---
_id: '931'
abstract:
- lang: eng
text: 'In many adult tissues, stem cells and differentiated cells are not homogeneously
distributed: stem cells are arranged in periodic "niches," and differentiated
cells are constantly produced and migrate out of these niches. In this article,
we provide a general theoretical framework to study mixtures of dividing and actively
migrating particles, which we apply to biological tissues. We show in particular
that the interplay between the stresses arising from active cell migration and
stem cell division give rise to robust stem cell patterns. The instability of
the tissue leads to spatial patterns which are either steady or oscillating in
time. The wavelength of the instability has an order of magnitude consistent with
the biological observations. We also discuss the implications of these results
for future in vitro and in vivo experiments.'
acknowledgement: The authors thank Jacques Prost and Pierre Recho for helpful discussions,
as well as the Labex CelTisPhyBio and all its members. E.H. acknowledges for funding
a Young Researcher Prize from the Bettencourt-Schueller Fondation, and a Junior
Research Fellowship from Trinity College, Cambridge.
article_processing_charge: No
author:
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Alice
full_name: Coucke, Alice
last_name: Coucke
- first_name: Jean
full_name: Joanny, Jean
last_name: Joanny
citation:
ama: Hannezo EB, Coucke A, Joanny J. Interplay of migratory and division forces
as a generic mechanism for stem cell patterns. Physical Review E Statistical
Nonlinear and Soft Matter Physics. 2016;93(2). doi:10.1103/PhysRevE.93.022405
apa: Hannezo, E. B., Coucke, A., & Joanny, J. (2016). Interplay of migratory
and division forces as a generic mechanism for stem cell patterns. Physical
Review E Statistical Nonlinear and Soft Matter Physics. American Institute
of Physics. https://doi.org/10.1103/PhysRevE.93.022405
chicago: Hannezo, Edouard B, Alice Coucke, and Jean Joanny. “Interplay of Migratory
and Division Forces as a Generic Mechanism for Stem Cell Patterns.” Physical
Review E Statistical Nonlinear and Soft Matter Physics. American Institute
of Physics, 2016. https://doi.org/10.1103/PhysRevE.93.022405.
ieee: E. B. Hannezo, A. Coucke, and J. Joanny, “Interplay of migratory and division
forces as a generic mechanism for stem cell patterns,” Physical Review E Statistical
Nonlinear and Soft Matter Physics, vol. 93, no. 2. American Institute of Physics,
2016.
ista: Hannezo EB, Coucke A, Joanny J. 2016. Interplay of migratory and division
forces as a generic mechanism for stem cell patterns. Physical Review E Statistical
Nonlinear and Soft Matter Physics. 93(2).
mla: Hannezo, Edouard B., et al. “Interplay of Migratory and Division Forces as
a Generic Mechanism for Stem Cell Patterns.” Physical Review E Statistical
Nonlinear and Soft Matter Physics, vol. 93, no. 2, American Institute of Physics,
2016, doi:10.1103/PhysRevE.93.022405.
short: E.B. Hannezo, A. Coucke, J. Joanny, Physical Review E Statistical Nonlinear
and Soft Matter Physics 93 (2016).
date_created: 2018-12-11T11:49:16Z
date_published: 2016-02-28T00:00:00Z
date_updated: 2021-01-12T08:22:00Z
day: '28'
doi: 10.1103/PhysRevE.93.022405
extern: '1'
intvolume: ' 93'
issue: '2'
language:
- iso: eng
month: '02'
oa_version: None
publication: Physical Review E Statistical Nonlinear and Soft Matter Physics
publication_status: published
publisher: American Institute of Physics
publist_id: '6509'
status: public
title: Interplay of migratory and division forces as a generic mechanism for stem
cell patterns
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 93
year: '2016'
...
---
_id: '932'
abstract:
- lang: eng
text: Epithelial sheets are crucial components of all metazoan animals, enclosing
organs and protecting the animal from its environment. Epithelial homeostasis
poses unique challenges, as addition of new cells and loss of old cells must be
achieved without disrupting the fluid-tight barrier and apicobasal polarity of
the epithelium. Several studies have identified cell biological mechanisms underlying
extrusion of cells from epithelia, but far less is known of the converse mechanism
by which new cells are added. Here, we combine molecular, pharmacological, and
laser-dissection experiments with theoretical modeling to characterize forces
driving emergence of an apical surface as single nascent cells are added to a
vertebrate epithelium in vivo. We find that this process involves the interplay
between cell-autonomous actin-generated pushing forces in the emerging cell and
mechanical properties of neighboring cells. Our findings define the forces driving
this cell behavior, contributing to a more comprehensive understanding of epithelial
homeostasis.
acknowledgement: We thank J. Bear, B. Goldstein, A. Ewald, and D. Soroldoni for critical
reading. This work was funded by an EMBO Long Term Fellowship to J.S., a Research
Fellowship from Trinity College, Cambridge and a Bettencourt-Schueller Foundation
Young Researcher Prize to E.H., a Cancer Institute NSW Early Career Researcher fellowship
(13/ECF/1–25) and a Cancer Australia/Cure Cancer Australia Foundation project grant
(1070498) to M.B., and grants from the NHLBI (HL117164) and NIGMS (GM074104) to
J.B.W. J.B.W. was an early career scientist of the Howard Hughes Medical Institute.
This work was initiated at the New Quantitative Approaches to Morphogenesis Workshop
at UCSB, which is funded in part by the National Science Foundation (PHY11-25915)
and the NIGMS (GM067110-05).
article_processing_charge: No
author:
- first_name: Jakub
full_name: Sedzinski, Jakub
last_name: Sedzinski
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Fan
full_name: Tu, Fan
last_name: Tu
- first_name: Maté
full_name: Biro, Maté
last_name: Biro
- first_name: John
full_name: Wallingford, John
last_name: Wallingford
citation:
ama: Sedzinski J, Hannezo EB, Tu F, Biro M, Wallingford J. Emergence of an Apical
Epithelial Cell Surface In Vivo. Developmental Cell. 2016;36(1):24-35.
doi:10.1016/j.devcel.2015.12.013
apa: Sedzinski, J., Hannezo, E. B., Tu, F., Biro, M., & Wallingford, J. (2016).
