---
_id: '834'
abstract:
- lang: eng
text: 'Thermal and many-body localized phases are separated by a dynamical phase
transition of a new kind. We analyze the distribution of off-diagonal matrix elements
of local operators across this transition in two different models of disordered
spin chains. We show that the behavior of matrix elements can be used to characterize
the breakdown of thermalization and to extract the many-body Thouless energy.
We find that upon increasing the disorder strength the system enters a critical
region around the many-body localization transition. The properties of the system
in this region are: (i) the Thouless energy becomes smaller than the level spacing,
(ii) the matrix elements show critical dependence on the energy difference, and
(iii) the matrix elements, viewed as amplitudes of a fictitious wave function,
exhibit strong multifractality. This critical region decreases with the system
size, which we interpret as evidence for a diverging correlation length at the
many-body localization transition. Our findings show that the correlation length
becomes larger than the accessible system sizes in a broad range of disorder strength
values and shed light on the critical behavior near the many-body localization
transition.'
acknowledgement: We acknowledge useful discussions with V. Kravtsov, T. Grover,
and R. Vasseur. M.S. was supported by Gordon and Betty Moore Foundation’s EPiQS
Initiative through Grant GBMF4307. M.S. and D.A. acknowledge hospitality of KITP, where parts of
this work were completed (supported in part by the National Science Foundation under
Grant No. NSF PHY11-25915)
article_number: '104201'
article_processing_charge: No
author:
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Papic
full_name: Zlatko, Papic
last_name: Zlatko
- first_name: Dmitry
full_name: Abanin, Dmitry
last_name: Abanin
citation:
ama: Serbyn M, Zlatko P, Abanin D. Thouless energy and multifractality across the
many-body localization transition. Physical Review B - Condensed Matter and
Materials Physics. 2017;96(10). doi:10.1103/PhysRevB.96.104201
apa: Serbyn, M., Zlatko, P., & Abanin, D. (2017). Thouless energy and multifractality
across the many-body localization transition. Physical Review B - Condensed
Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.96.104201
chicago: Serbyn, Maksym, Papic Zlatko, and Dmitry Abanin. “Thouless Energy and Multifractality
across the Many-Body Localization Transition.” Physical Review B - Condensed
Matter and Materials Physics. American Physical Society, 2017. https://doi.org/10.1103/PhysRevB.96.104201.
ieee: M. Serbyn, P. Zlatko, and D. Abanin, “Thouless energy and multifractality
across the many-body localization transition,” Physical Review B - Condensed
Matter and Materials Physics, vol. 96, no. 10. American Physical Society,
2017.
ista: Serbyn M, Zlatko P, Abanin D. 2017. Thouless energy and multifractality across
the many-body localization transition. Physical Review B - Condensed Matter and
Materials Physics. 96(10), 104201.
mla: Serbyn, Maksym, et al. “Thouless Energy and Multifractality across the Many-Body
Localization Transition.” Physical Review B - Condensed Matter and Materials
Physics, vol. 96, no. 10, 104201, American Physical Society, 2017, doi:10.1103/PhysRevB.96.104201.
short: M. Serbyn, P. Zlatko, D. Abanin, Physical Review B - Condensed Matter and
Materials Physics 96 (2017).
date_created: 2018-12-11T11:48:45Z
date_published: 2017-09-06T00:00:00Z
date_updated: 2023-09-26T15:51:54Z
day: '06'
department:
- _id: MaSe
doi: 10.1103/PhysRevB.96.104201
external_id:
isi:
- '000409429300004'
intvolume: ' 96'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1610.02389
month: '09'
oa: 1
oa_version: Submitted Version
publication: Physical Review B - Condensed Matter and Materials Physics
publication_identifier:
issn:
- '24699950'
publication_status: published
publisher: American Physical Society
publist_id: '6814'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Thouless energy and multifractality across the many-body localization transition
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 96
year: '2017'
...
---
_id: '835'
abstract:
- lang: eng
text: An outstanding question in animal development, tissue homeostasis and disease
is how cell populations adapt to sensory inputs. During Drosophila larval development,
hematopoietic sites are in direct contact with sensory neuron clusters of the
peripheral nervous system (PNS), and blood cells (hemocytes) require the PNS for
their survival and recruitment to these microenvironments, known as Hematopoietic
Pockets. Here we report that Activin-β, a TGF-β family ligand, is expressed by
sensory neurons of the PNS and regulates the proliferation and adhesion of hemocytes.
These hemocyte responses depend on PNS activity, as shown by agonist treatment
and transient silencing of sensory neurons. Activin-β has a key role in this regulation,
which is apparent from reporter expression and mutant analyses. This mechanism
of local sensory neurons controlling blood cell adaptation invites evolutionary
parallels with vertebrate hematopoietic progenitors and the independent myeloid
system of tissue macrophages, whose regulation by local microenvironments remain
undefined.
article_number: '15990'
article_processing_charge: No
author:
- first_name: Kalpana
full_name: Makhijani, Kalpana
last_name: Makhijani
- first_name: Brandy
full_name: Alexander, Brandy
last_name: Alexander
- first_name: Deepti
full_name: Rao, Deepti
last_name: Rao
- first_name: Sophia
full_name: Petraki, Sophia
last_name: Petraki
- first_name: Leire
full_name: Herboso, Leire
last_name: Herboso
- first_name: Katelyn
full_name: Kukar, Katelyn
last_name: Kukar
- first_name: Itrat
full_name: Batool, Itrat
last_name: Batool
- first_name: Stephanie
full_name: Wachner, Stephanie
id: 2A95E7B0-F248-11E8-B48F-1D18A9856A87
last_name: Wachner
- first_name: Katrina
full_name: Gold, Katrina
last_name: Gold
- first_name: Corinna
full_name: Wong, Corinna
last_name: Wong
- first_name: Michael
full_name: O'Connor, Michael
last_name: O'Connor
- first_name: Katja
full_name: Brückner, Katja
last_name: Brückner
citation:
ama: Makhijani K, Alexander B, Rao D, et al. Regulation of Drosophila hematopoietic
sites by Activin-β from active sensory neurons. Nature Communications.
2017;8. doi:10.1038/ncomms15990
apa: Makhijani, K., Alexander, B., Rao, D., Petraki, S., Herboso, L., Kukar, K.,
… Brückner, K. (2017). Regulation of Drosophila hematopoietic sites by Activin-β
from active sensory neurons. Nature Communications. Nature Publishing Group.
https://doi.org/10.1038/ncomms15990
chicago: Makhijani, Kalpana, Brandy Alexander, Deepti Rao, Sophia Petraki, Leire
Herboso, Katelyn Kukar, Itrat Batool, et al. “Regulation of Drosophila Hematopoietic
Sites by Activin-β from Active Sensory Neurons.” Nature Communications.
Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms15990.
ieee: K. Makhijani et al., “Regulation of Drosophila hematopoietic sites
by Activin-β from active sensory neurons,” Nature Communications, vol.
8. Nature Publishing Group, 2017.
ista: Makhijani K, Alexander B, Rao D, Petraki S, Herboso L, Kukar K, Batool I,
Wachner S, Gold K, Wong C, O’Connor M, Brückner K. 2017. Regulation of Drosophila
hematopoietic sites by Activin-β from active sensory neurons. Nature Communications.
8, 15990.
mla: Makhijani, Kalpana, et al. “Regulation of Drosophila Hematopoietic Sites by
Activin-β from Active Sensory Neurons.” Nature Communications, vol. 8,
15990, Nature Publishing Group, 2017, doi:10.1038/ncomms15990.
short: K. Makhijani, B. Alexander, D. Rao, S. Petraki, L. Herboso, K. Kukar, I.
Batool, S. Wachner, K. Gold, C. Wong, M. O’Connor, K. Brückner, Nature Communications
8 (2017).
date_created: 2018-12-11T11:48:45Z
date_published: 2017-07-27T00:00:00Z
date_updated: 2023-09-26T15:51:28Z
day: '27'
ddc:
- '570'
- '576'
- '616'
doi: 10.1038/ncomms15990
extern: '1'
external_id:
isi:
- '000406360100001'
file:
- access_level: open_access
checksum: 99a3d63308d4250eda0a35341171f80e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:32Z
date_updated: 2020-07-14T12:48:12Z
file_id: '5153'
file_name: IST-2017-859-v1+1_ncomms15990.pdf
file_size: 3027104
relation: main_file
file_date_updated: 2020-07-14T12:48:12Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
issn:
- '20411723'
publication_status: published
publisher: Nature Publishing Group
publist_id: '6813'
pubrep_id: '859'
quality_controlled: '1'
status: public
title: Regulation of Drosophila hematopoietic sites by Activin-β from active sensory
neurons
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 8
year: '2017'
...
---
_id: '836'
abstract:
- lang: eng
text: Recent research has examined how to study the topological features of a continuous
self-map by means of the persistence of the eigenspaces, for given eigenvalues,
of the endomorphism induced in homology over a field. This raised the question
of how to select dynamically significant eigenvalues. The present paper aims to
answer this question, giving an algorithm that computes the persistence of eigenspaces
for every eigenvalue simultaneously, also expressing said eigenspaces as direct
sums of “finite” and “singular” subspaces.
alternative_title:
- PROMS
article_processing_charge: No
author:
- first_name: Marc
full_name: Ethier, Marc
last_name: Ethier
- first_name: Grzegorz
full_name: Jablonski, Grzegorz
id: 4483EF78-F248-11E8-B48F-1D18A9856A87
last_name: Jablonski
orcid: 0000-0002-3536-9866
- first_name: Marian
full_name: Mrozek, Marian
last_name: Mrozek
citation:
ama: 'Ethier M, Jablonski G, Mrozek M. Finding eigenvalues of self-maps with the
Kronecker canonical form. In: Special Sessions in Applications of Computer
Algebra. Vol 198. Springer; 2017:119-136. doi:10.1007/978-3-319-56932-1_8'
apa: 'Ethier, M., Jablonski, G., & Mrozek, M. (2017). Finding eigenvalues of
self-maps with the Kronecker canonical form. In Special Sessions in Applications
of Computer Algebra (Vol. 198, pp. 119–136). Kalamata, Greece: Springer. https://doi.org/10.1007/978-3-319-56932-1_8'
chicago: Ethier, Marc, Grzegorz Jablonski, and Marian Mrozek. “Finding Eigenvalues
of Self-Maps with the Kronecker Canonical Form.” In Special Sessions in Applications
of Computer Algebra, 198:119–36. Springer, 2017. https://doi.org/10.1007/978-3-319-56932-1_8.
ieee: M. Ethier, G. Jablonski, and M. Mrozek, “Finding eigenvalues of self-maps
with the Kronecker canonical form,” in Special Sessions in Applications of
Computer Algebra, Kalamata, Greece, 2017, vol. 198, pp. 119–136.
ista: 'Ethier M, Jablonski G, Mrozek M. 2017. Finding eigenvalues of self-maps with
the Kronecker canonical form. Special Sessions in Applications of Computer Algebra.
