---
_id: '8262'
abstract:
- lang: eng
text: "Background: The genus Burkholderia consists of species that occupy remarkably
diverse ecological niches. Its best known members are important pathogens, B.
mallei and B. pseudomallei, which cause glanders and melioidosis, respectively.
Burkholderia genomes are unusual due to their multichromosomal organization, generally
comprised of 2-3 chromosomes.\r\n\r\nResults: We performed integrated genomic
analysis of 127 Burkholderia strains. The pan-genome is open with the saturation
to be reached between 86,000 and 88,000 genes. The reconstructed rearrangements
indicate a strong avoidance of intra-replichore inversions that is likely caused
by selection against the transfer of large groups of genes between the leading
and the lagging strands. Translocated genes also tend to retain their position
in the leading or the lagging strand, and this selection is stronger for large
syntenies. Integrated reconstruction of chromosome rearrangements in the context
of strains phylogeny reveals parallel rearrangements that may indicate inversion-based
phase variation and integration of new genomic islands. In particular, we detected
parallel inversions in the second chromosomes of B. pseudomallei with breakpoints
formed by genes encoding membrane components of multidrug resistance complex,
that may be linked to a phase variation mechanism. Two genomic islands, spreading
horizontally between chromosomes, were detected in the B. cepacia group.\r\n\r\nConclusions:
This study demonstrates the power of integrated analysis of pan-genomes, chromosome
rearrangements, and selection regimes. Non-random inversion patterns indicate
selective pressure, inversions are particularly frequent in a recent pathogen
B. mallei, and, together with periods of positive selection at other branches,
may indicate adaptation to new niches. One such adaptation could be a possible
phase variation mechanism in B. pseudomallei."
article_number: '965'
article_processing_charge: No
article_type: original
author:
- first_name: Olga
full_name: Bochkareva, Olga
id: C4558D3C-6102-11E9-A62E-F418E6697425
last_name: Bochkareva
orcid: 0000-0003-1006-6639
- first_name: Elena V.
full_name: Moroz, Elena V.
last_name: Moroz
- first_name: Iakov I.
full_name: Davydov, Iakov I.
last_name: Davydov
- first_name: Mikhail S.
full_name: Gelfand, Mikhail S.
last_name: Gelfand
citation:
ama: Bochkareva O, Moroz EV, Davydov II, Gelfand MS. Genome rearrangements and selection
in multi-chromosome bacteria Burkholderia spp. BMC Genomics. 2018;19. doi:10.1186/s12864-018-5245-1
apa: Bochkareva, O., Moroz, E. V., Davydov, I. I., & Gelfand, M. S. (2018).
Genome rearrangements and selection in multi-chromosome bacteria Burkholderia
spp. BMC Genomics. Springer Nature. https://doi.org/10.1186/s12864-018-5245-1
chicago: Bochkareva, Olga, Elena V. Moroz, Iakov I. Davydov, and Mikhail S. Gelfand.
“Genome Rearrangements and Selection in Multi-Chromosome Bacteria Burkholderia
Spp.” BMC Genomics. Springer Nature, 2018. https://doi.org/10.1186/s12864-018-5245-1.
ieee: O. Bochkareva, E. V. Moroz, I. I. Davydov, and M. S. Gelfand, “Genome rearrangements
and selection in multi-chromosome bacteria Burkholderia spp.,” BMC Genomics,
vol. 19. Springer Nature, 2018.
ista: Bochkareva O, Moroz EV, Davydov II, Gelfand MS. 2018. Genome rearrangements
and selection in multi-chromosome bacteria Burkholderia spp. BMC Genomics. 19,
965.
mla: Bochkareva, Olga, et al. “Genome Rearrangements and Selection in Multi-Chromosome
Bacteria Burkholderia Spp.” BMC Genomics, vol. 19, 965, Springer Nature,
2018, doi:10.1186/s12864-018-5245-1.
short: O. Bochkareva, E.V. Moroz, I.I. Davydov, M.S. Gelfand, BMC Genomics 19 (2018).
date_created: 2020-08-15T11:02:08Z
date_published: 2018-12-27T00:00:00Z
date_updated: 2023-02-23T13:28:52Z
day: '27'
doi: 10.1186/s12864-018-5245-1
extern: '1'
intvolume: ' 19'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1186/s12864-018-5245-1
month: '12'
oa: 1
oa_version: Published Version
publication: BMC Genomics
publication_identifier:
issn:
- 1471-2164
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Genome rearrangements and selection in multi-chromosome bacteria Burkholderia
spp.
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 19
year: '2018'
...
---
_id: '8265'
abstract:
- lang: eng
text: Genome rearrangements have played an important role in the evolution of Yersinia
pestis from its progenitor Yersinia pseudotuberculosis. Traditional phylogenetic
trees for Y. pestis based on sequence comparison have short internal branches
and low bootstrap supports as only a small number of nucleotide substitutions
have occurred. On the other hand, even a small number of genome rearrangements
may resolve topological ambiguities in a phylogenetic tree. We reconstructed phylogenetic
trees based on genome rearrangements using several popular approaches such as
Maximum likelihood for Gene Order and the Bayesian model of genome rearrangements
by inversions. We also reconciled phylogenetic trees for each of the three CRISPR
loci to obtain an integrated scenario of the CRISPR cassette evolution. Analysis
of contradictions between the obtained evolutionary trees yielded numerous parallel
inversions and gain/loss events. Our data indicate that an integrated analysis
of sequence-based and inversion-based trees enhances the resolution of phylogenetic
reconstruction. In contrast, reconstructions of strain relationships based on
solely CRISPR loci may not be reliable, as the history is obscured by large deletions,
obliterating the order of spacer gains. Similarly, numerous parallel gene losses
preclude reconstruction of phylogeny based on gene content.
article_number: e4545
article_processing_charge: No
article_type: original
author:
- first_name: Olga
full_name: Bochkareva, Olga
id: C4558D3C-6102-11E9-A62E-F418E6697425
last_name: Bochkareva
orcid: 0000-0003-1006-6639
- first_name: Natalia O.
full_name: Dranenko, Natalia O.
last_name: Dranenko
- first_name: Elena S.
full_name: Ocheredko, Elena S.
last_name: Ocheredko
- first_name: German M.
full_name: Kanevsky, German M.
last_name: Kanevsky
- first_name: Yaroslav N.
full_name: Lozinsky, Yaroslav N.
last_name: Lozinsky
- first_name: Vera A.
full_name: Khalaycheva, Vera A.
last_name: Khalaycheva
- first_name: Irena I.
full_name: Artamonova, Irena I.
last_name: Artamonova
- first_name: Mikhail S.
full_name: Gelfand, Mikhail S.
last_name: Gelfand
citation:
ama: Bochkareva O, Dranenko NO, Ocheredko ES, et al. Genome rearrangements and phylogeny
reconstruction in Yersinia pestis. PeerJ. 2018;6. doi:10.7717/peerj.4545
apa: Bochkareva, O., Dranenko, N. O., Ocheredko, E. S., Kanevsky, G. M., Lozinsky,
Y. N., Khalaycheva, V. A., … Gelfand, M. S. (2018). Genome rearrangements and
phylogeny reconstruction in Yersinia pestis. PeerJ. PeerJ. https://doi.org/10.7717/peerj.4545
chicago: Bochkareva, Olga, Natalia O. Dranenko, Elena S. Ocheredko, German M. Kanevsky,
Yaroslav N. Lozinsky, Vera A. Khalaycheva, Irena I. Artamonova, and Mikhail S.
Gelfand. “Genome Rearrangements and Phylogeny Reconstruction in Yersinia Pestis.”
PeerJ. PeerJ, 2018. https://doi.org/10.7717/peerj.4545.
ieee: O. Bochkareva et al., “Genome rearrangements and phylogeny reconstruction
in Yersinia pestis,” PeerJ, vol. 6. PeerJ, 2018.
ista: Bochkareva O, Dranenko NO, Ocheredko ES, Kanevsky GM, Lozinsky YN, Khalaycheva
VA, Artamonova II, Gelfand MS. 2018. Genome rearrangements and phylogeny reconstruction
in Yersinia pestis. PeerJ. 6, e4545.
mla: Bochkareva, Olga, et al. “Genome Rearrangements and Phylogeny Reconstruction
in Yersinia Pestis.” PeerJ, vol. 6, e4545, PeerJ, 2018, doi:10.7717/peerj.4545.
short: O. Bochkareva, N.O. Dranenko, E.S. Ocheredko, G.M. Kanevsky, Y.N. Lozinsky,
V.A. Khalaycheva, I.I. Artamonova, M.S. Gelfand, PeerJ 6 (2018).
date_created: 2020-08-15T11:08:23Z
date_published: 2018-03-27T00:00:00Z
date_updated: 2023-02-23T13:28:57Z
day: '27'
doi: 10.7717/peerj.4545
extern: '1'
external_id:
pmid:
- '29607260'
intvolume: ' 6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.7717/peerj.4545
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: PeerJ
publication_identifier:
issn:
- 2167-8359
publication_status: published
publisher: PeerJ
quality_controlled: '1'
status: public
title: Genome rearrangements and phylogeny reconstruction in Yersinia pestis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2018'
...
