---
_id: '5771'
abstract:
- lang: eng
text: Retroviruses such as HIV-1 assemble and bud from infected cells in an immature,
non-infectious form. Subsequently, a series of proteolytic cleavages catalysed
by the viral protease leads to a spectacular structural rearrangement of the viral
particle into a mature form that is competent to fuse with and infect a new cell.
Maturation involves changes in the structures of protein domains, in the interactions
between protein domains, and in the architecture of the viral components that
are assembled by the proteins. Tight control of proteolytic cleavages at different
sites is required for successful maturation, and the process is a major target
of antiretroviral drugs. Here we will describe what is known about the structures
of immature and mature retrovirus particles, and about the maturation process
by which one transitions into the other. Despite a wealth of available data, fundamental
questions about retroviral maturation remain unanswered.
author:
- first_name: Simone
full_name: Mattei, Simone
last_name: Mattei
- first_name: Florian
full_name: Schur, Florian
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: John AG
full_name: Briggs, John AG
last_name: Briggs
citation:
ama: Mattei S, Schur FK, Briggs JA. Retrovirus maturation—an extraordinary structural
transformation. Current Opinion in Virology. 2016;18(6):27-35. doi:10.1016/j.coviro.2016.02.008
apa: Mattei, S., Schur, F. K., & Briggs, J. A. (2016). Retrovirus maturation—an
extraordinary structural transformation. Current Opinion in Virology. Elsevier.
https://doi.org/10.1016/j.coviro.2016.02.008
chicago: Mattei, Simone, Florian KM Schur, and John AG Briggs. “Retrovirus Maturation—an
Extraordinary Structural Transformation.” Current Opinion in Virology.
Elsevier, 2016. https://doi.org/10.1016/j.coviro.2016.02.008.
ieee: S. Mattei, F. K. Schur, and J. A. Briggs, “Retrovirus maturation—an extraordinary
structural transformation,” Current Opinion in Virology, vol. 18, no. 6.
Elsevier, pp. 27–35, 2016.
ista: Mattei S, Schur FK, Briggs JA. 2016. Retrovirus maturation—an extraordinary
structural transformation. Current Opinion in Virology. 18(6), 27–35.
mla: Mattei, Simone, et al. “Retrovirus Maturation—an Extraordinary Structural Transformation.”
Current Opinion in Virology, vol. 18, no. 6, Elsevier, 2016, pp. 27–35,
doi:10.1016/j.coviro.2016.02.008.
short: S. Mattei, F.K. Schur, J.A. Briggs, Current Opinion in Virology 18 (2016)
27–35.
date_created: 2018-12-20T21:13:59Z
date_published: 2016-03-22T00:00:00Z
date_updated: 2021-01-12T08:03:22Z
day: '22'
ddc:
- '570'
doi: 10.1016/j.coviro.2016.02.008
extern: '1'
file:
- access_level: open_access
checksum: 320939d28ebd1adfb122338019892508
content_type: application/pdf
creator: dernst
date_created: 2019-01-09T13:05:44Z
date_updated: 2020-07-14T12:47:11Z
file_id: '5812'
file_name: 2016_CurrentOpinion_Mattei.pdf
file_size: 1773842
relation: main_file
file_date_updated: 2020-07-14T12:47:11Z
fulldoi: https://doi.org/10.1016/j.coviro.2016.02.008
has_accepted_license: '1'
intvolume: ' 18'
issue: '6'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 27-35
publication: Current Opinion in Virology
publication_identifier:
issn:
- 1879-6257
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Retrovirus maturation—an extraordinary structural transformation
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2016'
...
---
_id: '5805'
abstract:
- lang: eng
text: Discretization of sphere in the integer space follows a particular discretization
scheme, which, in principle, conforms to some topological model. This eventually
gives rise to interesting topological properties of a discrete spherical surface,
which need to be investigated for its analytical characterization. This paper
presents some novel results on the local topological properties of the naive model
of discrete sphere. They follow from the bijection of each quadraginta octant
of naive sphere with its projection map called f -map on the corresponding functional
plane and from the characterization of certain jumps in the f-map. As an application,
we have shown how these properties can be used in designing an efficient reconstruction
algorithm for a naive spherical surface from an input voxel set when it is sparse
or noisy.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Nabhasmita
full_name: Sen, Nabhasmita
last_name: Sen
- first_name: Ranita
full_name: Biswas, Ranita
id: 3C2B033E-F248-11E8-B48F-1D18A9856A87
last_name: Biswas
orcid: 0000-0002-5372-7890
- first_name: Partha
full_name: Bhowmick, Partha
last_name: Bhowmick
citation:
ama: 'Sen N, Biswas R, Bhowmick P. On some local topological properties of naive
discrete sphere. In: Computational Topology in Image Context. Vol 9667.
Cham: Springer Nature; 2016:253-264. doi:10.1007/978-3-319-39441-1_23'
apa: 'Sen, N., Biswas, R., & Bhowmick, P. (2016). On some local topological
properties of naive discrete sphere. In Computational Topology in Image Context
(Vol. 9667, pp. 253–264). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-39441-1_23'
chicago: 'Sen, Nabhasmita, Ranita Biswas, and Partha Bhowmick. “On Some Local Topological
Properties of Naive Discrete Sphere.” In Computational Topology in Image Context,
9667:253–64. Cham: Springer Nature, 2016. https://doi.org/10.1007/978-3-319-39441-1_23.'
ieee: 'N. Sen, R. Biswas, and P. Bhowmick, “On some local topological properties
of naive discrete sphere,” in Computational Topology in Image Context,
vol. 9667, Cham: Springer Nature, 2016, pp. 253–264.'
ista: 'Sen N, Biswas R, Bhowmick P. 2016.On some local topological properties of
naive discrete sphere. In: Computational Topology in Image Context. LNCS, vol.
9667, 253–264.'
mla: Sen, Nabhasmita, et al. “On Some Local Topological Properties of Naive Discrete
Sphere.” Computational Topology in Image Context, vol. 9667, Springer Nature,
2016, pp. 253–64, doi:10.1007/978-3-319-39441-1_23.
short: N. Sen, R. Biswas, P. Bhowmick, in:, Computational Topology in Image Context,
Springer Nature, Cham, 2016, pp. 253–264.
conference:
end_date: 2016-06-17
location: Marseille, France
name: 'CTIC: Computational Topology in Image Context'
start_date: 2016-06-15
date_created: 2019-01-08T20:44:24Z
date_published: 2016-06-02T00:00:00Z
date_updated: 2022-01-28T08:01:22Z
day: '02'
department:
- _id: HeEd
doi: 10.1007/978-3-319-39441-1_23
extern: '1'
fulldoi: https://doi.org/10.1007/978-3-319-39441-1_23
intvolume: ' 9667'
language:
- iso: eng
month: '06'
oa_version: None
page: 253-264
place: Cham
publication: Computational Topology in Image Context
publication_identifier:
eisbn:
- 978-3-319-39441-1
eissn:
- 1611-3349
isbn:
- 978-3-319-39440-4
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: On some local topological properties of naive discrete sphere
type: book_chapter
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 9667
year: '2016'
...
---
_id: '5806'
abstract:
- lang: eng
text: Although the concept of functional plane for naive plane is studied and reported
in the literature in great detail, no similar study is yet found for naive sphere.
This article exposes the first study in this line, opening up further prospects
of analyzing the topological properties of sphere in the discrete space. We show
that each quadraginta octant Q of a naive sphere forms a bijection with its projected
pixel set on a unique coordinate plane, which thereby serves as the functional
plane of Q, and hence gives rise to merely mono-jumps during back projection.
The other two coordinate planes serve as para-functional and dia-functional planes
for Q, as the former is ‘mono-jumping’ but not bijective, whereas the latter holds
neither of the two. Owing to this, the quadraginta octants form symmetry groups
and subgroups with equivalent jump conditions. We also show a potential application
in generating a special class of discrete 3D circles based on back projection
and jump bridging by Steiner voxels. A circle in this class possesses 4-symmetry,
uniqueness, and bounded distance from the underlying real sphere and real plane.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Ranita
full_name: Biswas, Ranita
id: 3C2B033E-F248-11E8-B48F-1D18A9856A87
last_name: Biswas
orcid: 0000-0002-5372-7890
- first_name: Partha
full_name: Bhowmick, Partha
last_name: Bhowmick
citation:
ama: 'Biswas R, Bhowmick P. On functionality of quadraginta octants of naive sphere
with application to circle drawing. In: Discrete Geometry for Computer Imagery.
Vol 9647. Cham: Springer Nature; 2016:256-267. doi:10.1007/978-3-319-32360-2_20'
apa: 'Biswas, R., & Bhowmick, P. (2016). On functionality of quadraginta octants
of naive sphere with application to circle drawing. In Discrete Geometry for
Computer Imagery (Vol. 9647, pp. 256–267). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-32360-2_20'
chicago: 'Biswas, Ranita, and Partha Bhowmick. “On Functionality of Quadraginta
Octants of Naive Sphere with Application to Circle Drawing.” In Discrete Geometry
for Computer Imagery, 9647:256–67. Cham: Springer Nature, 2016. https://doi.org/10.1007/978-3-319-32360-2_20.'
ieee: R. Biswas and P. Bhowmick, “On functionality of quadraginta octants of naive
sphere with application to circle drawing,” in Discrete Geometry for Computer
Imagery, Nantes, France, 2016, vol. 9647, pp. 256–267.
ista: 'Biswas R, Bhowmick P. 2016. On functionality of quadraginta octants of naive
sphere with application to circle drawing. Discrete Geometry for Computer Imagery.
DGCI: International Conference on Discrete Geometry for Computer Imagery, LNCS,
vol. 9647, 256–267.'
mla: Biswas, Ranita, and Partha Bhowmick. “On Functionality of Quadraginta Octants
of Naive Sphere with Application to Circle Drawing.” Discrete Geometry for
Computer Imagery, vol. 9647, Springer Nature, 2016, pp. 256–67, doi:10.1007/978-3-319-32360-2_20.
short: R. Biswas, P. Bhowmick, in:, Discrete Geometry for Computer Imagery, Springer
Nature, Cham, 2016, pp. 256–267.
conference:
end_date: 2016-04-20
location: Nantes, France
name: 'DGCI: International Conference on Discrete Geometry for Computer Imagery'
start_date: 2016-04-18
date_created: 2019-01-08T20:44:37Z
date_published: 2016-04-09T00:00:00Z
date_updated: 2022-01-28T08:10:11Z
day: '09'
department:
- _id: HeEd
doi: 10.1007/978-3-319-32360-2_20
extern: '1'
fulldoi: https://doi.org/10.1007/978-3-319-32360-2_20
intvolume: ' 9647'
language:
- iso: eng
month: '04'
oa_version: None
page: 256-267
place: Cham
publication: Discrete Geometry for Computer Imagery
publication_identifier:
eisbn:
- 978-3-319-32360-2
isbn:
- 978-3-319-32359-6
issn:
- 0302-9743
- 1611-3349
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: On functionality of quadraginta octants of naive sphere with application to
circle drawing
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 9647
year: '2016'
...
