---
_id: '1607'
abstract:
- lang: eng
text: We consider the core algorithmic problems related to verification of systems
with respect to three classical quantitative properties, namely, the mean-payoff
property, the ratio property, and the minimum initial credit for energy property.
The algorithmic problem given a graph and a quantitative property asks to compute
the optimal value (the infimum value over all traces) from every node of the graph.
We consider graphs with constant treewidth, and it is well-known that the control-flow
graphs of most programs have constant treewidth. Let n denote the number of nodes
of a graph, m the number of edges (for constant treewidth graphs m=O(n)) and W
the largest absolute value of the weights. Our main theoretical results are as
follows. First, for constant treewidth graphs we present an algorithm that approximates
the mean-payoff value within a multiplicative factor of ϵ in time O(n⋅log(n/ϵ))
and linear space, as compared to the classical algorithms that require quadratic
time. Second, for the ratio property we present an algorithm that for constant
treewidth graphs works in time O(n⋅log(|a⋅b|))=O(n⋅log(n⋅W)), when the output
is ab, as compared to the previously best known algorithm with running time O(n2⋅log(n⋅W)).
Third, for the minimum initial credit problem we show that (i) for general graphs
the problem can be solved in O(n2⋅m) time and the associated decision problem
can be solved in O(n⋅m) time, improving the previous known O(n3⋅m⋅log(n⋅W)) and
O(n2⋅m) bounds, respectively; and (ii) for constant treewidth graphs we present
an algorithm that requires O(n⋅logn) time, improving the previous known O(n4⋅log(n⋅W))
bound. We have implemented some of our algorithms and show that they present a
significant speedup on standard benchmarks.
acknowledgement: 'The research was partly supported by Austrian Science Fund (FWF)
Grant No P23499- N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant
(279307: Graph Games), and Microsoft faculty fellows award.'
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
citation:
ama: 'Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. Faster algorithms for quantitative
verification in constant treewidth graphs. In: Vol 9206. Springer; 2015:140-157.
doi:10.1007/978-3-319-21690-4_9'
apa: 'Chatterjee, K., Ibsen-Jensen, R., & Pavlogiannis, A. (2015). Faster algorithms
for quantitative verification in constant treewidth graphs (Vol. 9206, pp. 140–157).
Presented at the CAV: Computer Aided Verification, San Francisco, CA, USA: Springer.
https://doi.org/10.1007/978-3-319-21690-4_9'
chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis.
“Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs,”
9206:140–57. Springer, 2015. https://doi.org/10.1007/978-3-319-21690-4_9.
ieee: 'K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, “Faster algorithms for
quantitative verification in constant treewidth graphs,” presented at the CAV:
Computer Aided Verification, San Francisco, CA, USA, 2015, vol. 9206, pp. 140–157.'
ista: 'Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2015. Faster algorithms for
quantitative verification in constant treewidth graphs. CAV: Computer Aided Verification,
LNCS, vol. 9206, 140–157.'
mla: Chatterjee, Krishnendu, et al. Faster Algorithms for Quantitative Verification
in Constant Treewidth Graphs. Vol. 9206, Springer, 2015, pp. 140–57, doi:10.1007/978-3-319-21690-4_9.
short: K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, in:, Springer, 2015, pp.
140–157.
conference:
end_date: 2015-07-24
location: San Francisco, CA, USA
name: 'CAV: Computer Aided Verification'
start_date: 2015-07-18
date_created: 2018-12-11T11:52:59Z
date_published: 2015-07-16T00:00:00Z
date_updated: 2023-09-07T12:01:59Z
day: '16'
department:
- _id: KrCh
doi: 10.1007/978-3-319-21690-4_9
ec_funded: 1
intvolume: ' 9206'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1504.07384
month: '07'
oa: 1
oa_version: Preprint
page: 140 - 157
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'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication_status: published
publisher: Springer
publist_id: '5560'
quality_controlled: '1'
related_material:
record:
- id: '5430'
relation: earlier_version
status: public
- id: '5437'
relation: earlier_version
status: public
- id: '821'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Faster algorithms for quantitative verification in constant treewidth graphs
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9206
year: '2015'
...
