---
_id: '1722'
abstract:
- lang: eng
text: Morphogens are secreted signalling molecules that act in a graded manner to
control the pattern of cellular differentiation in developing tissues. An example
is Sonic hedgehog (Shh), which acts in several developing vertebrate tissues,
including the central nervous system, to provide positional information during
embryonic patterning. Here we address how Shh signalling assigns the positional
identities of distinct neuronal subtype progenitors throughout the ventral neural
tube. Assays of intracellular signal transduction and gene expression indicate
that the duration as well as level of signalling is critical for morphogen interpretation.
Progenitors of the ventral neuronal subtypes are established sequentially, with
progressively more ventral identities requiring correspondingly higher levels
and longer periods of Shh signalling. Moreover, cells remain sensitive to changes
in Shh signalling for an extended time, reverting to antecedent identities if
signalling levels fall below a threshold. Thus, the duration of signalling is
important not only for the assignment but also for the refinement and maintenance
of positional identity. Together the data suggest a dynamic model for ventral
neural tube patterning in which positional information corresponds to the time
integral of Shh signalling. This suggests an alternative to conventional models
of morphogen action that rely solely on the level of signalling.
acknowledgement: 'NS was supported by a Marie Curie Fellowship (PIIF-GA-2008-219939)
and the Mochida Memorial Foundation for Medical and Pharmaceutical Research. Support
for VR was provided by an EMBO LTF, for AK by a FEBS LTF. ED was supported by the
Wellcome Trust (#080630). Work in the lab of JB is supported by the Medical Research
Council (UK). AP is a CNRS (Centre National de la Recherche Scientifique) Investigator.
This work was supported by grants from the Ministère de la Recherche (ACI Grant
#0220575) and the Association pour la Recherche sur le Cancer (Grant #4679) to AP.
BGN was supported by grants from the Whitehall Foundation (2004-05-90-APL), the
March of Dimes Foundation (5-FY2006-281), the Muscular Dystrophy Association (92901),
and the NINDS (NS053976)'
author:
- first_name: Éric
full_name: Dessaud, Éric
last_name: Dessaud
- first_name: Vanessa
full_name: Ribes, Vanessa
last_name: Ribes
- first_name: Nikolaos
full_name: Balaskas, Nikolaos
last_name: Balaskas
- first_name: Linlin
full_name: Yang, Linlin
last_name: Yang
- first_name: Alessandra
full_name: Pierani, Alessandra
last_name: Pierani
- first_name: Anna
full_name: Anna Kicheva
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
- first_name: Bennett
full_name: Novitch, Bennett
last_name: Novitch
- first_name: James
full_name: Briscoe, James
last_name: Briscoe
- first_name: Noriaki
full_name: Sasai, Noriaki
last_name: Sasai
citation:
ama: Dessaud É, Ribes V, Balaskas N, et al. Dynamic assignment and maintenance of
positional identity in the ventral neural tube by the morphogen sonic hedgehog.
PLoS Biology. 2010;8(6). doi:10.1371/journal.pbio.1000382
apa: Dessaud, É., Ribes, V., Balaskas, N., Yang, L., Pierani, A., Kicheva, A., …
Sasai, N. (2010). Dynamic assignment and maintenance of positional identity in
the ventral neural tube by the morphogen sonic hedgehog. PLoS Biology.
Public Library of Science. https://doi.org/10.1371/journal.pbio.1000382
chicago: Dessaud, Éric, Vanessa Ribes, Nikolaos Balaskas, Linlin Yang, Alessandra
Pierani, Anna Kicheva, Bennett Novitch, James Briscoe, and Noriaki Sasai. “Dynamic
Assignment and Maintenance of Positional Identity in the Ventral Neural Tube by
the Morphogen Sonic Hedgehog.” PLoS Biology. Public Library of Science,
2010. https://doi.org/10.1371/journal.pbio.1000382.
ieee: É. Dessaud et al., “Dynamic assignment and maintenance of positional
identity in the ventral neural tube by the morphogen sonic hedgehog,” PLoS
Biology, vol. 8, no. 6. Public Library of Science, 2010.
ista: Dessaud É, Ribes V, Balaskas N, Yang L, Pierani A, Kicheva A, Novitch B, Briscoe
J, Sasai N. 2010. Dynamic assignment and maintenance of positional identity in
the ventral neural tube by the morphogen sonic hedgehog. PLoS Biology. 8(6).
mla: Dessaud, Éric, et al. “Dynamic Assignment and Maintenance of Positional Identity
in the Ventral Neural Tube by the Morphogen Sonic Hedgehog.” PLoS Biology,
vol. 8, no. 6, Public Library of Science, 2010, doi:10.1371/journal.pbio.1000382.
short: É. Dessaud, V. Ribes, N. Balaskas, L. Yang, A. Pierani, A. Kicheva, B. Novitch,
J. Briscoe, N. Sasai, PLoS Biology 8 (2010).
date_created: 2018-12-11T11:53:39Z
date_published: 2010-06-01T00:00:00Z
date_updated: 2021-01-12T06:52:46Z
day: '01'
doi: 10.1371/journal.pbio.1000382
extern: 1
intvolume: ' 8'
issue: '6'
month: '06'
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '5408'
quality_controlled: 0
status: public
title: Dynamic assignment and maintenance of positional identity in the ventral neural
tube by the morphogen sonic hedgehog
type: journal_article
volume: 8
year: '2010'
...
---
_id: '1752'
abstract:
- lang: eng
text: The epitaxial growth of germanium on silicon leads to the self-assembly of
SiGe nanocrystals by a process that allows the size, composition and position
of the nanocrystals to be controlled. This level of control, combined with an
inherent compatibility with silicon technology, could prove useful in nanoelectronic
applications. Here, we report the confinement of holes in quantum-dot devices
made by directly contacting individual SiGe nanocrystals with aluminium electrodes,
and the production of hybrid superconductor- semiconductor devices, such as resonant
supercurrent transistors, when the quantum dot is strongly coupled to the electrodes.
Charge transport measurements on weakly coupled quantum dots reveal discrete energy
spectra, with the confined hole states displaying anisotropic gyromagnetic factors
and strong spin-orbit coupling with pronounced dependences on gate voltage and
magnetic field.
acknowledgement: We also acknowledge support from the Agence Nationale de la Recherche
(through the ACCESS and COHESION projects). G.K. acknowledges further support from
the Deutsche Forschungsgemeinschaft (grant no. KA 2922/1-1)
author:
- first_name: Georgios
full_name: Georgios Katsaros
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
- first_name: Panayotis
full_name: Spathis, Panayotis N
last_name: Spathis
- first_name: Mathieu
full_name: Stoffel, Mathieu
last_name: Stoffel
- first_name: Frank
full_name: Fournel, Frank
last_name: Fournel
- first_name: Massimo
full_name: Mongillo, Massimo
last_name: Mongillo
- first_name: Vincent
full_name: Bouchiat, Vincent
last_name: Bouchiat
- first_name: François
full_name: Lefloch, François
last_name: Lefloch
- first_name: Armando
full_name: Rastelli, Armando
last_name: Rastelli
- first_name: Oliver
full_name: Schmidt, Oliver G
last_name: Schmidt
- first_name: Silvano
full_name: De Franceschi, Silvano
last_name: De Franceschi
citation:
ama: Katsaros G, Spathis P, Stoffel M, et al. Hybrid superconductor-semiconductor
devices made from self-assembled SiGe nanocrystals on silicon. Nature Nanotechnology.
2010;5(6):458-464. doi:10.1038/nnano.2010.84
apa: Katsaros, G., Spathis, P., Stoffel, M., Fournel, F., Mongillo, M., Bouchiat,
V., … De Franceschi, S. (2010). Hybrid superconductor-semiconductor devices made
from self-assembled SiGe nanocrystals on silicon. Nature Nanotechnology.
Nature Publishing Group. https://doi.org/10.1038/nnano.2010.84
chicago: Katsaros, Georgios, Panayotis Spathis, Mathieu Stoffel, Frank Fournel,
Massimo Mongillo, Vincent Bouchiat, François Lefloch, Armando Rastelli, Oliver
Schmidt, and Silvano De Franceschi. “Hybrid Superconductor-Semiconductor Devices
Made from Self-Assembled SiGe Nanocrystals on Silicon.” Nature Nanotechnology.
Nature Publishing Group, 2010. https://doi.org/10.1038/nnano.2010.84.
ieee: G. Katsaros et al., “Hybrid superconductor-semiconductor devices made
from self-assembled SiGe nanocrystals on silicon,” Nature Nanotechnology,
vol. 5, no. 6. Nature Publishing Group, pp. 458–464, 2010.
ista: Katsaros G, Spathis P, Stoffel M, Fournel F, Mongillo M, Bouchiat V, Lefloch
F, Rastelli A, Schmidt O, De Franceschi S. 2010. Hybrid superconductor-semiconductor
devices made from self-assembled SiGe nanocrystals on silicon. Nature Nanotechnology.
5(6), 458–464.
mla: Katsaros, Georgios, et al. “Hybrid Superconductor-Semiconductor Devices Made
from Self-Assembled SiGe Nanocrystals on Silicon.” Nature Nanotechnology,
vol. 5, no. 6, Nature Publishing Group, 2010, pp. 458–64, doi:10.1038/nnano.2010.84.
short: G. Katsaros, P. Spathis, M. Stoffel, F. Fournel, M. Mongillo, V. Bouchiat,
F. Lefloch, A. Rastelli, O. Schmidt, S. De Franceschi, Nature Nanotechnology 5
(2010) 458–464.
date_created: 2018-12-11T11:53:49Z
date_published: 2010-06-01T00:00:00Z
date_updated: 2021-01-12T06:52:59Z
day: '01'
doi: 10.1038/nnano.2010.84
extern: 1
intvolume: ' 5'
issue: '6'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1005.1816
month: '06'
oa: 1
page: 458 - 464
publication: Nature Nanotechnology
publication_status: published
publisher: Nature Publishing Group
publist_id: '5372'
quality_controlled: 0
status: public
title: Hybrid superconductor-semiconductor devices made from self-assembled SiGe nanocrystals
on silicon
type: journal_article
volume: 5
year: '2010'
...