---
_id: '8274'
abstract:
- lang: eng
text: 'Background/Aim: Our aim was to investigate the crosstalk between tumor and
immune cells (M2 macrophages) and its effects on cyclo-oxygenase-2 (COX2) regulation
in canine mammary tumors (CMT). Materials and Methods: Sh1b CMT cells and human
BT474 mammary or HT29 colon cancer cells were co-cultured with canine peripheral
blood mononuclear cells (PBMCs) or with macrophage-like differentiated THP1 monocytes
(dTHP1). Intracellular COX2 expression by PBMCs, dTHP1 and cancer cells was evaluated
by flow cytometry. Results: Co-culturing of Sh1b and canine PBMCs induced COX2
overexpression in CMT cells. In turn, COX2 expression by PBMCs, mostly CD68+ macrophages,
was attenuated by co-culture with Sh1b (p=0.0001). In accordance, co-culture with
dTHP1 prompted intracellular production of COX2 in both Sh1b CMT cells and HT29
human colon cancer cells and reduced production of COX2 in BT474 human mammary
cancer cells. The intracellular COX2 expression from dTHP1 decreased when treated
with conditioned medium from cultured Sh1b and HT29 cancer cells. Conclusion:
Bidirectional COX2 regulation between cancer and monocytes/macrophages might shape
a tolerogenic tumor microenvironment in CMT.'
article_processing_charge: No
article_type: original
author:
- first_name: Maria Isabel
full_name: Carvalho, Maria Isabel
last_name: Carvalho
- first_name: Rodolfo
full_name: Bianchini, Rodolfo
last_name: Bianchini
- first_name: Judit
full_name: Fazekas-Singer, Judit
id: 36432834-F248-11E8-B48F-1D18A9856A87
last_name: Fazekas-Singer
orcid: 0000-0002-8777-3502
- first_name: Ina
full_name: Herrmann, Ina
last_name: Herrmann
- first_name: Irene
full_name: Flickinger, Irene
last_name: Flickinger
- first_name: Johann G.
full_name: Thalhammer, Johann G.
last_name: Thalhammer
- first_name: Isabel
full_name: Pires, Isabel
last_name: Pires
- first_name: Erika
full_name: Jensen-Jarolim, Erika
last_name: Jensen-Jarolim
- first_name: Felisbina L.
full_name: Queiroga, Felisbina L.
last_name: Queiroga
citation:
ama: Carvalho MI, Bianchini R, Singer J, et al. Bidirectional regulation of COX-2
expression between cancer cells and macrophages. Anticancer Research. 2018;38(5):2811-2817.
doi:10.21873/anticanres.12525
apa: Carvalho, M. I., Bianchini, R., Singer, J., Herrmann, I., Flickinger, I., Thalhammer,
J. G., … Queiroga, F. L. (2018). Bidirectional regulation of COX-2 expression
between cancer cells and macrophages. Anticancer Research. International
Institute of Anticancer Research. https://doi.org/10.21873/anticanres.12525
chicago: Carvalho, Maria Isabel, Rodolfo Bianchini, Judit Singer, Ina Herrmann,
Irene Flickinger, Johann G. Thalhammer, Isabel Pires, Erika Jensen-Jarolim, and
Felisbina L. Queiroga. “Bidirectional Regulation of COX-2 Expression between Cancer
Cells and Macrophages.” Anticancer Research. International Institute of
Anticancer Research, 2018. https://doi.org/10.21873/anticanres.12525.
ieee: M. I. Carvalho et al., “Bidirectional regulation of COX-2 expression
between cancer cells and macrophages,” Anticancer Research, vol. 38, no.
5. International Institute of Anticancer Research, pp. 2811–2817, 2018.
ista: Carvalho MI, Bianchini R, Singer J, Herrmann I, Flickinger I, Thalhammer JG,
Pires I, Jensen-Jarolim E, Queiroga FL. 2018. Bidirectional regulation of COX-2
expression between cancer cells and macrophages. Anticancer Research. 38(5), 2811–2817.
mla: Carvalho, Maria Isabel, et al. “Bidirectional Regulation of COX-2 Expression
between Cancer Cells and Macrophages.” Anticancer Research, vol. 38, no.
5, International Institute of Anticancer Research, 2018, pp. 2811–17, doi:10.21873/anticanres.12525.
short: M.I. Carvalho, R. Bianchini, J. Singer, I. Herrmann, I. Flickinger, J.G.
Thalhammer, I. Pires, E. Jensen-Jarolim, F.L. Queiroga, Anticancer Research 38
(2018) 2811–2817.
date_created: 2020-08-17T07:13:55Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2021-01-12T08:17:52Z
day: '01'
doi: 10.21873/anticanres.12525
extern: '1'
intvolume: ' 38'
issue: '5'
language:
- iso: eng
month: '05'
oa_version: None
page: 2811-2817
publication: Anticancer Research
publication_identifier:
eissn:
- 1791-7530
issn:
- 0250-7005
publication_status: published
publisher: International Institute of Anticancer Research
quality_controlled: '1'
status: public
title: Bidirectional regulation of COX-2 expression between cancer cells and macrophages
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 38
year: '2018'
...
---
_id: '8298'
abstract:
- lang: eng
text: Sharding, or partitioning the system’s state so that different subsets of
participants handle it, is a proven approach to building distributed systems whose
total capacity scales horizontally with the number of participants. Many distributed
ledgers have adopted this approach to increase their performance, however, they
focus on the permissionless setting that assumes the existence of a strong adversary.
In this paper, we deploy channels for permissioned blockchains. Our first contribution
is to adapt sharding on asset-management applications for the permissioned setting,
while preserving liveness and safety even on transactions spanning across-channels.
Our second contribution is to leverage channels as a confidentiality boundary,
enabling different organizations and consortia to preserve their privacy within
their channels and still be part of a bigger collaborative ecosystem. To make
our system concrete we map it on top of Hyperledger Fabric.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Elli
full_name: Androulaki, Elli
last_name: Androulaki
- first_name: Christian
full_name: Cachin, Christian
last_name: Cachin
- first_name: Angelo
full_name: De Caro, Angelo
last_name: De Caro
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
citation:
ama: 'Androulaki E, Cachin C, De Caro A, Kokoris Kogias E. Channels: Horizontal
scaling and confidentiality on permissioned blockchains. In: Computer Security.
Vol 11098. Springer Nature; 2018:111-131. doi:10.1007/978-3-319-99073-6_6'
apa: 'Androulaki, E., Cachin, C., De Caro, A., & Kokoris Kogias, E. (2018).
Channels: Horizontal scaling and confidentiality on permissioned blockchains.
In Computer Security (Vol. 11098, pp. 111–131). Barcelona, Spain: Springer
Nature. https://doi.org/10.1007/978-3-319-99073-6_6'
chicago: 'Androulaki, Elli, Christian Cachin, Angelo De Caro, and Eleftherios Kokoris
Kogias. “Channels: Horizontal Scaling and Confidentiality on Permissioned Blockchains.”
In Computer Security, 11098:111–31. Springer Nature, 2018. https://doi.org/10.1007/978-3-319-99073-6_6.'
ieee: 'E. Androulaki, C. Cachin, A. De Caro, and E. Kokoris Kogias, “Channels: Horizontal
scaling and confidentiality on permissioned blockchains,” in Computer Security,
Barcelona, Spain, 2018, vol. 11098, pp. 111–131.'
ista: 'Androulaki E, Cachin C, De Caro A, Kokoris Kogias E. 2018. Channels: Horizontal
scaling and confidentiality on permissioned blockchains. Computer Security. ESORICS:
European Symposium on Research in Computer Security, LNCS, vol. 11098, 111–131.'
mla: 'Androulaki, Elli, et al. “Channels: Horizontal Scaling and Confidentiality
on Permissioned Blockchains.” Computer Security, vol. 11098, Springer Nature,
2018, pp. 111–31, doi:10.1007/978-3-319-99073-6_6.'
short: E. Androulaki, C. Cachin, A. De Caro, E. Kokoris Kogias, in:, Computer Security,
Springer Nature, 2018, pp. 111–131.
conference:
end_date: 2018-09-07
location: Barcelona, Spain
name: 'ESORICS: European Symposium on Research in Computer Security'
start_date: 2018-09-03
date_created: 2020-08-26T11:47:34Z
date_published: 2018-08-08T00:00:00Z
date_updated: 2021-01-12T08:17:57Z
day: '08'
doi: 10.1007/978-3-319-99073-6_6
extern: '1'
intvolume: ' 11098'
language:
- iso: eng
month: '08'
oa_version: None
page: 111-131
publication: Computer Security
publication_identifier:
eisbn:
- '9783319990736'
isbn:
- '9783319990729'
issn:
- 0302-9743
- 1611-3349
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: 'Channels: Horizontal scaling and confidentiality on permissioned blockchains'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11098
year: '2018'
...
---
_id: '8297'
abstract:
- lang: eng
text: "Designing a secure permissionless distributed ledger (blockchain) that performs
on par with centralized payment\r\nprocessors, such as Visa, is a challenging
task. Most existing distributed ledgers are unable to scale-out, i.e., to grow
their totalprocessing capacity with the number of validators; and those that do,
compromise security or decentralization. We present OmniLedger, a novel scale-out
distributed ledger that preserves longterm security under permissionless operation.
It ensures security and correctness by using a bias-resistant public-randomness
protocol for choosing large, statistically representative shards that process
transactions, and by introducing an efficient crossshard commit protocol that
atomically handles transactions affecting multiple shards. OmniLedger also optimizes
performance via parallel intra-shard transaction processing, ledger pruning via
collectively-signed state blocks, and low-latency “trust-butverify” \r\nvalidation
for low-value transactions. An evaluation ofour experimental prototype shows that
OmniLedger’s throughput\r\nscales linearly in the number of active validators,
supporting Visa-level workloads and beyond, while confirming typical transactions
in under two seconds."
article_processing_charge: No
author:
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
- first_name: Philipp
full_name: Jovanovic, Philipp
last_name: Jovanovic
- first_name: Linus
full_name: Gasser, Linus
last_name: Gasser
- first_name: Nicolas
full_name: Gailly, Nicolas
last_name: Gailly
- first_name: Ewa
full_name: Syta, Ewa
last_name: Syta
- first_name: Bryan
full_name: Ford, Bryan
last_name: Ford
citation:
ama: 'Kokoris Kogias E, Jovanovic P, Gasser L, Gailly N, Syta E, Ford B. OmniLedger:
A secure, scale-out, decentralized ledger via sharding. In: 2018 IEEE Symposium
on Security and Privacy. IEEE; 2018:583-598. doi:10.1109/sp.2018.000-5'
apa: 'Kokoris Kogias, E., Jovanovic, P., Gasser, L., Gailly, N., Syta, E., &
Ford, B. (2018). OmniLedger: A secure, scale-out, decentralized ledger via sharding.
In 2018 IEEE Symposium on Security and Privacy (pp. 583–598). San Francisco,
CA, United States: IEEE. https://doi.org/10.1109/sp.2018.000-5'
chicago: 'Kokoris Kogias, Eleftherios, Philipp Jovanovic, Linus Gasser, Nicolas
Gailly, Ewa Syta, and Bryan Ford. “OmniLedger: A Secure, Scale-out, Decentralized
Ledger via Sharding.” In 2018 IEEE Symposium on Security and Privacy, 583–98.
IEEE, 2018. https://doi.org/10.1109/sp.2018.000-5.'
ieee: 'E. Kokoris Kogias, P. Jovanovic, L. Gasser, N. Gailly, E. Syta, and B. Ford,
“OmniLedger: A secure, scale-out, decentralized ledger via sharding,” in 2018
IEEE Symposium on Security and Privacy, San Francisco, CA, United States,
2018, pp. 583–598.'
ista: 'Kokoris Kogias E, Jovanovic P, Gasser L, Gailly N, Syta E, Ford B. 2018.
