---
OA_type: closed access
_id: '17973'
abstract:
- lang: eng
text: Here we study the stability and rupture of molecular junctions under high
voltage bias at the single molecule/single bond level using the scanning tunneling
microscope-based break-junction technique. We synthesize carbon-, silicon-, and
germanium-based molecular wires terminated by aurophilic linker groups and study
how the molecular backbone and linker group affect the probability of voltage-induced
junction rupture. First, we find that junctions formed with covalent S–Au bonds
are robust under high voltage and their rupture does not demonstrate bias dependence
within our bias range. In contrast, junctions formed through donor–acceptor bonds
rupture more frequently, and their rupture probability demonstrates a strong bias
dependence. Moreover, we find that the junction rupture probability increases
significantly above ∼1 V in junctions formed from methylthiol-terminated disilanes
and digermanes, indicating a voltage-induced rupture of individual Si–Si and Ge–Ge
bonds. Finally, we compare the rupture probabilities of the thiol-terminated silane
derivatives containing Si–Si, Si–C, and Si–O bonds and find that Si–C backbones
have higher probabilities of sustaining the highest voltage. These results establish
a new method for studying electric field breakdown phenomena at the single molecule
level.
article_processing_charge: No
article_type: original
author:
- first_name: Haixing
full_name: Li, Haixing
last_name: Li
- first_name: Timothy A.
full_name: Su, Timothy A.
last_name: Su
- first_name: Vivian
full_name: Zhang, Vivian
last_name: Zhang
- first_name: Michael L.
full_name: Steigerwald, Michael L.
last_name: Steigerwald
- first_name: Colin
full_name: Nuckolls, Colin
last_name: Nuckolls
- first_name: Latha
full_name: Venkataraman, Latha
id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf
last_name: Venkataraman
orcid: 0000-0002-6957-6089
citation:
ama: Li H, Su TA, Zhang V, Steigerwald ML, Nuckolls C, Venkataraman L. Electric
field breakdown in single molecule junctions. Journal of the American Chemical
Society. 2015;137(15):5028-5033. doi:10.1021/ja512523r
apa: Li, H., Su, T. A., Zhang, V., Steigerwald, M. L., Nuckolls, C., & Venkataraman,
L. (2015). Electric field breakdown in single molecule junctions. Journal of
the American Chemical Society. American Chemical Society. https://doi.org/10.1021/ja512523r
chicago: Li, Haixing, Timothy A. Su, Vivian Zhang, Michael L. Steigerwald, Colin
Nuckolls, and Latha Venkataraman. “Electric Field Breakdown in Single Molecule
Junctions.” Journal of the American Chemical Society. American Chemical
Society, 2015. https://doi.org/10.1021/ja512523r.
ieee: H. Li, T. A. Su, V. Zhang, M. L. Steigerwald, C. Nuckolls, and L. Venkataraman,
“Electric field breakdown in single molecule junctions,” Journal of the American
Chemical Society, vol. 137, no. 15. American Chemical Society, pp. 5028–5033,
2015.
ista: Li H, Su TA, Zhang V, Steigerwald ML, Nuckolls C, Venkataraman L. 2015. Electric
field breakdown in single molecule junctions. Journal of the American Chemical
Society. 137(15), 5028–5033.
mla: Li, Haixing, et al. “Electric Field Breakdown in Single Molecule Junctions.”
Journal of the American Chemical Society, vol. 137, no. 15, American Chemical
Society, 2015, pp. 5028–33, doi:10.1021/ja512523r.
short: H. Li, T.A. Su, V. Zhang, M.L. Steigerwald, C. Nuckolls, L. Venkataraman,
Journal of the American Chemical Society 137 (2015) 5028–5033.
date_created: 2024-09-09T10:04:02Z
date_published: 2015-02-12T00:00:00Z
date_updated: 2024-12-18T12:10:06Z
day: '12'
doi: 10.1021/ja512523r
extern: '1'
external_id:
pmid:
- '25675085'
intvolume: ' 137'
issue: '15'
language:
- iso: eng
month: '02'
oa_version: None
page: 5028-5033
pmid: 1
publication: Journal of the American Chemical Society
publication_identifier:
eissn:
- 1520-5126
issn:
- 0002-7863
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Electric field breakdown in single molecule junctions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 137
year: '2015'
...
---
OA_type: closed access
_id: '17974'
abstract:
- lang: eng
text: Guest editors Dirk M. Guldi, Hiroshi Nishihara and Latha Venkataraman introduce
the Molecular Wires issue of "Chemical Society Reviews".
article_processing_charge: No
article_type: letter_note
author:
- first_name: Dirk M.
full_name: Guldi, Dirk M.
last_name: Guldi
- first_name: Hiroshi
full_name: Nishihara, Hiroshi
last_name: Nishihara
- first_name: Latha
full_name: Venkataraman, Latha
id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf
last_name: Venkataraman
orcid: 0000-0002-6957-6089
citation:
ama: Guldi DM, Nishihara H, Venkataraman L. Molecular wires. Chemical Society
Reviews. 2015;44(4):842-844. doi:10.1039/c5cs90010g
apa: Guldi, D. M., Nishihara, H., & Venkataraman, L. (2015). Molecular wires.
Chemical Society Reviews. Royal Society of Chemistry. https://doi.org/10.1039/c5cs90010g
chicago: Guldi, Dirk M., Hiroshi Nishihara, and Latha Venkataraman. “Molecular Wires.”
Chemical Society Reviews. Royal Society of Chemistry, 2015. https://doi.org/10.1039/c5cs90010g.
ieee: D. M. Guldi, H. Nishihara, and L. Venkataraman, “Molecular wires,” Chemical
Society Reviews, vol. 44, no. 4. Royal Society of Chemistry, pp. 842–844,
2015.
ista: Guldi DM, Nishihara H, Venkataraman L. 2015. Molecular wires. Chemical Society
Reviews. 44(4), 842–844.
mla: Guldi, Dirk M., et al. “Molecular Wires.” Chemical Society Reviews,
vol. 44, no. 4, Royal Society of Chemistry, 2015, pp. 842–44, doi:10.1039/c5cs90010g.
short: D.M. Guldi, H. Nishihara, L. Venkataraman, Chemical Society Reviews 44 (2015)
842–844.
date_created: 2024-09-09T10:53:55Z
date_published: 2015-01-30T00:00:00Z
date_updated: 2025-01-02T13:26:36Z
day: '30'
doi: 10.1039/c5cs90010g
extern: '1'
external_id:
pmid:
- '25636152'
intvolume: ' 44'
issue: '4'
language:
- iso: eng
month: '01'
oa_version: None
page: 842-844
pmid: 1
publication: Chemical Society Reviews
publication_identifier:
eissn:
- 1460-4744
issn:
- 0306-0012
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Molecular wires
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 44
year: '2015'
...
---
OA_type: closed access
_id: '17975'
abstract:
- lang: eng
text: A new intersection between reaction chemistry and electronic circuitry is
emerging from the ultraminiaturization of electronic devices. Over decades chemists
have developed a nuanced understanding of stereoelectronics to establish how the
electronic properties of molecules relate to their conformation; the recent advent
of single-molecule break-junction techniques provides the means to alter this
conformation with a level of control previously unimagined. Here we unite these
ideas by demonstrating the first single-molecule switch that operates through
a stereoelectronic effect. We demonstrate this behaviour in permethyloligosilanes
with methylthiomethyl electrode linkers. The strong σ conjugation in the oligosilane
backbone couples the stereoelectronic properties of the sulfur–methylene σ bonds
that terminate the molecule. Theoretical calculations support the existence of
three distinct dihedral conformations that differ drastically in their electronic
character. We can shift between these three species by simply lengthening or compressing
the molecular junction, and, in doing so, we can switch conductance digitally
between two states.
article_processing_charge: No
article_type: original
author:
- first_name: Timothy A.
full_name: Su, Timothy A.
last_name: Su
- first_name: Haixing
full_name: Li, Haixing
last_name: Li
- first_name: Michael L.
full_name: Steigerwald, Michael L.
last_name: Steigerwald
- first_name: Latha
full_name: Venkataraman, Latha
id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf
last_name: Venkataraman
orcid: 0000-0002-6957-6089
- first_name: Colin
full_name: Nuckolls, Colin
last_name: Nuckolls
citation:
ama: Su TA, Li H, Steigerwald ML, Venkataraman L, Nuckolls C. Stereoelectronic switching
in single-molecule junctions. Nature Chemistry. 2015;7(3):215-220. doi:10.1038/nchem.2180
apa: Su, T. A., Li, H., Steigerwald, M. L., Venkataraman, L., & Nuckolls, C.
(2015). Stereoelectronic switching in single-molecule junctions. Nature Chemistry.
Springer Nature. https://doi.org/10.1038/nchem.2180
chicago: Su, Timothy A., Haixing Li, Michael L. Steigerwald, Latha Venkataraman,
and Colin Nuckolls. “Stereoelectronic Switching in Single-Molecule Junctions.”
Nature Chemistry. Springer Nature, 2015. https://doi.org/10.1038/nchem.2180.
ieee: T. A. Su, H. Li, M. L. Steigerwald, L. Venkataraman, and C. Nuckolls, “Stereoelectronic
switching in single-molecule junctions,” Nature Chemistry, vol. 7, no.
3. Springer Nature, pp. 215–220, 2015.
ista: Su TA, Li H, Steigerwald ML, Venkataraman L, Nuckolls C. 2015. Stereoelectronic
switching in single-molecule junctions. Nature Chemistry. 7(3), 215–220.
mla: Su, Timothy A., et al. “Stereoelectronic Switching in Single-Molecule Junctions.”
