---
_id: '13374'
abstract:
- lang: eng
text: Confining molecules to volumes only slightly larger than the molecules themselves
can profoundly alter their properties. Molecular switches—entities that can be
toggled between two or more forms upon exposure to an external stimulus—often
require conformational freedom to isomerize. Therefore, placing these switches
in confined spaces can render them non-operational. To preserve the switchability
of these species under confinement, we work with a water-soluble coordination
cage that is flexible enough to adapt its shape to the conformation of the encapsulated
guest. We show that owing to its flexibility, the cage is not only capable of
accommodating—and solubilizing in water—several light-responsive spiropyran-based
molecular switches, but, more importantly, it also provides an environment suitable
for the efficient, reversible photoisomerization of the bound guests. Our findings
pave the way towards studying various molecular switching processes in confined
environments.
article_number: '641'
article_processing_charge: No
article_type: original
author:
- first_name: Dipak
full_name: Samanta, Dipak
last_name: Samanta
- first_name: Daria
full_name: Galaktionova, Daria
last_name: Galaktionova
- first_name: Julius
full_name: Gemen, Julius
last_name: Gemen
- first_name: Linda J. W.
full_name: Shimon, Linda J. W.
last_name: Shimon
- first_name: Yael
full_name: Diskin-Posner, Yael
last_name: Diskin-Posner
- first_name: Liat
full_name: Avram, Liat
last_name: Avram
- first_name: Petr
full_name: Král, Petr
last_name: Král
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Samanta D, Galaktionova D, Gemen J, et al. Reversible chromism of spiropyran
in the cavity of a flexible coordination cage. Nature Communications. 2018;9.
doi:10.1038/s41467-017-02715-6
apa: Samanta, D., Galaktionova, D., Gemen, J., Shimon, L. J. W., Diskin-Posner,
Y., Avram, L., … Klajn, R. (2018). Reversible chromism of spiropyran in the cavity
of a flexible coordination cage. Nature Communications. Springer Nature.
https://doi.org/10.1038/s41467-017-02715-6
chicago: Samanta, Dipak, Daria Galaktionova, Julius Gemen, Linda J. W. Shimon, Yael
Diskin-Posner, Liat Avram, Petr Král, and Rafal Klajn. “Reversible Chromism of
Spiropyran in the Cavity of a Flexible Coordination Cage.” Nature Communications.
Springer Nature, 2018. https://doi.org/10.1038/s41467-017-02715-6.
ieee: D. Samanta et al., “Reversible chromism of spiropyran in the cavity
of a flexible coordination cage,” Nature Communications, vol. 9. Springer
Nature, 2018.
ista: Samanta D, Galaktionova D, Gemen J, Shimon LJW, Diskin-Posner Y, Avram L,
Král P, Klajn R. 2018. Reversible chromism of spiropyran in the cavity of a flexible
coordination cage. Nature Communications. 9, 641.
mla: Samanta, Dipak, et al. “Reversible Chromism of Spiropyran in the Cavity of
a Flexible Coordination Cage.” Nature Communications, vol. 9, 641, Springer
Nature, 2018, doi:10.1038/s41467-017-02715-6.
short: D. Samanta, D. Galaktionova, J. Gemen, L.J.W. Shimon, Y. Diskin-Posner, L.
Avram, P. Král, R. Klajn, Nature Communications 9 (2018).
date_created: 2023-08-01T09:39:32Z
date_published: 2018-02-13T00:00:00Z
date_updated: 2023-08-07T10:54:05Z
day: '13'
doi: 10.1038/s41467-017-02715-6
extern: '1'
external_id:
pmid:
- '29440687'
intvolume: ' 9'
keyword:
- General Physics and Astronomy
- General Biochemistry
- Genetics and Molecular Biology
- General Chemistry
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41467-017-02715-6
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41467-018-03701-2
scopus_import: '1'
status: public
title: Reversible chromism of spiropyran in the cavity of a flexible coordination
cage
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2018'
...
---
_id: '13376'
abstract:
- lang: eng
text: Efficient molecular switching in confined spaces is critical for the successful
development of artificial molecular machines. However, molecular switching events
often entail large structural changes and therefore require conformational freedom,
which is typically limited under confinement conditions. Here, we investigated
the behavior of azobenzene—the key building block of light-controlled molecular
machines—in a confined environment that is flexible and can adapt its shape to
that of the bound guest. To this end, we encapsulated several structurally diverse
azobenzenes within the cavity of a flexible, water-soluble coordination cage,
and investigated their light-responsive behavior. Using UV/Vis absorption spectroscopy
and a combination of NMR methods, we showed that each of the encapsulated azobenzenes
exhibited distinct switching properties. An azobenzene forming a 1:1 host–guest
inclusion complex could be efficiently photoisomerized in a reversible fashion.
In contrast, successful switching in inclusion complexes incorporating two azobenzene
guests was dependent on the availability of free cages in the system, and it involved
reversible trafficking of azobenzene between the cages. In the absence of extra
cages, photoswitching was either suppressed or it involved expulsion of azobenzene
from the cage and consequently its precipitation from the solution. This finding
was utilized to develop an information storage medium in which messages could
be written and erased in a reversible fashion using light.
article_processing_charge: No
article_type: original
author:
- first_name: Dipak
full_name: Samanta, Dipak
last_name: Samanta
- first_name: Julius
full_name: Gemen, Julius
last_name: Gemen
- first_name: Zonglin
full_name: Chu, Zonglin
last_name: Chu
- first_name: Yael
full_name: Diskin-Posner, Yael
last_name: Diskin-Posner
- first_name: Linda J. W.
full_name: Shimon, Linda J. W.
last_name: Shimon
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Samanta D, Gemen J, Chu Z, Diskin-Posner Y, Shimon LJW, Klajn R. Reversible
photoswitching of encapsulated azobenzenes in water. Proceedings of the National
Academy of Sciences. 2018;115(38):9379-9384. doi:10.1073/pnas.1712787115
apa: Samanta, D., Gemen, J., Chu, Z., Diskin-Posner, Y., Shimon, L. J. W., &
Klajn, R. (2018). Reversible photoswitching of encapsulated azobenzenes in water.
Proceedings of the National Academy of Sciences. Proceedings of the National
Academy of Sciences. https://doi.org/10.1073/pnas.1712787115
chicago: Samanta, Dipak, Julius Gemen, Zonglin Chu, Yael Diskin-Posner, Linda J.
W. Shimon, and Rafal Klajn. “Reversible Photoswitching of Encapsulated Azobenzenes
in Water.” Proceedings of the National Academy of Sciences. Proceedings
of the National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1712787115.
ieee: D. Samanta, J. Gemen, Z. Chu, Y. Diskin-Posner, L. J. W. Shimon, and R. Klajn,
“Reversible photoswitching of encapsulated azobenzenes in water,” Proceedings
of the National Academy of Sciences, vol. 115, no. 38. Proceedings of the
National Academy of Sciences, pp. 9379–9384, 2018.
ista: Samanta D, Gemen J, Chu Z, Diskin-Posner Y, Shimon LJW, Klajn R. 2018. Reversible
photoswitching of encapsulated azobenzenes in water. Proceedings of the National
Academy of Sciences. 115(38), 9379–9384.
mla: Samanta, Dipak, et al. “Reversible Photoswitching of Encapsulated Azobenzenes
in Water.” Proceedings of the National Academy of Sciences, vol. 115, no.
38, Proceedings of the National Academy of Sciences, 2018, pp. 9379–84, doi:10.1073/pnas.1712787115.
short: D. Samanta, J. Gemen, Z. Chu, Y. Diskin-Posner, L.J.W. Shimon, R. Klajn,
Proceedings of the National Academy of Sciences 115 (2018) 9379–9384.
date_created: 2023-08-01T09:40:00Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2023-08-07T10:58:11Z
day: '01'
doi: 10.1073/pnas.1712787115
extern: '1'
external_id:
pmid:
- '29717041'
intvolume: ' 115'
issue: '38'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1712787115
month: '05'
oa: 1
oa_version: Published Version
page: 9379-9384
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Reversible photoswitching of encapsulated azobenzenes in water
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 115
year: '2018'
...
---
_id: '14284'
abstract:
- lang: eng
text: Pore-forming toxins (PFT) are virulence factors that transform from soluble
to membrane-bound states. The Yersinia YaxAB system represents a family of binary
α-PFTs with orthologues in human, insect, and plant pathogens, with unknown structures.
YaxAB was shown to be cytotoxic and likely involved in pathogenesis, though the
molecular basis for its two-component lytic mechanism remains elusive. Here, we
present crystal structures of YaxA and YaxB, together with a cryo-electron microscopy
map of the YaxAB complex. Our structures reveal a pore predominantly composed
of decamers of YaxA–YaxB heterodimers. Both subunits bear membrane-active moieties,
but only YaxA is capable of binding to membranes by itself. YaxB can subsequently
be recruited to membrane-associated YaxA and induced to present its lytic transmembrane
helices. Pore formation can progress by further oligomerization of YaxA–YaxB dimers.
Our results allow for a comparison between pore assemblies belonging to the wider
ClyA-like family of α-PFTs, highlighting diverse pore architectures.
article_number: '1806'
article_processing_charge: No
article_type: original
author:
- first_name: Bastian
full_name: Bräuning, Bastian
last_name: Bräuning
- first_name: Eva
full_name: Bertosin, Eva
last_name: Bertosin
- first_name: Florian M
full_name: Praetorius, Florian M
id: dfec9381-4341-11ee-8fd8-faa02bba7d62
last_name: Praetorius
- first_name: Christian
full_name: Ihling, Christian
last_name: Ihling
- first_name: Alexandra
full_name: Schatt, Alexandra
last_name: Schatt
- first_name: Agnes
full_name: Adler, Agnes
last_name: Adler
- first_name: Klaus
full_name: Richter, Klaus
last_name: Richter
- first_name: Andrea
full_name: Sinz, Andrea
last_name: Sinz
- first_name: Hendrik
full_name: Dietz, Hendrik
last_name: Dietz
- first_name: Michael
full_name: Groll, Michael
last_name: Groll
citation:
ama: Bräuning B, Bertosin E, Praetorius FM, et al. Structure and mechanism of the
two-component α-helical pore-forming toxin YaxAB. Nature Communications.
