first_name: Daniela
full_name: Rus, Daniela
last_name: Rus
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
citation:
ama: Lechner M, Amini A, Rus D, Henzinger TA. Revisiting the adversarial robustness-accuracy
tradeoff in robot learning. IEEE Robotics and Automation Letters. 2023;8(3):1595-1602.
doi:10.1109/LRA.2023.3240930
apa: Lechner, M., Amini, A., Rus, D., & Henzinger, T. A. (2023). Revisiting
the adversarial robustness-accuracy tradeoff in robot learning. IEEE Robotics
and Automation Letters. Institute of Electrical and Electronics Engineers.
https://doi.org/10.1109/LRA.2023.3240930
chicago: Lechner, Mathias, Alexander Amini, Daniela Rus, and Thomas A Henzinger.
“Revisiting the Adversarial Robustness-Accuracy Tradeoff in Robot Learning.” IEEE
Robotics and Automation Letters. Institute of Electrical and Electronics Engineers,
2023. https://doi.org/10.1109/LRA.2023.3240930.
ieee: M. Lechner, A. Amini, D. Rus, and T. A. Henzinger, “Revisiting the adversarial
robustness-accuracy tradeoff in robot learning,” IEEE Robotics and Automation
Letters, vol. 8, no. 3. Institute of Electrical and Electronics Engineers,
pp. 1595–1602, 2023.
ista: Lechner M, Amini A, Rus D, Henzinger TA. 2023. Revisiting the adversarial
robustness-accuracy tradeoff in robot learning. IEEE Robotics and Automation Letters.
8(3), 1595–1602.
mla: Lechner, Mathias, et al. “Revisiting the Adversarial Robustness-Accuracy Tradeoff
in Robot Learning.” IEEE Robotics and Automation Letters, vol. 8, no. 3,
Institute of Electrical and Electronics Engineers, 2023, pp. 1595–602, doi:10.1109/LRA.2023.3240930.
short: M. Lechner, A. Amini, D. Rus, T.A. Henzinger, IEEE Robotics and Automation
Letters 8 (2023) 1595–1602.
date_created: 2023-03-05T23:01:04Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2023-08-01T13:36:50Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1109/LRA.2023.3240930
external_id:
arxiv:
- '2204.07373'
isi:
- '000936534100012'
file:
- access_level: open_access
checksum: 5a75dcd326ea66685de2b1aaec259e85
content_type: application/pdf
creator: cchlebak
date_created: 2023-03-07T12:22:23Z
date_updated: 2023-03-07T12:22:23Z
file_id: '12714'
file_name: 2023_IEEERobAutLetters_Lechner.pdf
file_size: 944052
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success: 1
file_date_updated: 2023-03-07T12:22:23Z
has_accepted_license: '1'
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isi: 1
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- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 1595-1602
publication: IEEE Robotics and Automation Letters
publication_identifier:
eissn:
- 2377-3766
publication_status: published
publisher: Institute of Electrical and Electronics Engineers
quality_controlled: '1'
related_material:
record:
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relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Revisiting the adversarial robustness-accuracy tradeoff in robot learning
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: 8
year: '2023'
...
---
_id: '12737'
abstract:
- lang: eng
text: The substitution of heavier, more metallic atoms into classical organic ligand
frameworks provides an important strategy for tuning ligand properties, such as
ligand bite and donor character, and is the basis for the emerging area of main-group
supramolecular chemistry. In this paper, we explore two new ligands [E(2-Me-8-qy)3]
[E = Sb (1), Bi (2); qy = quinolyl], allowing a fundamental comparison of their
coordination behavior with classical tris(2-pyridyl) ligands of the type [E′(2-py)3]
(E = a range of bridgehead atoms and groups, py = pyridyl). A range of new coordination
modes to Cu+, Ag+, and Au+ is seen for 1 and 2, in the absence of steric constraints
at the bridgehead and with their more remote N-donor atoms. A particular feature
is the adaptive nature of these new ligands, with the ability to adjust coordination
mode in response to the hard–soft character of coordinated metal ions, influenced
also by the character of the bridgehead atom (Sb or Bi). These features can be
seen in a comparison between [Cu2{Sb(2-Me-8-qy)3}2](PF6)2 (1·CuPF6) and [Cu{Bi(2-Me-8-qy)3}](PF6)
(2·CuPF6), the first containing a dimeric cation in which 1 adopts an unprecedented
intramolecular N,N,Sb-coordination mode while in the second, 2 adopts an unusual
N,N,(π-)C coordination mode. In contrast, the previously reported analogous ligands
[E(6-Me-2-py)3] (E = Sb, Bi; 2-py = 2-pyridyl) show a tris-chelating mode in their
complexes with CuPF6, which is typical for the extensive tris(2-pyridyl) family
with a range of metals. The greater polarity of the Bi–C bond in 2 results in
ligand transfer reactions with Au(I). Although this reactivity is not in itself
unusual, the characterization of several products by single-crystal X-ray diffraction
provides snapshots of the ligand transfer reaction involved, with one of the products
(the bimetallic complex [(BiCl){ClAu2(2-Me-8-qy)3}] (8)) containing a Au2Bi core
in which the shortest Au → Bi donor–acceptor bond to date is observed.