OmniLedger: A secure, scale-out, decentralized ledger via sharding. 2018 IEEE
Symposium on Security and Privacy. SP: Symposium on Security and Privacy, 583–598.'
mla: 'Kokoris Kogias, Eleftherios, et al. “OmniLedger: A Secure, Scale-out, Decentralized
Ledger via Sharding.” 2018 IEEE Symposium on Security and Privacy, IEEE,
2018, pp. 583–98, doi:10.1109/sp.2018.000-5.'
short: E. Kokoris Kogias, P. Jovanovic, L. Gasser, N. Gailly, E. Syta, B. Ford,
in:, 2018 IEEE Symposium on Security and Privacy, IEEE, 2018, pp. 583–598.
conference:
end_date: 2018-05-24
location: San Francisco, CA, United States
name: 'SP: Symposium on Security and Privacy'
start_date: 2018-05-20
date_created: 2020-08-26T11:46:35Z
date_published: 2018-07-26T00:00:00Z
date_updated: 2021-01-12T08:17:56Z
day: '26'
doi: 10.1109/sp.2018.000-5
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2017/406
month: '07'
oa: 1
oa_version: Preprint
page: 583-598
publication: 2018 IEEE Symposium on Security and Privacy
publication_identifier:
isbn:
- '9781538643532'
issn:
- 2375-1207
publication_status: published
publisher: IEEE
quality_controlled: '1'
status: public
title: 'OmniLedger: A secure, scale-out, decentralized ledger via sharding'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '8443'
abstract:
- lang: eng
text: Characterizing the structure of membrane proteins (MPs) generally requires
extraction from their native environment, most commonly with detergents. Yet,
the physicochemical properties of detergent micelles and lipid bilayers differ
markedly and could alter the structural organization of MPs, albeit without general
rules. Dodecylphosphocholine (DPC) is the most widely used detergent for MP structure
determination by NMR, but the physiological relevance of several prominent structures
has been questioned, though indirectly, by other biophysical techniques, e.g.,
functional/thermostability assay (TSA) and molecular dynamics (MD) simulations.
Here, we resolve unambiguously this controversy by probing the functional relevance
of three different mitochondrial carriers (MCs) in DPC at the atomic level, using
an exhaustive set of solution-NMR experiments, complemented by functional/TSA
and MD data. Our results provide atomic-level insight into the structure, substrate
interaction and dynamics of the detergent–membrane protein complexes and demonstrates
cogently that, while high-resolution NMR signals can be obtained for MCs in DPC,
they systematically correspond to nonfunctional states.
article_processing_charge: No
article_type: original
author:
- first_name: Vilius
full_name: Kurauskas, Vilius
last_name: Kurauskas
- first_name: Audrey
full_name: Hessel, Audrey
last_name: Hessel
- first_name: Peixiang
full_name: Ma, Peixiang
last_name: Ma
- first_name: Paola
full_name: Lunetti, Paola
last_name: Lunetti
- first_name: Katharina
full_name: Weinhäupl, Katharina
last_name: Weinhäupl
- first_name: Lionel
full_name: Imbert, Lionel
last_name: Imbert
- first_name: Bernhard
full_name: Brutscher, Bernhard
last_name: Brutscher
- first_name: Martin S.
full_name: King, Martin S.
last_name: King
- first_name: Rémy
full_name: Sounier, Rémy
last_name: Sounier
- first_name: Vincenza
full_name: Dolce, Vincenza
last_name: Dolce
- first_name: Edmund R. S.
full_name: Kunji, Edmund R. S.
last_name: Kunji
- first_name: Loredana
full_name: Capobianco, Loredana
last_name: Capobianco
- first_name: Christophe
full_name: Chipot, Christophe
last_name: Chipot
- first_name: François
full_name: Dehez, François
last_name: Dehez
- first_name: Beate
full_name: Bersch, Beate
last_name: Bersch
- 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, Hessel A, Ma P, et al. How detergent impacts membrane proteins:
Atomic-level views of mitochondrial carriers in dodecylphosphocholine. The
Journal of Physical Chemistry Letters. 2018;9(5):933-938. doi:10.1021/acs.jpclett.8b00269'
apa: 'Kurauskas, V., Hessel, A., Ma, P., Lunetti, P., Weinhäupl, K., Imbert, L.,
… Schanda, P. (2018). How detergent impacts membrane proteins: Atomic-level views
of mitochondrial carriers in dodecylphosphocholine. The Journal of Physical
Chemistry Letters. American Chemical Society. https://doi.org/10.1021/acs.jpclett.8b00269'
chicago: 'Kurauskas, Vilius, Audrey Hessel, Peixiang Ma, Paola Lunetti, Katharina
Weinhäupl, Lionel Imbert, Bernhard Brutscher, et al. “How Detergent Impacts Membrane
Proteins: Atomic-Level Views of Mitochondrial Carriers in Dodecylphosphocholine.”
The Journal of Physical Chemistry Letters. American Chemical Society, 2018.
https://doi.org/10.1021/acs.jpclett.8b00269.'
ieee: 'V. Kurauskas et al., “How detergent impacts membrane proteins: Atomic-level
views of mitochondrial carriers in dodecylphosphocholine,” The Journal of Physical
Chemistry Letters, vol. 9, no. 5. American Chemical Society, pp. 933–938,
2018.'
ista: 'Kurauskas V, Hessel A, Ma P, Lunetti P, Weinhäupl K, Imbert L, Brutscher
B, King MS, Sounier R, Dolce V, Kunji ERS, Capobianco L, Chipot C, Dehez F, Bersch
B, Schanda P. 2018. How detergent impacts membrane proteins: Atomic-level views
of mitochondrial carriers in dodecylphosphocholine. The Journal of Physical Chemistry
Letters. 9(5), 933–938.'
mla: 'Kurauskas, Vilius, et al. “How Detergent Impacts Membrane Proteins: Atomic-Level
Views of Mitochondrial Carriers in Dodecylphosphocholine.” The Journal of Physical
Chemistry Letters, vol. 9, no. 5, American Chemical Society, 2018, pp. 933–38,
doi:10.1021/acs.jpclett.8b00269.'
short: V. Kurauskas, A. Hessel, P. Ma, P. Lunetti, K. Weinhäupl, L. Imbert, B. Brutscher,
M.S. King, R. Sounier, V. Dolce, E.R.S. Kunji, L. Capobianco, C. Chipot, F. Dehez,
B. Bersch, P. Schanda, The Journal of Physical Chemistry Letters 9 (2018) 933–938.
date_created: 2020-09-18T10:05:45Z
date_published: 2018-02-03T00:00:00Z
date_updated: 2021-01-12T08:19:18Z
day: '03'
doi: 10.1021/acs.jpclett.8b00269
extern: '1'
intvolume: ' 9'
issue: '5'
keyword:
- General Materials Science
language:
- iso: eng
month: '02'
oa_version: None
page: 933-938
publication: The Journal of Physical Chemistry Letters
publication_identifier:
issn:
- 1948-7185
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
status: public
title: 'How detergent impacts membrane proteins: Atomic-level views of mitochondrial
carriers in dodecylphosphocholine'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2018'
...
---
_id: '8440'
abstract:
- lang: eng
text: Mycobacterium tuberculosis can remain dormant in the host, an ability that
explains the failure of many current tuberculosis treatments. Recently, the natural
products cyclomarin, ecumicin, and lassomycin have been shown to efficiently kill
Mycobacterium tuberculosis persisters. Their target is the N-terminal domain of
the hexameric AAA+ ATPase ClpC1, which recognizes, unfolds, and translocates protein
substrates, such as proteins containing phosphorylated arginine residues, to the
ClpP1P2 protease for degradation. Surprisingly, these antibiotics do not inhibit
ClpC1 ATPase activity, and how they cause cell death is still unclear. Here, using
NMR and small-angle X-ray scattering, we demonstrate that arginine-phosphate binding
to the ClpC1 N-terminal domain induces millisecond dynamics. We show that these
dynamics are caused by conformational changes and do not result from unfolding
or oligomerization of this domain. Cyclomarin binding to this domain specifically
blocked these N-terminal dynamics. On the basis of these results, we propose a
mechanism of action involving cyclomarin-induced restriction of ClpC1 dynamics,
which modulates the chaperone enzymatic activity leading eventually to cell death.
article_processing_charge: No
article_type: original
author:
- first_name: Katharina
full_name: Weinhäupl, Katharina
last_name: Weinhäupl
- first_name: Martha
full_name: Brennich, Martha
last_name: Brennich
- first_name: Uli
full_name: Kazmaier, Uli
last_name: Kazmaier
- first_name: Joel
full_name: Lelievre, Joel
last_name: Lelievre
- first_name: Lluis
full_name: Ballell, Lluis
last_name: Ballell
- first_name: Alfred
full_name: Goldberg, Alfred
last_name: Goldberg
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Hugo
full_name: Fraga, Hugo
last_name: Fraga
citation:
ama: Weinhäupl K, Brennich M, Kazmaier U, et al. The antibiotic cyclomarin blocks
arginine-phosphate–induced millisecond dynamics in the N-terminal domain of ClpC1
from Mycobacterium tuberculosis. Journal of Biological Chemistry. 2018;293(22):8379-8393.
doi:10.1074/jbc.ra118.002251
apa: Weinhäupl, K., Brennich, M., Kazmaier, U., Lelievre, J., Ballell, L., Goldberg,
A., … Fraga, H. (2018). The antibiotic cyclomarin blocks arginine-phosphate–induced
millisecond dynamics in the N-terminal domain of ClpC1 from Mycobacterium tuberculosis.
Journal of Biological Chemistry. American Society for Biochemistry &
Molecular Biology. https://doi.org/10.1074/jbc.ra118.002251
chicago: Weinhäupl, Katharina, Martha Brennich, Uli Kazmaier, Joel Lelievre, Lluis
Ballell, Alfred Goldberg, Paul Schanda, and Hugo Fraga. “The Antibiotic Cyclomarin
Blocks Arginine-Phosphate–Induced Millisecond Dynamics in the N-Terminal Domain
of ClpC1 from Mycobacterium Tuberculosis.” Journal of Biological Chemistry.
American Society for Biochemistry & Molecular Biology, 2018. https://doi.org/10.1074/jbc.ra118.002251.
ieee: K. Weinhäupl et al., “The antibiotic cyclomarin blocks arginine-phosphate–induced
millisecond dynamics in the N-terminal domain of ClpC1 from Mycobacterium tuberculosis,”
Journal of Biological Chemistry, vol. 293, no. 22. American Society for
Biochemistry & Molecular Biology, pp. 8379–8393, 2018.
ista: Weinhäupl K, Brennich M, Kazmaier U, Lelievre J, Ballell L, Goldberg A, Schanda
P, Fraga H. 2018. The antibiotic cyclomarin blocks arginine-phosphate–induced
millisecond dynamics in the N-terminal domain of ClpC1 from Mycobacterium tuberculosis.
