---
_id: '9668'
abstract:
- lang: eng
text: Estimating the homogeneous ice nucleation rate from undercooled liquid water
is crucial for understanding many important physical phenomena and technological
applications, and challenging for both experiments and theory. From a theoretical
point of view, difficulties arise due to the long time scales required, as well
as the numerous nucleation pathways involved to form ice nuclei with different
stacking disorders. We computed the homogeneous ice nucleation rate at a physically
relevant undercooling for a single-site water model, taking into account the diffuse
nature of ice–water interfaces, stacking disorders in ice nuclei, and the addition
rate of particles to the critical nucleus. We disentangled and investigated the
relative importance of all the terms, including interfacial free energy, entropic
contributions and the kinetic prefactor, that contribute to the overall nucleation
rate. Breaking down the problem into pieces not only provides physical insights
into ice nucleation, but also sheds light on the long-standing discrepancy between
different theoretical predictions, as well as between theoretical and experimental
determinations of the nucleation rate. Moreover, we pinpoint the main shortcomings
and suggest strategies to systematically improve the existing simulation methods.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Christoph
full_name: Dellago, Christoph
last_name: Dellago
- first_name: Michele
full_name: Ceriotti, Michele
last_name: Ceriotti
citation:
ama: 'Cheng B, Dellago C, Ceriotti M. Theoretical prediction of the homogeneous
ice nucleation rate: Disentangling thermodynamics and kinetics. Physical Chemistry
Chemical Physics. 2018;20(45):28732-28740. doi:10.1039/c8cp04561e'
apa: 'Cheng, B., Dellago, C., & Ceriotti, M. (2018). Theoretical prediction
of the homogeneous ice nucleation rate: Disentangling thermodynamics and kinetics.
Physical Chemistry Chemical Physics. Royal Society of Chemistry. https://doi.org/10.1039/c8cp04561e'
chicago: 'Cheng, Bingqing, Christoph Dellago, and Michele Ceriotti. “Theoretical
Prediction of the Homogeneous Ice Nucleation Rate: Disentangling Thermodynamics
and Kinetics.” Physical Chemistry Chemical Physics. Royal Society of Chemistry,
2018. https://doi.org/10.1039/c8cp04561e.'
ieee: 'B. Cheng, C. Dellago, and M. Ceriotti, “Theoretical prediction of the homogeneous
ice nucleation rate: Disentangling thermodynamics and kinetics,” Physical Chemistry
Chemical Physics, vol. 20, no. 45. Royal Society of Chemistry, pp. 28732–28740,
2018.'
ista: 'Cheng B, Dellago C, Ceriotti M. 2018. Theoretical prediction of the homogeneous
ice nucleation rate: Disentangling thermodynamics and kinetics. Physical Chemistry
Chemical Physics. 20(45), 28732–28740.'
mla: 'Cheng, Bingqing, et al. “Theoretical Prediction of the Homogeneous Ice Nucleation
Rate: Disentangling Thermodynamics and Kinetics.” Physical Chemistry Chemical
Physics, vol. 20, no. 45, Royal Society of Chemistry, 2018, pp. 28732–40,
doi:10.1039/c8cp04561e.'
short: B. Cheng, C. Dellago, M. Ceriotti, Physical Chemistry Chemical Physics 20
(2018) 28732–28740.
date_created: 2021-07-15T12:51:44Z
date_published: 2018-12-07T00:00:00Z
date_updated: 2021-08-09T12:36:47Z
day: '07'
doi: 10.1039/c8cp04561e
extern: '1'
external_id:
arxiv:
- '1807.05551'
pmid:
- '30412211'
intvolume: ' 20'
issue: '45'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1807.05551
month: '12'
oa: 1
oa_version: Preprint
page: 28732-28740
pmid: 1
publication: Physical Chemistry Chemical Physics
publication_identifier:
eissn:
- 1463-9084
issn:
- 1463-9076
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Theoretical prediction of the homogeneous ice nucleation rate: Disentangling
thermodynamics and kinetics'
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 20
year: '2018'
...
---
_id: '9687'
abstract:
- lang: eng
text: The Gibbs free energy is the fundamental thermodynamic potential underlying
the relative stability of different states of matter under constant-pressure conditions.
However, computing this quantity from atomic-scale simulations is far from trivial,
so the potential energy of a system is often used as a proxy. In this paper, we
use a combination of thermodynamic integration methods to accurately evaluate
the Gibbs free energies associated with defects in crystals, including the vacancy
formation energy in bcc iron, and the stacking fault energy in fcc nickel, iron,
and cobalt. We quantify the importance of entropic and anharmonic effects in determining
the free energies of defects at high temperatures, and show that the potential
energy approximation as well as the harmonic approximation may produce inaccurate
or even qualitatively wrong results. Our calculations manifest the necessity to
employ accurate free energy methods such as thermodynamic integration to estimate
the stability of crystallographic defects at high temperatures.
article_number: '054102'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Michele
full_name: Ceriotti, Michele
last_name: Ceriotti
citation:
ama: 'Cheng B, Ceriotti M. Computing the absolute Gibbs free energy in atomistic
simulations: Applications to defects in solids. Physical Review B. 2018;97(5).
doi:10.1103/physrevb.97.054102'
apa: 'Cheng, B., & Ceriotti, M. (2018). Computing the absolute Gibbs free energy
in atomistic simulations: Applications to defects in solids. Physical Review
B. American Physical Society. https://doi.org/10.1103/physrevb.97.054102'
chicago: 'Cheng, Bingqing, and Michele Ceriotti. “Computing the Absolute Gibbs Free
Energy in Atomistic Simulations: Applications to Defects in Solids.” Physical
Review B. American Physical Society, 2018. https://doi.org/10.1103/physrevb.97.054102.'
ieee: 'B. Cheng and M. Ceriotti, “Computing the absolute Gibbs free energy in atomistic
simulations: Applications to defects in solids,” Physical Review B, vol.
97, no. 5. American Physical Society, 2018.'
ista: 'Cheng B, Ceriotti M. 2018. Computing the absolute Gibbs free energy in atomistic
simulations: Applications to defects in solids. Physical Review B. 97(5), 054102.'
mla: 'Cheng, Bingqing, and Michele Ceriotti. “Computing the Absolute Gibbs Free
Energy in Atomistic Simulations: Applications to Defects in Solids.” Physical
Review B, vol. 97, no. 5, 054102, American Physical Society, 2018, doi:10.1103/physrevb.97.054102.'
short: B. Cheng, M. Ceriotti, Physical Review B 97 (2018).
date_created: 2021-07-19T09:39:48Z
date_published: 2018-02-01T00:00:00Z
date_updated: 2021-08-09T12:38:26Z
day: '01'
doi: 10.1103/physrevb.97.054102
extern: '1'
external_id:
arxiv:
- '1710.02815'
intvolume: ' 97'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1710.02815
month: '02'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Computing the absolute Gibbs free energy in atomistic simulations: Applications
to defects in solids'
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 97
year: '2018'
...
---
_id: '10'
abstract:
- lang: eng
text: Genomic imprinting is an epigenetic process that leads to parent of origin-specific
gene expression in a subset of genes. Imprinted genes are essential for brain
development, and deregulation of imprinting is associated with neurodevelopmental
diseases and the pathogenesis of psychiatric disorders. However, the cell-type
specificity of imprinting at single cell resolution, and how imprinting and thus
gene dosage regulates neuronal circuit assembly is still largely unknown. Here,
MADM (Mosaic Analysis with Double Markers) technology was employed to assess genomic
imprinting at single cell level. By visualizing MADM-induced uniparental disomies
(UPDs) in distinct colors at single cell level in genetic mosaic animals, this
experimental paradigm provides a unique quantitative platform to systematically
assay the UPD-mediated imbalances in imprinted gene expression at unprecedented
resolution. An experimental pipeline based on FACS, RNA-seq and bioinformatics
analysis was established and applied to systematically map cell-type-specific
‘imprintomes’ in the mouse brain. The results revealed that parental-specific
expression of imprinted genes per se is rarely cell-type-specific even at the
individual cell level. Conversely, when we extended the comparison to downstream
responses resulting from imbalanced imprinted gene expression, we discovered an
unexpectedly high degree of cell-type specificity. Furthermore, we determined
a novel function of genomic imprinting in cortical astrocyte production and in
olfactory bulb (OB) granule cell generation. These results suggest important functional
implication of genomic imprinting for generating cell-type diversity in the brain.
In addition, MADM provides a powerful tool to study candidate genes by concomitant
genetic manipulation and fluorescent labelling of single cells. MADM-based candidate
gene approach was utilized to identify potential imprinted genes involved in the
generation of cortical astrocytes and OB granule cells. We investigated p57Kip2,
a maternally expressed gene and known cell cycle regulator. Although we found
that p57Kip2 does not play a role in these processes, we detected an unexpected
function of the paternal allele previously thought to be silent. Finally, we took
advantage of a key property of MADM which is to allow unambiguous investigation
of environmental impact on single cells. The experimental pipeline based on FACS
and RNA-seq analysis of MADM-labeled cells was established to probe the functional
differences of single cell loss of gene function compared to global loss of function
on a transcriptional level. With this method, both common and distinct responses
were isolated due to cell-autonomous and non-autonomous effects acting on genotypically
identical cells. As a result, transcriptional changes were identified which result
solely from the surrounding environment. Using the MADM technology to study genomic
imprinting at single cell resolution, we have identified cell-type-specific gene
expression, novel gene function and the impact of environment on single cell transcriptomes.
Together, these provide important insights to the understanding of mechanisms
regulating cell-type specificity and thus diversity in the brain.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Susanne
full_name: Laukoter, Susanne
id: 2D6B7A9A-F248-11E8-B48F-1D18A9856A87
last_name: Laukoter
orcid: 0000-0002-7903-3010
citation:
ama: Laukoter S. Role of genomic imprinting in cerebral cortex development. 2018:1-139.
doi:10.15479/AT:ISTA:th1057
apa: Laukoter, S. (2018). Role of genomic imprinting in cerebral cortex development.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th1057
chicago: Laukoter, Susanne. “Role of Genomic Imprinting in Cerebral Cortex Development.”
Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th1057.
ieee: S. Laukoter, “Role of genomic imprinting in cerebral cortex development,”
Institute of Science and Technology Austria, 2018.
ista: Laukoter S. 2018. Role of genomic imprinting in cerebral cortex development.
Institute of Science and Technology Austria.
mla: Laukoter, Susanne. Role of Genomic Imprinting in Cerebral Cortex Development.