acknowledgement: The authors thank the Walters-Kundert Studentship of Selwyn College
(scholarship for J.E.W.), the Leverhulme Trust (R.G.-R. and D.S.W., grant RPG-2017-146),
the Australian Research Council (A.L.C., DE200100450), the Spanish Ministry of Science
and Innovation (MCI) and the Spanish Ministry of Science, Innovation and Universities
(MCIU) (R.G.-R., PID2021-124691NB-I00, funded by MCIN/AEI/10.13039/501100011033/FEDER,
UE and PGC2018-096880-A-I00, MCIU/AEI/FEDER), The University of Valladolid and Santander
Bank (Fellowship for A.G.-R.), and the U.K. EPSRC and The Royal Dutch Shell plc.
(I-Case award for R.B.J., EP/R511870/1) for financial support. Calculations were
carried out on an in-house Odyssey HPC cluster (Cambridge), and the authors are
grateful for the calculation time used.
article_processing_charge: No
article_type: original
author:
- first_name: Álvaro
full_name: García-Romero, Álvaro
last_name: García-Romero
- first_name: Jessica E.
full_name: Waters, Jessica E.
last_name: Waters
- first_name: Rajesh B
full_name: Jethwa, Rajesh B
id: 4cc538d5-803f-11ed-ab7e-8139573aad8f
last_name: Jethwa
orcid: 0000-0002-0404-4356
- first_name: Andrew D.
full_name: Bond, Andrew D.
last_name: Bond
- first_name: Annie L.
full_name: Colebatch, Annie L.
last_name: Colebatch
- first_name: Raúl
full_name: García-Rodríguez, Raúl
last_name: García-Rodríguez
- first_name: Dominic S.
full_name: Wright, Dominic S.
last_name: Wright
citation:
ama: García-Romero Á, Waters JE, Jethwa RB, et al. Highly adaptive nature of group
15 tris(quinolyl) ligands─studies with coinage metals. Inorganic Chemistry.
2023;62(11):4625-4636. doi:10.1021/acs.inorgchem.3c00057
apa: García-Romero, Á., Waters, J. E., Jethwa, R. B., Bond, A. D., Colebatch, A.
L., García-Rodríguez, R., & Wright, D. S. (2023). Highly adaptive nature of
group 15 tris(quinolyl) ligands─studies with coinage metals. Inorganic Chemistry.
American Chemical Society. https://doi.org/10.1021/acs.inorgchem.3c00057
chicago: García-Romero, Álvaro, Jessica E. Waters, Rajesh B Jethwa, Andrew D. Bond,
Annie L. Colebatch, Raúl García-Rodríguez, and Dominic S. Wright. “Highly Adaptive
Nature of Group 15 Tris(Quinolyl) Ligands─studies with Coinage Metals.” Inorganic
Chemistry. American Chemical Society, 2023. https://doi.org/10.1021/acs.inorgchem.3c00057.
ieee: Á. García-Romero et al., “Highly adaptive nature of group 15 tris(quinolyl)
ligands─studies with coinage metals,” Inorganic Chemistry, vol. 62, no.
11. American Chemical Society, pp. 4625–4636, 2023.
ista: García-Romero Á, Waters JE, Jethwa RB, Bond AD, Colebatch AL, García-Rodríguez
R, Wright DS. 2023. Highly adaptive nature of group 15 tris(quinolyl) ligands─studies
with coinage metals. Inorganic Chemistry. 62(11), 4625–4636.
mla: García-Romero, Álvaro, et al. “Highly Adaptive Nature of Group 15 Tris(Quinolyl)
Ligands─studies with Coinage Metals.” Inorganic Chemistry, vol. 62, no.
11, American Chemical Society, 2023, pp. 4625–36, doi:10.1021/acs.inorgchem.3c00057.
short: Á. García-Romero, J.E. Waters, R.B. Jethwa, A.D. Bond, A.L. Colebatch, R.
García-Rodríguez, D.S. Wright, Inorganic Chemistry 62 (2023) 4625–4636.
date_created: 2023-03-19T23:00:59Z
date_published: 2023-03-08T00:00:00Z
date_updated: 2023-08-01T13:42:59Z
day: '08'
department:
- _id: StFr
doi: 10.1021/acs.inorgchem.3c00057
external_id:
isi:
- '000956110300001'
pmid:
- '36883367'
intvolume: ' 62'
isi: 1
issue: '11'
language:
- iso: eng
month: '03'
oa_version: None
page: 4625-4636
pmid: 1
publication: Inorganic Chemistry
publication_identifier:
eissn:
- 1520-510X
issn:
- 0020-1669
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage
metals
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 62
year: '2023'
...
---
_id: '12723'
abstract:
- lang: eng
text: 'Lead halide perovskites enjoy a number of remarkable optoelectronic properties.