Journal of Biological Chemistry. 293(22), 8379–8393.
mla: Weinhäupl, Katharina, et al. “The Antibiotic Cyclomarin Blocks Arginine-Phosphate–Induced
Millisecond Dynamics in the N-Terminal Domain of ClpC1 from Mycobacterium Tuberculosis.”
Journal of Biological Chemistry, vol. 293, no. 22, American Society for
Biochemistry & Molecular Biology, 2018, pp. 8379–93, doi:10.1074/jbc.ra118.002251.
short: K. Weinhäupl, M. Brennich, U. Kazmaier, J. Lelievre, L. Ballell, A. Goldberg,
P. Schanda, H. Fraga, Journal of Biological Chemistry 293 (2018) 8379–8393.
date_created: 2020-09-18T10:05:18Z
date_published: 2018-06-01T00:00:00Z
date_updated: 2021-01-12T08:19:17Z
day: '01'
doi: 10.1074/jbc.ra118.002251
extern: '1'
intvolume: ' 293'
issue: '22'
keyword:
- Cell Biology
- Biochemistry
- Molecular Biology
language:
- iso: eng
month: '06'
oa_version: None
page: 8379-8393
publication: Journal of Biological Chemistry
publication_identifier:
issn:
- 0021-9258
- 1083-351X
publication_status: published
publisher: American Society for Biochemistry & Molecular Biology
quality_controlled: '1'
status: public
title: The antibiotic cyclomarin blocks arginine-phosphate–induced millisecond dynamics
in the N-terminal domain of ClpC1 from Mycobacterium tuberculosis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 293
year: '2018'
...
---
_id: '8442'
abstract:
- lang: eng
text: Membrane proteins perform a host of vital cellular functions. Deciphering
the molecular mechanisms whereby they fulfill these functions requires detailed
biophysical and structural investigations. Detergents have proven pivotal to extract
the protein from its native surroundings. Yet, they provide a milieu that departs
significantly from that of the biological membrane, to the extent that the structure,
the dynamics, and the interactions of membrane proteins in detergents may considerably
vary, as compared to the native environment. Understanding the impact of detergents
on membrane proteins is, therefore, crucial to assess the biological relevance
of results obtained in detergents. Here, we review the strengths and weaknesses
of alkyl phosphocholines (or foscholines), the most widely used detergent in solution-NMR
studies of membrane proteins. While this class of detergents is often successful
for membrane protein solubilization, a growing list of examples points to destabilizing
and denaturing properties, in particular for α-helical membrane proteins. Our
comprehensive analysis stresses the importance of stringent controls when working
with this class of detergents and when analyzing the structure and dynamics of
membrane proteins in alkyl phosphocholine detergents.
article_processing_charge: No
article_type: original
author:
- first_name: Christophe
full_name: Chipot, Christophe
last_name: Chipot
- first_name: François
full_name: Dehez, François
last_name: Dehez
- first_name: Jason R.
full_name: Schnell, Jason R.
last_name: Schnell
- first_name: Nicole
full_name: Zitzmann, Nicole
last_name: Zitzmann
- first_name: Eva
full_name: Pebay-Peyroula, Eva
last_name: Pebay-Peyroula
- first_name: Laurent J.
full_name: Catoire, Laurent J.
last_name: Catoire
- first_name: Bruno
full_name: Miroux, Bruno
last_name: Miroux
- first_name: Edmund R. S.
full_name: Kunji, Edmund R. S.
last_name: Kunji
- first_name: Gianluigi
full_name: Veglia, Gianluigi
last_name: Veglia
- first_name: Timothy A.
full_name: Cross, Timothy A.
last_name: Cross
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: 'Chipot C, Dehez F, Schnell JR, et al. Perturbations of native membrane protein
structure in alkyl phosphocholine detergents: A critical assessment of NMR and
biophysical studies. Chemical Reviews. 2018;118(7):3559-3607. doi:10.1021/acs.chemrev.7b00570'
apa: 'Chipot, C., Dehez, F., Schnell, J. R., Zitzmann, N., Pebay-Peyroula, E., Catoire,
L. J., … Schanda, P. (2018). Perturbations of native membrane protein structure
in alkyl phosphocholine detergents: A critical assessment of NMR and biophysical
studies. Chemical Reviews. American Chemical Society. https://doi.org/10.1021/acs.chemrev.7b00570'
chicago: 'Chipot, Christophe, François Dehez, Jason R. Schnell, Nicole Zitzmann,
Eva Pebay-Peyroula, Laurent J. Catoire, Bruno Miroux, et al. “Perturbations of
Native Membrane Protein Structure in Alkyl Phosphocholine Detergents: A Critical
Assessment of NMR and Biophysical Studies.” Chemical Reviews. American
Chemical Society, 2018. https://doi.org/10.1021/acs.chemrev.7b00570.'
ieee: 'C. Chipot et al., “Perturbations of native membrane protein structure
in alkyl phosphocholine detergents: A critical assessment of NMR and biophysical
studies,” Chemical Reviews, vol. 118, no. 7. American Chemical Society,
pp. 3559–3607, 2018.'
ista: 'Chipot C, Dehez F, Schnell JR, Zitzmann N, Pebay-Peyroula E, Catoire LJ,
Miroux B, Kunji ERS, Veglia G, Cross TA, Schanda P. 2018. Perturbations of native
membrane protein structure in alkyl phosphocholine detergents: A critical assessment
of NMR and biophysical studies. Chemical Reviews. 118(7), 3559–3607.'
mla: 'Chipot, Christophe, et al. “Perturbations of Native Membrane Protein Structure
in Alkyl Phosphocholine Detergents: A Critical Assessment of NMR and Biophysical
Studies.” Chemical Reviews, vol. 118, no. 7, American Chemical Society,
2018, pp. 3559–607, doi:10.1021/acs.chemrev.7b00570.'
short: C. Chipot, F. Dehez, J.R. Schnell, N. Zitzmann, E. Pebay-Peyroula, L.J. Catoire,
B. Miroux, E.R.S. Kunji, G. Veglia, T.A. Cross, P. Schanda, Chemical Reviews 118
(2018) 3559–3607.
date_created: 2020-09-18T10:05:35Z
date_published: 2018-02-28T00:00:00Z
date_updated: 2021-01-12T08:19:18Z
day: '28'
doi: 10.1021/acs.chemrev.7b00570
extern: '1'
intvolume: ' 118'
issue: '7'
keyword:
- General Chemistry
language:
- iso: eng
month: '02'
oa_version: None
page: 3559-3607
publication: Chemical Reviews
publication_identifier:
issn:
- 0009-2665
- 1520-6890
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
status: public
title: 'Perturbations of native membrane protein structure in alkyl phosphocholine
detergents: A critical assessment of NMR and biophysical studies'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 118
year: '2018'
...
---
_id: '8441'
abstract:
- lang: eng
text: Solid-state near-rotary-resonance measurements of the spin–lattice relaxation
rate in the rotating frame (R1ρ) is a powerful NMR technique for studying molecular
dynamics in the microsecond time scale. The small difference between the spin-lock
(SL) and magic-angle-spinning (MAS) frequencies allows sampling very slow motions,
at the same time it brings up some methodological challenges. In this work, several
issues affecting correct measurements and analysis of 15N R1ρ data are considered
in detail. Among them are signal amplitude as a function of the difference between
SL and MAS frequencies, “dead time” in the initial part of the relaxation decay
caused by transient spin-dynamic oscillations, measurements under HORROR condition
and proper treatment of the multi-exponential relaxation decays. The multiple
15N R1ρ measurements at different SL fields and temperatures have been conducted
in 1D mode (i.e. without site-specific resolution) for a set of four different
microcrystalline protein samples (GB1, SH3, MPD-ubiquitin and cubic-PEG-ubiquitin)
to study the overall protein rocking in a crystal. While the amplitude of this
motion varies very significantly, its correlation time for all four sample is
practically the same, 30–50 μs. The amplitude of the rocking motion correlates
with the packing density of a protein crystal. It has been suggested that the
rocking motion is not diffusive but likely a jump-like dynamic process.
article_processing_charge: No
article_type: original
author:
- first_name: Alexey
full_name: Krushelnitsky, Alexey
last_name: Krushelnitsky
- first_name: Diego
full_name: Gauto, Diego
last_name: Gauto
- first_name: Diana C.
full_name: Rodriguez Camargo, Diana C.
last_name: Rodriguez Camargo
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Kay
full_name: Saalwächter, Kay
last_name: Saalwächter
citation:
ama: 'Krushelnitsky A, Gauto D, Rodriguez Camargo DC, Schanda P, Saalwächter K.
Microsecond motions probed by near-rotary-resonance R1ρ 15N MAS NMR experiments:
The model case of protein overall-rocking in crystals. Journal of Biomolecular
NMR. 2018;71(1):53-67. doi:10.1007/s10858-018-0191-4'
apa: 'Krushelnitsky, A., Gauto, D., Rodriguez Camargo, D. C., Schanda, P., &
Saalwächter, K. (2018). Microsecond motions probed by near-rotary-resonance R1ρ
15N MAS NMR experiments: The model case of protein overall-rocking in crystals.
Journal of Biomolecular NMR. Springer Nature. https://doi.org/10.1007/s10858-018-0191-4'
chicago: 'Krushelnitsky, Alexey, Diego Gauto, Diana C. Rodriguez Camargo, Paul Schanda,
and Kay Saalwächter. “Microsecond Motions Probed by Near-Rotary-Resonance R1ρ
15N MAS NMR Experiments: The Model Case of Protein Overall-Rocking in Crystals.”
Journal of Biomolecular NMR. Springer Nature, 2018. https://doi.org/10.1007/s10858-018-0191-4.'
ieee: 'A. Krushelnitsky, D. Gauto, D. C. Rodriguez Camargo, P. Schanda, and K. Saalwächter,
“Microsecond motions probed by near-rotary-resonance R1ρ 15N MAS NMR experiments:
The model case of protein overall-rocking in crystals,” Journal of Biomolecular
NMR, vol. 71, no. 1. Springer Nature, pp. 53–67, 2018.'
ista: 'Krushelnitsky A, Gauto D, Rodriguez Camargo DC, Schanda P, Saalwächter K.