2018;9. doi:10.1038/s41467-018-04139-2
apa: Bräuning, B., Bertosin, E., Praetorius, F. M., Ihling, C., Schatt, A., Adler,
A., … Groll, M. (2018). Structure and mechanism of the two-component α-helical
pore-forming toxin YaxAB. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-04139-2
chicago: Bräuning, Bastian, Eva Bertosin, Florian M Praetorius, Christian Ihling,
Alexandra Schatt, Agnes Adler, Klaus Richter, Andrea Sinz, Hendrik Dietz, and
Michael Groll. “Structure and Mechanism of the Two-Component α-Helical Pore-Forming
Toxin YaxAB.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-04139-2.
ieee: B. Bräuning et al., “Structure and mechanism of the two-component α-helical
pore-forming toxin YaxAB,” Nature Communications, vol. 9. Springer Nature,
2018.
ista: Bräuning B, Bertosin E, Praetorius FM, Ihling C, Schatt A, Adler A, Richter
K, Sinz A, Dietz H, Groll M. 2018. Structure and mechanism of the two-component
α-helical pore-forming toxin YaxAB. Nature Communications. 9, 1806.
mla: Bräuning, Bastian, et al. “Structure and Mechanism of the Two-Component α-Helical
Pore-Forming Toxin YaxAB.” Nature Communications, vol. 9, 1806, Springer
Nature, 2018, doi:10.1038/s41467-018-04139-2.
short: B. Bräuning, E. Bertosin, F.M. Praetorius, C. Ihling, A. Schatt, A. Adler,
K. Richter, A. Sinz, H. Dietz, M. Groll, Nature Communications 9 (2018).
date_created: 2023-09-06T12:07:33Z
date_published: 2018-05-04T00:00:00Z
date_updated: 2023-11-07T11:46:12Z
day: '04'
doi: 10.1038/s41467-018-04139-2
extern: '1'
external_id:
pmid:
- '29728606'
intvolume: ' 9'
keyword:
- General Physics and Astronomy
- General Biochemistry
- Genetics and Molecular Biology
- General Chemistry
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41467-018-04139-2
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structure and mechanism of the two-component α-helical pore-forming toxin YaxAB
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2018'
...
---
_id: '9135'
abstract:
- lang: eng
text: Idealized simulations of tropical moist convection have revealed that clouds
can spontaneously clump together in a process called self-aggregation. This results
in a state where a moist cloudy region with intense deep convection is surrounded
by extremely dry subsiding air devoid of deep convection. Because of the idealized
settings of the simulations where it was discovered, the relevance of self-aggregation
to the real world is still debated. Here, we show that self-aggregation feedbacks
play a leading-order role in the spontaneous genesis of tropical cyclones in cloud-resolving
simulations. Those feedbacks accelerate the cyclogenesis process by a factor of
2, and the feedbacks contributing to the cyclone formation show qualitative and
quantitative agreement with the self-aggregation process. Once the cyclone is
formed, wind-induced surface heat exchange (WISHE) effects dominate, although
we find that self-aggregation feedbacks have a small but nonnegligible contribution
to the maintenance of the mature cyclone. Our results suggest that self-aggregation,
and the framework developed for its study, can help shed more light into the physical
processes leading to cyclogenesis and cyclone intensification. In particular,
our results point out the importance of the longwave radiative cooling outside
the cyclone.
article_processing_charge: No
article_type: original
author:
- first_name: Caroline J
full_name: Muller, Caroline J
id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b
last_name: Muller
orcid: 0000-0001-5836-5350
- first_name: David M.
full_name: Romps, David M.
last_name: Romps
citation:
ama: Muller CJ, Romps DM. Acceleration of tropical cyclogenesis by self-aggregation
feedbacks. Proceedings of the National Academy of Sciences. 2018;115(12):2930-2935.
doi:10.1073/pnas.1719967115
apa: Muller, C. J., & Romps, D. M. (2018). Acceleration of tropical cyclogenesis
by self-aggregation feedbacks. Proceedings of the National Academy of Sciences.
Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1719967115
chicago: Muller, Caroline J, and David M. Romps. “Acceleration of Tropical Cyclogenesis
by Self-Aggregation Feedbacks.” Proceedings of the National Academy of Sciences.
Proceedings of the National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1719967115.
ieee: C. J. Muller and D. M. Romps, “Acceleration of tropical cyclogenesis by self-aggregation
feedbacks,” Proceedings of the National Academy of Sciences, vol. 115,
no. 12. Proceedings of the National Academy of Sciences, pp. 2930–2935, 2018.
ista: Muller CJ, Romps DM. 2018. Acceleration of tropical cyclogenesis by self-aggregation
feedbacks. Proceedings of the National Academy of Sciences. 115(12), 2930–2935.
mla: Muller, Caroline J., and David M. Romps. “Acceleration of Tropical Cyclogenesis
by Self-Aggregation Feedbacks.” Proceedings of the National Academy of Sciences,
vol. 115, no. 12, Proceedings of the National Academy of Sciences, 2018, pp. 2930–35,
doi:10.1073/pnas.1719967115.
short: C.J. Muller, D.M. Romps, Proceedings of the National Academy of Sciences
115 (2018) 2930–2935.
date_created: 2021-02-15T14:18:16Z
date_published: 2018-03-20T00:00:00Z
date_updated: 2022-01-24T12:39:49Z
day: '20'
doi: 10.1073/pnas.1719967115
extern: '1'
intvolume: ' 115'
issue: '12'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1719967115
month: '03'
oa: 1
oa_version: Published Version
page: 2930-2935
publication: Proceedings of the National Academy of Sciences
publication_identifier:
issn:
- 0027-8424
- 1091-6490
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
status: public
title: Acceleration of tropical cyclogenesis by self-aggregation feedbacks
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 115
year: '2018'
...
---
_id: '9471'
abstract:
- lang: eng
text: The DEMETER (DME) DNA glycosylase catalyzes genome-wide DNA demethylation
and is required for endosperm genomic imprinting and embryo viability. Targets
of DME-mediated DNA demethylation reside in small, euchromatic, AT-rich transposons
and at the boundaries of large transposons, but how DME interacts with these diverse
chromatin states is unknown. The STRUCTURE SPECIFIC RECOGNITION PROTEIN 1 (SSRP1)
subunit of the chromatin remodeler FACT (facilitates chromatin transactions),
was previously shown to be involved in the DME-dependent regulation of genomic
imprinting in Arabidopsis endosperm. Therefore, to investigate the interaction
between DME and chromatin, we focused on the activity of the two FACT subunits,
SSRP1 and SUPPRESSOR of TY16 (SPT16), during reproduction in Arabidopsis. We found
that FACT colocalizes with nuclear DME in vivo, and that DME has two classes of
target sites, the first being euchromatic and accessible to DME, but the second,
representing over half of DME targets, requiring the action of FACT for DME-mediated
DNA demethylation genome-wide. Our results show that the FACT-dependent DME targets
are GC-rich heterochromatin domains with high nucleosome occupancy enriched with
H3K9me2 and H3K27me1. Further, we demonstrate that heterochromatin-associated
linker histone H1 specifically mediates the requirement for FACT at a subset of
DME-target loci. Overall, our results demonstrate that FACT is required for DME
targeting by facilitating its access to heterochromatin.
article_processing_charge: No
article_type: original
author:
- first_name: Jennifer M.
full_name: Frost, Jennifer M.
last_name: Frost
- first_name: M. Yvonne
full_name: Kim, M. Yvonne
last_name: Kim
- first_name: Guen Tae
full_name: Park, Guen Tae
last_name: Park
- first_name: Ping-Hung
full_name: Hsieh, Ping-Hung
last_name: Hsieh
- first_name: Miyuki
full_name: Nakamura, Miyuki
last_name: Nakamura
- first_name: Samuel J. H.
full_name: Lin, Samuel J. H.
last_name: Lin
- first_name: Hyunjin
full_name: Yoo, Hyunjin
last_name: Yoo
- first_name: Jaemyung
full_name: Choi, Jaemyung
last_name: Choi
- first_name: Yoko
full_name: Ikeda, Yoko
last_name: Ikeda
- first_name: Tetsu
full_name: Kinoshita, Tetsu
last_name: Kinoshita
- first_name: Yeonhee
full_name: Choi, Yeonhee
last_name: Choi
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
citation:
ama: Frost JM, Kim MY, Park GT, et al. FACT complex is required for DNA demethylation
at heterochromatin during reproduction in Arabidopsis. Proceedings of the National
Academy of Sciences. 2018;115(20):E4720-E4729. doi:10.1073/pnas.1713333115
apa: Frost, J. M., Kim, M. Y., Park, G. T., Hsieh, P.-H., Nakamura, M., Lin, S.
J. H., … Fischer, R. L. (2018). FACT complex is required for DNA demethylation
at heterochromatin during reproduction in Arabidopsis. Proceedings of the National
Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1713333115
chicago: Frost, Jennifer M., M. Yvonne Kim, Guen Tae Park, Ping-Hung Hsieh, Miyuki
Nakamura, Samuel J. H. Lin, Hyunjin Yoo, et al. “FACT Complex Is Required for
DNA Demethylation at Heterochromatin during Reproduction in Arabidopsis.” Proceedings
of the National Academy of Sciences. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1713333115.
ieee: J. M. Frost et al., “FACT complex is required for DNA demethylation
at heterochromatin during reproduction in Arabidopsis,” Proceedings of the
National Academy of Sciences, vol. 115, no. 20. National Academy of Sciences,
pp. E4720–E4729, 2018.
ista: Frost JM, Kim MY, Park GT, Hsieh P-H, Nakamura M, Lin SJH, Yoo H, Choi J,
Ikeda Y, Kinoshita T, Choi Y, Zilberman D, Fischer RL. 2018. FACT complex is required
for DNA demethylation at heterochromatin during reproduction in Arabidopsis. Proceedings
of the National Academy of Sciences. 115(20), E4720–E4729.
mla: Frost, Jennifer M., et al. “FACT Complex Is Required for DNA Demethylation
at Heterochromatin during Reproduction in Arabidopsis.” Proceedings of the
National Academy of Sciences, vol. 115, no. 20, National Academy of Sciences,
2018, pp. E4720–29, doi:10.1073/pnas.1713333115.
short: J.M. Frost, M.Y. Kim, G.T. Park, P.-H. Hsieh, M. Nakamura, S.J.H. Lin, H.