---
_id: '5809'
abstract:
- lang: eng
text: A discrete spherical circle is a topologically well-connected 3D circle in
the integer space, which belongs to a discrete sphere as well as a discrete plane.
It is one of the most important 3D geometric primitives, but has not possibly
yet been studied up to its merit. This paper is a maiden exposition of some of
its elementary properties, which indicates a sense of its profound theoretical
prospects in the framework of digital geometry. We have shown how different types
of discretization can lead to forbidden and admissible classes, when one attempts
to define the discretization of a spherical circle in terms of intersection between
a discrete sphere and a discrete plane. Several fundamental theoretical results
have been presented, the algorithm for construction of discrete spherical circles
has been discussed, and some test results have been furnished to demonstrate its
practicality and usefulness.
article_processing_charge: No
author:
- first_name: Ranita
full_name: Biswas, Ranita
id: 3C2B033E-F248-11E8-B48F-1D18A9856A87
last_name: Biswas
orcid: 0000-0002-5372-7890
- first_name: Partha
full_name: Bhowmick, Partha
last_name: Bhowmick
- first_name: Valentin E.
full_name: Brimkov, Valentin E.
last_name: Brimkov
citation:
ama: 'Biswas R, Bhowmick P, Brimkov VE. On the connectivity and smoothness of discrete
spherical circles. In: Combinatorial Image Analysis. Vol 9448. Cham: Springer
Nature; 2016:86-100. doi:10.1007/978-3-319-26145-4_7'
apa: 'Biswas, R., Bhowmick, P., & Brimkov, V. E. (2016). On the connectivity
and smoothness of discrete spherical circles. In Combinatorial image analysis
(Vol. 9448, pp. 86–100). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-26145-4_7'
chicago: 'Biswas, Ranita, Partha Bhowmick, and Valentin E. Brimkov. “On the Connectivity
and Smoothness of Discrete Spherical Circles.” In Combinatorial Image Analysis,
9448:86–100. Cham: Springer Nature, 2016. https://doi.org/10.1007/978-3-319-26145-4_7.'
ieee: 'R. Biswas, P. Bhowmick, and V. E. Brimkov, “On the connectivity and smoothness
of discrete spherical circles,” in Combinatorial image analysis, vol. 9448,
Cham: Springer Nature, 2016, pp. 86–100.'
ista: 'Biswas R, Bhowmick P, Brimkov VE. 2016.On the connectivity and smoothness
of discrete spherical circles. In: Combinatorial image analysis. vol. 9448, 86–100.'
mla: Biswas, Ranita, et al. “On the Connectivity and Smoothness of Discrete Spherical
Circles.” Combinatorial Image Analysis, vol. 9448, Springer Nature, 2016,
pp. 86–100, doi:10.1007/978-3-319-26145-4_7.
short: R. Biswas, P. Bhowmick, V.E. Brimkov, in:, Combinatorial Image Analysis,
Springer Nature, Cham, 2016, pp. 86–100.
conference:
end_date: 2015-11-27
location: Kolkata, India
name: 'IWCIA: International Workshop on Combinatorial Image Analysis'
start_date: 2015-11-24
date_created: 2019-01-08T20:45:19Z
date_published: 2016-01-06T00:00:00Z
date_updated: 2022-01-28T08:13:03Z
day: '06'
department:
- _id: HeEd
doi: 10.1007/978-3-319-26145-4_7
extern: '1'
fulldoi: https://doi.org/10.1007/978-3-319-26145-4_7
intvolume: ' 9448'
language:
- iso: eng
month: '01'
oa_version: None
page: 86-100
place: Cham
publication: Combinatorial image analysis
publication_identifier:
eisbn:
- 978-3-319-26145-4
eissn:
- 1611-3349
isbn:
- 978-3-319-26144-7
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: On the connectivity and smoothness of discrete spherical circles
type: book_chapter
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 9448
year: '2016'
...
---
OA_place: repository
OA_type: green
_id: '587'
abstract:
- lang: eng
text: Quantum metrology exploits entangled states of particles to improve sensing
precision beyond the limit achievable with uncorrelated particles. All previous
methods required detection noise levels below this standard quantum limit to realize
the benefits of the intrinsic sensitivity provided by these states.We experimentally
demonstrate a widely applicable method for entanglement-enhanced measurements
without low-noise detection. The method involves an intermediate quantum phase
magnification step that eases implementation complexity. We used it to perform
squeezed-state metrology 8 decibels below the standard quantum limit with a detection
system that has a noise floor 10 decibels above the standard quantum limit.
article_processing_charge: No
arxiv: 1
author:
- first_name: Onur
full_name: Hosten, Onur
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
- first_name: Rajiv
full_name: Krishnakumar, Rajiv
last_name: Krishnakumar
- first_name: Nils
full_name: Engelsen, Nils
last_name: Engelsen
- first_name: Mark
full_name: Kasevich, Mark
last_name: Kasevich
citation:
ama: Hosten O, Krishnakumar R, Engelsen N, Kasevich M. Quantum Phase Magnification.
Vol 352. American Association for the Advancement of Science; 2016:1552-1555.
doi:10.1126/science.aaf3397
apa: Hosten, O., Krishnakumar, R., Engelsen, N., & Kasevich, M. (2016). Quantum
phase magnification (Vol. 352, pp. 1552–1555). American Association for the
Advancement of Science. https://doi.org/10.1126/science.aaf3397
chicago: Hosten, Onur, Rajiv Krishnakumar, Nils Engelsen, and Mark Kasevich. Quantum
Phase Magnification. Vol. 352. American Association for the Advancement of
Science, 2016. https://doi.org/10.1126/science.aaf3397.
ieee: O. Hosten, R. Krishnakumar, N. Engelsen, and M. Kasevich, Quantum phase
magnification, vol. 352. American Association for the Advancement of Science,
2016, pp. 1552–1555.
ista: Hosten O, Krishnakumar R, Engelsen N, Kasevich M. 2016. Quantum phase magnification,
American Association for the Advancement of Science,p.
mla: Hosten, Onur, et al. Quantum Phase Magnification. Vol. 352, American
Association for the Advancement of Science, 2016, pp. 1552–55, doi:10.1126/science.aaf3397.
short: O. Hosten, R. Krishnakumar, N. Engelsen, M. Kasevich, Quantum Phase Magnification,
American Association for the Advancement of Science, 2016.
date_created: 2018-12-11T11:47:21Z
date_published: 2016-06-24T00:00:00Z
date_updated: 2026-05-20T07:21:32Z
day: '24'
doi: 10.1126/science.aaf3397
extern: '1'
external_id:
arxiv:
- '1601.07683'
pmid:
- '27339982'
fulldoi: https://doi.org/10.1126/science.aaf3397
intvolume: ' 352'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.1601.07683'
month: '06'
oa: 1
oa_version: Preprint
page: 1552 - 1555
pmid: 1
publication_identifier:
eisbn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '7214'
status: public
title: Quantum phase magnification
type: report
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 352
year: '2016'
...
---
OA_type: closed access
_id: '588'
abstract:
- lang: eng
text: Quantum metrology uses quantum entanglement - correlations in the properties
of microscopic systems - to improve the statistical precision of physical measurements.
When measuring a signal, such as the phase shift of a light beam or an atomic
state, a prominent limitation to achievable precision arises from the noise associated
with the counting of uncorrelated probe particles. This noise, commonly referred
to as shot noise or projection noise, gives rise to the standard quantum limit
(SQL) to phase resolution. However, it can be mitigated down to the fundamental
Heisenberg limit by entangling the probe particles. Despite considerable experimental
progress in a variety of physical systems, a question that persists is whether
these methods can achieve performance levels that compare favourably with optimized
conventional (non-entangled) systems. Here we demonstrate an approach that achieves
unprecedented levels of metrological improvement using half a million 87Rb atoms
in their 'clock' states. The ensemble is 20.1 ± 0.3 decibels (100-fold) spin-squeezed
via an optical-cavity-based measurement. We directly resolve small microwave-induced
rotations 18.5 ± 0.3 decibels (70-fold) beyond the SQL. The single-shot phase
resolution of 147 microradians achieved by the apparatus is better than that achieved
by the best engineered cold atom sensors despite lower atom numbers. We infer
entanglement of more than 680 ± 35 particles in the atomic ensemble. Applications
include atomic clocks, inertial sensors, and fundamental physics experiments such
as tests of general relativity or searches for electron electric dipole moment.
To this end, we demonstrate an atomic clock measurement with a quantum enhancement
of 10.5 ± 0.3 decibels (11-fold), limited by the phase noise of our microwave
source.
article_processing_charge: No
article_type: original
author:
- first_name: Onur
full_name: Hosten, Onur
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
- first_name: Nils
full_name: Engelsen, Nils
last_name: Engelsen
- first_name: Rajiv
full_name: Krishnakumar, Rajiv
last_name: Krishnakumar
- first_name: Mark
full_name: Kasevich, Mark
last_name: Kasevich
citation:
ama: Hosten O, Engelsen N, Krishnakumar R, Kasevich M. Measurement noise 100 times
lower than the quantum-projection limit using entangled atoms. Nature.
2016;529:505-508. doi:10.1038/nature16176
apa: Hosten, O., Engelsen, N., Krishnakumar, R., & Kasevich, M. (2016). Measurement
noise 100 times lower than the quantum-projection limit using entangled atoms.
Nature. Springer Nature. https://doi.org/10.1038/nature16176
chicago: Hosten, Onur, Nils Engelsen, Rajiv Krishnakumar, and Mark Kasevich. “Measurement
Noise 100 Times Lower than the Quantum-Projection Limit Using Entangled Atoms.”
Nature. Springer Nature, 2016. https://doi.org/10.1038/nature16176.
ieee: O. Hosten, N. Engelsen, R. Krishnakumar, and M. Kasevich, “Measurement noise
100 times lower than the quantum-projection limit using entangled atoms,” Nature,
vol. 529. Springer Nature, pp. 505–508, 2016.
ista: Hosten O, Engelsen N, Krishnakumar R, Kasevich M. 2016. Measurement noise
100 times lower than the quantum-projection limit using entangled atoms. Nature.