To explain their origin, it is necessary to study how electromagnetic fields interact
with these systems. We address this problem here by studying two classical quantities:
Faraday rotation and the complex refractive index in a paradigmatic perovskite
CH3NH3PbBr3 in a broad wavelength range. We find that the minimal coupling of
electromagnetic fields to the k⋅p Hamiltonian is insufficient to describe the
observed data even on the qualitative level. To amend this, we demonstrate that
there exists a relevant atomic-level coupling between electromagnetic fields and
the spin degree of freedom. This spin-electric coupling allows for quantitative
description of a number of previous as well as present experimental data. In particular,
we use it here to show that the Faraday effect in lead halide perovskites is dominated
by the Zeeman splitting of the energy levels and has a substantial beyond-Becquerel
contribution. Finally, we present general symmetry-based phenomenological arguments
that in the low-energy limit our effective model includes all basis coupling terms
to the electromagnetic field in the linear order.'
article_number: '106901'
article_processing_charge: No
article_type: original
author:
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
- first_name: Abhishek
full_name: Shiva Kumar, Abhishek
id: 5e9a6931-eb97-11eb-a6c2-e96f7058d77a
last_name: Shiva Kumar
- first_name: Dusan
full_name: Lorenc, Dusan
id: 40D8A3E6-F248-11E8-B48F-1D18A9856A87
last_name: Lorenc
- first_name: Younes
full_name: Ashourishokri, Younes
id: e32c111f-f6e0-11ea-865d-eb955baea334
last_name: Ashourishokri
- first_name: Ayan A.
full_name: Zhumekenov, Ayan A.
last_name: Zhumekenov
- first_name: Osman M.
full_name: Bakr, Osman M.
last_name: Bakr
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Zhanybek
full_name: Alpichshev, Zhanybek
id: 45E67A2A-F248-11E8-B48F-1D18A9856A87
last_name: Alpichshev
orcid: 0000-0002-7183-5203
citation:
ama: Volosniev A, Shiva Kumar A, Lorenc D, et al. Spin-electric coupling in lead
halide perovskites. Physical Review Letters. 2023;130(10). doi:10.1103/physrevlett.130.106901
apa: Volosniev, A., Shiva Kumar, A., Lorenc, D., Ashourishokri, Y., Zhumekenov,
A. A., Bakr, O. M., … Alpichshev, Z. (2023). Spin-electric coupling in lead halide
perovskites. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.130.106901
chicago: Volosniev, Artem, Abhishek Shiva Kumar, Dusan Lorenc, Younes Ashourishokri,
Ayan A. Zhumekenov, Osman M. Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev.
“Spin-Electric Coupling in Lead Halide Perovskites.” Physical Review Letters.
American Physical Society, 2023. https://doi.org/10.1103/physrevlett.130.106901.
ieee: A. Volosniev et al., “Spin-electric coupling in lead halide perovskites,”
Physical Review Letters, vol. 130, no. 10. American Physical Society, 2023.
ista: Volosniev A, Shiva Kumar A, Lorenc D, Ashourishokri Y, Zhumekenov AA, Bakr
OM, Lemeshko M, Alpichshev Z. 2023. Spin-electric coupling in lead halide perovskites.
Physical Review Letters. 130(10), 106901.
mla: Volosniev, Artem, et al. “Spin-Electric Coupling in Lead Halide Perovskites.”
Physical Review Letters, vol. 130, no. 10, 106901, American Physical Society,
2023, doi:10.1103/physrevlett.130.106901.
short: A. Volosniev, A. Shiva Kumar, D. Lorenc, Y. Ashourishokri, A.A. Zhumekenov,
O.M. Bakr, M. Lemeshko, Z. Alpichshev, Physical Review Letters 130 (2023).
date_created: 2023-03-14T13:11:59Z
date_published: 2023-03-10T00:00:00Z
date_updated: 2023-08-01T13:39:04Z
day: '10'
department:
- _id: GradSch
- _id: ZhAl
- _id: MiLe
doi: 10.1103/physrevlett.130.106901
external_id:
arxiv:
- '2203.09443'
isi:
- '000982435900002'
intvolume: ' 130'
isi: 1
issue: '10'
keyword:
- General Physics and Astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2203.09443
month: '03'
oa: 1
oa_version: Preprint
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Spin-electric coupling in lead halide perovskites
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 130
year: '2023'
...
---
_id: '12724'
abstract:
- lang: eng
text: 'We use general symmetry-based arguments to construct an effective model suitable
for studying optical properties of lead halide perovskites. To build the model,
we identify an atomic-level interaction between electromagnetic fields and the
spin degree of freedom that should be added to a minimally coupled k⋅p Hamiltonian.