2018. Microsecond motions probed by near-rotary-resonance R1ρ 15N MAS NMR experiments:
The model case of protein overall-rocking in crystals. Journal of Biomolecular
NMR. 71(1), 53–67.'
mla: 'Krushelnitsky, Alexey, et al. “Microsecond Motions Probed by Near-Rotary-Resonance
R1ρ 15N MAS NMR Experiments: The Model Case of Protein Overall-Rocking in Crystals.”
Journal of Biomolecular NMR, vol. 71, no. 1, Springer Nature, 2018, pp.
53–67, doi:10.1007/s10858-018-0191-4.'
short: A. Krushelnitsky, D. Gauto, D.C. Rodriguez Camargo, P. Schanda, K. Saalwächter,
Journal of Biomolecular NMR 71 (2018) 53–67.
date_created: 2020-09-18T10:05:28Z
date_published: 2018-05-30T00:00:00Z
date_updated: 2021-01-12T08:19:17Z
day: '30'
doi: 10.1007/s10858-018-0191-4
extern: '1'
intvolume: ' 71'
issue: '1'
language:
- iso: eng
month: '05'
oa_version: Published Version
page: 53-67
publication: Journal of Biomolecular NMR
publication_identifier:
issn:
- 0925-2738
- 1573-5001
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: 'Microsecond motions probed by near-rotary-resonance R1ρ 15N MAS NMR experiments:
The model case of protein overall-rocking in crystals'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 71
year: '2018'
...
---
_id: '8439'
abstract:
- lang: eng
text: Lipopolysaccharides (LPS) are complex glycolipids forming the outside layer
of Gram-negative bacteria. Their hydrophobic and heterogeneous nature greatly
hampers their structural study in an environment similar to the bacterial surface.
We have studied LPS purified from E. coli and pathogenic P. aeruginosa with long
O-antigen polysaccharides assembled in solution as vesicles or elongated micelles.
Solid-state NMR with magic-angle spinning permitted the identification of NMR
signals arising from regions with different flexibilities in the LPS, from the
lipid components to the O-antigen polysaccharides. Atomic scale data on the LPS
enabled the study of the interaction of gentamicin antibiotic bound to P. aeruginosa
LPS, for which we could confirm that a specific oligosaccharide is involved in
the antibiotic binding. The possibility to study LPS alone and bound to a ligand
when it is assembled in membrane-like structures opens great prospects for the
investigation of proteins and antibiotics that specifically target such an important
molecule at the surface of Gram-negative bacteria.
article_processing_charge: No
article_type: original
author:
- first_name: Cedric
full_name: Laguri, Cedric
last_name: Laguri
- first_name: Alba
full_name: Silipo, Alba
last_name: Silipo
- first_name: Alessandra M.
full_name: Martorana, Alessandra M.
last_name: Martorana
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Roberta
full_name: Marchetti, Roberta
last_name: Marchetti
- first_name: Alessandra
full_name: Polissi, Alessandra
last_name: Polissi
- first_name: Antonio
full_name: Molinaro, Antonio
last_name: Molinaro
- first_name: Jean-Pierre
full_name: Simorre, Jean-Pierre
last_name: Simorre
citation:
ama: Laguri C, Silipo A, Martorana AM, et al. Solid state NMR studies of intact
lipopolysaccharide endotoxin. ACS Chemical Biology. 2018;13(8):2106-2113.
doi:10.1021/acschembio.8b00271
apa: Laguri, C., Silipo, A., Martorana, A. M., Schanda, P., Marchetti, R., Polissi,
A., … Simorre, J.-P. (2018). Solid state NMR studies of intact lipopolysaccharide
endotoxin. ACS Chemical Biology. American Chemical Society. https://doi.org/10.1021/acschembio.8b00271
chicago: Laguri, Cedric, Alba Silipo, Alessandra M. Martorana, Paul Schanda, Roberta
Marchetti, Alessandra Polissi, Antonio Molinaro, and Jean-Pierre Simorre. “Solid
State NMR Studies of Intact Lipopolysaccharide Endotoxin.” ACS Chemical Biology.
American Chemical Society, 2018. https://doi.org/10.1021/acschembio.8b00271.
ieee: C. Laguri et al., “Solid state NMR studies of intact lipopolysaccharide
endotoxin,” ACS Chemical Biology, vol. 13, no. 8. American Chemical Society,
pp. 2106–2113, 2018.
ista: Laguri C, Silipo A, Martorana AM, Schanda P, Marchetti R, Polissi A, Molinaro
A, Simorre J-P. 2018. Solid state NMR studies of intact lipopolysaccharide endotoxin.
ACS Chemical Biology. 13(8), 2106–2113.
mla: Laguri, Cedric, et al. “Solid State NMR Studies of Intact Lipopolysaccharide
Endotoxin.” ACS Chemical Biology, vol. 13, no. 8, American Chemical Society,
2018, pp. 2106–13, doi:10.1021/acschembio.8b00271.
short: C. Laguri, A. Silipo, A.M. Martorana, P. Schanda, R. Marchetti, A. Polissi,
A. Molinaro, J.-P. Simorre, ACS Chemical Biology 13 (2018) 2106–2113.
date_created: 2020-09-18T10:05:09Z
date_published: 2018-07-02T00:00:00Z
date_updated: 2021-01-12T08:19:16Z
day: '02'
doi: 10.1021/acschembio.8b00271
extern: '1'
intvolume: ' 13'
issue: '8'
keyword:
- Molecular Medicine
- Biochemistry
- General Medicine
language:
- iso: eng
month: '07'
oa_version: None
page: 2106-2113
publication: ACS Chemical Biology
publication_identifier:
issn:
- 1554-8929
- 1554-8937
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
status: public
title: Solid state NMR studies of intact lipopolysaccharide endotoxin
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2018'
...
---
_id: '8547'
abstract:
- lang: eng
text: The cerebral cortex contains multiple hierarchically organized areas with
distinctive cytoarchitectonical patterns, but the cellular mechanisms underlying
the emergence of this diversity remain unclear. Here, we have quantitatively investigated
the neuronal output of individual progenitor cells in the ventricular zone of
the developing mouse neocortex using a combination of methods that together circumvent
the biases and limitations of individual approaches. We found that individual
cortical progenitor cells show a high degree of stochasticity and generate pyramidal
cell lineages that adopt a wide range of laminar configurations. Mathematical
modelling these lineage data suggests that a small number of progenitor cell populations,
each generating pyramidal cells following different stochastic developmental programs,
suffice to generate the heterogenous complement of pyramidal cell lineages that
collectively build the complex cytoarchitecture of the neocortex.
acknowledgement: We thank I. Andrew and S.E. Bae for excellent technical assistance,
F. Gage for plasmids, and K. Nave (Nex-Cre) for mouse colonies. We thank members
of the Marín and Rico laboratories for stimulating discussions and ideas. Our research
on this topic is supported by grants from the European Research Council (ERC-2017-AdG
787355 to O.M and ERC2016-CoG 725780 to S.H.) and Wellcome Trust (103714MA) to O.M.
L.L. was the recipient of an EMBO long-term postdoctoral fellowship, R.B. received
support from FWF Lise-Meitner program (M 2416) and F.K.W. was supported by an EMBO
postdoctoral fellowship and is currently a Marie Skłodowska-Curie Fellow from the
European Commission under the H2020 Programme.
article_processing_charge: No
author:
- first_name: Alfredo
full_name: Llorca, Alfredo
last_name: Llorca
- first_name: Gabriele
full_name: Ciceri, Gabriele
last_name: Ciceri
- first_name: Robert J
full_name: Beattie, Robert J
id: 2E26DF60-F248-11E8-B48F-1D18A9856A87
last_name: Beattie
orcid: 0000-0002-8483-8753
- first_name: Fong K.
full_name: Wong, Fong K.
last_name: Wong
- first_name: Giovanni
full_name: Diana, Giovanni
last_name: Diana
- first_name: Eleni
full_name: Serafeimidou, Eleni
last_name: Serafeimidou
- first_name: Marian
full_name: Fernández-Otero, Marian
last_name: Fernández-Otero
- first_name: Carmen
full_name: Streicher, Carmen
id: 36BCB99C-F248-11E8-B48F-1D18A9856A87
last_name: Streicher
- first_name: Sebastian J.
full_name: Arnold, Sebastian J.
last_name: Arnold
- first_name: Martin
full_name: Meyer, Martin
last_name: Meyer
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Miguel
full_name: Maravall, Miguel
last_name: Maravall
- first_name: Oscar
full_name: Marín, Oscar
last_name: Marín
citation:
ama: Llorca A, Ciceri G, Beattie RJ, et al. Heterogeneous progenitor cell behaviors
underlie the assembly of neocortical cytoarchitecture. bioRxiv. doi:10.1101/494088
apa: Llorca, A., Ciceri, G., Beattie, R. J., Wong, F. K., Diana, G., Serafeimidou,
E., … Marín, O. (n.d.). Heterogeneous progenitor cell behaviors underlie the assembly
of neocortical cytoarchitecture. bioRxiv. Cold Spring Harbor Laboratory.
https://doi.org/10.1101/494088
chicago: Llorca, Alfredo, Gabriele Ciceri, Robert J Beattie, Fong K. Wong, Giovanni
Diana, Eleni Serafeimidou, Marian Fernández-Otero, et al. “Heterogeneous Progenitor
Cell Behaviors Underlie the Assembly of Neocortical Cytoarchitecture.” BioRxiv.
Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/494088.
ieee: A. Llorca et al., “Heterogeneous progenitor cell behaviors underlie
the assembly of neocortical cytoarchitecture,” bioRxiv. Cold Spring Harbor
Laboratory.
ista: Llorca A, Ciceri G, Beattie RJ, Wong FK, Diana G, Serafeimidou E, Fernández-Otero
M, Streicher C, Arnold SJ, Meyer M, Hippenmeyer S, Maravall M, Marín O. Heterogeneous
progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture.
bioRxiv, 10.1101/494088.
mla: Llorca, Alfredo, et al. “Heterogeneous Progenitor Cell Behaviors Underlie the
Assembly of Neocortical Cytoarchitecture.” BioRxiv, Cold Spring Harbor
Laboratory, doi:10.1101/494088.
short: A. Llorca, G. Ciceri, R.J. Beattie, F.K. Wong, G. Diana, E. Serafeimidou,
M. Fernández-Otero, C. Streicher, S.J. Arnold, M. Meyer, S. Hippenmeyer, M. Maravall,
O. Marín, BioRxiv (n.d.).
date_created: 2020-09-21T12:01:50Z
date_published: 2018-12-13T00:00:00Z
date_updated: 2021-01-12T08:20:00Z
day: '13'
department:
- _id: SiHi
doi: 10.1101/494088
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/494088
month: '12'
oa: 1
oa_version: Preprint
project:
- _id: 260018B0-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '725780'
name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
- _id: 264E56E2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02416
name: Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex
publication: bioRxiv
publication_status: submitted
publisher: Cold Spring Harbor Laboratory
status: public
title: Heterogeneous progenitor cell behaviors underlie the assembly of neocortical
cytoarchitecture
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '86'
abstract:
- lang: eng
text: Responsiveness—the requirement that every request to a system be eventually
handled—is one of the fundamental liveness properties of a reactive system. Average
response time is a quantitative measure for the responsiveness requirement used
commonly in performance evaluation. We show how average response time can be computed
on state-transition graphs, on Markov chains, and on game graphs. In all three
cases, we give polynomial-time algorithms.
acknowledgement: 'This research was supported in part by the Austrian Science Fund
(FWF) under grants S11402-N23, S11407-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein
Award), ERC Start grant (279307: Graph Games), Vienna Science and Technology Fund
(WWTF) through project ICT15-003 and by the National Science Centre (NCN), Poland
under grant 2014/15/D/ST6/04543.'