Yoo, J. Choi, Y. Ikeda, T. Kinoshita, Y. Choi, D. Zilberman, R.L. Fischer, Proceedings
of the National Academy of Sciences 115 (2018) E4720–E4729.
date_created: 2021-06-07T06:11:28Z
date_published: 2018-05-15T00:00:00Z
date_updated: 2021-12-14T07:53:40Z
day: '15'
ddc:
- '580'
department:
- _id: DaZi
doi: 10.1073/pnas.1713333115
extern: '1'
external_id:
pmid:
- '29712855'
file:
- access_level: open_access
checksum: 810260dc0e3cc3033e15c19ad0dc123e
content_type: application/pdf
creator: asandaue
date_created: 2021-06-07T06:16:38Z
date_updated: 2021-06-07T06:16:38Z
file_id: '9472'
file_name: 2018_PNAS_Frost.pdf
file_size: 3045260
relation: main_file
success: 1
file_date_updated: 2021-06-07T06:16:38Z
has_accepted_license: '1'
intvolume: ' 115'
issue: '20'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: E4720-E4729
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- relation: earlier_version
url: 'https://doi.org/10.1101/187674 '
scopus_import: '1'
status: public
title: FACT complex is required for DNA demethylation at heterochromatin during reproduction
in Arabidopsis
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 115
year: '2018'
...
---
_id: '13381'
abstract:
- lang: eng
text: Self-assembly of inorganic nanoparticles has been used to prepare hundreds
of different colloidal crystals, but almost invariably with the restriction that
the particles must be densely packed. Here, we show that non–close-packed nanoparticle
arrays can be fabricated through the selective removal of one of two components
comprising binary nanoparticle superlattices. First, a variety of binary nanoparticle
superlattices were prepared at the liquid-air interface, including several arrangements
that were previously unknown. Molecular dynamics simulations revealed the particular
role of the liquid in templating the formation of superlattices not achievable
through self-assembly in bulk solution. Second, upon stabilization, all of these
binary superlattices could be transformed into distinct “nanoallotropes”—nanoporous
materials having the same chemical composition but differing in their nanoscale
architectures.
article_processing_charge: No
article_type: original
author:
- first_name: Thumu
full_name: Udayabhaskararao, Thumu
last_name: Udayabhaskararao
- first_name: Thomas
full_name: Altantzis, Thomas
last_name: Altantzis
- first_name: Lothar
full_name: Houben, Lothar
last_name: Houben
- first_name: Marc
full_name: Coronado-Puchau, Marc
last_name: Coronado-Puchau
- first_name: Judith
full_name: Langer, Judith
last_name: Langer
- first_name: Ronit
full_name: Popovitz-Biro, Ronit
last_name: Popovitz-Biro
- first_name: Luis M.
full_name: Liz-Marzán, Luis M.
last_name: Liz-Marzán
- first_name: Lela
full_name: Vuković, Lela
last_name: Vuković
- first_name: Petr
full_name: Král, Petr
last_name: Král
- first_name: Sara
full_name: Bals, Sara
last_name: Bals
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Udayabhaskararao T, Altantzis T, Houben L, et al. Tunable porous nanoallotropes
prepared by post-assembly etching of binary nanoparticle superlattices. Science.
2017;358(6362):514-518. doi:10.1126/science.aan6046
apa: Udayabhaskararao, T., Altantzis, T., Houben, L., Coronado-Puchau, M., Langer,
J., Popovitz-Biro, R., … Klajn, R. (2017). Tunable porous nanoallotropes prepared
by post-assembly etching of binary nanoparticle superlattices. Science.
American Association for the Advancement of Science. https://doi.org/10.1126/science.aan6046
chicago: Udayabhaskararao, Thumu, Thomas Altantzis, Lothar Houben, Marc Coronado-Puchau,
Judith Langer, Ronit Popovitz-Biro, Luis M. Liz-Marzán, et al. “Tunable Porous
Nanoallotropes Prepared by Post-Assembly Etching of Binary Nanoparticle Superlattices.”
Science. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/science.aan6046.
ieee: T. Udayabhaskararao et al., “Tunable porous nanoallotropes prepared
by post-assembly etching of binary nanoparticle superlattices,” Science,
vol. 358, no. 6362. American Association for the Advancement of Science, pp. 514–518,
2017.
ista: Udayabhaskararao T, Altantzis T, Houben L, Coronado-Puchau M, Langer J, Popovitz-Biro
R, Liz-Marzán LM, Vuković L, Král P, Bals S, Klajn R. 2017. Tunable porous nanoallotropes
prepared by post-assembly etching of binary nanoparticle superlattices. Science.
358(6362), 514–518.
mla: Udayabhaskararao, Thumu, et al. “Tunable Porous Nanoallotropes Prepared by
Post-Assembly Etching of Binary Nanoparticle Superlattices.” Science, vol.
358, no. 6362, American Association for the Advancement of Science, 2017, pp.
514–18, doi:10.1126/science.aan6046.
short: T. Udayabhaskararao, T. Altantzis, L. Houben, M. Coronado-Puchau, J. Langer,
R. Popovitz-Biro, L.M. Liz-Marzán, L. Vuković, P. Král, S. Bals, R. Klajn, Science
358 (2017) 514–518.
date_created: 2023-08-01T09:41:16Z
date_published: 2017-10-27T00:00:00Z
date_updated: 2023-08-07T11:25:00Z
day: '27'
doi: 10.1126/science.aan6046
extern: '1'
external_id:
pmid:
- '29074773'
intvolume: ' 358'
issue: '6362'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://repository.uantwerpen.be/docman/irua/8d722e/147242_2018_06_07.pdf
month: '10'
oa: 1
oa_version: Submitted Version
page: 514-518
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tunable porous nanoallotropes prepared by post-assembly etching of binary nanoparticle
superlattices
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 358
year: '2017'
...
---
_id: '13384'
abstract:
- lang: eng
text: Although methane is a volatile gas, it can be efficiently trapped in ice,
which can then be readily set on fire. Beyond the curiosity of this “burning ice,”
caged methane is of great importance as one of the world's largest natural gas
resources. In these materials, known as clathrates, methane molecules are tightly
bound in nanometer-sized, regularly interspaced cages. Other inorganic materials,
such as the silica mineral chibaite, can similarly encapsulate methane and higher
hydrocarbons. Simple organic compounds have also been found to trap various organic
molecules upon crystallization.
article_processing_charge: No
article_type: original
author:
- first_name: Dipak
full_name: Samanta, Dipak
last_name: Samanta
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Samanta D, Klajn R. Clathrates grow up. Science. 2017;355(6328):912-912.
doi:10.1126/science.aam7927
apa: Samanta, D., & Klajn, R. (2017). Clathrates grow up. Science. American
Association for the Advancement of Science. https://doi.org/10.1126/science.aam7927
chicago: Samanta, Dipak, and Rafal Klajn. “Clathrates Grow Up.” Science.
American Association for the Advancement of Science, 2017. https://doi.org/10.1126/science.aam7927.
ieee: D. Samanta and R. Klajn, “Clathrates grow up,” Science, vol. 355, no.
6328. American Association for the Advancement of Science, pp. 912–912, 2017.
ista: Samanta D, Klajn R. 2017. Clathrates grow up. Science. 355(6328), 912–912.
mla: Samanta, Dipak, and Rafal Klajn. “Clathrates Grow Up.” Science, vol.
355, no. 6328, American Association for the Advancement of Science, 2017, pp.
912–912, doi:10.1126/science.aam7927.
short: D. Samanta, R. Klajn, Science 355 (2017) 912–912.
date_created: 2023-08-01T09:41:55Z
date_published: 2017-03-03T00:00:00Z
date_updated: 2023-08-07T12:23:03Z
day: '03'
doi: 10.1126/science.aam7927
extern: '1'
external_id:
pmid:
- '28254902'
intvolume: ' 355'
issue: '6328'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '03'
oa_version: None
page: 912-912
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Clathrates grow up
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 355
year: '2017'
...
---
_id: '14005'
abstract:
- lang: eng
text: Strong-field photoelectron holography and laser-induced electron diffraction
(LIED) are two powerful emerging methods for probing the ultrafast dynamics of
molecules. However, both of them have remained restricted to static systems and
to nuclear dynamics induced by strong-field ionization. Here we extend these promising
methods to image purely electronic valence-shell dynamics in molecules using photoelectron
holography. In the same experiment, we use LIED and photoelectron holography simultaneously,
to observe coupled electronic-rotational dynamics taking place on similar timescales.
These results offer perspectives for imaging ultrafast dynamics of molecules on
femtosecond to attosecond timescales.
article_number: '15651'
article_processing_charge: No
article_type: original
author:
- first_name: Samuel G.
full_name: Walt, Samuel G.
last_name: Walt
- first_name: Niraghatam
full_name: Bhargava Ram, Niraghatam
last_name: Bhargava Ram
- first_name: Marcos
full_name: Atala, Marcos
last_name: Atala
- first_name: Nikolay I
full_name: Shvetsov-Shilovski, Nikolay I
last_name: Shvetsov-Shilovski
- first_name: Aaron
full_name: von Conta, Aaron
last_name: von Conta
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: Manfred
full_name: Lein, Manfred
last_name: Lein
- first_name: Hans Jakob
full_name: Wörner, Hans Jakob
last_name: Wörner
citation:
ama: Walt SG, Bhargava Ram N, Atala M, et al. Dynamics of valence-shell electrons
and nuclei probed by strong-field holography and rescattering. Nature Communications.
2017;8. doi:10.1038/ncomms15651
apa: Walt, S. G., Bhargava Ram, N., Atala, M., Shvetsov-Shilovski, N. I., von Conta,
A., Baykusheva, D. R., … Wörner, H. J. (2017). Dynamics of valence-shell electrons
and nuclei probed by strong-field holography and rescattering. Nature Communications.
Springer Nature. https://doi.org/10.1038/ncomms15651
chicago: Walt, Samuel G., Niraghatam Bhargava Ram, Marcos Atala, Nikolay I Shvetsov-Shilovski,
Aaron von Conta, Denitsa Rangelova Baykusheva, Manfred Lein, and Hans Jakob Wörner.