---
_id: '1753'
abstract:
- lang: eng
text: We investigate electronic transport in n-i-n GaN nanowires with and without
AlN double barriers. The nanowires are grown by catalyst-free, plasma-assisted
molecular beam epitaxy enabling abrupt GaN/AlN interfaces as well as longitudinal
n-type doping modulation. At low temperature, transport in n-i-n GaN nanowires
is dominated by the Coulomb blockade effect. Carriers are confined in the undoped
middle region, forming single or multiple islands with a characteristic length
of ∼100 nm. The incorporation of two AlN tunnel barriers causes confinement to
occur within the GaN dot in between. In the case of a 6 nm thick dot and 2 nm
thick barriers, we observe characteristic signatures of Coulomb-blockaded transport
in single quantum dots with discrete energy states. For thinner dots and barriers,
Coulomb-blockade effects do not play a significant role while the onset of resonant
tunneling via the confined quantum levels is accompanied by a negative differential
resistance surviving up to ∼150 K.
acknowledgement: This research was partly funded by the Agence Nationale de la Recherche
through the COHESION project. G.K. acknowledges further support from the Deutsche
Forschungsgemeinschaft (Grant KA 2922/1-1)
author:
- first_name: Rudeeson
full_name: Songmuang, Rudeeson
last_name: Songmuang
- first_name: Georgios
full_name: Georgios Katsaros
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
- first_name: Eva
full_name: Monroy, Eva
last_name: Monroy
- first_name: Panayotis
full_name: Spathis, Panayotis N
last_name: Spathis
- first_name: Catherine
full_name: Bougerol, Catherine
last_name: Bougerol
- first_name: Massimo
full_name: Mongillo, Massimo
last_name: Mongillo
- first_name: Silvano
full_name: De Franceschi, Silvano
last_name: De Franceschi
citation:
ama: Songmuang R, Katsaros G, Monroy E, et al. Quantum transport in GaN/AlN double-barrier
heterostructure nanowires. Nano Letters. 2010;10(9):3545-3550. doi:10.1021/nl1017578
apa: Songmuang, R., Katsaros, G., Monroy, E., Spathis, P., Bougerol, C., Mongillo,
M., & De Franceschi, S. (2010). Quantum transport in GaN/AlN double-barrier
heterostructure nanowires. Nano Letters. American Chemical Society. https://doi.org/10.1021/nl1017578
chicago: Songmuang, Rudeeson, Georgios Katsaros, Eva Monroy, Panayotis Spathis,
Catherine Bougerol, Massimo Mongillo, and Silvano De Franceschi. “Quantum Transport
in GaN/AlN Double-Barrier Heterostructure Nanowires.” Nano Letters. American
Chemical Society, 2010. https://doi.org/10.1021/nl1017578.
ieee: R. Songmuang et al., “Quantum transport in GaN/AlN double-barrier heterostructure
nanowires,” Nano Letters, vol. 10, no. 9. American Chemical Society, pp.
3545–3550, 2010.
ista: Songmuang R, Katsaros G, Monroy E, Spathis P, Bougerol C, Mongillo M, De Franceschi
S. 2010. Quantum transport in GaN/AlN double-barrier heterostructure nanowires.
Nano Letters. 10(9), 3545–3550.
mla: Songmuang, Rudeeson, et al. “Quantum Transport in GaN/AlN Double-Barrier Heterostructure
Nanowires.” Nano Letters, vol. 10, no. 9, American Chemical Society, 2010,
pp. 3545–50, doi:10.1021/nl1017578.
short: R. Songmuang, G. Katsaros, E. Monroy, P. Spathis, C. Bougerol, M. Mongillo,
S. De Franceschi, Nano Letters 10 (2010) 3545–3550.
date_created: 2018-12-11T11:53:49Z
date_published: 2010-09-08T00:00:00Z
date_updated: 2021-01-12T06:52:59Z
day: '08'
doi: 10.1021/nl1017578
extern: 1
intvolume: ' 10'
issue: '9'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1005.3637
month: '09'
oa: 1
page: 3545 - 3550
publication: Nano Letters
publication_status: published
publisher: American Chemical Society
publist_id: '5371'
quality_controlled: 0
status: public
title: Quantum transport in GaN/AlN double-barrier heterostructure nanowires
type: journal_article
volume: 10
year: '2010'
...
---
_id: '17639'
abstract:
- lang: eng
text: It has been proposed that primordial gas in early dark matter halos, with
virial temperatures above 10^4 K, can avoid fragmentation and undergo rapid collapse,
possibly resulting in a supermassive black hole (SMBH). This requires the gas
to avoid cooling and to remain at temperatures near T=10^4 K. We show that this
condition can be satisfied in the presence of a sufficiently strong primordial
magnetic field, which heats the collapsing gas via ambipolar diffusion. If the
field has a strength above B = 3.6 (comoving) nG, the collapsing gas is kept warm
(T=10^4K) until it reaches the critical density n_crit=10^3 cm^{-3} at which the
roto-vibrational states of H_2 approach local thermodynamic equilibrium. H_2-cooling
then remains inefficient, and the gas temperature stays near 10^4K, even as it
continues to collapse to higher densities. The critical magnetic field strength
required to permanently suppress H_2-cooling is somewhat higher than upper limit
of approx. 2 nG from the cosmic microwave background (CMB). However, it can be
realized in the rare (2-3)-sigma regions of the spatially fluctuating B-field;
these regions contain a sufficient number of halos to account for the z=6 quasar
BHs.
article_processing_charge: No
article_type: original
author:
- first_name: Shiv
full_name: Sethi, Shiv
last_name: Sethi
- first_name: Zoltán
full_name: Haiman, Zoltán
id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36
last_name: Haiman
- first_name: Kanhaiya
full_name: Pandey, Kanhaiya
last_name: Pandey
citation:
ama: Sethi S, Haiman Z, Pandey K. Supermassive black hole formation at high redshifts
through a primordial magnetic field. The Astrophysical Journal. 2010;721(1):615-621.
doi:10.1088/0004-637x/721/1/615
apa: Sethi, S., Haiman, Z., & Pandey, K. (2010). Supermassive black hole formation
at high redshifts through a primordial magnetic field. The Astrophysical Journal.
American Astronomical Society. https://doi.org/10.1088/0004-637x/721/1/615
chicago: Sethi, Shiv, Zoltán Haiman, and Kanhaiya Pandey. “Supermassive Black Hole
Formation at High Redshifts through a Primordial Magnetic Field.” The Astrophysical
Journal. American Astronomical Society, 2010. https://doi.org/10.1088/0004-637x/721/1/615.
ieee: S. Sethi, Z. Haiman, and K. Pandey, “Supermassive black hole formation at
high redshifts through a primordial magnetic field,” The Astrophysical Journal,
vol. 721, no. 1. American Astronomical Society, pp. 615–621, 2010.
ista: Sethi S, Haiman Z, Pandey K. 2010. Supermassive black hole formation at high
redshifts through a primordial magnetic field. The Astrophysical Journal. 721(1),
615–621.
mla: Sethi, Shiv, et al. “Supermassive Black Hole Formation at High Redshifts through
a Primordial Magnetic Field.” The Astrophysical Journal, vol. 721, no.
1, American Astronomical Society, 2010, pp. 615–21, doi:10.1088/0004-637x/721/1/615.
short: S. Sethi, Z. Haiman, K. Pandey, The Astrophysical Journal 721 (2010) 615–621.
date_created: 2024-09-06T07:16:56Z
date_published: 2010-08-31T00:00:00Z
date_updated: 2024-09-24T11:43:48Z
day: '31'
doi: 10.1088/0004-637x/721/1/615
extern: '1'
intvolume: ' 721'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1088/0004-637x/721/1/615
month: '08'
oa: 1
oa_version: Published Version
page: 615-621
publication: The Astrophysical Journal
publication_identifier:
issn:
- 0004-637X
- 1538-4357
publication_status: published
publisher: American Astronomical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Supermassive black hole formation at high redshifts through a primordial magnetic
field
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 721
year: '2010'
...
---
_id: '17648'
abstract:
- lang: eng
text: In the absence of H_2 molecules, the primordial gas in early dark matter halos
with virial temperatures just above T_vir >~ 10^4 K cools by collisional excitation
of atomic H. Although it cools efficiently, this gas remains relatively hot, at
a temperature near T ~ 8000 K, and consequently might be able to avoid fragmentation
and collapse directly into a supermassive black hole (SMBH). In order for H_2--formation
and cooling to be strongly suppressed, the gas must be irradiated by a sufficiently
intense ultraviolet (UV) flux. We performed a suite of three--dimensional hydrodynamical
adaptive mesh refinement (AMR) simulations of gas collapse in three different
protogalactic halos with T_vir >~ 10^4 K, irradiated by a UV flux with various
intensities and spectra. We determined the critical specific intensity, Jcrit,
required to suppress H_2 cooling in each of the three halos. For a hard spectrum
representative of metal--free stars, we find (in units of 10^{-21} erg s^{-1}
Hz^{-1} sr^{-1} cm^{-2}) 10^4Monthly Notices of the Royal Astronomical Society.
