---
_id: '10883'
abstract:
- lang: eng
text: 'Solving parity games, which are equivalent to modal μ-calculus model checking,
is a central algorithmic problem in formal methods, with applications in reactive
synthesis, program repair, verification of branching-time properties, etc. Besides
the standard compu- tation model with the explicit representation of games, another
important theoretical model of computation is that of set-based symbolic algorithms.
Set-based symbolic algorithms use basic set operations and one-step predecessor
operations on the implicit description of games, rather than the explicit representation.
The significance of symbolic algorithms is that they provide scalable algorithms
for large finite-state systems, as well as for infinite-state systems with finite
quotient. Consider parity games on graphs with n vertices and parity conditions
with d priorities. While there is a rich literature of explicit algorithms for
parity games, the main results for set-based symbolic algorithms are as follows:
(a) the basic algorithm that requires O(nd) symbolic operations and O(d) symbolic
space; and (b) an improved algorithm that requires O(nd/3+1) symbolic operations
and O(n) symbolic space. In this work, our contributions are as follows: (1) We
present a black-box set-based symbolic algorithm based on the explicit progress
measure algorithm. Two important consequences of our algorithm are as follows:
(a) a set-based symbolic algorithm for parity games that requires quasi-polynomially
many symbolic operations and O(n) symbolic space; and (b) any future improvement
in progress measure based explicit algorithms immediately imply an efficiency
improvement in our set-based symbolic algorithm for parity games. (2) We present
a set-based symbolic algorithm that requires quasi-polynomially many symbolic
operations and O(d · log n) symbolic space. Moreover, for the important special
case of d ≤ log n, our algorithm requires only polynomially many symbolic operations
and poly-logarithmic symbolic space.'
acknowledgement: 'A. S. is fully supported by the Vienna Science and Technology Fund
(WWTF) through project ICT15-003. K.C. is supported by the Austrian Science Fund
(FWF) NFN Grant No S11407-N23 (RiSE/SHiNE) and an ERC Starting grant (279307: Graph
Games). For M.H the research leading to these results has received funding from
the European Research Council under the European Union’s Seventh Framework Programme
(FP/2007-2013) /ERC Grant Agreement no. 340506.'
alternative_title:
- EPiC Series in Computing
article_processing_charge: No
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Wolfgang
full_name: Dvořák, Wolfgang
last_name: Dvořák
- 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: Svozil, Alexander
last_name: Svozil
citation:
ama: 'Chatterjee K, Dvořák W, Henzinger M, Svozil A. Quasipolynomial set-based symbolic
algorithms for parity games. In: 22nd International Conference on Logic for
Programming, Artificial Intelligence and Reasoning. Vol 57. EasyChair; 2018:233-253.
doi:10.29007/5z5k'
apa: 'Chatterjee, K., Dvořák, W., Henzinger, M., & Svozil, A. (2018). Quasipolynomial
set-based symbolic algorithms for parity games. In 22nd International Conference
on Logic for Programming, Artificial Intelligence and Reasoning (Vol. 57,
pp. 233–253). Awassa, Ethiopia: EasyChair. https://doi.org/10.29007/5z5k'
chicago: Chatterjee, Krishnendu, Wolfgang Dvořák, Monika Henzinger, and Alexander
Svozil. “Quasipolynomial Set-Based Symbolic Algorithms for Parity Games.” In 22nd
International Conference on Logic for Programming, Artificial Intelligence and
Reasoning, 57:233–53. EasyChair, 2018. https://doi.org/10.29007/5z5k.
ieee: K. Chatterjee, W. Dvořák, M. Henzinger, and A. Svozil, “Quasipolynomial set-based
symbolic algorithms for parity games,” in 22nd International Conference on
Logic for Programming, Artificial Intelligence and Reasoning, Awassa, Ethiopia,
2018, vol. 57, pp. 233–253.
ista: 'Chatterjee K, Dvořák W, Henzinger M, Svozil A. 2018. Quasipolynomial set-based
symbolic algorithms for parity games. 22nd International Conference on Logic for
Programming, Artificial Intelligence and Reasoning. LPAR: Logic for Programming,
Artificial Intelligence and Reasoning, EPiC Series in Computing, vol. 57, 233–253.'
mla: Chatterjee, Krishnendu, et al. “Quasipolynomial Set-Based Symbolic Algorithms
for Parity Games.” 22nd International Conference on Logic for Programming,
Artificial Intelligence and Reasoning, vol. 57, EasyChair, 2018, pp. 233–53,
doi:10.29007/5z5k.
short: K. Chatterjee, W. Dvořák, M. Henzinger, A. Svozil, in:, 22nd International
Conference on Logic for Programming, Artificial Intelligence and Reasoning, EasyChair,
2018, pp. 233–253.
conference:
end_date: 2018-11-21
location: Awassa, Ethiopia
name: 'LPAR: Logic for Programming, Artificial Intelligence and Reasoning'
start_date: 2018-11-17
date_created: 2022-03-18T12:46:32Z
date_published: 2018-10-23T00:00:00Z
date_updated: 2025-07-10T11:50:02Z
day: '23'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.29007/5z5k
ec_funded: 1
external_id:
arxiv:
- '1909.04983'
file:
- access_level: open_access
checksum: 1229aa8640bd6db610c85decf2265480
content_type: application/pdf
creator: dernst
date_created: 2022-05-17T07:51:08Z
date_updated: 2022-05-17T07:51:08Z
file_id: '11392'
file_name: 2018_EPiCs_Chatterjee.pdf
file_size: 720893
relation: main_file
success: 1
file_date_updated: 2022-05-17T07:51:08Z
has_accepted_license: '1'
intvolume: ' 57'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 233-253
project:
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: 22nd International Conference on Logic for Programming, Artificial Intelligence
and Reasoning
publication_identifier:
issn:
- 2398-7340
publication_status: published
publisher: EasyChair
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quasipolynomial set-based symbolic algorithms for parity games
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 57
year: '2018'
...
---
_id: '1092'
abstract:
- lang: eng
text: 'A graphical model encodes conditional independence relations via the Markov
properties. For an undirected graph these conditional independence relations can
be represented by a simple polytope known as the graph associahedron, which can
be constructed as a Minkowski sum of standard simplices. We show that there is
an analogous polytope for conditional independence relations coming from a regular
Gaussian model, and it can be defined using multiinformation or relative entropy.