ACA: Applications of Computer Algebra, PROMS, vol. 198, 119–136.'
mla: Ethier, Marc, et al. “Finding Eigenvalues of Self-Maps with the Kronecker Canonical
Form.” Special Sessions in Applications of Computer Algebra, vol. 198,
Springer, 2017, pp. 119–36, doi:10.1007/978-3-319-56932-1_8.
short: M. Ethier, G. Jablonski, M. Mrozek, in:, Special Sessions in Applications
of Computer Algebra, Springer, 2017, pp. 119–136.
conference:
end_date: 2015-07-23
location: Kalamata, Greece
name: 'ACA: Applications of Computer Algebra'
start_date: 2015-07-20
date_created: 2018-12-11T11:48:46Z
date_published: 2017-07-27T00:00:00Z
date_updated: 2023-09-26T15:50:52Z
day: '27'
department:
- _id: HeEd
doi: 10.1007/978-3-319-56932-1_8
ec_funded: 1
external_id:
isi:
- '000434088200008'
intvolume: ' 198'
isi: 1
language:
- iso: eng
month: '07'
oa_version: None
page: 119 - 136
project:
- _id: 255D761E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '318493'
name: Topological Complex Systems
publication: Special Sessions in Applications of Computer Algebra
publication_identifier:
isbn:
- 978-331956930-7
publication_status: published
publisher: Springer
publist_id: '6812'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Finding eigenvalues of self-maps with the Kronecker canonical form
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 198
year: '2017'
...
---
_id: '837'
abstract:
- lang: eng
text: 'The hippocampus is a key brain region for memory and notably for spatial
memory, and is needed for both spatial working and reference memories. Hippocampal
place cells selectively discharge in specific locations of the environment to
form mnemonic represen tations of space. Several behavioral protocols have been
designed to test spatial memory which requires the experimental subject to utilize
working memory and reference memory. However, less is known about how these memory
traces are presented in the hippo campus, especially considering tasks that require
both spatial working and long -term reference memory demand. The aim of my thesis
was to elucidate how spatial working memory, reference memory, and the combination
of both are represented in the hippocampus. In this thesis, using a radial eight
-arm maze, I examined how the combined demand on these memories influenced place
cell assemblies while reference memories were partially updated by changing some
of the reward- arms. This was contrasted with task varian ts requiring working
or reference memories only. Reference memory update led to gradual place field
shifts towards the rewards on the switched arms. Cells developed enhanced firing
in passes between newly -rewarded arms as compared to those containing an unchanged
reward. The working memory task did not show such gradual changes. Place assemblies
on occasions replayed trajectories of the maze; at decision points the next arm
choice was preferentially replayed in tasks needing reference memory while in
the pure working memory task the previously visited arm was replayed. Hence trajectory
replay only reflected the decision of the animal in tasks needing reference memory
update. At the reward locations, in all three tasks outbound trajectories of the
current arm were preferentially replayed, showing the animals’ next path to the
center. At reward locations trajectories were replayed preferentially in reverse
temporal order. Moreover, in the center reverse replay was seen in the working
memory task but in the other tasks forward replay was seen. Hence, the direction
of reactivation was determined by the goal locations so that part of the trajectory
which was closer to the goal was reactivated later in an HSE while places further
away from the goal were reactivated earlier. Altogether my work demonstrated that
reference memory update triggers several levels of reorganization of the hippocampal
cognitive map which are not seen in simpler working memory demand s. Moreover,
hippocampus is likely to be involved in spatial decisions through reactivating
planned trajectories when reference memory recall is required for such a decision. '
acknowledgement: 'I am very grateful for the opportunity I have had as a graduate
student to explore and incredibly interesting branch of neuroscience, and for the
people who made it possible. Firstly, I would like to offer my thanks to my supervisor
Professor Jozsef Csicsvari for his great support, guidance and patience offered
over the years. The door to his office was always open whenever I had questions.
I have learned a lot from him about carefully designing experiments, asking interesting
questions and how to integrate results into a broader picture. I also express my
gratitude to the remarkable post- doc , Dr. Joseph O’Neill. He is a gre at scientific
role model who is always willing to teach , and advice and talk through problems
with his full attention. Many thanks to my wonderful “office mates” over the years
and their support and encouragement, Alice Avernhe, Philipp Schönenberger, Desiree
Dickerson, Karel Blahna, Charlotte Boccara, Igor Gridchyn, Peter Baracskay, Krisztián
Kovács, Dámaris Rangel, Karola Käfer and Federico Stella. They were the ones in
the lab for the many useful discussions about science and for making the laboratory
such a nice and friendly place to work in. A special thank goes to Michael LoBianco
and Jago Wallenschus for wonderful technical support. I would also like to thank
Professor Peter Jonas and Professor David M Bannerman for being my qualifying exam
and thesi s committee members despite their busy schedule. I am also very thankful
to IST Austria for their support all throughout my PhD. '
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Haibing
full_name: Xu, Haibing
id: 310349D0-F248-11E8-B48F-1D18A9856A87
last_name: Xu
citation:
ama: Xu H. Reactivation of the hippocampal cognitive map in goal-directed spatial
tasks. 2017. doi:10.15479/AT:ISTA:th_858
apa: Xu, H. (2017). Reactivation of the hippocampal cognitive map in goal-directed
spatial tasks. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_858
chicago: Xu, Haibing. “Reactivation of the Hippocampal Cognitive Map in Goal-Directed
Spatial Tasks.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_858.
ieee: H. Xu, “Reactivation of the hippocampal cognitive map in goal-directed spatial
tasks,” Institute of Science and Technology Austria, 2017.
ista: Xu H. 2017. Reactivation of the hippocampal cognitive map in goal-directed
spatial tasks. Institute of Science and Technology Austria.
mla: Xu, Haibing. Reactivation of the Hippocampal Cognitive Map in Goal-Directed
Spatial Tasks. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_858.
short: H. Xu, Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial
Tasks, Institute of Science and Technology Austria, 2017.
date_created: 2018-12-11T11:48:46Z
date_published: 2017-08-23T00:00:00Z
date_updated: 2023-09-07T12:06:38Z
day: '23'
ddc:
- '571'
degree_awarded: PhD
department:
- _id: JoCs
doi: 10.15479/AT:ISTA:th_858
file:
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date_created: 2019-04-05T08:59:51Z
date_updated: 2020-07-14T12:48:12Z
file_id: '6213'
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date_updated: 2020-07-14T12:48:12Z
file_id: '6214'
file_name: 2017_Xu_Thesis_IST.pdf
file_size: 11668613
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file_date_updated: 2020-07-14T12:48:12Z
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '93'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6811'
pubrep_id: '858'
related_material:
record:
- id: '5828'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
title: Reactivation of the hippocampal cognitive map in goal-directed spatial tasks
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: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '838'
abstract:
- lang: eng
text: 'In this thesis we discuss the exact security of message authentications codes
HMAC , NMAC , and PMAC . NMAC is a mode of operation which turns a fixed input-length
keyed hash function f into a variable input-length function. A practical single-key
variant of NMAC called HMAC is a very popular and widely deployed message authentication
code (MAC). PMAC is a block-cipher based mode of operation, which also happens
to be the most famous fully parallel MAC. NMAC was introduced by Bellare, Canetti
and Krawczyk Crypto’96, who proved it to be a secure pseudorandom function (PRF),
and thus also a MAC, under two assumptions. Unfortunately, for many instantiations
of HMAC one of them has been found to be wrong. To restore the provable guarantees
for NMAC , Bellare [Crypto’06] showed its security without this assumption. PMAC
was introduced by Black and Rogaway at Eurocrypt 2002. If instantiated with a
pseudorandom permutation over n -bit strings, PMAC constitutes a provably secure
variable input-length PRF. For adversaries making q queries, each of length at
most ` (in n -bit blocks), and of total length σ ≤ q` , the original paper proves
an upper bound on the distinguishing advantage of O ( σ 2 / 2 n ), while the currently
best bound is O ( qσ/ 2 n ). In this work we show that this bound is tight by
giving an attack with advantage Ω( q 2 `/ 2 n ). In the PMAC construction one
initially XORs a mask to every message block, where the mask for the i th block
is computed as τ i := γ i · L , where L is a (secret) random value, and γ i is
the i -th codeword of the Gray code. Our attack applies more generally to any
sequence of γ i ’s which contains a large coset of a subgroup of GF (2 n ). As
for NMAC , our first contribution is a simpler and uniform proof: If f is an ε
-secure PRF (against q queries) and a δ - non-adaptively secure PRF (against q
queries), then NMAC f is an ( ε + `qδ )-secure PRF against q queries of length
at most ` blocks each. We also show that this ε + `qδ bound is basically tight
by constructing an f for which an attack with advantage `qδ exists. Moreover,
we analyze the PRF-security of a modification of NMAC called NI by An and Bellare
that avoids the constant rekeying on multi-block messages in NMAC and allows for
an information-theoretic analysis. We carry out such an analysis, obtaining a
tight `q 2 / 2 c bound for this step, improving over the trivial bound of ` 2
q 2 / 2 c . Finally, we investigate, if the security of PMAC can be further improved
by using τ i ’s that are k -wise independent, for k > 1 (the original has k
= 1). We observe that the security of PMAC will not increase in general if k =
2, and then prove that the security increases to O ( q 2 / 2 n ), if the k = 4.