2010;402(2):1249-1262. doi:10.1111/j.1365-2966.2009.15960.x'
apa: 'Shang, C., Bryan, G. L., & Haiman, Z. (2010). Supermassive black hole
formation by direct collapse: keeping protogalactic gas H2 free in dark matter
haloes with virial temperatures T_vir > rsim10^4 K . Monthly Notices of
the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1111/j.1365-2966.2009.15960.x'
chicago: 'Shang, Cien, Greg L. Bryan, and Zoltán Haiman. “Supermassive Black Hole
Formation by Direct Collapse: Keeping Protogalactic Gas H2 Free in Dark Matter
Haloes with Virial Temperatures T_vir > Rsim10^4 K .” Monthly Notices of
the Royal Astronomical Society. Oxford University Press, 2010. https://doi.org/10.1111/j.1365-2966.2009.15960.x.'
ieee: 'C. Shang, G. L. Bryan, and Z. Haiman, “Supermassive black hole formation
by direct collapse: keeping protogalactic gas H2 free in dark matter haloes with
virial temperatures T_vir > rsim10^4 K ,” Monthly Notices of the Royal
Astronomical Society, vol. 402, no. 2. Oxford University Press, pp. 1249–1262,
2010.'
ista: 'Shang C, Bryan GL, Haiman Z. 2010. Supermassive black hole formation by direct
collapse: keeping protogalactic gas H2 free in dark matter haloes with virial
temperatures T_vir > rsim10^4 K . Monthly Notices of the Royal Astronomical
Society. 402(2), 1249–1262.'
mla: 'Shang, Cien, et al. “Supermassive Black Hole Formation by Direct Collapse:
Keeping Protogalactic Gas H2 Free in Dark Matter Haloes with Virial Temperatures
T_vir > Rsim10^4 K .” Monthly Notices of the Royal Astronomical Society,
vol. 402, no. 2, Oxford University Press, 2010, pp. 1249–62, doi:10.1111/j.1365-2966.2009.15960.x.'
short: C. Shang, G.L. Bryan, Z. Haiman, Monthly Notices of the Royal Astronomical
Society 402 (2010) 1249–1262.
date_created: 2024-09-06T07:26:50Z
date_published: 2010-02-02T00:00:00Z
date_updated: 2024-09-24T12:49:06Z
day: '02'
doi: 10.1111/j.1365-2966.2009.15960.x
extern: '1'
intvolume: ' 402'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/j.1365-2966.2009.15960.x
month: '02'
oa: 1
oa_version: Published Version
page: 1249-1262
publication: Monthly Notices of the Royal Astronomical Society
publication_identifier:
issn:
- 0035-8711
- 1365-2966
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Supermassive black hole formation by direct collapse: keeping protogalactic
gas H2 free in dark matter haloes with virial temperatures T_vir > rsim10^4 K '
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 402
year: '2010'
...
---
_id: '17664'
abstract:
- lang: eng
text: Supermassive black holes (SMBHs) are common in local galactic nuclei, and
SMBHs as massive as several billion solar masses already exist at redshift z=6.
These earliest SMBHs may arise by the combination of Eddington-limited growth
and mergers of stellar-mass seed BHs left behind by the first generation of metal-free
stars, or by the rapid direct collapse of gas in rare special environments where
the gas can avoid fragmenting into stars. In this contribution, I review these
two competing scenarios. I also briefly mention some more exotic ideas and how
the different models may be distinguished in the future by LISA and other instruments.
article_processing_charge: No
arxiv: 1
author:
- first_name: Zoltán
full_name: Haiman, Zoltán
id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36
last_name: Haiman
- first_name: Daniel J.
full_name: Whalen, Daniel J.
last_name: Whalen
- first_name: Volker
full_name: Bromm, Volker
last_name: Bromm
- first_name: Naoki
full_name: Yoshida, Naoki
last_name: Yoshida
citation:
ama: 'Haiman Z, Whalen DJ, Bromm V, Yoshida N. The origin and detection of high-redshift
supermassive black holes. In: AIP Conference Proceedings. Vol 1294. American
Institute of Physics; 2010:215-224. doi:10.1063/1.3518857'
apa: 'Haiman, Z., Whalen, D. J., Bromm, V., & Yoshida, N. (2010). The origin
and detection of high-redshift supermassive black holes. In AIP Conference
Proceedings (Vol. 1294, pp. 215–224). Austin, TX, United States: American
Institute of Physics. https://doi.org/10.1063/1.3518857'
chicago: Haiman, Zoltán, Daniel J. Whalen, Volker Bromm, and Naoki Yoshida. “The
Origin and Detection of High-Redshift Supermassive Black Holes.” In AIP Conference
Proceedings, 1294:215–24. American Institute of Physics, 2010. https://doi.org/10.1063/1.3518857.
ieee: Z. Haiman, D. J. Whalen, V. Bromm, and N. Yoshida, “The origin and detection
of high-redshift supermassive black holes,” in AIP Conference Proceedings,
Austin, TX, United States, 2010, vol. 1294, no. 1, pp. 215–224.
ista: 'Haiman Z, Whalen DJ, Bromm V, Yoshida N. 2010. The origin and detection of
high-redshift supermassive black holes. AIP Conference Proceedings. The First
Stars and Galaxies: Challenges for the Next Decade vol. 1294, 215–224.'
mla: Haiman, Zoltán, et al. “The Origin and Detection of High-Redshift Supermassive
Black Holes.” AIP Conference Proceedings, vol. 1294, no. 1, American Institute
of Physics, 2010, pp. 215–24, doi:10.1063/1.3518857.
short: Z. Haiman, D.J. Whalen, V. Bromm, N. Yoshida, in:, AIP Conference Proceedings,
American Institute of Physics, 2010, pp. 215–224.
conference:
end_date: 2010-03-11
location: Austin, TX, United States
name: 'The First Stars and Galaxies: Challenges for the Next Decade'
start_date: 2010-03-08
date_created: 2024-09-06T07:41:39Z
date_published: 2010-11-03T00:00:00Z
date_updated: 2024-09-25T07:40:43Z
day: '03'
doi: 10.1063/1.3518857
extern: '1'
external_id:
arxiv:
- '1007.4741'
intvolume: ' 1294'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.1007.4741'
month: '11'
oa: 1
oa_version: Preprint
page: 215-224
publication: AIP Conference Proceedings
publication_identifier:
issn:
- 0094-243X
publication_status: published
publisher: American Institute of Physics
quality_controlled: '1'
scopus_import: '1'
status: public
title: The origin and detection of high-redshift supermassive black holes
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 1294
year: '2010'
...
---
_id: '17665'
abstract:
- lang: eng
text: Finding electromagnetic (EM) counterparts of future gravitational wave (GW)
sources would bring rich scientific benefits. A promising possibility, in the
case of the coalescence of a supermassive black hole binary (SMBHB), is that the
prompt emission from merger-induced disturbances in a supersonic circumbinary
disc may be detectable. We follow the post-merger evolution of a thin, zero-viscosity
circumbinary gas disc with two-dimensional simulations, using the hydrodynamic
code flash. We analyse perturbations arising from the 530 km s−1 recoil of a 106
M⊙ binary, oriented in the plane of the disc, assuming either a non-radiative
gamma-law or a pseudo-isothermal equation of state for the gas. We find that a
single-armed spiral shock wave forms and propagates outwards, sweeping up ∼40
per cent of the mass of the disc. The morphology and evolution of the perturbations
agrees well with those of caustics predicted to occur in a collisionless disc.
Assuming that the disc radiates nearly instantaneously to maintain a constant
temperature, we estimate the amount of dissipation and corresponding post-merger
light curve. The luminosity rises steadily on the time-scale of months, and reaches
few ×1043 erg s−1, corresponding to ≈10 per cent of the Eddington luminosity of
the central SMBHB. We also analyse the case in which gravitational wave emission
results in a 5 per cent mass loss in the merger remnant. The mass loss reduces
the shock overdensities and the overall luminosity of the disc by ≈15–20 per cent,
without any other major effects on the spiral shock pattern.
alternative_title:
- Gas disc response to black hole merger
article_processing_charge: No
article_type: original
author:
- first_name: Lia R.
full_name: Corrales, Lia R.
last_name: Corrales
- first_name: Zoltán
full_name: Haiman, Zoltán
id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36
last_name: Haiman
- first_name: Andrew
full_name: MacFadyen, Andrew
last_name: MacFadyen
citation:
ama: Corrales LR, Haiman Z, MacFadyen A. Hydrodynamical response of a circumbinary
gas disc to black hole recoil and mass loss. Monthly Notices of the Royal Astronomical
Society. 2010;404(2):947-962. doi:10.1111/j.1365-2966.2010.16324.x
apa: Corrales, L. R., Haiman, Z., & MacFadyen, A. (2010). Hydrodynamical response
of a circumbinary gas disc to black hole recoil and mass loss. Monthly Notices
of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1111/j.1365-2966.2010.16324.x
chicago: Corrales, Lia R., Zoltán Haiman, and Andrew MacFadyen. “Hydrodynamical
Response of a Circumbinary Gas Disc to Black Hole Recoil and Mass Loss.” Monthly
Notices of the Royal Astronomical Society. Oxford University Press, 2010.
https://doi.org/10.1111/j.1365-2966.2010.16324.x.
ieee: L. R. Corrales, Z. Haiman, and A. MacFadyen, “Hydrodynamical response of a
circumbinary gas disc to black hole recoil and mass loss,” Monthly Notices
of the Royal Astronomical Society, vol. 404, no. 2. Oxford University Press,
pp. 947–962, 2010.
ista: Corrales LR, Haiman Z, MacFadyen A. 2010. Hydrodynamical response of a circumbinary
gas disc to black hole recoil and mass loss. Monthly Notices of the Royal Astronomical
Society. 404(2), 947–962.
mla: Corrales, Lia R., et al. “Hydrodynamical Response of a Circumbinary Gas Disc
to Black Hole Recoil and Mass Loss.” Monthly Notices of the Royal Astronomical
Society, vol. 404, no. 2, Oxford University Press, 2010, pp. 947–62, doi:10.1111/j.1365-2966.2010.16324.x.
short: L.R. Corrales, Z. Haiman, A. MacFadyen, Monthly Notices of the Royal Astronomical
Society 404 (2010) 947–962.
date_created: 2024-09-06T07:43:45Z
date_published: 2010-05-04T00:00:00Z
date_updated: 2024-09-25T07:43:38Z
day: '04'
doi: 10.1111/j.1365-2966.2010.16324.x
extern: '1'
intvolume: ' 404'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/j.1365-2966.2010.16324.x
month: '05'
oa: 1
oa_version: Published Version
page: 947-962
publication: Monthly Notices of the Royal Astronomical Society
publication_identifier:
issn:
- 0035-8711
- 1365-2966
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Hydrodynamical response of a circumbinary gas disc to black hole recoil and
mass loss
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 404
year: '2010'
...