“Dynamics of Valence-Shell Electrons and Nuclei Probed by Strong-Field Holography
and Rescattering.” Nature Communications. Springer Nature, 2017. https://doi.org/10.1038/ncomms15651.
ieee: S. G. Walt et al., “Dynamics of valence-shell electrons and nuclei
probed by strong-field holography and rescattering,” Nature Communications,
vol. 8. Springer Nature, 2017.
ista: Walt SG, Bhargava Ram N, Atala M, Shvetsov-Shilovski NI, von Conta A, Baykusheva
DR, Lein M, Wörner HJ. 2017. Dynamics of valence-shell electrons and nuclei probed
by strong-field holography and rescattering. Nature Communications. 8, 15651.
mla: Walt, Samuel G., et al. “Dynamics of Valence-Shell Electrons and Nuclei Probed
by Strong-Field Holography and Rescattering.” Nature Communications, vol.
8, 15651, Springer Nature, 2017, doi:10.1038/ncomms15651.
short: S.G. Walt, N. Bhargava Ram, M. Atala, N.I. Shvetsov-Shilovski, A. von Conta,
D.R. Baykusheva, M. Lein, H.J. Wörner, Nature Communications 8 (2017).
date_created: 2023-08-10T06:36:09Z
date_published: 2017-06-15T00:00:00Z
date_updated: 2023-08-22T08:26:06Z
day: '15'
doi: 10.1038/ncomms15651
extern: '1'
external_id:
pmid:
- '28643771'
intvolume: ' 8'
keyword:
- General Physics and Astronomy
- General Biochemistry
- Genetics and Molecular Biology
- General Chemistry
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/ncomms15651
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamics of valence-shell electrons and nuclei probed by strong-field holography
and rescattering
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2017'
...
---
_id: '14008'
abstract:
- lang: eng
text: Time-resolved x-ray absorption spectroscopy (TR-XAS) has so far practically
been limited to large-scale facilities, to subpicosecond temporal resolution,
and to the condensed phase. We report the realization of TR-XAS with a temporal
resolution in the low femtosecond range by developing a tabletop high-harmonic
source reaching up to 350 electron volts, thus partially covering the spectral
region of 280 to 530 electron volts, where water is transmissive. We used this
source to follow previously unexamined light-induced chemical reactions in the
lowest electronic states of isolated CF4+ and SF6+ molecules in the gas phase.
By probing element-specific core-to-valence transitions at the carbon K-edge or
the sulfur L-edges, we characterized their reaction paths and observed the effect
of symmetry breaking through the splitting of absorption bands and Rydberg-valence
mixing induced by the geometry changes.
article_processing_charge: No
article_type: original
author:
- first_name: Yoann
full_name: Pertot, Yoann
last_name: Pertot
- first_name: Cédric
full_name: Schmidt, Cédric
last_name: Schmidt
- first_name: Mary
full_name: Matthews, Mary
last_name: Matthews
- first_name: Adrien
full_name: Chauvet, Adrien
last_name: Chauvet
- first_name: Martin
full_name: Huppert, Martin
last_name: Huppert
- first_name: Vit
full_name: Svoboda, Vit
last_name: Svoboda
- first_name: Aaron
full_name: von Conta, Aaron
last_name: von Conta
- first_name: Andres
full_name: Tehlar, Andres
last_name: Tehlar
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: Jean-Pierre
full_name: Wolf, Jean-Pierre
last_name: Wolf
- first_name: Hans Jakob
full_name: Wörner, Hans Jakob
last_name: Wörner
citation:
ama: Pertot Y, Schmidt C, Matthews M, et al. Time-resolved x-ray absorption spectroscopy
with a water window high-harmonic source. Science. 2017;355(6322):264-267.
doi:10.1126/science.aah6114
apa: Pertot, Y., Schmidt, C., Matthews, M., Chauvet, A., Huppert, M., Svoboda, V.,
… Wörner, H. J. (2017). Time-resolved x-ray absorption spectroscopy with a water
window high-harmonic source. Science. American Association for the Advancement
of Science. https://doi.org/10.1126/science.aah6114
chicago: Pertot, Yoann, Cédric Schmidt, Mary Matthews, Adrien Chauvet, Martin Huppert,
Vit Svoboda, Aaron von Conta, et al. “Time-Resolved x-Ray Absorption Spectroscopy
with a Water Window High-Harmonic Source.” Science. American Association
for the Advancement of Science, 2017. https://doi.org/10.1126/science.aah6114.
ieee: Y. Pertot et al., “Time-resolved x-ray absorption spectroscopy with
a water window high-harmonic source,” Science, vol. 355, no. 6322. American
Association for the Advancement of Science, pp. 264–267, 2017.
ista: Pertot Y, Schmidt C, Matthews M, Chauvet A, Huppert M, Svoboda V, von Conta
A, Tehlar A, Baykusheva DR, Wolf J-P, Wörner HJ. 2017. Time-resolved x-ray absorption
spectroscopy with a water window high-harmonic source. Science. 355(6322), 264–267.
mla: Pertot, Yoann, et al. “Time-Resolved x-Ray Absorption Spectroscopy with a Water
Window High-Harmonic Source.” Science, vol. 355, no. 6322, American Association
for the Advancement of Science, 2017, pp. 264–67, doi:10.1126/science.aah6114.
short: Y. Pertot, C. Schmidt, M. Matthews, A. Chauvet, M. Huppert, V. Svoboda, A.
von Conta, A. Tehlar, D.R. Baykusheva, J.-P. Wolf, H.J. Wörner, Science 355 (2017)
264–267.
date_created: 2023-08-10T06:36:39Z
date_published: 2017-01-05T00:00:00Z
date_updated: 2023-08-22T08:34:38Z
day: '05'
doi: 10.1126/science.aah6114
extern: '1'
external_id:
pmid:
- '28059713'
intvolume: ' 355'
issue: '6322'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '01'
oa_version: None
page: 264-267
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Time-resolved x-ray absorption spectroscopy with a water window high-harmonic
source
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 355
year: '2017'
...
---
_id: '10373'
abstract:
- lang: eng
text: 'Electric charges are conserved. The same would be expected to hold for magnetic
charges, yet magnetic monopoles have never been observed. It is therefore surprising
that the laws of nonequilibrium thermodynamics, combined with Maxwell’s equations,
suggest that colloidal particles heated or cooled in certain polar or paramagnetic
solvents may behave as if they carry an electric/magnetic charge. Here, we present
numerical simulations that show that the field distribution around a pair of such
heated/cooled colloidal particles agrees quantitatively with the theoretical predictions
for a pair of oppositely charged electric or magnetic monopoles. However, in other
respects, the nonequilibrium colloidal particles do not behave as monopoles: They
cannot be moved by a homogeneous applied field. The numerical evidence for the
monopole-like fields around heated/cooled colloidal particles is crucial because
the experimental and numerical determination of forces between such colloidal
particles would be complicated by the presence of other effects, such as thermophoresis.'
acknowledgement: P.W. acknowledges many invaluable discussions with Martin Neumann,
Chao Zhang, Michiel Sprik, Aleks Reinhardt, Carl Pölking, and Tine Curk. We acknowledge
financial support from the Austrian Academy of Sciences through a doctoral (DOC)
fellowship (to P.W.), the Austrian Science Fund (FWF) within the Spezialforschungsbereich
Vienna Computational Materials Laboratory (Project F41) (C.D.), and the European
Union Early Training Network NANOTRANS (Grant 674979 to D. Frenkel). The results
presented here have been achieved in part using the Vienna Scientific Cluster.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Peter
full_name: Wirnsberger, Peter
last_name: Wirnsberger
- first_name: Domagoj
full_name: Fijan, Domagoj
last_name: Fijan
- first_name: Roger A.
full_name: Lightwood, Roger A.
last_name: Lightwood
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Christoph
full_name: Dellago, Christoph
last_name: Dellago
- first_name: Daan
full_name: Frenkel, Daan
last_name: Frenkel
citation:
ama: Wirnsberger P, Fijan D, Lightwood RA, Šarić A, Dellago C, Frenkel D. Numerical
evidence for thermally induced monopoles. Proceedings of the National Academy
of Sciences. 2017;114(19):4911-4914. doi:10.1073/pnas.1621494114
apa: Wirnsberger, P., Fijan, D., Lightwood, R. A., Šarić, A., Dellago, C., &
Frenkel, D. (2017). Numerical evidence for thermally induced monopoles. Proceedings
of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1621494114
chicago: Wirnsberger, Peter, Domagoj Fijan, Roger A. Lightwood, Anđela Šarić, Christoph
Dellago, and Daan Frenkel. “Numerical Evidence for Thermally Induced Monopoles.”
Proceedings of the National Academy of Sciences. National Academy of Sciences,
2017. https://doi.org/10.1073/pnas.1621494114.
ieee: P. Wirnsberger, D. Fijan, R. A. Lightwood, A. Šarić, C. Dellago, and D. Frenkel,
“Numerical evidence for thermally induced monopoles,” Proceedings of the National
Academy of Sciences, vol. 114, no. 19. National Academy of Sciences, pp. 4911–4914,
2017.
ista: Wirnsberger P, Fijan D, Lightwood RA, Šarić A, Dellago C, Frenkel D. 2017.
Numerical evidence for thermally induced monopoles. Proceedings of the National
Academy of Sciences. 114(19), 4911–4914.
mla: Wirnsberger, Peter, et al. “Numerical Evidence for Thermally Induced Monopoles.”
Proceedings of the National Academy of Sciences, vol. 114, no. 19, National
Academy of Sciences, 2017, pp. 4911–14, doi:10.1073/pnas.1621494114.
short: P. Wirnsberger, D. Fijan, R.A. Lightwood, A. Šarić, C. Dellago, D. Frenkel,
Proceedings of the National Academy of Sciences 114 (2017) 4911–4914.
date_created: 2021-11-29T09:28:24Z
date_published: 2017-04-24T00:00:00Z
date_updated: 2021-11-29T09:59:12Z
day: '24'
doi: 10.1073/pnas.1621494114
extern: '1'
external_id:
arxiv:
- '1610.06840'
pmid:
- '28439003'
intvolume: ' 114'
issue: '19'
keyword:
- multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.pnas.org/content/114/19/4911
month: '04'
oa: 1
oa_version: Published Version
page: 4911-4914
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Numerical evidence for thermally induced monopoles
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 114
year: '2017'
...