---
_id: '1609'
abstract:
- lang: eng
text: The synthesis problem asks for the automatic construction of a system from
its specification. In the traditional setting, the system is “constructed from
scratch” rather than composed from reusable components. However, this is rare
in practice, and almost every non-trivial software system relies heavily on the
use of libraries of reusable components. Recently, Lustig and Vardi introduced
dataflow and controlflow synthesis from libraries of reusable components. They
proved that dataflow synthesis is undecidable, while controlflow synthesis is
decidable. The problem of controlflow synthesis from libraries of probabilistic
components was considered by Nain, Lustig and Vardi, and was shown to be decidable
for qualitative analysis (that asks that the specification be satisfied with probability
1). Our main contribution for controlflow synthesis from probabilistic components
is to establish better complexity bounds for the qualitative analysis problem,
and to show that the more general quantitative problem is undecidable. For the
qualitative analysis, we show that the problem (i) is EXPTIME-complete when the
specification is given as a deterministic parity word automaton, improving the
previously known 2EXPTIME upper bound; and (ii) belongs to UP ∩ coUP and is parity-games
hard, when the specification is given directly as a parity condition on the components,
improving the previously known EXPTIME upper bound.
acknowledgement: 'This research was supported by Austrian Science Fund (FWF) Grant
No P23499- N23, FWF NFN Grant No S11407-N23 (SHiNE), ERC Start grant (279307: Graph
Games), EU FP7 Project Cassting, NSF grants CNS 1049862 and CCF-1139011, by NSF
Expeditions in Computing project “ExCAPE: Expeditions in Computer Augmented Program
Engineering”, by BSF grant 9800096, and by gift from Intel.'
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Laurent
full_name: Doyen, Laurent
last_name: Doyen
- first_name: Moshe
full_name: Vardi, Moshe
last_name: Vardi
citation:
ama: 'Chatterjee K, Doyen L, Vardi M. The complexity of synthesis from probabilistic
components. In: 42nd International Colloquium. Vol 9135. Springer Nature;
2015:108-120. doi:10.1007/978-3-662-47666-6_9'
apa: 'Chatterjee, K., Doyen, L., & Vardi, M. (2015). The complexity of synthesis
from probabilistic components. In 42nd International Colloquium (Vol. 9135,
pp. 108–120). Kyoto, Japan: Springer Nature. https://doi.org/10.1007/978-3-662-47666-6_9'
chicago: Chatterjee, Krishnendu, Laurent Doyen, and Moshe Vardi. “The Complexity
of Synthesis from Probabilistic Components.” In 42nd International Colloquium,
9135:108–20. Springer Nature, 2015. https://doi.org/10.1007/978-3-662-47666-6_9.
ieee: K. Chatterjee, L. Doyen, and M. Vardi, “The complexity of synthesis from probabilistic
components,” in 42nd International Colloquium, Kyoto, Japan, 2015, vol.
9135, pp. 108–120.
ista: 'Chatterjee K, Doyen L, Vardi M. 2015. The complexity of synthesis from probabilistic
components. 42nd International Colloquium. ICALP: Automata, Languages and Programming,
LNCS, vol. 9135, 108–120.'
mla: Chatterjee, Krishnendu, et al. “The Complexity of Synthesis from Probabilistic
Components.” 42nd International Colloquium, vol. 9135, Springer Nature,
2015, pp. 108–20, doi:10.1007/978-3-662-47666-6_9.
short: K. Chatterjee, L. Doyen, M. Vardi, in:, 42nd International Colloquium, Springer
Nature, 2015, pp. 108–120.
conference:
end_date: 2015-07-10
location: Kyoto, Japan
name: 'ICALP: Automata, Languages and Programming'
start_date: 2015-07-06
date_created: 2018-12-11T11:53:00Z
date_published: 2015-06-20T00:00:00Z
date_updated: 2022-02-01T15:04:44Z
day: '20'
department:
- _id: KrCh
doi: 10.1007/978-3-662-47666-6_9
ec_funded: 1
intvolume: ' 9135'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1502.04844
month: '06'
oa: 1
oa_version: Preprint
page: 108 - 120
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _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: 42nd International Colloquium
publication_identifier:
isbn:
- 978-3-662-47665-9
publication_status: published
publisher: Springer Nature
publist_id: '5557'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The complexity of synthesis from probabilistic components
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 9135
year: '2015'
...