---
_id: '17686'
abstract:
- lang: eng
text: The coalescence of a supermassive black hole binary (SMBHB) is thought to
be accompanied by an electromagnetic (EM) afterglow, produced by the viscous infall
of the surrounding circumbinary gas disk after the merger. It has been proposed
that once the merger has been detected in gravitational waves (GWs) by LISA, follow-up
EM searches for this afterglow can help identify the EM counterpart of the LISA
source. Here we study whether the afterglows may be sufficiently bright and numerous
to be detectable in EM surveys alone. The viscous afterglow, which lasts for years
to decades for SMBHBs in LISA's sensitivity window, is characterized by rapid
increases in both the bolometric luminosity and in the spectral hardness of the
source. If quasar activity is triggered by the same major galaxy mergers that
produce SMBHBs, then the afterglow could be interpreted as a signature of the
birth of a quasar. Using an idealized model for the post-merger viscous spreading
of the circumbinary disk and the resulting light curve, and using the observed
luminosity function of quasars as a proxy for the SMBHB merger rate, we delineate
the survey requirements for identifying such birthing quasars. If circumbinary
disks have a high disk surface density and viscosity, an all-sky soft X-ray survey
with a sensitivity of ~<3x10^-14 erg s^-1 cm^-2 and a time resolution of ~months
could identify dozens of birthing quasars with sustained brightening rates of
>10%/yr. If >1% of the X-ray emission is reprocessed into optical frequencies,
birthing quasars could also be identified in optical transient surveys such as
the LSST. Distinguishing a birthing quasar from other variable sources may be
facilitated by the monotonic hardening of its spectrum, but will likely remain
challenging. This reinforces the notion that joint EM-plus-GW observations offer
the best prospects for identifying the EM signatures of SMBHB mergers.
article_processing_charge: No
article_type: original
author:
- first_name: Takamitsu
full_name: Tanaka, Takamitsu
last_name: Tanaka
- first_name: Zoltán
full_name: Haiman, Zoltán
id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36
last_name: Haiman
- first_name: Kristen
full_name: Menou, Kristen
last_name: Menou
citation:
ama: Tanaka T, Haiman Z, Menou K. Witnessing the birth of a quasar. The Astronomical
Journal. 2010;140(2):642-651. doi:10.1088/0004-6256/140/2/642
apa: Tanaka, T., Haiman, Z., & Menou, K. (2010). Witnessing the birth of a quasar.
The Astronomical Journal. American Astronomical Society. https://doi.org/10.1088/0004-6256/140/2/642
chicago: Tanaka, Takamitsu, Zoltán Haiman, and Kristen Menou. “Witnessing the Birth
of a Quasar.” The Astronomical Journal. American Astronomical Society,
2010. https://doi.org/10.1088/0004-6256/140/2/642.
ieee: T. Tanaka, Z. Haiman, and K. Menou, “Witnessing the birth of a quasar,” The
Astronomical Journal, vol. 140, no. 2. American Astronomical Society, pp.
642–651, 2010.
ista: Tanaka T, Haiman Z, Menou K. 2010. Witnessing the birth of a quasar. The Astronomical
Journal. 140(2), 642–651.
mla: Tanaka, Takamitsu, et al. “Witnessing the Birth of a Quasar.” The Astronomical
Journal, vol. 140, no. 2, American Astronomical Society, 2010, pp. 642–51,
doi:10.1088/0004-6256/140/2/642.
short: T. Tanaka, Z. Haiman, K. Menou, The Astronomical Journal 140 (2010) 642–651.
date_created: 2024-09-06T08:21:37Z
date_published: 2010-07-15T00:00:00Z
date_updated: 2024-09-25T09:22:09Z
day: '15'
doi: 10.1088/0004-6256/140/2/642
extern: '1'
intvolume: ' 140'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1088/0004-6256/140/2/642
month: '07'
oa: 1
oa_version: Published Version
page: 642-651
publication: The Astronomical Journal
publication_identifier:
issn:
- 0004-6256
- 1538-3881
publication_status: published
publisher: American Astronomical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Witnessing the birth of a quasar
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 140
year: '2010'
...
---
_id: '17695'
abstract:
- lang: eng
text: Clusters of galaxies have been extensively used to determine cosmological
parameters. A major difficulty in making the best use of Sunyaev–Zel'dovich (SZ)
and X-ray observations of clusters for cosmology is that using X-ray observations
it is difficult to measure the temperature distribution and therefore determine
the density distribution in individual clusters of galaxies out to the virial
radius. Observations with the new generation of SZ instruments are a promising
alternative approach. We use clusters of galaxies drawn from high-resolution adaptive
mesh refinement cosmological simulations to study how well we should be able to
constrain the large-scale distribution of the intracluster gas (ICG) in individual
massive relaxed clusters using AMiBA in its configuration with 13 1.2 m diameter
dishes (AMiBA13) along with X-ray observations. We show that non-isothermal β
models provide a good description of the ICG in our simulated relaxed clusters.
We use simulated X-ray observations to estimate the quality of constraints on
the distribution of gas density, and simulated SZ visibilities (AMiBA13 observations)
for constraints on the large-scale temperature distribution of the ICG. We find
that AMiBA13 visibilities should constrain the scale radius of the temperature
distribution to about 50% accuracy. We conclude that the upgraded AMiBA, AMiBA13,
should be a powerful instrument to constrain the large-scale distribution of the
ICG.
article_processing_charge: No
article_type: original
author:
- first_name: Sandor M.
full_name: Molnar, Sandor M.
last_name: Molnar
- first_name: Keiichi
full_name: Umetsu, Keiichi
last_name: Umetsu
- first_name: Mark
full_name: Birkinshaw, Mark
last_name: Birkinshaw
- first_name: Greg
full_name: Bryan, Greg
last_name: Bryan
- first_name: Zoltán
full_name: Haiman, Zoltán
id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36
last_name: Haiman
- first_name: Nathan
full_name: Hearn, Nathan
last_name: Hearn
- first_name: Cien
full_name: Shang, Cien
last_name: Shang
- first_name: Paul T. P.
full_name: Ho, Paul T. P.
last_name: Ho
- first_name: Chih-Wei Locutus
full_name: Huang, Chih-Wei Locutus
last_name: Huang
- first_name: Patrick M.
full_name: Koch, Patrick M.
last_name: Koch
- first_name: Yu-Wei
full_name: Victor Liao, Yu-Wei
last_name: Victor Liao
- first_name: Kai-Yang
full_name: Lin, Kai-Yang
last_name: Lin
- first_name: Guo-Chin
full_name: Liu, Guo-Chin
last_name: Liu
- first_name: Hiroaki
full_name: Nishioka, Hiroaki
last_name: Nishioka
- first_name: Fu-Cheng
full_name: Wang, Fu-Cheng
last_name: Wang
- first_name: Jiun-Huei Proty
full_name: Wu, Jiun-Huei Proty
last_name: Wu
citation:
ama: Molnar SM, Umetsu K, Birkinshaw M, et al. Constraining intracluster gas models
with AMiBA13. The Astrophysical Journal. 2010;723(2):1272-1285. doi:10.1088/0004-637x/723/2/1272
apa: Molnar, S. M., Umetsu, K., Birkinshaw, M., Bryan, G., Haiman, Z., Hearn, N.,
… Wu, J.-H. P. (2010). Constraining intracluster gas models with AMiBA13. The
Astrophysical Journal. American Astronomical Society. https://doi.org/10.1088/0004-637x/723/2/1272
chicago: Molnar, Sandor M., Keiichi Umetsu, Mark Birkinshaw, Greg Bryan, Zoltán
Haiman, Nathan Hearn, Cien Shang, et al. “Constraining Intracluster Gas Models
with AMiBA13.” The Astrophysical Journal. American Astronomical Society,
2010. https://doi.org/10.1088/0004-637x/723/2/1272.
ieee: S. M. Molnar et al., “Constraining intracluster gas models with AMiBA13,”
The Astrophysical Journal, vol. 723, no. 2. American Astronomical Society,
pp. 1272–1285, 2010.
ista: Molnar SM, Umetsu K, Birkinshaw M, Bryan G, Haiman Z, Hearn N, Shang C, Ho
PTP, Huang C-WL, Koch PM, Victor Liao Y-W, Lin K-Y, Liu G-C, Nishioka H, Wang
F-C, Wu J-HP. 2010. Constraining intracluster gas models with AMiBA13. The Astrophysical
Journal. 723(2), 1272–1285.
mla: Molnar, Sandor M., et al. “Constraining Intracluster Gas Models with AMiBA13.”
The Astrophysical Journal, vol. 723, no. 2, American Astronomical Society,
2010, pp. 1272–85, doi:10.1088/0004-637x/723/2/1272.
short: S.M. Molnar, K. Umetsu, M. Birkinshaw, G. Bryan, Z. Haiman, N. Hearn, C.
Shang, P.T.P. Ho, C.-W.L. Huang, P.M. Koch, Y.-W. Victor Liao, K.-Y. Lin, G.-C.
Liu, H. Nishioka, F.-C. Wang, J.-H.P. Wu, The Astrophysical Journal 723 (2010)
1272–1285.
date_created: 2024-09-06T08:41:14Z
date_published: 2010-10-20T00:00:00Z
date_updated: 2024-09-25T10:08:14Z
day: '20'
doi: 10.1088/0004-637x/723/2/1272
extern: '1'
intvolume: ' 723'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1088/0004-637x/723/2/1272
month: '10'
oa: 1
oa_version: Published Version
page: 1272-1285
publication: The Astrophysical Journal
publication_identifier:
issn:
- 0004-637X
- 1538-4357
publication_status: published
publisher: American Astronomical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Constraining intracluster gas models with AMiBA13
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 723
year: '2010'
...