---
_id: '9477'
abstract:
- lang: eng
text: Cytosine methylation is a DNA modification with important regulatory functions
in eukaryotes. In flowering plants, sexual reproduction is accompanied by extensive
DNA demethylation, which is required for proper gene expression in the endosperm,
a nutritive extraembryonic seed tissue. Endosperm arises from a fusion of a sperm
cell carried in the pollen and a female central cell. Endosperm DNA demethylation
is observed specifically on the chromosomes inherited from the central cell in
Arabidopsis thaliana, rice, and maize, and requires the DEMETER DNA demethylase
in Arabidopsis. DEMETER is expressed in the central cell before fertilization,
suggesting that endosperm demethylation patterns are inherited from the central
cell. Down-regulation of the MET1 DNA methyltransferase has also been proposed
to contribute to central cell demethylation. However, with the exception of three
maize genes, central cell DNA methylation has not been directly measured, leaving
the origin and mechanism of endosperm demethylation uncertain. Here, we report
genome-wide analysis of DNA methylation in the central cells of Arabidopsis and
rice—species that diverged 150 million years ago—as well as in rice egg cells.
We find that DNA demethylation in both species is initiated in central cells,
which requires DEMETER in Arabidopsis. However, we do not observe a global reduction
of CG methylation that would be indicative of lowered MET1 activity; on the contrary,
CG methylation efficiency is elevated in female gametes compared with nonsexual
tissues. Our results demonstrate that locus-specific, active DNA demethylation
in the central cell is the origin of maternal chromosome hypomethylation in the
endosperm.
article_processing_charge: No
article_type: original
author:
- first_name: Kyunghyuk
full_name: Park, Kyunghyuk
last_name: Park
- first_name: M. Yvonne
full_name: Kim, M. Yvonne
last_name: Kim
- first_name: Martin
full_name: Vickers, Martin
last_name: Vickers
- first_name: Jin-Sup
full_name: Park, Jin-Sup
last_name: Park
- first_name: Youbong
full_name: Hyun, Youbong
last_name: Hyun
- first_name: Takashi
full_name: Okamoto, Takashi
last_name: Okamoto
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Yeonhee
full_name: Choi, Yeonhee
last_name: Choi
- first_name: Stefan
full_name: Scholten, Stefan
last_name: Scholten
citation:
ama: Park K, Kim MY, Vickers M, et al. DNA demethylation is initiated in the central
cells of Arabidopsis and rice. Proceedings of the National Academy of Sciences.
2016;113(52):15138-15143. doi:10.1073/pnas.1619047114
apa: Park, K., Kim, M. Y., Vickers, M., Park, J.-S., Hyun, Y., Okamoto, T., … Scholten,
S. (2016). DNA demethylation is initiated in the central cells of Arabidopsis
and rice. Proceedings of the National Academy of Sciences. National Academy
of Sciences. https://doi.org/10.1073/pnas.1619047114
chicago: Park, Kyunghyuk, M. Yvonne Kim, Martin Vickers, Jin-Sup Park, Youbong Hyun,
Takashi Okamoto, Daniel Zilberman, et al. “DNA Demethylation Is Initiated in the
Central Cells of Arabidopsis and Rice.” Proceedings of the National Academy
of Sciences. National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1619047114.
ieee: K. Park et al., “DNA demethylation is initiated in the central cells
of Arabidopsis and rice,” Proceedings of the National Academy of Sciences,
vol. 113, no. 52. National Academy of Sciences, pp. 15138–15143, 2016.
ista: Park K, Kim MY, Vickers M, Park J-S, Hyun Y, Okamoto T, Zilberman D, Fischer
RL, Feng X, Choi Y, Scholten S. 2016. DNA demethylation is initiated in the central
cells of Arabidopsis and rice. Proceedings of the National Academy of Sciences.
113(52), 15138–15143.
mla: Park, Kyunghyuk, et al. “DNA Demethylation Is Initiated in the Central Cells
of Arabidopsis and Rice.” Proceedings of the National Academy of Sciences,
vol. 113, no. 52, National Academy of Sciences, 2016, pp. 15138–43, doi:10.1073/pnas.1619047114.
short: K. Park, M.Y. Kim, M. Vickers, J.-S. Park, Y. Hyun, T. Okamoto, D. Zilberman,
R.L. Fischer, X. Feng, Y. Choi, S. Scholten, Proceedings of the National Academy
of Sciences 113 (2016) 15138–15143.
date_created: 2021-06-07T07:10:59Z
date_published: 2016-12-27T00:00:00Z
date_updated: 2023-05-08T11:00:07Z
day: '27'
department:
- _id: DaZi
- _id: XiFe
doi: 10.1073/pnas.1619047114
extern: '1'
external_id:
pmid:
- '27956642'
intvolume: ' 113'
issue: '52'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1619047114
month: '12'
oa: 1
oa_version: Published Version
page: 15138-15143
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA demethylation is initiated in the central cells of Arabidopsis and rice
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2016'
...
---
_id: '10377'
abstract:
- lang: eng
text: The interplay of membrane proteins is vital for many biological processes,
such as cellular transport, cell division, and signal transduction between nerve
cells. Theoretical considerations have led to the idea that the membrane itself
mediates protein self-organization in these processes through minimization of
membrane curvature energy. Here, we present a combined experimental and numerical
study in which we quantify these interactions directly for the first time. In
our experimental model system we control the deformation of a lipid membrane by
adhering colloidal particles. Using confocal microscopy, we establish that these
membrane deformations cause an attractive interaction force leading to reversible
binding. The attraction extends over 2.5 times the particle diameter and has a
strength of three times the thermal energy (−3.3 kBT). Coarse-grained Monte-Carlo
simulations of the system are in excellent agreement with the experimental results
and prove that the measured interaction is independent of length scale. Our combined
experimental and numerical results reveal membrane curvature as a common physical
origin for interactions between any membrane-deforming objects, from nanometre-sized
proteins to micrometre-sized particles.
acknowledgement: This work was supported by the Netherlands Organisation for Scientific
Research (NWO/OCW), as part of the Frontiers of Nanoscience program and VENI grant
680-47-431. We thank Jeroen Appel and Wim Pomp for advice on the protocol design
and Marcel Winter and Ruben Verweij for experimental support.
article_number: '32825'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Casper
full_name: van der Wel, Casper
last_name: van der Wel
- first_name: Afshin
full_name: Vahid, Afshin
last_name: Vahid
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Timon
full_name: Idema, Timon
last_name: Idema
- first_name: Doris
full_name: Heinrich, Doris
last_name: Heinrich
- first_name: Daniela J.
full_name: Kraft, Daniela J.
last_name: Kraft
citation:
ama: van der Wel C, Vahid A, Šarić A, Idema T, Heinrich D, Kraft DJ. Lipid membrane-mediated
attraction between curvature inducing objects. Scientific Reports. 2016;6(1).
doi:10.1038/srep32825
apa: van der Wel, C., Vahid, A., Šarić, A., Idema, T., Heinrich, D., & Kraft,
D. J. (2016). Lipid membrane-mediated attraction between curvature inducing objects.
Scientific Reports. Springer Nature. https://doi.org/10.1038/srep32825
chicago: Wel, Casper van der, Afshin Vahid, Anđela Šarić, Timon Idema, Doris Heinrich,
and Daniela J. Kraft. “Lipid Membrane-Mediated Attraction between Curvature Inducing
Objects.” Scientific Reports. Springer Nature, 2016. https://doi.org/10.1038/srep32825.
ieee: C. van der Wel, A. Vahid, A. Šarić, T. Idema, D. Heinrich, and D. J. Kraft,
“Lipid membrane-mediated attraction between curvature inducing objects,” Scientific
Reports, vol. 6, no. 1. Springer Nature, 2016.
ista: van der Wel C, Vahid A, Šarić A, Idema T, Heinrich D, Kraft DJ. 2016. Lipid
membrane-mediated attraction between curvature inducing objects. Scientific Reports.
6(1), 32825.
mla: van der Wel, Casper, et al. “Lipid Membrane-Mediated Attraction between Curvature
Inducing Objects.” Scientific Reports, vol. 6, no. 1, 32825, Springer Nature,
2016, doi:10.1038/srep32825.
short: C. van der Wel, A. Vahid, A. Šarić, T. Idema, D. Heinrich, D.J. Kraft, Scientific
Reports 6 (2016).
date_created: 2021-11-29T10:34:08Z
date_published: 2016-09-13T00:00:00Z
date_updated: 2021-11-29T11:08:15Z
day: '13'
ddc:
- '540'
doi: 10.1038/srep32825
extern: '1'
external_id:
arxiv:
- '1603.04644'
pmid:
- '27618764'
file:
- access_level: open_access
checksum: d6cf16dd511e15726b001e7cc287cf1d
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-29T10:50:00Z
date_updated: 2021-11-29T10:50:00Z
file_id: '10379'
file_name: 2016_SciRep_vanderWel.pdf
file_size: 1598289
relation: main_file
success: 1
file_date_updated: 2021-11-29T10:50:00Z
has_accepted_license: '1'
intvolume: ' 6'
issue: '1'
keyword:
- multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.nature.com/articles/srep32825
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
publication: Scientific Reports
publication_identifier:
issn:
- 2045-2322
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/srep37382
scopus_import: '1'
status: public
title: Lipid membrane-mediated attraction between curvature inducing objects
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: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 6
year: '2016'
...
---
_id: '12618'
abstract:
- lang: eng
text: Mountain ranges are the world’s natural water towers and provide water resources
for millions of people. However, their hydrological balance and possible future
changes in river flow remain poorly understood because of high meteorological
variability, physical inaccessibility, and the complex interplay between climate,
cryosphere, and hydrological processes. Here, we use a state-of-the art glacio-hydrological
model informed by data from high-altitude observations and the latest climate
change scenarios to quantify the climate change impact on water resources of two
contrasting catchments vulnerable to changes in the cryosphere. The two study
catchments are located in the Central Andes of Chile and in the Nepalese Himalaya
in close vicinity of densely populated areas. Although both sites reveal a strong
decrease in glacier area, they show a remarkably different hydrological response
to projected climate change. In the Juncal catchment in Chile, runoff is likely
to sharply decrease in the future and the runoff seasonality is sensitive to projected
climatic changes. In the Langtang catchment in Nepal, future water availability
is on the rise for decades to come with limited shifts between seasons. Owing
to the high spatiotemporal resolution of the simulations and process complexity
included in the modeling, the response times and the mechanisms underlying the
variations in glacier area and river flow can be well constrained. The projections
indicate that climate change adaptation in Central Chile should focus on dealing
with a reduction in water availability, whereas in Nepal preparedness for flood
extremes should be the policy priority.
article_processing_charge: No
article_type: original
author:
- first_name: Silvan
full_name: Ragettli, Silvan
last_name: Ragettli
- first_name: Walter W.
full_name: Immerzeel, Walter W.
last_name: Immerzeel
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
citation:
ama: Ragettli S, Immerzeel WW, Pellicciotti F. Contrasting climate change impact
on river flows from high-altitude catchments in the Himalayan and Andes Mountains.