Emergence of an Apical Epithelial Cell Surface In Vivo. Developmental Cell.
Cell Press. https://doi.org/10.1016/j.devcel.2015.12.013
chicago: Sedzinski, Jakub, Edouard B Hannezo, Fan Tu, Maté Biro, and John Wallingford.
“Emergence of an Apical Epithelial Cell Surface In Vivo.” Developmental Cell.
Cell Press, 2016. https://doi.org/10.1016/j.devcel.2015.12.013.
ieee: J. Sedzinski, E. B. Hannezo, F. Tu, M. Biro, and J. Wallingford, “Emergence
of an Apical Epithelial Cell Surface In Vivo,” Developmental Cell, vol.
36, no. 1. Cell Press, pp. 24–35, 2016.
ista: Sedzinski J, Hannezo EB, Tu F, Biro M, Wallingford J. 2016. Emergence of an
Apical Epithelial Cell Surface In Vivo. Developmental Cell. 36(1), 24–35.
mla: Sedzinski, Jakub, et al. “Emergence of an Apical Epithelial Cell Surface In
Vivo.” Developmental Cell, vol. 36, no. 1, Cell Press, 2016, pp. 24–35,
doi:10.1016/j.devcel.2015.12.013.
short: J. Sedzinski, E.B. Hannezo, F. Tu, M. Biro, J. Wallingford, Developmental
Cell 36 (2016) 24–35.
date_created: 2018-12-11T11:49:16Z
date_published: 2016-01-12T00:00:00Z
date_updated: 2021-01-12T08:22:00Z
day: '12'
doi: 10.1016/j.devcel.2015.12.013
extern: '1'
intvolume: ' 36'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 24 - 35
publication: Developmental Cell
publication_status: published
publisher: Cell Press
publist_id: '6510'
status: public
title: Emergence of an Apical Epithelial Cell Surface In Vivo
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 36
year: '2016'
...
---
_id: '9456'
abstract:
- lang: eng
text: The discovery of introns four decades ago was one of the most unexpected findings
in molecular biology. Introns are sequences interrupting genes that must be removed
as part of messenger RNA production. Genome sequencing projects have shown that
most eukaryotic genes contain at least one intron, and frequently many. Comparison
of these genomes reveals a history of long evolutionary periods during which few
introns were gained, punctuated by episodes of rapid, extensive gain. However,
although several detailed mechanisms for such episodic intron generation have
been proposed, none has been empirically supported on a genomic scale. Here we
show how short, non-autonomous DNA transposons independently generated hundreds
to thousands of introns in the prasinophyte Micromonas pusilla and the pelagophyte
Aureococcus anophagefferens. Each transposon carries one splice site. The other
splice site is co-opted from the gene sequence that is duplicated upon transposon
insertion, allowing perfect splicing out of the RNA. The distributions of sequences
that can be co-opted are biased with respect to codons, and phasing of transposon-generated
introns is similarly biased. These transposons insert between pre-existing nucleosomes,
so that multiple nearby insertions generate nucleosome-sized intervening segments.
Thus, transposon insertion and sequence co-option may explain the intron phase
biases and prevalence of nucleosome-sized exons observed in eukaryotes. Overall,
the two independent examples of proliferating elements illustrate a general DNA
transposon mechanism that can plausibly account for episodes of rapid, extensive
intron gain during eukaryotic evolution.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Jason T.
full_name: Huff, Jason T.
last_name: Huff
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Scott W.
full_name: Roy, Scott W.
last_name: Roy
citation:
ama: Huff JT, Zilberman D, Roy SW. Mechanism for DNA transposons to generate introns
on genomic scales. Nature. 2016;538(7626):533-536. doi:10.1038/nature20110
apa: Huff, J. T., Zilberman, D., & Roy, S. W. (2016). Mechanism for DNA transposons
to generate introns on genomic scales. Nature. Springer Nature . https://doi.org/10.1038/nature20110
chicago: Huff, Jason T., Daniel Zilberman, and Scott W. Roy. “Mechanism for DNA
Transposons to Generate Introns on Genomic Scales.” Nature. Springer Nature
, 2016. https://doi.org/10.1038/nature20110.
ieee: J. T. Huff, D. Zilberman, and S. W. Roy, “Mechanism for DNA transposons to
generate introns on genomic scales,” Nature, vol. 538, no. 7626. Springer
Nature , pp. 533–536, 2016.
ista: Huff JT, Zilberman D, Roy SW. 2016. Mechanism for DNA transposons to generate
introns on genomic scales. Nature. 538(7626), 533–536.
mla: Huff, Jason T., et al. “Mechanism for DNA Transposons to Generate Introns on
Genomic Scales.” Nature, vol. 538, no. 7626, Springer Nature , 2016, pp.
533–36, doi:10.1038/nature20110.
short: J.T. Huff, D. Zilberman, S.W. Roy, Nature 538 (2016) 533–536.
date_created: 2021-06-04T11:34:55Z
date_published: 2016-10-27T00:00:00Z
date_updated: 2021-12-14T07:55:30Z
day: '27'
department:
- _id: DaZi
doi: 10.1038/nature20110
extern: '1'
external_id:
pmid:
- '27760113'
intvolume: ' 538'
issue: '7626'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5684705/
month: '10'
oa: 1
oa_version: Submitted Version
page: 533-536
pmid: 1
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: 'Springer Nature '
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mechanism for DNA transposons to generate introns on genomic scales
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 538
year: '2016'
...