Due to simple extension attacks, this is the best bound one can hope for, using
any distribution on the masks. Whether k = 3 is already sufficient to get this
level of security is left as an open problem. Keywords: Message authentication
codes, Pseudorandom functions, HMAC, PMAC. '
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Michal
full_name: Rybar, Michal
id: 2B3E3DE8-F248-11E8-B48F-1D18A9856A87
last_name: Rybar
citation:
ama: Rybar M. (The exact security of) Message authentication codes. 2017. doi:10.15479/AT:ISTA:th_828
apa: Rybar, M. (2017). (The exact security of) Message authentication codes.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_828
chicago: Rybar, Michal. “(The Exact Security of) Message Authentication Codes.”
Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_828.
ieee: M. Rybar, “(The exact security of) Message authentication codes,” Institute
of Science and Technology Austria, 2017.
ista: Rybar M. 2017. (The exact security of) Message authentication codes. Institute
of Science and Technology Austria.
mla: Rybar, Michal. (The Exact Security of) Message Authentication Codes.
Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_828.
short: M. Rybar, (The Exact Security of) Message Authentication Codes, Institute
of Science and Technology Austria, 2017.
date_created: 2018-12-11T11:48:46Z
date_published: 2017-06-26T00:00:00Z
date_updated: 2023-09-07T12:02:28Z
day: '26'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: KrPi
doi: 10.15479/AT:ISTA:th_828
file:
- access_level: open_access
checksum: ff8639ec4bded6186f44c7bd3ee26804
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creator: system
date_created: 2018-12-12T10:10:13Z
date_updated: 2020-07-14T12:48:12Z
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file_size: 847400
relation: main_file
- access_level: closed
checksum: 3462101745ce8ad199c2d0f75dae4a7e
content_type: application/zip
creator: dernst
date_created: 2019-04-05T08:24:11Z
date_updated: 2020-07-14T12:48:12Z
file_id: '6202'
file_name: 2017_Thesis_Rybar_source.zip
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file_date_updated: 2020-07-14T12:48:12Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '86'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6810'
pubrep_id: '828'
related_material:
record:
- id: '2082'
relation: part_of_dissertation
status: public
- id: '6196'
relation: part_of_dissertation
status: public
status: public
title: (The exact security of) Message authentication codes
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '839'
abstract:
- lang: eng
text: 'This thesis describes a brittle fracture simulation method for visual effects
applications. Building upon a symmetric Galerkin boundary element method, we first
compute stress intensity factors following the theory of linear elastic fracture
mechanics. We then use these stress intensities to simulate the motion of a propagating
crack front at a significantly higher resolution than the overall deformation
of the breaking object. Allowing for spatial variations of the material''s toughness
during crack propagation produces visually realistic, highly-detailed fracture
surfaces. Furthermore, we introduce approximations for stress intensities and
crack opening displacements, resulting in both practical speed-up and theoretically
superior runtime complexity compared to previous methods. While we choose a quasi-static
approach to fracture mechanics, ignoring dynamic deformations, we also couple
our fracture simulation framework to a standard rigid-body dynamics solver, enabling
visual effects artists to simulate both large scale motion, as well as fracturing
due to collision forces in a combined system. As fractures inside of an object
grow, their geometry must be represented both in the coarse boundary element mesh,
as well as at the desired fine output resolution. Using a boundary element method,
we avoid complicated volumetric meshing operations. Instead we describe a simple
set of surface meshing operations that allow us to progressively add cracks to
the mesh of an object and still re-use all previously computed entries of the
linear boundary element system matrix. On the high resolution level, we opt for
an implicit surface representation. We then describe how to capture fracture surfaces
during crack propagation, as well as separate the individual fragments resulting
from the fracture process, based on this implicit representation. We show results
obtained with our method, either solving the full boundary element system in every
time step, or alternatively using our fast approximations. These results demonstrate
that both of these methods perform well in basic test cases and produce realistic
fracture surfaces. Furthermore we show that our fast approximations substantially
out-perform the standard approach in more demanding scenarios. Finally, these
two methods naturally combine, using the full solution while the problem size
is manageably small and switching to the fast approximations later on. The resulting
hybrid method gives the user a direct way to choose between speed and accuracy
of the simulation. '
acknowledgement: "ERC H2020 programme (grant agreement no. 638176)\r\nFirst of all,
let me thank my committee members, especially my supervisor, Chris\r\nWojtan, for
supporting me throughout my PhD. Obviously, none of this work would\r\nhave been
possible without you.\r\nFurthermore, Thank You to all the people who have contributed
to this work in various\r\nways, in particular Martin Schanz and his group for providing
and supporting the\r\nHyENA boundary element library, as well as Eder Miguel and
Morten Bojsen-Hansen\r\nfor (repeatedly) proof reading and providing valuable suggestions
during the writing\r\nof this thesis.\r\nI would also like to thank Bernd Bickel,
and all the members – past and present – of his\r\nand Chris’ research groups at
IST Austria for always providing honest and insightful\r\nfeedback throughout many
joint group meetings, as well as Christopher Batty, Eitan\r\nGrinspun, and Fang
Da for many insights into boundary element methods during our\r\ncollaboration.\r\nAs
only virtual objects have been harmed in the process of creating this work, I would\r\nlike
to acknowledge the Stanford scanning repository for providing the “Bunny” and\r\n“Armadillo”
models, the AIM@SHAPE repository for “Pierre’s hand, watertight”, and\r\nS. Gainsbourg
for the “Column” via Archive3D.net. Sorry for breaking these models\r\nin many different
ways.\r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: David
full_name: Hahn, David
id: 357A6A66-F248-11E8-B48F-1D18A9856A87
last_name: Hahn
citation:
ama: Hahn D. Brittle fracture simulation with boundary elements for computer graphics.
2017. doi:10.15479/AT:ISTA:th_855
apa: Hahn, D. (2017). Brittle fracture simulation with boundary elements for
computer graphics. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_855
chicago: Hahn, David. “Brittle Fracture Simulation with Boundary Elements for Computer
Graphics.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_855.
ieee: D. Hahn, “Brittle fracture simulation with boundary elements for computer
graphics,” Institute of Science and Technology Austria, 2017.
ista: Hahn D. 2017. Brittle fracture simulation with boundary elements for computer
graphics. Institute of Science and Technology Austria.
mla: Hahn, David. Brittle Fracture Simulation with Boundary Elements for Computer
Graphics. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_855.
short: D. Hahn, Brittle Fracture Simulation with Boundary Elements for Computer
Graphics, Institute of Science and Technology Austria, 2017.
date_created: 2018-12-11T11:48:47Z
date_published: 2017-08-14T00:00:00Z
date_updated: 2024-02-21T13:48:02Z
day: '14'
ddc:
- '004'
- '005'
- '006'
- '531'
- '621'
degree_awarded: PhD
department:
- _id: ChWo
doi: 10.15479/AT:ISTA:th_855
ec_funded: 1
file:
- access_level: open_access
checksum: 6c1ae8c90bfaba5e089417fefbc4a272
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:46Z
date_updated: 2020-07-14T12:48:13Z
file_id: '5100'
file_name: IST-2017-855-v1+1_thesis_online_pdfA.pdf
file_size: 14596191
relation: main_file
- access_level: closed
checksum: 421672f68d563b029869c5cf1713f919
content_type: application/zip
creator: dernst
date_created: 2019-04-05T08:40:30Z
date_updated: 2020-07-14T12:48:13Z
file_id: '6207'
file_name: 2017_thesis_Hahn_source.zip
file_size: 15060566
relation: source_file
file_date_updated: 2020-07-14T12:48:13Z
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '124'
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: Efficient Simulation of Natural Phenomena at Extremely Large Scales
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6809'
pubrep_id: '855'
related_material:
record:
- id: '1362'
relation: part_of_dissertation
status: public
- id: '1633'
relation: part_of_dissertation
status: public
- id: '5568'
relation: popular_science
status: public
status: public
supervisor:
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
title: Brittle fracture simulation with boundary elements for computer graphics
tmp:
image: /images/cc_by_sa.png
legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode
name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC
BY-SA 4.0)
short: CC BY-SA (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '84'
abstract:
- lang: eng
text: The advent of high-throughput technologies and the concurrent advances in
information sciences have led to a data revolution in biology. This revolution
is most significant in molecular biology, with an increase in the number and scale
of the “omics” projects over the last decade. Genomics projects, for example,
have produced impressive advances in our knowledge of the information concealed
into genomes, from the many genes that encode for the proteins that are responsible
for most if not all cellular functions, to the noncoding regions that are now
known to provide regulatory functions. Proteomics initiatives help to decipher
the role of post-translation modifications on the protein structures and provide
maps of protein-protein interactions, while functional genomics is the field that
attempts to make use of the data produced by these projects to understand protein
functions. The biggest challenge today is to assimilate the wealth of information
provided by these initiatives into a conceptual framework that will help us decipher
life. For example, the current views of the relationship between protein structure
and function remain fragmented. We know of their sequences, more and more about
their structures, we have information on their biological activities, but we have
difficulties connecting this dotted line into an informed whole. We lack the experimental
and computational tools for directly studying protein structure, function, and
dynamics at the molecular and supra-molecular levels. In this chapter, we review
some of the current developments in building the computational tools that are
needed, focusing on the role that geometry and topology play in these efforts.
One of our goals is to raise the general awareness about the importance of geometric
methods in elucidating the mysterious foundations of our very existence. Another
goal is the broadening of what we consider a geometric algorithm. There is plenty
of valuable no-man’s-land between combinatorial and numerical algorithms, and
it seems opportune to explore this land with a computational-geometric frame of
mind.
article_processing_charge: No
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Patrice
full_name: Koehl, Patrice
last_name: Koehl
citation:
ama: 'Edelsbrunner H, Koehl P. Computational topology for structural molecular biology.
In: Toth C, O’Rourke J, Goodman J, eds. Handbook of Discrete and Computational
Geometry, Third Edition. Handbook of Discrete and Computational Geometry.