As a first application, we study two basic optical characteristics of the material:
the Verdet constant and the refractive index. Beyond these linear characteristics
of the material, the model is suitable for calculating nonlinear effects such
as the third-order optical susceptibility. Analysis of this quantity shows that
the geometrical properties of the spin-electric term imply isotropic optical response
of the system, and that optical anisotropy of lead halide perovskites is a manifestation
of hopping of charge carriers. To illustrate this, we discuss third-harmonic generation.'
article_number: '125201'
article_processing_charge: No
article_type: original
author:
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
- first_name: Abhishek
full_name: Shiva Kumar, Abhishek
id: 5e9a6931-eb97-11eb-a6c2-e96f7058d77a
last_name: Shiva Kumar
- first_name: Dusan
full_name: Lorenc, Dusan
id: 40D8A3E6-F248-11E8-B48F-1D18A9856A87
last_name: Lorenc
- first_name: Younes
full_name: Ashourishokri, Younes
id: e32c111f-f6e0-11ea-865d-eb955baea334
last_name: Ashourishokri
- first_name: Ayan
full_name: Zhumekenov, Ayan
last_name: Zhumekenov
- first_name: Osman M.
full_name: Bakr, Osman M.
last_name: Bakr
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Zhanybek
full_name: Alpichshev, Zhanybek
id: 45E67A2A-F248-11E8-B48F-1D18A9856A87
last_name: Alpichshev
orcid: 0000-0002-7183-5203
citation:
ama: Volosniev A, Shiva Kumar A, Lorenc D, et al. Effective model for studying optical
properties of lead halide perovskites. Physical Review B. 2023;107(12).
doi:10.1103/physrevb.107.125201
apa: Volosniev, A., Shiva Kumar, A., Lorenc, D., Ashourishokri, Y., Zhumekenov,
A., Bakr, O. M., … Alpichshev, Z. (2023). Effective model for studying optical
properties of lead halide perovskites. Physical Review B. American Physical
Society. https://doi.org/10.1103/physrevb.107.125201
chicago: Volosniev, Artem, Abhishek Shiva Kumar, Dusan Lorenc, Younes Ashourishokri,
Ayan Zhumekenov, Osman M. Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev. “Effective
Model for Studying Optical Properties of Lead Halide Perovskites.” Physical
Review B. American Physical Society, 2023. https://doi.org/10.1103/physrevb.107.125201.
ieee: A. Volosniev et al., “Effective model for studying optical properties
of lead halide perovskites,” Physical Review B, vol. 107, no. 12. American
Physical Society, 2023.
ista: Volosniev A, Shiva Kumar A, Lorenc D, Ashourishokri Y, Zhumekenov A, Bakr
OM, Lemeshko M, Alpichshev Z. 2023. Effective model for studying optical properties
of lead halide perovskites. Physical Review B. 107(12), 125201.
mla: Volosniev, Artem, et al. “Effective Model for Studying Optical Properties of
Lead Halide Perovskites.” Physical Review B, vol. 107, no. 12, 125201,
American Physical Society, 2023, doi:10.1103/physrevb.107.125201.
short: A. Volosniev, A. Shiva Kumar, D. Lorenc, Y. Ashourishokri, A. Zhumekenov,
O.M. Bakr, M. Lemeshko, Z. Alpichshev, Physical Review B 107 (2023).
date_created: 2023-03-14T13:13:05Z
date_published: 2023-03-15T00:00:00Z
date_updated: 2023-08-01T13:39:47Z
day: '15'
department:
- _id: GradSch
- _id: ZhAl
- _id: MiLe
doi: 10.1103/physrevb.107.125201
external_id:
arxiv:
- '2204.04022'
isi:
- '000972602200006'
intvolume: ' 107'
isi: 1
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2204.04022
month: '03'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Effective model for studying optical properties of lead halide perovskites
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 107
year: '2023'
...
---
_id: '12759'
abstract:
- lang: eng
text: Stereological methods for estimating the 3D particle size and density from
2D projections are essential to many research fields. These methods are, however,
prone to errors arising from undetected particle profiles due to sectioning and
limited resolution, known as ‘lost caps’. A potential solution developed by Keiding,
Jensen, and Ranek in 1972, which we refer to as the Keiding model, accounts for
lost caps by quantifying the smallest detectable profile in terms of its limiting
‘cap angle’ (ϕ), a size-independent measure of a particle’s distance from the
section surface. However, this simple solution has not been widely adopted nor
tested. Rather, model-independent design-based stereological methods, which do
not explicitly account for lost caps, have come to the fore. Here, we provide
the first experimental validation of the Keiding model by comparing the size and
density of particles estimated from 2D projections with direct measurement from
3D EM reconstructions of the same tissue. We applied the Keiding model to estimate
the size and density of somata, nuclei and vesicles in the cerebellum of mice
and rats, where high packing density can be problematic for design-based methods.
Our analysis reveals a Gaussian distribution for ϕ rather than a single value.
Nevertheless, curve fits of the Keiding model to the 2D diameter distribution
accurately estimate the mean ϕ and 3D diameter distribution. While systematic
testing using simulations revealed an upper limit to determining ϕ, our analysis
shows that estimated ϕ can be used to determine the 3D particle density from the
2D density under a wide range of conditions, and this method is potentially more
accurate than minimum-size-based lost-cap corrections and disector methods. Our
results show the Keiding model provides an efficient means of accurately estimating
the size and density of particles from 2D projections even under conditions of
a high density.