---
_id: '9473'
abstract:
- lang: eng
text: Cytosine DNA methylation regulates the expression of eukaryotic genes and
transposons. Methylation is copied by methyltransferases after DNA replication,
which results in faithful transmission of methylation patterns during cell division
and, at least in flowering plants, across generations. Transgenerational inheritance
is mediated by a small group of cells that includes gametes and their progenitors.
However, methylation is usually analyzed in somatic tissues that do not contribute
to the next generation, and the mechanisms of transgenerational inheritance are
inferred from such studies. To gain a better understanding of how DNA methylation
is inherited, we analyzed purified Arabidopsis thaliana sperm and vegetative cells-the
cell types that comprise pollen-with mutations in the DRM, CMT2, and CMT3 methyltransferases.
We find that DNA methylation dependency on these enzymes is similar in sperm,
vegetative cells, and somatic tissues, although DRM activity extends into heterochromatin
in vegetative cells, likely reflecting transcription of heterochromatic transposons
in this cell type. We also show that lack of histone H1, which elevates heterochromatic
DNA methylation in somatic tissues, does not have this effect in pollen. Instead,
levels of CG methylation in wild-type sperm and vegetative cells, as well as in
wild-type microspores from which both pollen cell types originate, are substantially
higher than in wild-type somatic tissues and similar to those of H1-depleted roots.
Our results demonstrate that the mechanisms of methylation maintenance are similar
between pollen and somatic cells, but the efficiency of CG methylation is higher
in pollen, allowing methylation patterns to be accurately inherited across generations.
article_processing_charge: No
article_type: original
author:
- first_name: Ping-Hung
full_name: Hsieh, Ping-Hung
last_name: Hsieh
- first_name: Shengbo
full_name: He, Shengbo
last_name: He
- first_name: Toby
full_name: Buttress, Toby
last_name: Buttress
- first_name: Hongbo
full_name: Gao, Hongbo
last_name: Gao
- first_name: Matthew
full_name: Couchman, Matthew
last_name: Couchman
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
citation:
ama: Hsieh P-H, He S, Buttress T, et al. Arabidopsis male sexual lineage exhibits
more robust maintenance of CG methylation than somatic tissues. Proceedings
of the National Academy of Sciences. 2016;113(52):15132-15137. doi:10.1073/pnas.1619074114
apa: Hsieh, P.-H., He, S., Buttress, T., Gao, H., Couchman, M., Fischer, R. L.,
… Feng, X. (2016). Arabidopsis male sexual lineage exhibits more robust maintenance
of CG methylation than somatic tissues. Proceedings of the National Academy
of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1619074114
chicago: Hsieh, Ping-Hung, Shengbo He, Toby Buttress, Hongbo Gao, Matthew Couchman,
Robert L. Fischer, Daniel Zilberman, and Xiaoqi Feng. “Arabidopsis Male Sexual
Lineage Exhibits More Robust Maintenance of CG Methylation than Somatic Tissues.”
Proceedings of the National Academy of Sciences. National Academy of Sciences,
2016. https://doi.org/10.1073/pnas.1619074114.
ieee: P.-H. Hsieh et al., “Arabidopsis male sexual lineage exhibits more
robust maintenance of CG methylation than somatic tissues,” Proceedings of
the National Academy of Sciences, vol. 113, no. 52. National Academy of Sciences,
pp. 15132–15137, 2016.
ista: Hsieh P-H, He S, Buttress T, Gao H, Couchman M, Fischer RL, Zilberman D, Feng
X. 2016. Arabidopsis male sexual lineage exhibits more robust maintenance of CG
methylation than somatic tissues. Proceedings of the National Academy of Sciences.
113(52), 15132–15137.
mla: Hsieh, Ping-Hung, et al. “Arabidopsis Male Sexual Lineage Exhibits More Robust
Maintenance of CG Methylation than Somatic Tissues.” Proceedings of the National
Academy of Sciences, vol. 113, no. 52, National Academy of Sciences, 2016,
pp. 15132–37, doi:10.1073/pnas.1619074114.
short: P.-H. Hsieh, S. He, T. Buttress, H. Gao, M. Couchman, R.L. Fischer, D. Zilberman,
X. Feng, Proceedings of the National Academy of Sciences 113 (2016) 15132–15137.
date_created: 2021-06-07T06:21:39Z
date_published: 2016-12-27T00:00:00Z
date_updated: 2023-05-08T11:00:40Z
day: '27'
department:
- _id: DaZi
- _id: XiFe
doi: 10.1073/pnas.1619074114
extern: '1'
external_id:
pmid:
- '27956643'
intvolume: ' 113'
issue: '52'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1619074114
month: '12'
oa: 1
oa_version: Published Version
page: 15132-15137
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation
than somatic tissues
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2016'
...
---
_id: '9477'
abstract:
- lang: eng
text: Cytosine methylation is a DNA modification with important regulatory functions
in eukaryotes. In flowering plants, sexual reproduction is accompanied by extensive
DNA demethylation, which is required for proper gene expression in the endosperm,
a nutritive extraembryonic seed tissue. Endosperm arises from a fusion of a sperm
cell carried in the pollen and a female central cell. Endosperm DNA demethylation
is observed specifically on the chromosomes inherited from the central cell in
Arabidopsis thaliana, rice, and maize, and requires the DEMETER DNA demethylase
in Arabidopsis. DEMETER is expressed in the central cell before fertilization,
suggesting that endosperm demethylation patterns are inherited from the central
cell. Down-regulation of the MET1 DNA methyltransferase has also been proposed
to contribute to central cell demethylation. However, with the exception of three
maize genes, central cell DNA methylation has not been directly measured, leaving
the origin and mechanism of endosperm demethylation uncertain. Here, we report
genome-wide analysis of DNA methylation in the central cells of Arabidopsis and
rice—species that diverged 150 million years ago—as well as in rice egg cells.