For directed acyclic graphical models we give a construction of this polytope
as a Minkowski sum of matroid polytopes. Finally, we apply this geometric insight
to construct a new ordering-based search algorithm for causal inference via directed
acyclic graphical models. '
author:
- first_name: Fatemeh
full_name: Mohammadi, Fatemeh
id: 2C29581E-F248-11E8-B48F-1D18A9856A87
last_name: Mohammadi
- first_name: Caroline
full_name: Uhler, Caroline
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
- first_name: Charles
full_name: Wang, Charles
last_name: Wang
- first_name: Josephine
full_name: Yu, Josephine
last_name: Yu
citation:
ama: Mohammadi F, Uhler C, Wang C, Yu J. Generalized permutohedra from probabilistic
graphical models. SIAM Journal on Discrete Mathematics. 2018;32(1):64-93.
doi:10.1137/16M107894X
apa: Mohammadi, F., Uhler, C., Wang, C., & Yu, J. (2018). Generalized permutohedra
from probabilistic graphical models. SIAM Journal on Discrete Mathematics.
SIAM. https://doi.org/10.1137/16M107894X
chicago: Mohammadi, Fatemeh, Caroline Uhler, Charles Wang, and Josephine Yu. “Generalized
Permutohedra from Probabilistic Graphical Models.” SIAM Journal on Discrete
Mathematics. SIAM, 2018. https://doi.org/10.1137/16M107894X.
ieee: F. Mohammadi, C. Uhler, C. Wang, and J. Yu, “Generalized permutohedra from
probabilistic graphical models,” SIAM Journal on Discrete Mathematics,
vol. 32, no. 1. SIAM, pp. 64–93, 2018.
ista: Mohammadi F, Uhler C, Wang C, Yu J. 2018. Generalized permutohedra from probabilistic
graphical models. SIAM Journal on Discrete Mathematics. 32(1), 64–93.
mla: Mohammadi, Fatemeh, et al. “Generalized Permutohedra from Probabilistic Graphical
Models.” SIAM Journal on Discrete Mathematics, vol. 32, no. 1, SIAM, 2018,
pp. 64–93, doi:10.1137/16M107894X.
short: F. Mohammadi, C. Uhler, C. Wang, J. Yu, SIAM Journal on Discrete Mathematics
32 (2018) 64–93.
date_created: 2018-12-11T11:50:06Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2021-01-12T06:48:13Z
day: '01'
doi: 10.1137/16M107894X
extern: '1'
intvolume: ' 32'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1606.01814
month: '01'
oa: 1
oa_version: Preprint
page: 64-93
publication: SIAM Journal on Discrete Mathematics
publication_status: published
publisher: SIAM
publist_id: '6284'
quality_controlled: '1'
status: public
title: Generalized permutohedra from probabilistic graphical models
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2018'
...
---
_id: '11'
abstract:
- lang: eng
text: We report on a novel strategy to derive mean-field limits of quantum mechanical
systems in which a large number of particles weakly couple to a second-quantized
radiation field. The technique combines the method of counting and the coherent
state approach to study the growth of the correlations among the particles and
in the radiation field. As an instructional example, we derive the Schrödinger–Klein–Gordon
system of equations from the Nelson model with ultraviolet cutoff and possibly
massless scalar field. In particular, we prove the convergence of the reduced
density matrices (of the nonrelativistic particles and the field bosons) associated
with the exact time evolution to the projectors onto the solutions of the Schrödinger–Klein–Gordon
equations in trace norm. Furthermore, we derive explicit bounds on the rate of
convergence of the one-particle reduced density matrix of the nonrelativistic
particles in Sobolev norm.
arxiv: 1
author:
- first_name: Nikolai K
full_name: Leopold, Nikolai K
id: 4BC40BEC-F248-11E8-B48F-1D18A9856A87
last_name: Leopold
orcid: 0000-0002-0495-6822
- first_name: Peter
full_name: Pickl, Peter
last_name: Pickl
citation:
ama: 'Leopold NK, Pickl P. Mean-field limits of particles in interaction with quantised
radiation fields. In: Vol 270. Springer; 2018:185-214. doi:10.1007/978-3-030-01602-9_9'
apa: 'Leopold, N. K., & Pickl, P. (2018). Mean-field limits of particles in
interaction with quantised radiation fields (Vol. 270, pp. 185–214). Presented
at the MaLiQS: Macroscopic Limits of Quantum Systems, Munich, Germany: Springer.
https://doi.org/10.1007/978-3-030-01602-9_9'
chicago: Leopold, Nikolai K, and Peter Pickl. “Mean-Field Limits of Particles in
Interaction with Quantised Radiation Fields,” 270:185–214. Springer, 2018. https://doi.org/10.1007/978-3-030-01602-9_9.
ieee: 'N. K. Leopold and P. Pickl, “Mean-field limits of particles in interaction
with quantised radiation fields,” presented at the MaLiQS: Macroscopic Limits
of Quantum Systems, Munich, Germany, 2018, vol. 270, pp. 185–214.'
ista: 'Leopold NK, Pickl P. 2018. Mean-field limits of particles in interaction
with quantised radiation fields. MaLiQS: Macroscopic Limits of Quantum Systems
vol. 270, 185–214.'
mla: Leopold, Nikolai K., and Peter Pickl. Mean-Field Limits of Particles in
Interaction with Quantised Radiation Fields. Vol. 270, Springer, 2018, pp.
185–214, doi:10.1007/978-3-030-01602-9_9.
short: N.K. Leopold, P. Pickl, in:, Springer, 2018, pp. 185–214.
conference:
end_date: 2017-04-01
location: Munich, Germany
name: 'MaLiQS: Macroscopic Limits of Quantum Systems'
start_date: 2017-03-30
date_created: 2018-12-11T11:44:08Z
date_published: 2018-10-27T00:00:00Z
date_updated: 2021-01-12T06:48:16Z
day: '27'
department:
- _id: RoSe
doi: 10.1007/978-3-030-01602-9_9
ec_funded: 1
external_id:
arxiv:
- '1806.10843'
intvolume: ' 270'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1806.10843
month: '10'
oa: 1
oa_version: Preprint
page: 185 - 214
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication_status: published
publisher: Springer
publist_id: '8045'
quality_controlled: '1'
scopus_import: 1
status: public
title: Mean-field limits of particles in interaction with quantised radiation fields
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 270
year: '2018'
...