Nature Chemistry, vol. 7, no. 3, Springer Nature, 2015, pp. 215–20, doi:10.1038/nchem.2180.
short: T.A. Su, H. Li, M.L. Steigerwald, L. Venkataraman, C. Nuckolls, Nature Chemistry
7 (2015) 215–220.
date_created: 2024-09-09T10:54:59Z
date_published: 2015-02-16T00:00:00Z
date_updated: 2025-01-02T13:28:51Z
day: '16'
doi: 10.1038/nchem.2180
extern: '1'
external_id:
pmid:
- '25698330'
intvolume: ' 7'
issue: '3'
language:
- iso: eng
month: '02'
oa_version: None
page: 215-220
pmid: 1
publication: Nature Chemistry
publication_identifier:
eissn:
- 1755-4349
issn:
- 1755-4330
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Stereoelectronic switching in single-molecule junctions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2015'
...
---
OA_type: closed access
_id: '17976'
abstract:
- lang: eng
text: To develop advanced materials for electronic devices, it is of utmost importance
to design organic building blocks with tunable functionality and to study their
properties at the molecular level. For organic electronic and photovoltaic applications,
the ability to vary the nature of charge carriers and so create either electron
donors or acceptors is critical. Here we demonstrate that charge carriers in single-molecule
junctions can be tuned within a family of molecules that contain electron-deficient
thiophene-1,1-dioxide (TDO) building blocks. Oligomers of TDO were designed to
increase electron affinity and maintain delocalized frontier orbitals while significantly
decreasing the transport gap. Through thermopower measurements we show that the
dominant charge carriers change from holes to electrons as the number of TDO units
is increased. This results in a unique system in which the charge carrier depends
on the backbone length, and provides a new means to tune p- and n-type transport
in organic materials.
article_processing_charge: No
article_type: original
author:
- first_name: Emma J.
full_name: Dell, Emma J.
last_name: Dell
- first_name: Brian
full_name: Capozzi, Brian
last_name: Capozzi
- first_name: Jianlong
full_name: Xia, Jianlong
last_name: Xia
- first_name: Latha
full_name: Venkataraman, Latha
id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf
last_name: Venkataraman
orcid: 0000-0002-6957-6089
- first_name: Luis M.
full_name: Campos, Luis M.
last_name: Campos
citation:
ama: Dell EJ, Capozzi B, Xia J, Venkataraman L, Campos LM. Molecular length dictates
the nature of charge carriers in single-molecule junctions of oxidized oligothiophenes.
Nature Chemistry. 2015;7(3):209-214. doi:10.1038/nchem.2160
apa: Dell, E. J., Capozzi, B., Xia, J., Venkataraman, L., & Campos, L. M. (2015).
Molecular length dictates the nature of charge carriers in single-molecule junctions
of oxidized oligothiophenes. Nature Chemistry. Springer Nature. https://doi.org/10.1038/nchem.2160
chicago: Dell, Emma J., Brian Capozzi, Jianlong Xia, Latha Venkataraman, and Luis
M. Campos. “Molecular Length Dictates the Nature of Charge Carriers in Single-Molecule
Junctions of Oxidized Oligothiophenes.” Nature Chemistry. Springer Nature,
2015. https://doi.org/10.1038/nchem.2160.
ieee: E. J. Dell, B. Capozzi, J. Xia, L. Venkataraman, and L. M. Campos, “Molecular
length dictates the nature of charge carriers in single-molecule junctions of
oxidized oligothiophenes,” Nature Chemistry, vol. 7, no. 3. Springer Nature,
pp. 209–214, 2015.
ista: Dell EJ, Capozzi B, Xia J, Venkataraman L, Campos LM. 2015. Molecular length
dictates the nature of charge carriers in single-molecule junctions of oxidized
oligothiophenes. Nature Chemistry. 7(3), 209–214.
mla: Dell, Emma J., et al. “Molecular Length Dictates the Nature of Charge Carriers
in Single-Molecule Junctions of Oxidized Oligothiophenes.” Nature Chemistry,
vol. 7, no. 3, Springer Nature, 2015, pp. 209–14, doi:10.1038/nchem.2160.
short: E.J. Dell, B. Capozzi, J. Xia, L. Venkataraman, L.M. Campos, Nature Chemistry
7 (2015) 209–214.
date_created: 2024-09-09T10:55:42Z
date_published: 2015-02-02T00:00:00Z
date_updated: 2025-01-02T13:35:46Z
day: '02'
doi: 10.1038/nchem.2160
extern: '1'
external_id:
pmid:
- '25698329'
intvolume: ' 7'
issue: '3'
language:
- iso: eng
month: '02'
oa_version: None
page: 209-214
pmid: 1
publication: Nature Chemistry
publication_identifier:
eissn:
- 1755-4349
issn:
- 1755-4330
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Molecular length dictates the nature of charge carriers in single-molecule
junctions of oxidized oligothiophenes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2015'
...
---
_id: '1802'
abstract:
- lang: eng
text: Noncoding variants in the human MIR137 gene locus increase schizophrenia risk
with genome-wide significance. However, the functional consequence of these risk
alleles is unknown. Here we examined induced human neurons harboring the minor
alleles of four disease-associated single nucleotide polymorphisms in MIR137.
We observed increased MIR137 levels compared to those in major allele–carrying
cells. microRNA-137 gain of function caused downregulation of the presynaptic
target genes complexin-1 (Cplx1), Nsf and synaptotagmin-1 (Syt1), leading to impaired
vesicle release. In vivo, miR-137 gain of function resulted in changes in synaptic
vesicle pool distribution, impaired induction of mossy fiber long-term potentiation
and deficits in hippocampus-dependent learning and memory. By sequestering endogenous
miR-137, we were able to ameliorate the synaptic phenotypes. Moreover, reinstatement
of Syt1 expression partially restored synaptic plasticity, demonstrating the importance
of Syt1 as a miR-137 target. Our data provide new insight into the mechanism by
which miR-137 dysregulation can impair synaptic plasticity in the hippocampus.
acknowledgement: S.S. was supported by a Human Frontier Science Program (HFSP) long-term
postdoctoral fellowship and a Swiss National Science Foundation fellowship for prospective
researchers. E.J.K. was supported by a Simons Foundation Postdoctoral Fellowship.
A.R. was supported by a NARSAD Young Investigator Award. This work was supported
by a Seed Grant from the Simons Center for the Social Brain and US National Institutes
of Health grant RO1 MH 091115 to L.-H.T.
author:
- first_name: Sandra
full_name: Sandra Siegert
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
- first_name: Jinsoo
full_name: Seo, Jinsoo
last_name: Seo
- first_name: Ester
full_name: Kwon, Ester J
last_name: Kwon
- first_name: Andrii
full_name: Rudenko, Andrii
last_name: Rudenko
- first_name: Sukhee
full_name: Cho, Sukhee
last_name: Cho
- first_name: Wenyuan
full_name: Wang, Wenyuan
last_name: Wang
- first_name: Zachary
full_name: Flood, Zachary C
last_name: Flood
- first_name: Anthony
full_name: Martorell, Anthony J
last_name: Martorell
- first_name: Maria
full_name: Ericsson, Maria
last_name: Ericsson
- first_name: Alison
full_name: Mungenast, Alison E
last_name: Mungenast
- first_name: Lihuei
full_name: Tsai, Lihuei
last_name: Tsai
citation:
ama: Siegert S, Seo J, Kwon E, et al. The schizophrenia risk gene product miR-137
alters presynaptic plasticity. Nature Neuroscience. 2015;18:1008-1016.
doi:10.1038/nn.4023
apa: Siegert, S., Seo, J., Kwon, E., Rudenko, A., Cho, S., Wang, W., … Tsai, L.
(2015). The schizophrenia risk gene product miR-137 alters presynaptic plasticity.
Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.4023
chicago: Siegert, Sandra, Jinsoo Seo, Ester Kwon, Andrii Rudenko, Sukhee Cho, Wenyuan
Wang, Zachary Flood, et al. “The Schizophrenia Risk Gene Product MiR-137 Alters
Presynaptic Plasticity.” Nature Neuroscience. Nature Publishing Group,
2015. https://doi.org/10.1038/nn.4023.
ieee: S. Siegert et al., “The schizophrenia risk gene product miR-137 alters
presynaptic plasticity,” Nature Neuroscience, vol. 18. Nature Publishing
Group, pp. 1008–1016, 2015.
ista: Siegert S, Seo J, Kwon E, Rudenko A, Cho S, Wang W, Flood Z, Martorell A,
Ericsson M, Mungenast A, Tsai L. 2015. The schizophrenia risk gene product miR-137
alters presynaptic plasticity. Nature Neuroscience. 18, 1008–1016.
mla: Siegert, Sandra, et al. “The Schizophrenia Risk Gene Product MiR-137 Alters
Presynaptic Plasticity.” Nature Neuroscience, vol. 18, Nature Publishing
Group, 2015, pp. 1008–16, doi:10.1038/nn.4023.
short: S. Siegert, J. Seo, E. Kwon, A. Rudenko, S. Cho, W. Wang, Z. Flood, A. Martorell,
M. Ericsson, A. Mungenast, L. Tsai, Nature Neuroscience 18 (2015) 1008–1016.
date_created: 2018-12-11T11:54:05Z
date_published: 2015-07-01T00:00:00Z
date_updated: 2021-01-12T06:53:18Z
day: '01'
doi: 10.1038/nn.4023
extern: 1
intvolume: ' 18'
month: '07'
page: 1008 - 1016
publication: Nature Neuroscience
publication_status: published
publisher: Nature Publishing Group
publist_id: '5308'
quality_controlled: 0
status: public
title: The schizophrenia risk gene product miR-137 alters presynaptic plasticity
type: journal_article
volume: 18
year: '2015'
...