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: "We thank the IST Austria Electron Microscopy Facility for technical
support, and Diccon Coyle, Andrea Lőrincz and Zoltan Nusser for their helpful comments
and discussions.\r\nFunding for JSR and RAS was from the Wellcome Trust (203048;
224499; https://\r\nwellcome.org/). RAS is in receipt of a Wellcome Trust Principal
Research Fellowship (224499).\r\nFunding for CBM and PJ was from Fond zur Förderung
der Wissenschaftlichen Forschung (V\r\n739-B27 Elise-Richter Programme to CBM, Z
312-B27 Wittgenstein Award to PJ; \r\nhttps://www.fwf.ac.at). PJ received funding
from the European Research Council (ERC; https://erc.europa.eu) under the European
Union’s Horizon 2020 research and innovation programme (grant agreement no. 692692).
NH was supported by a European\r\nResearch Council Advanced Grant (ERC-AG787157)."
article_number: e0277148
article_processing_charge: No
article_type: original
author:
- first_name: Jason Seth
full_name: Rothman, Jason Seth
last_name: Rothman
- first_name: Carolina
full_name: Borges Merjane, Carolina
id: 4305C450-F248-11E8-B48F-1D18A9856A87
last_name: Borges Merjane
orcid: 0000-0003-0005-401X
- first_name: Noemi
full_name: Holderith, Noemi
last_name: Holderith
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: R.
full_name: Angus Silver, R.
last_name: Angus Silver
citation:
ama: Rothman JS, Borges Merjane C, Holderith N, Jonas PM, Angus Silver R. Validation
of a stereological method for estimating particle size and density from 2D projections
with high accuracy. PLoS ONE. 2023;18(3 March). doi:10.1371/journal.pone.0277148
apa: Rothman, J. S., Borges Merjane, C., Holderith, N., Jonas, P. M., & Angus
Silver, R. (2023). Validation of a stereological method for estimating particle
size and density from 2D projections with high accuracy. PLoS ONE. Public
Library of Science. https://doi.org/10.1371/journal.pone.0277148
chicago: Rothman, Jason Seth, Carolina Borges Merjane, Noemi Holderith, Peter M
Jonas, and R. Angus Silver. “Validation of a Stereological Method for Estimating
Particle Size and Density from 2D Projections with High Accuracy.” PLoS ONE.
Public Library of Science, 2023. https://doi.org/10.1371/journal.pone.0277148.
ieee: J. S. Rothman, C. Borges Merjane, N. Holderith, P. M. Jonas, and R. Angus
Silver, “Validation of a stereological method for estimating particle size and
density from 2D projections with high accuracy,” PLoS ONE, vol. 18, no.
3 March. Public Library of Science, 2023.
ista: Rothman JS, Borges Merjane C, Holderith N, Jonas PM, Angus Silver R. 2023.
Validation of a stereological method for estimating particle size and density
from 2D projections with high accuracy. PLoS ONE. 18(3 March), e0277148.
mla: Rothman, Jason Seth, et al. “Validation of a Stereological Method for Estimating
Particle Size and Density from 2D Projections with High Accuracy.” PLoS ONE,
vol. 18, no. 3 March, e0277148, Public Library of Science, 2023, doi:10.1371/journal.pone.0277148.
short: J.S. Rothman, C. Borges Merjane, N. Holderith, P.M. Jonas, R. Angus Silver,
PLoS ONE 18 (2023).
date_created: 2023-03-26T22:01:07Z
date_published: 2023-03-17T00:00:00Z
date_updated: 2023-08-01T13:46:39Z
day: '17'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1371/journal.pone.0277148
ec_funded: 1
external_id:
isi:
- '001024737400001'
file:
- access_level: open_access
checksum: 2380331ec27cc87808826fc64419ac1c
content_type: application/pdf
creator: dernst
date_created: 2023-03-27T06:51:09Z
date_updated: 2023-03-27T06:51:09Z
file_id: '12770'
file_name: 2023_PLoSOne_Rothman.pdf
file_size: 7290413
relation: main_file
success: 1
file_date_updated: 2023-03-27T06:51:09Z
has_accepted_license: '1'
intvolume: ' 18'
isi: 1
issue: 3 March
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glumatergic synapse
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: The Wittgenstein Prize
- _id: 2696E7FE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: V00739
name: Structural plasticity at mossy fiber-CA3 synapses
publication: PLoS ONE
publication_identifier:
eissn:
- 1932-6203
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Validation of a stereological method for estimating particle size and density
from 2D projections with high accuracy
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: 18
year: '2023'
...
---
_id: '12756'
abstract:
- lang: eng
text: ESCRT-III family proteins form composite polymers that deform and cut membrane
tubes in the context of a wide range of cell biological processes across the tree
of life. In reconstituted systems, sequential changes in the composition of ESCRT-III
polymers induced by the AAA–adenosine triphosphatase Vps4 have been shown to remodel
membranes. However, it is not known how composite ESCRT-III polymers are organized
and remodeled in space and time in a cellular context. Taking advantage of the
relative simplicity of the ESCRT-III–dependent division system in Sulfolobus acidocaldarius,
one of the closest experimentally tractable prokaryotic relatives of eukaryotes,
we use super-resolution microscopy, electron microscopy, and computational modeling
to show how CdvB/CdvB1/CdvB2 proteins form a precisely patterned composite ESCRT-III
division ring, which undergoes stepwise Vps4-dependent disassembly and contracts
to cut cells into two. These observations lead us to suggest sequential changes
in a patterned composite polymer as a general mechanism of ESCRT-III–dependent
membrane remodeling.