Institute of Science and Technology Austria, 2018, pp. 1–139, doi:10.15479/AT:ISTA:th1057.
short: S. Laukoter, Role of Genomic Imprinting in Cerebral Cortex Development, Institute
of Science and Technology Austria, 2018.
date_created: 2018-12-11T11:44:08Z
date_published: 2018-11-21T00:00:00Z
date_updated: 2023-09-07T12:40:44Z
day: '21'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: SiHi
doi: 10.15479/AT:ISTA:th1057
file:
- access_level: closed
checksum: 41fdbf5fdce312802935d88a8ad9932c
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: dernst
date_created: 2019-05-10T07:47:04Z
date_updated: 2019-11-23T23:30:03Z
embargo_to: open_access
file_id: '6396'
file_name: Thesis_LaukoterSusanne_FINAL.docx
file_size: 17949175
relation: source_file
- access_level: open_access
checksum: 53001a9a0c9e570e598d861bb0af28aa
content_type: application/pdf
creator: dernst
date_created: 2019-05-10T07:47:04Z
date_updated: 2021-02-11T11:17:16Z
embargo: 2019-11-21
file_id: '6397'
file_name: Thesis_LaukoterSusanne_FINAL.pdf
file_size: 21187245
relation: main_file
file_date_updated: 2021-02-11T11:17:16Z
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 1 - 139
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '8046'
pubrep_id: '1057'
status: public
supervisor:
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
title: Role of genomic imprinting in cerebral cortex development
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '1012'
abstract:
- lang: eng
text: We prove a new central limit theorem (CLT) for the difference of linear eigenvalue
statistics of a Wigner random matrix H and its minor H and find that the fluctuation
is much smaller than the fluctuations of the individual linear statistics, as
a consequence of the strong correlation between the eigenvalues of H and H. In
particular, our theorem identifies the fluctuation of Kerov's rectangular Young
diagrams, defined by the interlacing eigenvalues ofH and H, around their asymptotic
shape, the Vershik'Kerov'Logan'Shepp curve. Young diagrams equipped with the Plancherel
measure follow the same limiting shape. For this, algebraically motivated, ensemble
a CLT has been obtained in Ivanov and Olshanski [20] which is structurally similar
to our result but the variance is different, indicating that the analogy between
the two models has its limitations. Moreover, our theorem shows that Borodin's
result [7] on the convergence of the spectral distribution of Wigner matrices
to a Gaussian free field also holds in derivative sense.
article_processing_charge: No
arxiv: 1
author:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Dominik J
full_name: Schröder, Dominik J
id: 408ED176-F248-11E8-B48F-1D18A9856A87
last_name: Schröder
orcid: 0000-0002-2904-1856
citation:
ama: Erdös L, Schröder DJ. Fluctuations of rectangular young diagrams of interlacing
wigner eigenvalues. International Mathematics Research Notices. 2018;2018(10):3255-3298.
doi:10.1093/imrn/rnw330
apa: Erdös, L., & Schröder, D. J. (2018). Fluctuations of rectangular young
diagrams of interlacing wigner eigenvalues. International Mathematics Research
Notices. Oxford University Press. https://doi.org/10.1093/imrn/rnw330
chicago: Erdös, László, and Dominik J Schröder. “Fluctuations of Rectangular Young
Diagrams of Interlacing Wigner Eigenvalues.” International Mathematics Research
Notices. Oxford University Press, 2018. https://doi.org/10.1093/imrn/rnw330.
ieee: L. Erdös and D. J. Schröder, “Fluctuations of rectangular young diagrams of
interlacing wigner eigenvalues,” International Mathematics Research Notices,
vol. 2018, no. 10. Oxford University Press, pp. 3255–3298, 2018.
ista: Erdös L, Schröder DJ. 2018. Fluctuations of rectangular young diagrams of
interlacing wigner eigenvalues. International Mathematics Research Notices. 2018(10),
3255–3298.
mla: Erdös, László, and Dominik J. Schröder. “Fluctuations of Rectangular Young
Diagrams of Interlacing Wigner Eigenvalues.” International Mathematics Research
Notices, vol. 2018, no. 10, Oxford University Press, 2018, pp. 3255–98, doi:10.1093/imrn/rnw330.
short: L. Erdös, D.J. Schröder, International Mathematics Research Notices 2018
(2018) 3255–3298.
date_created: 2018-12-11T11:49:41Z
date_published: 2018-05-18T00:00:00Z
date_updated: 2023-09-22T09:44:21Z
day: '18'
department:
- _id: LaEr
doi: 10.1093/imrn/rnw330
ec_funded: 1
external_id:
arxiv:
- '1608.05163'
isi:
- '000441668300009'
intvolume: ' 2018'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1608.05163
month: '05'
oa: 1
oa_version: Preprint
page: 3255-3298
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: International Mathematics Research Notices
publication_identifier:
issn:
- '10737928'
publication_status: published
publisher: Oxford University Press
publist_id: '6383'
quality_controlled: '1'
related_material:
record:
- id: '6179'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Fluctuations of rectangular young diagrams of interlacing wigner eigenvalues
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2018
year: '2018'
...
---
_id: '10286'
abstract:
- lang: eng
text: 'In this paper, we evaluate clock signals generated in ring oscillators and
self-timed rings and the way their jitter can be transformed into random numbers.
We show that counting the periods of the jittery clock signal produces random
numbers of significantly better quality than the methods in which the jittery
signal is simply sampled (the case in almost all current methods). Moreover, we
use the counter values to characterize and continuously monitor the source of
randomness. However, instead of using the widely used statistical variance, we
propose to use Allan variance to do so. There are two main advantages: Allan variance
is insensitive to low frequency noises such as flicker noise that are known to
be autocorrelated and significantly less circuitry is required for its computation
than that used to compute commonly used variance. We also show that it is essential
to use a differential principle of randomness extraction from the jitter based
on the use of two identical oscillators to avoid autocorrelations originating
from external and internal global jitter sources and that this fact is valid for
both kinds of rings. Last but not least, we propose a method of statistical testing
based on high order Markov model to show the reduced dependencies when the proposed
randomness extraction is applied.'
article_processing_charge: No
article_type: original
author:
- first_name: Elie Noumon
full_name: Allini, Elie Noumon
last_name: Allini
- first_name: Maciej
full_name: Skórski, Maciej
id: EC09FA6A-02D0-11E9-8223-86B7C91467DD
last_name: Skórski
- first_name: Oto
full_name: Petura, Oto
last_name: Petura
- first_name: Florent
full_name: Bernard, Florent
last_name: Bernard
- first_name: Marek
full_name: Laban, Marek
last_name: Laban
- first_name: Viktor
full_name: Fischer, Viktor
last_name: Fischer
citation:
ama: Allini EN, Skórski M, Petura O, Bernard F, Laban M, Fischer V. Evaluation and
monitoring of free running oscillators serving as source of randomness. IACR
Transactions on Cryptographic Hardware and Embedded Systems. 2018;2018(3):214-242.
doi:10.13154/tches.v2018.i3.214-242
apa: Allini, E. N., Skórski, M., Petura, O., Bernard, F., Laban, M., & Fischer,
V. (2018). Evaluation and monitoring of free running oscillators serving as source
of randomness. IACR Transactions on Cryptographic Hardware and Embedded Systems.
International Association for Cryptologic Research. https://doi.org/10.13154/tches.v2018.i3.214-242
chicago: Allini, Elie Noumon, Maciej Skórski, Oto Petura, Florent Bernard, Marek
Laban, and Viktor Fischer. “Evaluation and Monitoring of Free Running Oscillators
Serving as Source of Randomness.” IACR Transactions on Cryptographic Hardware
and Embedded Systems. International Association for Cryptologic Research,
2018. https://doi.org/10.13154/tches.v2018.i3.214-242.
ieee: E. N. Allini, M. Skórski, O. Petura, F. Bernard, M. Laban, and V. Fischer,
“Evaluation and monitoring of free running oscillators serving as source of randomness,”
IACR Transactions on Cryptographic Hardware and Embedded Systems, vol.
2018, no. 3. International Association for Cryptologic Research, pp. 214–242,
2018.
ista: Allini EN, Skórski M, Petura O, Bernard F, Laban M, Fischer V. 2018. Evaluation
and monitoring of free running oscillators serving as source of randomness. IACR
Transactions on Cryptographic Hardware and Embedded Systems. 2018(3), 214–242.
mla: Allini, Elie Noumon, et al. “Evaluation and Monitoring of Free Running Oscillators
Serving as Source of Randomness.” IACR Transactions on Cryptographic Hardware
and Embedded Systems, vol. 2018, no. 3, International Association for Cryptologic
Research, 2018, pp. 214–42, doi:10.13154/tches.v2018.i3.214-242.
short: E.N. Allini, M. Skórski, O. Petura, F. Bernard, M. Laban, V. Fischer, IACR
Transactions on Cryptographic Hardware and Embedded Systems 2018 (2018) 214–242.
date_created: 2021-11-14T23:01:25Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2021-11-15T10:48:49Z
day: '01'
ddc:
- '000'
department:
- _id: KrPi
doi: 10.13154/tches.v2018.i3.214-242
file:
- access_level: open_access
checksum: b816b848f046c48a8357700d9305dce5
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-15T10:27:29Z
date_updated: 2021-11-15T10:27:29Z
file_id: '10289'
file_name: 2018_IACR_Allini.pdf
file_size: 955755
relation: main_file
success: 1
file_date_updated: 2021-11-15T10:27:29Z
has_accepted_license: '1'
intvolume: ' 2018'
issue: '3'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '01'
oa: 1
oa_version: Published Version
page: 214-242
publication: IACR Transactions on Cryptographic Hardware and Embedded Systems
publication_identifier:
eissn:
- 2569-2925
publication_status: published
publisher: International Association for Cryptologic Research
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evaluation and monitoring of free running oscillators serving as source of
randomness
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: 2018
year: '2018'
...
---
_id: '10357'
abstract:
- lang: eng
text: The misfolding and aggregation of proteins into linear fibrils is widespread
in human biology, for example, in connection with amyloid formation and the pathology
of neurodegenerative disorders such as Alzheimer’s and Parkinson’s diseases. The
oligomeric species that are formed in the early stages of protein aggregation
are of great interest, having been linked with the cellular toxicity associated
with these conditions. However, these species are not characterized in any detail
experimentally, and their properties are not well understood. Many of these species
have been found to have approximately spherical morphology and to be held together
by hydrophobic interactions. We present here an analytical statistical mechanical
model of globular oligomer formation from simple idealized amphiphilic protein
monomers and show that this correlates well with Monte Carlo simulations of oligomer
formation. We identify the controlling parameters of the model, which are closely
related to simple quantities that may be fitted directly from experiment. We predict
that globular oligomers are unlikely to form at equilibrium in many polypeptide
systems but instead form transiently in the early stages of amyloid formation.