529, 505–508.
mla: Hosten, Onur, et al. “Measurement Noise 100 Times Lower than the Quantum-Projection
Limit Using Entangled Atoms.” Nature, vol. 529, Springer Nature, 2016,
pp. 505–08, doi:10.1038/nature16176.
short: O. Hosten, N. Engelsen, R. Krishnakumar, M. Kasevich, Nature 529 (2016) 505–508.
date_created: 2018-12-11T11:47:21Z
date_published: 2016-01-28T00:00:00Z
date_updated: 2026-05-20T07:16:23Z
day: '28'
doi: 10.1038/nature16176
extern: '1'
external_id:
pmid:
- ' 26751056'
fulldoi: https://doi.org/10.1038/nature16176
intvolume: ' 529'
language:
- iso: eng
month: '01'
oa_version: None
page: 505 - 508
pmid: 1
publication: Nature
publication_identifier:
eissn:
- ' 1476-4687'
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
publist_id: '7215'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Measurement noise 100 times lower than the quantum-projection limit using entangled
atoms
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 529
year: '2016'
...
---
_id: '592'
abstract:
- lang: eng
text: We create up to 20 dB spin-squeezed states of atomic ensembles using an optical
cavity-based measurement. The prepared states are suitable for atomic sensors
that require free space release of the atoms.
article_processing_charge: No
author:
- first_name: Nils
full_name: Engelsen, Nils
last_name: Engelsen
- first_name: Onur
full_name: Hosten, Onur
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
- first_name: Rajiv
full_name: Krishnakumar, Rajiv
last_name: Krishnakumar
- first_name: Mark
full_name: Kasevich, Mark
last_name: Kasevich
citation:
ama: 'Engelsen N, Hosten O, Krishnakumar R, Kasevich M. Engineering spin squeezed
states for quantum-enhanced atom interferometry. In: IEEE; 2016.'
apa: 'Engelsen, N., Hosten, O., Krishnakumar, R., & Kasevich, M. (2016). Engineering
spin squeezed states for quantum-enhanced atom interferometry. Presented at the
CLEO: Conference on Lasers and Electro Optics, San Jose, CA, United States: IEEE.'
chicago: Engelsen, Nils, Onur Hosten, Rajiv Krishnakumar, and Mark Kasevich. “Engineering
Spin Squeezed States for Quantum-Enhanced Atom Interferometry.” IEEE, 2016.
ieee: 'N. Engelsen, O. Hosten, R. Krishnakumar, and M. Kasevich, “Engineering spin
squeezed states for quantum-enhanced atom interferometry,” presented at the CLEO:
Conference on Lasers and Electro Optics, San Jose, CA, United States, 2016.'
ista: 'Engelsen N, Hosten O, Krishnakumar R, Kasevich M. 2016. Engineering spin
squeezed states for quantum-enhanced atom interferometry. CLEO: Conference on
Lasers and Electro Optics.'
mla: Engelsen, Nils, et al. Engineering Spin Squeezed States for Quantum-Enhanced
Atom Interferometry. IEEE, 2016.
short: N. Engelsen, O. Hosten, R. Krishnakumar, M. Kasevich, in:, IEEE, 2016.
conference:
end_date: 2016-06-10
location: San Jose, CA, United States
name: 'CLEO: Conference on Lasers and Electro Optics'
start_date: 2016-06-05
date_created: 2018-12-11T11:47:23Z
date_published: 2016-12-16T00:00:00Z
date_updated: 2021-01-12T08:05:15Z
day: '16'
extern: '1'
language:
- iso: eng
main_file_link:
- url: http://ieeexplore.ieee.org/document/7787611/
month: '12'
oa_version: None
publication_status: published
publisher: IEEE
publist_id: '7213'
quality_controlled: '1'
status: public
title: Engineering spin squeezed states for quantum-enhanced atom interferometry
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
OA_type: closed access
_id: '602'
abstract:
- lang: eng
text: RNA polymerase (Pol) II produces messenger RNA during transcription of protein-coding
genes in all eukaryotic cells. The Pol II structure is known at high resolution
from X-ray crystallography for two yeast species1-3. Structural studies of mammalian
Pol II, however, remain limited to low-resolution electron microscopy analysis
of human Pol II and its complexes with various proteins4-10. Here we report the
3.4 Å resolution cryo-electron microscopy structure of mammalian Pol II in the
form of a transcribing complex comprising DNA template and RNA transcript. We
use bovine Pol II, which is identical to the human enzyme except for seven amino-acid
residues. The obtained atomic model closely resembles its yeast counterpart, but
also reveals unknown features. Binding of nucleic acids to the polymerase involves
'induced fit' of the mobile Pol II clamp and active centre region. DNA downstream
of the transcription bubble contacts a conserved 'TPSA motif' in the jaw domain
of the Pol II subunit RPB5, an interaction that is apparently already established
during transcription initiation7. Upstream DNA emanates from the active centre
cleft at an angle of approximately 105° with respect to downstream DNA. This position
of upstream DNA allows for binding of the general transcription elongation factor
DSIF (SPT4-SPT5) that we localize over the active centre cleft in a conserved
position on the clamp domain of Pol II. Our results define the structure of mammalian
Pol II in its functional state, indicate that previous crystallographic analysis
of yeast Pol II is relevant for understanding gene transcription in all eukaryotes,
and provide a starting point for a mechanistic analysis of human transcription.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Carrie A
full_name: Bernecky, Carrie A
id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
last_name: Bernecky
orcid: 0000-0003-0893-7036
- first_name: Franz
full_name: Herzog, Franz
last_name: Herzog
- first_name: Wolfgang
full_name: Baumeister, Wolfgang
last_name: Baumeister
- first_name: Jürgen
full_name: Plitzko, Jürgen
last_name: Plitzko
- first_name: Patrick
full_name: Cramer, Patrick
last_name: Cramer
citation:
ama: Bernecky C, Herzog F, Baumeister W, Plitzko J, Cramer P. Structure of transcribing
mammalian RNA polymerase II. Nature. 2016;529:551-554. doi:10.1038/nature16482
apa: Bernecky, C., Herzog, F., Baumeister, W., Plitzko, J., & Cramer, P. (2016).
Structure of transcribing mammalian RNA polymerase II. Nature. Springer
Nature. https://doi.org/10.1038/nature16482
chicago: Bernecky, Carrie, Franz Herzog, Wolfgang Baumeister, Jürgen Plitzko, and
Patrick Cramer. “Structure of Transcribing Mammalian RNA Polymerase II.” Nature.
Springer Nature, 2016. https://doi.org/10.1038/nature16482.
ieee: C. Bernecky, F. Herzog, W. Baumeister, J. Plitzko, and P. Cramer, “Structure
of transcribing mammalian RNA polymerase II,” Nature, vol. 529. Springer
Nature, pp. 551–554, 2016.
ista: Bernecky C, Herzog F, Baumeister W, Plitzko J, Cramer P. 2016. Structure of
transcribing mammalian RNA polymerase II. Nature. 529, 551–554.
mla: Bernecky, Carrie, et al. “Structure of Transcribing Mammalian RNA Polymerase
II.” Nature, vol. 529, Springer Nature, 2016, pp. 551–54, doi:10.1038/nature16482.
short: C. Bernecky, F. Herzog, W. Baumeister, J. Plitzko, P. Cramer, Nature 529
(2016) 551–554.
date_created: 2018-12-11T11:47:26Z
date_published: 2016-01-28T00:00:00Z
date_updated: 2026-05-20T07:26:38Z
day: '28'
doi: 10.1038/nature16482
extern: '1'
external_id:
pmid:
- '26789250'
fulldoi: https://doi.org/10.1038/nature16482
intvolume: ' 529'
language:
- iso: eng
month: '01'
oa_version: None
page: 551 - 554
pmid: 1
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
publist_id: '7205'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structure of transcribing mammalian RNA polymerase II
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 529
year: '2016'
...
---
OA_place: publisher
OA_type: gold
_id: '19814'
abstract:
- lang: eng
text: Metallic transition-metal dichalcogenides (TMDCs) are benchmark systems for
studying and controlling intertwined electronic orders in solids, with superconductivity
developing from a charge-density wave state. The interplay between such phases
is thought to play a critical role in the unconventional superconductivity of
cuprates, Fe-based and heavy-fermion systems, yet even for the more moderately-correlated
TMDCs, their nature and origins have proved controversial. Here, we study a prototypical
example, 2H-NbSe2, by spin- and angle-resolved photoemission and first-principles
theory. We find that the normal state, from which its hallmark collective phases
emerge, is characterized by quasiparticles whose spin is locked to their valley
pseudospin. This results from a combination of strong spin–orbit interactions
and local inversion symmetry breaking, while interlayer coupling further drives
a rich three-dimensional momentum dependence of the underlying Fermi-surface spin
texture. These findings necessitate a re-investigation of the nature of charge
order and superconducting pairing in NbSe2 and related TMDCs.
article_number: '11711'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: L.
full_name: Bawden, L.
last_name: Bawden
- first_name: S. P.
full_name: Cooil, S. P.
last_name: Cooil
- first_name: F.
full_name: Mazzola, F.
last_name: Mazzola
- first_name: J. M.
full_name: Riley, J. M.
last_name: Riley
- first_name: L. J.
full_name: Collins-McIntyre, L. J.
last_name: Collins-McIntyre
- first_name: Veronika
full_name: Sunko, Veronika
id: 23cb1cf6-2c7a-11ef-91a4-f72fc19f20b3
last_name: Sunko
orcid: 0000-0003-2724-3523
- first_name: K. W. B.
full_name: Hunvik, K. W. B.
last_name: Hunvik
- first_name: M.
full_name: Leandersson, M.
last_name: Leandersson
- first_name: C. M.
full_name: Polley, C. M.
last_name: Polley
- first_name: T.
full_name: Balasubramanian, T.
last_name: Balasubramanian
- first_name: T. K.
full_name: Kim, T. K.
last_name: Kim
- first_name: M.
full_name: Hoesch, M.
last_name: Hoesch
- first_name: J. W.
full_name: Wells, J. W.
last_name: Wells
- first_name: G.
full_name: Balakrishnan, G.
last_name: Balakrishnan
- first_name: M. S.
full_name: Bahramy, M. S.
last_name: Bahramy
- first_name: P. D. C.
full_name: King, P. D. C.
last_name: King
citation:
ama: Bawden L, Cooil SP, Mazzola F, et al. Spin-valley locking in the normal state
of a transition-metal dichalcogenide superconductor. Nature Communications.