acknowledgement: "We thank Y. Liu and V. Hale for help with electron cryotomography;
the Medical Research Council (MRC) LMB Electron Microscopy Facility for access,
training, and support; and T. Darling and J. Grimmett at the MRC LMB for help with
computing infrastructure. We also thank the Flow Cytometry Facility and the MRC
LMB for training and support.\r\n F.H. and G.T.-R. were supported by a grant from
the Wellcome Trust (203276/Z/16/Z). A.C. was supported by an EMBO long-term fellowship:
ALTF_1041-2021. J.T. was supported by a grant from the VW Foundation (94933). A.A.P.
was supported by the Wellcome Trust (203276/Z/16/Z) and the HFSP (LT001027/2019).
B.B. received support from the MRC LMB, the Wellcome Trust (203276/Z/16/Z), the
VW Foundation (94933), the Life Sciences–Moore-Simons Foundation (735929LPI), and
a Gordon and Betty Moore Foundation’s Symbiosis in Aquatic Systems Initiative (9346).
A.Š. and X.J. acknowledge funding from the European Research Council (ERC) under
the European Union’s Horizon 2020 research and innovation programme (grant no. 802960).
L.H.-K. acknowledges support from Biotechnology and Biological Sciences Research
Council LIDo Programme. T.N. and J.L. were supported by the MRC (U105184326) and
the Wellcome Trust (203276/Z/16/Z)."
article_number: eade5224
article_processing_charge: No
article_type: original
author:
- first_name: Fredrik
full_name: Hurtig, Fredrik
last_name: Hurtig
- first_name: Thomas C.Q.
full_name: Burgers, Thomas C.Q.
last_name: Burgers
- first_name: Alice
full_name: Cezanne, Alice
last_name: Cezanne
- first_name: Xiuyun
full_name: Jiang, Xiuyun
last_name: Jiang
- first_name: Frank N.
full_name: Mol, Frank N.
last_name: Mol
- first_name: Jovan
full_name: Traparić, Jovan
last_name: Traparić
- first_name: Andre Arashiro
full_name: Pulschen, Andre Arashiro
last_name: Pulschen
- first_name: Tim
full_name: Nierhaus, Tim
last_name: Nierhaus
- first_name: Gabriel
full_name: Tarrason-Risa, Gabriel
last_name: Tarrason-Risa
- first_name: Lena
full_name: Harker-Kirschneck, Lena
last_name: Harker-Kirschneck
- first_name: Jan
full_name: Löwe, Jan
last_name: Löwe
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Rifka
full_name: Vlijm, Rifka
last_name: Vlijm
- first_name: Buzz
full_name: Baum, Buzz
last_name: Baum
citation:
ama: Hurtig F, Burgers TCQ, Cezanne A, et al. The patterned assembly and stepwise
Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell
division. Science Advances. 2023;9(11). doi:10.1126/sciadv.ade5224
apa: Hurtig, F., Burgers, T. C. Q., Cezanne, A., Jiang, X., Mol, F. N., Traparić,
J., … Baum, B. (2023). The patterned assembly and stepwise Vps4-mediated disassembly
of composite ESCRT-III polymers drives archaeal cell division. Science Advances.
American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.ade5224
chicago: Hurtig, Fredrik, Thomas C.Q. Burgers, Alice Cezanne, Xiuyun Jiang, Frank
N. Mol, Jovan Traparić, Andre Arashiro Pulschen, et al. “The Patterned Assembly
and Stepwise Vps4-Mediated Disassembly of Composite ESCRT-III Polymers Drives
Archaeal Cell Division.” Science Advances. American Association for the
Advancement of Science, 2023. https://doi.org/10.1126/sciadv.ade5224.
ieee: F. Hurtig et al., “The patterned assembly and stepwise Vps4-mediated
disassembly of composite ESCRT-III polymers drives archaeal cell division,” Science
Advances, vol. 9, no. 11. American Association for the Advancement of Science,
2023.
ista: Hurtig F, Burgers TCQ, Cezanne A, Jiang X, Mol FN, Traparić J, Pulschen AA,
Nierhaus T, Tarrason-Risa G, Harker-Kirschneck L, Löwe J, Šarić A, Vlijm R, Baum
B. 2023. The patterned assembly and stepwise Vps4-mediated disassembly of composite
ESCRT-III polymers drives archaeal cell division. Science Advances. 9(11), eade5224.
mla: Hurtig, Fredrik, et al. “The Patterned Assembly and Stepwise Vps4-Mediated
Disassembly of Composite ESCRT-III Polymers Drives Archaeal Cell Division.” Science
Advances, vol. 9, no. 11, eade5224, American Association for the Advancement
of Science, 2023, doi:10.1126/sciadv.ade5224.
short: F. Hurtig, T.C.Q. Burgers, A. Cezanne, X. Jiang, F.N. Mol, J. Traparić, A.A.