PNAS. 2016;113(33):9222-9227. doi:10.1073/pnas.1606526113
apa: Ragettli, S., Immerzeel, W. W., & Pellicciotti, F. (2016). Contrasting
climate change impact on river flows from high-altitude catchments in the Himalayan
and Andes Mountains. PNAS. Proceedings of the National Academy of Sciences.
https://doi.org/10.1073/pnas.1606526113
chicago: Ragettli, Silvan, Walter W. Immerzeel, and Francesca Pellicciotti. “Contrasting
Climate Change Impact on River Flows from High-Altitude Catchments in the Himalayan
and Andes Mountains.” PNAS. Proceedings of the National Academy of Sciences,
2016. https://doi.org/10.1073/pnas.1606526113.
ieee: S. Ragettli, W. W. Immerzeel, and F. Pellicciotti, “Contrasting climate change
impact on river flows from high-altitude catchments in the Himalayan and Andes
Mountains,” PNAS, vol. 113, no. 33. Proceedings of the National Academy
of Sciences, pp. 9222–9227, 2016.
ista: Ragettli S, Immerzeel WW, Pellicciotti F. 2016. Contrasting climate change
impact on river flows from high-altitude catchments in the Himalayan and Andes
Mountains. PNAS. 113(33), 9222–9227.
mla: Ragettli, Silvan, et al. “Contrasting Climate Change Impact on River Flows
from High-Altitude Catchments in the Himalayan and Andes Mountains.” PNAS,
vol. 113, no. 33, Proceedings of the National Academy of Sciences, 2016, pp. 9222–27,
doi:10.1073/pnas.1606526113.
short: S. Ragettli, W.W. Immerzeel, F. Pellicciotti, PNAS 113 (2016) 9222–9227.
date_created: 2023-02-20T08:14:58Z
date_published: 2016-08-01T00:00:00Z
date_updated: 2023-02-24T10:48:43Z
day: '01'
doi: 10.1073/pnas.1606526113
extern: '1'
external_id:
pmid:
- '27482082'
intvolume: ' 113'
issue: '33'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1606526113
month: '08'
oa: 1
oa_version: Published Version
page: 9222-9227
pmid: 1
publication: PNAS
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Contrasting climate change impact on river flows from high-altitude catchments
in the Himalayan and Andes Mountains
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2016'
...
---
_id: '14013'
abstract:
- lang: eng
text: The ultrafast motion of electrons and holes after light-matter interaction
is fundamental to a broad range of chemical and biophysical processes. We advanced
high-harmonic spectroscopy to resolve spatially and temporally the migration of
an electron hole immediately after ionization of iodoacetylene while simultaneously
demonstrating extensive control over the process. A multidimensional approach,
based on the measurement and accurate theoretical description of both even and
odd harmonic orders, enabled us to reconstruct both quantum amplitudes and phases
of the electronic states with a resolution of ~100 attoseconds. We separately
reconstructed quasi-field-free and laser-controlled charge migration as a function
of the spatial orientation of the molecule and determined the shape of the hole
created by ionization. Our technique opens the prospect of laser control over
electronic primary processes.
article_processing_charge: No
article_type: original
author:
- first_name: P. M.
full_name: Kraus, P. M.
last_name: Kraus
- first_name: B.
full_name: Mignolet, B.
last_name: Mignolet
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: A.
full_name: Rupenyan, A.
last_name: Rupenyan
- first_name: L.
full_name: Horný, L.
last_name: Horný
- first_name: E. F.
full_name: Penka, E. F.
last_name: Penka
- first_name: G.
full_name: Grassi, G.
last_name: Grassi
- first_name: O. I.
full_name: Tolstikhin, O. I.
last_name: Tolstikhin
- first_name: J.
full_name: Schneider, J.
last_name: Schneider
- first_name: F.
full_name: Jensen, F.
last_name: Jensen
- first_name: L. B.
full_name: Madsen, L. B.
last_name: Madsen
- first_name: A. D.
full_name: Bandrauk, A. D.
last_name: Bandrauk
- first_name: F.
full_name: Remacle, F.
last_name: Remacle
- first_name: H. J.
full_name: Wörner, H. J.
last_name: Wörner
citation:
ama: Kraus PM, Mignolet B, Baykusheva DR, et al. Measurement and laser control of
attosecond charge migration in ionized iodoacetylene. Science. 2015;350(6262):790-795.
doi:10.1126/science.aab2160
apa: Kraus, P. M., Mignolet, B., Baykusheva, D. R., Rupenyan, A., Horný, L., Penka,
E. F., … Wörner, H. J. (2015). Measurement and laser control of attosecond charge
migration in ionized iodoacetylene. Science. American Association for the
Advancement of Science. https://doi.org/10.1126/science.aab2160
chicago: Kraus, P. M., B. Mignolet, Denitsa Rangelova Baykusheva, A. Rupenyan, L.
Horný, E. F. Penka, G. Grassi, et al. “Measurement and Laser Control of Attosecond
Charge Migration in Ionized Iodoacetylene.” Science. American Association
for the Advancement of Science, 2015. https://doi.org/10.1126/science.aab2160.
ieee: P. M. Kraus et al., “Measurement and laser control of attosecond charge
migration in ionized iodoacetylene,” Science, vol. 350, no. 6262. American
Association for the Advancement of Science, pp. 790–795, 2015.
ista: Kraus PM, Mignolet B, Baykusheva DR, Rupenyan A, Horný L, Penka EF, Grassi
G, Tolstikhin OI, Schneider J, Jensen F, Madsen LB, Bandrauk AD, Remacle F, Wörner
HJ. 2015. Measurement and laser control of attosecond charge migration in ionized
iodoacetylene. Science. 350(6262), 790–795.
mla: Kraus, P. M., et al. “Measurement and Laser Control of Attosecond Charge Migration
in Ionized Iodoacetylene.” Science, vol. 350, no. 6262, American Association
for the Advancement of Science, 2015, pp. 790–95, doi:10.1126/science.aab2160.
short: P.M. Kraus, B. Mignolet, D.R. Baykusheva, A. Rupenyan, L. Horný, E.F. Penka,
G. Grassi, O.I. Tolstikhin, J. Schneider, F. Jensen, L.B. Madsen, A.D. Bandrauk,
F. Remacle, H.J. Wörner, Science 350 (2015) 790–795.
date_created: 2023-08-10T06:37:35Z
date_published: 2015-10-22T00:00:00Z
date_updated: 2023-08-22T08:47:39Z
day: '22'
doi: 10.1126/science.aab2160
extern: '1'
external_id:
pmid:
- '26494175'
intvolume: ' 350'
issue: '6262'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '10'
oa_version: None
page: 790-795
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Measurement and laser control of attosecond charge migration in ionized iodoacetylene
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 350
year: '2015'
...
---
_id: '14016'
abstract:
- lang: eng
text: All attosecond time-resolved measurements have so far relied on the use of
intense near-infrared laser pulses. In particular, attosecond streaking, laser-induced
electron diffraction and high-harmonic generation all make use of non-perturbative
light–matter interactions. Remarkably, the effect of the strong laser field on
the studied sample has often been neglected in previous studies. Here we use high-harmonic
spectroscopy to measure laser-induced modifications of the electronic structure
of molecules. We study high-harmonic spectra of spatially oriented CH3F and CH3Br
as generic examples of polar polyatomic molecules. We accurately measure intensity
ratios of even and odd-harmonic orders, and of the emission from aligned and unaligned
molecules. We show that these robust observables reveal a substantial modification
of the molecular electronic structure by the external laser field. Our insights
offer new challenges and opportunities for a range of emerging strong-field attosecond
spectroscopies.
article_number: '7039'
article_processing_charge: No
article_type: original
author:
- first_name: P. M.
full_name: Kraus, P. M.
last_name: Kraus
- first_name: O. I.
full_name: Tolstikhin, O. I.
last_name: Tolstikhin
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: A.
full_name: Rupenyan, A.
last_name: Rupenyan
- first_name: J.
full_name: Schneider, J.
last_name: Schneider
- first_name: C. Z.
full_name: Bisgaard, C. Z.
last_name: Bisgaard
- first_name: T.
full_name: Morishita, T.
last_name: Morishita
- first_name: F.
full_name: Jensen, F.
last_name: Jensen
- first_name: L. B.
full_name: Madsen, L. B.
last_name: Madsen
- first_name: H. J.
full_name: Wörner, H. J.
last_name: Wörner
citation:
ama: Kraus PM, Tolstikhin OI, Baykusheva DR, et al. Observation of laser-induced
electronic structure in oriented polyatomic molecules. Nature Communications.
2015;6. doi:10.1038/ncomms8039
apa: Kraus, P. M., Tolstikhin, O. I., Baykusheva, D. R., Rupenyan, A., Schneider,
J., Bisgaard, C. Z., … Wörner, H. J. (2015). Observation of laser-induced electronic
structure in oriented polyatomic molecules. Nature Communications. Springer
Nature. https://doi.org/10.1038/ncomms8039
chicago: Kraus, P. M., O. I. Tolstikhin, Denitsa Rangelova Baykusheva, A. Rupenyan,
J. Schneider, C. Z. Bisgaard, T. Morishita, F. Jensen, L. B. Madsen, and H. J.
Wörner. “Observation of Laser-Induced Electronic Structure in Oriented Polyatomic
Molecules.” Nature Communications. Springer Nature, 2015. https://doi.org/10.1038/ncomms8039.
ieee: P. M. Kraus et al., “Observation of laser-induced electronic structure
in oriented polyatomic molecules,” Nature Communications, vol. 6. Springer
Nature, 2015.
ista: Kraus PM, Tolstikhin OI, Baykusheva DR, Rupenyan A, Schneider J, Bisgaard
CZ, Morishita T, Jensen F, Madsen LB, Wörner HJ. 2015. Observation of laser-induced
electronic structure in oriented polyatomic molecules. Nature Communications.