2016;7. doi:10.1038/ncomms11711
apa: Bawden, L., Cooil, S. P., Mazzola, F., Riley, J. M., Collins-McIntyre, L. J.,
Sunko, V., … King, P. D. C. (2016). Spin-valley locking in the normal state of
a transition-metal dichalcogenide superconductor. Nature Communications.
Springer Nature. https://doi.org/10.1038/ncomms11711
chicago: Bawden, L., S. P. Cooil, F. Mazzola, J. M. Riley, L. J. Collins-McIntyre,
Veronika Sunko, K. W. B. Hunvik, et al. “Spin-Valley Locking in the Normal State
of a Transition-Metal Dichalcogenide Superconductor.” Nature Communications.
Springer Nature, 2016. https://doi.org/10.1038/ncomms11711.
ieee: L. Bawden et al., “Spin-valley locking in the normal state of a transition-metal
dichalcogenide superconductor,” Nature Communications, vol. 7. Springer
Nature, 2016.
ista: Bawden L, Cooil SP, Mazzola F, Riley JM, Collins-McIntyre LJ, Sunko V, Hunvik
KWB, Leandersson M, Polley CM, Balasubramanian T, Kim TK, Hoesch M, Wells JW,
Balakrishnan G, Bahramy MS, King PDC. 2016. Spin-valley locking in the normal
state of a transition-metal dichalcogenide superconductor. Nature Communications.
7, 11711.
mla: Bawden, L., et al. “Spin-Valley Locking in the Normal State of a Transition-Metal
Dichalcogenide Superconductor.” Nature Communications, vol. 7, 11711, Springer
Nature, 2016, doi:10.1038/ncomms11711.
short: L. Bawden, S.P. Cooil, F. Mazzola, J.M. Riley, L.J. Collins-McIntyre, V.
Sunko, K.W.B. Hunvik, M. Leandersson, C.M. Polley, T. Balasubramanian, T.K. Kim,
M. Hoesch, J.W. Wells, G. Balakrishnan, M.S. Bahramy, P.D.C. King, Nature Communications
7 (2016).
date_created: 2025-06-10T09:15:34Z
date_published: 2016-05-23T00:00:00Z
date_updated: 2025-06-10T13:10:23Z
day: '23'
ddc:
- '530'
doi: 10.1038/ncomms11711
extern: '1'
external_id:
arxiv:
- '1603.05207'
fulldoi: https://doi.org/10.1038/ncomms11711
has_accepted_license: '1'
intvolume: ' 7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/ncomms11711
month: '05'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Spin-valley locking in the normal state of a transition-metal dichalcogenide
superconductor
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2016'
...
---
OA_type: closed access
_id: '19990'
abstract:
- lang: eng
text: Visualizing molecular localization at high resolution contributes to understanding
of their functions and roles in physiological and pathological conditions. Sodium
dodecyl sulfate-digested freeze-fracture replica labeling (SDS-FRL) is a powerful
electron microscopy method to study high-resolution two-dimensional distribution
of transmembrane proteins and their tightly associated proteins on platinum-carbon
replica. During treatment with SDS, unfixed proteins and intracellular organelle
are dissolved and integral membrane proteins captured and stabilized by carbon
and platinum deposition are denatured, retaining most of their antigenicity, and
exposed on exoplasmic and protoplasmic surfaces of lipid monolayers. The exposure
of these antigens on the surface of replica facilitates the accessibility of antibodies
and therefore provides higher labeling efficiency than those obtained with other
immunoelectron microscopy techniques. In this chapter, we describe the protocols
of SDS-FRL adapted for mammalian brain samples and an additional procedure for
fluorescence-guided electron microscopy for replica immunolabeling.
acknowledgement: We thank Mitsuru Ikeda for preparing replica images used in Fig.
2.
article_processing_charge: No
author:
- first_name: Harumi
full_name: Harada, Harumi
id: 2E55CDF2-F248-11E8-B48F-1D18A9856A87
last_name: Harada
orcid: 0000-0001-7429-7896
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
citation:
ama: 'Harada H, Shigemoto R. High-Resolution Localization of Membrane Proteins by
SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL). In: Receptor and Ion
Channel Detection in the Brain. Neuromethods. Springer Nature; 2016:233-245.
doi:10.1007/978-1-4939-3064-7_17'
apa: Harada, H., & Shigemoto, R. (2016). High-Resolution Localization of Membrane
Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL). In Receptor
and Ion Channel Detection in the Brain (pp. 233–245). Springer Nature. https://doi.org/10.1007/978-1-4939-3064-7_17
chicago: Harada, Harumi, and Ryuichi Shigemoto. “High-Resolution Localization of
Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL).”
In Receptor and Ion Channel Detection in the Brain, 233–45. Neuromethods.
Springer Nature, 2016. https://doi.org/10.1007/978-1-4939-3064-7_17.
ieee: H. Harada and R. Shigemoto, “High-Resolution Localization of Membrane Proteins
by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL),” in Receptor and
Ion Channel Detection in the Brain, Springer Nature, 2016, pp. 233–245.
ista: 'Harada H, Shigemoto R. 2016.High-Resolution Localization of Membrane Proteins
by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL). In: Receptor and Ion
Channel Detection in the Brain. , 233–245.'
mla: Harada, Harumi, and Ryuichi Shigemoto. “High-Resolution Localization of Membrane
Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL).” Receptor
and Ion Channel Detection in the Brain, Springer Nature, 2016, pp. 233–45,
doi:10.1007/978-1-4939-3064-7_17.
short: H. Harada, R. Shigemoto, in:, Receptor and Ion Channel Detection in the Brain,
Springer Nature, 2016, pp. 233–245.
corr_author: '1'
date_created: 2025-07-10T13:56:06Z
date_published: 2016-02-02T00:00:00Z
date_updated: 2026-04-07T08:32:03Z
day: '02'
department:
- _id: RySh
doi: 10.1007/978-1-4939-3064-7_17
fulldoi: https://doi.org/10.1007/978-1-4939-3064-7_17
language:
- iso: eng
month: '02'
oa_version: None
page: 233-245
publication: Receptor and Ion Channel Detection in the Brain
publication_identifier:
eisbn:
- '9781493930647'
eissn:
- 1940-6045
isbn:
- '9781493930630'
issn:
- 0893-2336
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
series_title: Neuromethods
status: public
title: High-Resolution Localization of Membrane Proteins by SDS-Digested Freeze-Fracture
Replica Labeling (SDS-FRL)
type: book_chapter
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2016'
...
---
OA_type: closed access
_id: '19991'
abstract:
- lang: eng
text: 'When applying machine learning techniques to real-world problems, prior knowledge
plays a crucial role in enriching the learning system. This prior knowledge is
typically defined by domain experts and can be integrated into machine learning
algorithms in a variety of ways: as a preference of certain prediction functions
over others, as a Bayesian prior over parameters, or as additional information
about the samples in the training set used for learning a prediction function.
The latter setup is called learning using privileged information (LUPI) and was
adopted by Vapnik and Vashist in (Neural Netw, 2009). Formally, LUPI refers to
the setting when, in addition to the main data modality, the learning system has
access to an extra source of information about the training examples. The additional
source of information is only available during training and therefore is called
privileged. The main goal of LUPI is to utilize privileged information and to
learn a better model in the main data modality than one would learn without the
privileged source. As an illustration, for protein classification based on amino-acid
sequences, the protein tertiary structure can be considered additional information.
Another example is recognizing objects in images; the textual information in the
form of image tags contains additional object descriptions and can be used as
privileged.'
article_processing_charge: No
author:
- first_name: Viktoriia
full_name: Sharmanska, Viktoriia
id: 2EA6D09E-F248-11E8-B48F-1D18A9856A87
last_name: Sharmanska
orcid: 0000-0003-0192-9308
- first_name: Novi
full_name: Quadrianto, Novi
last_name: Quadrianto
citation:
ama: 'Sharmanska V, Quadrianto N. Learning Using Privileged Information. In: Encyclopedia
of Machine Learning and Data Mining. Springer Nature; 2016:1-4. doi:10.1007/978-1-4899-7502-7_892-1'
apa: Sharmanska, V., & Quadrianto, N. (2016). Learning Using Privileged Information.
In Encyclopedia of Machine Learning and Data Mining (pp. 1–4). Springer
Nature. https://doi.org/10.1007/978-1-4899-7502-7_892-1
chicago: Sharmanska, Viktoriia, and Novi Quadrianto. “Learning Using Privileged
Information.” In Encyclopedia of Machine Learning and Data Mining, 1–4.
Springer Nature, 2016. https://doi.org/10.1007/978-1-4899-7502-7_892-1.
ieee: V. Sharmanska and N. Quadrianto, “Learning Using Privileged Information,”
in Encyclopedia of Machine Learning and Data Mining, Springer Nature, 2016,
pp. 1–4.
ista: 'Sharmanska V, Quadrianto N. 2016.Learning Using Privileged Information. In:
Encyclopedia of Machine Learning and Data Mining. , 1–4.'
mla: Sharmanska, Viktoriia, and Novi Quadrianto. “Learning Using Privileged Information.”
Encyclopedia of Machine Learning and Data Mining, Springer Nature, 2016,
pp. 1–4, doi:10.1007/978-1-4899-7502-7_892-1.
short: V. Sharmanska, N. Quadrianto, in:, Encyclopedia of Machine Learning and Data
Mining, Springer Nature, 2016, pp. 1–4.
corr_author: '1'
date_created: 2025-07-10T13:57:52Z
date_published: 2016-07-06T00:00:00Z
date_updated: 2025-09-23T10:53:13Z
day: '06'
department:
- _id: ChLa
doi: 10.1007/978-1-4899-7502-7_892-1
fulldoi: https://doi.org/10.1007/978-1-4899-7502-7_892-1
language:
- iso: eng
month: '07'
oa_version: None
page: 1-4
publication: Encyclopedia of Machine Learning and Data Mining
publication_identifier:
eisbn:
- '9781489975027'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Learning Using Privileged Information
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '100'
abstract:
- lang: eng
text: We introduce a scheme for preparation, manipulation, and read out of Majorana
zero modes in semiconducting wires with mesoscopic superconducting islands. Our
approach synthesizes recent advances in materials growth with tools commonly used
in quantum-dot experiments, including gate control of tunnel barriers and Coulomb
effects, charge sensing, and charge pumping. We outline a sequence of milestones
interpolating between zero-mode detection and quantum computing that includes
(1) detection of fusion rules for non-Abelian anyons using either proximal charge
sensors or pumped current, (2) validation of a prototype topological qubit, and
(3) demonstration of non-Abelian statistics by braiding in a branched geometry.