---
_id: '11063'
abstract:
- lang: eng
text: The total number of nuclear pore complexes (NPCs) per nucleus varies greatly
between different cell types and is known to change during cell differentiation
and cell transformation. However, the underlying mechanisms that control how many
nuclear transport channels are assembled into a given nuclear envelope remain
unclear. Here, we report that depletion of the NPC basket protein Tpr, but not
Nup153, dramatically increases the total NPC number in various cell types. This
negative regulation of Tpr occurs via a phosphorylation cascade of extracellular
signal-regulated kinase (ERK), the central kinase of the mitogen-activated protein
kinase (MAPK) pathway. Tpr serves as a scaffold for ERK to phosphorylate the nucleoporin
(Nup) Nup153, which is critical for early stages of NPC biogenesis. Our results
reveal a critical role of the Nup Tpr in coordinating signal transduction pathways
during cell proliferation and the dynamic organization of the nucleus.
article_processing_charge: No
article_type: original
author:
- first_name: Asako
full_name: McCloskey, Asako
last_name: McCloskey
- first_name: Arkaitz
full_name: Ibarra, Arkaitz
last_name: Ibarra
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: McCloskey A, Ibarra A, Hetzer M. Tpr regulates the total number of nuclear
pore complexes per cell nucleus. Genes & Development. 2018;32(19-20):1321-1331.
doi:10.1101/gad.315523.118
apa: McCloskey, A., Ibarra, A., & Hetzer, M. (2018). Tpr regulates the total
number of nuclear pore complexes per cell nucleus. Genes & Development.
Cold Spring Harbor Laboratory. https://doi.org/10.1101/gad.315523.118
chicago: McCloskey, Asako, Arkaitz Ibarra, and Martin Hetzer. “Tpr Regulates the
Total Number of Nuclear Pore Complexes per Cell Nucleus.” Genes & Development.
Cold Spring Harbor Laboratory, 2018. https://doi.org/10.1101/gad.315523.118.
ieee: A. McCloskey, A. Ibarra, and M. Hetzer, “Tpr regulates the total number of
nuclear pore complexes per cell nucleus,” Genes & Development, vol.
32, no. 19–20. Cold Spring Harbor Laboratory, pp. 1321–1331, 2018.
ista: McCloskey A, Ibarra A, Hetzer M. 2018. Tpr regulates the total number of nuclear
pore complexes per cell nucleus. Genes & Development. 32(19–20), 1321–1331.
mla: McCloskey, Asako, et al. “Tpr Regulates the Total Number of Nuclear Pore Complexes
per Cell Nucleus.” Genes & Development, vol. 32, no. 19–20, Cold Spring
Harbor Laboratory, 2018, pp. 1321–31, doi:10.1101/gad.315523.118.
short: A. McCloskey, A. Ibarra, M. Hetzer, Genes & Development 32 (2018) 1321–1331.
date_created: 2022-04-07T07:45:30Z
date_published: 2018-09-18T00:00:00Z
date_updated: 2024-10-14T11:19:35Z
day: '18'
doi: 10.1101/gad.315523.118
extern: '1'
external_id:
pmid:
- '30228202'
intvolume: ' 32'
issue: 19-20
keyword:
- Developmental Biology
- Genetics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/gad.315523.118
month: '09'
oa: 1
oa_version: Published Version
page: 1321-1331
pmid: 1
publication: Genes & Development
publication_identifier:
issn:
- 0890-9369
- 1549-5477
publication_status: published
publisher: Cold Spring Harbor Laboratory
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tpr regulates the total number of nuclear pore complexes per cell nucleus
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2018'
...
---
_id: '11064'
abstract:
- lang: eng
text: Biomarkers of aging can be used to assess the health of individuals and to
study aging and age-related diseases. We generate a large dataset of genome-wide
RNA-seq profiles of human dermal fibroblasts from 133 people aged 1 to 94 years
old to test whether signatures of aging are encoded within the transcriptome.
We develop an ensemble machine learning method that predicts age to a median error
of 4 years, outperforming previous methods used to predict age. The ensemble was
further validated by testing it on ten progeria patients, and our method is the
only one that predicts accelerated aging in these patients.
article_number: '221'
article_processing_charge: No
article_type: original
author:
- first_name: Jason G.
full_name: Fleischer, Jason G.
last_name: Fleischer
- first_name: Roberta
full_name: Schulte, Roberta
last_name: Schulte
- first_name: Hsiao H.
full_name: Tsai, Hsiao H.
last_name: Tsai
- first_name: Swati
full_name: Tyagi, Swati
last_name: Tyagi
- first_name: Arkaitz
full_name: Ibarra, Arkaitz
last_name: Ibarra
- first_name: Maxim N.
full_name: Shokhirev, Maxim N.
last_name: Shokhirev
- first_name: Ling
full_name: Huang, Ling
last_name: Huang
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
- first_name: Saket
full_name: Navlakha, Saket
last_name: Navlakha
citation:
ama: Fleischer JG, Schulte R, Tsai HH, et al. Predicting age from the transcriptome
of human dermal fibroblasts. Genome Biology. 2018;19. doi:10.1186/s13059-018-1599-6
apa: Fleischer, J. G., Schulte, R., Tsai, H. H., Tyagi, S., Ibarra, A., Shokhirev,
M. N., … Navlakha, S. (2018). Predicting age from the transcriptome of human dermal
fibroblasts. Genome Biology. BioMed Central. https://doi.org/10.1186/s13059-018-1599-6
chicago: Fleischer, Jason G., Roberta Schulte, Hsiao H. Tsai, Swati Tyagi, Arkaitz
Ibarra, Maxim N. Shokhirev, Ling Huang, Martin Hetzer, and Saket Navlakha. “Predicting
Age from the Transcriptome of Human Dermal Fibroblasts.” Genome Biology.