We find that DNA demethylation in both species is initiated in central cells,
which requires DEMETER in Arabidopsis. However, we do not observe a global reduction
of CG methylation that would be indicative of lowered MET1 activity; on the contrary,
CG methylation efficiency is elevated in female gametes compared with nonsexual
tissues. Our results demonstrate that locus-specific, active DNA demethylation
in the central cell is the origin of maternal chromosome hypomethylation in the
endosperm.
article_processing_charge: No
article_type: original
author:
- first_name: Kyunghyuk
full_name: Park, Kyunghyuk
last_name: Park
- first_name: M. Yvonne
full_name: Kim, M. Yvonne
last_name: Kim
- first_name: Martin
full_name: Vickers, Martin
last_name: Vickers
- first_name: Jin-Sup
full_name: Park, Jin-Sup
last_name: Park
- first_name: Youbong
full_name: Hyun, Youbong
last_name: Hyun
- first_name: Takashi
full_name: Okamoto, Takashi
last_name: Okamoto
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Yeonhee
full_name: Choi, Yeonhee
last_name: Choi
- first_name: Stefan
full_name: Scholten, Stefan
last_name: Scholten
citation:
ama: Park K, Kim MY, Vickers M, et al. DNA demethylation is initiated in the central
cells of Arabidopsis and rice. Proceedings of the National Academy of Sciences.
2016;113(52):15138-15143. doi:10.1073/pnas.1619047114
apa: Park, K., Kim, M. Y., Vickers, M., Park, J.-S., Hyun, Y., Okamoto, T., … Scholten,
S. (2016). DNA demethylation is initiated in the central cells of Arabidopsis
and rice. Proceedings of the National Academy of Sciences. National Academy
of Sciences. https://doi.org/10.1073/pnas.1619047114
chicago: Park, Kyunghyuk, M. Yvonne Kim, Martin Vickers, Jin-Sup Park, Youbong Hyun,
Takashi Okamoto, Daniel Zilberman, et al. “DNA Demethylation Is Initiated in the
Central Cells of Arabidopsis and Rice.” Proceedings of the National Academy
of Sciences. National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1619047114.
ieee: K. Park et al., “DNA demethylation is initiated in the central cells
of Arabidopsis and rice,” Proceedings of the National Academy of Sciences,
vol. 113, no. 52. National Academy of Sciences, pp. 15138–15143, 2016.
ista: Park K, Kim MY, Vickers M, Park J-S, Hyun Y, Okamoto T, Zilberman D, Fischer
RL, Feng X, Choi Y, Scholten S. 2016. DNA demethylation is initiated in the central
cells of Arabidopsis and rice. Proceedings of the National Academy of Sciences.
113(52), 15138–15143.
mla: Park, Kyunghyuk, et al. “DNA Demethylation Is Initiated in the Central Cells
of Arabidopsis and Rice.” Proceedings of the National Academy of Sciences,
vol. 113, no. 52, National Academy of Sciences, 2016, pp. 15138–43, doi:10.1073/pnas.1619047114.
short: K. Park, M.Y. Kim, M. Vickers, J.-S. Park, Y. Hyun, T. Okamoto, D. Zilberman,
R.L. Fischer, X. Feng, Y. Choi, S. Scholten, Proceedings of the National Academy
of Sciences 113 (2016) 15138–15143.
date_created: 2021-06-07T07:10:59Z
date_published: 2016-12-27T00:00:00Z
date_updated: 2023-05-08T11:00:07Z
day: '27'
department:
- _id: DaZi
- _id: XiFe
doi: 10.1073/pnas.1619047114
extern: '1'
external_id:
pmid:
- '27956642'
intvolume: ' 113'
issue: '52'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1619047114
month: '12'
oa: 1
oa_version: Published Version
page: 15138-15143
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA demethylation is initiated in the central cells of Arabidopsis and rice
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2016'
...
---
_id: '948'
abstract:
- lang: eng
text: Experience constantly shapes neural circuits through a variety of plasticity
mechanisms. While the functional roles of some plasticity mechanisms are well-understood,
it remains unclear how changes in neural excitability contribute to learning.
Here, we develop a normative interpretation of intrinsic plasticity (IP) as a
key component of unsupervised learning. We introduce a novel generative mixture
model that accounts for the class-specific statistics of stimulus intensities,
and we derive a neural circuit that learns the input classes and their intensities.
We will analytically show that inference and learning for our generative model
can be achieved by a neural circuit with intensity-sensitive neurons equipped
with a specific form of IP. Numerical experiments verify our analytical derivations
and show robust behavior for artificial and natural stimuli. Our results link
IP to non-trivial input statistics, in particular the statistics of stimulus intensities
for classes to which a neuron is sensitive. More generally, our work paves the
way toward new classification algorithms that are robust to intensity variations.
acknowledgement: DFG Cluster of Excellence EXC 1077/1 (Hearing4all) and LU 1196/5-1
(JL and TM), People Programme (Marie Curie Actions) FP7/2007-2013 grant agreement
no. 291734 (CS)
alternative_title:
- Advances in Neural Information Processing Systems
author:
- first_name: Travis
full_name: Monk, Travis
last_name: Monk
- first_name: Cristina
full_name: Savin, Cristina
id: 3933349E-F248-11E8-B48F-1D18A9856A87
last_name: Savin
- first_name: Jörg
full_name: Lücke, Jörg
last_name: Lücke
citation:
ama: 'Monk T, Savin C, Lücke J. Neurons equipped with intrinsic plasticity learn
stimulus intensity statistics. In: Vol 29. Neural Information Processing Systems;
2016:4285-4293.'
apa: 'Monk, T., Savin, C., & Lücke, J. (2016). Neurons equipped with intrinsic
plasticity learn stimulus intensity statistics (Vol. 29, pp. 4285–4293). Presented
at the NIPS: Neural Information Processing Systems, Barcelona, Spaine: Neural
Information Processing Systems.'
chicago: Monk, Travis, Cristina Savin, and Jörg Lücke. “Neurons Equipped with Intrinsic
Plasticity Learn Stimulus Intensity Statistics,” 29:4285–93. Neural Information
Processing Systems, 2016.