The first two milestones require only a single wire with two islands, and additionally
enable sensitive measurements of the system\'s excitation gap, quasiparticle poisoning
rates, residual Majorana zero-mode splittings, and topological-qubit coherence
times. These pre-braiding experiments can be adapted to other manipulation and
read out schemes as well.
acknowledgement: We acknowledge support from Microsoft Research, the National Science
Foundation through Grant No. DMR-1341822 (J. A.); the Alfred P. Sloan Foundation
(J. A.); the Caltech Institute for Quantum Information and Matter, an NSF Physics
Frontiers Center with support of the Gordon and Betty Moore Foundation through Grant
No. GBMF1250; the Walter Burke Institute for Theoretical Physics at Caltech; the
NSERC PGSD program (D. A.); the Crafoord Foundation (M. L. and M. H.) and the Swedish
Research Council (M. L.); The Danish National Research Foundation, and the Villum
Foundation (C. M.); The Danish Council for Independent Research/Natural Sciences,
and Danmarks Nationalbank (J. F.). Part of this work was performed at the Aspen
Center for Physics, which is supported by National Science Foundation Grant No.
PHY-1066293 (R. V. M.).
article_number: '031016'
author:
- first_name: David
full_name: Aasen, David
last_name: Aasen
- first_name: Michael
full_name: Hell, Michael
last_name: Hell
- first_name: Ryan
full_name: Mishmash, Ryan
last_name: Mishmash
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
- first_name: Jeroen
full_name: Danon, Jeroen
last_name: Danon
- first_name: Martin
full_name: Leijnse, Martin
last_name: Leijnse
- first_name: Thomas
full_name: Jespersen, Thomas
last_name: Jespersen
- first_name: Joshua
full_name: Folk, Joshua
last_name: Folk
- first_name: Charles
full_name: Marcs, Charles
last_name: Marcs
- first_name: Karsten
full_name: Flensberg, Karsten
last_name: Flensberg
- first_name: Jason
full_name: Alicea, Jason
last_name: Alicea
citation:
ama: Aasen D, Hell M, Mishmash R, et al. Milestones toward Majorana-based quantum
computing. Physical Review X. 2016;6(3). doi:10.1103/PhysRevX.6.031016
apa: Aasen, D., Hell, M., Mishmash, R., Higginbotham, A. P., Danon, J., Leijnse,
M., … Alicea, J. (2016). Milestones toward Majorana-based quantum computing. Physical
Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.6.031016
chicago: Aasen, David, Michael Hell, Ryan Mishmash, Andrew P Higginbotham, Jeroen
Danon, Martin Leijnse, Thomas Jespersen, et al. “Milestones toward Majorana-Based
Quantum Computing.” Physical Review X. American Physical Society, 2016.
https://doi.org/10.1103/PhysRevX.6.031016.
ieee: D. Aasen et al., “Milestones toward Majorana-based quantum computing,”
Physical Review X, vol. 6, no. 3. American Physical Society, 2016.
ista: Aasen D, Hell M, Mishmash R, Higginbotham AP, Danon J, Leijnse M, Jespersen
T, Folk J, Marcs C, Flensberg K, Alicea J. 2016. Milestones toward Majorana-based
quantum computing. Physical Review X. 6(3), 031016.
mla: Aasen, David, et al. “Milestones toward Majorana-Based Quantum Computing.”
Physical Review X, vol. 6, no. 3, 031016, American Physical Society, 2016,
doi:10.1103/PhysRevX.6.031016.
short: D. Aasen, M. Hell, R. Mishmash, A.P. Higginbotham, J. Danon, M. Leijnse,
T. Jespersen, J. Folk, C. Marcs, K. Flensberg, J. Alicea, Physical Review X 6
(2016).
date_created: 2018-12-11T11:44:37Z
date_published: 2016-08-03T00:00:00Z
date_updated: 2021-01-12T06:47:33Z
day: '03'
ddc:
- '530'
doi: 10.1103/PhysRevX.6.031016
extern: '1'
file:
- access_level: open_access
content_type: application/pdf
creator: kschuh
date_created: 2019-05-15T14:12:31Z
date_updated: 2019-05-15T14:12:31Z
file_id: '6458'
file_name: 2016_PhysRevX_Aasen.pdf
file_size: 2142676
relation: main_file
success: 1
file_date_updated: 2019-05-15T14:12:31Z
fulldoi: https://doi.org/10.1103/PhysRevX.6.031016
has_accepted_license: '1'
intvolume: ' 6'
issue: '3'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication: Physical Review X
publication_status: published
publisher: American Physical Society
publist_id: '7954'
quality_controlled: '1'
status: public
title: Milestones toward Majorana-based quantum computing
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2016'
...
---
_id: '1008'
abstract:
- lang: eng
text: Feedback loops in biological networks, among others, enable differentiation
and cell cycle progression, and increase robustness in signal transduction. In
natural networks, feedback loops are often complex and intertwined, making it
challenging to identify which loops are mainly responsible for an observed behavior.
However, minimal synthetic replicas could allow for such identification. Here,
we engineered a synthetic permease-inducer-repressor system in Saccharomyces cerevisiae
to analyze if a transport-mediated positive feedback loop could be a core mechanism
for the switch-like behavior in the regulation of metabolic gene networks such
as the S. cerevisiae GAL system or the Escherichia coli lac operon. We characterized
the synthetic circuit using deterministic and stochastic mathematical models.
Similar to its natural counterparts, our synthetic system shows bistable and hysteretic
behavior, and the inducer concentration range for bistability as well as the switching
rates between the two stable states depend on the repressor concentration. Our
results indicate that a generic permease–inducer–repressor circuit with a single
feedback loop is sufficient to explain the experimentally observed bistable behavior
of the natural systems. We anticipate that the approach of reimplementing natural
systems with orthogonal parts to identify crucial network components is applicable
to other natural systems such as signaling pathways.
acknowledgement: We thank Julio Polaina (Instituto de Agroqu ı ́ mica y Tecnolog ı
́ a de Alimentos, C.S.I.C., Paterna, Spain) for the gift of plasmid pMR4, Gregor
W. Schmidt for provision of and support with the micro fl uidic device, Markus Du
̈ rr for the cell tracking R script, and Lukas Widmer for the script for MEIGO using
“ parfor ” in MATLAB. We acknowledge the members of the Stelling group for discussions,
comments, and support.
article_processing_charge: No
author:
- first_name: Robert
full_name: Gnügge, Robert
last_name: Gnügge
- first_name: Lekshmi
full_name: Dharmarajan, Lekshmi
last_name: Dharmarajan
- first_name: Moritz
full_name: Lang, Moritz
id: 29E0800A-F248-11E8-B48F-1D18A9856A87
last_name: Lang
- first_name: Jörg
full_name: Stelling, Jörg
last_name: Stelling
citation:
ama: Gnügge R, Dharmarajan L, Lang M, Stelling J. An orthogonal permease–inducer–repressor
feedback loop shows bistability. ACS Synthetic Biology. 2016;5(10):1098-1107.
doi:10.1021/acssynbio.6b00013
apa: Gnügge, R., Dharmarajan, L., Lang, M., & Stelling, J. (2016). An orthogonal
permease–inducer–repressor feedback loop shows bistability. ACS Synthetic Biology.
American Chemical Society. https://doi.org/10.1021/acssynbio.6b00013
chicago: Gnügge, Robert, Lekshmi Dharmarajan, Moritz Lang, and Jörg Stelling. “An
Orthogonal Permease–Inducer–Repressor Feedback Loop Shows Bistability.” ACS
Synthetic Biology. American Chemical Society, 2016. https://doi.org/10.1021/acssynbio.6b00013.
ieee: R. Gnügge, L. Dharmarajan, M. Lang, and J. Stelling, “An orthogonal permease–inducer–repressor
feedback loop shows bistability,” ACS Synthetic Biology, vol. 5, no. 10.
American Chemical Society, pp. 1098–1107, 2016.
ista: Gnügge R, Dharmarajan L, Lang M, Stelling J. 2016. An orthogonal permease–inducer–repressor
feedback loop shows bistability. ACS Synthetic Biology. 5(10), 1098–1107.
mla: Gnügge, Robert, et al. “An Orthogonal Permease–Inducer–Repressor Feedback Loop
Shows Bistability.” ACS Synthetic Biology, vol. 5, no. 10, American Chemical
Society, 2016, pp. 1098–107, doi:10.1021/acssynbio.6b00013.
short: R. Gnügge, L. Dharmarajan, M. Lang, J. Stelling, ACS Synthetic Biology 5
(2016) 1098–1107.
date_created: 2018-12-11T11:49:40Z
date_published: 2016-05-05T00:00:00Z
date_updated: 2025-09-22T14:20:45Z
day: '05'
department:
- _id: CaGu
doi: 10.1021/acssynbio.6b00013
external_id:
isi:
- '000386196100008'
fulldoi: https://doi.org/10.1021/acssynbio.6b00013
intvolume: ' 5'
isi: 1
issue: '10'
language:
- iso: eng
month: '05'
oa_version: None
page: 1098 - 1107
publication: ACS Synthetic Biology
publication_status: published
publisher: American Chemical Society
publist_id: '6390'
quality_controlled: '1'
status: public
title: An orthogonal permease–inducer–repressor feedback loop shows bistability
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 5
year: '2016'
...
---
_id: '101'
abstract:
- lang: eng
text: Majorana zero modes are quasiparticle excitations in condensed matter systems
that have been proposed as building blocks of fault-tolerant quantum computers.