---
_id: '17697'
abstract:
- lang: eng
text: We propose counting peaks in weak lensing (WL) maps, as a function of their
height, to probe models of dark energy and to constrain cosmological parameters.
Because peaks can be identified in two-dimensional WL maps directly, they can
provide constraints that are free from potential selection effects and biases
involved in identifying and determining the masses of galaxy clusters. We have
run cosmological N-body simulations to produce WL convergence maps in three models
with different constant values of the dark energy equation of state parameter,
w=-0.8, -1, and -1.2, with a fixed normalization of the primordial power spectrum
(corresponding to present-day normalizations of sigma8=0.742, 0.798, and 0.839,
respectively). By comparing the number of WL peaks in 8 convergence bins in the
range of -0.1 < kappa < 0.2, in multiple realizations of a single simulated 3x3
degree field, we show that the first (last) pair of models can be distinguished
at the 95% (85%) confidence level. A survey with depth and area (20,000 sq. degrees),
comparable to those expected from LSST, should have a factor of approx. 50 better
parameter sensitivity. We find that relatively low-amplitude peaks (kappa = 0.03),
which typically do not correspond to a single collapsed halo along the line of
sight, account for most of this sensitivity. We study a range of smoothing scales
and source galaxy redshifts (z_s). With a fixed source galaxy density of 15/arcmin^2,
the best results are provided by the smallest scale we can reliably simulate,
1 arcminute, and z_s=2 provides substantially better sensitivity than z_s< 1.5.
article_number: '043519'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Jan M.
full_name: Kratochvil, Jan M.
last_name: Kratochvil
- first_name: Zoltán
full_name: Haiman, Zoltán
id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36
last_name: Haiman
- first_name: Morgan
full_name: May, Morgan
last_name: May
citation:
ama: Kratochvil JM, Haiman Z, May M. Probing cosmology with weak lensing peak counts.
Physical Review D. 2010;81(4). doi:10.1103/physrevd.81.043519
apa: Kratochvil, J. M., Haiman, Z., & May, M. (2010). Probing cosmology with
weak lensing peak counts. Physical Review D. American Physical Society.
https://doi.org/10.1103/physrevd.81.043519
chicago: Kratochvil, Jan M., Zoltán Haiman, and Morgan May. “Probing Cosmology with
Weak Lensing Peak Counts.” Physical Review D. American Physical Society,
2010. https://doi.org/10.1103/physrevd.81.043519.
ieee: J. M. Kratochvil, Z. Haiman, and M. May, “Probing cosmology with weak lensing
peak counts,” Physical Review D, vol. 81, no. 4. American Physical Society,
2010.
ista: Kratochvil JM, Haiman Z, May M. 2010. Probing cosmology with weak lensing
peak counts. Physical Review D. 81(4), 043519.
mla: Kratochvil, Jan M., et al. “Probing Cosmology with Weak Lensing Peak Counts.”
Physical Review D, vol. 81, no. 4, 043519, American Physical Society, 2010,
doi:10.1103/physrevd.81.043519.
short: J.M. Kratochvil, Z. Haiman, M. May, Physical Review D 81 (2010).
date_created: 2024-09-06T08:43:22Z
date_published: 2010-02-10T00:00:00Z
date_updated: 2024-09-25T11:14:37Z
day: '10'
doi: 10.1103/physrevd.81.043519
extern: '1'
external_id:
arxiv:
- '0907.0486'
intvolume: ' 81'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.0907.0486'
month: '02'
oa: 1
oa_version: Preprint
publication: Physical Review D
publication_identifier:
issn:
- 1550-7998
- 1550-2368
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Probing cosmology with weak lensing peak counts
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 81
year: '2010'
...
---
_id: '1772'
abstract:
- lang: eng
text: We present the realization of a cavity quantum electrodynamics setup in which
photons of strongly different lifetimes are engineered in different harmonic modes
of the same cavity. We achieve this in a superconducting transmission line resonator
with superconducting qubits coupled to the different modes. One cavity mode is
strongly coupled to a detection line for qubit state readout, while a second long
lifetime mode is used for photon storage and coherent quantum operations. We demonstrate
sideband-based measurement of photon coherence, generation of n photon Fock states
and the scaling of the sideband Rabi frequency with √n using a scheme that may
be extended to realize sideband-based two-qubit logic gates.
acknowledgement: This work was supported financially by the Swiss National Science
Foundation, by the EC via the EuroSQIP project and by ETH Zurich
author:
- first_name: Peter
full_name: Leek, Peter J
last_name: Leek
- first_name: Matthias
full_name: Baur, Matthias P
last_name: Baur
- first_name: Johannes M
full_name: Johannes Fink
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- first_name: R
full_name: Bianchetti, R
last_name: Bianchetti
- first_name: L.
full_name: Steffen, L. Kraig
last_name: Steffen
- first_name: Stefan
full_name: Filipp, Stefan
last_name: Filipp
- first_name: Andreas
full_name: Wallraff, Andreas
last_name: Wallraff
citation:
ama: Leek P, Baur M, Fink JM, et al. Cavity quantum electrodynamics with separate
photon storage and qubit readout modes. Physical Review Letters. 2010;104(10).
doi:10.1103/PhysRevLett.104.100504
apa: Leek, P., Baur, M., Fink, J. M., Bianchetti, R., Steffen, L., Filipp, S., &
Wallraff, A. (2010). Cavity quantum electrodynamics with separate photon storage
and qubit readout modes. Physical Review Letters. American Physical Society.
https://doi.org/10.1103/PhysRevLett.104.100504
chicago: Leek, Peter, Matthias Baur, Johannes M Fink, R Bianchetti, L. Steffen,
Stefan Filipp, and Andreas Wallraff. “Cavity Quantum Electrodynamics with Separate
Photon Storage and Qubit Readout Modes.” Physical Review Letters. American
Physical Society, 2010. https://doi.org/10.1103/PhysRevLett.104.100504.
ieee: P. Leek et al., “Cavity quantum electrodynamics with separate photon
storage and qubit readout modes,” Physical Review Letters, vol. 104, no.
10. American Physical Society, 2010.
ista: Leek P, Baur M, Fink JM, Bianchetti R, Steffen L, Filipp S, Wallraff A. 2010.
Cavity quantum electrodynamics with separate photon storage and qubit readout
modes. Physical Review Letters. 104(10).
mla: Leek, Peter, et al. “Cavity Quantum Electrodynamics with Separate Photon Storage
and Qubit Readout Modes.” Physical Review Letters, vol. 104, no. 10, American
Physical Society, 2010, doi:10.1103/PhysRevLett.104.100504.
short: P. Leek, M. Baur, J.M. Fink, R. Bianchetti, L. Steffen, S. Filipp, A. Wallraff,
Physical Review Letters 104 (2010).
date_created: 2018-12-11T11:53:55Z
date_published: 2010-03-10T00:00:00Z
date_updated: 2021-01-12T06:53:06Z
day: '10'
doi: 10.1103/PhysRevLett.104.100504
extern: 1
intvolume: ' 104'
issue: '10'
month: '03'
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '5345'
quality_controlled: 0
status: public
title: Cavity quantum electrodynamics with separate photon storage and qubit readout
modes
type: journal_article
volume: 104
year: '2010'
...
---
_id: '1773'
abstract:
- lang: eng
text: The quantum properties of electromagnetic, mechanical or other harmonic oscillators
can be revealed by investigating their strong coherent coupling to a single quantum
two level system in an approach known as cavity quantum electrodynamics (QED).
At temperatures much lower than the characteristic energy level spacing the observation
of vacuum Rabi oscillations or mode splittings with one or a few quanta asserts
the quantum nature of the oscillator. Here, we study how the classical response
of a cavity QED system emerges from the quantum one when its thermal occupation-or
effective temperature-is raised gradually over 5 orders of magnitude. In this
way we explore in detail the continuous quantum-to-classical crossover and demonstrate
how to extract effective cavity field temperatures from both spectroscopic and
time-resolved vacuum Rabi measurements.
acknowledgement: This work was supported by SNF, EuroSQIP and ETHZ. L. S. B. acknowledges
support by LPS/NSA under ARO contract No. W911NF-05-1-0365 and the NSF under grant
No. DMR-0653377
author:
- first_name: Johannes M
full_name: Johannes Fink
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- first_name: L.
full_name: Steffen, L. Kraig
last_name: Steffen
- first_name: Peter
full_name: Studer, Peter
last_name: Studer
- first_name: Lev
full_name: Bishop, Lev S
last_name: Bishop
- first_name: Matthias
full_name: Baur, Matthias P
last_name: Baur
- first_name: R
full_name: Bianchetti, R
last_name: Bianchetti
- first_name: Deniz
full_name: Bozyigit, Deniz
last_name: Bozyigit
- first_name: C
full_name: Lang, C
last_name: Lang
- first_name: Stefan
full_name: Filipp, Stefan
last_name: Filipp
- first_name: Peter
full_name: Leek, Peter J
last_name: Leek
- first_name: Andreas
full_name: Wallraff, Andreas
last_name: Wallraff
citation:
ama: Fink JM, Steffen L, Studer P, et al. Quantum-to-classical transition in cavity
quantum electrodynamics. Physical Review Letters. 2010;105(16). doi:10.1103/PhysRevLett.105.163601
apa: Fink, J. M., Steffen, L., Studer, P., Bishop, L., Baur, M., Bianchetti, R.,
… Wallraff, A. (2010). Quantum-to-classical transition in cavity quantum electrodynamics.
Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.105.163601
chicago: Fink, Johannes M, L. Steffen, Peter Studer, Lev Bishop, Matthias Baur,
R Bianchetti, Deniz Bozyigit, et al. “Quantum-to-Classical Transition in Cavity
Quantum Electrodynamics.” Physical Review Letters. American Physical Society,
2010. https://doi.org/10.1103/PhysRevLett.105.163601.
ieee: J. M. Fink et al., “Quantum-to-classical transition in cavity quantum
electrodynamics,” Physical Review Letters, vol. 105, no. 16. American Physical
Society, 2010.
ista: Fink JM, Steffen L, Studer P, Bishop L, Baur M, Bianchetti R, Bozyigit D,
Lang C, Filipp S, Leek P, Wallraff A. 2010. Quantum-to-classical transition in
cavity quantum electrodynamics. Physical Review Letters. 105(16).
mla: Fink, Johannes M., et al. “Quantum-to-Classical Transition in Cavity Quantum
Electrodynamics.” Physical Review Letters, vol. 105, no. 16, American Physical
Society, 2010, doi:10.1103/PhysRevLett.105.163601.
short: J.M. Fink, L. Steffen, P. Studer, L. Bishop, M. Baur, R. Bianchetti, D. Bozyigit,
C. Lang, S. Filipp, P. Leek, A. Wallraff, Physical Review Letters 105 (2010).
date_created: 2018-12-11T11:53:56Z
date_published: 2010-10-14T00:00:00Z
date_updated: 2021-01-12T06:53:07Z
day: '14'
doi: 10.1103/PhysRevLett.105.163601
extern: 1
intvolume: ' 105'
issue: '16'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1003.1161
month: '10'
oa: 1
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '5343'
quality_controlled: 0
status: public
title: Quantum-to-classical transition in cavity quantum electrodynamics
type: journal_article
volume: 105
year: '2010'
...
---
_id: '1774'
abstract:
- lang: eng
text: A number of superconducting qubits, such as the transmon or the phase qubit,
have an energy level structure with small anharmonicity. This allows for convenient
access of higher excited states with similar frequencies. However, special care
has to be taken to avoid unwanted higher-level populations when using short control
pulses. Here we demonstrate the preparation of arbitrary three level superposition
states using optimal control techniques in a transmon. Performing dispersive readout,
we extract the populations of all three levels of the qutrit and study the coherence
of its excited states. Finally we demonstrate full quantum state tomography of
the prepared qutrit states and evaluate the fidelities of a set of states, finding
on average 95%.
acknowledgement: This work was supported by SNF, ETHZ, the Austrian Science Foundation
(FWF), and the EU projects SOLID and GEOMDISS. A. B. is supported by NSERC, the
Alfred P. Sloan Foundation, and CIFAR
author:
- first_name: R
full_name: Bianchetti, R
last_name: Bianchetti
- first_name: Stefan
full_name: Filipp, Stefan
last_name: Filipp
- first_name: Matthias
full_name: Baur, Matthias P
last_name: Baur
- first_name: Johannes M
full_name: Johannes Fink
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- first_name: C
full_name: Lang, C
last_name: Lang
- first_name: L.
full_name: Steffen, L. Kraig
last_name: Steffen
- first_name: Maxime
full_name: Boissonneault, Maxime
last_name: Boissonneault
- first_name: Alexandre
full_name: Blais, Alexandre
last_name: Blais
- first_name: Andreas
full_name: Wallraff, Andreas
last_name: Wallraff
citation:
ama: Bianchetti R, Filipp S, Baur M, et al. Control and tomography of a three level
superconducting artificial atom. Physical Review Letters. 2010;105(22).
doi:10.1103/PhysRevLett.105.223601
apa: Bianchetti, R., Filipp, S., Baur, M., Fink, J. M., Lang, C., Steffen, L., …
Wallraff, A. (2010). Control and tomography of a three level superconducting artificial
atom. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.105.223601
chicago: Bianchetti, R, Stefan Filipp, Matthias Baur, Johannes M Fink, C Lang, L.
Steffen, Maxime Boissonneault, Alexandre Blais, and Andreas Wallraff. “Control
and Tomography of a Three Level Superconducting Artificial Atom.” Physical
Review Letters. American Physical Society, 2010. https://doi.org/10.1103/PhysRevLett.105.223601.
ieee: R. Bianchetti et al., “Control and tomography of a three level superconducting
artificial atom,” Physical Review Letters, vol. 105, no. 22. American Physical
Society, 2010.
ista: Bianchetti R, Filipp S, Baur M, Fink JM, Lang C, Steffen L, Boissonneault
M, Blais A, Wallraff A. 2010. Control and tomography of a three level superconducting
artificial atom. Physical Review Letters. 105(22).
mla: Bianchetti, R., et al. “Control and Tomography of a Three Level Superconducting
Artificial Atom.” Physical Review Letters, vol. 105, no. 22, American Physical
Society, 2010, doi:10.1103/PhysRevLett.105.223601.
short: R. Bianchetti, S. Filipp, M. Baur, J.M. Fink, C. Lang, L. Steffen, M. Boissonneault,
A. Blais, A. Wallraff, Physical Review Letters 105 (2010).
date_created: 2018-12-11T11:53:56Z
date_published: 2010-11-24T00:00:00Z
date_updated: 2021-01-12T06:53:07Z
day: '24'
doi: 10.1103/PhysRevLett.105.223601
extern: 1
intvolume: ' 105'
issue: '22'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1004.5504
month: '11'
oa: 1
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '5341'
quality_controlled: 0
status: public
title: Control and tomography of a three level superconducting artificial atom
type: journal_article
volume: 105
year: '2010'
...
---
_id: '7703'
abstract:
- lang: eng
text: By combining gene expression profiling with image registration, Tomer et al.
(2010) find that the mushroom body of the segmented worm Platynereis dumerilii
shares many features with the mammalian cerebral cortex. The authors propose that
the mushroom body and cortex evolved from the same structure in the common ancestor
of vertebrates and invertebrates.
article_processing_charge: No
article_type: original
author:
- first_name: Lora Beatrice Jaeger
full_name: Sweeney, Lora Beatrice Jaeger
id: 56BE8254-C4F0-11E9-8E45-0B23E6697425
last_name: Sweeney
orcid: 0000-0001-9242-5601
- first_name: Liqun
full_name: Luo, Liqun
last_name: Luo
citation:
ama: 'Sweeney LB, Luo L. ‘Fore brain: A hint of the ancestral cortex. Cell.
2010;142(5):679-681. doi:10.1016/j.cell.2010.08.024'
apa: 'Sweeney, L. B., & Luo, L. (2010). ‘Fore brain: A hint of the ancestral
cortex. Cell. Elsevier. https://doi.org/10.1016/j.cell.2010.08.024'
chicago: 'Sweeney, Lora B., and Liqun Luo. “‘Fore Brain: A Hint of the Ancestral
Cortex.” Cell. Elsevier, 2010. https://doi.org/10.1016/j.cell.2010.08.024.'
ieee: 'L. B. Sweeney and L. Luo, “‘Fore brain: A hint of the ancestral cortex,”
Cell, vol. 142, no. 5. Elsevier, pp. 679–681, 2010.'
ista: 'Sweeney LB, Luo L. 2010. ‘Fore brain: A hint of the ancestral cortex. Cell.
142(5), 679–681.'
mla: 'Sweeney, Lora B., and Liqun Luo. “‘Fore Brain: A Hint of the Ancestral Cortex.”
Cell, vol. 142, no. 5, Elsevier, 2010, pp. 679–81, doi:10.1016/j.cell.2010.08.024.'
short: L.B. Sweeney, L. Luo, Cell 142 (2010) 679–681.
date_created: 2020-04-30T10:36:52Z
date_published: 2010-09-03T00:00:00Z
date_updated: 2024-01-31T10:14:59Z
day: '03'
doi: 10.1016/j.cell.2010.08.024
extern: '1'
intvolume: ' 142'
issue: '5'
language:
- iso: eng
month: '09'
oa_version: None
page: 679-681
publication: Cell
publication_identifier:
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: '‘Fore brain: A hint of the ancestral cortex'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 142
year: '2010'
...
---
_id: '8472'
abstract:
- lang: eng
text: Characterization of protein dynamics by solid-state NMR spectroscopy requires
robust and accurate measurement protocols, which are not yet fully developed.
In this study, we investigate the backbone dynamics of microcrystalline ubiquitin
using different approaches. A rotational-echo double-resonance type (REDOR-type)
methodology allows one to accurately measure 1H−15N order parameters in highly
deuterated samples. We show that the systematic errors in the REDOR experiment
are as low as 1% or even less, giving access to accurate data for the amplitudes
of backbone mobility. Combining such dipolar-coupling-derived order parameters
with autocorrelated and cross-correlated 15N relaxation rates, we are able to
quantitate amplitudes and correlation times of backbone dynamics on picosecond
and nanosecond time scales in a residue-resolved manner. While the mobility on
picosecond time scales appears to have rather uniform amplitude throughout the
protein, we unambiguously identify and quantitate nanosecond mobility with order
parameters S2 as low as 0.8 in some regions of the protein, where nanosecond dynamics
has also been revealed in solution state. The methodology used here, a combination
of accurate dipolar-coupling measurements and different relaxation parameters,
yields details about dynamics on different time scales and can be applied to solid
protein samples such as amyloid fibrils or membrane proteins.
article_processing_charge: No
article_type: original
author:
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Beat H.
full_name: Meier, Beat H.
last_name: Meier
- first_name: Matthias
full_name: Ernst, Matthias
last_name: Ernst
citation:
ama: Schanda P, Meier BH, Ernst M. Quantitative analysis of protein backbone dynamics
in microcrystalline ubiquitin by solid-state NMR spectroscopy. Journal of the
American Chemical Society. 2010;132(45):15957-15967. doi:10.1021/ja100726a
apa: Schanda, P., Meier, B. H., & Ernst, M. (2010). Quantitative analysis of
protein backbone dynamics in microcrystalline ubiquitin by solid-state NMR spectroscopy.
Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/ja100726a
chicago: Schanda, Paul, Beat H. Meier, and Matthias Ernst. “Quantitative Analysis
of Protein Backbone Dynamics in Microcrystalline Ubiquitin by Solid-State NMR
Spectroscopy.” Journal of the American Chemical Society. American Chemical
Society, 2010. https://doi.org/10.1021/ja100726a.
ieee: P. Schanda, B. H. Meier, and M. Ernst, “Quantitative analysis of protein backbone
dynamics in microcrystalline ubiquitin by solid-state NMR spectroscopy,” Journal
of the American Chemical Society, vol. 132, no. 45. American Chemical Society,
pp. 15957–15967, 2010.
ista: Schanda P, Meier BH, Ernst M. 2010. Quantitative analysis of protein backbone
dynamics in microcrystalline ubiquitin by solid-state NMR spectroscopy. Journal
of the American Chemical Society. 132(45), 15957–15967.
mla: Schanda, Paul, et al. “Quantitative Analysis of Protein Backbone Dynamics in
Microcrystalline Ubiquitin by Solid-State NMR Spectroscopy.” Journal of the
American Chemical Society, vol. 132, no. 45, American Chemical Society, 2010,
pp. 15957–67, doi:10.1021/ja100726a.
short: P. Schanda, B.H. Meier, M. Ernst, Journal of the American Chemical Society
132 (2010) 15957–15967.
date_created: 2020-09-18T10:11:13Z
date_published: 2010-10-26T00:00:00Z
date_updated: 2021-01-12T08:19:30Z
day: '26'
doi: 10.1021/ja100726a
extern: '1'
intvolume: ' 132'
issue: '45'
language:
- iso: eng
month: '10'
oa_version: None
page: 15957-15967
publication: Journal of the American Chemical Society
publication_identifier:
issn:
- 0002-7863
- 1520-5126
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
status: public
title: Quantitative analysis of protein backbone dynamics in microcrystalline ubiquitin
by solid-state NMR spectroscopy
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 132
year: '2010'
...
---
_id: '8473'
abstract:
- lang: eng
text: β2-microglobulin (β2m), the light chain of class I major histocompatibility
complex, is responsible for the dialysis-related amyloidosis and, in patients
undergoing long term dialysis, the full-length and chemically unmodified β2m converts
into amyloid fibrils. The protein, belonging to the immunoglobulin superfamily,
in common to other members of this family, experiences during its folding a long-lived
intermediate associated to the trans-to-cis isomerization of Pro-32 that has been
addressed as the precursor of the amyloid fibril formation. In this respect, previous
studies on the W60G β2m mutant, showing that the lack of Trp-60 prevents fibril
formation in mild aggregating condition, prompted us to reinvestigate the refolding
kinetics of wild type and W60G β2m at atomic resolution by real-time NMR. The
analysis, conducted at ambient temperature by the band selective flip angle short
transient real-time two-dimensional NMR techniques and probing the β2m states
every 15 s, revealed a more complex folding energy landscape than previously reported
for wild type β2m, involving more than a single intermediate species, and shedding
new light into the fibrillogenic pathway. Moreover, a significant difference in
the kinetic scheme previously characterized by optical spectroscopic methods was
discovered for the W60G β2m mutant.
article_processing_charge: No
article_type: original
author:
- first_name: Alessandra
full_name: Corazza, Alessandra
last_name: Corazza
- first_name: Enrico
full_name: Rennella, Enrico
last_name: Rennella
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Maria Chiara
full_name: Mimmi, Maria Chiara
last_name: Mimmi
- first_name: Thomas
full_name: Cutuil, Thomas
last_name: Cutuil
- first_name: Sara
full_name: Raimondi, Sara
last_name: Raimondi
- first_name: Sofia
full_name: Giorgetti, Sofia
last_name: Giorgetti
- first_name: Federico
full_name: Fogolari, Federico
last_name: Fogolari
- first_name: Paolo
full_name: Viglino, Paolo
last_name: Viglino
- first_name: Lucio
full_name: Frydman, Lucio
last_name: Frydman
- first_name: Maayan
full_name: Gal, Maayan
last_name: Gal
- first_name: Vittorio
full_name: Bellotti, Vittorio
last_name: Bellotti
- first_name: Bernhard
full_name: Brutscher, Bernhard
last_name: Brutscher
- first_name: Gennaro
full_name: Esposito, Gennaro
last_name: Esposito
citation:
ama: Corazza A, Rennella E, Schanda P, et al. Native-unlike long-lived intermediates
along the folding pathway of the amyloidogenic protein β2-Microglobulin revealed
by real-time two-dimensional NMR. Journal of Biological Chemistry. 2010;285(8):5827-5835.
doi:10.1074/jbc.m109.061168
apa: Corazza, A., Rennella, E., Schanda, P., Mimmi, M. C., Cutuil, T., Raimondi,
S., … Esposito, G. (2010). Native-unlike long-lived intermediates along the folding
pathway of the amyloidogenic protein β2-Microglobulin revealed by real-time two-dimensional
NMR. Journal of Biological Chemistry. American Society for Biochemistry
& Molecular Biology. https://doi.org/10.1074/jbc.m109.061168
chicago: Corazza, Alessandra, Enrico Rennella, Paul Schanda, Maria Chiara Mimmi,
Thomas Cutuil, Sara Raimondi, Sofia Giorgetti, et al. “Native-Unlike Long-Lived
Intermediates along the Folding Pathway of the Amyloidogenic Protein Β2-Microglobulin
Revealed by Real-Time Two-Dimensional NMR.” Journal of Biological Chemistry.
American Society for Biochemistry & Molecular Biology, 2010. https://doi.org/10.1074/jbc.m109.061168.
ieee: A. Corazza et al., “Native-unlike long-lived intermediates along the
folding pathway of the amyloidogenic protein β2-Microglobulin revealed by real-time
two-dimensional NMR,” Journal of Biological Chemistry, vol. 285, no. 8.
American Society for Biochemistry & Molecular Biology, pp. 5827–5835, 2010.
ista: Corazza A, Rennella E, Schanda P, Mimmi MC, Cutuil T, Raimondi S, Giorgetti
S, Fogolari F, Viglino P, Frydman L, Gal M, Bellotti V, Brutscher B, Esposito
G. 2010. Native-unlike long-lived intermediates along the folding pathway of the
amyloidogenic protein β2-Microglobulin revealed by real-time two-dimensional NMR.
Journal of Biological Chemistry. 285(8), 5827–5835.
mla: Corazza, Alessandra, et al. “Native-Unlike Long-Lived Intermediates along the
Folding Pathway of the Amyloidogenic Protein Β2-Microglobulin Revealed by Real-Time
Two-Dimensional NMR.” Journal of Biological Chemistry, vol. 285, no. 8,
American Society for Biochemistry & Molecular Biology, 2010, pp. 5827–35,
doi:10.1074/jbc.m109.061168.
short: A. Corazza, E. Rennella, P. Schanda, M.C. Mimmi, T. Cutuil, S. Raimondi,
S. Giorgetti, F. Fogolari, P. Viglino, L. Frydman, M. Gal, V. Bellotti, B. Brutscher,
G. Esposito, Journal of Biological Chemistry 285 (2010) 5827–5835.
date_created: 2020-09-18T10:11:23Z
date_published: 2010-02-19T00:00:00Z
date_updated: 2021-01-12T08:19:31Z
day: '19'
doi: 10.1074/jbc.m109.061168
extern: '1'
intvolume: ' 285'
issue: '8'
keyword:
- Cell Biology
- Biochemistry
- Molecular Biology
language:
- iso: eng
month: '02'
oa_version: None
page: 5827-5835
publication: Journal of Biological Chemistry
publication_identifier:
issn:
- 0021-9258
- 1083-351X
publication_status: published
publisher: American Society for Biochemistry & Molecular Biology
quality_controlled: '1'
status: public
title: Native-unlike long-lived intermediates along the folding pathway of the amyloidogenic
protein β2-Microglobulin revealed by real-time two-dimensional NMR
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 285
year: '2010'
...
---
_id: '8506'
article_processing_charge: No
author:
- first_name: Brian R.
full_name: Hunt, Brian R.
last_name: Hunt
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
citation:
ama: 'Hunt BR, Kaloshin V. Prevalence. In: Handbook of Dynamical Systems.
Vol 3. Elsevier; 2010:43-87. doi:10.1016/s1874-575x(10)00310-3'
apa: Hunt, B. R., & Kaloshin, V. (2010). Prevalence. In Handbook of Dynamical
Systems (Vol. 3, pp. 43–87). Elsevier. https://doi.org/10.1016/s1874-575x(10)00310-3
chicago: Hunt, Brian R., and Vadim Kaloshin. “Prevalence.” In Handbook of Dynamical
Systems, 3:43–87. Elsevier, 2010. https://doi.org/10.1016/s1874-575x(10)00310-3.
ieee: B. R. Hunt and V. Kaloshin, “Prevalence,” in Handbook of Dynamical Systems,
vol. 3, Elsevier, 2010, pp. 43–87.
ista: 'Hunt BR, Kaloshin V. 2010.Prevalence. In: Handbook of Dynamical Systems.
vol. 3, 43–87.'
mla: Hunt, Brian R., and Vadim Kaloshin. “Prevalence.” Handbook of Dynamical
Systems, vol. 3, Elsevier, 2010, pp. 43–87, doi:10.1016/s1874-575x(10)00310-3.
short: B.R. Hunt, V. Kaloshin, in:, Handbook of Dynamical Systems, Elsevier, 2010,
pp. 43–87.
date_created: 2020-09-18T10:47:48Z
date_published: 2010-01-01T00:00:00Z
date_updated: 2021-01-12T08:19:45Z
day: '01'
doi: 10.1016/s1874-575x(10)00310-3
extern: '1'
intvolume: ' 3'
language:
- iso: eng
month: '01'
oa_version: None
page: 43-87
publication: Handbook of Dynamical Systems
publication_identifier:
isbn:
- '9780444531414'
issn:
- 1874-575X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Prevalence
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2010'
...