ieee: 'T. Monk, C. Savin, and J. Lücke, “Neurons equipped with intrinsic plasticity
learn stimulus intensity statistics,” presented at the NIPS: Neural Information
Processing Systems, Barcelona, Spaine, 2016, vol. 29, pp. 4285–4293.'
ista: 'Monk T, Savin C, Lücke J. 2016. Neurons equipped with intrinsic plasticity
learn stimulus intensity statistics. NIPS: Neural Information Processing Systems,
Advances in Neural Information Processing Systems, vol. 29, 4285–4293.'
mla: Monk, Travis, et al. Neurons Equipped with Intrinsic Plasticity Learn Stimulus
Intensity Statistics. Vol. 29, Neural Information Processing Systems, 2016,
pp. 4285–93.
short: T. Monk, C. Savin, J. Lücke, in:, Neural Information Processing Systems,
2016, pp. 4285–4293.
conference:
end_date: 2016-12-10
location: Barcelona, Spaine
name: 'NIPS: Neural Information Processing Systems'
start_date: 2016-12-05
date_created: 2018-12-11T11:49:21Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2021-01-12T08:22:08Z
day: '01'
department:
- _id: GaTk
ec_funded: 1
intvolume: ' 29'
language:
- iso: eng
main_file_link:
- url: https://papers.nips.cc/paper/6582-neurons-equipped-with-intrinsic-plasticity-learn-stimulus-intensity-statistics
month: '01'
oa_version: None
page: 4285 - 4293
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: Neural Information Processing Systems
publist_id: '6469'
quality_controlled: '1'
scopus_import: 1
status: public
title: Neurons equipped with intrinsic plasticity learn stimulus intensity statistics
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2016'
...
---
_id: '9591'
abstract:
- lang: eng
text: We give several results showing that different discrete structures typically
gain certain spanning substructures (in particular, Hamilton cycles) after a modest
random perturbation. First, we prove that adding linearly many random edges to
a dense k-uniform hypergraph ensures the (asymptotically almost sure) existence
of a perfect matching or a loose Hamilton cycle. The proof involves an interesting
application of Szemerédi's Regularity Lemma, which might be independently useful.
We next prove that digraphs with certain strong expansion properties are pancyclic,
and use this to show that adding a linear number of random edges typically makes
a dense digraph pancyclic. Finally, we prove that perturbing a certain (minimum-degree-dependent)
number of random edges in a tournament typically ensures the existence of multiple
edge-disjoint Hamilton cycles. All our results are tight.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Michael
full_name: Krivelevich, Michael
last_name: Krivelevich
- first_name: Matthew Alan
full_name: Kwan, Matthew Alan
id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
last_name: Kwan
orcid: 0000-0002-4003-7567
- first_name: Benny
full_name: Sudakov, Benny
last_name: Sudakov
citation:
ama: Krivelevich M, Kwan MA, Sudakov B. Cycles and matchings in randomly perturbed
digraphs and hypergraphs. Combinatorics, Probability and Computing. 2016;25(6):909-927.
doi:10.1017/s0963548316000079
apa: Krivelevich, M., Kwan, M. A., & Sudakov, B. (2016). Cycles and matchings
in randomly perturbed digraphs and hypergraphs. Combinatorics, Probability
and Computing. Cambridge University Press. https://doi.org/10.1017/s0963548316000079
chicago: Krivelevich, Michael, Matthew Alan Kwan, and Benny Sudakov. “Cycles and
Matchings in Randomly Perturbed Digraphs and Hypergraphs.” Combinatorics, Probability
and Computing. Cambridge University Press, 2016. https://doi.org/10.1017/s0963548316000079.
ieee: M. Krivelevich, M. A. Kwan, and B. Sudakov, “Cycles and matchings in randomly
perturbed digraphs and hypergraphs,” Combinatorics, Probability and Computing,
vol. 25, no. 6. Cambridge University Press, pp. 909–927, 2016.
ista: Krivelevich M, Kwan MA, Sudakov B. 2016. Cycles and matchings in randomly
perturbed digraphs and hypergraphs. Combinatorics, Probability and Computing.
25(6), 909–927.
mla: Krivelevich, Michael, et al. “Cycles and Matchings in Randomly Perturbed Digraphs
and Hypergraphs.” Combinatorics, Probability and Computing, vol. 25, no.
6, Cambridge University Press, 2016, pp. 909–27, doi:10.1017/s0963548316000079.
short: M. Krivelevich, M.A. Kwan, B. Sudakov, Combinatorics, Probability and Computing
25 (2016) 909–927.
date_created: 2021-06-22T12:35:13Z
date_published: 2016-11-01T00:00:00Z
date_updated: 2023-02-23T14:02:07Z
day: '01'
doi: 10.1017/s0963548316000079
extern: '1'
external_id:
arxiv:
- '1501.04816'
intvolume: ' 25'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1501.04816
month: '11'
oa: 1
oa_version: Preprint
page: 909-927
publication: Combinatorics, Probability and Computing
publication_identifier:
eissn:
- 1469-2163
issn:
- 0963-5483
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cycles and matchings in randomly perturbed digraphs and hypergraphs
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 25
year: '2016'
...