They are expected to exhibit non-Abelian particle statistics, in contrast to the
usual statistics of fermions and bosons, enabling quantum operations to be performed
by braiding isolated modes around one another. Quantum braiding operations are
topologically protected insofar as these modes are pinned near zero energy, with
the departure from zero expected to be exponentially small as the modes become
spatially separated. Following theoretical proposals, several experiments have
identified signatures of Majorana modes in nanowires with proximity-induced superconductivity
and atomic chains, with small amounts of mode splitting potentially explained
by hybridization of Majorana modes. Here, we use Coulomb-blockade spectroscopy
in an InAs nanowire segment with epitaxial aluminium, which forms a proximity-induced
superconducting Coulomb island (a â ∼ Majorana islandâ (tm)) that is isolated
from normal-metal leads by tunnel barriers, to measure the splitting of near-zero-energy
Majorana modes. We observe exponential suppression of energy splitting with increasing
wire length. For short devices of a few hundred nanometres, sub-gap state energies
oscillate as the magnetic field is varied, as is expected for hybridized Majorana
modes. Splitting decreases by a factor of about ten for each half a micrometre
of increased wire length. For devices longer than about one micrometre, transport
in strong magnetic fields occurs through a zero-energy state that is energetically
isolated from a continuum, yielding uniformly spaced Coulomb-blockade conductance
peaks, consistent with teleportation via Majorana modes. Our results help to explain
the trivial-to-topological transition in finite systems and to quantify the scaling
of topological protection with end-mode separation.
acknowledgement: This research was supported by Microsoft Project Q, the Danish National
Research Foundation, the Lundbeck Foundation, the Carlsberg Foundation and the European
Commission. C.M.M. acknowledges support from the Villum Foundation.
arxiv: 1
author:
- first_name: S M
full_name: Albrecht, S M
last_name: Albrecht
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
- first_name: Thomas
full_name: Jespersen, Thomas
last_name: Jespersen
- first_name: Morten
full_name: Madsen, Morten
last_name: Madsen
- first_name: Ferdinand
full_name: Kuemmeth, Ferdinand
last_name: Kuemmeth
- first_name: Jesper
full_name: Nygård, Jesper
last_name: Nygård
- first_name: Peter
full_name: Krogstrup, Peter
last_name: Krogstrup
- first_name: Charles
full_name: Marcus, Charles
last_name: Marcus
citation:
ama: Albrecht SM, Higginbotham AP, Jespersen T, et al. Exponential protection of
zero modes in Majorana islands. Nature. 2016;531(7593):206-209. doi:10.1038/nature17162
apa: Albrecht, S. M., Higginbotham, A. P., Jespersen, T., Madsen, M., Kuemmeth,
F., Nygård, J., … Marcus, C. (2016). Exponential protection of zero modes in Majorana
islands. Nature. Nature Publishing Group. https://doi.org/10.1038/nature17162
chicago: Albrecht, S M, Andrew P Higginbotham, Thomas Jespersen, Morten Madsen,
Ferdinand Kuemmeth, Jesper Nygård, Peter Krogstrup, and Charles Marcus. “Exponential
Protection of Zero Modes in Majorana Islands.” Nature. Nature Publishing
Group, 2016. https://doi.org/10.1038/nature17162.
ieee: S. M. Albrecht et al., “Exponential protection of zero modes in Majorana
islands,” Nature, vol. 531, no. 7593. Nature Publishing Group, pp. 206–209,
2016.
ista: Albrecht SM, Higginbotham AP, Jespersen T, Madsen M, Kuemmeth F, Nygård J,
Krogstrup P, Marcus C. 2016. Exponential protection of zero modes in Majorana
islands. Nature. 531(7593), 206–209.
mla: Albrecht, S. M., et al. “Exponential Protection of Zero Modes in Majorana Islands.”
Nature, vol. 531, no. 7593, Nature Publishing Group, 2016, pp. 206–09,
doi:10.1038/nature17162.
short: S.M. Albrecht, A.P. Higginbotham, T. Jespersen, M. Madsen, F. Kuemmeth, J.
Nygård, P. Krogstrup, C. Marcus, Nature 531 (2016) 206–209.
date_created: 2018-12-11T11:44:38Z
date_published: 2016-03-10T00:00:00Z
date_updated: 2021-01-12T06:47:37Z
day: '10'
doi: 10.1038/nature17162
extern: '1'
external_id:
arxiv:
- '1603.03217'
fulldoi: https://doi.org/10.1038/nature17162
intvolume: ' 531'
issue: '7593'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1603.03217
month: '03'
oa: 1
oa_version: Submitted Version
page: 206 - 209
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '7953'
quality_controlled: '1'
status: public
title: Exponential protection of zero modes in Majorana islands
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 531
year: '2016'
...
---
_id: '102'
abstract:
- lang: eng
text: 'Recent experiments have produced mounting evidence of Majorana zero modes
in nanowire-superconductor hybrids. Signatures of an expected topological phase
transition accompanying the onset of these modes nevertheless remain elusive.
We investigate a fundamental question concerning this issue: Do well-formed Majorana
modes necessarily entail a sharp phase transition in these setups? Assuming reasonable
parameters, we argue that finite-size effects can dramatically smooth this putative
transition into a crossover, even in systems large enough to support well-localized
Majorana modes. We propose overcoming such finite-size effects by examining the
behavior of low-lying excited states through tunneling spectroscopy. In particular,
the excited-state energies exhibit characteristic field and density dependence,
and scaling with system size, that expose an approaching topological phase transition.
We suggest several experiments for extracting the predicted behavior. As a useful
byproduct, the protocols also allow one to measure the wire''s spin-orbit coupling
directly in its superconducting environment.'
article_number: '245404'
arxiv: 1
author:
- first_name: Ryan
full_name: Mishmash, Ryan
last_name: Mishmash
- first_name: David
full_name: Aasen, David
last_name: Aasen
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
- first_name: Jason
full_name: Alicea, Jason
last_name: Alicea
citation:
ama: Mishmash R, Aasen D, Higginbotham AP, Alicea J. Approaching a topological phase
transition in Majorana nanowires. Physical Review B. 2016;93(24). doi:10.1103/PhysRevB.93.245404
apa: Mishmash, R., Aasen, D., Higginbotham, A. P., & Alicea, J. (2016). Approaching
a topological phase transition in Majorana nanowires. Physical Review B.
American Physical Society. https://doi.org/10.1103/PhysRevB.93.245404
chicago: Mishmash, Ryan, David Aasen, Andrew P Higginbotham, and Jason Alicea. “Approaching
a Topological Phase Transition in Majorana Nanowires.” Physical Review B.
American Physical Society, 2016. https://doi.org/10.1103/PhysRevB.93.245404.
ieee: R. Mishmash, D. Aasen, A. P. Higginbotham, and J. Alicea, “Approaching a topological
phase transition in Majorana nanowires,” Physical Review B, vol. 93, no.
24. American Physical Society, 2016.
ista: Mishmash R, Aasen D, Higginbotham AP, Alicea J. 2016. Approaching a topological
phase transition in Majorana nanowires. Physical Review B. 93(24), 245404.
mla: Mishmash, Ryan, et al. “Approaching a Topological Phase Transition in Majorana
Nanowires.” Physical Review B, vol. 93, no. 24, 245404, American Physical
Society, 2016, doi:10.1103/PhysRevB.93.245404.
short: R. Mishmash, D. Aasen, A.P. Higginbotham, J. Alicea, Physical Review B 93
(2016).
date_created: 2018-12-11T11:44:38Z
date_published: 2016-06-08T00:00:00Z
date_updated: 2021-01-12T06:47:42Z
day: '08'
doi: 10.1103/PhysRevB.93.245404
extern: '1'
external_id:
arxiv:
- '1601.07908'
fulldoi: https://doi.org/10.1103/PhysRevB.93.245404
intvolume: ' 93'
issue: '24'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1601.07908
month: '06'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_status: published
publisher: American Physical Society
publist_id: '7952'
quality_controlled: '1'
status: public
title: Approaching a topological phase transition in Majorana nanowires
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 93
year: '2016'
...
---
_id: '10376'
abstract:
- lang: eng
text: Nucleation processes are at the heart of a large number of phenomena, from
cloud formation to protein crystallization. A recently emerging area where nucleation
is highly relevant is the initiation of filamentous protein self-assembly, a process
that has broad implications in many research areas ranging from medicine to nanotechnology.
As such, spontaneous nucleation of protein fibrils has received much attention
in recent years with many theoretical and experimental studies focusing on the
underlying physical principles. In this paper we make a step forward in this direction
and explore the early time behaviour of filamentous protein growth in the context
of nucleation theory. We first provide an overview of the thermodynamics and kinetics
of spontaneous nucleation of protein filaments in the presence of one relevant
degree of freedom, namely the cluster size. In this case, we review how key kinetic
observables, such as the reaction order of spontaneous nucleation, are directly
related to the physical size of the critical nucleus. We then focus on the increasingly
prominent case of filament nucleation that includes a conformational conversion
of the nucleating building-block as an additional slow step in the nucleation
process. Using computer simulations, we study the concentration dependence of
the nucleation rate. We find that, under these circumstances, the reaction order
of spontaneous nucleation with respect to the free monomer does no longer relate
to the overall physical size of the nucleating aggregate but rather to the portion
of the aggregate that actively participates in the conformational conversion.
Our results thus provide a novel interpretation of the common kinetic descriptors
of protein filament formation, including the reaction order of the nucleation
step or the scaling exponent of lag times, and put into perspective current theoretical
descriptions of protein aggregation.
acknowledgement: We acknowledge support from the Human Frontier Science Program and
Emmanuel College (A.Š.), St John’s and Peterhouse Colleges (T.C.T.M.), the Swiss
National Science Foundation (T.C.T.M.), the Biotechnology and Biological Sciences
Research Council (T.P.J.K.), the Frances and Augustus Newman Foundation (T.P.J.K.),
the European Research Council (T.C.T.M., T.P.J.K., and D.F.), and the Engineering
and Physical Sciences Research Council (D.F.).
article_number: '211926'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Thomas C. T.
full_name: Michaels, Thomas C. T.
last_name: Michaels
- first_name: Alessio
full_name: Zaccone, Alessio
last_name: Zaccone
- first_name: Tuomas P. J.
full_name: Knowles, Tuomas P. J.
last_name: Knowles
- first_name: Daan
full_name: Frenkel, Daan
last_name: Frenkel
citation:
ama: 'Šarić A, Michaels TCT, Zaccone A, Knowles TPJ, Frenkel D. Kinetics of spontaneous
filament nucleation via oligomers: Insights from theory and simulation. The
Journal of Chemical Physics. 2016;145(21). doi:10.1063/1.4965040'
apa: 'Šarić, A., Michaels, T. C. T., Zaccone, A., Knowles, T. P. J., & Frenkel,
D. (2016). Kinetics of spontaneous filament nucleation via oligomers: Insights
from theory and simulation. The Journal of Chemical Physics. American Institute
of Physics. https://doi.org/10.1063/1.4965040'
chicago: 'Šarić, Anđela, Thomas C. T. Michaels, Alessio Zaccone, Tuomas P. J. Knowles,
and Daan Frenkel. “Kinetics of Spontaneous Filament Nucleation via Oligomers:
Insights from Theory and Simulation.” The Journal of Chemical Physics.