6, 7039.
mla: Kraus, P. M., et al. “Observation of Laser-Induced Electronic Structure in
Oriented Polyatomic Molecules.” Nature Communications, vol. 6, 7039, Springer
Nature, 2015, doi:10.1038/ncomms8039.
short: P.M. Kraus, O.I. Tolstikhin, D.R. Baykusheva, A. Rupenyan, J. Schneider,
C.Z. Bisgaard, T. Morishita, F. Jensen, L.B. Madsen, H.J. Wörner, Nature Communications
6 (2015).
date_created: 2023-08-10T06:38:01Z
date_published: 2015-05-05T00:00:00Z
date_updated: 2023-08-22T08:52:56Z
day: '05'
doi: 10.1038/ncomms8039
extern: '1'
external_id:
pmid:
- '25940229'
intvolume: ' 6'
keyword:
- General Physics and Astronomy
- General Biochemistry
- Genetics and Molecular Biology
- General Chemistry
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/ncomms8039
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Observation of laser-induced electronic structure in oriented polyatomic molecules
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2015'
...
---
_id: '13400'
abstract:
- lang: eng
text: Organizing inorganic nanocrystals into complex architectures is challenging
and typically relies on preexisting templates, such as properly folded DNA or
polypeptide chains. We found that under carefully controlled conditions, cubic
nanocrystals of magnetite self-assemble into arrays of helical superstructures
in a template-free manner with >99% yield. Computer simulations revealed that
the formation of helices is determined by the interplay of van der Waals and magnetic
dipole-dipole interactions, Zeeman coupling, and entropic forces and can be attributed
to spontaneous formation of chiral nanocube clusters. Neighboring helices within
their densely packed ensembles tended to adopt the same handedness in order to
maximize packing, thus revealing a novel mechanism of symmetry breaking and chirality
amplification.
article_processing_charge: No
article_type: original
author:
- first_name: Gurvinder
full_name: Singh, Gurvinder
last_name: Singh
- first_name: Henry
full_name: Chan, Henry
last_name: Chan
- first_name: Artem
full_name: Baskin, Artem
last_name: Baskin
- first_name: Elijah
full_name: Gelman, Elijah
last_name: Gelman
- first_name: Nikita
full_name: Repnin, Nikita
last_name: Repnin
- first_name: Petr
full_name: Král, Petr
last_name: Král
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Singh G, Chan H, Baskin A, et al. Self-assembly of magnetite nanocubes into
helical superstructures. Science. 2014;345(6201):1149-1153. doi:10.1126/science.1254132
apa: Singh, G., Chan, H., Baskin, A., Gelman, E., Repnin, N., Král, P., & Klajn,
R. (2014). Self-assembly of magnetite nanocubes into helical superstructures.
Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1254132
chicago: Singh, Gurvinder, Henry Chan, Artem Baskin, Elijah Gelman, Nikita Repnin,
Petr Král, and Rafal Klajn. “Self-Assembly of Magnetite Nanocubes into Helical
Superstructures.” Science. American Association for the Advancement of
Science, 2014. https://doi.org/10.1126/science.1254132.
ieee: G. Singh et al., “Self-assembly of magnetite nanocubes into helical
superstructures,” Science, vol. 345, no. 6201. American Association for
the Advancement of Science, pp. 1149–1153, 2014.
ista: Singh G, Chan H, Baskin A, Gelman E, Repnin N, Král P, Klajn R. 2014. Self-assembly
of magnetite nanocubes into helical superstructures. Science. 345(6201), 1149–1153.
mla: Singh, Gurvinder, et al. “Self-Assembly of Magnetite Nanocubes into Helical
Superstructures.” Science, vol. 345, no. 6201, American Association for
the Advancement of Science, 2014, pp. 1149–53, doi:10.1126/science.1254132.
short: G. Singh, H. Chan, A. Baskin, E. Gelman, N. Repnin, P. Král, R. Klajn, Science
345 (2014) 1149–1153.
date_created: 2023-08-01T09:45:56Z
date_published: 2014-07-24T00:00:00Z
date_updated: 2023-08-08T07:23:05Z
day: '24'
doi: 10.1126/science.1254132
extern: '1'
external_id:
pmid:
- '25061133'
intvolume: ' 345'
issue: '6201'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '07'
oa_version: None
page: 1149-1153
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Self-assembly of magnetite nanocubes into helical superstructures
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 345
year: '2014'
...
---
_id: '13402'
abstract:
- lang: eng
text: Nanoporous frameworks are polymeric materials built from rigid molecules,
which give rise to their nanoporous structures with applications in gas sorption
and storage, catalysis and others. Conceptually new applications could emerge,
should these beneficial properties be manipulated by external stimuli in a reversible
manner. One approach to render nanoporous frameworks responsive to external signals
would be to immobilize molecular switches within their nanopores. Although the
majority of molecular switches require conformational freedom to isomerize, and
switching in the solid state is prohibited, the nanopores may provide enough room
for the switches to efficiently isomerize. Here we describe two families of nanoporous
materials incorporating the spiropyran molecular switch. These materials exhibit
a variety of interesting properties, including reversible photochromism and acidochromism
under solvent-free conditions, light-controlled capture and release of metal ions,
as well reversible chromism induced by solvation/desolvation.
article_number: '3588'
article_processing_charge: No
article_type: original
author:
- first_name: Pintu K.
full_name: Kundu, Pintu K.
last_name: Kundu
- first_name: Gregory L.
full_name: Olsen, Gregory L.
last_name: Olsen
- first_name: Vladimir
full_name: Kiss, Vladimir
last_name: Kiss
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Kundu PK, Olsen GL, Kiss V, Klajn R. Nanoporous frameworks exhibiting multiple
stimuli responsiveness. Nature Communications. 2014;5. doi:10.1038/ncomms4588
apa: Kundu, P. K., Olsen, G. L., Kiss, V., & Klajn, R. (2014). Nanoporous frameworks
exhibiting multiple stimuli responsiveness. Nature Communications. Springer
Nature. https://doi.org/10.1038/ncomms4588
chicago: Kundu, Pintu K., Gregory L. Olsen, Vladimir Kiss, and Rafal Klajn. “Nanoporous
Frameworks Exhibiting Multiple Stimuli Responsiveness.” Nature Communications.
Springer Nature, 2014. https://doi.org/10.1038/ncomms4588.
ieee: P. K. Kundu, G. L. Olsen, V. Kiss, and R. Klajn, “Nanoporous frameworks exhibiting
multiple stimuli responsiveness,” Nature Communications, vol. 5. Springer
Nature, 2014.
ista: Kundu PK, Olsen GL, Kiss V, Klajn R. 2014. Nanoporous frameworks exhibiting
multiple stimuli responsiveness. Nature Communications. 5, 3588.
mla: Kundu, Pintu K., et al. “Nanoporous Frameworks Exhibiting Multiple Stimuli
Responsiveness.” Nature Communications, vol. 5, 3588, Springer Nature,
2014, doi:10.1038/ncomms4588.
short: P.K. Kundu, G.L. Olsen, V. Kiss, R. Klajn, Nature Communications 5 (2014).
date_created: 2023-08-01T09:46:27Z
date_published: 2014-04-07T00:00:00Z
date_updated: 2023-08-08T07:28:10Z
day: '07'
doi: 10.1038/ncomms4588
extern: '1'
external_id:
pmid:
- '24709950'
intvolume: ' 5'
keyword:
- General Physics and Astronomy
- General Biochemistry
- Genetics and Molecular Biology
- General Chemistry
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/ncomms4588
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nanoporous frameworks exhibiting multiple stimuli responsiveness
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2014'
...
---
_id: '10382'
abstract:
- lang: eng
text: 'Protein oligomers have been implicated as toxic agents in a wide range of
amyloid-related diseases. However, it has remained unsolved whether the oligomers
are a necessary step in the formation of amyloid fibrils or just a dangerous byproduct.
Analogously, it has not been resolved if the amyloid nucleation process is a classical
one-step nucleation process or a two-step process involving prenucleation clusters.
We use coarse-grained computer simulations to study the effect of nonspecific
attractions between peptides on the primary nucleation process underlying amyloid
fibrillization. We find that, for peptides that do not attract, the classical
one-step nucleation mechanism is possible but only at nonphysiologically high
peptide concentrations. At low peptide concentrations, which mimic the physiologically
relevant regime, attractive interpeptide interactions are essential for fibril
formation. Nucleation then inevitably takes place through a two-step mechanism
involving prefibrillar oligomers. We show that oligomers not only help peptides
meet each other but also, create an environment that facilitates the conversion
of monomers into the β-sheet–rich form characteristic of fibrils. Nucleation typically
does not proceed through the most prevalent oligomers but through an oligomer
size that is only observed in rare fluctuations, which is why such aggregates
might be hard to capture experimentally. Finally, we find that the nucleation
of amyloid fibrils cannot be described by classical nucleation theory: in the
two-step mechanism, the critical nucleus size increases with increases in both
concentration and interpeptide interactions, which is in direct contrast with
predictions from classical nucleation theory.'
acknowledgement: We thank Michele Vendruscolo, Iskra Staneva, and William M. Jacobs,
for helpful discussions. A.Š. acknowledges support from the Human Frontier Science
Program and Emmanuel College. Y.C.C. and D.F. are supported by Engineering and Physical
Sciences Research Council Programme Grant EP/I001352/1. T.P.J.K. acknowledges the
Frances and Augustus Newman Foundation, the European Research Council, and the Biotechnology
and Biological Sciences Research Council. D.F. acknowledges European Research Council
Advanced Grant 227758.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Yassmine C.
full_name: Chebaro, Yassmine C.
last_name: Chebaro
- first_name: Tuomas P. J.
full_name: Knowles, Tuomas P. J.
last_name: Knowles
- first_name: Daan
full_name: Frenkel, Daan
last_name: Frenkel
citation:
ama: Šarić A, Chebaro YC, Knowles TPJ, Frenkel D. Crucial role of nonspecific interactions
in amyloid nucleation. Proceedings of the National Academy of Sciences.
2014;111(50):17869-17874. doi:10.1073/pnas.1410159111
apa: Šarić, A., Chebaro, Y. C., Knowles, T. P. J., & Frenkel, D. (2014). Crucial
role of nonspecific interactions in amyloid nucleation. Proceedings of the
National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1410159111
chicago: Šarić, Anđela, Yassmine C. Chebaro, Tuomas P. J. Knowles, and Daan Frenkel.