BioMed Central, 2018. https://doi.org/10.1186/s13059-018-1599-6.
ieee: J. G. Fleischer et al., “Predicting age from the transcriptome of human
dermal fibroblasts,” Genome Biology, vol. 19. BioMed Central, 2018.
ista: Fleischer JG, Schulte R, Tsai HH, Tyagi S, Ibarra A, Shokhirev MN, Huang L,
Hetzer M, Navlakha S. 2018. Predicting age from the transcriptome of human dermal
fibroblasts. Genome Biology. 19, 221.
mla: Fleischer, Jason G., et al. “Predicting Age from the Transcriptome of Human
Dermal Fibroblasts.” Genome Biology, vol. 19, 221, BioMed Central, 2018,
doi:10.1186/s13059-018-1599-6.
short: J.G. Fleischer, R. Schulte, H.H. Tsai, S. Tyagi, A. Ibarra, M.N. Shokhirev,
L. Huang, M. Hetzer, S. Navlakha, Genome Biology 19 (2018).
date_created: 2022-04-07T07:45:40Z
date_published: 2018-12-20T00:00:00Z
date_updated: 2024-10-14T11:20:00Z
day: '20'
doi: 10.1186/s13059-018-1599-6
extern: '1'
external_id:
pmid:
- '30567591'
intvolume: ' 19'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1186/s13059-018-1599-6
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
publication: Genome Biology
publication_identifier:
issn:
- 1474-760X
publication_status: published
publisher: BioMed Central
quality_controlled: '1'
scopus_import: '1'
status: public
title: Predicting age from the transcriptome of human dermal fibroblasts
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 19
year: '2018'
...
---
OA_place: publisher
OA_type: diamond
_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.
corr_author: '1'
date_created: 2021-11-14T23:01:25Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2025-05-20T09:40:25Z
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
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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
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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'
...
---
OA_place: publisher
OA_type: hybrid
_id: '10417'
abstract:
- lang: eng
text: "We present a new dynamic partial-order reduction method for stateless model
checking of concurrent programs. A common approach for exploring program behaviors
relies on enumerating the traces of the program, without storing the visited states
(aka stateless exploration). As the number of distinct traces grows exponentially,
dynamic partial-order reduction (DPOR) techniques have been successfully used
to partition the space of traces into equivalence classes (Mazurkiewicz partitioning),
with the goal of exploring only few representative traces from each class.\r\n\r\nWe
introduce a new equivalence on traces under sequential consistency semantics,
which we call the observation equivalence. Two traces are observationally equivalent
if every read event observes the same write event in both traces. While the traditional
Mazurkiewicz equivalence is control-centric, our new definition is data-centric.
We show that our observation equivalence is coarser than the Mazurkiewicz equivalence,
and in many cases even exponentially coarser. We devise a DPOR exploration of
the trace space, called data-centric DPOR, based on the observation equivalence."
acknowledgement: "The research was partly supported by Austrian Science Fund (FWF)
Grant No P23499- N23, FWF\r\nNFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant
(279307: Graph Games), and Czech\r\nScience Foundation grant GBP202/12/G061."
article_number: '31'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Marek
full_name: Chalupa, Marek
last_name: Chalupa
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Nishant
full_name: Sinha, Nishant
last_name: Sinha
- first_name: Kapil
full_name: Vaidya, Kapil
last_name: Vaidya
citation:
ama: Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. Data-centric dynamic
partial order reduction. Proceedings of the ACM on Programming Languages.
2018;2(POPL). doi:10.1145/3158119
apa: 'Chalupa, M., Chatterjee, K., Pavlogiannis, A., Sinha, N., & Vaidya, K.
(2018). Data-centric dynamic partial order reduction. Proceedings of the ACM
on Programming Languages. Los Angeles, CA, United States: Association for
Computing Machinery. https://doi.org/10.1145/3158119'
chicago: Chalupa, Marek, Krishnendu Chatterjee, Andreas Pavlogiannis, Nishant Sinha,
and Kapil Vaidya. “Data-Centric Dynamic Partial Order Reduction.” Proceedings
of the ACM on Programming Languages. Association for Computing Machinery,
2018. https://doi.org/10.1145/3158119.
ieee: M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, and K. Vaidya, “Data-centric
dynamic partial order reduction,” Proceedings of the ACM on Programming Languages,
vol. 2, no. POPL. Association for Computing Machinery, 2018.
ista: Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. 2018. Data-centric
dynamic partial order reduction. Proceedings of the ACM on Programming Languages.
2(POPL), 31.
mla: Chalupa, Marek, et al. “Data-Centric Dynamic Partial Order Reduction.” Proceedings
of the ACM on Programming Languages, vol. 2, no. POPL, 31, Association for
Computing Machinery, 2018, doi:10.1145/3158119.
short: M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, K. Vaidya, Proceedings
of the ACM on Programming Languages 2 (2018).
conference:
end_date: 2018-01-13
location: Los Angeles, CA, United States
name: 'POPL: Programming Languages'
start_date: 2018-01-07
date_created: 2021-12-05T23:01:49Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2025-05-20T09:45:10Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1145/3158119
ec_funded: 1
external_id:
arxiv:
- '1610.01188'
file:
- access_level: open_access
checksum: b27ab1745f6dba2387deb785798a657c
content_type: application/pdf
creator: dernst
date_created: 2025-05-20T09:44:47Z
date_updated: 2025-05-20T09:44:47Z
file_id: '19716'
file_name: 2018_ACM_Chalupa.pdf
file_size: 388891
relation: main_file
success: 1
file_date_updated: 2025-05-20T09:44:47Z
has_accepted_license: '1'
intvolume: ' 2'
issue: POPL
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: Proceedings of the ACM on Programming Languages
publication_identifier:
eissn:
- 2475-1421
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
record:
- id: '5448'
relation: earlier_version
status: public
- id: '5456'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Data-centric dynamic partial order reduction
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2018'
...
---
OA_type: closed access
_id: '21094'
abstract:
- lang: eng
text: The X-ray crystal structures of a decamer sequence d(CGCGTACGCG)2 and a tetradecamer
sequence d(CGCGCGTACGCGCG)2 are presented here. Both sequences are alternating
pyrimidine-purine repeat sequences and they form disordered, pseudo-continuous
left handed Z-type helices. They demonstrate interesting variants of the ‘bundles
of columns of helices’ mode of packing.
article_processing_charge: No
article_type: original
author:
- first_name: S.
full_name: Karthik, S.
last_name: Karthik
- first_name: Pradeep K
full_name: Mandal, Pradeep K
id: 6a3def15-d4b4-11ef-9fa9-a24c1f545ec3
last_name: Mandal
orcid: 0000-0001-5996-956X
- first_name: A.
full_name: Thirugnanasambandam, A.
last_name: Thirugnanasambandam
- first_name: N.
full_name: Gautham, N.
last_name: Gautham
citation:
ama: Karthik S, Mandal PK, Thirugnanasambandam A, Gautham N. Crystal structures
of disordered Z-type helices. Nucleosides, Nucleotides & Nucleic Acids.