Taylor & Francis; 2017:1709-1735. doi:10.1201/9781315119601'
apa: Edelsbrunner, H., & Koehl, P. (2017). Computational topology for structural
molecular biology. In C. Toth, J. O’Rourke, & J. Goodman (Eds.), Handbook
of Discrete and Computational Geometry, Third Edition (pp. 1709–1735). Taylor
& Francis. https://doi.org/10.1201/9781315119601
chicago: Edelsbrunner, Herbert, and Patrice Koehl. “Computational Topology for Structural
Molecular Biology.” In Handbook of Discrete and Computational Geometry, Third
Edition, edited by Csaba Toth, Joseph O’Rourke, and Jacob Goodman, 1709–35.
Handbook of Discrete and Computational Geometry. Taylor & Francis, 2017. https://doi.org/10.1201/9781315119601.
ieee: H. Edelsbrunner and P. Koehl, “Computational topology for structural molecular
biology,” in Handbook of Discrete and Computational Geometry, Third Edition,
C. Toth, J. O’Rourke, and J. Goodman, Eds. Taylor & Francis, 2017, pp. 1709–1735.
ista: 'Edelsbrunner H, Koehl P. 2017.Computational topology for structural molecular
biology. In: Handbook of Discrete and Computational Geometry, Third Edition. ,
1709–1735.'
mla: Edelsbrunner, Herbert, and Patrice Koehl. “Computational Topology for Structural
Molecular Biology.” Handbook of Discrete and Computational Geometry, Third
Edition, edited by Csaba Toth et al., Taylor & Francis, 2017, pp. 1709–35,
doi:10.1201/9781315119601.
short: H. Edelsbrunner, P. Koehl, in:, C. Toth, J. O’Rourke, J. Goodman (Eds.),
Handbook of Discrete and Computational Geometry, Third Edition, Taylor & Francis,
2017, pp. 1709–1735.
date_created: 2018-12-11T11:44:32Z
date_published: 2017-11-09T00:00:00Z
date_updated: 2023-10-16T11:15:22Z
day: '09'
department:
- _id: HeEd
doi: 10.1201/9781315119601
editor:
- first_name: Csaba
full_name: Toth, Csaba
last_name: Toth
- first_name: Joseph
full_name: O'Rourke, Joseph
last_name: O'Rourke
- first_name: Jacob
full_name: Goodman, Jacob
last_name: Goodman
language:
- iso: eng
month: '11'
oa_version: None
page: 1709 - 1735
publication: Handbook of Discrete and Computational Geometry, Third Edition
publication_identifier:
eisbn:
- '9781498711425'
publication_status: published
publisher: Taylor & Francis
publist_id: '7970'
quality_controlled: '1'
scopus_import: '1'
series_title: Handbook of Discrete and Computational Geometry
status: public
title: Computational topology for structural molecular biology
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '840'
abstract:
- lang: eng
text: Heavy holes confined in quantum dots are predicted to be promising candidates
for the realization of spin qubits with long coherence times. Here we focus on
such heavy-hole states confined in germanium hut wires. By tuning the growth density
of the latter we can realize a T-like structure between two neighboring wires.
Such a structure allows the realization of a charge sensor, which is electrostatically
and tunnel coupled to a quantum dot, with charge-transfer signals as high as 0.3
e. By integrating the T-like structure into a radiofrequency reflectometry setup,
single-shot measurements allowing the extraction of hole tunneling times are performed.
The extracted tunneling times of less than 10 μs are attributed to the small effective
mass of Ge heavy-hole states and pave the way toward projective spin readout measurements.
acknowledged_ssus:
- _id: M-Shop
article_processing_charge: No
author:
- first_name: Lada
full_name: Vukusic, Lada
id: 31E9F056-F248-11E8-B48F-1D18A9856A87
last_name: Vukusic
orcid: 0000-0003-2424-8636
- first_name: Josip
full_name: Kukucka, Josip
id: 3F5D8856-F248-11E8-B48F-1D18A9856A87
last_name: Kukucka
- first_name: Hannes
full_name: Watzinger, Hannes
id: 35DF8E50-F248-11E8-B48F-1D18A9856A87
last_name: Watzinger
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
citation:
ama: Vukušić L, Kukucka J, Watzinger H, Katsaros G. Fast hole tunneling times in
germanium hut wires probed by single-shot reflectometry. Nano Letters.
2017;17(9):5706-5710. doi:10.1021/acs.nanolett.7b02627
apa: Vukušić, L., Kukucka, J., Watzinger, H., & Katsaros, G. (2017). Fast hole
tunneling times in germanium hut wires probed by single-shot reflectometry. Nano
Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.7b02627
chicago: Vukušić, Lada, Josip Kukucka, Hannes Watzinger, and Georgios Katsaros.
“Fast Hole Tunneling Times in Germanium Hut Wires Probed by Single-Shot Reflectometry.”
Nano Letters. American Chemical Society, 2017. https://doi.org/10.1021/acs.nanolett.7b02627.
ieee: L. Vukušić, J. Kukucka, H. Watzinger, and G. Katsaros, “Fast hole tunneling
times in germanium hut wires probed by single-shot reflectometry,” Nano Letters,
vol. 17, no. 9. American Chemical Society, pp. 5706–5710, 2017.
ista: Vukušić L, Kukucka J, Watzinger H, Katsaros G. 2017. Fast hole tunneling times
in germanium hut wires probed by single-shot reflectometry. Nano Letters. 17(9),
5706–5710.
mla: Vukušić, Lada, et al. “Fast Hole Tunneling Times in Germanium Hut Wires Probed
by Single-Shot Reflectometry.” Nano Letters, vol. 17, no. 9, American Chemical
Society, 2017, pp. 5706–10, doi:10.1021/acs.nanolett.7b02627.
short: L. Vukušić, J. Kukucka, H. Watzinger, G. Katsaros, Nano Letters 17 (2017)
5706–5710.
date_created: 2018-12-11T11:48:47Z
date_published: 2017-08-10T00:00:00Z
date_updated: 2023-09-26T15:50:22Z
day: '10'
ddc:
- '539'
department:
- _id: GeKa
doi: 10.1021/acs.nanolett.7b02627
ec_funded: 1
external_id:
isi:
- '000411043500078'
file:
- access_level: open_access
checksum: 761371a0129b2aa442424b9561450ece
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:33Z
date_updated: 2020-07-14T12:48:13Z
file_id: '4951'
file_name: IST-2017-865-v1+1_acs.nanolett.7b02627.pdf
file_size: 2449546
relation: main_file
file_date_updated: 2020-07-14T12:48:13Z
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
issue: '9'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 5706 - 5710
project:
- _id: 25517E86-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '335497'
name: Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires
publication: Nano Letters
publication_identifier:
issn:
- '15306984'
publication_status: published
publisher: American Chemical Society
publist_id: '6808'
pubrep_id: '865'
quality_controlled: '1'
related_material:
record:
- id: '7977'
relation: popular_science
- id: '69'
relation: dissertation_contains
status: public
- id: '7996'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 17
year: '2017'
...
---
_id: '8423'
abstract:
- lang: eng
text: In this paper we show that for a generic strictly convex domain, one can recover
the eigendata corresponding to Aubry–Mather periodic orbits of the induced billiard
map from the (maximal) marked length spectrum of the domain.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Guan
full_name: Huang, Guan
last_name: Huang
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: Alfonso
full_name: Sorrentino, Alfonso
last_name: Sorrentino
citation:
ama: Huang G, Kaloshin V, Sorrentino A. On the marked length spectrum of generic
strictly convex billiard tables. Duke Mathematical Journal. 2017;167(1):175-209.
doi:10.1215/00127094-2017-0038
apa: Huang, G., Kaloshin, V., & Sorrentino, A. (2017). On the marked length
spectrum of generic strictly convex billiard tables. Duke Mathematical Journal.
Duke University Press. https://doi.org/10.1215/00127094-2017-0038
chicago: Huang, Guan, Vadim Kaloshin, and Alfonso Sorrentino. “On the Marked Length
Spectrum of Generic Strictly Convex Billiard Tables.” Duke Mathematical Journal.
Duke University Press, 2017. https://doi.org/10.1215/00127094-2017-0038.
ieee: G. Huang, V. Kaloshin, and A. Sorrentino, “On the marked length spectrum of
generic strictly convex billiard tables,” Duke Mathematical Journal, vol.
167, no. 1. Duke University Press, pp. 175–209, 2017.
ista: Huang G, Kaloshin V, Sorrentino A. 2017. On the marked length spectrum of
generic strictly convex billiard tables. Duke Mathematical Journal. 167(1), 175–209.
mla: Huang, Guan, et al. “On the Marked Length Spectrum of Generic Strictly Convex
Billiard Tables.” Duke Mathematical Journal, vol. 167, no. 1, Duke University
Press, 2017, pp. 175–209, doi:10.1215/00127094-2017-0038.
short: G. Huang, V. Kaloshin, A. Sorrentino, Duke Mathematical Journal 167 (2017)
175–209.
date_created: 2020-09-17T10:42:42Z
date_published: 2017-12-08T00:00:00Z
date_updated: 2021-01-12T08:19:11Z
day: '08'
doi: 10.1215/00127094-2017-0038
extern: '1'
external_id:
arxiv:
- '1603.08838'
intvolume: ' 167'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1603.08838
month: '12'
oa: 1
oa_version: Preprint
page: 175-209
publication: Duke Mathematical Journal
publication_identifier:
issn:
- 0012-7094
publication_status: published
publisher: Duke University Press
quality_controlled: '1'
status: public
title: On the marked length spectrum of generic strictly convex billiard tables
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 167
year: '2017'
...
---
_id: '8427'
abstract:
- lang: eng
text: We show that any sufficiently (finitely) smooth ℤ₂-symmetric strictly convex
domain sufficiently close to a circle is dynamically spectrally rigid; i.e., all
deformations among domains in the same class that preserve the length of all periodic
orbits of the associated billiard flow must necessarily be isometric deformations.
This gives a partial answer to a question of P. Sarnak.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Jacopo
full_name: De Simoi, Jacopo
last_name: De Simoi
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: Qiaoling
full_name: Wei, Qiaoling
last_name: Wei
citation:
ama: De Simoi J, Kaloshin V, Wei Q. Dynamical spectral rigidity among Z2-symmetric
strictly convex domains close to a circle. Annals of Mathematics. 2017;186(1):277-314.
doi:10.4007/annals.2017.186.1.7
apa: De Simoi, J., Kaloshin, V., & Wei, Q. (2017). Dynamical spectral rigidity
among Z2-symmetric strictly convex domains close to a circle. Annals of Mathematics.