---
_id: '1803'
abstract:
- lang: eng
text: Repeated stress has been suggested to underlie learning and memory deficits
via the basolateral amygdala (BLA) and the hippocampus; however, the functional
contribution of BLA inputs to the hippocampus and their molecular repercussions
are not well understood. Here we show that repeated stress is accompanied by generation
of the Cdk5 (cyclin-dependent kinase 5)-activator p25, up-regulation and phosphorylation
of glucocorticoid receptors, increased HDAC2 expression, and reduced expression
of memoryrelated genes in the hippocampus. A combination of optogenetic and pharmacosynthetic
approaches shows that BLA activation is both necessary and sufficient for stress-associated
molecular changes and memory impairments. Furthermore, we show that this effect
relies on direct glutamatergic projections from the BLA to the dorsal hippocampus.
Finally, we show that p25 generation is necessary for the stress-induced memory
dysfunction. Taken together, our data provide a neural circuit model for stress-induced
hippocampal memory deficits through BLA activity-dependent p25 generation.
acknowledgement: |-
AG047661; NIH; Schweizerische Nationalfonds zur Förderung der Wissenschaftlichen Forschung
NS051874; NIH; Schweizerische Nationalfonds zur Förderung der Wissenschaftlichen Forschung
SNSF; Schweizerische Nationalfonds zur Förderung der Wissenschaftlichen Forschung
author:
- first_name: Damien
full_name: Rei, Damien
last_name: Rei
- first_name: Xenos
full_name: Mason, Xenos
last_name: Mason
- first_name: Jinsoo
full_name: Seo, Jinsoo
last_name: Seo
- first_name: Johannes
full_name: Gräff, Johannes
last_name: Gräff
- first_name: Andrii
full_name: Rudenko, Andrii
last_name: Rudenko
- first_name: Jùn
full_name: Wang, Jùn
last_name: Wang
- first_name: Richard
full_name: Rueda, Richard
last_name: Rueda
- first_name: Sandra
full_name: Sandra Siegert
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
- first_name: Sukhee
full_name: Cho, Sukhee
last_name: Cho
- first_name: Rebecca
full_name: Canter, Rebecca G
last_name: Canter
- first_name: Alison
full_name: Mungenast, Alison E
last_name: Mungenast
- first_name: Karl
full_name: Deisseroth, Karl A
last_name: Deisseroth
- first_name: Lihuei
full_name: Tsai, Lihuei
last_name: Tsai
citation:
ama: Rei D, Mason X, Seo J, et al. Basolateral amygdala bidirectionally modulates
stress induced hippocampal learning and memory deficits through a p25/Cdk5-dependent
pathway. PNAS. 2015;112(23):7291-7296. doi:10.1073/pnas.1415845112
apa: Rei, D., Mason, X., Seo, J., Gräff, J., Rudenko, A., Wang, J., … Tsai, L. (2015).
Basolateral amygdala bidirectionally modulates stress induced hippocampal learning
and memory deficits through a p25/Cdk5-dependent pathway. PNAS. National
Academy of Sciences. https://doi.org/10.1073/pnas.1415845112
chicago: Rei, Damien, Xenos Mason, Jinsoo Seo, Johannes Gräff, Andrii Rudenko, Jùn
Wang, Richard Rueda, et al. “Basolateral Amygdala Bidirectionally Modulates Stress
Induced Hippocampal Learning and Memory Deficits through a P25/Cdk5-Dependent
Pathway.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1415845112.
ieee: D. Rei et al., “Basolateral amygdala bidirectionally modulates stress
induced hippocampal learning and memory deficits through a p25/Cdk5-dependent
pathway,” PNAS, vol. 112, no. 23. National Academy of Sciences, pp. 7291–7296,
2015.
ista: Rei D, Mason X, Seo J, Gräff J, Rudenko A, Wang J, Rueda R, Siegert S, Cho
S, Canter R, Mungenast A, Deisseroth K, Tsai L. 2015. Basolateral amygdala bidirectionally
modulates stress induced hippocampal learning and memory deficits through a p25/Cdk5-dependent
pathway. PNAS. 112(23), 7291–7296.
mla: Rei, Damien, et al. “Basolateral Amygdala Bidirectionally Modulates Stress
Induced Hippocampal Learning and Memory Deficits through a P25/Cdk5-Dependent
Pathway.” PNAS, vol. 112, no. 23, National Academy of Sciences, 2015, pp.
7291–96, doi:10.1073/pnas.1415845112.
short: D. Rei, X. Mason, J. Seo, J. Gräff, A. Rudenko, J. Wang, R. Rueda, S. Siegert,
S. Cho, R. Canter, A. Mungenast, K. Deisseroth, L. Tsai, PNAS 112 (2015) 7291–7296.
date_created: 2018-12-11T11:54:06Z
date_published: 2015-06-09T00:00:00Z
date_updated: 2021-01-12T06:53:18Z
day: '09'
doi: 10.1073/pnas.1415845112
extern: 1
intvolume: ' 112'
issue: '23'
month: '06'
page: 7291 - 7296
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '5307'
quality_controlled: 0
status: public
title: Basolateral amygdala bidirectionally modulates stress induced hippocampal learning
and memory deficits through a p25/Cdk5-dependent pathway
type: journal_article
volume: 112
year: '2015'
...
---
_id: '1804'
abstract:
- lang: eng
text: It is known that in classical fluids turbulence typically occurs at high Reynolds
numbers. But can turbulence occur at low Reynolds numbers? Here we investigate
the transition to turbulence in the classic Taylor-Couette system in which the
rotating fluids are manufactured ferrofluids with magnetized nanoparticles embedded
in liquid carriers. We find that, in the presence of a magnetic field transverse
to the symmetry axis of the system, turbulence can occur at Reynolds numbers that
are at least one order of magnitude smaller than those in conventional fluids.
This is established by extensive computational ferrohydrodynamics through a detailed
investigation of transitions in the flow structure, and characterization of behaviors
of physical quantities such as the energy, the wave number, and the angular momentum
through the bifurcations. A finding is that, as the magnetic field is increased,
onset of turbulence can be determined accurately and reliably. Our results imply
that experimental investigation of turbulence may be feasible by using ferrofluids.
Our study of transition to and evolution of turbulence in the Taylor-Couette ferrofluidic
flow system provides insights into the challenging problem of turbulence control.
article_number: '10781'
article_processing_charge: No
author:
- first_name: Sebastian
full_name: Altmeyer, Sebastian
id: 2EE67FDC-F248-11E8-B48F-1D18A9856A87
last_name: Altmeyer
orcid: 0000-0001-5964-0203
- first_name: Younghae
full_name: Do, Younghae
last_name: Do
- first_name: Ying
full_name: Lai, Ying
last_name: Lai
citation:
ama: Altmeyer S, Do Y, Lai Y. Transition to turbulence in Taylor-Couette ferrofluidic
flow. Scientific Reports. 2015;5. doi:10.1038/srep10781
apa: Altmeyer, S., Do, Y., & Lai, Y. (2015). Transition to turbulence in Taylor-Couette
ferrofluidic flow. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep10781
chicago: Altmeyer, Sebastian, Younghae Do, and Ying Lai. “Transition to Turbulence
in Taylor-Couette Ferrofluidic Flow.” Scientific Reports. Nature Publishing
Group, 2015. https://doi.org/10.1038/srep10781.
ieee: S. Altmeyer, Y. Do, and Y. Lai, “Transition to turbulence in Taylor-Couette
ferrofluidic flow,” Scientific Reports, vol. 5. Nature Publishing Group,
2015.
ista: Altmeyer S, Do Y, Lai Y. 2015. Transition to turbulence in Taylor-Couette
ferrofluidic flow. Scientific Reports. 5, 10781.
mla: Altmeyer, Sebastian, et al. “Transition to Turbulence in Taylor-Couette Ferrofluidic
Flow.” Scientific Reports, vol. 5, 10781, Nature Publishing Group, 2015,
doi:10.1038/srep10781.
short: S. Altmeyer, Y. Do, Y. Lai, Scientific Reports 5 (2015).
corr_author: '1'
date_created: 2018-12-11T11:54:06Z
date_published: 2015-06-12T00:00:00Z
date_updated: 2025-09-29T10:58:13Z
day: '12'
ddc:
- '530'
department:
- _id: BjHo
doi: 10.1038/srep10781
external_id:
isi:
- '000356150200001'
file:
- access_level: open_access
checksum: 7716f582f8c9d82d8f2bf80bf896b440
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:26Z
date_updated: 2020-07-14T12:45:16Z
file_id: '5280'
file_name: IST-2016-450-v1+1_srep10781.pdf
file_size: 2449723
relation: main_file
file_date_updated: 2020-07-14T12:45:16Z
has_accepted_license: '1'
intvolume: ' 5'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '5306'
pubrep_id: '450'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Transition to turbulence in Taylor-Couette ferrofluidic flow
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 5
year: '2015'
...
---
OA_place: publisher
OA_type: free access
_id: '1805'
abstract:
- lang: eng
text: 'We consider the problem of deciding whether the persistent homology group
of a simplicial pair (K,L) can be realized as the homology H∗(X) of some complex
X with L ⊂ X ⊂ K. We show that this problem is NP-complete even if K is embedded
in double-struck R3. As a consequence, we show that it is NP-hard to simplify
level and sublevel sets of scalar functions on double-struck S3 within a given
tolerance constraint. This problem has relevance to the visualization of medical
images by isosurfaces. We also show an implication to the theory of well groups
of scalar functions: not every well group can be realized by some level set, and
deciding whether a well group can be realized is NP-hard.'
article_processing_charge: No
article_type: original
author:
- first_name: Dominique
full_name: Attali, Dominique
last_name: Attali
- first_name: Ulrich
full_name: Bauer, Ulrich
id: 2ADD483A-F248-11E8-B48F-1D18A9856A87
last_name: Bauer
orcid: 0000-0002-9683-0724
- first_name: Olivier
full_name: Devillers, Olivier
last_name: Devillers
- first_name: Marc
full_name: Glisse, Marc
last_name: Glisse
- first_name: André
full_name: Lieutier, André
last_name: Lieutier
citation:
ama: 'Attali D, Bauer U, Devillers O, Glisse M, Lieutier A. Homological reconstruction
and simplification in R3. Computational Geometry: Theory and Applications.