Pulschen, T. Nierhaus, G. Tarrason-Risa, L. Harker-Kirschneck, J. Löwe, A. Šarić,
R. Vlijm, B. Baum, Science Advances 9 (2023).
date_created: 2023-03-26T22:01:06Z
date_published: 2023-03-17T00:00:00Z
date_updated: 2023-08-01T13:45:54Z
day: '17'
ddc:
- '570'
department:
- _id: AnSa
doi: 10.1126/sciadv.ade5224
ec_funded: 1
external_id:
isi:
- '000968083500010'
file:
- access_level: open_access
checksum: 6d7dbe9ed86a116c8a002d62971202c5
content_type: application/pdf
creator: dernst
date_created: 2023-03-27T06:24:49Z
date_updated: 2023-03-27T06:24:49Z
file_id: '12768'
file_name: 2023_ScienceAdvances_Hurtig.pdf
file_size: 1826471
relation: main_file
success: 1
file_date_updated: 2023-03-27T06:24:49Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '11'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: eba2549b-77a9-11ec-83b8-a81e493eae4e
call_identifier: H2020
grant_number: '802960'
name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines'
publication: Science Advances
publication_identifier:
eissn:
- 2375-2548
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: The patterned assembly and stepwise Vps4-mediated disassembly of composite
ESCRT-III polymers drives archaeal cell division
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 9
year: '2023'
...
---
_id: '12758'
abstract:
- lang: eng
text: AlphaFold changed the field of structural biology by achieving three-dimensional
(3D) structure prediction from protein sequence at experimental quality. The astounding
success even led to claims that the protein folding problem is “solved”. However,
protein folding problem is more than just structure prediction from sequence.
Presently, it is unknown if the AlphaFold-triggered revolution could help to solve
other problems related to protein folding. Here we assay the ability of AlphaFold
to predict the impact of single mutations on protein stability (ΔΔG) and function.
To study the question we extracted the pLDDT and metrics from AlphaFold
predictions before and after single mutation in a protein and correlated the predicted
change with the experimentally known ΔΔG values. Additionally, we correlated the
same AlphaFold pLDDT metrics with the impact of a single mutation on structure
using a large scale dataset of single mutations in GFP with the experimentally
assayed levels of fluorescence. We found a very weak or no correlation between
AlphaFold output metrics and change of protein stability or fluorescence. Our
results imply that AlphaFold may not be immediately applied to other problems
or applications in protein folding.
acknowledgement: The authors acknowledge the use of Zhores supercomputer [28] for
obtaining the results presented in this paper.The authors thank Zimin Foundation
and Petrovax for support of the presented study at the School of Molecular and Theoretical
Biology 2021.
article_number: e0282689
article_processing_charge: No
article_type: original
author:
- first_name: Marina A.
full_name: Pak, Marina A.
last_name: Pak
- first_name: Karina A.
full_name: Markhieva, Karina A.
last_name: Markhieva
- first_name: Mariia S.
full_name: Novikova, Mariia S.
last_name: Novikova
- first_name: Dmitry S.
full_name: Petrov, Dmitry S.
last_name: Petrov
- first_name: Ilya S.
full_name: Vorobyev, Ilya S.
last_name: Vorobyev
- first_name: Ekaterina
full_name: Maksimova, Ekaterina
id: 2FBE0DE4-F248-11E8-B48F-1D18A9856A87
last_name: Maksimova
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Dmitry N.
full_name: Ivankov, Dmitry N.
last_name: Ivankov
citation:
ama: Pak MA, Markhieva KA, Novikova MS, et al. Using AlphaFold to predict the impact
of single mutations on protein stability and function. PLoS ONE. 2023;18(3).
doi:10.1371/journal.pone.0282689
apa: Pak, M. A., Markhieva, K. A., Novikova, M. S., Petrov, D. S., Vorobyev, I.
S., Maksimova, E., … Ivankov, D. N. (2023). Using AlphaFold to predict the impact
of single mutations on protein stability and function. PLoS ONE. Public
Library of Science. https://doi.org/10.1371/journal.pone.0282689
chicago: Pak, Marina A., Karina A. Markhieva, Mariia S. Novikova, Dmitry S. Petrov,
Ilya S. Vorobyev, Ekaterina Maksimova, Fyodor Kondrashov, and Dmitry N. Ivankov.
“Using AlphaFold to Predict the Impact of Single Mutations on Protein Stability
and Function.” PLoS ONE. Public Library of Science, 2023. https://doi.org/10.1371/journal.pone.0282689.
ieee: M. A. Pak et al., “Using AlphaFold to predict the impact of single
mutations on protein stability and function,” PLoS ONE, vol. 18, no. 3.