Annals of Mathematics. https://doi.org/10.4007/annals.2017.186.1.7
chicago: De Simoi, Jacopo, Vadim Kaloshin, and Qiaoling Wei. “Dynamical Spectral
Rigidity among Z2-Symmetric Strictly Convex Domains Close to a Circle.” Annals
of Mathematics. Annals of Mathematics, 2017. https://doi.org/10.4007/annals.2017.186.1.7.
ieee: J. De Simoi, V. Kaloshin, and Q. Wei, “Dynamical spectral rigidity among Z2-symmetric
strictly convex domains close to a circle,” Annals of Mathematics, vol.
186, no. 1. Annals of Mathematics, pp. 277–314, 2017.
ista: De Simoi J, Kaloshin V, Wei Q. 2017. Dynamical spectral rigidity among Z2-symmetric
strictly convex domains close to a circle. Annals of Mathematics. 186(1), 277–314.
mla: De Simoi, Jacopo, et al. “Dynamical Spectral Rigidity among Z2-Symmetric Strictly
Convex Domains Close to a Circle.” Annals of Mathematics, vol. 186, no.
1, Annals of Mathematics, 2017, pp. 277–314, doi:10.4007/annals.2017.186.1.7.
short: J. De Simoi, V. Kaloshin, Q. Wei, Annals of Mathematics 186 (2017) 277–314.
date_created: 2020-09-17T10:46:42Z
date_published: 2017-07-01T00:00:00Z
date_updated: 2021-01-12T08:19:12Z
day: '01'
doi: 10.4007/annals.2017.186.1.7
extern: '1'
external_id:
arxiv:
- '1606.00230'
intvolume: ' 186'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1606.00230
month: '07'
oa: 1
oa_version: Preprint
page: 277-314
publication: Annals of Mathematics
publication_identifier:
issn:
- 0003-486X
publication_status: published
publisher: Annals of Mathematics
quality_controlled: '1'
status: public
title: Dynamical spectral rigidity among Z2-symmetric strictly convex domains close
to a circle
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 186
year: '2017'
...
---
_id: '8444'
abstract:
- lang: eng
text: Biophysical investigation of membrane proteins generally requires their extraction
from native sources using detergents, a step that can lead, possibly irreversibly,
to protein denaturation. The propensity of dodecylphosphocholine (DPC), a detergent
widely utilized in NMR studies of membrane proteins, to distort their structure
has been the subject of much controversy. It has been recently proposed that the
binding specificity of the yeast mitochondrial ADP/ATP carrier (yAAC3) toward
cardiolipins is preserved in DPC, thereby suggesting that DPC is a suitable environment
in which to study membrane proteins. In this communication, we used all-atom molecular
dynamics simulations to investigate the specific binding of cardiolipins to yAAC3.
Our data demonstrate that the interaction interface observed in a native-like
environment differs markedly from that inferred from an NMR investigation in DPC,
implying that in this detergent, the protein structure is distorted. We further
investigated yAAC3 solubilized in DPC and in the milder dodecylmaltoside with
thermal-shift assays. The loss of thermal transition observed in DPC confirms
that the protein is no longer properly folded in this environment.
article_processing_charge: No
article_type: original
author:
- first_name: François
full_name: Dehez, François
last_name: Dehez
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Martin S.
full_name: King, Martin S.
last_name: King
- first_name: Edmund R.S.
full_name: Kunji, Edmund R.S.
last_name: Kunji
- first_name: Christophe
full_name: Chipot, Christophe
last_name: Chipot
citation:
ama: Dehez F, Schanda P, King MS, Kunji ERS, Chipot C. Mitochondrial ADP/ATP carrier
in dodecylphosphocholine binds cardiolipins with non-native affinity. Biophysical
Journal. 2017;113(11):2311-2315. doi:10.1016/j.bpj.2017.09.019
apa: Dehez, F., Schanda, P., King, M. S., Kunji, E. R. S., & Chipot, C. (2017).
Mitochondrial ADP/ATP carrier in dodecylphosphocholine binds cardiolipins with
non-native affinity. Biophysical Journal. Elsevier. https://doi.org/10.1016/j.bpj.2017.09.019
chicago: Dehez, François, Paul Schanda, Martin S. King, Edmund R.S. Kunji, and Christophe
Chipot. “Mitochondrial ADP/ATP Carrier in Dodecylphosphocholine Binds Cardiolipins
with Non-Native Affinity.” Biophysical Journal. Elsevier, 2017. https://doi.org/10.1016/j.bpj.2017.09.019.
ieee: F. Dehez, P. Schanda, M. S. King, E. R. S. Kunji, and C. Chipot, “Mitochondrial
ADP/ATP carrier in dodecylphosphocholine binds cardiolipins with non-native affinity,”
Biophysical Journal, vol. 113, no. 11. Elsevier, pp. 2311–2315, 2017.
ista: Dehez F, Schanda P, King MS, Kunji ERS, Chipot C. 2017. Mitochondrial ADP/ATP
carrier in dodecylphosphocholine binds cardiolipins with non-native affinity.
Biophysical Journal. 113(11), 2311–2315.
mla: Dehez, François, et al. “Mitochondrial ADP/ATP Carrier in Dodecylphosphocholine
Binds Cardiolipins with Non-Native Affinity.” Biophysical Journal, vol.
113, no. 11, Elsevier, 2017, pp. 2311–15, doi:10.1016/j.bpj.2017.09.019.
short: F. Dehez, P. Schanda, M.S. King, E.R.S. Kunji, C. Chipot, Biophysical Journal
113 (2017) 2311–2315.
date_created: 2020-09-18T10:05:54Z
date_published: 2017-12-05T00:00:00Z
date_updated: 2021-01-12T08:19:18Z
day: '05'
doi: 10.1016/j.bpj.2017.09.019
extern: '1'
intvolume: ' 113'
issue: '11'
keyword:
- Biophysics
language:
- iso: eng
month: '12'
oa_version: None
page: 2311-2315
publication: Biophysical Journal
publication_identifier:
issn:
- 0006-3495
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Mitochondrial ADP/ATP carrier in dodecylphosphocholine binds cardiolipins with
non-native affinity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2017'
...
---
_id: '8445'
abstract:
- lang: eng
text: Proteins perform their functions in solution but their structures are most
frequently studied inside crystals. Here we probe how the crystal packing alters
microsecond dynamics, using solid-state NMR measurements and multi-microsecond
MD simulations of different crystal forms of ubiquitin. In particular, near-rotary-resonance
relaxation dispersion (NERRD) experiments probe angular backbone motion, while
Bloch–McConnell relaxation dispersion data report on fluctuations of the local
electronic environment. These experiments and simulations reveal that the packing
of the protein can significantly alter the thermodynamics and kinetics of local
conformational exchange. Moreover, we report small-amplitude reorientational motion
of protein molecules in the crystal lattice with an ~3–5° amplitude on a tens-of-microseconds
time scale in one of the crystals, but not in others. An intriguing possibility
arises that overall motion is to some extent coupled to local dynamics. Our study
highlights the importance of considering the packing when analyzing dynamics of
crystalline proteins.
article_number: '145'
article_processing_charge: No
article_type: original
author:
- first_name: Vilius
full_name: Kurauskas, Vilius
last_name: Kurauskas
- first_name: Sergei A.
full_name: Izmailov, Sergei A.
last_name: Izmailov
- first_name: Olga N.
full_name: Rogacheva, Olga N.
last_name: Rogacheva
- first_name: Audrey
full_name: Hessel, Audrey
last_name: Hessel
- first_name: Isabel
full_name: Ayala, Isabel
last_name: Ayala
- first_name: Joyce
full_name: Woodhouse, Joyce
last_name: Woodhouse
- first_name: Anastasya
full_name: Shilova, Anastasya
last_name: Shilova
- first_name: Yi
full_name: Xue, Yi
last_name: Xue
- first_name: Tairan
full_name: Yuwen, Tairan
last_name: Yuwen
- first_name: Nicolas
full_name: Coquelle, Nicolas
last_name: Coquelle
- first_name: Jacques-Philippe
full_name: Colletier, Jacques-Philippe
last_name: Colletier
- first_name: Nikolai R.
full_name: Skrynnikov, Nikolai R.
last_name: Skrynnikov
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Kurauskas V, Izmailov SA, Rogacheva ON, et al. Slow conformational exchange
and overall rocking motion in ubiquitin protein crystals. Nature Communications.
2017;8. doi:10.1038/s41467-017-00165-8
apa: Kurauskas, V., Izmailov, S. A., Rogacheva, O. N., Hessel, A., Ayala, I., Woodhouse,
J., … Schanda, P. (2017). Slow conformational exchange and overall rocking motion
in ubiquitin protein crystals. Nature Communications. Springer Nature.
https://doi.org/10.1038/s41467-017-00165-8
chicago: Kurauskas, Vilius, Sergei A. Izmailov, Olga N. Rogacheva, Audrey Hessel,
Isabel Ayala, Joyce Woodhouse, Anastasya Shilova, et al. “Slow Conformational
Exchange and Overall Rocking Motion in Ubiquitin Protein Crystals.” Nature
Communications. Springer Nature, 2017. https://doi.org/10.1038/s41467-017-00165-8.
ieee: V. Kurauskas et al., “Slow conformational exchange and overall rocking
motion in ubiquitin protein crystals,” Nature Communications, vol. 8. Springer
Nature, 2017.
ista: Kurauskas V, Izmailov SA, Rogacheva ON, Hessel A, Ayala I, Woodhouse J, Shilova
A, Xue Y, Yuwen T, Coquelle N, Colletier J-P, Skrynnikov NR, Schanda P. 2017.
Slow conformational exchange and overall rocking motion in ubiquitin protein crystals.