2018;38(4):279-293. doi:10.1080/15257770.2018.1517883
apa: Karthik, S., Mandal, P. K., Thirugnanasambandam, A., & Gautham, N. (2018).
Crystal structures of disordered Z-type helices. Nucleosides, Nucleotides &
Nucleic Acids. Informa UK Limited. https://doi.org/10.1080/15257770.2018.1517883
chicago: Karthik, S., Pradeep K Mandal, A. Thirugnanasambandam, and N. Gautham.
“Crystal Structures of Disordered Z-Type Helices.” Nucleosides, Nucleotides
& Nucleic Acids. Informa UK Limited, 2018. https://doi.org/10.1080/15257770.2018.1517883.
ieee: S. Karthik, P. K. Mandal, A. Thirugnanasambandam, and N. Gautham, “Crystal
structures of disordered Z-type helices,” Nucleosides, Nucleotides &
Nucleic Acids, vol. 38, no. 4. Informa UK Limited, pp. 279–293, 2018.
ista: Karthik S, Mandal PK, Thirugnanasambandam A, Gautham N. 2018. Crystal structures
of disordered Z-type helices. Nucleosides, Nucleotides & Nucleic Acids.
38(4), 279–293.
mla: Karthik, S., et al. “Crystal Structures of Disordered Z-Type Helices.” Nucleosides,
Nucleotides & Nucleic Acids, vol. 38, no. 4, Informa UK Limited, 2018,
pp. 279–93, doi:10.1080/15257770.2018.1517883.
short: S. Karthik, P.K. Mandal, A. Thirugnanasambandam, N. Gautham, Nucleosides,
Nucleotides & Nucleic Acids 38 (2018) 279–293.
date_created: 2026-01-29T21:15:08Z
date_published: 2018-12-27T00:00:00Z
date_updated: 2026-02-20T08:27:39Z
day: '27'
doi: 10.1080/15257770.2018.1517883
extern: '1'
external_id:
pmid:
- '30588873'
has_accepted_license: '1'
intvolume: ' 38'
issue: '4'
language:
- iso: eng
month: '12'
oa_version: None
page: 279-293
pmid: 1
publication: Nucleosides, Nucleotides & Nucleic Acids
publication_identifier:
eissn:
- 1532-2335
issn:
- 1525-7770
publication_status: published
publisher: Informa UK Limited
quality_controlled: '1'
status: public
title: Crystal structures of disordered Z-type helices
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 38
year: '2018'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '21096'
abstract:
- lang: eng
text: 'By using a combination of readily accessible experimental and computational
experiments in water, we explored the factors governing the association between
polyanionic dyn[4]arene and a series of α,ω-alkyldiammonium ions of increasing
chain length. We found that the lock-and-key concept based on the best match between
the apolar and polar regions of the molecular partners failed to explain the observed
selectivities. Instead, the dissection of the energetic and structural contributions
demonstrated that the binding events were actually guided by two crucial solvent-related
phenomena as the chain length of the guest increases: the expected decrease of
the enthalpic cost of guest desolvation and the unexpected increase of the favourable
enthalpy of complex solvation. By bringing to light the decisive enthalpic impact
of complex solvation during the binding of polyelectrolytes by inclusion, this
study may provide a missing piece to a puzzle that one day could display the global
picture of molecular recognition in water.'
article_processing_charge: No
article_type: original
author:
- first_name: Emeric
full_name: Jeamet, Emeric
last_name: Jeamet
- first_name: Jean
full_name: Septavaux, Jean
last_name: Septavaux
- first_name: Alexandre
full_name: Héloin, Alexandre
last_name: Héloin
- first_name: Marion
full_name: Donnier-Maréchal, Marion
last_name: Donnier-Maréchal
- first_name: Melissa
full_name: Dumartin, Melissa
last_name: Dumartin
- first_name: Benjamin
full_name: Ourri, Benjamin
last_name: Ourri
- first_name: Pradeep K
full_name: Mandal, Pradeep K
id: 6a3def15-d4b4-11ef-9fa9-a24c1f545ec3
last_name: Mandal
orcid: 0000-0001-5996-956X
- first_name: Ivan
full_name: Huc, Ivan
last_name: Huc
- first_name: Emmanuelle
full_name: Bignon, Emmanuelle
last_name: Bignon
- first_name: Elise
full_name: Dumont, Elise
last_name: Dumont
- first_name: Christophe
full_name: Morell, Christophe
last_name: Morell
- first_name: Jean-Patrick
full_name: Francoia, Jean-Patrick
last_name: Francoia
- first_name: Florent
full_name: Perret, Florent
last_name: Perret
- first_name: Laurent
full_name: Vial, Laurent
last_name: Vial
- first_name: Julien
full_name: Leclaire, Julien
last_name: Leclaire
citation:
ama: Jeamet E, Septavaux J, Héloin A, et al. Wetting the lock and key enthalpically
favours polyelectrolyte binding. Chemical Science. 2018;10(1):277-283.
doi:10.1039/c8sc02966k
apa: Jeamet, E., Septavaux, J., Héloin, A., Donnier-Maréchal, M., Dumartin, M.,
Ourri, B., … Leclaire, J. (2018). Wetting the lock and key enthalpically favours
polyelectrolyte binding. Chemical Science. Royal Society of Chemistry.
https://doi.org/10.1039/c8sc02966k
chicago: Jeamet, Emeric, Jean Septavaux, Alexandre Héloin, Marion Donnier-Maréchal,
Melissa Dumartin, Benjamin Ourri, Pradeep K Mandal, et al. “Wetting the Lock and
Key Enthalpically Favours Polyelectrolyte Binding.” Chemical Science. Royal
Society of Chemistry, 2018. https://doi.org/10.1039/c8sc02966k.
ieee: E. Jeamet et al., “Wetting the lock and key enthalpically favours polyelectrolyte
binding,” Chemical Science, vol. 10, no. 1. Royal Society of Chemistry,
pp. 277–283, 2018.
ista: Jeamet E, Septavaux J, Héloin A, Donnier-Maréchal M, Dumartin M, Ourri B,
Mandal PK, Huc I, Bignon E, Dumont E, Morell C, Francoia J-P, Perret F, Vial L,
Leclaire J. 2018. Wetting the lock and key enthalpically favours polyelectrolyte
binding. Chemical Science. 10(1), 277–283.
mla: Jeamet, Emeric, et al. “Wetting the Lock and Key Enthalpically Favours Polyelectrolyte
Binding.” Chemical Science, vol. 10, no. 1, Royal Society of Chemistry,
2018, pp. 277–83, doi:10.1039/c8sc02966k.
short: E. Jeamet, J. Septavaux, A. Héloin, M. Donnier-Maréchal, M. Dumartin, B.