American Institute of Physics, 2016. https://doi.org/10.1063/1.4965040.'
ieee: 'A. Šarić, T. C. T. Michaels, A. Zaccone, T. P. J. Knowles, and D. Frenkel,
“Kinetics of spontaneous filament nucleation via oligomers: Insights from theory
and simulation,” The Journal of Chemical Physics, vol. 145, no. 21. American
Institute of Physics, 2016.'
ista: 'Šarić A, Michaels TCT, Zaccone A, Knowles TPJ, Frenkel D. 2016. Kinetics
of spontaneous filament nucleation via oligomers: Insights from theory and simulation.
The Journal of Chemical Physics. 145(21), 211926.'
mla: 'Šarić, Anđela, et al. “Kinetics of Spontaneous Filament Nucleation via Oligomers:
Insights from Theory and Simulation.” The Journal of Chemical Physics,
vol. 145, no. 21, 211926, American Institute of Physics, 2016, doi:10.1063/1.4965040.'
short: A. Šarić, T.C.T. Michaels, A. Zaccone, T.P.J. Knowles, D. Frenkel, The Journal
of Chemical Physics 145 (2016).
date_created: 2021-11-29T10:01:57Z
date_published: 2016-12-01T00:00:00Z
date_updated: 2021-11-29T10:33:11Z
day: '01'
doi: 10.1063/1.4965040
extern: '1'
external_id:
arxiv:
- '1610.02320'
pmid:
- '28799382'
fulldoi: https://doi.org/10.1063/1.4965040
intvolume: ' 145'
issue: '21'
keyword:
- physical and theoretical chemistry
- general physics and astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1610.02320
month: '12'
oa: 1
oa_version: Preprint
pmid: 1
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: American Institute of Physics
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Kinetics of spontaneous filament nucleation via oligomers: Insights from theory
and simulation'
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 145
year: '2016'
...
---
_id: '10377'
abstract:
- lang: eng
text: The interplay of membrane proteins is vital for many biological processes,
such as cellular transport, cell division, and signal transduction between nerve
cells. Theoretical considerations have led to the idea that the membrane itself
mediates protein self-organization in these processes through minimization of
membrane curvature energy. Here, we present a combined experimental and numerical
study in which we quantify these interactions directly for the first time. In
our experimental model system we control the deformation of a lipid membrane by
adhering colloidal particles. Using confocal microscopy, we establish that these
membrane deformations cause an attractive interaction force leading to reversible
binding. The attraction extends over 2.5 times the particle diameter and has a
strength of three times the thermal energy (−3.3 kBT). Coarse-grained Monte-Carlo
simulations of the system are in excellent agreement with the experimental results
and prove that the measured interaction is independent of length scale. Our combined
experimental and numerical results reveal membrane curvature as a common physical
origin for interactions between any membrane-deforming objects, from nanometre-sized
proteins to micrometre-sized particles.
acknowledgement: This work was supported by the Netherlands Organisation for Scientific
Research (NWO/OCW), as part of the Frontiers of Nanoscience program and VENI grant
680-47-431. We thank Jeroen Appel and Wim Pomp for advice on the protocol design
and Marcel Winter and Ruben Verweij for experimental support.
article_number: '32825'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Casper
full_name: van der Wel, Casper
last_name: van der Wel
- first_name: Afshin
full_name: Vahid, Afshin
last_name: Vahid
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Timon
full_name: Idema, Timon
last_name: Idema
- first_name: Doris
full_name: Heinrich, Doris
last_name: Heinrich
- first_name: Daniela J.
full_name: Kraft, Daniela J.
last_name: Kraft
citation:
ama: van der Wel C, Vahid A, Šarić A, Idema T, Heinrich D, Kraft DJ. Lipid membrane-mediated
attraction between curvature inducing objects. Scientific Reports. 2016;6(1).
doi:10.1038/srep32825
apa: van der Wel, C., Vahid, A., Šarić, A., Idema, T., Heinrich, D., & Kraft,
D. J. (2016). Lipid membrane-mediated attraction between curvature inducing objects.
Scientific Reports. Springer Nature. https://doi.org/10.1038/srep32825
chicago: Wel, Casper van der, Afshin Vahid, Anđela Šarić, Timon Idema, Doris Heinrich,
and Daniela J. Kraft. “Lipid Membrane-Mediated Attraction between Curvature Inducing
Objects.” Scientific Reports. Springer Nature, 2016. https://doi.org/10.1038/srep32825.
ieee: C. van der Wel, A. Vahid, A. Šarić, T. Idema, D. Heinrich, and D. J. Kraft,
“Lipid membrane-mediated attraction between curvature inducing objects,” Scientific
Reports, vol. 6, no. 1. Springer Nature, 2016.
ista: van der Wel C, Vahid A, Šarić A, Idema T, Heinrich D, Kraft DJ. 2016. Lipid
membrane-mediated attraction between curvature inducing objects. Scientific Reports.
6(1), 32825.
mla: van der Wel, Casper, et al. “Lipid Membrane-Mediated Attraction between Curvature
Inducing Objects.” Scientific Reports, vol. 6, no. 1, 32825, Springer Nature,
2016, doi:10.1038/srep32825.
short: C. van der Wel, A. Vahid, A. Šarić, T. Idema, D. Heinrich, D.J. Kraft, Scientific
Reports 6 (2016).
date_created: 2021-11-29T10:34:08Z
date_published: 2016-09-13T00:00:00Z
date_updated: 2021-11-29T11:08:15Z
day: '13'
ddc:
- '540'
doi: 10.1038/srep32825
extern: '1'
external_id:
arxiv:
- '1603.04644'
pmid:
- '27618764'
file:
- access_level: open_access
checksum: d6cf16dd511e15726b001e7cc287cf1d
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-29T10:50:00Z
date_updated: 2021-11-29T10:50:00Z
file_id: '10379'
file_name: 2016_SciRep_vanderWel.pdf
file_size: 1598289
relation: main_file
success: 1
file_date_updated: 2021-11-29T10:50:00Z
fulldoi: https://doi.org/10.1038/srep32825
has_accepted_license: '1'
intvolume: ' 6'
issue: '1'
keyword:
- multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.nature.com/articles/srep32825
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
publication: Scientific Reports
publication_identifier:
issn:
- 2045-2322
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/srep37382
scopus_import: '1'
status: public
title: Lipid membrane-mediated attraction between curvature inducing objects
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 6
year: '2016'
...
---
_id: '10378'
abstract:
- lang: eng
text: The ability of biological molecules to replicate themselves is the foundation
of life, requiring a complex cellular machinery. However, a range of aberrant
processes involve the self-replication of pathological protein structures without
any additional assistance. One example is the autocatalytic generation of pathological
protein aggregates, including amyloid fibrils, involved in neurodegenerative disorders.
Here, we use computer simulations to identify the necessary requirements for the
self-replication of fibrillar assemblies of proteins. We establish that a key
physical determinant for this process is the affinity of proteins for the surfaces
of fibrils. We find that self-replication can take place only in a very narrow
regime of inter-protein interactions, implying a high level of sensitivity to
system parameters and experimental conditions. We then compare our theoretical
predictions with kinetic and biosensor measurements of fibrils formed from the
Aβ peptide associated with Alzheimer’s disease. Our results show a quantitative
connection between the kinetics of self-replication and the surface coverage of
fibrils by monomeric proteins. These findings reveal the fundamental physical
requirements for the formation of supra-molecular structures able to replicate
themselves, and shed light on mechanisms in play in the proliferation of protein
aggregates in nature.
acknowledgement: We acknowledge support from the Human Frontier Science Program and
Emmanuel College (A.Š.), the Leverhulme Trust and Magdalene College (A.K.B.), St
John’s College (T.C.T.M.), the Biotechnology and Biological Sciences Research Council
(T.P.J.K. and C.M.D.), the Frances and Augustus Newman Foundation (T.P.J.K.), the
European Research Council (T.P.J.K., T.C.T.M., S.L. and D.F.), and the Engineering
and Physical Sciences Research Council (D.F.).
article_processing_charge: No
article_type: original
author:
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Alexander K.
full_name: Buell, Alexander K.
last_name: Buell
- first_name: Georg
full_name: Meisl, Georg
last_name: Meisl
- first_name: Thomas C. T.
full_name: Michaels, Thomas C. T.
last_name: Michaels
- first_name: Christopher M.
full_name: Dobson, Christopher M.
last_name: Dobson
- first_name: Sara
full_name: Linse, Sara
last_name: Linse
- first_name: Tuomas P. J.
full_name: Knowles, Tuomas P. J.
last_name: Knowles
- first_name: Daan
full_name: Frenkel, Daan
last_name: Frenkel
citation:
ama: Šarić A, Buell AK, Meisl G, et al. Physical determinants of the self-replication
of protein fibrils. Nature Physics. 2016;12(9):874-880. doi:10.1038/nphys3828
apa: Šarić, A., Buell, A. K., Meisl, G., Michaels, T. C. T., Dobson, C. M., Linse,
S., … Frenkel, D. (2016). Physical determinants of the self-replication of protein
fibrils. Nature Physics. Springer Nature. https://doi.org/10.1038/nphys3828
chicago: Šarić, Anđela, Alexander K. Buell, Georg Meisl, Thomas C. T. Michaels,
Christopher M. Dobson, Sara Linse, Tuomas P. J. Knowles, and Daan Frenkel. “Physical
Determinants of the Self-Replication of Protein Fibrils.” Nature Physics.
Springer Nature, 2016. https://doi.org/10.1038/nphys3828.
ieee: A. Šarić et al., “Physical determinants of the self-replication of
protein fibrils,” Nature Physics, vol. 12, no. 9. Springer Nature, pp.
874–880, 2016.
ista: Šarić A, Buell AK, Meisl G, Michaels TCT, Dobson CM, Linse S, Knowles TPJ,
Frenkel D. 2016. Physical determinants of the self-replication of protein fibrils.
Nature Physics. 12(9), 874–880.
mla: Šarić, Anđela, et al. “Physical Determinants of the Self-Replication of Protein
Fibrils.” Nature Physics, vol. 12, no. 9, Springer Nature, 2016, pp. 874–80,
doi:10.1038/nphys3828.
short: A. Šarić, A.K. Buell, G. Meisl, T.C.T. Michaels, C.M. Dobson, S. Linse, T.P.J.