---
_id: '1610'
abstract:
- lang: eng
text: The edit distance between two words w1, w2 is the minimal number of word operations
(letter insertions, deletions, and substitutions) necessary to transform w1 to
w2. The edit distance generalizes to languages L1,L2, where the edit distance
is the minimal number k such that for every word from L1 there exists a word in
L2 with edit distance at most k. We study the edit distance computation problem
between pushdown automata and their subclasses. The problem of computing edit
distance to pushdown automata is undecidable, and in practice, the interesting
question is to compute the edit distance from a pushdown automaton (the implementation,
a standard model for programs with recursion) to a regular language (the specification).
In this work, we present a complete picture of decidability and complexity for
deciding whether, for a given threshold k, the edit distance from a pushdown automaton
to a finite automaton is at most k.
alternative_title:
- LNCS
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: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Jan
full_name: Otop, Jan
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
citation:
ama: 'Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. Edit distance for pushdown
automata. In: 42nd International Colloquium. Vol 9135. Springer Nature;
2015:121-133. doi:10.1007/978-3-662-47666-6_10'
apa: 'Chatterjee, K., Henzinger, T. A., Ibsen-Jensen, R., & Otop, J. (2015).
Edit distance for pushdown automata. In 42nd International Colloquium (Vol.
9135, pp. 121–133). Kyoto, Japan: Springer Nature. https://doi.org/10.1007/978-3-662-47666-6_10'
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, Rasmus Ibsen-Jensen, and Jan
Otop. “Edit Distance for Pushdown Automata.” In 42nd International Colloquium,
9135:121–33. Springer Nature, 2015. https://doi.org/10.1007/978-3-662-47666-6_10.
ieee: K. Chatterjee, T. A. Henzinger, R. Ibsen-Jensen, and J. Otop, “Edit distance
for pushdown automata,” in 42nd International Colloquium, Kyoto, Japan,
2015, vol. 9135, no. Part II, pp. 121–133.
ista: 'Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. 2015. Edit distance for
pushdown automata. 42nd International Colloquium. ICALP: Automata, Languages and
Programming, LNCS, vol. 9135, 121–133.'
mla: Chatterjee, Krishnendu, et al. “Edit Distance for Pushdown Automata.” 42nd
International Colloquium, vol. 9135, no. Part II, Springer Nature, 2015, pp.
121–33, doi:10.1007/978-3-662-47666-6_10.
short: K. Chatterjee, T.A. Henzinger, R. Ibsen-Jensen, J. Otop, in:, 42nd International
Colloquium, Springer Nature, 2015, pp. 121–133.
conference:
end_date: 2015-07-10
location: Kyoto, Japan
name: 'ICALP: Automata, Languages and Programming'
start_date: 2015-07-06
date_created: 2018-12-11T11:53:01Z
date_published: 2015-07-01T00:00:00Z
date_updated: 2023-02-23T12:26:24Z
day: '01'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1007/978-3-662-47666-6_10
ec_funded: 1
external_id:
arxiv:
- '1504.08259'
intvolume: ' 9135'
issue: Part II
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1504.08259
month: '07'
oa: 1
oa_version: None
page: 121 - 133
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _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'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication: 42nd International Colloquium
publication_identifier:
isbn:
- 978-3-662-47665-9
publication_status: published
publisher: Springer Nature
publist_id: '5556'
pubrep_id: '321'
quality_controlled: '1'
related_material:
record:
- id: '465'
relation: later_version
status: public
- id: '5438'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Edit distance for pushdown automata
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 9135
year: '2015'
...
---
_id: '1611'
abstract:
- lang: eng
text: Biosensors for signaling molecules allow the study of physiological processes
by bringing together the fields of protein engineering, fluorescence imaging,
and cell biology. Construction of genetically encoded biosensors generally relies
on the availability of a binding "core" that is both specific and stable,
which can then be combined with fluorescent molecules to create a sensor. However,
binding proteins with the desired properties are often not available in nature
and substantial improvement to sensors can be required, particularly with regard
to their durability. Ancestral protein reconstruction is a powerful protein-engineering
tool able to generate highly stable and functional proteins. In this work, we
sought to establish the utility of ancestral protein reconstruction to biosensor
development, beginning with the construction of an l-arginine biosensor. l-arginine,
as the immediate precursor to nitric oxide, is an important molecule in many physiological
contexts including brain function. Using a combination of ancestral reconstruction
and circular permutation, we constructed a Förster resonance energy transfer (FRET)
biosensor for l-arginine (cpFLIPR). cpFLIPR displays high sensitivity and specificity,
with a Kd of ∼14 μM and a maximal dynamic range of 35%. Importantly, cpFLIPR was
highly robust, enabling accurate l-arginine measurement at physiological temperatures.