---
_id: '9654'
abstract:
- lang: eng
text: RNA polymerase I (Pol I) is a highly processive enzyme that transcribes ribosomal
DNA (rDNA) and regulates growth of eukaryotic cells. Crystal structures of free
Pol I from the yeast Saccharomyces cerevisiae have revealed dimers of the enzyme
stabilized by a 'connector' element and an expanded cleft containing the active
centre in an inactive conformation. The central bridge helix was unfolded and
a Pol-I-specific 'expander' element occupied the DNA-template-binding site. The
structure of Pol I in its active transcribing conformation has yet to be determined,
whereas structures of Pol II and Pol III have been solved with bound DNA template
and RNA transcript. Here we report structures of active transcribing Pol I from
yeast solved by two different cryo-electron microscopy approaches. A single-particle
structure at 3.8 Å resolution reveals a contracted active centre cleft with bound
DNA and RNA, and a narrowed pore beneath the active site that no longer holds
the RNA-cleavage-stimulating domain of subunit A12.2. A structure at 29 Å resolution
that was determined from cryo-electron tomograms of Pol I enzymes transcribing
cellular rDNA confirms contraction of the cleft and reveals that incoming and
exiting rDNA enclose an angle of around 150°. The structures suggest a model for
the regulation of transcription elongation in which contracted and expanded polymerase
conformations are associated with active and inactive states, respectively.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Simon
full_name: Neyer, Simon
last_name: Neyer
- first_name: Michael
full_name: Kunz, Michael
last_name: Kunz
- first_name: Christian
full_name: Geiss, Christian
last_name: Geiss
- first_name: Merle
full_name: Hantsche, Merle
last_name: Hantsche
- first_name: Victor-Valentin
full_name: Hodirnau, Victor-Valentin
id: 3661B498-F248-11E8-B48F-1D18A9856A87
last_name: Hodirnau
- first_name: Anja
full_name: Seybert, Anja
last_name: Seybert
- first_name: Christoph
full_name: Engel, Christoph
last_name: Engel
- first_name: Margot P.
full_name: Scheffer, Margot P.
last_name: Scheffer
- first_name: Patrick
full_name: Cramer, Patrick
last_name: Cramer
- first_name: Achilleas S.
full_name: Frangakis, Achilleas S.
last_name: Frangakis
citation:
ama: Neyer S, Kunz M, Geiss C, et al. Structure of RNA polymerase I transcribing
ribosomal DNA genes. Nature. 2016;540(7634):607-610. doi:10.1038/nature20561
apa: Neyer, S., Kunz, M., Geiss, C., Hantsche, M., Hodirnau, V.-V., Seybert, A.,
… Frangakis, A. S. (2016). Structure of RNA polymerase I transcribing ribosomal
DNA genes. Nature. Springer Nature. https://doi.org/10.1038/nature20561
chicago: Neyer, Simon, Michael Kunz, Christian Geiss, Merle Hantsche, Victor-Valentin
Hodirnau, Anja Seybert, Christoph Engel, Margot P. Scheffer, Patrick Cramer, and
Achilleas S. Frangakis. “Structure of RNA Polymerase I Transcribing Ribosomal
DNA Genes.” Nature. Springer Nature, 2016. https://doi.org/10.1038/nature20561.
ieee: S. Neyer et al., “Structure of RNA polymerase I transcribing ribosomal
DNA genes,” Nature, vol. 540, no. 7634. Springer Nature, pp. 607–610, 2016.
ista: Neyer S, Kunz M, Geiss C, Hantsche M, Hodirnau V-V, Seybert A, Engel C, Scheffer
MP, Cramer P, Frangakis AS. 2016. Structure of RNA polymerase I transcribing ribosomal
DNA genes. Nature. 540(7634), 607–610.
mla: Neyer, Simon, et al. “Structure of RNA Polymerase I Transcribing Ribosomal
DNA Genes.” Nature, vol. 540, no. 7634, Springer Nature, 2016, pp. 607–10,
doi:10.1038/nature20561.
short: S. Neyer, M. Kunz, C. Geiss, M. Hantsche, V.-V. Hodirnau, A. Seybert, C.
Engel, M.P. Scheffer, P. Cramer, A.S. Frangakis, Nature 540 (2016) 607–610.
date_created: 2021-07-14T09:04:24Z
date_published: 2016-12-22T00:00:00Z
date_updated: 2021-07-22T09:22:20Z
day: '22'
doi: 10.1038/nature20561
extern: '1'
external_id:
pmid:
- '27842382'
intvolume: ' 540'
issue: '7634'
language:
- iso: eng
month: '12'
oa_version: None
page: 607-610
pmid: 1
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structure of RNA polymerase I transcribing ribosomal DNA genes
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 540
year: '2016'
...
---
_id: '9681'
abstract:
- lang: eng
text: One of the most prominent consequences of the quantum nature of light atomic
nuclei is that their kinetic energy does not follow a Maxwell–Boltzmann distribution.
Deep inelastic neutron scattering (DINS) experiments can measure this effect.
Thus, the nuclear quantum kinetic energy can be probed directly in both ordered
and disordered samples. However, the relation between the quantum kinetic energy
and the atomic environment is a very indirect one, and cross-validation with theoretical
modeling is therefore urgently needed. Here, we use state of the art path integral
molecular dynamics techniques to compute the kinetic energy of hydrogen and oxygen
nuclei in liquid, solid, and gas-phase water close to the triple point, comparing
three different interatomic potentials and validating our results against equilibrium
isotope fractionation measurements. We will then show how accurate simulations
can draw a link between extremely precise fractionation experiments and DINS,
therefore establishing a reliable benchmark for future measurements and providing
key insights to increase further the accuracy of interatomic potentials for water.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Jörg
full_name: Behler, Jörg
last_name: Behler
- first_name: Michele
full_name: Ceriotti, Michele
last_name: Ceriotti
citation:
ama: 'Cheng B, Behler J, Ceriotti M. Nuclear quantum effects in water at the triple
point: Using theory as a link between experiments. The Journal of Physical
Chemistry Letters. 2016;7(12):2210-2215. doi:10.1021/acs.jpclett.6b00729'
apa: 'Cheng, B., Behler, J., & Ceriotti, M. (2016). Nuclear quantum effects
in water at the triple point: Using theory as a link between experiments. The
Journal of Physical Chemistry Letters. American Chemical Society. https://doi.org/10.1021/acs.jpclett.6b00729'
chicago: 'Cheng, Bingqing, Jörg Behler, and Michele Ceriotti. “Nuclear Quantum Effects
in Water at the Triple Point: Using Theory as a Link between Experiments.” The
Journal of Physical Chemistry Letters. American Chemical Society, 2016. https://doi.org/10.1021/acs.jpclett.6b00729.'