2015;48(8):606-621. doi:10.1016/j.comgeo.2014.08.010'
apa: 'Attali, D., Bauer, U., Devillers, O., Glisse, M., & Lieutier, A. (2015).
Homological reconstruction and simplification in R3. Computational Geometry:
Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2014.08.010'
chicago: 'Attali, Dominique, Ulrich Bauer, Olivier Devillers, Marc Glisse, and André
Lieutier. “Homological Reconstruction and Simplification in R3.” Computational
Geometry: Theory and Applications. Elsevier, 2015. https://doi.org/10.1016/j.comgeo.2014.08.010.'
ieee: 'D. Attali, U. Bauer, O. Devillers, M. Glisse, and A. Lieutier, “Homological
reconstruction and simplification in R3,” Computational Geometry: Theory and
Applications, vol. 48, no. 8. Elsevier, pp. 606–621, 2015.'
ista: 'Attali D, Bauer U, Devillers O, Glisse M, Lieutier A. 2015. Homological reconstruction
and simplification in R3. Computational Geometry: Theory and Applications. 48(8),
606–621.'
mla: 'Attali, Dominique, et al. “Homological Reconstruction and Simplification in
R3.” Computational Geometry: Theory and Applications, vol. 48, no. 8, Elsevier,
2015, pp. 606–21, doi:10.1016/j.comgeo.2014.08.010.'
short: 'D. Attali, U. Bauer, O. Devillers, M. Glisse, A. Lieutier, Computational
Geometry: Theory and Applications 48 (2015) 606–621.'
corr_author: '1'
date_created: 2018-12-11T11:54:06Z
date_published: 2015-06-03T00:00:00Z
date_updated: 2025-09-23T09:18:30Z
day: '03'
department:
- _id: HeEd
doi: 10.1016/j.comgeo.2014.08.010
ec_funded: 1
external_id:
isi:
- '000357353200006'
intvolume: ' 48'
isi: 1
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.comgeo.2014.08.010
month: '06'
oa: 1
oa_version: Published Version
page: 606 - 621
project:
- _id: 255D761E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '318493'
name: Topological Complex Systems
publication: 'Computational Geometry: Theory and Applications'
publication_status: published
publisher: Elsevier
publist_id: '5305'
quality_controlled: '1'
related_material:
record:
- id: '2812'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Homological reconstruction and simplification in R3
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 48
year: '2015'
...
---
_id: '1807'
abstract:
- lang: eng
text: We study a double Cahn-Hilliard type functional related to the Gross-Pitaevskii
energy of two-components Bose-Einstein condensates. In the case of large but same
order intercomponent and intracomponent coupling strengths, we prove Γ-convergence
to a perimeter minimisation functional with an inhomogeneous surface tension.
We study the asymptotic behavior of the surface tension as the ratio between the
intercomponent and intracomponent coupling strengths becomes very small or very
large and obtain good agreement with the physical literature. We obtain as a consequence,
symmetry breaking of the minimisers for the harmonic potential.
article_processing_charge: No
arxiv: 1
author:
- first_name: Michael
full_name: Goldman, Michael
last_name: Goldman
- first_name: Jimena
full_name: Royo-Letelier, Jimena
id: 4D3BED28-F248-11E8-B48F-1D18A9856A87
last_name: Royo-Letelier
citation:
ama: Goldman M, Royo-Letelier J. Sharp interface limit for two components Bose-Einstein
condensates. ESAIM - Control, Optimisation and Calculus of Variations.
2015;21(3):603-624. doi:10.1051/cocv/2014040
apa: Goldman, M., & Royo-Letelier, J. (2015). Sharp interface limit for two
components Bose-Einstein condensates. ESAIM - Control, Optimisation and Calculus
of Variations. EDP Sciences. https://doi.org/10.1051/cocv/2014040
chicago: Goldman, Michael, and Jimena Royo-Letelier. “Sharp Interface Limit for
Two Components Bose-Einstein Condensates.” ESAIM - Control, Optimisation and
Calculus of Variations. EDP Sciences, 2015. https://doi.org/10.1051/cocv/2014040.
ieee: M. Goldman and J. Royo-Letelier, “Sharp interface limit for two components
Bose-Einstein condensates,” ESAIM - Control, Optimisation and Calculus of Variations,
vol. 21, no. 3. EDP Sciences, pp. 603–624, 2015.
ista: Goldman M, Royo-Letelier J. 2015. Sharp interface limit for two components
Bose-Einstein condensates. ESAIM - Control, Optimisation and Calculus of Variations.
21(3), 603–624.
mla: Goldman, Michael, and Jimena Royo-Letelier. “Sharp Interface Limit for Two
Components Bose-Einstein Condensates.” ESAIM - Control, Optimisation and Calculus
of Variations, vol. 21, no. 3, EDP Sciences, 2015, pp. 603–24, doi:10.1051/cocv/2014040.
short: M. Goldman, J. Royo-Letelier, ESAIM - Control, Optimisation and Calculus
of Variations 21 (2015) 603–624.
corr_author: '1'
date_created: 2018-12-11T11:54:07Z
date_published: 2015-05-01T00:00:00Z
date_updated: 2025-09-23T10:45:09Z
day: '01'
department:
- _id: RoSe
doi: 10.1051/cocv/2014040
external_id:
arxiv:
- '1401.1727'
isi:
- '000356012000001'
intvolume: ' 21'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1401.1727
month: '05'
oa: 1
oa_version: Preprint
page: 603 - 624
publication: ESAIM - Control, Optimisation and Calculus of Variations
publication_status: published
publisher: EDP Sciences
publist_id: '5303'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sharp interface limit for two components Bose-Einstein condensates
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 21
year: '2015'
...
---
_id: '1808'
article_number: '7'
article_processing_charge: No
author:
- first_name: Ashutosh
full_name: Gupta, Ashutosh
id: 335E5684-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: Gupta A, Henzinger TA. Guest editors’ introduction to special issue on computational
methods in systems biology. ACM Transactions on Modeling and Computer Simulation.
2015;25(2). doi:10.1145/2745799
apa: Gupta, A., & Henzinger, T. A. (2015). Guest editors’ introduction to special
issue on computational methods in systems biology. ACM Transactions on Modeling
and Computer Simulation. ACM. https://doi.org/10.1145/2745799
chicago: Gupta, Ashutosh, and Thomas A Henzinger. “Guest Editors’ Introduction to
Special Issue on Computational Methods in Systems Biology.” ACM Transactions
on Modeling and Computer Simulation. ACM, 2015. https://doi.org/10.1145/2745799.
ieee: A. Gupta and T. A. Henzinger, “Guest editors’ introduction to special issue
on computational methods in systems biology,” ACM Transactions on Modeling
and Computer Simulation, vol. 25, no. 2. ACM, 2015.
ista: Gupta A, Henzinger TA. 2015. Guest editors’ introduction to special issue
on computational methods in systems biology. ACM Transactions on Modeling and
Computer Simulation. 25(2), 7.
mla: Gupta, Ashutosh, and Thomas A. Henzinger. “Guest Editors’ Introduction to Special
Issue on Computational Methods in Systems Biology.” ACM Transactions on Modeling
and Computer Simulation, vol. 25, no. 2, 7, ACM, 2015, doi:10.1145/2745799.
short: A. Gupta, T.A. Henzinger, ACM Transactions on Modeling and Computer Simulation
25 (2015).
date_created: 2018-12-11T11:54:07Z
date_published: 2015-05-01T00:00:00Z
date_updated: 2025-09-23T09:11:51Z
day: '01'
department:
- _id: ToHe
doi: 10.1145/2745799
external_id:
isi:
- '000354789200001'
intvolume: ' 25'
isi: 1
issue: '2'
language:
- iso: eng
month: '05'
oa_version: None
publication: ACM Transactions on Modeling and Computer Simulation
publication_status: published
publisher: ACM
publist_id: '5302'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Guest editors' introduction to special issue on computational methods in systems
biology
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 25
year: '2015'
...