“Crucial Role of Nonspecific Interactions in Amyloid Nucleation.” Proceedings
of the National Academy of Sciences. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1410159111.
ieee: A. Šarić, Y. C. Chebaro, T. P. J. Knowles, and D. Frenkel, “Crucial role of
nonspecific interactions in amyloid nucleation,” Proceedings of the National
Academy of Sciences, vol. 111, no. 50. National Academy of Sciences, pp. 17869–17874,
2014.
ista: Šarić A, Chebaro YC, Knowles TPJ, Frenkel D. 2014. Crucial role of nonspecific
interactions in amyloid nucleation. Proceedings of the National Academy of Sciences.
111(50), 17869–17874.
mla: Šarić, Anđela, et al. “Crucial Role of Nonspecific Interactions in Amyloid
Nucleation.” Proceedings of the National Academy of Sciences, vol. 111,
no. 50, National Academy of Sciences, 2014, pp. 17869–74, doi:10.1073/pnas.1410159111.
short: A. Šarić, Y.C. Chebaro, T.P.J. Knowles, D. Frenkel, Proceedings of the National
Academy of Sciences 111 (2014) 17869–17874.
date_created: 2021-11-29T13:09:53Z
date_published: 2014-12-01T00:00:00Z
date_updated: 2021-11-29T13:29:05Z
day: '01'
doi: 10.1073/pnas.1410159111
extern: '1'
external_id:
arxiv:
- '1412.0897'
pmid:
- '25453085'
intvolume: ' 111'
issue: '50'
keyword:
- multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.pnas.org/content/111/50/17869
month: '12'
oa: 1
oa_version: Published Version
page: 17869-17874
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Crucial role of nonspecific interactions in amyloid nucleation
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 111
year: '2014'
...
---
_id: '9055'
abstract:
- lang: eng
text: Spontaneous formation of colonies of bacteria or flocks of birds are examples
of self-organization in active living matter. Here, we demonstrate a form of self-organization
from nonequilibrium driving forces in a suspension of synthetic photoactivated
colloidal particles. They lead to two-dimensional "living crystals," which form,
break, explode, and re-form elsewhere. The dynamic assembly results from a competition
between self-propulsion of particles and an attractive interaction induced respectively
by osmotic and phoretic effects and activated by light. We measured a transition
from normal to giant-number fluctuations. Our experiments are quantitatively described
by simple numerical simulations. We show that the existence of the living crystals
is intrinsically related to the out-of-equilibrium collisions of the self-propelled
particles.
article_processing_charge: No
article_type: original
author:
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
- first_name: S.
full_name: Sacanna, S.
last_name: Sacanna
- first_name: A. P.
full_name: Steinberg, A. P.
last_name: Steinberg
- first_name: D. J.
full_name: Pine, D. J.
last_name: Pine
- first_name: P. M.
full_name: Chaikin, P. M.
last_name: Chaikin
citation:
ama: Palacci JA, Sacanna S, Steinberg AP, Pine DJ, Chaikin PM. Living crystals of
light-activated colloidal surfers. Science. 2013;339(6122):936-940. doi:10.1126/science.1230020
apa: Palacci, J. A., Sacanna, S., Steinberg, A. P., Pine, D. J., & Chaikin,
P. M. (2013). Living crystals of light-activated colloidal surfers. Science.
American Association for the Advancement of Science . https://doi.org/10.1126/science.1230020
chicago: Palacci, Jérémie A, S. Sacanna, A. P. Steinberg, D. J. Pine, and P. M.
Chaikin. “Living Crystals of Light-Activated Colloidal Surfers.” Science.
American Association for the Advancement of Science , 2013. https://doi.org/10.1126/science.1230020.
ieee: J. A. Palacci, S. Sacanna, A. P. Steinberg, D. J. Pine, and P. M. Chaikin,
“Living crystals of light-activated colloidal surfers,” Science, vol. 339,
no. 6122. American Association for the Advancement of Science , pp. 936–940, 2013.
ista: Palacci JA, Sacanna S, Steinberg AP, Pine DJ, Chaikin PM. 2013. Living crystals
of light-activated colloidal surfers. Science. 339(6122), 936–940.
mla: Palacci, Jérémie A., et al. “Living Crystals of Light-Activated Colloidal Surfers.”
Science, vol. 339, no. 6122, American Association for the Advancement of
Science , 2013, pp. 936–40, doi:10.1126/science.1230020.
short: J.A. Palacci, S. Sacanna, A.P. Steinberg, D.J. Pine, P.M. Chaikin, Science
339 (2013) 936–940.
date_created: 2021-02-01T14:37:29Z
date_published: 2013-02-22T00:00:00Z
date_updated: 2022-08-25T14:57:43Z
day: '22'
doi: 10.1126/science.1230020
extern: '1'
external_id:
pmid:
- '23371555'
intvolume: ' 339'
issue: '6122'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '02'
oa_version: None
page: 936-940
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: 'American Association for the Advancement of Science '
quality_controlled: '1'
scopus_import: '1'
status: public
title: Living crystals of light-activated colloidal surfers
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 339
year: '2013'
...
---
_id: '9481'
abstract:
- lang: eng
text: Arabidopsis thaliana endosperm, a transient tissue that nourishes the embryo,
exhibits extensive localized DNA demethylation on maternally inherited chromosomes.
Demethylation mediates parent-of-origin–specific (imprinted) gene expression but
is apparently unnecessary for the extensive accumulation of maternally biased
small RNA (sRNA) molecules detected in seeds. Endosperm DNA in the distantly related
monocots rice and maize is likewise locally hypomethylated, but whether this hypomethylation
is generally parent-of-origin specific is unknown. Imprinted expression of sRNA
also remains uninvestigated in monocot seeds. Here, we report high-coverage sequencing
of the Kitaake rice cultivar that enabled us to show that localized hypomethylation
in rice endosperm occurs solely on the maternal genome, preferring regions of
high DNA accessibility. Maternally expressed imprinted genes are enriched for
hypomethylation at putative promoter regions and transcriptional termini and paternally
expressed genes at promoters and gene bodies, mirroring our recent results in
A. thaliana. However, unlike in A. thaliana, rice endosperm sRNA populations are
dominated by specific strong sRNA-producing loci, and imprinted 24-nt sRNAs are
expressed from both parental genomes and correlate with hypomethylation. Overlaps
between imprinted sRNA loci and imprinted genes expressed from opposite alleles
suggest that sRNAs may regulate genomic imprinting. Whereas sRNAs in seedling
tissues primarily originate from small class II (cut-and-paste) transposable elements,
those in endosperm are more uniformly derived, including sequences from other
transposon classes, as well as genic and intergenic regions. Our data indicate
that the endosperm exhibits a unique pattern of sRNA expression and suggest that
localized hypomethylation of maternal endosperm DNA is conserved in flowering
plants.
article_processing_charge: No
article_type: original
author:
- first_name: Jessica A.
full_name: Rodrigues, Jessica A.
last_name: Rodrigues
- first_name: Randy
full_name: Ruan, Randy
last_name: Ruan
- first_name: Toshiro
full_name: Nishimura, Toshiro
last_name: Nishimura
- first_name: Manoj K.
full_name: Sharma, Manoj K.
last_name: Sharma
- first_name: Rita
full_name: Sharma, Rita
last_name: Sharma
- first_name: Pamela C
full_name: Ronald, Pamela C
last_name: Ronald
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Rodrigues JA, Ruan R, Nishimura T, et al. Imprinted expression of genes and
small RNA is associated with localized hypomethylation of the maternal genome
in rice endosperm. Proceedings of the National Academy of Sciences. 2013;110(19):7934-7939.
doi:10.1073/pnas.1306164110
apa: Rodrigues, J. A., Ruan, R., Nishimura, T., Sharma, M. K., Sharma, R., Ronald,
P. C., … Zilberman, D. (2013). Imprinted expression of genes and small RNA is
associated with localized hypomethylation of the maternal genome in rice endosperm.
Proceedings of the National Academy of Sciences. National Academy of Sciences.
https://doi.org/10.1073/pnas.1306164110
chicago: Rodrigues, Jessica A., Randy Ruan, Toshiro Nishimura, Manoj K. Sharma,
Rita Sharma, Pamela C Ronald, Robert L. Fischer, and Daniel Zilberman. “Imprinted
Expression of Genes and Small RNA Is Associated with Localized Hypomethylation
of the Maternal Genome in Rice Endosperm.” Proceedings of the National Academy
of Sciences. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1306164110.
ieee: J. A. Rodrigues et al., “Imprinted expression of genes and small RNA
is associated with localized hypomethylation of the maternal genome in rice endosperm,”
Proceedings of the National Academy of Sciences, vol. 110, no. 19. National
Academy of Sciences, pp. 7934–7939, 2013.
ista: Rodrigues JA, Ruan R, Nishimura T, Sharma MK, Sharma R, Ronald PC, Fischer
RL, Zilberman D. 2013. Imprinted expression of genes and small RNA is associated
with localized hypomethylation of the maternal genome in rice endosperm. Proceedings
of the National Academy of Sciences. 110(19), 7934–7939.
mla: Rodrigues, Jessica A., et al. “Imprinted Expression of Genes and Small RNA
Is Associated with Localized Hypomethylation of the Maternal Genome in Rice Endosperm.”
Proceedings of the National Academy of Sciences, vol. 110, no. 19, National
Academy of Sciences, 2013, pp. 7934–39, doi:10.1073/pnas.1306164110.
short: J.A. Rodrigues, R. Ruan, T. Nishimura, M.K. Sharma, R. Sharma, P.C. Ronald,
R.L. Fischer, D. Zilberman, Proceedings of the National Academy of Sciences 110
(2013) 7934–7939.
date_created: 2021-06-07T07:31:02Z
date_published: 2013-05-07T00:00:00Z
date_updated: 2021-12-14T08:26:44Z
day: '07'
department:
- _id: DaZi
doi: 10.1073/pnas.1306164110
extern: '1'
external_id:
pmid:
- '23613580'
intvolume: ' 110'
issue: '19'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1306164110
month: '05'
oa: 1
oa_version: Published Version
page: 7934-7939
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Imprinted expression of genes and small RNA is associated with localized hypomethylation
of the maternal genome in rice endosperm
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 110
year: '2013'
...