We contrast the globular model of oligomer formation to a well-established model
of linear oligomer formation, highlighting how the differing ensemble properties
of linear and globular oligomers offer a potential strategy for characterizing
oligomers from experimental measurements.
acknowledgement: We acknowledge support from the Schiff Foundation (A.J.D.), the Royal
Society (A.Š.), the Academy of Medical Sciences and Wellcome Trust (A.Š.), Peterhouse,
Cambridge (T.C.T.M.), the Swiss National Science foundation (T.C.T.M.), the Wellcome
Trust (T.P.J.K.), the Cambridge Centre for Misfolding Diseases (T.P.J.K.), the BBSRC
(T.P.J.K.), the Frances and Augustus Newman foundation (T.P.J.K.). The research
leading to these results has received funding from the European Research Council
under the European Union’s Seventh Framework Programme (Grant FP7/2007-2013) through
the ERC Grant PhysProt (Agreement No. 337969). We thank Daan Frenkel for several
useful discussions.
article_processing_charge: No
article_type: original
author:
- first_name: Alexander J.
full_name: Dear, Alexander J.
last_name: Dear
- 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: Christopher M.
full_name: Dobson, Christopher M.
last_name: Dobson
- first_name: Tuomas P. J.
full_name: Knowles, Tuomas P. J.
last_name: Knowles
citation:
ama: Dear AJ, Šarić A, Michaels TCT, Dobson CM, Knowles TPJ. Statistical mechanics
of globular oligomer formation by protein molecules. The Journal of Physical
Chemistry B. 2018;122(49):11721-11730. doi:10.1021/acs.jpcb.8b07805
apa: Dear, A. J., Šarić, A., Michaels, T. C. T., Dobson, C. M., & Knowles, T.
P. J. (2018). Statistical mechanics of globular oligomer formation by protein
molecules. The Journal of Physical Chemistry B. American Chemical Society.
https://doi.org/10.1021/acs.jpcb.8b07805
chicago: Dear, Alexander J., Anđela Šarić, Thomas C. T. Michaels, Christopher M.
Dobson, and Tuomas P. J. Knowles. “Statistical Mechanics of Globular Oligomer
Formation by Protein Molecules.” The Journal of Physical Chemistry B. American
Chemical Society, 2018. https://doi.org/10.1021/acs.jpcb.8b07805.
ieee: A. J. Dear, A. Šarić, T. C. T. Michaels, C. M. Dobson, and T. P. J. Knowles,
“Statistical mechanics of globular oligomer formation by protein molecules,” The
Journal of Physical Chemistry B, vol. 122, no. 49. American Chemical Society,
pp. 11721–11730, 2018.
ista: Dear AJ, Šarić A, Michaels TCT, Dobson CM, Knowles TPJ. 2018. Statistical
mechanics of globular oligomer formation by protein molecules. The Journal of
Physical Chemistry B. 122(49), 11721–11730.
mla: Dear, Alexander J., et al. “Statistical Mechanics of Globular Oligomer Formation
by Protein Molecules.” The Journal of Physical Chemistry B, vol. 122, no.
49, American Chemical Society, 2018, pp. 11721–30, doi:10.1021/acs.jpcb.8b07805.
short: A.J. Dear, A. Šarić, T.C.T. Michaels, C.M. Dobson, T.P.J. Knowles, The Journal
of Physical Chemistry B 122 (2018) 11721–11730.
date_created: 2021-11-26T11:55:12Z
date_published: 2018-10-18T00:00:00Z
date_updated: 2021-11-26T12:40:02Z
day: '18'
doi: 10.1021/acs.jpcb.8b07805
extern: '1'
external_id:
pmid:
- '30336667'
intvolume: ' 122'
issue: '49'
keyword:
- materials chemistry
language:
- iso: eng
month: '10'
oa_version: None
page: 11721-11730
pmid: 1
publication: The Journal of Physical Chemistry B
publication_identifier:
eissn:
- 1520-5207
issn:
- 1520-6106
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Statistical mechanics of globular oligomer formation by protein molecules
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 122
year: '2018'
...
---
_id: '10358'
abstract:
- lang: eng
text: Probing reaction mechanisms of supramolecular processes in soft and biological
matter, such as protein aggregation, is inherently challenging. This is because
these processes involve multiple molecular mechanisms that are associated with
the rearrangement of large numbers of weak bonds, resulting in complex free energy
landscapes with many kinetic barriers. Reaction rate measurements at different
temperatures can offer unprecedented insights into the underlying molecular mechanisms.
However, to be able to interpret such measurements, a key challenge is to establish
which properties of the complex free energy landscapes are probed by the reaction
rate. Here, we present a reaction rate theory for supramolecular kinetics based
on Kramers theory of diffusive reactions over multiple kinetic barriers. We find
that reaction rates for protein aggregation are of the Arrhenius–Eyring type and
that the associated activation energies probe only one relevant barrier along
the respective free energy landscapes. We apply this advancement to interpret,
in experiments and in coarse-grained computer simulations, reaction rates of amyloid
aggregation in terms of molecular mechanisms and associated thermodynamic signatures.
These results suggest a practical extension of the concept of rate-determining
steps for complex supramolecular processes and establish a general platform for
probing the underlying energy landscape using kinetic measurements.
acknowledgement: We thank Claudia Flandoli for the help with illustrations.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Thomas C. T.
full_name: Michaels, Thomas C. T.
last_name: Michaels
- first_name: Lucie X.
full_name: Liu, Lucie X.
last_name: Liu
- first_name: Samo
full_name: Curk, Samo
last_name: Curk
- first_name: Peter G.
full_name: Bolhuis, Peter G.
last_name: Bolhuis
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Tuomas P. J.
full_name: Knowles, Tuomas P. J.
last_name: Knowles
citation:
ama: 'Michaels TCT, Liu LX, Curk S, Bolhuis PG, Šarić A, Knowles TPJ. Reaction rate
theory for supramolecular kinetics: application to protein aggregation. Molecular
Physics. 2018;116(21-22):3055-3065. doi:10.1080/00268976.2018.1474280'
apa: 'Michaels, T. C. T., Liu, L. X., Curk, S., Bolhuis, P. G., Šarić, A., &
Knowles, T. P. J. (2018). Reaction rate theory for supramolecular kinetics: application
to protein aggregation. Molecular Physics. Taylor & Francis. https://doi.org/10.1080/00268976.2018.1474280'
chicago: 'Michaels, Thomas C. T., Lucie X. Liu, Samo Curk, Peter G. Bolhuis, Anđela
Šarić, and Tuomas P. J. Knowles. “Reaction Rate Theory for Supramolecular Kinetics:
Application to Protein Aggregation.” Molecular Physics. Taylor & Francis,
2018. https://doi.org/10.1080/00268976.2018.1474280.'
ieee: 'T. C. T. Michaels, L. X. Liu, S. Curk, P. G. Bolhuis, A. Šarić, and T. P.
J. Knowles, “Reaction rate theory for supramolecular kinetics: application to
protein aggregation,” Molecular Physics, vol. 116, no. 21–22. Taylor &
Francis, pp. 3055–3065, 2018.'
ista: 'Michaels TCT, Liu LX, Curk S, Bolhuis PG, Šarić A, Knowles TPJ. 2018. Reaction
rate theory for supramolecular kinetics: application to protein aggregation. Molecular
Physics. 116(21–22), 3055–3065.'
mla: 'Michaels, Thomas C. T., et al. “Reaction Rate Theory for Supramolecular Kinetics:
Application to Protein Aggregation.” Molecular Physics, vol. 116, no. 21–22,
Taylor & Francis, 2018, pp. 3055–65, doi:10.1080/00268976.2018.1474280.'
short: T.C.T. Michaels, L.X. Liu, S. Curk, P.G. Bolhuis, A. Šarić, T.P.J. Knowles,
Molecular Physics 116 (2018) 3055–3065.
date_created: 2021-11-26T12:08:02Z
date_published: 2018-05-24T00:00:00Z
date_updated: 2021-11-26T12:39:58Z
day: '24'
doi: 10.1080/00268976.2018.1474280
extern: '1'
external_id:
arxiv:
- '1803.04851'
intvolume: ' 116'
issue: 21-22
keyword:
- physical chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1803.04851
month: '05'
oa: 1
oa_version: Preprint
page: 3055-3065
publication: Molecular Physics
publication_identifier:
eissn:
- 1362-3028
issn:
- 0026-8976
publication_status: published
publisher: Taylor & Francis
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Reaction rate theory for supramolecular kinetics: application to protein aggregation'
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 116
year: '2018'
...
---
_id: '10359'
abstract:
- lang: eng
text: Biological membranes typically contain a large number of different components
dispersed in small concentrations in the main membrane phase, including proteins,
sugars, and lipids of varying geometrical properties. Most of these components
do not bind the cargo. Here, we show that such “inert” components can be crucial
for the precise control of cross-membrane trafficking. Using a statistical mechanics
model and molecular dynamics simulations, we demonstrate that the presence of
inert membrane components of small isotropic curvatures dramatically influences
cargo endocytosis, even if the total spontaneous curvature of such a membrane
remains unchanged. Curved lipids, such as cholesterol, as well as asymmetrically
included proteins and tethered sugars can, therefore, actively participate in
the control of the membrane trafficking of nanoscopic cargo. We find that even
a low-level expression of curved inert membrane components can determine the membrane
selectivity toward the cargo size and can be used to selectively target membranes
of certain compositions. Our results suggest a robust and general method of controlling
cargo trafficking by adjusting the membrane composition without needing to alter
the concentration of receptors or the average membrane curvature. This study indicates
that cells can prepare for any trafficking event by incorporating curved inert
components in either of the membrane leaflets.
acknowledgement: We acknowledge discussions with Giuseppe Battaglia as well as support
from the Herchel Smith scholarship (T.C.), the CAS PIFI fellowship (T.C.), the UCL
Institute for the Physics of Living Systems (T.C. and A.Š.), the Austrian Academy
of Sciences through a DOC fellowship (P.W.), the European Union Horizon 2020 programme
under ETN grant no. 674979-NANOTRANS and FET grant no. 766972-NANOPHLOW (J.D. and
D.F.), the Engineering and Physical Sciences Research Council (D.F. and A.Š.), the
Academy of Medical Sciences and Wellcome Trust (A.Š.), and the Royal Society (A.Š.).
We thank Claudia Flandoli for help with Figure 1.
article_processing_charge: No
article_type: original
author:
- first_name: Tine
full_name: Curk, Tine
last_name: Curk
- first_name: Peter
full_name: Wirnsberger, Peter
last_name: Wirnsberger
- first_name: Jure
full_name: Dobnikar, Jure
last_name: Dobnikar
- first_name: Daan
full_name: Frenkel, Daan
last_name: Frenkel
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
citation:
ama: Curk T, Wirnsberger P, Dobnikar J, Frenkel D, Šarić A. Controlling cargo trafficking
in multicomponent membranes. Nano Letters. 2018;18(9):5350-5356. doi:10.1021/acs.nanolett.8b00786
apa: Curk, T., Wirnsberger, P., Dobnikar, J., Frenkel, D., & Šarić, A. (2018).