---
_id: '1809'
abstract:
- lang: eng
text: 'Background: Indirect genetic effects (IGEs) occur when genes expressed in
one individual alter the expression of traits in social partners. Previous studies
focused on the evolutionary consequences and evolutionary dynamics of IGEs, using
equilibrium solutions to predict phenotypes in subsequent generations. However,
whether or not such steady states may be reached may depend on the dynamics of
interactions themselves. Results: In our study, we focus on the dynamics of social
interactions and indirect genetic effects and investigate how they modify phenotypes
over time. Unlike previous IGE studies, we do not analyse evolutionary dynamics;
rather we consider within-individual phenotypic changes, also referred to as phenotypic
plasticity. We analyse iterative interactions, when individuals interact in a
series of discontinuous events, and investigate the stability of steady state
solutions and the dependence on model parameters, such as population size, strength,
and the nature of interactions. We show that for interactions where a feedback
loop occurs, the possible parameter space of interaction strength is fairly limited,
affecting the evolutionary consequences of IGEs. We discuss the implications of
our results for current IGE model predictions and their limitations.'
article_processing_charge: No
author:
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
orcid: 0000-0002-2519-824X
- first_name: Reinmar
full_name: Hager, Reinmar
last_name: Hager
citation:
ama: Trubenova B, Novak S, Hager R. Indirect genetic effects and the dynamics of
social interactions. PLoS One. 2015;10(5). doi:10.1371/journal.pone.0126907
apa: Trubenova, B., Novak, S., & Hager, R. (2015). Indirect genetic effects
and the dynamics of social interactions. PLoS One. Public Library of Science.
https://doi.org/10.1371/journal.pone.0126907
chicago: Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Indirect Genetic
Effects and the Dynamics of Social Interactions.” PLoS One. Public Library
of Science, 2015. https://doi.org/10.1371/journal.pone.0126907.
ieee: B. Trubenova, S. Novak, and R. Hager, “Indirect genetic effects and the dynamics
of social interactions,” PLoS One, vol. 10, no. 5. Public Library of Science,
2015.
ista: Trubenova B, Novak S, Hager R. 2015. Indirect genetic effects and the dynamics
of social interactions. PLoS One. 10(5).
mla: Trubenova, Barbora, et al. “Indirect Genetic Effects and the Dynamics of Social
Interactions.” PLoS One, vol. 10, no. 5, Public Library of Science, 2015,
doi:10.1371/journal.pone.0126907.
short: B. Trubenova, S. Novak, R. Hager, PLoS One 10 (2015).
corr_author: '1'
date_created: 2018-12-11T11:54:07Z
date_published: 2015-05-18T00:00:00Z
date_updated: 2025-09-23T09:21:54Z
day: '18'
ddc:
- '570'
- '576'
department:
- _id: NiBa
doi: 10.1371/journal.pone.0126907
external_id:
isi:
- '000354917300064'
file:
- access_level: open_access
checksum: d3a4a58ef4bd3b3e2f32b7fd7af4a743
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:07Z
date_updated: 2020-07-14T12:45:17Z
file_id: '4730'
file_name: IST-2016-453-v1+1_journal.pone.0126907.pdf
file_size: 2748982
relation: main_file
file_date_updated: 2020-07-14T12:45:17Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '5299'
pubrep_id: '453'
quality_controlled: '1'
related_material:
record:
- id: '9715'
relation: research_data
status: public
- id: '9772'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Indirect genetic effects and the dynamics of social interactions
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 10
year: '2015'
...
---
_id: '1810'
abstract:
- lang: eng
text: Combining antibiotics is a promising strategy for increasing treatment efficacy
and for controlling resistance evolution. When drugs are combined, their effects
on cells may be amplified or weakened, that is the drugs may show synergistic
or antagonistic interactions. Recent work revealed the underlying mechanisms of
such drug interactions by elucidating the drugs'; joint effects on cell physiology.
Moreover, new treatment strategies that use drug combinations to exploit evolutionary
tradeoffs were shown to affect the rate of resistance evolution in predictable
ways. High throughput studies have further identified drug candidates based on
their interactions with established antibiotics and general principles that enable
the prediction of drug interactions were suggested. Overall, the conceptual and
technical foundation for the rational design of potent drug combinations is rapidly
developing.
article_processing_charge: No
author:
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: 'Bollenbach MT. Antimicrobial interactions: Mechanisms and implications for
drug discovery and resistance evolution. Current Opinion in Microbiology.
2015;27:1-9. doi:10.1016/j.mib.2015.05.008'
apa: 'Bollenbach, M. T. (2015). Antimicrobial interactions: Mechanisms and implications
for drug discovery and resistance evolution. Current Opinion in Microbiology.
Elsevier. https://doi.org/10.1016/j.mib.2015.05.008'
chicago: 'Bollenbach, Mark Tobias. “Antimicrobial Interactions: Mechanisms and Implications
for Drug Discovery and Resistance Evolution.” Current Opinion in Microbiology.
Elsevier, 2015. https://doi.org/10.1016/j.mib.2015.05.008.'
ieee: 'M. T. Bollenbach, “Antimicrobial interactions: Mechanisms and implications
for drug discovery and resistance evolution,” Current Opinion in Microbiology,
vol. 27. Elsevier, pp. 1–9, 2015.'
ista: 'Bollenbach MT. 2015. Antimicrobial interactions: Mechanisms and implications
for drug discovery and resistance evolution. Current Opinion in Microbiology.
27, 1–9.'
mla: 'Bollenbach, Mark Tobias. “Antimicrobial Interactions: Mechanisms and Implications
for Drug Discovery and Resistance Evolution.” Current Opinion in Microbiology,
vol. 27, Elsevier, 2015, pp. 1–9, doi:10.1016/j.mib.2015.05.008.'
short: M.T. Bollenbach, Current Opinion in Microbiology 27 (2015) 1–9.
corr_author: '1'
date_created: 2018-12-11T11:54:08Z
date_published: 2015-06-01T00:00:00Z
date_updated: 2025-09-23T07:55:38Z
day: '01'
ddc:
- '570'
department:
- _id: ToBo
doi: 10.1016/j.mib.2015.05.008
ec_funded: 1
external_id:
isi:
- '000365065400003'
file:
- access_level: open_access
checksum: 1683bb0f42ef892a5b3b71a050d65d25
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:23Z
date_updated: 2020-07-14T12:45:17Z
file_id: '5277'
file_name: IST-2016-493-v1+1_1-s2.0-S1369527415000594-main.pdf
file_size: 1047255
relation: main_file
file_date_updated: 2020-07-14T12:45:17Z
has_accepted_license: '1'
intvolume: ' 27'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 1 - 9
project:
- _id: 25E9AF9E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27201-B22
name: Revealing the mechanisms underlying drug interactions
- _id: 25E83C2C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '303507'
name: Optimality principles in responses to antibiotics
- _id: 25EB3A80-B435-11E9-9278-68D0E5697425
grant_number: RGP0042/2013
name: Revealing the fundamental limits of cell growth
publication: Current Opinion in Microbiology
publication_status: published
publisher: Elsevier
publist_id: '5298'
pubrep_id: '493'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Antimicrobial interactions: Mechanisms and implications for drug discovery
and resistance evolution'
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 27
year: '2015'
...
---
_id: '1811'
abstract:
- lang: eng
text: Atomic form factors are widely used for the characterization of targets and
specimens, from crystallography to biology. By using recent mathematical results,
here we derive an analytical expression for the atomic form factor within the
independent particle model constructed from nonrelativistic screened hydrogenic
wave functions. The range of validity of this analytical expression is checked
by comparing the analytically obtained form factors with the ones obtained within
the Hartee-Fock method. As an example, we apply our analytical expression for
the atomic form factor to evaluate the differential cross section for Rayleigh
scattering off neutral atoms.
acknowledgement: The research leading to these results has received funding from the
People Programme (Marie Curie Actions) of the European Union’s Seventh Framework
Programme (FP7/2007-2013) under REA grant agreement n◦ [291734]. F.F. acknowledges
support by Fundação de Amparo à Pesquisa do estado de Minas Gerais (FAPEMIG), by
Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), and by the
Austrian Science Fund (FWF) through the START Grant No. Y 591-N16.
article_number: '052105'
article_processing_charge: No
arxiv: 1
author:
- first_name: Laleh
full_name: Safari, Laleh
id: 3C325E5E-F248-11E8-B48F-1D18A9856A87
last_name: Safari
- first_name: José
full_name: Santos, José
last_name: Santos
- first_name: Pedro
full_name: Amaro, Pedro
last_name: Amaro
- first_name: Kari
full_name: Jänkälä, Kari
last_name: Jänkälä
- first_name: Filippo
full_name: Fratini, Filippo
last_name: Fratini
citation:
ama: 'Safari L, Santos J, Amaro P, Jänkälä K, Fratini F. Analytical evaluation of
atomic form factors: Application to Rayleigh scattering. Journal of Mathematical
Physics. 2015;56(5). doi:10.1063/1.4921227'
apa: 'Safari, L., Santos, J., Amaro, P., Jänkälä, K., & Fratini, F. (2015).
Analytical evaluation of atomic form factors: Application to Rayleigh scattering.
Journal of Mathematical Physics. American Institute of Physics. https://doi.org/10.1063/1.4921227'
chicago: 'Safari, Laleh, José Santos, Pedro Amaro, Kari Jänkälä, and Filippo Fratini.
“Analytical Evaluation of Atomic Form Factors: Application to Rayleigh Scattering.”
Journal of Mathematical Physics. American Institute of Physics, 2015. https://doi.org/10.1063/1.4921227.'
ieee: 'L. Safari, J. Santos, P. Amaro, K. Jänkälä, and F. Fratini, “Analytical evaluation
of atomic form factors: Application to Rayleigh scattering,” Journal of Mathematical
Physics, vol. 56, no. 5. American Institute of Physics, 2015.'
ista: 'Safari L, Santos J, Amaro P, Jänkälä K, Fratini F. 2015. Analytical evaluation
of atomic form factors: Application to Rayleigh scattering. Journal of Mathematical
Physics. 56(5), 052105.'
mla: 'Safari, Laleh, et al. “Analytical Evaluation of Atomic Form Factors: Application
to Rayleigh Scattering.” Journal of Mathematical Physics, vol. 56, no.
5, 052105, American Institute of Physics, 2015, doi:10.1063/1.4921227.'
short: L. Safari, J. Santos, P. Amaro, K. Jänkälä, F. Fratini, Journal of Mathematical
Physics 56 (2015).
corr_author: '1'
date_created: 2018-12-11T11:54:08Z
date_published: 2015-05-20T00:00:00Z
date_updated: 2025-09-23T07:53:00Z
day: '20'
department:
- _id: MiLe
doi: 10.1063/1.4921227
ec_funded: 1
external_id:
arxiv:
- '1409.0110'
isi:
- '000355920800016'
intvolume: ' 56'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1409.0110
month: '05'
oa: 1
oa_version: Preprint
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Journal of Mathematical Physics
publication_status: published
publisher: American Institute of Physics
publist_id: '5295'
scopus_import: '1'
status: public
title: 'Analytical evaluation of atomic form factors: Application to Rayleigh scattering'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 56
year: '2015'
...