Nature Communications. 8, 145.
mla: Kurauskas, Vilius, et al. “Slow Conformational Exchange and Overall Rocking
Motion in Ubiquitin Protein Crystals.” Nature Communications, vol. 8, 145,
Springer Nature, 2017, doi:10.1038/s41467-017-00165-8.
short: V. Kurauskas, S.A. Izmailov, O.N. Rogacheva, A. Hessel, I. Ayala, J. Woodhouse,
A. Shilova, Y. Xue, T. Yuwen, N. Coquelle, J.-P. Colletier, N.R. Skrynnikov, P.
Schanda, Nature Communications 8 (2017).
date_created: 2020-09-18T10:06:01Z
date_published: 2017-07-27T00:00:00Z
date_updated: 2021-01-12T08:19:19Z
day: '27'
doi: 10.1038/s41467-017-00165-8
extern: '1'
intvolume: ' 8'
language:
- iso: eng
month: '07'
oa_version: Published Version
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Slow conformational exchange and overall rocking motion in ubiquitin protein
crystals
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2017'
...
---
_id: '8446'
abstract:
- lang: eng
text: Solid‐state NMR spectroscopy can provide insight into protein structure and
dynamics at the atomic level without inherent protein size limitations. However,
a major hurdle to studying large proteins by solid‐state NMR spectroscopy is related
to spectral complexity and resonance overlap, which increase with molecular weight
and severely hamper the assignment process. Here the use of two sets of experiments
is shown to expand the tool kit of 1H‐detected assignment approaches, which correlate
a given amide pair either to the two adjacent CO–CA pairs (4D hCOCANH/hCOCAcoNH),
or to the amide 1H of the neighboring residue (3D HcocaNH/HcacoNH, which can be
extended to 5D). The experiments are based on efficient coherence transfers between
backbone atoms using INEPT transfers between carbons and cross‐polarization for
heteronuclear transfers. The utility of these experiments is exemplified with
application to assemblies of deuterated, fully amide‐protonated proteins from
approximately 20 to 60 kDa monomer, at magic‐angle spinning (MAS) frequencies
from approximately 40 to 55 kHz. These experiments will also be applicable to
protonated proteins at higher MAS frequencies. The resonance assignment of a domain
within the 50.4 kDa bacteriophage T5 tube protein pb6 is reported, and this is
compared to NMR assignments of the isolated domain in solution. This comparison
reveals contacts of this domain to the core of the polymeric tail tube assembly.
article_processing_charge: No
article_type: original
author:
- first_name: Hugo
full_name: Fraga, Hugo
last_name: Fraga
- first_name: Charles‐Adrien
full_name: Arnaud, Charles‐Adrien
last_name: Arnaud
- first_name: Diego F.
full_name: Gauto, Diego F.
last_name: Gauto
- first_name: Maxime
full_name: Audin, Maxime
last_name: Audin
- first_name: Vilius
full_name: Kurauskas, Vilius
last_name: Kurauskas
- first_name: Pavel
full_name: Macek, Pavel
last_name: Macek
- first_name: Carsten
full_name: Krichel, Carsten
last_name: Krichel
- first_name: Jia‐Ying
full_name: Guan, Jia‐Ying
last_name: Guan
- first_name: Jerome
full_name: Boisbouvier, Jerome
last_name: Boisbouvier
- first_name: Remco
full_name: Sprangers, Remco
last_name: Sprangers
- first_name: Cécile
full_name: Breyton, Cécile
last_name: Breyton
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Fraga H, Arnaud C, Gauto DF, et al. Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D
correlation experiments for resonance assignment of large proteins. ChemPhysChem.
2017;18(19):2697-2703. doi:10.1002/cphc.201700572
apa: Fraga, H., Arnaud, C., Gauto, D. F., Audin, M., Kurauskas, V., Macek, P., …
Schanda, P. (2017). Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D correlation experiments
for resonance assignment of large proteins. ChemPhysChem. Wiley. https://doi.org/10.1002/cphc.201700572
chicago: Fraga, Hugo, Charles‐Adrien Arnaud, Diego F. Gauto, Maxime Audin, Vilius
Kurauskas, Pavel Macek, Carsten Krichel, et al. “Solid‐state NMR H–N–(C)–H and
H–N–C–C 3D/4D Correlation Experiments for Resonance Assignment of Large Proteins.”
ChemPhysChem. Wiley, 2017. https://doi.org/10.1002/cphc.201700572.
ieee: H. Fraga et al., “Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D correlation
experiments for resonance assignment of large proteins,” ChemPhysChem,
vol. 18, no. 19. Wiley, pp. 2697–2703, 2017.
ista: Fraga H, Arnaud C, Gauto DF, Audin M, Kurauskas V, Macek P, Krichel C, Guan
J, Boisbouvier J, Sprangers R, Breyton C, Schanda P. 2017. Solid‐state NMR H–N–(C)–H
and H–N–C–C 3D/4D correlation experiments for resonance assignment of large proteins.
ChemPhysChem. 18(19), 2697–2703.
mla: Fraga, Hugo, et al. “Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D Correlation
Experiments for Resonance Assignment of Large Proteins.” ChemPhysChem,
vol. 18, no. 19, Wiley, 2017, pp. 2697–703, doi:10.1002/cphc.201700572.
short: H. Fraga, C. Arnaud, D.F. Gauto, M. Audin, V. Kurauskas, P. Macek, C. Krichel,
J. Guan, J. Boisbouvier, R. Sprangers, C. Breyton, P. Schanda, ChemPhysChem 18
(2017) 2697–2703.
date_created: 2020-09-18T10:06:09Z
date_published: 2017-08-09T00:00:00Z
date_updated: 2021-01-12T08:19:19Z
day: '09'
doi: 10.1002/cphc.201700572
extern: '1'
intvolume: ' 18'
issue: '19'
keyword:
- Physical and Theoretical Chemistry
- Atomic and Molecular Physics
- and Optics
language:
- iso: eng
month: '08'
oa_version: None
page: 2697-2703
publication: ChemPhysChem
publication_identifier:
issn:
- 1439-4235
- 1439-7641
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D correlation experiments for resonance
assignment of large proteins
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2017'
...
---
_id: '8447'
abstract:
- lang: eng
text: 'Solid-state NMR spectroscopy can provide site-resolved information about
protein dynamics over many time scales. Here we combine protein deuteration, fast
magic-angle spinning (~45–60 kHz) and proton detection to study dynamics of ubiquitin
in microcrystals, and in particular a mutant in a region that undergoes microsecond
motions in a β-turn region in the wild-type protein. We use 15N R1ρ relaxation
measurements as a function of the radio-frequency (RF) field strength, i.e. relaxation
dispersion, to probe how the G53A mutation alters these dynamics. We report a
population-inversion of conformational states: the conformation that in the wild-type
protein is populated only sparsely becomes the predominant state. We furthermore
explore the potential to use amide-1H R1ρ relaxation to obtain insight into dynamics.
We show that while quantitative interpretation of 1H relaxation remains beyond
reach under the experimental conditions, due to coherent contributions to decay,
one may extract qualitative information about flexibility.'
article_processing_charge: No
article_type: original
author:
- first_name: Diego F.
full_name: Gauto, Diego F.
last_name: Gauto
- first_name: Audrey
full_name: Hessel, Audrey
last_name: Hessel
- first_name: Petra
full_name: Rovó, Petra
last_name: Rovó
- first_name: Vilius
full_name: Kurauskas, Vilius
last_name: Kurauskas
- first_name: Rasmus
full_name: Linser, Rasmus
last_name: Linser
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: 'Gauto DF, Hessel A, Rovó P, Kurauskas V, Linser R, Schanda P. Protein conformational
dynamics studied by 15N and 1HR1ρ relaxation dispersion: Application to wild-type
and G53A ubiquitin crystals. Solid State Nuclear Magnetic Resonance. 2017;87(10):86-95.
doi:10.1016/j.ssnmr.2017.04.002'
apa: 'Gauto, D. F., Hessel, A., Rovó, P., Kurauskas, V., Linser, R., & Schanda,
P. (2017). Protein conformational dynamics studied by 15N and 1HR1ρ relaxation
dispersion: Application to wild-type and G53A ubiquitin crystals. Solid State
Nuclear Magnetic Resonance. Elsevier. https://doi.org/10.1016/j.ssnmr.2017.04.002'
chicago: 'Gauto, Diego F., Audrey Hessel, Petra Rovó, Vilius Kurauskas, Rasmus Linser,
and Paul Schanda. “Protein Conformational Dynamics Studied by 15N and 1HR1ρ Relaxation
Dispersion: Application to Wild-Type and G53A Ubiquitin Crystals.” Solid State
Nuclear Magnetic Resonance. Elsevier, 2017. https://doi.org/10.1016/j.ssnmr.2017.04.002.'
ieee: 'D. F. Gauto, A. Hessel, P. Rovó, V. Kurauskas, R. Linser, and P. Schanda,
“Protein conformational dynamics studied by 15N and 1HR1ρ relaxation dispersion:
Application to wild-type and G53A ubiquitin crystals,” Solid State Nuclear
Magnetic Resonance, vol. 87, no. 10. Elsevier, pp. 86–95, 2017.'
ista: 'Gauto DF, Hessel A, Rovó P, Kurauskas V, Linser R, Schanda P. 2017. Protein
conformational dynamics studied by 15N and 1HR1ρ relaxation dispersion: Application
to wild-type and G53A ubiquitin crystals. Solid State Nuclear Magnetic Resonance.
87(10), 86–95.'
mla: 'Gauto, Diego F., et al. “Protein Conformational Dynamics Studied by 15N and
1HR1ρ Relaxation Dispersion: Application to Wild-Type and G53A Ubiquitin Crystals.”
Solid State Nuclear Magnetic Resonance, vol. 87, no. 10, Elsevier, 2017,
pp. 86–95, doi:10.1016/j.ssnmr.2017.04.002.'
short: D.F. Gauto, A. Hessel, P. Rovó, V. Kurauskas, R. Linser, P. Schanda, Solid
State Nuclear Magnetic Resonance 87 (2017) 86–95.
date_created: 2020-09-18T10:06:18Z
date_published: 2017-10-01T00:00:00Z
date_updated: 2021-01-12T08:19:20Z
day: '01'
doi: 10.1016/j.ssnmr.2017.04.002
extern: '1'
intvolume: ' 87'
issue: '10'
keyword:
- Nuclear and High Energy Physics
- Instrumentation
- General Chemistry
- Radiation
language:
- iso: eng
month: '10'
oa_version: None
page: 86-95
publication: Solid State Nuclear Magnetic Resonance
publication_identifier:
issn:
- 0926-2040
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: 'Protein conformational dynamics studied by 15N and 1HR1ρ relaxation dispersion:
Application to wild-type and G53A ubiquitin crystals'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 87
year: '2017'
...