Controlling cargo trafficking in multicomponent membranes. Nano Letters.
American Chemical Society. https://doi.org/10.1021/acs.nanolett.8b00786
chicago: Curk, Tine, Peter Wirnsberger, Jure Dobnikar, Daan Frenkel, and Anđela
Šarić. “Controlling Cargo Trafficking in Multicomponent Membranes.” Nano Letters.
American Chemical Society, 2018. https://doi.org/10.1021/acs.nanolett.8b00786.
ieee: T. Curk, P. Wirnsberger, J. Dobnikar, D. Frenkel, and A. Šarić, “Controlling
cargo trafficking in multicomponent membranes,” Nano Letters, vol. 18,
no. 9. American Chemical Society, pp. 5350–5356, 2018.
ista: Curk T, Wirnsberger P, Dobnikar J, Frenkel D, Šarić A. 2018. Controlling cargo
trafficking in multicomponent membranes. Nano Letters. 18(9), 5350–5356.
mla: Curk, Tine, et al. “Controlling Cargo Trafficking in Multicomponent Membranes.”
Nano Letters, vol. 18, no. 9, American Chemical Society, 2018, pp. 5350–56,
doi:10.1021/acs.nanolett.8b00786.
short: T. Curk, P. Wirnsberger, J. Dobnikar, D. Frenkel, A. Šarić, Nano Letters
18 (2018) 5350–5356.
date_created: 2021-11-26T12:15:47Z
date_published: 2018-04-18T00:00:00Z
date_updated: 2021-11-26T15:14:08Z
day: '18'
doi: 10.1021/acs.nanolett.8b00786
extern: '1'
external_id:
pmid:
- '29667410'
intvolume: ' 18'
issue: '9'
keyword:
- mechanical engineering
- condensed matter physics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1712.10147
month: '04'
oa: 1
oa_version: Preprint
page: 5350-5356
pmid: 1
publication: Nano Letters
publication_identifier:
eissn:
- 1530-6992
issn:
- 1530-6984
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Controlling cargo trafficking in multicomponent membranes
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 18
year: '2018'
...
---
_id: '10360'
abstract:
- lang: eng
text: Mapping free-energy landscapes has proved to be a powerful tool for studying
reaction mechanisms. Many complex biomolecular assembly processes, however, have
remained challenging to access using this approach, including the aggregation
of peptides and proteins into amyloid fibrils implicated in a range of disorders.
Here, we generalize the strategy used to probe free-energy landscapes in protein
folding to determine the activation energies and entropies that characterize each
of the molecular steps in the aggregation of the amyloid-β peptide (Aβ42), which
is associated with Alzheimer’s disease. Our results reveal that interactions between
monomeric Aβ42 and amyloid fibrils during fibril-dependent secondary nucleation
fundamentally reverse the thermodynamic signature of this process relative to
primary nucleation, even though both processes generate aggregates from soluble
peptides. By mapping the energetic and entropic contributions along the reaction
trajectories, we show that the catalytic efficiency of Aβ42 fibril surfaces results
from the enthalpic stabilization of adsorbing peptides in conformations amenable
to nucleation, resulting in a dramatic lowering of the activation energy for nucleation.
acknowledgement: We thank B. Jönsson and I. André for helpful discussions. We acknowledge
financial support from the Schiff Foundation (S.I.A.C.), St John’s College, Cambridge
(S.I.A.C.), the Royal Physiographic Society (R.C.), the Research School FLÄK of
Lund University (S.L., R.C.), the Swedish Research Council (S.L.) and its Linneaus
Centre Organizing Molecular Matter (S.L.), the Crafoord Foundation (S.L.), Alzheimerfonden
(S.L.), the European Research Council (S.L.), NanoLund (S.L.), Knut and Alice Wallenberg
Foundation (S.L.), Peterhouse, Cambridge (T.C.T.M.), the Swiss National Science
Foundation (T.C.T.M.), Magdalene College, Cambridge (A.K.B.), the Leverhulme Trust
(A.K.B.), the Royal Society (A.Š.), the Academy of Medical Sciences (A.Š.), the
Wellcome Trust (C.M.D., T.P.J.K., A.Š.), and the Centre for Misfolding Diseases
(C.M.D., T.P.J.K, M.V.). A.K.B. thanks the Alzheimer Forschung Initiative (AFI).
article_processing_charge: No
article_type: original
author:
- first_name: Samuel I. A.
full_name: Cohen, Samuel I. A.
last_name: Cohen
- first_name: Risto
full_name: Cukalevski, Risto
last_name: Cukalevski
- first_name: Thomas C. T.
full_name: Michaels, Thomas C. T.
last_name: Michaels
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Mattias
full_name: Törnquist, Mattias
last_name: Törnquist
- first_name: Michele
full_name: Vendruscolo, Michele
last_name: Vendruscolo
- first_name: Christopher M.
full_name: Dobson, Christopher M.
last_name: Dobson
- first_name: Alexander K.
full_name: Buell, Alexander K.
last_name: Buell
- first_name: Tuomas P. J.
full_name: Knowles, Tuomas P. J.
last_name: Knowles
- first_name: Sara
full_name: Linse, Sara
last_name: Linse
citation:
ama: Cohen SIA, Cukalevski R, Michaels TCT, et al. Distinct thermodynamic signatures
of oligomer generation in the aggregation of the amyloid-β peptide. Nature
Chemistry. 2018;10(5):523-531. doi:10.1038/s41557-018-0023-x
apa: Cohen, S. I. A., Cukalevski, R., Michaels, T. C. T., Šarić, A., Törnquist,
M., Vendruscolo, M., … Linse, S. (2018). Distinct thermodynamic signatures of
oligomer generation in the aggregation of the amyloid-β peptide. Nature Chemistry.
Springer Nature. https://doi.org/10.1038/s41557-018-0023-x
chicago: Cohen, Samuel I. A., Risto Cukalevski, Thomas C. T. Michaels, Anđela Šarić,
Mattias Törnquist, Michele Vendruscolo, Christopher M. Dobson, Alexander K. Buell,
Tuomas P. J. Knowles, and Sara Linse. “Distinct Thermodynamic Signatures of Oligomer
Generation in the Aggregation of the Amyloid-β Peptide.” Nature Chemistry.
Springer Nature, 2018. https://doi.org/10.1038/s41557-018-0023-x.
ieee: S. I. A. Cohen et al., “Distinct thermodynamic signatures of oligomer
generation in the aggregation of the amyloid-β peptide,” Nature Chemistry,
vol. 10, no. 5. Springer Nature, pp. 523–531, 2018.
ista: Cohen SIA, Cukalevski R, Michaels TCT, Šarić A, Törnquist M, Vendruscolo M,
Dobson CM, Buell AK, Knowles TPJ, Linse S. 2018. Distinct thermodynamic signatures
of oligomer generation in the aggregation of the amyloid-β peptide. Nature Chemistry.
10(5), 523–531.
mla: Cohen, Samuel I. A., et al. “Distinct Thermodynamic Signatures of Oligomer
Generation in the Aggregation of the Amyloid-β Peptide.” Nature Chemistry,
vol. 10, no. 5, Springer Nature, 2018, pp. 523–31, doi:10.1038/s41557-018-0023-x.
short: S.I.A. Cohen, R. Cukalevski, T.C.T. Michaels, A. Šarić, M. Törnquist, M.
Vendruscolo, C.M. Dobson, A.K. Buell, T.P.J. Knowles, S. Linse, Nature Chemistry
10 (2018) 523–531.
date_created: 2021-11-26T12:41:38Z
date_published: 2018-03-26T00:00:00Z
date_updated: 2021-11-26T15:14:00Z
day: '26'
doi: 10.1038/s41557-018-0023-x
extern: '1'
external_id:
pmid:
- '29581486'
intvolume: ' 10'
issue: '5'
keyword:
- general chemical engineering
- general chemistry
language:
- iso: eng
month: '03'
oa_version: None
page: 523-531
pmid: 1
publication: Nature Chemistry
publication_identifier:
eissn:
- 1755-4349
issn:
- 1755-4330
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Distinct thermodynamic signatures of oligomer generation in the aggregation
of the amyloid-β peptide
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 10
year: '2018'
...
---
_id: '10361'
abstract:
- lang: eng
text: Understanding how normally soluble peptides and proteins aggregate to form
amyloid fibrils is central to many areas of modern biomolecular science, ranging
from the development of functional biomaterials to the design of rational therapeutic
strategies against increasingly prevalent medical conditions such as Alzheimer's
and Parkinson's diseases. As such, there is a great need to develop models to
mechanistically describe how amyloid fibrils are formed from precursor peptides
and proteins. Here we review and discuss how ideas and concepts from chemical
reaction kinetics can help to achieve this objective. In particular, we show how
a combination of theory, experiments, and computer simulations, based on chemical
kinetics, provides a general formalism for uncovering, at the molecular level,
the mechanistic steps that underlie the phenomenon of amyloid fibril formation.
acknowledgement: "We acknowledge support from the Swiss National Science Foundation
(T.C.T.M.); Peterhouse,\r\nCambridge (T.C.T.M.); the Royal Society (A.S.); the Academy
of Medical Sciences (A.S.); the\r\nWellcome Trust (A.S., M.V., C.M.D., T.P.J.K.);
the Cambridge Centre for Misfolding Diseases\r\n(M.V., C.M.D., T.P.J.K.); the Biotechnology
and Biological Sciences Research Council (C.M.D.,\r\nT.P.J.K.); and the Frances
and Augustus Newman Foundation (T.P.J.K.). The research leading\r\nto these results
has received funding from the European Research Council (ERC) under the\r\nEuropean
Union’s Seventh Framework Programme (FP7/2007-2013) through the ERC grant\r\nPhysProt
(337969)."
article_processing_charge: No
article_type: original
author:
- first_name: Thomas C.T.
full_name: Michaels, Thomas C.T.
last_name: Michaels
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Johnny
full_name: Habchi, Johnny
last_name: Habchi
- first_name: Sean
full_name: Chia, Sean
last_name: Chia
- first_name: Georg
full_name: Meisl, Georg
last_name: Meisl
- first_name: Michele
full_name: Vendruscolo, Michele
last_name: Vendruscolo
- first_name: Christopher M.
full_name: Dobson, Christopher M.
last_name: Dobson
- first_name: Tuomas P.J.
full_name: Knowles, Tuomas P.J.
last_name: Knowles
citation:
ama: Michaels TCT, Šarić A, Habchi J, et al. Chemical kinetics for bridging molecular
mechanisms and macroscopic measurements of amyloid fibril formation. Annual
Review of Physical Chemistry. 2018;69(1):273-298. doi:10.1146/annurev-physchem-050317-021322
apa: Michaels, T. C. T., Šarić, A., Habchi, J., Chia, S., Meisl, G., Vendruscolo,
M., … Knowles, T. P. J. (2018). Chemical kinetics for bridging molecular mechanisms
and macroscopic measurements of amyloid fibril formation. Annual Review of
Physical Chemistry. Annual Reviews. https://doi.org/10.1146/annurev-physchem-050317-021322
chicago: Michaels, Thomas C.T., Anđela Šarić, Johnny Habchi, Sean Chia, Georg Meisl,
Michele Vendruscolo, Christopher M. Dobson, and Tuomas P.J. Knowles. “Chemical
Kinetics for Bridging Molecular Mechanisms and Macroscopic Measurements of Amyloid
Fibril Formation.” Annual Review of Physical Chemistry. Annual Reviews,
2018. https://doi.org/10.1146/annurev-physchem-050317-021322.
ieee: T. C. T. Michaels et al., “Chemical kinetics for bridging molecular
mechanisms and macroscopic measurements of amyloid fibril formation,” Annual
Review of Physical Chemistry, vol. 69, no. 1. Annual Reviews, pp. 273–298,
2018.
ista: Michaels TCT, Šarić A, Habchi J, Chia S, Meisl G, Vendruscolo M, Dobson CM,
Knowles TPJ. 2018. Chemical kinetics for bridging molecular mechanisms and macroscopic
measurements of amyloid fibril formation. Annual Review of Physical Chemistry.