---
_id: '1812'
abstract:
- lang: eng
text: "We investigate the occurrence of rotons in a quadrupolar Bose–Einstein condensate
confined to two dimensions. Depending on the particle density, the ratio of the
contact and quadrupole–quadrupole interactions, and the alignment of the quadrupole
moments with respect to the confinement plane, the dispersion relation features
two or four point-like roton minima or one ring-shaped minimum. We map out the
entire parameter space of the roton behavior and identify the instability regions.
We propose to observe the exotic rotons by monitoring the characteristic density
wave dynamics resulting from a short local perturbation, and discuss the possibilities
to detect the predicted effects in state-of-the-art experiments with ultracold
homonuclear molecules.\r\n"
article_number: '045005'
article_processing_charge: No
author:
- first_name: Martin
full_name: Lahrz, Martin
last_name: Lahrz
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Ludwig
full_name: Mathey, Ludwig
last_name: Mathey
citation:
ama: Lahrz M, Lemeshko M, Mathey L. Exotic roton excitations in quadrupolar Bose–Einstein
condensates . New Journal of Physics. 2015;17(4). doi:10.1088/1367-2630/17/4/045005
apa: Lahrz, M., Lemeshko, M., & Mathey, L. (2015). Exotic roton excitations
in quadrupolar Bose–Einstein condensates . New Journal of Physics. IOP
Publishing. https://doi.org/10.1088/1367-2630/17/4/045005
chicago: Lahrz, Martin, Mikhail Lemeshko, and Ludwig Mathey. “Exotic Roton Excitations
in Quadrupolar Bose–Einstein Condensates .” New Journal of Physics. IOP
Publishing, 2015. https://doi.org/10.1088/1367-2630/17/4/045005.
ieee: M. Lahrz, M. Lemeshko, and L. Mathey, “Exotic roton excitations in quadrupolar
Bose–Einstein condensates ,” New Journal of Physics, vol. 17, no. 4. IOP
Publishing, 2015.
ista: Lahrz M, Lemeshko M, Mathey L. 2015. Exotic roton excitations in quadrupolar
Bose–Einstein condensates . New Journal of Physics. 17(4), 045005.
mla: Lahrz, Martin, et al. “Exotic Roton Excitations in Quadrupolar Bose–Einstein
Condensates .” New Journal of Physics, vol. 17, no. 4, 045005, IOP Publishing,
2015, doi:10.1088/1367-2630/17/4/045005.
short: M. Lahrz, M. Lemeshko, L. Mathey, New Journal of Physics 17 (2015).
date_created: 2018-12-11T11:54:09Z
date_published: 2015-04-01T00:00:00Z
date_updated: 2025-09-23T08:45:19Z
day: '01'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1088/1367-2630/17/4/045005
external_id:
isi:
- '000354022400001'
file:
- access_level: open_access
checksum: 551f751a75b39b89a1db2f7f498f9a49
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:59Z
date_updated: 2020-07-14T12:45:17Z
file_id: '5184'
file_name: IST-2016-446-v1+1_document.pdf
file_size: 1900925
relation: main_file
file_date_updated: 2020-07-14T12:45:17Z
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: New Journal of Physics
publication_status: published
publisher: IOP Publishing
publist_id: '5294'
pubrep_id: '446'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Exotic roton excitations in quadrupolar Bose–Einstein condensates '
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 17
year: '2015'
...
---
_id: '1813'
abstract:
- lang: eng
text: We develop a microscopic theory describing a quantum impurity whose rotational
degree of freedom is coupled to a many-particle bath. We approach the problem
by introducing the concept of an “angulon”—a quantum rotor dressed by a quantum
field—and reveal its quasiparticle properties using a combination of variational
and diagrammatic techniques. Our theory predicts renormalization of the impurity
rotational structure, such as that observed in experiments with molecules in superfluid
helium droplets, in terms of a rotational Lamb shift induced by the many-particle
environment. Furthermore, we discover a rich many-body-induced fine structure,
emerging in rotational spectra due to a redistribution of angular momentum within
the quantum many-body system.
article_number: '203001'
article_processing_charge: No
arxiv: 1
author:
- first_name: Richard
full_name: Schmidt, Richard
last_name: Schmidt
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Schmidt R, Lemeshko M. Rotation of quantum impurities in the presence of a
many-body environment. Physical Review Letters. 2015;114(20). doi:10.1103/PhysRevLett.114.203001
apa: Schmidt, R., & Lemeshko, M. (2015). Rotation of quantum impurities in the
presence of a many-body environment. Physical Review Letters. American
Physical Society. https://doi.org/10.1103/PhysRevLett.114.203001
chicago: Schmidt, Richard, and Mikhail Lemeshko. “Rotation of Quantum Impurities
in the Presence of a Many-Body Environment.” Physical Review Letters. American
Physical Society, 2015. https://doi.org/10.1103/PhysRevLett.114.203001.
ieee: R. Schmidt and M. Lemeshko, “Rotation of quantum impurities in the presence
of a many-body environment,” Physical Review Letters, vol. 114, no. 20.
American Physical Society, 2015.
ista: Schmidt R, Lemeshko M. 2015. Rotation of quantum impurities in the presence
of a many-body environment. Physical Review Letters. 114(20), 203001.
mla: Schmidt, Richard, and Mikhail Lemeshko. “Rotation of Quantum Impurities in
the Presence of a Many-Body Environment.” Physical Review Letters, vol.
114, no. 20, 203001, American Physical Society, 2015, doi:10.1103/PhysRevLett.114.203001.
short: R. Schmidt, M. Lemeshko, Physical Review Letters 114 (2015).
corr_author: '1'
date_created: 2018-12-11T11:54:09Z
date_published: 2015-05-18T00:00:00Z
date_updated: 2025-09-23T10:40:28Z
day: '18'
department:
- _id: MiLe
doi: 10.1103/PhysRevLett.114.203001
external_id:
arxiv:
- '1502.03447'
isi:
- '000354969900003'
intvolume: ' 114'
isi: 1
issue: '20'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1502.03447
month: '05'
oa: 1
oa_version: Preprint
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '5293'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Rotation of quantum impurities in the presence of a many-body environment
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 114
year: '2015'
...
---
_id: '1814'
abstract:
- lang: eng
text: 'We present an efficient wavefront tracking algorithm for animating bodies
of water that interact with their environment. Our contributions include: a novel
wavefront tracking technique that enables dispersion, refraction, reflection,
and diffraction in the same simulation; a unique multivalued function interpolation
method that enables our simulations to elegantly sidestep the Nyquist limit; a
dispersion approximation for efficiently amplifying the number of simulated waves
by several orders of magnitude; and additional extensions that allow for time-dependent
effects and interactive artistic editing of the resulting animation. Our contributions
combine to give us multitudes more wave details than similar algorithms, while
maintaining high frame rates and allowing close camera zooms.'
article_number: '27'
article_processing_charge: No
author:
- first_name: Stefan
full_name: Jeschke, Stefan
id: 44D6411A-F248-11E8-B48F-1D18A9856A87
last_name: Jeschke
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: Jeschke S, Wojtan C. Water wave animation via wavefront parameter interpolation.
ACM Transactions on Graphics. 2015;34(3). doi:10.1145/2714572
apa: Jeschke, S., & Wojtan, C. (2015). Water wave animation via wavefront parameter
interpolation. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2714572
chicago: Jeschke, Stefan, and Chris Wojtan. “Water Wave Animation via Wavefront
Parameter Interpolation.” ACM Transactions on Graphics. ACM, 2015. https://doi.org/10.1145/2714572.
ieee: S. Jeschke and C. Wojtan, “Water wave animation via wavefront parameter interpolation,”
ACM Transactions on Graphics, vol. 34, no. 3. ACM, 2015.
ista: Jeschke S, Wojtan C. 2015. Water wave animation via wavefront parameter interpolation.
ACM Transactions on Graphics. 34(3), 27.
mla: Jeschke, Stefan, and Chris Wojtan. “Water Wave Animation via Wavefront Parameter
Interpolation.” ACM Transactions on Graphics, vol. 34, no. 3, 27, ACM,
2015, doi:10.1145/2714572.
short: S. Jeschke, C. Wojtan, ACM Transactions on Graphics 34 (2015).
corr_author: '1'
date_created: 2018-12-11T11:54:09Z
date_published: 2015-04-01T00:00:00Z
date_updated: 2025-09-29T11:05:55Z
day: '01'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/2714572
ec_funded: 1
external_id:
isi:
- '000354800700004'
file:
- access_level: open_access
checksum: 67c9f4fa370def68cdf31299e48bc91f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:15Z
date_updated: 2020-07-14T12:45:17Z
file_id: '4933'
file_name: IST-2016-575-v1+1_wavefront_preprint.pdf
file_size: 23712153
relation: main_file
file_date_updated: 2020-07-14T12:45:17Z
has_accepted_license: '1'
intvolume: ' 34'
isi: 1
issue: '3'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Submitted Version
project:
- _id: 25357BD2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 24352-N23
name: 'Deep Pictures: Creating Visual and Haptic Vector Images'
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: 'Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large
Scales'
publication: ACM Transactions on Graphics
publication_status: published
publisher: ACM
publist_id: '5292'
pubrep_id: '575'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Water wave animation via wavefront parameter interpolation
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 34
year: '2015'
...