---
_id: '8448'
abstract:
- lang: eng
text: We present an improved fast mixing device based on the rapid mixing of two
solutions inside the NMR probe, as originally proposed by Hore and coworkers (J.
Am. Chem. Soc. 125 (2003) 12484–12492). Such a device is important for off-equilibrium
studies of molecular kinetics by multidimensional real-time NMR spectrsocopy.
The novelty of this device is that it allows removing the injector from the NMR
detection volume after mixing, and thus provides good magnetic field homogeneity
independently of the initial sample volume placed in the NMR probe. The apparatus
is simple to build, inexpensive, and can be used without any hardware modification
on any type of liquid-state NMR spectrometer. We demonstrate the performance of
our fast mixing device in terms of improved magnetic field homogeneity, and show
an application to the study of protein folding and the structural characterization
of transiently populated folding intermediates.
article_processing_charge: No
article_type: original
author:
- first_name: Rémi
full_name: Franco, Rémi
last_name: Franco
- first_name: Adrien
full_name: Favier, Adrien
last_name: Favier
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Bernhard
full_name: Brutscher, Bernhard
last_name: Brutscher
citation:
ama: Franco R, Favier A, Schanda P, Brutscher B. Optimized fast mixing device for
real-time NMR applications. Journal of Magnetic Resonance. 2017;281(8):125-129.
doi:10.1016/j.jmr.2017.05.016
apa: Franco, R., Favier, A., Schanda, P., & Brutscher, B. (2017). Optimized
fast mixing device for real-time NMR applications. Journal of Magnetic Resonance.
Elsevier. https://doi.org/10.1016/j.jmr.2017.05.016
chicago: Franco, Rémi, Adrien Favier, Paul Schanda, and Bernhard Brutscher. “Optimized
Fast Mixing Device for Real-Time NMR Applications.” Journal of Magnetic Resonance.
Elsevier, 2017. https://doi.org/10.1016/j.jmr.2017.05.016.
ieee: R. Franco, A. Favier, P. Schanda, and B. Brutscher, “Optimized fast mixing
device for real-time NMR applications,” Journal of Magnetic Resonance,
vol. 281, no. 8. Elsevier, pp. 125–129, 2017.
ista: Franco R, Favier A, Schanda P, Brutscher B. 2017. Optimized fast mixing device
for real-time NMR applications. Journal of Magnetic Resonance. 281(8), 125–129.
mla: Franco, Rémi, et al. “Optimized Fast Mixing Device for Real-Time NMR Applications.”
Journal of Magnetic Resonance, vol. 281, no. 8, Elsevier, 2017, pp. 125–29,
doi:10.1016/j.jmr.2017.05.016.
short: R. Franco, A. Favier, P. Schanda, B. Brutscher, Journal of Magnetic Resonance
281 (2017) 125–129.
date_created: 2020-09-18T10:06:27Z
date_published: 2017-08-01T00:00:00Z
date_updated: 2021-01-12T08:19:20Z
day: '01'
doi: 10.1016/j.jmr.2017.05.016
extern: '1'
intvolume: ' 281'
issue: '8'
keyword:
- Nuclear and High Energy Physics
- Biophysics
- Biochemistry
- Condensed Matter Physics
language:
- iso: eng
month: '08'
oa_version: None
page: 125-129
publication: Journal of Magnetic Resonance
publication_identifier:
issn:
- 1090-7807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Optimized fast mixing device for real-time NMR applications
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 281
year: '2017'
...
---
_id: '8449'
abstract:
- lang: eng
text: Ensuring the correct folding of RNA molecules in the cell is of major importance
for a large variety of biological functions. Therefore, chaperone proteins that
assist RNA in adopting their functionally active states are abundant in all living
organisms. An important feature of RNA chaperone proteins is that they do not
require an external energy source to perform their activity, and that they interact
transiently and non-specifically with their RNA targets. So far, little is known
about the mechanistic details of the RNA chaperone activity of these proteins.
Prominent examples of RNA chaperones are bacterial cold shock proteins (Csp) that
have been reported to bind single-stranded RNA and DNA. Here, we have used advanced
NMR spectroscopy techniques to investigate at atomic resolution the RNA-melting
activity of CspA, the major cold shock protein of Escherichia coli, upon binding
to different RNA hairpins. Real-time NMR provides detailed information on the
folding kinetics and folding pathways. Finally, comparison of wild-type CspA with
single-point mutants and small peptides yields insights into the complementary
roles of aromatic and positively charged amino-acid side chains for the RNA chaperone
activity of the protein.
article_processing_charge: No
article_type: original
author:
- first_name: Enrico
full_name: Rennella, Enrico
last_name: Rennella
- first_name: Tomáš
full_name: Sára, Tomáš
last_name: Sára
- first_name: Michael
full_name: Juen, Michael
last_name: Juen
- first_name: Christoph
full_name: Wunderlich, Christoph
last_name: Wunderlich
- first_name: Lionel
full_name: Imbert, Lionel
last_name: Imbert
- first_name: Zsofia
full_name: Solyom, Zsofia
last_name: Solyom
- first_name: Adrien
full_name: Favier, Adrien
last_name: Favier
- first_name: Isabel
full_name: Ayala, Isabel
last_name: Ayala
- first_name: Katharina
full_name: Weinhäupl, Katharina
last_name: Weinhäupl
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Robert
full_name: Konrat, Robert
last_name: Konrat
- first_name: Christoph
full_name: Kreutz, Christoph
last_name: Kreutz
- first_name: Bernhard
full_name: Brutscher, Bernhard
last_name: Brutscher
citation:
ama: Rennella E, Sára T, Juen M, et al. RNA binding and chaperone activity of the
E.coli cold-shock protein CspA. Nucleic Acids Research. 2017;45(7):4255-4268.
doi:10.1093/nar/gkx044
apa: Rennella, E., Sára, T., Juen, M., Wunderlich, C., Imbert, L., Solyom, Z., …
Brutscher, B. (2017). RNA binding and chaperone activity of the E.coli cold-shock
protein CspA. Nucleic Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gkx044
chicago: Rennella, Enrico, Tomáš Sára, Michael Juen, Christoph Wunderlich, Lionel
Imbert, Zsofia Solyom, Adrien Favier, et al. “RNA Binding and Chaperone Activity
of the E.Coli Cold-Shock Protein CspA.” Nucleic Acids Research. Oxford
University Press, 2017. https://doi.org/10.1093/nar/gkx044.
ieee: E. Rennella et al., “RNA binding and chaperone activity of the E.coli
cold-shock protein CspA,” Nucleic Acids Research, vol. 45, no. 7. Oxford
University Press, pp. 4255–4268, 2017.
ista: Rennella E, Sára T, Juen M, Wunderlich C, Imbert L, Solyom Z, Favier A, Ayala
I, Weinhäupl K, Schanda P, Konrat R, Kreutz C, Brutscher B. 2017. RNA binding
and chaperone activity of the E.coli cold-shock protein CspA. Nucleic Acids Research.
45(7), 4255–4268.
mla: Rennella, Enrico, et al. “RNA Binding and Chaperone Activity of the E.Coli
Cold-Shock Protein CspA.” Nucleic Acids Research, vol. 45, no. 7, Oxford
University Press, 2017, pp. 4255–68, doi:10.1093/nar/gkx044.
short: E. Rennella, T. Sára, M. Juen, C. Wunderlich, L. Imbert, Z. Solyom, A. Favier,
I. Ayala, K. Weinhäupl, P. Schanda, R. Konrat, C. Kreutz, B. Brutscher, Nucleic
Acids Research 45 (2017) 4255–4268.
date_created: 2020-09-18T10:06:34Z
date_published: 2017-04-20T00:00:00Z
date_updated: 2021-01-12T08:19:20Z
day: '20'
doi: 10.1093/nar/gkx044
extern: '1'
intvolume: ' 45'
issue: '7'
language:
- iso: eng
month: '04'
oa_version: None
page: 4255-4268
publication: Nucleic Acids Research
publication_identifier:
issn:
- 0305-1048
- 1362-4962
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
status: public
title: RNA binding and chaperone activity of the E.coli cold-shock protein CspA
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 45
year: '2017'
...
---
_id: '8450'
abstract:
- lang: eng
text: Methyl groups are very useful probes of structure, dynamics, and interactions
in protein NMR spectroscopy. In particular, methyl-directed experiments provide
high sensitivity even in very large proteins, such as membrane proteins in a membrane-mimicking
environment. In this chapter, we discuss the approach for labeling methyl groups
in E. coli-based protein expression, as exemplified with the mitochondrial carrier
GGC.