Public Library of Science, 2023.
ista: Pak MA, Markhieva KA, Novikova MS, Petrov DS, Vorobyev IS, Maksimova E, Kondrashov
F, Ivankov DN. 2023. Using AlphaFold to predict the impact of single mutations
on protein stability and function. PLoS ONE. 18(3), e0282689.
mla: Pak, Marina A., et al. “Using AlphaFold to Predict the Impact of Single Mutations
on Protein Stability and Function.” PLoS ONE, vol. 18, no. 3, e0282689,
Public Library of Science, 2023, doi:10.1371/journal.pone.0282689.
short: M.A. Pak, K.A. Markhieva, M.S. Novikova, D.S. Petrov, I.S. Vorobyev, E. Maksimova,
F. Kondrashov, D.N. Ivankov, PLoS ONE 18 (2023).
date_created: 2023-03-26T22:01:07Z
date_published: 2023-03-16T00:00:00Z
date_updated: 2023-08-01T13:47:14Z
day: '16'
ddc:
- '570'
department:
- _id: FyKo
- _id: MaRo
doi: 10.1371/journal.pone.0282689
external_id:
isi:
- '000985134400106'
file:
- access_level: open_access
checksum: 0281bdfccf8d76c4e08dd011c603f6b6
content_type: application/pdf
creator: dernst
date_created: 2023-03-27T07:09:08Z
date_updated: 2023-03-27T07:09:08Z
file_id: '12771'
file_name: 2023_PLoSOne_Pak.pdf
file_size: 856625
relation: main_file
success: 1
file_date_updated: 2023-03-27T07:09:08Z
has_accepted_license: '1'
intvolume: ' 18'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication: PLoS ONE
publication_identifier:
eissn:
- 1932-6203
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Using AlphaFold to predict the impact of single mutations on protein stability
and function
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: 18
year: '2023'
...
---
_id: '12757'
abstract:
- lang: eng
text: My group and myself have studied respiratory complex I for almost 30 years,
starting in 1994 when it was known as a L-shaped giant ‘black box' of bioenergetics.
First breakthrough was the X-ray structure of the peripheral arm, followed by
structures of the membrane arm and finally the entire complex from Thermus thermophilus.
The developments in cryo-EM technology allowed us to solve the first complete
structure of the twice larger, ∼1 MDa mammalian enzyme in 2016. However, the mechanism
coupling, over large distances, the transfer of two electrons to pumping of four
protons across the membrane remained an enigma. Recently we have solved high-resolution
structures of mammalian and bacterial complex I under a range of redox conditions,
including catalytic turnover. This allowed us to propose a robust and universal
mechanism for complex I and related protein families. Redox reactions initially
drive conformational changes around the quinone cavity and a long-distance transfer
of substrate protons. These set up a stage for a series of electrostatically driven
proton transfers along the membrane arm (‘domino effect'), eventually resulting
in proton expulsion from the distal antiporter-like subunit. The mechanism radically
differs from previous suggestions, however, it naturally explains all the unusual
structural features of complex I. In this review I discuss the state of knowledge
on complex I, including the current most controversial issues.
article_processing_charge: No
article_type: review
author:
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: 'Sazanov LA. From the “black box” to “domino effect” mechanism: What have we
learned from the structures of respiratory complex I. The Biochemical Journal.
2023;480(5):319-333. doi:10.1042/BCJ20210285'
apa: 'Sazanov, L. A. (2023). From the “black box” to “domino effect” mechanism:
What have we learned from the structures of respiratory complex I. The Biochemical
Journal. Portland Press. https://doi.org/10.1042/BCJ20210285'
chicago: 'Sazanov, Leonid A. “From the ‘black Box’ to ‘Domino Effect’ Mechanism:
What Have We Learned from the Structures of Respiratory Complex I.” The Biochemical
Journal. Portland Press, 2023. https://doi.org/10.1042/BCJ20210285.'
ieee: 'L. A. Sazanov, “From the ‘black box’ to ‘domino effect’ mechanism: What have
we learned from the structures of respiratory complex I,” The Biochemical Journal,
vol. 480, no. 5. Portland Press, pp. 319–333, 2023.'
ista: 'Sazanov LA. 2023. From the ‘black box’ to ‘domino effect’ mechanism: What
have we learned from the structures of respiratory complex I. The Biochemical
Journal. 480(5), 319–333.'
mla: 'Sazanov, Leonid A. “From the ‘black Box’ to ‘Domino Effect’ Mechanism: What
Have We Learned from the Structures of Respiratory Complex I.” The Biochemical
Journal, vol. 480, no. 5, Portland Press, 2023, pp. 319–33, doi:10.1042/BCJ20210285.'
short: L.A. Sazanov, The Biochemical Journal 480 (2023) 319–333.
date_created: 2023-03-26T22:01:06Z
date_published: 2023-03-15T00:00:00Z
date_updated: 2023-08-01T13:45:12Z
day: '15'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.1042/BCJ20210285
external_id:
isi:
- '000957065700001'
pmid:
- '36920092'
has_accepted_license: '1'
intvolume: ' 480'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1042/BCJ20210285
month: '03'
oa: 1
oa_version: Published Version
page: 319-333
pmid: 1
publication: The Biochemical Journal
publication_identifier:
eissn:
- 1470-8728
issn:
- 0264-6021
publication_status: published
publisher: Portland Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'From the ''black box'' to ''domino effect'' mechanism: What have we learned
from the structures of respiratory complex I'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 480
year: '2023'
...