ieee: 'B. Cheng, J. Behler, and M. Ceriotti, “Nuclear quantum effects in water at
the triple point: Using theory as a link between experiments,” The Journal
of Physical Chemistry Letters, vol. 7, no. 12. American Chemical Society,
pp. 2210–2215, 2016.'
ista: 'Cheng B, Behler J, Ceriotti M. 2016. Nuclear quantum effects in water at
the triple point: Using theory as a link between experiments. The Journal of Physical
Chemistry Letters. 7(12), 2210–2215.'
mla: 'Cheng, Bingqing, et al. “Nuclear Quantum Effects in Water at the Triple Point:
Using Theory as a Link between Experiments.” The Journal of Physical Chemistry
Letters, vol. 7, no. 12, American Chemical Society, 2016, pp. 2210–15, doi:10.1021/acs.jpclett.6b00729.'
short: B. Cheng, J. Behler, M. Ceriotti, The Journal of Physical Chemistry Letters
7 (2016) 2210–2215.
date_created: 2021-07-19T08:57:32Z
date_published: 2016-06-16T00:00:00Z
date_updated: 2023-02-23T14:04:49Z
day: '16'
doi: 10.1021/acs.jpclett.6b00729
extern: '1'
external_id:
pmid:
- '27203358'
intvolume: ' 7'
issue: '12'
language:
- iso: eng
month: '06'
oa_version: None
page: 2210-2215
pmid: 1
publication: The Journal of Physical Chemistry Letters
publication_identifier:
eissn:
- 1948-7185
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Nuclear quantum effects in water at the triple point: Using theory as a link
between experiments'
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 7
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
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.
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: 2021-01-12T06:47:37Z
day: '05'
department:
- _id: CaGu
doi: 10.1021/acssynbio.6b00013
intvolume: ' 5'
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
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'
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'
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'
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
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'
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'
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'
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'
...
---
_id: '1057'
abstract:
- lang: eng
text: Far-field super-resolution fluorescence microscopy discerns fluorophores residing
closer than the diffraction barrier by briefly transferring them in different
(typically ON and OFF) states before detection. In coordinate-targeted super-resolution
variants, such as stimulated emission depletion (STED) microscopy, this state
difference is created by the intensity minima and maxima of an optical pattern,
causing all fluorophores to assume the off state, for instance, except at the
minima. Although strong spatial confinement of the on state enables high resolution,
it also subjects the fluorophores to excess intensities and state cycles at the
maxima. Here, we address these issues by driving the fluorophores into a second
off state that is inert to the excess light. By using reversibly switchable fluorescent
proteins as labels, our approach reduces bleaching and enhances resolution and
contrast in live-cell STED microscopy. Using two or more transitions to off states
is a useful strategy for augmenting the power of coordinate-targeted super-resolution
microscopy.
acknowledgement: We thank T. Gilat and E. Rothermel (both MPI) for help with preparing
samples, and J. Keller for discussion. J.G.D. acknowledges support by the European
Union through a Marie Curie fellowship PIEF-GA-2011-299283. S.W.H. acknowledges
support by the Körber Foundation.
article_processing_charge: No
author:
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Sven
full_name: Sidenstein, Sven
last_name: Sidenstein
- first_name: Carola
full_name: Gregor, Carola
last_name: Gregor
- first_name: Nicolai
full_name: Urban, Nicolai
last_name: Urban
- first_name: Peter
full_name: Ilgen, Peter
last_name: Ilgen
- first_name: Stefan
full_name: Jakobs, Stefan
last_name: Jakobs
- first_name: Stefan
full_name: Hell, Stefan
last_name: Hell
citation:
ama: Danzl JG, Sidenstein S, Gregor C, et al. Coordinate-targeted fluorescence nanoscopy
with multiple off states. Nature Photonics. 2016;10(2):122-128. doi:10.1038/nphoton.2015.266
apa: Danzl, J. G., Sidenstein, S., Gregor, C., Urban, N., Ilgen, P., Jakobs, S.,
& Hell, S. (2016). Coordinate-targeted fluorescence nanoscopy with multiple
off states. Nature Photonics. Nature Publishing Group. https://doi.org/10.1038/nphoton.2015.266
chicago: Danzl, Johann G, Sven Sidenstein, Carola Gregor, Nicolai Urban, Peter Ilgen,
Stefan Jakobs, and Stefan Hell. “Coordinate-Targeted Fluorescence Nanoscopy with
Multiple off States.” Nature Photonics. Nature Publishing Group, 2016.
https://doi.org/10.1038/nphoton.2015.266.
ieee: J. G. Danzl et al., “Coordinate-targeted fluorescence nanoscopy with
multiple off states,” Nature Photonics, vol. 10, no. 2. Nature Publishing
Group, pp. 122–128, 2016.
ista: Danzl JG, Sidenstein S, Gregor C, Urban N, Ilgen P, Jakobs S, Hell S. 2016.
Coordinate-targeted fluorescence nanoscopy with multiple off states. Nature Photonics.
10(2), 122–128.
mla: Danzl, Johann G., et al. “Coordinate-Targeted Fluorescence Nanoscopy with Multiple
off States.” Nature Photonics, vol. 10, no. 2, Nature Publishing Group,
2016, pp. 122–28, doi:10.1038/nphoton.2015.266.
short: J.G. Danzl, S. Sidenstein, C. Gregor, N. Urban, P. Ilgen, S. Jakobs, S. Hell,
Nature Photonics 10 (2016) 122–128.
date_created: 2018-12-11T11:49:55Z
date_published: 2016-02-01T00:00:00Z
date_updated: 2021-01-12T06:47:58Z
day: '01'
doi: 10.1038/nphoton.2015.266
extern: '1'
intvolume: ' 10'
issue: '2'
language:
- iso: eng
month: '02'
oa_version: None
page: 122 - 128
publication: Nature Photonics
publication_status: published
publisher: Nature Publishing Group
publist_id: '6331'
status: public
title: Coordinate-targeted fluorescence nanoscopy with multiple off states
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2016'
...