Knowles, D. Frenkel, Nature Physics 12 (2016) 874–880.
date_created: 2021-11-29T10:36:11Z
date_published: 2016-07-18T00:00:00Z
date_updated: 2021-11-29T11:07:25Z
day: '18'
doi: 10.1038/nphys3828
extern: '1'
external_id:
pmid:
- '31031819'
fulldoi: https://doi.org/10.1038/nphys3828
intvolume: ' 12'
issue: '9'
keyword:
- general physics and astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://discovery.ucl.ac.uk/id/eprint/1517406/
month: '07'
oa: 1
oa_version: Preprint
page: 874-880
pmid: 1
publication: Nature Physics
publication_identifier:
eissn:
- 1745-2481
issn:
- 1745-2473
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Physical determinants of the self-replication of protein fibrils
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 12
year: '2016'
...
---
_id: '10380'
abstract:
- lang: eng
text: Using non-equilibrium molecular dynamics simulations, it has been recently
demonstrated that water molecules align in response to an imposed temperature
gradient, resulting in an effective electric field. Here, we investigate how thermally
induced fields depend on the underlying treatment of long-ranged interactions.
For the short-ranged Wolf method and Ewald summation, we find the peak strength
of the field to range between 2 × 107 and 5 × 107 V/m for a temperature gradient
of 5.2 K/Å. Our value for the Wolf method is therefore an order of magnitude lower
than the literature value [J. A. Armstrong and F. Bresme, J. Chem. Phys. 139,
014504 (2013); J. Armstrong et al., J. Chem. Phys. 143, 036101 (2015)]. We show
that this discrepancy can be traced back to the use of an incorrect kernel in
the calculation of the electrostatic field. More seriously, we find that the Wolf
method fails to predict correct molecular orientations, resulting in dipole densities
with opposite sign to those computed using Ewald summation. By considering two
different multipole expansions, we show that, for inhomogeneous polarisations,
the quadrupole contribution can be significant and even outweigh the dipole contribution
to the field. Finally, we propose a more accurate way of calculating the electrostatic
potential and the field. In particular, we show that averaging the microscopic
field analytically to obtain the macroscopic Maxwell field reduces the error bars
by up to an order of magnitude. As a consequence, the simulation times required
to reach a given statistical accuracy decrease by up to two orders of magnitude.
acknowledgement: The authors should like to dedicate this paper to the memory of Simon
de Leeuw, who was a pioneer in the calculation of Coulomb effects in simulations.
P.W. would like to thank the Austrian Academy of Sciences for financial support
through a DOC Fellowship, and for covering the travel expenses for the CECAM workshop
in Zaragoza in May 2015, where these results were first presented. P.W. would also
like to thank Chao Zhang for pointing out the equivalence of the two expressions
for the electric field discussed in Sec. VI D, Michiel Sprik for emphasising the
importance of the quadrupole contribution in experimental studies of interfacial
systems, as well as Aleks Reinhardt and other members of the Frenkel and Dellago
groups for their advice. We further acknowledge support from the Federation of Austrian
Industry (IV) Carinthia (P.W.), the University of Zagreb and Erasmus SMP (D. Fijan),
the Human Frontier Science Program and Emmanuel College (A.Š.), the Austrian Science
Fund FWF within the SFB Vicom project F41 (C.D.), and the Engineering and Physical
Sciences Research Council Programme Grant No. EP/I001352/1 (D.F.). Additional data
related to this publication are available at the University of Cambridge data repository
(http://dx.doi.org/10.17863/CAM.118).
article_number: '224102'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: P.
full_name: Wirnsberger, P.
last_name: Wirnsberger
- first_name: D.
full_name: Fijan, D.
last_name: Fijan
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: M.
full_name: Neumann, M.
last_name: Neumann
- first_name: C.
full_name: Dellago, C.
last_name: Dellago
- first_name: D.
full_name: Frenkel, D.
last_name: Frenkel
citation:
ama: Wirnsberger P, Fijan D, Šarić A, Neumann M, Dellago C, Frenkel D. Non-equilibrium
simulations of thermally induced electric fields in water. The Journal of Chemical
Physics. 2016;144(22). doi:10.1063/1.4953036
apa: Wirnsberger, P., Fijan, D., Šarić, A., Neumann, M., Dellago, C., & Frenkel,
D. (2016). Non-equilibrium simulations of thermally induced electric fields in
water. The Journal of Chemical Physics. American Institute of Physics.
https://doi.org/10.1063/1.4953036
chicago: Wirnsberger, P., D. Fijan, Anđela Šarić, M. Neumann, C. Dellago, and D.
Frenkel. “Non-Equilibrium Simulations of Thermally Induced Electric Fields in
Water.” The Journal of Chemical Physics. American Institute of Physics,
2016. https://doi.org/10.1063/1.4953036.
ieee: P. Wirnsberger, D. Fijan, A. Šarić, M. Neumann, C. Dellago, and D. Frenkel,
“Non-equilibrium simulations of thermally induced electric fields in water,” The
Journal of Chemical Physics, vol. 144, no. 22. American Institute of Physics,
2016.
ista: Wirnsberger P, Fijan D, Šarić A, Neumann M, Dellago C, Frenkel D. 2016. Non-equilibrium
simulations of thermally induced electric fields in water. The Journal of Chemical
Physics. 144(22), 224102.
mla: Wirnsberger, P., et al. “Non-Equilibrium Simulations of Thermally Induced Electric
Fields in Water.” The Journal of Chemical Physics, vol. 144, no. 22, 224102,
American Institute of Physics, 2016, doi:10.1063/1.4953036.
short: P. Wirnsberger, D. Fijan, A. Šarić, M. Neumann, C. Dellago, D. Frenkel, The
Journal of Chemical Physics 144 (2016).
date_created: 2021-11-29T11:08:52Z
date_published: 2016-06-10T00:00:00Z
date_updated: 2021-11-29T13:09:08Z
day: '10'
doi: 10.1063/1.4953036
extern: '1'
external_id:
arxiv:
- '1602.02734'
pmid:
- '27305991'
fulldoi: https://doi.org/10.1063/1.4953036
intvolume: ' 144'
issue: '22'
keyword:
- physical and theoretical chemistry
- general physics and astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1602.02734
month: '06'
oa: 1
oa_version: Preprint
pmid: 1
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: American Institute of Physics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Non-equilibrium simulations of thermally induced electric fields in water
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 144
year: '2016'
...
---
_id: '10381'
abstract:
- lang: eng
text: We study phase behaviour of lipid-bilayer vesicles functionalised by ligand–receptor
complexes made of synthetic DNA by introducing a modelling framework and a dedicated
experimental platform. In particular, we perform Monte Carlo simulations that
combine a coarse grained description of the lipid bilayer with state of art analytical
models for multivalent ligand–receptor interactions. Using density of state calculations,
we derive the partition function in pairs of vesicles and compute the number of
ligand–receptor bonds as a function of temperature. Numerical results are compared
to microscopy and fluorimetry experiments on large unilamellar vesicles decorated
by DNA linkers carrying complementary overhangs. We find that vesicle aggregation
is suppressed when the total number of linkers falls below a threshold value.
Within the model proposed here, this is due to the higher configurational costs
required to form inter-vesicle bridges as compared to intra-vesicle loops, which
are in turn related to membrane deformability. Our findings and our numerical/experimental
methodologies are applicable to the rational design of liposomes used as functional
materials and drug delivery applications, as well as to study inter-membrane interactions
in living systems, such as cell adhesion.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Stephan Jan
full_name: Bachmann, Stephan Jan
last_name: Bachmann
- first_name: Jurij
full_name: Kotar, Jurij
last_name: Kotar
- first_name: Lucia
full_name: Parolini, Lucia
last_name: Parolini
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Pietro
full_name: Cicuta, Pietro
last_name: Cicuta
- first_name: Lorenzo
full_name: Di Michele, Lorenzo
last_name: Di Michele
- first_name: Bortolo Matteo
full_name: Mognetti, Bortolo Matteo
last_name: Mognetti
citation:
ama: Bachmann SJ, Kotar J, Parolini L, et al. Melting transition in lipid vesicles
functionalised by mobile DNA linkers. Soft Matter. 2016;12(37):7804-7817.
doi:10.1039/c6sm01515h
apa: Bachmann, S. J., Kotar, J., Parolini, L., Šarić, A., Cicuta, P., Di Michele,
L., & Mognetti, B. M. (2016). Melting transition in lipid vesicles functionalised
by mobile DNA linkers. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c6sm01515h
chicago: Bachmann, Stephan Jan, Jurij Kotar, Lucia Parolini, Anđela Šarić, Pietro
Cicuta, Lorenzo Di Michele, and Bortolo Matteo Mognetti. “Melting Transition in
Lipid Vesicles Functionalised by Mobile DNA Linkers.” Soft Matter. Royal
Society of Chemistry, 2016. https://doi.org/10.1039/c6sm01515h.
ieee: S. J. Bachmann et al., “Melting transition in lipid vesicles functionalised
by mobile DNA linkers,” Soft Matter, vol. 12, no. 37. Royal Society of
Chemistry, pp. 7804–7817, 2016.
ista: Bachmann SJ, Kotar J, Parolini L, Šarić A, Cicuta P, Di Michele L, Mognetti
BM. 2016. Melting transition in lipid vesicles functionalised by mobile DNA linkers.
Soft Matter. 12(37), 7804–7817.
mla: Bachmann, Stephan Jan, et al. “Melting Transition in Lipid Vesicles Functionalised
by Mobile DNA Linkers.” Soft Matter, vol. 12, no. 37, Royal Society of
Chemistry, 2016, pp. 7804–17, doi:10.1039/c6sm01515h.
short: S.J. Bachmann, J. Kotar, L. Parolini, A. Šarić, P. Cicuta, L. Di Michele,
B.M. Mognetti, Soft Matter 12 (2016) 7804–7817.
date_created: 2021-11-29T11:09:55Z
date_published: 2016-08-19T00:00:00Z
date_updated: 2021-11-29T13:09:00Z
day: '19'
doi: 10.1039/c6sm01515h
extern: '1'
external_id:
arxiv:
- '1608.05788'
pmid:
- '27722701'
fulldoi: https://doi.org/10.1039/c6sm01515h
intvolume: ' 12'
issue: '37'
keyword:
- condensed matter physics
- general chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1608.05788
month: '08'
oa: 1
oa_version: Preprint
page: 7804-7817
pmid: 1
publication: Soft Matter
publication_identifier:
eissn:
- 1744-6848
issn:
- 1744-683X
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Melting transition in lipid vesicles functionalised by mobile DNA linkers
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 12
year: '2016'
...