Ourri, P.K. Mandal, I. Huc, E. Bignon, E. Dumont, C. Morell, J.-P. Francoia, F.
Perret, L. Vial, J. Leclaire, Chemical Science 10 (2018) 277–283.
date_created: 2026-01-29T21:20:24Z
date_published: 2018-10-08T00:00:00Z
date_updated: 2026-02-23T10:00:16Z
day: '08'
doi: 10.1039/c8sc02966k
extern: '1'
has_accepted_license: '1'
intvolume: ' 10'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1039/C8SC02966K
month: '10'
oa: 1
oa_version: Published Version
page: 277-283
publication: Chemical Science
publication_identifier:
eissn:
- 2041-6539
issn:
- 2041-6520
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
status: public
title: Wetting the lock and key enthalpically favours polyelectrolyte binding
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/3.0/legalcode
name: Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0)
short: CC BY-NC (3.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2018'
...
---
OA_type: closed access
_id: '21097'
abstract:
- lang: eng
text: Translation, the mRNA-templated synthesis of peptides by the ribosome, can
be manipulated to incorporate variants of the 20 cognate amino acids. Such approaches
for expanding the range of chemical entities that can be produced by the ribosome
may accelerate the discovery of molecules that can perform functions for which
poorly folded, short peptidic sequences are ill suited. Here, we show that the
ribosome tolerates some artificial helical aromatic oligomers, so-called foldamers.
Using a flexible tRNA-acylation ribozyme—flexizyme—foldamers were attached to
tRNA, and the resulting acylated tRNAs were delivered to the ribosome to initiate
the synthesis of non-cyclic and cyclic foldamer–peptide hybrid molecules. Passing
through the ribosome exit tunnel requires the foldamers to unfold. Yet foldamers
encode sufficient folding information to influence the peptide structure once
translation is completed. We also show that in cyclic hybrids, the foldamer portion
can fold into a helix and force the peptide segment to adopt a constrained and
stretched conformation.
article_processing_charge: No
article_type: original
author:
- first_name: Joseph M.
full_name: Rogers, Joseph M.
last_name: Rogers
- first_name: Sunbum
full_name: Kwon, Sunbum
last_name: Kwon
- first_name: Simon J.
full_name: Dawson, Simon J.
last_name: Dawson
- first_name: Pradeep K
full_name: Mandal, Pradeep K
id: 6a3def15-d4b4-11ef-9fa9-a24c1f545ec3
last_name: Mandal
orcid: 0000-0001-5996-956X
- first_name: Hiroaki
full_name: Suga, Hiroaki
last_name: Suga
- first_name: Ivan
full_name: Huc, Ivan
last_name: Huc
citation:
ama: Rogers JM, Kwon S, Dawson SJ, Mandal PK, Suga H, Huc I. Ribosomal synthesis
and folding of peptide-helical aromatic foldamer hybrids. Nature Chemistry.
2018;10(4):405-412. doi:10.1038/s41557-018-0007-x
apa: Rogers, J. M., Kwon, S., Dawson, S. J., Mandal, P. K., Suga, H., & Huc,
I. (2018). Ribosomal synthesis and folding of peptide-helical aromatic foldamer
hybrids. Nature Chemistry. Springer Nature. https://doi.org/10.1038/s41557-018-0007-x
chicago: Rogers, Joseph M., Sunbum Kwon, Simon J. Dawson, Pradeep K Mandal, Hiroaki
Suga, and Ivan Huc. “Ribosomal Synthesis and Folding of Peptide-Helical Aromatic
Foldamer Hybrids.” Nature Chemistry. Springer Nature, 2018. https://doi.org/10.1038/s41557-018-0007-x.
ieee: J. M. Rogers, S. Kwon, S. J. Dawson, P. K. Mandal, H. Suga, and I. Huc, “Ribosomal
synthesis and folding of peptide-helical aromatic foldamer hybrids,” Nature
Chemistry, vol. 10, no. 4. Springer Nature, pp. 405–412, 2018.
ista: Rogers JM, Kwon S, Dawson SJ, Mandal PK, Suga H, Huc I. 2018. Ribosomal synthesis
and folding of peptide-helical aromatic foldamer hybrids. Nature Chemistry. 10(4),
405–412.
mla: Rogers, Joseph M., et al. “Ribosomal Synthesis and Folding of Peptide-Helical
Aromatic Foldamer Hybrids.” Nature Chemistry, vol. 10, no. 4, Springer
Nature, 2018, pp. 405–12, doi:10.1038/s41557-018-0007-x.
short: J.M. Rogers, S. Kwon, S.J. Dawson, P.K. Mandal, H. Suga, I. Huc, Nature Chemistry
10 (2018) 405–412.
date_created: 2026-01-29T21:27:38Z
date_published: 2018-03-19T00:00:00Z
date_updated: 2026-02-20T08:58:10Z
day: '19'
doi: 10.1038/s41557-018-0007-x
extern: '1'
external_id:
pmid:
- '29556052'
has_accepted_license: '1'
intvolume: ' 10'
issue: '4'
language:
- iso: eng
month: '03'
oa_version: None
page: 405-412
pmid: 1
publication: Nature Chemistry
publication_identifier:
eissn:
- 1755-4349
issn:
- 1755-4330
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41557-018-0086-8
status: public
title: Ribosomal synthesis and folding of peptide-helical aromatic foldamer hybrids
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2018'
...