---
_id: '8507'
abstract:
- lang: eng
text: "We study a Cr nearly integrable Hamiltonian system defined on \U0001D54B3
× ℝ3. Let and µΣ1 be the restriction of Lebesgue measure on \U0001D54B3 × ℝ3
to ∑. We prove there is a perturbation , and an orbit (q(t), p(t)): ℝ → \U0001D54B3
× ℝ3 of the Hamiltonian equation such that ."
article_processing_charge: No
author:
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: KE
full_name: ZHANG, KE
last_name: ZHANG
- first_name: YONG
full_name: ZHENG, YONG
last_name: ZHENG
citation:
ama: 'Kaloshin V, ZHANG K, ZHENG Y. Almost dense orbit on energy surface. In: XVIth
International Congress on Mathematical Physics. World Scientific; 2010:314-322.
doi:10.1142/9789814304634_0017'
apa: 'Kaloshin, V., ZHANG, K., & ZHENG, Y. (2010). Almost dense orbit on energy
surface. In XVIth International Congress on Mathematical Physics (pp. 314–322).
Prague, Czech Republic: World Scientific. https://doi.org/10.1142/9789814304634_0017'
chicago: Kaloshin, Vadim, KE ZHANG, and YONG ZHENG. “Almost Dense Orbit on Energy
Surface.” In XVIth International Congress on Mathematical Physics, 314–22.
World Scientific, 2010. https://doi.org/10.1142/9789814304634_0017.
ieee: V. Kaloshin, K. ZHANG, and Y. ZHENG, “Almost dense orbit on energy surface,”
in XVIth International Congress on Mathematical Physics, Prague, Czech
Republic, 2010, pp. 314–322.
ista: Kaloshin V, ZHANG K, ZHENG Y. 2010. Almost dense orbit on energy surface.
XVIth International Congress on Mathematical Physics. International Congress on
Mathematical Physics, 314–322.
mla: Kaloshin, Vadim, et al. “Almost Dense Orbit on Energy Surface.” XVIth International
Congress on Mathematical Physics, World Scientific, 2010, pp. 314–22, doi:10.1142/9789814304634_0017.
short: V. Kaloshin, K. ZHANG, Y. ZHENG, in:, XVIth International Congress on Mathematical
Physics, World Scientific, 2010, pp. 314–322.
conference:
end_date: 2009-08-08
location: Prague, Czech Republic
name: International Congress on Mathematical Physics
start_date: 2009-08-03
date_created: 2020-09-18T10:47:56Z
date_published: 2010-03-01T00:00:00Z
date_updated: 2021-01-12T08:19:46Z
day: '01'
doi: 10.1142/9789814304634_0017
extern: '1'
language:
- iso: eng
month: '03'
oa_version: None
page: 314-322
publication: XVIth International Congress on Mathematical Physics
publication_identifier:
isbn:
- '9789814304627'
- '9789814304634'
publication_status: published
publisher: World Scientific
quality_controlled: '1'
status: public
title: Almost dense orbit on energy surface
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '857'
abstract:
- lang: eng
text: 'The need to maintain the structural and functional integrity of an evolving
protein severely restricts the repertoire of acceptable amino-acid substitutions.
However, it is not known whether these restrictions impose a global limit on how
far homologous protein sequences can diverge from each other. Here we explore
the limits of protein evolution using sequence divergence data. We formulate a
computational approach to study the rate of divergence of distant protein sequences
and measure this rate for ancient proteins, those that were present in the last
universal common ancestor. We show that ancient proteins are still diverging from
each other, indicating an ongoing expansion of the protein sequence universe.
The slow rate of this divergence is imposed by the sparseness of functional protein
sequences in sequence space and the ruggedness of the protein fitness landscape:
98 per cent of sites cannot accept an amino-acid substitution at any given moment
but a vast majority of all sites may eventually be permitted to evolve when other,
compensatory, changes occur. Thus, 3.5 × 10 9 yr has not been enough to reach
the limit of divergent evolution of proteins, and for most proteins the limit
of sequence similarity imposed by common function may not exceed that of random
sequences.'
acknowledgement: |
We thank E. Koonin, Y. Wolf, A. Lobkovsky, D. Petrov, D. Ivankov, J. Sharpe, B. Lehner, Y. Jaeger, P. Vlasov, M. Ptitsyn and M. Roytberg for discussions and A. Kondrashov for extensive feedback on our manuscript. We thank D. Tawfik for inspiring us to start the investigation of the functional limits in sequence space.
author:
- first_name: Inna
full_name: Povolotskaya, Inna
last_name: Povolotskaya
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Povolotskaya I, Kondrashov F. Sequence space and the ongoing expansion of the
protein universe. Nature. 2010;465(7300):922-926. doi:10.1038/nature09105
apa: Povolotskaya, I., & Kondrashov, F. (2010). Sequence space and the ongoing
expansion of the protein universe. Nature. Nature Publishing Group. https://doi.org/10.1038/nature09105
chicago: Povolotskaya, Inna, and Fyodor Kondrashov. “Sequence Space and the Ongoing
Expansion of the Protein Universe.” Nature. Nature Publishing Group, 2010.
https://doi.org/10.1038/nature09105.
ieee: I. Povolotskaya and F. Kondrashov, “Sequence space and the ongoing expansion
of the protein universe,” Nature, vol. 465, no. 7300. Nature Publishing
Group, pp. 922–926, 2010.
ista: Povolotskaya I, Kondrashov F. 2010. Sequence space and the ongoing expansion
of the protein universe. Nature. 465(7300), 922–926.
mla: Povolotskaya, Inna, and Fyodor Kondrashov. “Sequence Space and the Ongoing
Expansion of the Protein Universe.” Nature, vol. 465, no. 7300, Nature
Publishing Group, 2010, pp. 922–26, doi:10.1038/nature09105.
short: I. Povolotskaya, F. Kondrashov, Nature 465 (2010) 922–926.
date_created: 2018-12-11T11:48:52Z
date_published: 2010-06-17T00:00:00Z
date_updated: 2021-01-12T08:20:05Z
day: '17'
doi: 10.1038/nature09105
extern: 1
intvolume: ' 465'
issue: '7300'
month: '06'
page: 922 - 926
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '6791'
quality_controlled: 0
status: public
title: Sequence space and the ongoing expansion of the protein universe
type: journal_article
volume: 465
year: '2010'
...
---
_id: '862'
abstract:
- lang: eng
text: A long-standing controversy in evolutionary biology is whether or not evolving
lineages can cross valleys on the fitness landscape that correspond to low-fitness
genotypes, which can eventually enable them to reach isolated fitness peaks1-9.
Here we study the fitness landscapes traversed by switches between different AU
and GC Watson-Crick nucleotide pairs at complementary sites of mitochondrial transfer
RNA stem regions in 83 mammalian species. We find that such Watson-Crick switches
occur 30-40 times more slowly than pairs of neutral substitutions, and that alleles
corresponding to GU and AC non-Watson-Crick intermediate states segregate within
human populations at low frequencies, similar to those of non-synonymous alleles.
Substitutions leading to a Watson-Crick switch are strongly correlated, especially
in mitochondrial tRNAs encoded on the GT-nucleotide-rich strand of the mitochondrial
genome. Using these data we estimate that a typical Watson-Crick switch involves
crossing a fitness valley of a depth of about 10-3 or even about 10-2, with AC
intermediates being slightly more deleterious than GU intermediates. This compensatory
evolution must proceed through rare intermediate variants that never reach fixation.
The ubiquitous nature of compensatory evolution in mammalian mitochondrial tRNAs
and other molecules implies that simultaneous fixation of two alleles that are
individually deleterious may be a common phenomenon at the molecular level.
acknowledgement: We thank H. Innan, M. Laessig, R. Guigo, I. Povolotskaya, D. Ivankov
and M. Breen for thoughtful discussions and critical reading of the manuscript.
author:
- first_name: Margarita
full_name: Meer, Margarita V
last_name: Meer
- first_name: Alexey
full_name: Kondrashov, Alexey S
last_name: Kondrashov
- first_name: Yael
full_name: Artzy-Randrup, Yael
last_name: Artzy Randrup
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Meer M, Kondrashov A, Artzy Randrup Y, Kondrashov F. Compensatory evolution
in mitochondrial tRNAs navigates valleys of low fitness. Nature. 2010;464(7286):279-282.
doi:10.1038/nature08691
apa: Meer, M., Kondrashov, A., Artzy Randrup, Y., & Kondrashov, F. (2010). Compensatory
evolution in mitochondrial tRNAs navigates valleys of low fitness. Nature.
Nature Publishing Group. https://doi.org/10.1038/nature08691
chicago: Meer, Margarita, Alexey Kondrashov, Yael Artzy Randrup, and Fyodor Kondrashov.
“Compensatory Evolution in Mitochondrial TRNAs Navigates Valleys of Low Fitness.”
Nature. Nature Publishing Group, 2010. https://doi.org/10.1038/nature08691.
ieee: M. Meer, A. Kondrashov, Y. Artzy Randrup, and F. Kondrashov, “Compensatory
evolution in mitochondrial tRNAs navigates valleys of low fitness,” Nature,
vol. 464, no. 7286. Nature Publishing Group, pp. 279–282, 2010.
ista: Meer M, Kondrashov A, Artzy Randrup Y, Kondrashov F. 2010. Compensatory evolution
in mitochondrial tRNAs navigates valleys of low fitness. Nature. 464(7286), 279–282.
mla: Meer, Margarita, et al. “Compensatory Evolution in Mitochondrial TRNAs Navigates
Valleys of Low Fitness.” Nature, vol. 464, no. 7286, Nature Publishing
Group, 2010, pp. 279–82, doi:10.1038/nature08691.
short: M. Meer, A. Kondrashov, Y. Artzy Randrup, F. Kondrashov, Nature 464 (2010)
279–282.
date_created: 2018-12-11T11:48:54Z
date_published: 2010-03-11T00:00:00Z
date_updated: 2021-01-12T08:20:20Z
day: '11'
doi: 10.1038/nature08691
extern: 1
intvolume: ' 464'
issue: '7286'
month: '03'
page: 279 - 282
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '6784'
quality_controlled: 0
status: public
title: Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness
type: journal_article
volume: 464
year: '2010'
...