---
_id: '1059'
abstract:
- lang: eng
text: A range of bright and photostable rhodamines and carbopyronines with absorption
maxima in the range of λ=500-630 nm were prepared, and enabled the specific labeling
of cytoskeletal filaments using HaloTag technology followed by staining with 1
μm solutions of the dye-ligand conjugates. The synthesis, photophysical parameters,
fluorogenic behavior, and structure-property relationships of the new dyes are
discussed. Light microscopy with stimulated emission depletion (STED) provided
one- and two-color images of living cells with an optical resolution of 40-60
nm.
acknowledgement: We thank Prof. Y. Okada (RIKEN Quantitative Biology Center, Osaka,
Japan) for the gift of β-tubulin-Halo plasmid, T. Gilat and Dr. E. Rothermel (MPIBPC,
Göttingen, Germany) for cell culture and transfection, M. Pulst, J. Bienert (MPIBPC),
Dr. M. John, Dr. H. Frauendorf, and co-workers (Institut für Organische und Biomolekulare
Chemie, Georg-August-Universität, Göttingen, Germany) for UV/Vis, NMR, and ESI-MS
spectra, Prof. M. L. Bossi (University of Buenos-Aires, Argentina) for measuring
fluorescence lifetimes, and Dr. S. Vos and Prof. P. Cramer (MPIBPC) for access to
a Tecan microplate reader. S.W.H. acknowledges a grant from the Bundesministerium
für Bildung und Forschung (BMBF 513) within the program “Optische Technologien für
Biowissenschaften und Gesundheit” (FKZ 13N11066). J.G.D. was supported by funds
from the People Programme (Marie Curie Actions) of the European Union's Seventh
Framework Programme (FP7/2007–2013; REA grant agreement PIEF-GA-2011-299283).
article_processing_charge: No
author:
- first_name: Alexey
full_name: Butkevich, Alexey
last_name: Butkevich
- first_name: Gyuzel
full_name: Mitronova, Gyuzel
last_name: Mitronova
- first_name: Sven
full_name: Sidenstein, Sven
last_name: Sidenstein
- first_name: Jessica
full_name: Klocke, Jessica
last_name: Klocke
- first_name: Dirk
full_name: Kamin, Dirk
last_name: Kamin
- first_name: Dirk
full_name: Meineke, Dirk
last_name: Meineke
- first_name: Elisa
full_name: D'Este, Elisa
last_name: D'Este
- first_name: Philip
full_name: Kraemer, Philip
last_name: Kraemer
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Vladimir
full_name: Belov, Vladimir
last_name: Belov
- first_name: Stefan
full_name: Hell, Stefan
last_name: Hell
citation:
ama: Butkevich A, Mitronova G, Sidenstein S, et al. Fluorescent rhodamines and fluorogenic
carbopyronines for super-resolution STED microscopy in living cells. Angewandte
Chemie - International Edition. 2016;55(10):3290-3294. doi:10.1002/anie.201511018
apa: Butkevich, A., Mitronova, G., Sidenstein, S., Klocke, J., Kamin, D., Meineke,
D., … Hell, S. (2016). Fluorescent rhodamines and fluorogenic carbopyronines for
super-resolution STED microscopy in living cells. Angewandte Chemie - International
Edition. Wiley-Blackwell. https://doi.org/10.1002/anie.201511018
chicago: Butkevich, Alexey, Gyuzel Mitronova, Sven Sidenstein, Jessica Klocke, Dirk
Kamin, Dirk Meineke, Elisa D’Este, et al. “Fluorescent Rhodamines and Fluorogenic
Carbopyronines for Super-Resolution STED Microscopy in Living Cells.” Angewandte
Chemie - International Edition. Wiley-Blackwell, 2016. https://doi.org/10.1002/anie.201511018.
ieee: A. Butkevich et al., “Fluorescent rhodamines and fluorogenic carbopyronines
for super-resolution STED microscopy in living cells,” Angewandte Chemie -
International Edition, vol. 55, no. 10. Wiley-Blackwell, pp. 3290–3294, 2016.
ista: Butkevich A, Mitronova G, Sidenstein S, Klocke J, Kamin D, Meineke D, D’Este
E, Kraemer P, Danzl JG, Belov V, Hell S. 2016. Fluorescent rhodamines and fluorogenic
carbopyronines for super-resolution STED microscopy in living cells. Angewandte
Chemie - International Edition. 55(10), 3290–3294.
mla: Butkevich, Alexey, et al. “Fluorescent Rhodamines and Fluorogenic Carbopyronines
for Super-Resolution STED Microscopy in Living Cells.” Angewandte Chemie -
International Edition, vol. 55, no. 10, Wiley-Blackwell, 2016, pp. 3290–94,
doi:10.1002/anie.201511018.
short: A. Butkevich, G. Mitronova, S. Sidenstein, J. Klocke, D. Kamin, D. Meineke,
E. D’Este, P. Kraemer, J.G. Danzl, V. Belov, S. Hell, Angewandte Chemie - International
Edition 55 (2016) 3290–3294.
date_created: 2018-12-11T11:49:55Z
date_published: 2016-03-01T00:00:00Z
date_updated: 2021-01-12T06:47:59Z
day: '01'
doi: 10.1002/anie.201511018
extern: '1'
intvolume: ' 55'
issue: '10'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '03'
oa_version: None
page: 3290 - 3294
publication: Angewandte Chemie - International Edition
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6330'
status: public
title: Fluorescent rhodamines and fluorogenic carbopyronines for super-resolution
STED microscopy in living cells
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2016'
...