---
OA_type: closed access
_id: '21152'
abstract:
- lang: eng
text: 'Phospholipase A2 (PLA2) is one of the rate limiting enzymes involved in the
production of arachidonic acid, a potent inflammatory mediator. PLA2 is widely
distributed all over the animal kingdom. It is also seen in inflammatory exudation
and venoms of different organisms. The studies demonstrated that PLA2 inhibitors
have broad spectrum activities that they can either be used against inflammation
or envenomation. In this study, the inhibitory activity of 1-napthaleneacetic
acid (NAA) against porcine pancreatic PLA2 has been explained through isothermal
titration calorimetry and enzyme kinetics studies. The atomic level of interactions
of NAA with PLA2 was also studied using X-ray crystallography. Apart from these
findings, the theoretical binding affinities and mode of interactions of two naphthalene-based
NSAIDs such as naproxen (NAP) and nabumetone (NAB) were studied through molecular
modeling. The studies proved that the selected ligands are binding at the doorway
of the active site cleft and hindering the substrate entry to the active site.
The study brings out a potential scaffold for the designing of broad spectrum
PLA2 inhibitors which can be used for inflammation or envenomation. '
article_processing_charge: No
article_type: original
author:
- first_name: Kalarickal V.
full_name: Dileep, Kalarickal V.
last_name: Dileep
- first_name: Chandran
full_name: Remya, Chandran
last_name: Remya
- first_name: Ignatius
full_name: Tintu, Ignatius
last_name: Tintu
- first_name: Pradeep K
full_name: Mandal, Pradeep K
id: 6a3def15-d4b4-11ef-9fa9-a24c1f545ec3
last_name: Mandal
orcid: 0000-0001-5996-956X
- first_name: Ponnuraj
full_name: Karthe, Ponnuraj
last_name: Karthe
- first_name: Madathilkovilakathu
full_name: Haridas, Madathilkovilakathu
last_name: Haridas
- first_name: Chittalakkottu
full_name: Sadasivan, Chittalakkottu
last_name: Sadasivan
citation:
ama: Dileep KV, Remya C, Tintu I, et al. Crystal structure of phospholipase A2 in
complex with 1‐naphthaleneacetic acid. IUBMB Life. 2018;70(10):995-1001.
doi:10.1002/iub.1924
apa: Dileep, K. V., Remya, C., Tintu, I., Mandal, P. K., Karthe, P., Haridas, M.,
& Sadasivan, C. (2018). Crystal structure of phospholipase A2 in complex with
1‐naphthaleneacetic acid. IUBMB Life. Wiley. https://doi.org/10.1002/iub.1924
chicago: Dileep, Kalarickal V., Chandran Remya, Ignatius Tintu, Pradeep K Mandal,
Ponnuraj Karthe, Madathilkovilakathu Haridas, and Chittalakkottu Sadasivan. “Crystal
Structure of Phospholipase A2 in Complex with 1‐naphthaleneacetic Acid.” IUBMB
Life. Wiley, 2018. https://doi.org/10.1002/iub.1924.
ieee: K. V. Dileep et al., “Crystal structure of phospholipase A2 in complex
with 1‐naphthaleneacetic acid,” IUBMB Life, vol. 70, no. 10. Wiley, pp.
995–1001, 2018.
ista: Dileep KV, Remya C, Tintu I, Mandal PK, Karthe P, Haridas M, Sadasivan C.
2018. Crystal structure of phospholipase A2 in complex with 1‐naphthaleneacetic
acid. IUBMB Life. 70(10), 995–1001.
mla: Dileep, Kalarickal V., et al. “Crystal Structure of Phospholipase A2 in Complex
with 1‐naphthaleneacetic Acid.” IUBMB Life, vol. 70, no. 10, Wiley, 2018,
pp. 995–1001, doi:10.1002/iub.1924.
short: K.V. Dileep, C. Remya, I. Tintu, P.K. Mandal, P. Karthe, M. Haridas, C. Sadasivan,
IUBMB Life 70 (2018) 995–1001.
date_created: 2026-02-06T12:12:20Z
date_published: 2018-10-01T00:00:00Z
date_updated: 2026-02-20T08:09:53Z
day: '01'
doi: 10.1002/iub.1924
extern: '1'
external_id:
pmid:
- '30120882'
has_accepted_license: '1'
intvolume: ' 70'
issue: '10'
language:
- iso: eng
month: '10'
oa_version: None
page: 995-1001
pmid: 1
publication: IUBMB Life
publication_identifier:
eissn:
- 1521-6551
issn:
- 1521-6543
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Crystal structure of phospholipase A2 in complex with 1‐naphthaleneacetic acid
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 70
year: '2018'
...
---
_id: '24'
abstract:
- lang: eng
text: Partially-observable Markov decision processes (POMDPs) with discounted-sum
payoff are a standard framework to model a wide range of problems related to decision
making under uncertainty. Traditionally, the goal has been to obtain policies
that optimize the expectation of the discounted-sum payoff. A key drawback of
the expectation measure is that even low probability events with extreme payoff
can significantly affect the expectation, and thus the obtained policies are not
necessarily risk-averse. An alternate approach is to optimize the probability
that the payoff is above a certain threshold, which allows obtaining risk-averse
policies, but ignores optimization of the expectation. We consider the expectation
optimization with probabilistic guarantee (EOPG) problem, where the goal is to
optimize the expectation ensuring that the payoff is above a given threshold with
at least a specified probability. We present several results on the EOPG problem,
including the first algorithm to solve it.
acknowledgement: "This research was supported by the Vienna Science and Technology
Fund (WWTF) grant ICT15-003; Austrian Science Fund (FWF): S11407-N23(RiSE/SHiNE);and
an ERC Start Grant (279307:Graph Games).\r\n"
article_processing_charge: No
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Adrian
full_name: Elgyütt, Adrian
id: 4A2E9DBA-F248-11E8-B48F-1D18A9856A87
last_name: Elgyütt
- first_name: Petr
full_name: Novotny, Petr
id: 3CC3B868-F248-11E8-B48F-1D18A9856A87
last_name: Novotny
- first_name: Owen
full_name: Rouillé, Owen
last_name: Rouillé
citation:
ama: 'Chatterjee K, Elgyütt A, Novotný P, Rouillé O. Expectation optimization with
probabilistic guarantees in POMDPs with discounted-sum objectives. In: Vol 2018.
IJCAI; 2018:4692-4699. doi:10.24963/ijcai.2018/652'
apa: 'Chatterjee, K., Elgyütt, A., Novotný, P., & Rouillé, O. (2018). Expectation
optimization with probabilistic guarantees in POMDPs with discounted-sum objectives
(Vol. 2018, pp. 4692–4699). Presented at the IJCAI: International Joint Conference
on Artificial Intelligence, Stockholm, Sweden: IJCAI. https://doi.org/10.24963/ijcai.2018/652'
chicago: Chatterjee, Krishnendu, Adrian Elgyütt, Petr Novotný, and Owen Rouillé.