---
_id: '1817'
abstract:
- lang: eng
text: 'Vertebrates have a unique 3D body shape in which correct tissue and organ
shape and alignment are essential for function. For example, vision requires the
lens to be centred in the eye cup which must in turn be correctly positioned in
the head. Tissue morphogenesis depends on force generation, force transmission
through the tissue, and response of tissues and extracellular matrix to force.
Although a century ago D''Arcy Thompson postulated that terrestrial animal body
shapes are conditioned by gravity, there has been no animal model directly demonstrating
how the aforementioned mechano-morphogenetic processes are coordinated to generate
a body shape that withstands gravity. Here we report a unique medaka fish (Oryzias
latipes) mutant, hirame (hir), which is sensitive to deformation by gravity. hir
embryos display a markedly flattened body caused by mutation of YAP, a nuclear
executor of Hippo signalling that regulates organ size. We show that actomyosin-mediated
tissue tension is reduced in hir embryos, leading to tissue flattening and tissue
misalignment, both of which contribute to body flattening. By analysing YAP function
in 3D spheroids of human cells, we identify the Rho GTPase activating protein
ARHGAP18 as an effector of YAP in controlling tissue tension. Together, these
findings reveal a previously unrecognised function of YAP in regulating tissue
shape and alignment required for proper 3D body shape. Understanding this morphogenetic
function of YAP could facilitate the use of embryonic stem cells to generate complex
organs requiring correct alignment of multiple tissues. '
article_processing_charge: No
author:
- first_name: Sean
full_name: Porazinski, Sean
last_name: Porazinski
- first_name: Huijia
full_name: Wang, Huijia
last_name: Wang
- first_name: Yoichi
full_name: Asaoka, Yoichi
last_name: Asaoka
- first_name: Martin
full_name: Behrndt, Martin
id: 3ECECA3A-F248-11E8-B48F-1D18A9856A87
last_name: Behrndt
- first_name: Tatsuo
full_name: Miyamoto, Tatsuo
last_name: Miyamoto
- first_name: Hitoshi
full_name: Morita, Hitoshi
id: 4C6E54C6-F248-11E8-B48F-1D18A9856A87
last_name: Morita
- first_name: Shoji
full_name: Hata, Shoji
last_name: Hata
- first_name: Takashi
full_name: Sasaki, Takashi
last_name: Sasaki
- first_name: Gabriel
full_name: Krens, Gabriel
id: 2B819732-F248-11E8-B48F-1D18A9856A87
last_name: Krens
orcid: 0000-0003-4761-5996
- first_name: Yumi
full_name: Osada, Yumi
last_name: Osada
- first_name: Satoshi
full_name: Asaka, Satoshi
last_name: Asaka
- first_name: Akihiro
full_name: Momoi, Akihiro
last_name: Momoi
- first_name: Sarah
full_name: Linton, Sarah
last_name: Linton
- first_name: Joel
full_name: Miesfeld, Joel
last_name: Miesfeld
- first_name: Brian
full_name: Link, Brian
last_name: Link
- first_name: Takeshi
full_name: Senga, Takeshi
last_name: Senga
- first_name: Atahualpa
full_name: Castillo Morales, Atahualpa
last_name: Castillo Morales
- first_name: Araxi
full_name: Urrutia, Araxi
last_name: Urrutia
- first_name: Nobuyoshi
full_name: Shimizu, Nobuyoshi
last_name: Shimizu
- first_name: Hideaki
full_name: Nagase, Hideaki
last_name: Nagase
- first_name: Shinya
full_name: Matsuura, Shinya
last_name: Matsuura
- first_name: Stefan
full_name: Bagby, Stefan
last_name: Bagby
- first_name: Hisato
full_name: Kondoh, Hisato
last_name: Kondoh
- first_name: Hiroshi
full_name: Nishina, Hiroshi
last_name: Nishina
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: Makoto
full_name: Furutani Seiki, Makoto
last_name: Furutani Seiki
citation:
ama: Porazinski S, Wang H, Asaoka Y, et al. YAP is essential for tissue tension
to ensure vertebrate 3D body shape. Nature. 2015;521(7551):217-221. doi:10.1038/nature14215
apa: Porazinski, S., Wang, H., Asaoka, Y., Behrndt, M., Miyamoto, T., Morita, H.,
… Furutani Seiki, M. (2015). YAP is essential for tissue tension to ensure vertebrate
3D body shape. Nature. Nature Publishing Group. https://doi.org/10.1038/nature14215
chicago: Porazinski, Sean, Huijia Wang, Yoichi Asaoka, Martin Behrndt, Tatsuo Miyamoto,
Hitoshi Morita, Shoji Hata, et al. “YAP Is Essential for Tissue Tension to Ensure
Vertebrate 3D Body Shape.” Nature. Nature Publishing Group, 2015. https://doi.org/10.1038/nature14215.
ieee: S. Porazinski et al., “YAP is essential for tissue tension to ensure
vertebrate 3D body shape,” Nature, vol. 521, no. 7551. Nature Publishing
Group, pp. 217–221, 2015.
ista: Porazinski S, Wang H, Asaoka Y, Behrndt M, Miyamoto T, Morita H, Hata S, Sasaki
T, Krens G, Osada Y, Asaka S, Momoi A, Linton S, Miesfeld J, Link B, Senga T,
Castillo Morales A, Urrutia A, Shimizu N, Nagase H, Matsuura S, Bagby S, Kondoh
H, Nishina H, Heisenberg C-PJ, Furutani Seiki M. 2015. YAP is essential for tissue
tension to ensure vertebrate 3D body shape. Nature. 521(7551), 217–221.
mla: Porazinski, Sean, et al. “YAP Is Essential for Tissue Tension to Ensure Vertebrate
3D Body Shape.” Nature, vol. 521, no. 7551, Nature Publishing Group, 2015,
pp. 217–21, doi:10.1038/nature14215.
short: S. Porazinski, H. Wang, Y. Asaoka, M. Behrndt, T. Miyamoto, H. Morita, S.
Hata, T. Sasaki, G. Krens, Y. Osada, S. Asaka, A. Momoi, S. Linton, J. Miesfeld,
B. Link, T. Senga, A. Castillo Morales, A. Urrutia, N. Shimizu, H. Nagase, S.
Matsuura, S. Bagby, H. Kondoh, H. Nishina, C.-P.J. Heisenberg, M. Furutani Seiki,
Nature 521 (2015) 217–221.
corr_author: '1'
date_created: 2018-12-11T11:54:10Z
date_published: 2015-03-16T00:00:00Z
date_updated: 2025-09-29T11:07:11Z
day: '16'
department:
- _id: CaHe
doi: 10.1038/nature14215
external_id:
isi:
- '000354377800058'
pmid:
- '25778702'
intvolume: ' 521'
isi: 1
issue: '7551'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4720436/
month: '03'
oa: 1
oa_version: Submitted Version
page: 217 - 221
pmid: 1
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '5289'
quality_controlled: '1'
scopus_import: '1'
status: public
title: YAP is essential for tissue tension to ensure vertebrate 3D body shape
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 521
year: '2015'
...
---
_id: '1818'
abstract:
- lang: eng
text: 'Why do species not adapt to ever-wider ranges of conditions, gradually expanding
their ecological niche and geographic range? Gene flow across environments has
two conflicting effects: although it increases genetic variation, which is a prerequisite
for adaptation, gene flow may swamp adaptation to local conditions. In 1956, Haldane
proposed that, when the environment varies across space, "swamping"
by gene flow creates a positive feedback between low population size and maladaptation,
leading to a sharp range margin. However, current deterministic theory shows that,
when variance can evolve, there is no such limit. Using simple analytical tools
and simulations, we show that genetic drift can generate a sharp margin to a species''
range, by reducing genetic variance below the level needed for adaptation to spatially
variable conditions. Aided by separation of ecological and evolutionary timescales,
the identified effective dimensionless parameters reveal a simple threshold that
predicts when adaptation at the range margin fails. Two observable parameters
determine the threshold: (i) the effective environmental gradient, which can be
measured by the loss of fitness due to dispersal to a different environment; and
(ii) the efficacy of selection relative to genetic drift. The theory predicts
sharp range margins even in the absence of abrupt changes in the environment.
Furthermore, it implies that gradual worsening of conditions across a species''
habitat may lead to a sudden range fragmentation, when adaptation to a wide span
of conditions within a single species becomes impossible.'
article_processing_charge: No
author:
- first_name: Jitka
full_name: Polechova, Jitka
id: 3BBFB084-F248-11E8-B48F-1D18A9856A87
last_name: Polechova
orcid: 0000-0003-0951-3112
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Polechova J, Barton NH. Limits to adaptation along environmental gradients.
PNAS. 2015;112(20):6401-6406. doi:10.1073/pnas.1421515112
apa: Polechova, J., & Barton, N. H. (2015). Limits to adaptation along environmental
gradients. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1421515112
chicago: Polechova, Jitka, and Nicholas H Barton. “Limits to Adaptation along Environmental
Gradients.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1421515112.
ieee: J. Polechova and N. H. Barton, “Limits to adaptation along environmental gradients,”
PNAS, vol. 112, no. 20. National Academy of Sciences, pp. 6401–6406, 2015.
ista: Polechova J, Barton NH. 2015. Limits to adaptation along environmental gradients.