69(1), 273–298.
mla: Michaels, Thomas C. T., et al. “Chemical Kinetics for Bridging Molecular Mechanisms
and Macroscopic Measurements of Amyloid Fibril Formation.” Annual Review of
Physical Chemistry, vol. 69, no. 1, Annual Reviews, 2018, pp. 273–98, doi:10.1146/annurev-physchem-050317-021322.
short: T.C.T. Michaels, A. Šarić, J. Habchi, S. Chia, G. Meisl, M. Vendruscolo,
C.M. Dobson, T.P.J. Knowles, Annual Review of Physical Chemistry 69 (2018) 273–298.
date_created: 2021-11-26T12:52:12Z
date_published: 2018-02-28T00:00:00Z
date_updated: 2021-11-26T15:58:19Z
day: '28'
doi: 10.1146/annurev-physchem-050317-021322
extern: '1'
external_id:
pmid:
- '29490200'
intvolume: ' 69'
issue: '1'
keyword:
- physical and theoretical chemistry
language:
- iso: eng
month: '02'
oa_version: None
page: 273-298
pmid: 1
publication: Annual Review of Physical Chemistry
publication_identifier:
eissn:
- 1545-1593
issn:
- 0066-426X
publication_status: published
publisher: Annual Reviews
quality_controlled: '1'
scopus_import: '1'
status: public
title: Chemical kinetics for bridging molecular mechanisms and macroscopic measurements
of amyloid fibril formation
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 69
year: '2018'
...
---
_id: '10362'
abstract:
- lang: eng
text: Nuclear pore complexes (NPCs) form gateways that control molecular exchange
between the nucleus and the cytoplasm. They impose a diffusion barrier to macromolecules
and enable the selective transport of nuclear transport receptors with bound cargo.
The underlying mechanisms that establish these permeability properties remain
to be fully elucidated but require unstructured nuclear pore proteins rich in
Phe-Gly (FG)-repeat domains of different types, such as FxFG and GLFG. While physical
modeling and in vitro approaches have provided a framework for explaining how
the FG network contributes to the barrier and transport properties of the NPC,
it remains unknown whether the number and/or the spatial positioning of different
FG-domains along a cylindrical, ∼40 nm diameter transport channel contributes
to their collective properties and function. To begin to answer these questions,
we have used DNA origami to build a cylinder that mimics the dimensions of the
central transport channel and can house a specified number of FG-domains at specific
positions with easily tunable design parameters, such as grafting density and
topology. We find the overall morphology of the FG-domain assemblies to be dependent
on their chemical composition, determined by the type and density of FG-repeat,
and on their architectural confinement provided by the DNA cylinder, largely consistent
with here presented molecular dynamics simulations based on a coarse-grained polymer
model. In addition, high-speed atomic force microscopy reveals local and reversible
FG-domain condensation that transiently occludes the lumen of the DNA central
channel mimics, suggestive of how the NPC might establish its permeability properties.
acknowledgement: We thank J. Edel and members of the Lusk, Lin and Hoogenboom lab
for discussion and acknowledge A. Pyne and R. Thorogate for support carrying out
the AFM experiments. This work was funded by the NIH (R21GM109466 to CPL, CL and
TJM, DP2GM114830 to CL, RO1GM105672 to CPL, and T32GM007223 to PDEF) and the UK
Engineering and Physical Sciences Research Council (EP/L015277/1, EP/L504889/1,
and EP/M028100/1).
article_processing_charge: No
article_type: original
author:
- first_name: Patrick D. Ellis
full_name: Fisher, Patrick D. Ellis
last_name: Fisher
- first_name: Qi
full_name: Shen, Qi
last_name: Shen
- first_name: Bernice
full_name: Akpinar, Bernice
last_name: Akpinar
- first_name: Luke K.
full_name: Davis, Luke K.
last_name: Davis
- first_name: Kenny Kwok Hin
full_name: Chung, Kenny Kwok Hin
last_name: Chung
- first_name: David
full_name: Baddeley, David
last_name: Baddeley
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Thomas J.
full_name: Melia, Thomas J.
last_name: Melia
- first_name: Bart W.
full_name: Hoogenboom, Bart W.
last_name: Hoogenboom
- first_name: Chenxiang
full_name: Lin, Chenxiang
last_name: Lin
- first_name: C. Patrick
full_name: Lusk, C. Patrick
last_name: Lusk
citation:
ama: Fisher PDE, Shen Q, Akpinar B, et al. A Programmable DNA origami platform for
organizing intrinsically disordered nucleoporins within nanopore confinement.
ACS Nano. 2018;12(2):1508-1518. doi:10.1021/acsnano.7b08044
apa: Fisher, P. D. E., Shen, Q., Akpinar, B., Davis, L. K., Chung, K. K. H., Baddeley,
D., … Lusk, C. P. (2018). A Programmable DNA origami platform for organizing intrinsically
disordered nucleoporins within nanopore confinement. ACS Nano. American
Chemical Society. https://doi.org/10.1021/acsnano.7b08044
chicago: Fisher, Patrick D. Ellis, Qi Shen, Bernice Akpinar, Luke K. Davis, Kenny
Kwok Hin Chung, David Baddeley, Anđela Šarić, et al. “A Programmable DNA Origami
Platform for Organizing Intrinsically Disordered Nucleoporins within Nanopore
Confinement.” ACS Nano. American Chemical Society, 2018. https://doi.org/10.1021/acsnano.7b08044.
ieee: P. D. E. Fisher et al., “A Programmable DNA origami platform for organizing
intrinsically disordered nucleoporins within nanopore confinement,” ACS Nano,
vol. 12, no. 2. American Chemical Society, pp. 1508–1518, 2018.
ista: Fisher PDE, Shen Q, Akpinar B, Davis LK, Chung KKH, Baddeley D, Šarić A, Melia
TJ, Hoogenboom BW, Lin C, Lusk CP. 2018. A Programmable DNA origami platform for
organizing intrinsically disordered nucleoporins within nanopore confinement.
ACS Nano. 12(2), 1508–1518.
mla: Fisher, Patrick D. Ellis, et al. “A Programmable DNA Origami Platform for Organizing
Intrinsically Disordered Nucleoporins within Nanopore Confinement.” ACS Nano,
vol. 12, no. 2, American Chemical Society, 2018, pp. 1508–18, doi:10.1021/acsnano.7b08044.
short: P.D.E. Fisher, Q. Shen, B. Akpinar, L.K. Davis, K.K.H. Chung, D. Baddeley,
A. Šarić, T.J. Melia, B.W. Hoogenboom, C. Lin, C.P. Lusk, ACS Nano 12 (2018) 1508–1518.
date_created: 2021-11-26T15:15:00Z
date_published: 2018-01-19T00:00:00Z
date_updated: 2021-11-26T15:57:02Z
day: '19'
doi: 10.1021/acsnano.7b08044
extern: '1'
external_id:
pmid:
- '29350911'
intvolume: ' 12'
issue: '2'
keyword:
- general physics and astronomy
language:
- iso: eng
month: '01'
oa_version: None
page: 1508-1518
pmid: 1
publication: ACS Nano
publication_identifier:
eissn:
- 1936-086X
issn:
- 1936-0851
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: A Programmable DNA origami platform for organizing intrinsically disordered
nucleoporins within nanopore confinement
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 12
year: '2018'
...
---
_id: '104'
abstract:
- lang: eng
text: The biotrophic pathogen Ustilago maydis, the causative agent of corn smut
disease, infects one of the most important crops worldwide – Zea mays. To successfully
colonize its host, U. maydis secretes proteins, known as effectors, that suppress
plant defense responses and facilitate the establishment of biotrophy. In this
work, we describe the U. maydis effector protein Cce1. Cce1 is essential for virulence
and is upregulated during infection. Through microscopic analysis and in vitro
assays, we show that Cce1 is secreted from hyphae during filamentous growth of
the fungus. Strikingly, Δcce1 mutants are blocked at early stages of infection
and induce callose deposition as a plant defense response. Cce1 is highly conserved
among smut fungi and the Ustilago bromivora ortholog complemented the virulence
defect of the SG200Δcce1 deletion strain. These data indicate that Cce1 is a core
effector with apoplastic localization that is essential for U. maydis to infect
its host.
acknowledgement: 'the Austrian Science Fund (FWF): [P27429‐B22, P27818‐B22, I 3033‐B22],
and the Austrian Academy of Science (OEAW).'
article_processing_charge: No
author:
- first_name: Denise
full_name: Seitner, Denise
last_name: Seitner
- first_name: Simon
full_name: Uhse, Simon
last_name: Uhse
- first_name: Michelle C
full_name: Gallei, Michelle C
id: 35A03822-F248-11E8-B48F-1D18A9856A87
last_name: Gallei
orcid: 0000-0003-1286-7368
- first_name: Armin
full_name: Djamei, Armin
last_name: Djamei
citation:
ama: Seitner D, Uhse S, Gallei MC, Djamei A. The core effector Cce1 is required
for early infection of maize by Ustilago maydis. Molecular Plant Pathology.
2018;19(10):2277-2287. doi:10.1111/mpp.12698
apa: Seitner, D., Uhse, S., Gallei, M. C., & Djamei, A. (2018). The core effector
Cce1 is required for early infection of maize by Ustilago maydis. Molecular
Plant Pathology. Wiley. https://doi.org/10.1111/mpp.12698
chicago: Seitner, Denise, Simon Uhse, Michelle C Gallei, and Armin Djamei. “The
Core Effector Cce1 Is Required for Early Infection of Maize by Ustilago Maydis.”