“Expectation Optimization with Probabilistic Guarantees in POMDPs with Discounted-Sum
Objectives,” 2018:4692–99. IJCAI, 2018. https://doi.org/10.24963/ijcai.2018/652.
ieee: 'K. Chatterjee, A. Elgyütt, P. Novotný, and O. Rouillé, “Expectation optimization
with probabilistic guarantees in POMDPs with discounted-sum objectives,” presented
at the IJCAI: International Joint Conference on Artificial Intelligence, Stockholm,
Sweden, 2018, vol. 2018, pp. 4692–4699.'
ista: 'Chatterjee K, Elgyütt A, Novotný P, Rouillé O. 2018. Expectation optimization
with probabilistic guarantees in POMDPs with discounted-sum objectives. IJCAI:
International Joint Conference on Artificial Intelligence vol. 2018, 4692–4699.'
mla: Chatterjee, Krishnendu, et al. Expectation Optimization with Probabilistic
Guarantees in POMDPs with Discounted-Sum Objectives. Vol. 2018, IJCAI, 2018,
pp. 4692–99, doi:10.24963/ijcai.2018/652.
short: K. Chatterjee, A. Elgyütt, P. Novotný, O. Rouillé, in:, IJCAI, 2018, pp.
4692–4699.
conference:
end_date: 2018-07-19
location: Stockholm, Sweden
name: 'IJCAI: International Joint Conference on Artificial Intelligence'
start_date: 2018-07-13
date_created: 2018-12-11T11:44:13Z
date_published: 2018-07-01T00:00:00Z
date_updated: 2025-04-14T13:51:04Z
day: '01'
department:
- _id: KrCh
- _id: ToHe
doi: 10.24963/ijcai.2018/652
ec_funded: 1
external_id:
arxiv:
- '1804.10601'
isi:
- '000764175404117'
intvolume: ' 2018'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1804.10601
month: '07'
oa: 1
oa_version: Preprint
page: 4692 - 4699
project:
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication_status: published
publisher: IJCAI
publist_id: '8031'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Expectation optimization with probabilistic guarantees in POMDPs with discounted-sum
objectives
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2018
year: '2018'
...
---
_id: '155'
abstract:
- lang: eng
text: There is currently significant interest in operating devices in the quantum
regime, where their behaviour cannot be explained through classical mechanics.
Quantum states, including entangled states, are fragile and easily disturbed by
excessive thermal noise. Here we address the question of whether it is possible
to create non-reciprocal devices that encourage the flow of thermal noise towards
or away from a particular quantum device in a network. Our work makes use of the
cascaded systems formalism to answer this question in the affirmative, showing
how a three-port device can be used as an effective thermal transistor, and illustrates
how this formalism maps onto an experimentally-realisable optomechanical system.
Our results pave the way to more resilient quantum devices and to the use of thermal
noise as a resource.
alternative_title:
- Proceedings of SPIE
article_number: 106721N
article_processing_charge: No
arxiv: 1
author:
- first_name: André
full_name: Xuereb, André
last_name: Xuereb
- first_name: Matteo
full_name: Aquilina, Matteo
last_name: Aquilina
- first_name: Shabir
full_name: Barzanjeh, Shabir
id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87
last_name: Barzanjeh
orcid: 0000-0003-0415-1423
citation:
ama: 'Xuereb A, Aquilina M, Barzanjeh S. Routing thermal noise through quantum networks.
In: Andrews DL, Ostendorf A, Bain AJ, Nunzi JM, eds. Vol 10672. SPIE; 2018. doi:10.1117/12.2309928'
apa: 'Xuereb, A., Aquilina, M., & Barzanjeh, S. (2018). Routing thermal noise
through quantum networks. In D. L. Andrews, A. Ostendorf, A. J. Bain, & J.
M. Nunzi (Eds.) (Vol. 10672). Presented at the SPIE: The international society
for optical engineering, Strasbourg, France: SPIE. https://doi.org/10.1117/12.2309928'
chicago: Xuereb, André, Matteo Aquilina, and Shabir Barzanjeh. “Routing Thermal
Noise through Quantum Networks.” edited by D L Andrews, A Ostendorf, A J Bain,
and J M Nunzi, Vol. 10672. SPIE, 2018. https://doi.org/10.1117/12.2309928.
ieee: 'A. Xuereb, M. Aquilina, and S. Barzanjeh, “Routing thermal noise through
quantum networks,” presented at the SPIE: The international society for optical
engineering, Strasbourg, France, 2018, vol. 10672.'
ista: 'Xuereb A, Aquilina M, Barzanjeh S. 2018. Routing thermal noise through quantum
networks. SPIE: The international society for optical engineering, Proceedings
of SPIE, vol. 10672, 106721N.'
mla: Xuereb, André, et al. Routing Thermal Noise through Quantum Networks.
Edited by D L Andrews et al., vol. 10672, 106721N, SPIE, 2018, doi:10.1117/12.2309928.
short: A. Xuereb, M. Aquilina, S. Barzanjeh, in:, D.L. Andrews, A. Ostendorf, A.J.
Bain, J.M. Nunzi (Eds.), SPIE, 2018.
conference:
end_date: 2018-04-26
location: Strasbourg, France
name: 'SPIE: The international society for optical engineering'
start_date: 2018-04-22
date_created: 2018-12-11T11:44:55Z
date_published: 2018-05-04T00:00:00Z
date_updated: 2023-09-18T08:12:24Z
day: '04'
department:
- _id: JoFi
doi: 10.1117/12.2309928
editor:
- first_name: D L
full_name: Andrews, D L
last_name: Andrews
- first_name: A
full_name: Ostendorf, A
last_name: Ostendorf
- first_name: A J
full_name: Bain, A J
last_name: Bain
- first_name: J M
full_name: Nunzi, J M
last_name: Nunzi
external_id:
arxiv:
- '1806.01000'
isi:
- '000453298500019'
intvolume: ' 10672'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1806.01000
month: '05'
oa: 1
oa_version: Preprint
publication_status: published
publisher: SPIE
publist_id: '7766'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Routing thermal noise through quantum networks
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10672
year: '2018'
...