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Jan
full_name: Otop, Jan
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
citation:
ama: 'Chatterjee K, Henzinger TA, Otop J. Computing average response time. In: Lohstroh
M, Derler P, Sirjani M, eds. Principles of Modeling. Vol 10760. Springer;
2018:143-161. doi:10.1007/978-3-319-95246-8_9'
apa: Chatterjee, K., Henzinger, T. A., & Otop, J. (2018). Computing average
response time. In M. Lohstroh, P. Derler, & M. Sirjani (Eds.), Principles
of Modeling (Vol. 10760, pp. 143–161). Springer. https://doi.org/10.1007/978-3-319-95246-8_9
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Computing Average
Response Time.” In Principles of Modeling, edited by Marten Lohstroh, Patricia
Derler, and Marjan Sirjani, 10760:143–61. Springer, 2018. https://doi.org/10.1007/978-3-319-95246-8_9.
ieee: K. Chatterjee, T. A. Henzinger, and J. Otop, “Computing average response time,”
in Principles of Modeling, vol. 10760, M. Lohstroh, P. Derler, and M. Sirjani,
Eds. Springer, 2018, pp. 143–161.
ista: 'Chatterjee K, Henzinger TA, Otop J. 2018.Computing average response time.
In: Principles of Modeling. LNCS, vol. 10760, 143–161.'
mla: Chatterjee, Krishnendu, et al. “Computing Average Response Time.” Principles
of Modeling, edited by Marten Lohstroh et al., vol. 10760, Springer, 2018,
pp. 143–61, doi:10.1007/978-3-319-95246-8_9.
short: K. Chatterjee, T.A. Henzinger, J. Otop, in:, M. Lohstroh, P. Derler, M. Sirjani
(Eds.), Principles of Modeling, Springer, 2018, pp. 143–161.
date_created: 2018-12-11T11:44:33Z
date_published: 2018-07-20T00:00:00Z
date_updated: 2021-01-12T08:20:14Z
day: '20'
ddc:
- '000'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1007/978-3-319-95246-8_9
ec_funded: 1
editor:
- first_name: Marten
full_name: Lohstroh, Marten
last_name: Lohstroh
- first_name: Patricia
full_name: Derler, Patricia
last_name: Derler
- first_name: Marjan
full_name: Sirjani, Marjan
last_name: Sirjani
file:
- access_level: open_access
checksum: 9995c6ce6957333baf616fc4f20be597
content_type: application/pdf
creator: dernst
date_created: 2019-11-19T08:22:18Z
date_updated: 2020-07-14T12:48:14Z
file_id: '7053'
file_name: 2018_PrinciplesModeling_Chatterjee.pdf
file_size: 516307
relation: main_file
file_date_updated: 2020-07-14T12:48:14Z
has_accepted_license: '1'
intvolume: ' 10760'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
page: 143 - 161
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
publication: Principles of Modeling
publication_status: published
publisher: Springer
publist_id: '7968'
quality_controlled: '1'
scopus_import: 1
status: public
title: Computing average response time
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10760
year: '2018'
...
---
_id: '9062'
abstract:
- lang: eng
text: 'Self-assembly is the autonomous organization of components into patterns
or structures: an essential ingredient of biology and a desired route to complex
organization1. At equilibrium, the structure is encoded through specific interactions2,3,4,5,6,7,8,
at an unfavourable entropic cost for the system. An alternative approach, widely
used by nature, uses energy input to bypass the entropy bottleneck and develop
features otherwise impossible at equilibrium9. Dissipative building blocks that
inject energy locally were made available by recent advances in colloidal science10,11
but have not been used to control self-assembly. Here we show the targeted formation
of self-powered microgears from active particles and their autonomous synchronization
into dynamical superstructures. We use a photoactive component that consumes fuel,
haematite, to devise phototactic microswimmers that form self-spinning microgears
following spatiotemporal light patterns. The gears are coupled via their chemical
clouds by diffusiophoresis12 and constitute the elementary bricks of synchronized
superstructures, which autonomously regulate their dynamics. The results are quantitatively
rationalized on the basis of a stochastic description of diffusio-phoretic oscillators
dynamically coupled by chemical gradients. Our findings harness non-equilibrium
phoretic phenomena to program interactions and direct self-assembly with fidelity
and specificity. It lays the groundwork for the autonomous construction of dynamical
architectures and functional micro-machinery.'
article_processing_charge: No
article_type: original
author:
- first_name: Antoine
full_name: Aubret, Antoine
last_name: Aubret
- first_name: Mena
full_name: Youssef, Mena
last_name: Youssef
- first_name: Stefano
full_name: Sacanna, Stefano
last_name: Sacanna
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
citation:
ama: Aubret A, Youssef M, Sacanna S, Palacci JA. Targeted assembly and synchronization
of self-spinning microgears. Nature Physics. 2018;14(11):1114-1118. doi:10.1038/s41567-018-0227-4
apa: Aubret, A., Youssef, M., Sacanna, S., & Palacci, J. A. (2018). Targeted
assembly and synchronization of self-spinning microgears. Nature Physics.
Springer Nature. https://doi.org/10.1038/s41567-018-0227-4
chicago: Aubret, Antoine, Mena Youssef, Stefano Sacanna, and Jérémie A Palacci.
“Targeted Assembly and Synchronization of Self-Spinning Microgears.” Nature
Physics. Springer Nature, 2018. https://doi.org/10.1038/s41567-018-0227-4.
ieee: A. Aubret, M. Youssef, S. Sacanna, and J. A. Palacci, “Targeted assembly and
synchronization of self-spinning microgears,” Nature Physics, vol. 14,
no. 11. Springer Nature, pp. 1114–1118, 2018.
ista: Aubret A, Youssef M, Sacanna S, Palacci JA. 2018. Targeted assembly and synchronization
of self-spinning microgears. Nature Physics. 14(11), 1114–1118.
mla: Aubret, Antoine, et al. “Targeted Assembly and Synchronization of Self-Spinning
Microgears.” Nature Physics, vol. 14, no. 11, Springer Nature, 2018, pp.
1114–18, doi:10.1038/s41567-018-0227-4.
short: A. Aubret, M. Youssef, S. Sacanna, J.A. Palacci, Nature Physics 14 (2018)
1114–1118.
date_created: 2021-02-02T13:52:49Z
date_published: 2018-11-01T00:00:00Z
date_updated: 2023-02-23T13:48:02Z
day: '01'
doi: 10.1038/s41567-018-0227-4
extern: '1'
external_id:
arxiv:
- '1810.01033'
intvolume: ' 14'
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1810.01033
month: '11'
oa: 1
oa_version: Preprint
page: 1114-1118
publication: Nature Physics
publication_identifier:
eissn:
- 1745-2481
issn:
- 1745-2473
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Targeted assembly and synchronization of self-spinning microgears
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 14
year: '2018'
...
---
_id: '9229'
alternative_title:
- Molecular and cellular neuroscience
article_processing_charge: No
article_type: letter_note
author:
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
citation:
ama: Danzl JG. Diffraction-unlimited optical imaging for synaptic physiology. Opera
Medica et Physiologica. 2018;4(S1):11. doi:10.20388/omp2018.00s1.001
apa: Danzl, J. G. (2018). Diffraction-unlimited optical imaging for synaptic physiology.
Opera Medica et Physiologica. Lobachevsky State University of Nizhny Novgorod.
https://doi.org/10.20388/omp2018.00s1.001
chicago: Danzl, Johann G. “Diffraction-Unlimited Optical Imaging for Synaptic Physiology.”
Opera Medica et Physiologica. Lobachevsky State University of Nizhny Novgorod,
2018. https://doi.org/10.20388/omp2018.00s1.001.
ieee: J. G. Danzl, “Diffraction-unlimited optical imaging for synaptic physiology,”
Opera Medica et Physiologica, vol. 4, no. S1. Lobachevsky State University
of Nizhny Novgorod, p. 11, 2018.
ista: Danzl JG. 2018. Diffraction-unlimited optical imaging for synaptic physiology.
Opera Medica et Physiologica. 4(S1), 11.
mla: Danzl, Johann G. “Diffraction-Unlimited Optical Imaging for Synaptic Physiology.”
Opera Medica et Physiologica, vol. 4, no. S1, Lobachevsky State University
of Nizhny Novgorod, 2018, p. 11, doi:10.20388/omp2018.00s1.001.
short: J.G. Danzl, Opera Medica et Physiologica 4 (2018) 11.
date_created: 2021-03-07T23:01:25Z
date_published: 2018-06-30T00:00:00Z
date_updated: 2021-12-03T07:31:05Z
day: '30'
department:
- _id: JoDa
doi: 10.20388/omp2018.00s1.001
intvolume: ' 4'
issue: S1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://operamedphys.org/content/molecular-and-cellular-neuroscience
month: '06'
oa: 1
oa_version: Published Version
page: '11'
publication: Opera Medica et Physiologica
publication_identifier:
eissn:
- 2500-2295
issn:
- 2500-2287
publication_status: published
publisher: Lobachevsky State University of Nizhny Novgorod
quality_controlled: '1'
scopus_import: '1'
status: public
title: Diffraction-unlimited optical imaging for synaptic physiology
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 4
year: '2018'
...
---
_id: '6005'
abstract:
- lang: eng
text: Network games are widely used as a model for selfish resource-allocation problems.