Molecular Plant Pathology. Wiley, 2018. https://doi.org/10.1111/mpp.12698.
ieee: D. Seitner, S. Uhse, M. C. Gallei, and A. Djamei, “The core effector Cce1
is required for early infection of maize by Ustilago maydis,” Molecular Plant
Pathology, vol. 19, no. 10. Wiley, pp. 2277–2287, 2018.
ista: Seitner D, Uhse S, Gallei MC, Djamei A. 2018. The core effector Cce1 is required
for early infection of maize by Ustilago maydis. Molecular Plant Pathology. 19(10),
2277–2287.
mla: Seitner, Denise, et al. “The Core Effector Cce1 Is Required for Early Infection
of Maize by Ustilago Maydis.” Molecular Plant Pathology, vol. 19, no. 10,
Wiley, 2018, pp. 2277–87, doi:10.1111/mpp.12698.
short: D. Seitner, S. Uhse, M.C. Gallei, A. Djamei, Molecular Plant Pathology 19
(2018) 2277–2287.
date_created: 2018-12-11T11:44:39Z
date_published: 2018-10-01T00:00:00Z
date_updated: 2023-09-19T10:06:42Z
day: '01'
ddc:
- '580'
department:
- _id: GradSch
doi: 10.1111/mpp.12698
external_id:
isi:
- '000445624100006'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2018-12-18T09:46:00Z
date_updated: 2018-12-18T09:46:00Z
file_id: '5740'
file_name: 2018_MolecPlantPath_Seitner.pdf
file_size: 682335
relation: main_file
success: 1
file_date_updated: 2018-12-18T09:46:00Z
has_accepted_license: '1'
intvolume: ' 19'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 2277 - 2287
publication: Molecular Plant Pathology
publication_status: published
publisher: Wiley
publist_id: '7950'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The core effector Cce1 is required for early infection of maize by Ustilago
maydis
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 19
year: '2018'
...
---
_id: '106'
abstract:
- lang: eng
text: The goal of this article is to introduce the reader to the theory of intrinsic
geometry of convex surfaces. We illustrate the power of the tools by proving a
theorem on convex surfaces containing an arbitrarily long closed simple geodesic.
Let us remind ourselves that a curve in a surface is called geodesic if every
sufficiently short arc of the curve is length minimizing; if, in addition, it
has no self-intersections, we call it simple geodesic. A tetrahedron with equal
opposite edges is called isosceles. The axiomatic method of Alexandrov geometry
allows us to work with the metrics of convex surfaces directly, without approximating
it first by a smooth or polyhedral metric. Such approximations destroy the closed
geodesics on the surface; therefore it is difficult (if at all possible) to apply
approximations in the proof of our theorem. On the other hand, a proof in the
smooth or polyhedral case usually admits a translation into Alexandrov’s language;
such translation makes the result more general. In fact, our proof resembles a
translation of the proof given by Protasov. Note that the main theorem implies
in particular that a smooth convex surface does not have arbitrarily long simple
closed geodesics. However we do not know a proof of this corollary that is essentially
simpler than the one presented below.
article_processing_charge: No
arxiv: 1
author:
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Anton
full_name: Petrunin, Anton
last_name: Petrunin
citation:
ama: Akopyan A, Petrunin A. Long geodesics on convex surfaces. Mathematical Intelligencer.
2018;40(3):26-31. doi:10.1007/s00283-018-9795-5
apa: Akopyan, A., & Petrunin, A. (2018). Long geodesics on convex surfaces.
Mathematical Intelligencer. Springer. https://doi.org/10.1007/s00283-018-9795-5
chicago: Akopyan, Arseniy, and Anton Petrunin. “Long Geodesics on Convex Surfaces.”
Mathematical Intelligencer. Springer, 2018. https://doi.org/10.1007/s00283-018-9795-5.
ieee: A. Akopyan and A. Petrunin, “Long geodesics on convex surfaces,” Mathematical
Intelligencer, vol. 40, no. 3. Springer, pp. 26–31, 2018.
ista: Akopyan A, Petrunin A. 2018. Long geodesics on convex surfaces. Mathematical
Intelligencer. 40(3), 26–31.
mla: Akopyan, Arseniy, and Anton Petrunin. “Long Geodesics on Convex Surfaces.”
Mathematical Intelligencer, vol. 40, no. 3, Springer, 2018, pp. 26–31,
doi:10.1007/s00283-018-9795-5.
short: A. Akopyan, A. Petrunin, Mathematical Intelligencer 40 (2018) 26–31.
date_created: 2018-12-11T11:44:40Z
date_published: 2018-09-01T00:00:00Z
date_updated: 2023-09-13T08:49:16Z
day: '01'
department:
- _id: HeEd
doi: 10.1007/s00283-018-9795-5
external_id:
arxiv:
- '1702.05172'
isi:
- '000444141200005'
intvolume: ' 40'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1702.05172
month: '09'
oa: 1
oa_version: Preprint
page: 26 - 31
publication: Mathematical Intelligencer
publication_status: published
publisher: Springer
publist_id: '7948'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Long geodesics on convex surfaces
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 40
year: '2018'
...
---
_id: '10626'
abstract:
- lang: eng
text: "Owing to their wide tunability, multiple internal degrees of freedom, and
low disorder, graphene heterostructures are emerging as a promising experimental
platform for fractional quantum Hall (FQH) studies. Here, we report FQH thermal
activation gap measurements in dual graphite-gated monolayer graphene devices
fabricated in an edgeless Corbino geometry. In devices with substrate-induced
sublattice splitting, we find a tunable crossover between single- and multicomponent
FQH states in the zero energy Landau level. Activation gaps in the single-component
regime show excellent agreement with numerical calculations using a single broadening
parameter \r\nΓ≈7.2K. In the first excited Landau level, in contrast, FQH gaps
are strongly influenced by Landau level mixing, and we observe an unexpected valley-ordered
state at integer filling ν=−4."
acknowledgement: We thank Cory Dean, S. Chen, Y. Zeng, M. Yankowitz, and J. Li for
discussing their unpublished data and for sharing the stack inversion technique.
The authors acknowledge further discussions of the results with I. Sodemann, M.
Zaletel, C. Nayak, and J. Jain. A. F. Y., H. P., H. Z., and E. M. S. were supported
by the ARO under awards 69188PHH and MURI W911NF-17-1-0323. A portion of this work
was performed at the National High Magnetic Field Laboratory, which is supported
by National Science Foundation Cooperative Agreement No. DMR-1644779 and the State
of Florida. K. W. and T. T. acknowledge support from the Elemental Strategy Initiative
conducted by the MEXT, Japan, and JSPS KAKENHI Grant No. JP15K21722. E. M. S. acknowledges
the support of the Elings Prize Fellowship in Science of the California Nanosystems
Institute at the University of California, Santa Barbara. A. F. Y. acknowledges
the support of the David and Lucile Packard Foundation.
article_number: '226801'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Hryhoriy
full_name: Polshyn, Hryhoriy
id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48
last_name: Polshyn
orcid: 0000-0001-8223-8896
- first_name: H.
full_name: Zhou, H.
last_name: Zhou
- first_name: E. M.
full_name: Spanton, E. M.
last_name: Spanton
- first_name: T.
full_name: Taniguchi, T.
last_name: Taniguchi
- first_name: K.
full_name: Watanabe, K.
last_name: Watanabe
- first_name: A. F.
full_name: Young, A. F.
last_name: Young
citation:
ama: Polshyn H, Zhou H, Spanton EM, Taniguchi T, Watanabe K, Young AF. Quantitative
transport measurements of fractional quantum Hall energy gaps in edgeless graphene
devices. Physical Review Letters. 2018;121(22). doi:10.1103/physrevlett.121.226801
apa: Polshyn, H., Zhou, H., Spanton, E. M., Taniguchi, T., Watanabe, K., & Young,
A. F. (2018). Quantitative transport measurements of fractional quantum Hall energy
gaps in edgeless graphene devices. Physical Review Letters. American Physical
Society. https://doi.org/10.1103/physrevlett.121.226801
chicago: Polshyn, Hryhoriy, H. Zhou, E. M. Spanton, T. Taniguchi, K. Watanabe, and
A. F. Young. “Quantitative Transport Measurements of Fractional Quantum Hall Energy
Gaps in Edgeless Graphene Devices.” Physical Review Letters. American Physical
Society, 2018. https://doi.org/10.1103/physrevlett.121.226801.
ieee: H. Polshyn, H. Zhou, E. M. Spanton, T. Taniguchi, K. Watanabe, and A. F. Young,
“Quantitative transport measurements of fractional quantum Hall energy gaps in
edgeless graphene devices,” Physical Review Letters, vol. 121, no. 22.
American Physical Society, 2018.
ista: Polshyn H, Zhou H, Spanton EM, Taniguchi T, Watanabe K, Young AF. 2018. Quantitative
transport measurements of fractional quantum Hall energy gaps in edgeless graphene
devices. Physical Review Letters. 121(22), 226801.
mla: Polshyn, Hryhoriy, et al. “Quantitative Transport Measurements of Fractional
Quantum Hall Energy Gaps in Edgeless Graphene Devices.” Physical Review Letters,
vol. 121, no. 22, 226801, American Physical Society, 2018, doi:10.1103/physrevlett.121.226801.
short: H. Polshyn, H. Zhou, E.M. Spanton, T. Taniguchi, K. Watanabe, A.F. Young,
Physical Review Letters 121 (2018).
date_created: 2022-01-14T12:15:47Z
date_published: 2018-11-28T00:00:00Z
date_updated: 2022-01-14T13:48:35Z
day: '28'
doi: 10.1103/physrevlett.121.226801
extern: '1'
external_id:
arxiv:
- '1805.04199'
intvolume: ' 121'
issue: '22'
keyword:
- general physics and astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1805.04199
month: '11'
oa: 1
oa_version: Preprint
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantitative transport measurements of fractional quantum Hall energy gaps
in edgeless graphene devices
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 121
year: '2018'
...
---
_id: '10627'
abstract:
- lang: eng
text: We present a scanning probe technique for measuring the dynamics of individual
fluxoid transitions in multiply connected superconducting structures. In these
measurements, a small magnetic particle attached to the tip of a silicon cantilever
is scanned over a micron-size superconducting ring fabricated from a thin aluminum
film. We find that near the superconducting transition temperature of the aluminum,
the dissipation and frequency of the cantilever changes significantly at particular
locations where the tip-induced magnetic flux penetrating the ring causes the
two lowest-energy fluxoid states to become nearly degenerate. In this regime,
we show that changes in the cantilever frequency and dissipation are well-described
by a stochastic resonance (SR) process, wherein small oscillations of the cantilever
in the presence of thermally activated phase slips (TAPS) in the ring give rise
to a dynamical force that modifies the mechanical properties of the cantilever.