PNAS. 112(20), 6401–6406.
mla: Polechova, Jitka, and Nicholas H. Barton. “Limits to Adaptation along Environmental
Gradients.” PNAS, vol. 112, no. 20, National Academy of Sciences, 2015,
pp. 6401–06, doi:10.1073/pnas.1421515112.
short: J. Polechova, N.H. Barton, PNAS 112 (2015) 6401–6406.
corr_author: '1'
date_created: 2018-12-11T11:54:11Z
date_published: 2015-05-19T00:00:00Z
date_updated: 2025-09-23T09:27:16Z
day: '19'
department:
- _id: NiBa
doi: 10.1073/pnas.1421515112
ec_funded: 1
external_id:
isi:
- '000354729500058'
pmid:
- '25941385'
intvolume: ' 112'
isi: 1
issue: '20'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443383/
month: '05'
oa: 1
oa_version: Submitted Version
page: 6401 - 6406
pmid: 1
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '5288'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Limits to adaptation along environmental gradients
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 112
year: '2015'
...
---
_id: '1819'
abstract:
- lang: eng
text: 'The sessile life style of plants creates the need to deal with an often adverse
environment, in which water availability can change on a daily basis, challenging
the cellular physiology and integrity. Changes in osmotic conditions disrupt the
equilibrium of the plasma membrane: hypoosmotic conditions increase and hyperosmotic
environment decrease the cell volume. Here, we show that short-term extracellular
osmotic treatments are closely followed by a shift in the balance between endocytosis
and exocytosis in root meristem cells. Acute hyperosmotic treatments (ionic and
nonionic) enhance clathrin-mediated endocytosis simultaneously attenuating exocytosis,
whereas hypoosmotic treatments have the opposite effects. In addition to clathrin
recruitment to the plasma membrane, components of early endocytic trafficking
are essential during hyperosmotic stress responses. Consequently, growth of seedlings
defective in elements of clathrin or early endocytic machinery is more sensitive
to hyperosmotic treatments. We also found that the endocytotic response to a change
of osmotic status in the environment is dominant over the presumably evolutionary
more recent regulatory effect of plant hormones, such as auxin. These results
imply that osmotic perturbation influences the balance between endocytosis and
exocytosis acting through clathrin-mediated endocytosis. We propose that tension
on the plasma membrane determines the addition or removal of membranes at the
cell surface, thus preserving cell integrity.'
acknowledgement: This work was supported by the European Research Council (project
ERC-2011-StG-20101109-PSDP); European Social Fund (CZ.1.07/2.3.00/20.0043) and the
Czech Science Foundation GAČR (GA13-40637S) to J.F.; project Postdoc I. (CZ.1.07/2.3.00/30.0009)
co-financed by the European Social Fund and the state budget of the Czech Republic
to M.Z. and T.N..
article_processing_charge: No
author:
- first_name: Marta
full_name: Zwiewka, Marta
last_name: Zwiewka
- first_name: Tomasz
full_name: Nodzyński, Tomasz
last_name: Nodzyński
- first_name: Stéphanie
full_name: Robert, Stéphanie
last_name: Robert
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Jiřĺ
full_name: Friml, Jiřĺ
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Zwiewka M, Nodzyński T, Robert S, Vanneste S, Friml J. Osmotic stress modulates
the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis
thaliana. Molecular Plant. 2015;8(8):1175-1187. doi:10.1016/j.molp.2015.03.007
apa: Zwiewka, M., Nodzyński, T., Robert, S., Vanneste, S., & Friml, J. (2015).
Osmotic stress modulates the balance between exocytosis and clathrin mediated
endocytosis in Arabidopsis thaliana. Molecular Plant. Elsevier. https://doi.org/10.1016/j.molp.2015.03.007
chicago: Zwiewka, Marta, Tomasz Nodzyński, Stéphanie Robert, Steffen Vanneste, and
Jiří Friml. “Osmotic Stress Modulates the Balance between Exocytosis and Clathrin
Mediated Endocytosis in Arabidopsis Thaliana.” Molecular Plant. Elsevier,
2015. https://doi.org/10.1016/j.molp.2015.03.007.
ieee: M. Zwiewka, T. Nodzyński, S. Robert, S. Vanneste, and J. Friml, “Osmotic stress
modulates the balance between exocytosis and clathrin mediated endocytosis in
Arabidopsis thaliana,” Molecular Plant, vol. 8, no. 8. Elsevier, pp. 1175–1187,
2015.
ista: Zwiewka M, Nodzyński T, Robert S, Vanneste S, Friml J. 2015. Osmotic stress
modulates the balance between exocytosis and clathrin mediated endocytosis in
Arabidopsis thaliana. Molecular Plant. 8(8), 1175–1187.
mla: Zwiewka, Marta, et al. “Osmotic Stress Modulates the Balance between Exocytosis
and Clathrin Mediated Endocytosis in Arabidopsis Thaliana.” Molecular Plant,
vol. 8, no. 8, Elsevier, 2015, pp. 1175–87, doi:10.1016/j.molp.2015.03.007.
short: M. Zwiewka, T. Nodzyński, S. Robert, S. Vanneste, J. Friml, Molecular Plant
8 (2015) 1175–1187.
corr_author: '1'
date_created: 2018-12-11T11:54:11Z
date_published: 2015-08-03T00:00:00Z
date_updated: 2025-09-23T09:47:17Z
day: '03'
department:
- _id: JiFr
doi: 10.1016/j.molp.2015.03.007
ec_funded: 1
external_id:
isi:
- '000359136100006'
intvolume: ' 8'
isi: 1
issue: '8'
language:
- iso: eng
month: '08'
oa_version: None
page: 1175 - 1187
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Molecular Plant
publication_status: published
publisher: Elsevier
publist_id: '5287'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Osmotic stress modulates the balance between exocytosis and clathrin mediated
endocytosis in Arabidopsis thaliana
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 8
year: '2015'
...
---
_id: '1820'
abstract:
- lang: eng
text: 'We consider partially observable Markov decision processes (POMDPs) with
a set of target states and every transition is associated with an integer cost.
The optimization objec- tive we study asks to minimize the expected total cost
till the target set is reached, while ensuring that the target set is reached
almost-surely (with probability 1). We show that for integer costs approximating
the optimal cost is undecidable. For positive costs, our results are as follows:
(i) we establish matching lower and upper bounds for the optimal cost and the
bound is double exponential; (ii) we show that the problem of approximating the
optimal cost is decidable and present ap- proximation algorithms developing on
the existing algorithms for POMDPs with finite-horizon objectives. While the worst-
case running time of our algorithm is double exponential, we present efficient
stopping criteria for the algorithm and show experimentally that it performs well
in many examples.'
acknowledgement: ' The research was partly supported by Austrian Science Fund (FWF)
Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307:
Graph Games), and Microsoft faculty fellows award.'
alternative_title:
- Artifical Intelligence
article_processing_charge: No
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Chmelik, Martin
id: 3624234E-F248-11E8-B48F-1D18A9856A87
last_name: Chmelik
- first_name: Raghav
full_name: Gupta, Raghav
last_name: Gupta
- first_name: Ayush
full_name: Kanodia, Ayush
last_name: Kanodia
citation:
ama: 'Chatterjee K, Chmelik M, Gupta R, Kanodia A. Optimal cost almost-sure reachability
in POMDPs. In: Proceedings of the Twenty-Ninth AAAI Conference on Artificial
Intelligence . Vol 5. AAAI Press; 2015:3496-3502.'
apa: 'Chatterjee, K., Chmelik, M., Gupta, R., & Kanodia, A. (2015). Optimal
cost almost-sure reachability in POMDPs. In Proceedings of the Twenty-Ninth
AAAI Conference on Artificial Intelligence (Vol. 5, pp. 3496–3502). Austin,
TX, USA: AAAI Press.'
chicago: Chatterjee, Krishnendu, Martin Chmelik, Raghav Gupta, and Ayush Kanodia.
“Optimal Cost Almost-Sure Reachability in POMDPs.” In Proceedings of the Twenty-Ninth
AAAI Conference on Artificial Intelligence , 5:3496–3502. AAAI Press, 2015.
ieee: K. Chatterjee, M. Chmelik, R. Gupta, and A. Kanodia, “Optimal cost almost-sure
reachability in POMDPs,” in Proceedings of the Twenty-Ninth AAAI Conference
on Artificial Intelligence , Austin, TX, USA, 2015, vol. 5, pp. 3496–3502.
ista: 'Chatterjee K, Chmelik M, Gupta R, Kanodia A. 2015. Optimal cost almost-sure
reachability in POMDPs. Proceedings of the Twenty-Ninth AAAI Conference on Artificial
Intelligence . IAAI: Innovative Applications of Artificial Intelligence, Artifical
Intelligence, vol. 5, 3496–3502.'
mla: Chatterjee, Krishnendu, et al. “Optimal Cost Almost-Sure Reachability in POMDPs.”
Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence
, vol. 5, AAAI Press, 2015, pp. 3496–502.
short: K. Chatterjee, M. Chmelik, R. Gupta, A. Kanodia, in:, Proceedings of the
Twenty-Ninth AAAI Conference on Artificial Intelligence , AAAI Press, 2015, pp.
3496–3502.
conference:
end_date: 2015-01-30
location: Austin, TX, USA
name: 'IAAI: Innovative Applications of Artificial Intelligence'
start_date: 2015-01-25
corr_author: '1'
date_created: 2018-12-11T11:54:11Z
date_published: 2015-06-01T00:00:00Z
date_updated: 2025-09-18T11:05:08Z
day: '01'
department:
- _id: KrCh
ec_funded: 1
external_id:
arxiv:
- '1411.3880'
isi:
- '000372683700002'
intvolume: ' 5'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1411.3880
month: '06'
oa: 1
oa_version: Preprint
page: 3496-3502
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: 'Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence '
publication_status: published
publisher: AAAI Press
publist_id: '5286'
quality_controlled: '1'
related_material:
record:
- id: '1529'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Optimal cost almost-sure reachability in POMDPs
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 5
year: '2015'
...