In the classicalmodel, each player selects a path connecting her source and target
vertices. The cost of traversingan edge depends on theload; namely, number of
players that traverse it. Thus, it abstracts the factthat different users may
use a resource at different times and for different durations, which playsan important
role in determining the costs of the users in reality. For example, when transmittingpackets
in a communication network, routing traffic in a road network, or processing a
task in aproduction system, actual sharing and congestion of resources crucially
depends on time.In [13], we introducedtimed network games, which add a time component
to network games.Each vertexvin the network is associated with a cost function,
mapping the load onvto theprice that a player pays for staying invfor one time
unit with this load. Each edge in thenetwork is guarded by the time intervals
in which it can be traversed, which forces the players tospend time in the vertices.
In this work we significantly extend the way time can be referred toin timed network
games. In the model we study, the network is equipped withclocks, and, as intimed
automata, edges are guarded by constraints on the values of the clocks, and their
traversalmay involve a reset of some clocks. We argue that the stronger model
captures many realisticnetworks. The addition of clocks breaks the techniques
we developed in [13] and we developnew techniques in order to show that positive
results on classic network games carry over to thestronger timed setting.
alternative_title:
- LIPIcs
article_number: '23'
article_processing_charge: No
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- first_name: Shibashis
full_name: Guha, Shibashis
last_name: Guha
- first_name: Orna
full_name: Kupferman, Orna
last_name: Kupferman
citation:
ama: 'Avni G, Guha S, Kupferman O. Timed network games with clocks. In: Vol 117.
Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPICS.MFCS.2018.23'
apa: 'Avni, G., Guha, S., & Kupferman, O. (2018). Timed network games with clocks
(Vol. 117). Presented at the MFCS: Mathematical Foundations of Computer Science,
Liverpool, United Kingdom: Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
https://doi.org/10.4230/LIPICS.MFCS.2018.23'
chicago: Avni, Guy, Shibashis Guha, and Orna Kupferman. “Timed Network Games with
Clocks,” Vol. 117. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPICS.MFCS.2018.23.
ieee: 'G. Avni, S. Guha, and O. Kupferman, “Timed network games with clocks,” presented
at the MFCS: Mathematical Foundations of Computer Science, Liverpool, United Kingdom,
2018, vol. 117.'
ista: 'Avni G, Guha S, Kupferman O. 2018. Timed network games with clocks. MFCS:
Mathematical Foundations of Computer Science, LIPIcs, vol. 117, 23.'
mla: Avni, Guy, et al. Timed Network Games with Clocks. Vol. 117, 23, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPICS.MFCS.2018.23.
short: G. Avni, S. Guha, O. Kupferman, in:, Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, 2018.
conference:
end_date: 2018-08-31
location: Liverpool, United Kingdom
name: 'MFCS: Mathematical Foundations of Computer Science'
start_date: 2018-08-27
date_created: 2019-02-14T14:12:09Z
date_published: 2018-08-01T00:00:00Z
date_updated: 2023-02-23T14:02:58Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.4230/LIPICS.MFCS.2018.23
file:
- access_level: open_access
checksum: 41ab2ae9b63f5eb49fa995250c0ba128
content_type: application/pdf
creator: dernst
date_created: 2019-02-14T14:22:04Z
date_updated: 2020-07-14T12:47:15Z
file_id: '6007'
file_name: 2018_LIPIcs_Avni.pdf
file_size: 542889
relation: main_file
file_date_updated: 2020-07-14T12:47:15Z
has_accepted_license: '1'
intvolume: ' 117'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 264B3912-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02369
name: Formal Methods meets Algorithmic Game Theory
publication_identifier:
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
related_material:
record:
- id: '963'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Timed network games with clocks
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 117
year: '2018'
...
---
_id: '9668'
abstract:
- lang: eng
text: Estimating the homogeneous ice nucleation rate from undercooled liquid water
is crucial for understanding many important physical phenomena and technological
applications, and challenging for both experiments and theory. From a theoretical
point of view, difficulties arise due to the long time scales required, as well
as the numerous nucleation pathways involved to form ice nuclei with different
stacking disorders. We computed the homogeneous ice nucleation rate at a physically
relevant undercooling for a single-site water model, taking into account the diffuse
nature of ice–water interfaces, stacking disorders in ice nuclei, and the addition
rate of particles to the critical nucleus. We disentangled and investigated the
relative importance of all the terms, including interfacial free energy, entropic
contributions and the kinetic prefactor, that contribute to the overall nucleation
rate. Breaking down the problem into pieces not only provides physical insights
into ice nucleation, but also sheds light on the long-standing discrepancy between
different theoretical predictions, as well as between theoretical and experimental
determinations of the nucleation rate. Moreover, we pinpoint the main shortcomings
and suggest strategies to systematically improve the existing simulation methods.
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: Christoph
full_name: Dellago, Christoph
last_name: Dellago
- first_name: Michele
full_name: Ceriotti, Michele
last_name: Ceriotti
citation:
ama: 'Cheng B, Dellago C, Ceriotti M. Theoretical prediction of the homogeneous
ice nucleation rate: Disentangling thermodynamics and kinetics. Physical Chemistry
Chemical Physics. 2018;20(45):28732-28740. doi:10.1039/c8cp04561e'
apa: 'Cheng, B., Dellago, C., & Ceriotti, M. (2018). Theoretical prediction
of the homogeneous ice nucleation rate: Disentangling thermodynamics and kinetics.
Physical Chemistry Chemical Physics. Royal Society of Chemistry. https://doi.org/10.1039/c8cp04561e'
chicago: 'Cheng, Bingqing, Christoph Dellago, and Michele Ceriotti. “Theoretical
Prediction of the Homogeneous Ice Nucleation Rate: Disentangling Thermodynamics
and Kinetics.” Physical Chemistry Chemical Physics. Royal Society of Chemistry,
2018. https://doi.org/10.1039/c8cp04561e.'
ieee: 'B. Cheng, C. Dellago, and M. Ceriotti, “Theoretical prediction of the homogeneous
ice nucleation rate: Disentangling thermodynamics and kinetics,” Physical Chemistry
Chemical Physics, vol. 20, no. 45. Royal Society of Chemistry, pp. 28732–28740,
2018.'
ista: 'Cheng B, Dellago C, Ceriotti M. 2018. Theoretical prediction of the homogeneous
ice nucleation rate: Disentangling thermodynamics and kinetics. Physical Chemistry
Chemical Physics. 20(45), 28732–28740.'
mla: 'Cheng, Bingqing, et al. “Theoretical Prediction of the Homogeneous Ice Nucleation
Rate: Disentangling Thermodynamics and Kinetics.” Physical Chemistry Chemical
Physics, vol. 20, no. 45, Royal Society of Chemistry, 2018, pp. 28732–40,
doi:10.1039/c8cp04561e.'
short: B. Cheng, C. Dellago, M. Ceriotti, Physical Chemistry Chemical Physics 20
(2018) 28732–28740.
date_created: 2021-07-15T12:51:44Z
date_published: 2018-12-07T00:00:00Z
date_updated: 2021-08-09T12:36:47Z
day: '07'
doi: 10.1039/c8cp04561e
extern: '1'
external_id:
arxiv:
- '1807.05551'
pmid:
- '30412211'
intvolume: ' 20'
issue: '45'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1807.05551
month: '12'
oa: 1
oa_version: Preprint
page: 28732-28740
pmid: 1
publication: Physical Chemistry Chemical Physics
publication_identifier:
eissn:
- 1463-9084
issn:
- 1463-9076
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Theoretical prediction of the homogeneous ice nucleation rate: Disentangling
thermodynamics and kinetics'
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 20
year: '2018'
...
---
_id: '9687'
abstract:
- lang: eng
text: The Gibbs free energy is the fundamental thermodynamic potential underlying
the relative stability of different states of matter under constant-pressure conditions.
However, computing this quantity from atomic-scale simulations is far from trivial,
so the potential energy of a system is often used as a proxy. In this paper, we
use a combination of thermodynamic integration methods to accurately evaluate
the Gibbs free energies associated with defects in crystals, including the vacancy
formation energy in bcc iron, and the stacking fault energy in fcc nickel, iron,
and cobalt. We quantify the importance of entropic and anharmonic effects in determining
the free energies of defects at high temperatures, and show that the potential
energy approximation as well as the harmonic approximation may produce inaccurate
or even qualitatively wrong results. Our calculations manifest the necessity to
employ accurate free energy methods such as thermodynamic integration to estimate
the stability of crystallographic defects at high temperatures.
article_number: '054102'
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: Michele
full_name: Ceriotti, Michele
last_name: Ceriotti
citation:
ama: 'Cheng B, Ceriotti M. Computing the absolute Gibbs free energy in atomistic
simulations: Applications to defects in solids. Physical Review B. 2018;97(5).
doi:10.1103/physrevb.97.054102'
apa: 'Cheng, B., & Ceriotti, M. (2018). Computing the absolute Gibbs free energy
in atomistic simulations: Applications to defects in solids. Physical Review
B. American Physical Society. https://doi.org/10.1103/physrevb.97.054102'
chicago: 'Cheng, Bingqing, and Michele Ceriotti. “Computing the Absolute Gibbs Free
Energy in Atomistic Simulations: Applications to Defects in Solids.” Physical
Review B. American Physical Society, 2018. https://doi.org/10.1103/physrevb.97.054102.'
ieee: 'B. Cheng and M. Ceriotti, “Computing the absolute Gibbs free energy in atomistic
simulations: Applications to defects in solids,” Physical Review B, vol.
97, no. 5. American Physical Society, 2018.'
ista: 'Cheng B, Ceriotti M. 2018. Computing the absolute Gibbs free energy in atomistic
simulations: Applications to defects in solids. Physical Review B. 97(5), 054102.'
mla: 'Cheng, Bingqing, and Michele Ceriotti. “Computing the Absolute Gibbs Free
Energy in Atomistic Simulations: Applications to Defects in Solids.” Physical
Review B, vol. 97, no. 5, 054102, American Physical Society, 2018, doi:10.1103/physrevb.97.054102.'
short: B. Cheng, M. Ceriotti, Physical Review B 97 (2018).
date_created: 2021-07-19T09:39:48Z
date_published: 2018-02-01T00:00:00Z
date_updated: 2021-08-09T12:38:26Z
day: '01'
doi: 10.1103/physrevb.97.054102
extern: '1'
external_id:
arxiv:
- '1710.02815'
intvolume: ' 97'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1710.02815
month: '02'
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: 'Computing the absolute Gibbs free energy in atomistic simulations: Applications
to defects in solids'
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 97
year: '2018'
...