Using the SR model, we calculate the average fluctuation rate of the TAPS as a
function of temperature over a 32-dB range in frequency, and we compare it to
the Langer-Ambegaokar-McCumber-Halperin theory for TAPS in one-dimensional superconducting
structures.
acknowledgement: "We are grateful to Nadya Mason for useful discussions. This work
was supported by the DOE Basic Energy Sciences under Contract No. DE-SC0012649,
the Department of Physics and the Frederick Seitz Materials Research Laboratory
Central Facilities at the University of Illinois.\r\n"
article_number: '184501'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Hryhoriy
full_name: Polshyn, Hryhoriy
id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48
last_name: Polshyn
orcid: 0000-0001-8223-8896
- first_name: Tyler R.
full_name: Naibert, Tyler R.
last_name: Naibert
- first_name: Raffi
full_name: Budakian, Raffi
last_name: Budakian
citation:
ama: Polshyn H, Naibert TR, Budakian R. Imaging phase slip dynamics in micron-size
superconducting rings. Physical Review B. 2018;97(18). doi:10.1103/physrevb.97.184501
apa: Polshyn, H., Naibert, T. R., & Budakian, R. (2018). Imaging phase slip
dynamics in micron-size superconducting rings. Physical Review B. American
Physical Society. https://doi.org/10.1103/physrevb.97.184501
chicago: Polshyn, Hryhoriy, Tyler R. Naibert, and Raffi Budakian. “Imaging Phase
Slip Dynamics in Micron-Size Superconducting Rings.” Physical Review B.
American Physical Society, 2018. https://doi.org/10.1103/physrevb.97.184501.
ieee: H. Polshyn, T. R. Naibert, and R. Budakian, “Imaging phase slip dynamics in
micron-size superconducting rings,” Physical Review B, vol. 97, no. 18.
American Physical Society, 2018.
ista: Polshyn H, Naibert TR, Budakian R. 2018. Imaging phase slip dynamics in micron-size
superconducting rings. Physical Review B. 97(18), 184501.
mla: Polshyn, Hryhoriy, et al. “Imaging Phase Slip Dynamics in Micron-Size Superconducting
Rings.” Physical Review B, vol. 97, no. 18, 184501, American Physical Society,
2018, doi:10.1103/physrevb.97.184501.
short: H. Polshyn, T.R. Naibert, R. Budakian, Physical Review B 97 (2018).
date_created: 2022-01-14T13:48:47Z
date_published: 2018-05-08T00:00:00Z
date_updated: 2022-01-14T13:58:24Z
day: '08'
doi: 10.1103/physrevb.97.184501
extern: '1'
external_id:
arxiv:
- '1703.08184'
intvolume: ' 97'
issue: '18'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1703.08184
month: '05'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Imaging phase slip dynamics in micron-size superconducting rings
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 97
year: '2018'
...
---
_id: '1064'
abstract:
- lang: eng
text: 'In 1945, A.W. Goodman and R.E. Goodman proved the following conjecture by
P. Erdős: Given a family of (round) disks of radii r1, … , rn in the plane, it
is always possible to cover them by a disk of radius R= ∑ ri, provided they cannot
be separated into two subfamilies by a straight line disjoint from the disks.
In this note we show that essentially the same idea may work for different analogues
and generalizations of their result. In particular, we prove the following: Given
a family of positive homothetic copies of a fixed convex body K⊂ Rd with homothety
coefficients τ1, … , τn> 0 , it is always possible to cover them by a translate
of d+12(∑τi)K, provided they cannot be separated into two subfamilies by a hyperplane
disjoint from the homothets.'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Alexey
full_name: Balitskiy, Alexey
last_name: Balitskiy
- first_name: Mikhail
full_name: Grigorev, Mikhail
last_name: Grigorev
citation:
ama: Akopyan A, Balitskiy A, Grigorev M. On the circle covering theorem by A.W.
Goodman and R.E. Goodman. Discrete & Computational Geometry. 2018;59(4):1001-1009.
doi:10.1007/s00454-017-9883-x
apa: Akopyan, A., Balitskiy, A., & Grigorev, M. (2018). On the circle covering
theorem by A.W. Goodman and R.E. Goodman. Discrete & Computational Geometry.
Springer. https://doi.org/10.1007/s00454-017-9883-x
chicago: Akopyan, Arseniy, Alexey Balitskiy, and Mikhail Grigorev. “On the Circle
Covering Theorem by A.W. Goodman and R.E. Goodman.” Discrete & Computational
Geometry. Springer, 2018. https://doi.org/10.1007/s00454-017-9883-x.
ieee: A. Akopyan, A. Balitskiy, and M. Grigorev, “On the circle covering theorem
by A.W. Goodman and R.E. Goodman,” Discrete & Computational Geometry,
vol. 59, no. 4. Springer, pp. 1001–1009, 2018.
ista: Akopyan A, Balitskiy A, Grigorev M. 2018. On the circle covering theorem by
A.W. Goodman and R.E. Goodman. Discrete & Computational Geometry. 59(4), 1001–1009.
mla: Akopyan, Arseniy, et al. “On the Circle Covering Theorem by A.W. Goodman and
R.E. Goodman.” Discrete & Computational Geometry, vol. 59, no. 4, Springer,
2018, pp. 1001–09, doi:10.1007/s00454-017-9883-x.
short: A. Akopyan, A. Balitskiy, M. Grigorev, Discrete & Computational Geometry
59 (2018) 1001–1009.
date_created: 2018-12-11T11:49:57Z
date_published: 2018-06-01T00:00:00Z
date_updated: 2023-09-20T12:08:51Z
day: '01'
ddc:
- '516'
- '000'
department:
- _id: HeEd
doi: 10.1007/s00454-017-9883-x
ec_funded: 1
external_id:
isi:
- '000432205500011'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2019-01-18T09:27:36Z
date_updated: 2019-01-18T09:27:36Z
file_id: '5844'
file_name: 2018_DiscreteComp_Akopyan.pdf
file_size: 482518
relation: main_file
success: 1
file_date_updated: 2019-01-18T09:27:36Z
has_accepted_license: '1'
intvolume: ' 59'
isi: 1
issue: '4'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 1001-1009
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Discrete & Computational Geometry
publication_identifier:
eissn:
- '14320444'
issn:
- '01795376'
publication_status: published
publisher: Springer
publist_id: '6324'
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the circle covering theorem by A.W. Goodman and R.E. Goodman
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 59
year: '2018'
...
---
_id: '11827'
abstract:
- lang: eng
text: We study the metric facility location problem with client insertions and deletions.
This setting differs from the classic dynamic facility location problem, where
the set of clients remains the same, but the metric space can change over time.
We show a deterministic algorithm that maintains a constant factor approximation
to the optimal solution in worst-case time O~(2^{O(kappa^2)}) per client insertion
or deletion in metric spaces while answering queries about the cost in O(1) time,
where kappa denotes the doubling dimension of the metric. For metric spaces with
bounded doubling dimension, the update time is polylogarithmic in the parameters
of the problem.
alternative_title:
- LIPIcs
article_number: '39'
article_processing_charge: No
arxiv: 1
author:
- first_name: 'Gramoz '
full_name: 'Goranci, Gramoz '
last_name: Goranci
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Dariusz
full_name: Leniowski, Dariusz
last_name: Leniowski
citation:
ama: 'Goranci G, Henzinger MH, Leniowski D. A tree structure for dynamic facility
location. In: 26th Annual European Symposium on Algorithms. Vol 112. Schloss
Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPICS.ESA.2018.39'
apa: 'Goranci, G., Henzinger, M. H., & Leniowski, D. (2018). A tree structure
for dynamic facility location. In 26th Annual European Symposium on Algorithms
(Vol. 112). Helsinki, Finland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
https://doi.org/10.4230/LIPICS.ESA.2018.39'
chicago: Goranci, Gramoz , Monika H Henzinger, and Dariusz Leniowski. “A Tree Structure
for Dynamic Facility Location.” In 26th Annual European Symposium on Algorithms,
Vol. 112. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPICS.ESA.2018.39.
ieee: G. Goranci, M. H. Henzinger, and D. Leniowski, “A tree structure for dynamic
facility location,” in 26th Annual European Symposium on Algorithms, Helsinki,
Finland, 2018, vol. 112.
ista: 'Goranci G, Henzinger MH, Leniowski D. 2018. A tree structure for dynamic
facility location. 26th Annual European Symposium on Algorithms. ESA: Annual European
Symposium on Algorithms, LIPIcs, vol. 112, 39.'
mla: Goranci, Gramoz, et al. “A Tree Structure for Dynamic Facility Location.” 26th
Annual European Symposium on Algorithms, vol. 112, 39, Schloss Dagstuhl -
Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPICS.ESA.2018.39.
short: G. Goranci, M.H. Henzinger, D. Leniowski, in:, 26th Annual European Symposium
on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.
conference:
end_date: 2018-08-22
location: Helsinki, Finland
name: 'ESA: Annual European Symposium on Algorithms'
start_date: 2018-08-20
date_created: 2022-08-12T08:20:57Z
date_published: 2018-08-14T00:00:00Z
date_updated: 2023-02-16T10:50:51Z
day: '14'
doi: 10.4230/LIPICS.ESA.2018.39
extern: '1'
external_id:
arxiv:
- '1909.06653'
intvolume: ' 112'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.4230/LIPIcs.ESA.2018.39
month: '08'
oa: 1
oa_version: Published Version
publication: 26th Annual European Symposium on Algorithms
publication_identifier:
isbn:
- '9783959770811'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: A tree structure for dynamic facility location
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2018'
...