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
author:
- first_name: Vilius
full_name: Kurauskas, Vilius
last_name: Kurauskas
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Remy
full_name: Sounier, Remy
last_name: Sounier
citation:
ama: 'Kurauskas V, Schanda P, Sounier R. Methyl-specific isotope labeling strategies
for NMR studies of membrane proteins. In: Membrane Protein Structure and Function
Characterization. Vol 1635. Springer Nature; 2017:109-123. doi:10.1007/978-1-4939-7151-0_6'
apa: Kurauskas, V., Schanda, P., & Sounier, R. (2017). Methyl-specific isotope
labeling strategies for NMR studies of membrane proteins. In Membrane protein
structure and function characterization (Vol. 1635, pp. 109–123). Springer
Nature. https://doi.org/10.1007/978-1-4939-7151-0_6
chicago: Kurauskas, Vilius, Paul Schanda, and Remy Sounier. “Methyl-Specific Isotope
Labeling Strategies for NMR Studies of Membrane Proteins.” In Membrane Protein
Structure and Function Characterization, 1635:109–23. Springer Nature, 2017.
https://doi.org/10.1007/978-1-4939-7151-0_6.
ieee: V. Kurauskas, P. Schanda, and R. Sounier, “Methyl-specific isotope labeling
strategies for NMR studies of membrane proteins,” in Membrane protein structure
and function characterization, vol. 1635, Springer Nature, 2017, pp. 109–123.
ista: 'Kurauskas V, Schanda P, Sounier R. 2017.Methyl-specific isotope labeling
strategies for NMR studies of membrane proteins. In: Membrane protein structure
and function characterization. Methods in Molecular Biology, vol. 1635, 109–123.'
mla: Kurauskas, Vilius, et al. “Methyl-Specific Isotope Labeling Strategies for
NMR Studies of Membrane Proteins.” Membrane Protein Structure and Function
Characterization, vol. 1635, Springer Nature, 2017, pp. 109–23, doi:10.1007/978-1-4939-7151-0_6.
short: V. Kurauskas, P. Schanda, R. Sounier, in:, Membrane Protein Structure and
Function Characterization, Springer Nature, 2017, pp. 109–123.
date_created: 2020-09-18T10:06:44Z
date_published: 2017-07-29T00:00:00Z
date_updated: 2022-08-26T09:14:20Z
day: '29'
doi: 10.1007/978-1-4939-7151-0_6
extern: '1'
intvolume: ' 1635'
language:
- iso: eng
month: '07'
oa_version: None
page: 109-123
publication: Membrane protein structure and function characterization
publication_identifier:
isbn:
- '9781493971497'
- '9781493971510'
issn:
- 1064-3745
- 1940-6029
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Methyl-specific isotope labeling strategies for NMR studies of membrane proteins
type: book_chapter
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 1635
year: '2017'
...
---
_id: '8451'
abstract:
- lang: eng
text: The structure, dynamics, and function of membrane proteins are intimately
linked to the properties of the membrane environment in which the proteins are
embedded. For structural and biophysical characterization, membrane proteins generally
need to be extracted from the membrane and reconstituted in a suitable membrane‐mimicking
environment. Ensuring functional and structural integrity in these environments
is often a major concern. The styrene/maleic acid co‐polymer has recently been
shown to be able to extract lipid/membrane protein patches directly from native
membranes to form nanosize discoidal proteolipid particles, also referred to as
native nanodiscs. In this work, we show that high‐resolution solid‐state NMR spectra
can be obtained from an integral membrane protein in native nanodiscs, as exemplified
by the 2×34 kDa bacterial cation diffusion facilitator CzcD.
article_processing_charge: No
article_type: original
author:
- first_name: Beate
full_name: Bersch, Beate
last_name: Bersch
- first_name: Jonas M.
full_name: Dörr, Jonas M.
last_name: Dörr
- first_name: Audrey
full_name: Hessel, Audrey
last_name: Hessel
- first_name: J. Antoinette
full_name: Killian, J. Antoinette
last_name: Killian
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Bersch B, Dörr JM, Hessel A, Killian JA, Schanda P. Proton-detected solid-state
NMR spectroscopy of a Zinc diffusion facilitator protein in native nanodiscs.
Angewandte Chemie International Edition. 2017;56(9):2508-2512. doi:10.1002/anie.201610441
apa: Bersch, B., Dörr, J. M., Hessel, A., Killian, J. A., & Schanda, P. (2017).
Proton-detected solid-state NMR spectroscopy of a Zinc diffusion facilitator protein
in native nanodiscs. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201610441
chicago: Bersch, Beate, Jonas M. Dörr, Audrey Hessel, J. Antoinette Killian, and
Paul Schanda. “Proton-Detected Solid-State NMR Spectroscopy of a Zinc Diffusion
Facilitator Protein in Native Nanodiscs.” Angewandte Chemie International Edition.
Wiley, 2017. https://doi.org/10.1002/anie.201610441.
ieee: B. Bersch, J. M. Dörr, A. Hessel, J. A. Killian, and P. Schanda, “Proton-detected
solid-state NMR spectroscopy of a Zinc diffusion facilitator protein in native
nanodiscs,” Angewandte Chemie International Edition, vol. 56, no. 9. Wiley,
pp. 2508–2512, 2017.
ista: Bersch B, Dörr JM, Hessel A, Killian JA, Schanda P. 2017. Proton-detected
solid-state NMR spectroscopy of a Zinc diffusion facilitator protein in native
nanodiscs. Angewandte Chemie International Edition. 56(9), 2508–2512.
mla: Bersch, Beate, et al. “Proton-Detected Solid-State NMR Spectroscopy of a Zinc
Diffusion Facilitator Protein in Native Nanodiscs.” Angewandte Chemie International
Edition, vol. 56, no. 9, Wiley, 2017, pp. 2508–12, doi:10.1002/anie.201610441.
short: B. Bersch, J.M. Dörr, A. Hessel, J.A. Killian, P. Schanda, Angewandte Chemie
International Edition 56 (2017) 2508–2512.
date_created: 2020-09-18T10:06:50Z
date_published: 2017-01-27T00:00:00Z
date_updated: 2021-01-12T08:19:22Z
day: '27'
doi: 10.1002/anie.201610441
extern: '1'
intvolume: ' 56'
issue: '9'
language:
- iso: eng
month: '01'
oa_version: None
page: 2508-2512
publication: Angewandte Chemie International Edition
publication_identifier:
issn:
- 1433-7851
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Proton-detected solid-state NMR spectroscopy of a Zinc diffusion facilitator
protein in native nanodiscs
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 56
year: '2017'
...
---
_id: '169'
abstract:
- lang: eng
text: We show that a twisted variant of Linnik’s conjecture on sums of Kloosterman
sums leads to an optimal covering exponent for S3.
article_processing_charge: No
arxiv: 1
author:
- first_name: Timothy D
full_name: Browning, Timothy D
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
- first_name: Vinay
full_name: Kumaraswamy, Vinay
last_name: Kumaraswamy
- first_name: Rapael
full_name: Steiner, Rapael
last_name: Steiner
citation:
ama: Browning TD, Kumaraswamy V, Steiner R. Twisted Linnik implies optimal covering
exponent for S3. International Mathematics Research Notices. 2017. doi:10.1093/imrn/rnx116
apa: Browning, T. D., Kumaraswamy, V., & Steiner, R. (2017). Twisted Linnik
implies optimal covering exponent for S3. International Mathematics Research
Notices. Oxford University Press. https://doi.org/10.1093/imrn/rnx116
chicago: Browning, Timothy D, Vinay Kumaraswamy, and Rapael Steiner. “Twisted Linnik
Implies Optimal Covering Exponent for S3.” International Mathematics Research
Notices. Oxford University Press, 2017. https://doi.org/10.1093/imrn/rnx116.
ieee: T. D. Browning, V. Kumaraswamy, and R. Steiner, “Twisted Linnik implies optimal
covering exponent for S3,” International Mathematics Research Notices.
Oxford University Press, 2017.
ista: Browning TD, Kumaraswamy V, Steiner R. 2017. Twisted Linnik implies optimal
covering exponent for S3. International Mathematics Research Notices.
mla: Browning, Timothy D., et al. “Twisted Linnik Implies Optimal Covering Exponent
for S3.” International Mathematics Research Notices, Oxford University
Press, 2017, doi:10.1093/imrn/rnx116.
short: T.D. Browning, V. Kumaraswamy, R. Steiner, International Mathematics Research
Notices (2017).
date_created: 2018-12-11T11:44:59Z
date_published: 2017-06-19T00:00:00Z
date_updated: 2021-01-12T06:52:32Z
day: '19'
doi: 10.1093/imrn/rnx116
extern: '1'
external_id:
arxiv:
- '1609.06097'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1609.06097
month: '06'
oa: 1
oa_version: None
publication: International Mathematics Research Notices
publication_status: published
publisher: Oxford University Press
publist_id: '7752'
quality_controlled: '1'
status: public
title: Twisted Linnik implies optimal covering exponent for S3
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '172'
abstract:
- lang: eng
text: We study strong approximation for some algebraic varieties over ℚ which are
defined using norm forms. This allows us to confirm a special case of a conjecture
due to Harpaz and Wittenberg.
article_processing_charge: No
arxiv: 1
author:
- first_name: Timothy D
full_name: Browning, Timothy D
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
- first_name: Damaris
full_name: Schindler, Damaris
last_name: Schindler
citation:
ama: Browning TD, Schindler D. Strong approximation and a conjecture of Harpaz and
Wittenberg. International Mathematics Research Notices. 2017. doi:10.1093/imrn/rnx252
apa: Browning, T. D., & Schindler, D. (2017). Strong approximation and a conjecture
of Harpaz and Wittenberg. International Mathematics Research Notices. Oxford
University Press. https://doi.org/10.1093/imrn/rnx252
chicago: Browning, Timothy D, and Damaris Schindler. “Strong Approximation and a
Conjecture of Harpaz and Wittenberg.” International Mathematics Research Notices.
Oxford University Press, 2017. https://doi.org/10.1093/imrn/rnx252.
ieee: T. D. Browning and D. Schindler, “Strong approximation and a conjecture of
Harpaz and Wittenberg,” International Mathematics Research Notices. Oxford
University Press, 2017.
ista: Browning TD, Schindler D. 2017. Strong approximation and a conjecture of Harpaz
and Wittenberg. International Mathematics Research Notices.
mla: Browning, Timothy D., and Damaris Schindler. “Strong Approximation and a Conjecture
of Harpaz and Wittenberg.” International Mathematics Research Notices,
Oxford University Press, 2017, doi:10.1093/imrn/rnx252.
short: T.D. Browning, D. Schindler, International Mathematics Research Notices (2017).
date_created: 2018-12-11T11:45:00Z
date_published: 2017-10-30T00:00:00Z
date_updated: 2021-01-12T06:52:45Z
day: '30'
doi: 10.1093/imrn/rnx252
extern: '1'
external_id:
arxiv:
- '1509.07744'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1509.07744
month: '10'
oa: 1
oa_version: None
publication: International Mathematics Research Notices
publication_status: published
publisher: Oxford University Press
publist_id: '7749'
quality_controlled: '1'
status: public
title: Strong approximation and a conjecture of Harpaz and Wittenberg
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...