---
_id: '315'
abstract:
- lang: eng
text: 'More than 100 years after Grigg’s influential analysis of species’ borders,
the causes of limits to species’ ranges still represent a puzzle that has never
been understood with clarity. The topic has become especially important recently
as many scientists have become interested in the potential for species’ ranges
to shift in response to climate change—and yet nearly all of those studies fail
to recognise or incorporate evolutionary genetics in a way that relates to theoretical
developments. I show that range margins can be understood based on just two measurable
parameters: (i) the fitness cost of dispersal—a measure of environmental heterogeneity—and
(ii) the strength of genetic drift, which reduces genetic diversity. Together,
these two parameters define an ‘expansion threshold’: adaptation fails when genetic
drift reduces genetic diversity below that required for adaptation to a heterogeneous
environment. When the key parameters drop below this expansion threshold locally,
a sharp range margin forms. When they drop below this threshold throughout the
species’ range, adaptation collapses everywhere, resulting in either extinction
or formation of a fragmented metapopulation. Because the effects of dispersal
differ fundamentally with dimension, the second parameter—the strength of genetic
drift—is qualitatively different compared to a linear habitat. In two-dimensional
habitats, genetic drift becomes effectively independent of selection. It decreases
with ‘neighbourhood size’—the number of individuals accessible by dispersal within
one generation. Moreover, in contrast to earlier predictions, which neglected
evolution of genetic variance and/or stochasticity in two dimensions, dispersal
into small marginal populations aids adaptation. This is because the reduction
of both genetic and demographic stochasticity has a stronger effect than the cost
of dispersal through increased maladaptation. The expansion threshold thus provides
a novel, theoretically justified, and testable prediction for formation of the
range margin and collapse of the species’ range.'
article_number: e2005372
author:
- first_name: Jitka
full_name: Polechova, Jitka
id: 3BBFB084-F248-11E8-B48F-1D18A9856A87
last_name: Polechova
orcid: 0000-0003-0951-3112
citation:
ama: Polechova J. Is the sky the limit? On the expansion threshold of a species’
range. PLoS Biology. 2018;16(6). doi:10.1371/journal.pbio.2005372
apa: Polechova, J. (2018). Is the sky the limit? On the expansion threshold of a
species’ range. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005372
chicago: Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of
a Species’ Range.” PLoS Biology. Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005372.
ieee: J. Polechova, “Is the sky the limit? On the expansion threshold of a species’
range,” PLoS Biology, vol. 16, no. 6. Public Library of Science, 2018.
ista: Polechova J. 2018. Is the sky the limit? On the expansion threshold of a species’
range. PLoS Biology. 16(6), e2005372.
mla: Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of a Species’
Range.” PLoS Biology, vol. 16, no. 6, e2005372, Public Library of Science,
2018, doi:10.1371/journal.pbio.2005372.
short: J. Polechova, PLoS Biology 16 (2018).
date_created: 2018-12-11T11:45:46Z
date_published: 2018-06-15T00:00:00Z
date_updated: 2023-02-23T14:10:16Z
day: '15'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1371/journal.pbio.2005372
file:
- access_level: open_access
checksum: 908c52751bba30c55ed36789e5e4c84d
content_type: application/pdf
creator: dernst
date_created: 2019-01-22T08:30:03Z
date_updated: 2020-07-14T12:46:01Z
file_id: '5870'
file_name: 2017_PLOS_Polechova.pdf
file_size: 6968201
relation: main_file
file_date_updated: 2020-07-14T12:46:01Z
has_accepted_license: '1'
intvolume: ' 16'
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: PLoS Biology
publication_identifier:
issn:
- '15449173'
publication_status: published
publisher: Public Library of Science
publist_id: '7550'
quality_controlled: '1'
related_material:
record:
- id: '9839'
relation: research_data
status: public
scopus_import: 1
status: public
title: Is the sky the limit? On the expansion threshold of a species’ range
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2018'
...
---
_id: '8417'
abstract:
- lang: eng
text: The restricted planar elliptic three body problem (RPETBP) describes the motion
of a massless particle (a comet or an asteroid) under the gravitational field
of two massive bodies (the primaries, say the Sun and Jupiter) revolving around
their center of mass on elliptic orbits with some positive eccentricity. The aim
of this paper is to show the existence of orbits whose angular momentum performs
arbitrary excursions in a large region. In particular, there exist diffusive orbits,
that is, with a large variation of angular momentum. The leading idea of the proof
consists in analyzing parabolic motions of the comet. By a well-known result of
McGehee, the union of future (resp. past) parabolic orbits is an analytic manifold
P+ (resp. P−). In a properly chosen coordinate system these manifolds are stable
(resp. unstable) manifolds of a manifold at infinity P∞, which we call the manifold
at parabolic infinity. On P∞ it is possible to define two scattering maps, which
contain the map structure of the homoclinic trajectories to it, i.e. orbits parabolic
both in the future and the past. Since the inner dynamics inside P∞ is trivial,
two different scattering maps are used. The combination of these two scattering
maps permits the design of the desired diffusive pseudo-orbits. Using shadowing
techniques and these pseudo orbits we show the existence of true trajectories
of the RPETBP whose angular momentum varies in any predetermined fashion.
article_processing_charge: No
article_type: original
author:
- first_name: Amadeu
full_name: Delshams, Amadeu
last_name: Delshams
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: Abraham
full_name: de la Rosa, Abraham
last_name: de la Rosa
- first_name: Tere M.
full_name: Seara, Tere M.
last_name: Seara
citation:
ama: Delshams A, Kaloshin V, de la Rosa A, Seara TM. Global instability in the restricted
planar elliptic three body problem. Communications in Mathematical Physics.
2018;366(3):1173-1228. doi:10.1007/s00220-018-3248-z
apa: Delshams, A., Kaloshin, V., de la Rosa, A., & Seara, T. M. (2018). Global
instability in the restricted planar elliptic three body problem. Communications
in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-018-3248-z
chicago: Delshams, Amadeu, Vadim Kaloshin, Abraham de la Rosa, and Tere M. Seara.
“Global Instability in the Restricted Planar Elliptic Three Body Problem.” Communications
in Mathematical Physics. Springer Nature, 2018. https://doi.org/10.1007/s00220-018-3248-z.
ieee: A. Delshams, V. Kaloshin, A. de la Rosa, and T. M. Seara, “Global instability
in the restricted planar elliptic three body problem,” Communications in Mathematical
Physics, vol. 366, no. 3. Springer Nature, pp. 1173–1228, 2018.
ista: Delshams A, Kaloshin V, de la Rosa A, Seara TM. 2018. Global instability in
the restricted planar elliptic three body problem. Communications in Mathematical
Physics. 366(3), 1173–1228.
mla: Delshams, Amadeu, et al. “Global Instability in the Restricted Planar Elliptic
Three Body Problem.” Communications in Mathematical Physics, vol. 366,
no. 3, Springer Nature, 2018, pp. 1173–228, doi:10.1007/s00220-018-3248-z.
short: A. Delshams, V. Kaloshin, A. de la Rosa, T.M. Seara, Communications in Mathematical
Physics 366 (2018) 1173–1228.
date_created: 2020-09-17T10:41:43Z
date_published: 2018-09-05T00:00:00Z
date_updated: 2021-01-12T08:19:08Z
day: '05'
doi: 10.1007/s00220-018-3248-z
extern: '1'
intvolume: ' 366'
issue: '3'
keyword:
- Mathematical Physics
- Statistical and Nonlinear Physics
language:
- iso: eng
month: '09'
oa_version: None
page: 1173-1228
publication: Communications in Mathematical Physics
publication_identifier:
issn:
- 0010-3616
- 1432-0916
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Global instability in the restricted planar elliptic three body problem
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 366
year: '2018'
...
---
_id: '8422'
abstract:
- lang: eng
text: 'The Birkhoff conjecture says that the boundary of a strictly convex integrable
billiard table is necessarily an ellipse. In this article, we consider a stronger
notion of integrability, namely integrability close to the boundary, and prove
a local version of this conjecture: a small perturbation of an ellipse of small
eccentricity which preserves integrability near the boundary, is itself an ellipse.
This extends the result in Avila et al. (Ann Math 184:527–558, ADK16), where integrability
was assumed on a larger set. In particular, it shows that (local) integrability
near the boundary implies global integrability. One of the crucial ideas in the
proof consists in analyzing Taylor expansion of the corresponding action-angle
coordinates with respect to the eccentricity parameter, deriving and studying
higher order conditions for the preservation of integrable rational caustics.'
article_processing_charge: No
article_type: original
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. Nearly circular domains which are integrable
close to the boundary are ellipses. Geometric and Functional Analysis.
2018;28(2):334-392. doi:10.1007/s00039-018-0440-4
apa: Huang, G., Kaloshin, V., & Sorrentino, A. (2018). Nearly circular domains
which are integrable close to the boundary are ellipses. Geometric and Functional
Analysis. Springer Nature. https://doi.org/10.1007/s00039-018-0440-4
chicago: Huang, Guan, Vadim Kaloshin, and Alfonso Sorrentino. “Nearly Circular Domains
Which Are Integrable Close to the Boundary Are Ellipses.” Geometric and Functional
Analysis. Springer Nature, 2018. https://doi.org/10.1007/s00039-018-0440-4.
ieee: G. Huang, V. Kaloshin, and A. Sorrentino, “Nearly circular domains which are
integrable close to the boundary are ellipses,” Geometric and Functional Analysis,
vol. 28, no. 2. Springer Nature, pp. 334–392, 2018.
ista: Huang G, Kaloshin V, Sorrentino A. 2018. Nearly circular domains which are
integrable close to the boundary are ellipses. Geometric and Functional Analysis.
28(2), 334–392.
mla: Huang, Guan, et al. “Nearly Circular Domains Which Are Integrable Close to
the Boundary Are Ellipses.” Geometric and Functional Analysis, vol. 28,
no. 2, Springer Nature, 2018, pp. 334–92, doi:10.1007/s00039-018-0440-4.
short: G. Huang, V. Kaloshin, A. Sorrentino, Geometric and Functional Analysis 28
(2018) 334–392.
date_created: 2020-09-17T10:42:30Z
date_published: 2018-03-18T00:00:00Z
date_updated: 2021-01-12T08:19:11Z
day: '18'
doi: 10.1007/s00039-018-0440-4
extern: '1'
external_id:
arxiv:
- '1705.10601'
intvolume: ' 28'
issue: '2'
keyword:
- Geometry and Topology
- Analysis
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1705.10601
month: '03'
oa: 1
oa_version: Preprint
page: 334-392
publication: Geometric and Functional Analysis
publication_identifier:
issn:
- 1016-443X
- 1420-8970
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Nearly circular domains which are integrable close to the boundary are ellipses
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 28
year: '2018'
...