---
_id: '11828'
abstract:
- lang: eng
text: "We consider the problem of dynamically maintaining (approximate) all-pairs
effective resistances in separable graphs, which are those that admit an n^{c}-separator
theorem for some c<1. We give a fully dynamic algorithm that maintains (1+epsilon)-approximations
of the all-pairs effective resistances of an n-vertex graph G undergoing edge
insertions and deletions with O~(sqrt{n}/epsilon^2) worst-case update time and
O~(sqrt{n}/epsilon^2) worst-case query time, if G is guaranteed to be sqrt{n}-separable
(i.e., it is taken from a class satisfying a sqrt{n}-separator theorem) and its
separator can be computed in O~(n) time. Our algorithm is built upon a dynamic
algorithm for maintaining approximate Schur complement that approximately preserves
pairwise effective resistances among a set of terminals for separable graphs,
which might be of independent interest.\r\nWe complement our result by proving
that for any two fixed vertices s and t, no incremental or decremental algorithm
can maintain the s-t effective resistance for sqrt{n}-separable graphs with worst-case
update time O(n^{1/2-delta}) and query time O(n^{1-delta}) for any delta>0, unless
the Online Matrix Vector Multiplication (OMv) conjecture is false.\r\nWe further
show that for general graphs, no incremental or decremental algorithm can maintain
the s-t effective resistance problem with worst-case update time O(n^{1-delta})
and query-time O(n^{2-delta}) for any delta >0, unless the OMv conjecture is false."
alternative_title:
- LIPIcs
article_number: '40'
article_processing_charge: No
arxiv: 1
author:
- first_name: Gramoz
full_name: Goranci, Gramoz
last_name: Goranci
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Pan
full_name: Peng, Pan
last_name: Peng
citation:
ama: 'Goranci G, Henzinger MH, Peng P. Dynamic effective resistances and approximate
schur complement on separable graphs. In: 26th Annual European Symposium on
Algorithms. Vol 112. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018.
doi:10.4230/LIPICS.ESA.2018.40'
apa: 'Goranci, G., Henzinger, M. H., & Peng, P. (2018). Dynamic effective resistances
and approximate schur complement on separable graphs. In 26th Annual European
Symposium on Algorithms (Vol. 112). Helsinki, Finland: Schloss Dagstuhl -
Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ESA.2018.40'
chicago: Goranci, Gramoz, Monika H Henzinger, and Pan Peng. “Dynamic Effective Resistances
and Approximate Schur Complement on Separable Graphs.” In 26th Annual European
Symposium on Algorithms, Vol. 112. Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, 2018. https://doi.org/10.4230/LIPICS.ESA.2018.40.
ieee: G. Goranci, M. H. Henzinger, and P. Peng, “Dynamic effective resistances and
approximate schur complement on separable graphs,” in 26th Annual European
Symposium on Algorithms, Helsinki, Finland, 2018, vol. 112.
ista: 'Goranci G, Henzinger MH, Peng P. 2018. Dynamic effective resistances and
approximate schur complement on separable graphs. 26th Annual European Symposium
on Algorithms. ESA: Annual European Symposium on Algorithms, LIPIcs, vol. 112,
40.'
mla: Goranci, Gramoz, et al. “Dynamic Effective Resistances and Approximate Schur
Complement on Separable Graphs.” 26th Annual European Symposium on Algorithms,
vol. 112, 40, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPICS.ESA.2018.40.
short: G. Goranci, M.H. Henzinger, P. Peng, in:, 26th Annual European Symposium
on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.
conference:
end_date: 2018-08-22
location: Helsinki, Finland
name: 'ESA: Annual European Symposium on Algorithms'
start_date: 2018-08-20
date_created: 2022-08-12T08:26:42Z
date_published: 2018-08-14T00:00:00Z
date_updated: 2023-02-16T11:08:08Z
day: '14'
doi: 10.4230/LIPICS.ESA.2018.40
extern: '1'
external_id:
arxiv:
- '1802.09111'
intvolume: ' 112'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.4230/LIPIcs.ESA.2018.40
month: '08'
oa: 1
oa_version: Published Version
publication: 26th Annual European Symposium on Algorithms
publication_identifier:
isbn:
- '9783959770811'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamic effective resistances and approximate schur complement on separable
graphs
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2018'
...
---
_id: '11872'
abstract:
- lang: eng
text: We design fast dynamic algorithms for proper vertex and edge colorings in
a graph undergoing edge insertions and deletions. In the static setting, there
are simple linear time algorithms for (Δ + 1)- vertex coloring and (2Δ – 1)-edge
coloring in a graph with maximum degree Δ. It is natural to ask if we can efficiently
maintain such colorings in the dynamic setting as well. We get the following three
results. (1) We present a randomized algorithm which maintains a (Δ + 1)-vertex
coloring with O(log Δ) expected amortized update time. (2) We present a deterministic
algorithm which maintains a (1 + o(1)Δ-vertex coloring with O(polylog Δ) amortized
update time. (3) We present a simple, deterministic algorithm which maintains
a (2Δ – 1)-edge coloring with O(log Δ) worst-case update time. This improves the
recent O(Δ)-edge coloring algorithm with worst-case update time [4].
article_processing_charge: No
arxiv: 1
author:
- first_name: Sayan
full_name: Bhattacharya, Sayan
last_name: Bhattacharya
- first_name: Deeparnab
full_name: Chakrabarty, Deeparnab
last_name: Chakrabarty
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Danupon
full_name: Nanongkai, Danupon
last_name: Nanongkai
citation:
ama: 'Bhattacharya S, Chakrabarty D, Henzinger MH, Nanongkai D. Dynamic algorithms
for graph coloring. In: 29th Annual ACM-SIAM Symposium on Discrete Algorithms.
Society for Industrial and Applied Mathematics; 2018:1-20. doi:10.1137/1.9781611975031.1'
apa: 'Bhattacharya, S., Chakrabarty, D., Henzinger, M. H., & Nanongkai, D. (2018).
Dynamic algorithms for graph coloring. In 29th Annual ACM-SIAM Symposium on
Discrete Algorithms (pp. 1–20). New Orleans, LA, United States: Society for
Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611975031.1'
chicago: Bhattacharya, Sayan, Deeparnab Chakrabarty, Monika H Henzinger, and Danupon
Nanongkai. “Dynamic Algorithms for Graph Coloring.” In 29th Annual ACM-SIAM
Symposium on Discrete Algorithms, 1–20. Society for Industrial and Applied
Mathematics, 2018. https://doi.org/10.1137/1.9781611975031.1.
ieee: S. Bhattacharya, D. Chakrabarty, M. H. Henzinger, and D. Nanongkai, “Dynamic
algorithms for graph coloring,” in 29th Annual ACM-SIAM Symposium on Discrete
Algorithms, New Orleans, LA, United States, 2018, pp. 1–20.
ista: 'Bhattacharya S, Chakrabarty D, Henzinger MH, Nanongkai D. 2018. Dynamic algorithms
for graph coloring. 29th Annual ACM-SIAM Symposium on Discrete Algorithms. SODA:
Symposium on Discrete Algorithms, 1–20.'
mla: Bhattacharya, Sayan, et al. “Dynamic Algorithms for Graph Coloring.” 29th
Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and
Applied Mathematics, 2018, pp. 1–20, doi:10.1137/1.9781611975031.1.
short: S. Bhattacharya, D. Chakrabarty, M.H. Henzinger, D. Nanongkai, in:, 29th
Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied
Mathematics, 2018, pp. 1–20.
conference:
end_date: 2018-01-10
location: New Orleans, LA, United States
name: 'SODA: Symposium on Discrete Algorithms'
start_date: 2018-01-07
date_created: 2022-08-16T12:07:14Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2023-02-17T11:39:01Z
day: '01'
doi: 10.1137/1.9781611975031.1
extern: '1'
external_id:
arxiv:
- '1711.04355'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1711.04355
month: '01'
oa: 1
oa_version: Preprint
page: 1 - 20
publication: 29th Annual ACM-SIAM Symposium on Discrete Algorithms
publication_identifier:
eisbn:
- 978-161197503-1
publication_status: published
publisher: Society for Industrial and Applied Mathematics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamic algorithms for graph coloring
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '11882'
abstract:
- lang: eng
text: The minimum cut problem for an undirected edge-weighted graph asks us to divide
its set of nodes into two blocks while minimizing the weight sum of the cut edges.
Here, we introduce a linear-time algorithm to compute near-minimum cuts. Our algorithm
is based on cluster contraction using label propagation and Padberg and Rinaldi's
contraction heuristics [SIAM Review, 1991]. We give both sequential and shared-memory
parallel implementations of our algorithm. Extensive experiments on both real-world
and generated instances show that our algorithm finds the optimal cut on nearly
all instances significantly faster than other state-of-the-art exact algorithms,
and our error rate is lower than that of other heuristic algorithms. In addition,
our parallel algorithm shows good scalability.
article_processing_charge: No
arxiv: 1
author:
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Alexander
full_name: Noe, Alexander
last_name: Noe
- first_name: Christian
full_name: Schulz, Christian
last_name: Schulz
- first_name: Darren
full_name: Strash, Darren
last_name: Strash
citation:
ama: 'Henzinger MH, Noe A, Schulz C, Strash D. Practical minimum cut algorithms.
In: 20th Workshop on Algorithm Engineering and Experiments. Society for
Industrial and Applied Mathematics; 2018:48-61. doi:10.1137/1.9781611975055.5'
apa: 'Henzinger, M. H., Noe, A., Schulz, C., & Strash, D. (2018). Practical
minimum cut algorithms. In 20th Workshop on Algorithm Engineering and Experiments
(pp. 48–61). New Orleans, LA, United States: Society for Industrial and Applied
Mathematics. https://doi.org/10.1137/1.9781611975055.5'
chicago: Henzinger, Monika H, Alexander Noe, Christian Schulz, and Darren Strash.
“Practical Minimum Cut Algorithms.” In 20th Workshop on Algorithm Engineering
and Experiments, 48–61. Society for Industrial and Applied Mathematics, 2018.
https://doi.org/10.1137/1.9781611975055.5.
ieee: M. H. Henzinger, A. Noe, C. Schulz, and D. Strash, “Practical minimum cut
algorithms,” in 20th Workshop on Algorithm Engineering and Experiments,
New Orleans, LA, United States, 2018, pp. 48–61.
ista: 'Henzinger MH, Noe A, Schulz C, Strash D. 2018. Practical minimum cut algorithms.
20th Workshop on Algorithm Engineering and Experiments. ALENEX: Symposium on Algorithm
Engineering and Experiments, 48–61.'
mla: Henzinger, Monika H., et al. “Practical Minimum Cut Algorithms.” 20th Workshop
on Algorithm Engineering and Experiments, Society for Industrial and Applied
Mathematics, 2018, pp. 48–61, doi:10.1137/1.9781611975055.5.
short: M.H. Henzinger, A. Noe, C. Schulz, D. Strash, in:, 20th Workshop on Algorithm
Engineering and Experiments, Society for Industrial and Applied Mathematics, 2018,
pp. 48–61.
conference:
end_date: 2018-01-08
location: New Orleans, LA, United States
name: 'ALENEX: Symposium on Algorithm Engineering and Experiments'
start_date: 2018-01-07
date_created: 2022-08-17T07:04:57Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2023-02-17T14:03:39Z
day: '01'
doi: 10.1137/1.9781611975055.5
extern: '1'
external_id:
arxiv:
- '1708.06127'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1708.06127
month: '01'
oa: 1
oa_version: Preprint
page: 48-61
publication: 20th Workshop on Algorithm Engineering and Experiments
publication_identifier:
eisbn:
- 978-1-61197-505-5
publication_status: published
publisher: Society for Industrial and Applied Mathematics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Practical minimum cut algorithms
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...