We established that cpFLIPR is compatible with two-photon excitation fluorescence
microscopy and report l-arginine concentrations in brain tissue.
author:
- first_name: Jason
full_name: Whitfield, Jason
last_name: Whitfield
- first_name: William
full_name: Zhang, William
last_name: Zhang
- first_name: Michel
full_name: Herde, Michel
last_name: Herde
- first_name: Ben
full_name: Clifton, Ben
last_name: Clifton
- first_name: Johanna
full_name: Radziejewski, Johanna
last_name: Radziejewski
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Christian
full_name: Henneberger, Christian
last_name: Henneberger
- first_name: Colin
full_name: Jackson, Colin
last_name: Jackson
citation:
ama: Whitfield J, Zhang W, Herde M, et al. Construction of a robust and sensitive
arginine biosensor through ancestral protein reconstruction. Protein Science.
2015;24(9):1412-1422. doi:10.1002/pro.2721
apa: Whitfield, J., Zhang, W., Herde, M., Clifton, B., Radziejewski, J., Janovjak,
H. L., … Jackson, C. (2015). Construction of a robust and sensitive arginine biosensor
through ancestral protein reconstruction. Protein Science. Wiley. https://doi.org/10.1002/pro.2721
chicago: Whitfield, Jason, William Zhang, Michel Herde, Ben Clifton, Johanna Radziejewski,
Harald L Janovjak, Christian Henneberger, and Colin Jackson. “Construction of
a Robust and Sensitive Arginine Biosensor through Ancestral Protein Reconstruction.”
Protein Science. Wiley, 2015. https://doi.org/10.1002/pro.2721.
ieee: J. Whitfield et al., “Construction of a robust and sensitive arginine
biosensor through ancestral protein reconstruction,” Protein Science, vol.
24, no. 9. Wiley, pp. 1412–1422, 2015.
ista: Whitfield J, Zhang W, Herde M, Clifton B, Radziejewski J, Janovjak HL, Henneberger
C, Jackson C. 2015. Construction of a robust and sensitive arginine biosensor
through ancestral protein reconstruction. Protein Science. 24(9), 1412–1422.
mla: Whitfield, Jason, et al. “Construction of a Robust and Sensitive Arginine Biosensor
through Ancestral Protein Reconstruction.” Protein Science, vol. 24, no.
9, Wiley, 2015, pp. 1412–22, doi:10.1002/pro.2721.
short: J. Whitfield, W. Zhang, M. Herde, B. Clifton, J. Radziejewski, H.L. Janovjak,
C. Henneberger, C. Jackson, Protein Science 24 (2015) 1412–1422.
date_created: 2018-12-11T11:53:01Z
date_published: 2015-09-01T00:00:00Z
date_updated: 2021-01-12T06:52:00Z
day: '01'
department:
- _id: HaJa
doi: 10.1002/pro.2721
external_id:
pmid:
- '26061224'
intvolume: ' 24'
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4570536/
month: '09'
oa: 1
oa_version: Submitted Version
page: 1412 - 1422
pmid: 1
project:
- _id: 255BFFFA-B435-11E9-9278-68D0E5697425
grant_number: RGY0084/2012
name: In situ real-time imaging of neurotransmitter signaling using designer optical
sensors (HFSP Young Investigator)
publication: Protein Science
publication_status: published
publisher: Wiley
publist_id: '5555'
quality_controlled: '1'
scopus_import: 1
status: public
title: Construction of a robust and sensitive arginine biosensor through ancestral
protein reconstruction
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2015'
...
---
_id: '1614'
abstract:
- lang: eng
text: 'GABAergic perisoma-inhibiting fast-spiking interneurons (PIIs) effectively
control the activity of large neuron populations by their wide axonal arborizations.
It is generally assumed that the output of one PII to its target cells is strong
and rapid. Here, we show that, unexpectedly, both strength and time course of
PII-mediated perisomatic inhibition change with distance between synaptically
connected partners in the rodent hippocampus. Synaptic signals become weaker due
to lower contact numbers and decay more slowly with distance, very likely resulting
from changes in GABAA receptor subunit composition. When distance-dependent synaptic
inhibition is introduced to a rhythmically active neuronal network model, randomly
driven principal cell assemblies are strongly synchronized by the PIIs, leading
to higher precision in principal cell spike times than in a network with uniform
synaptic inhibition. '
author:
- first_name: Michael
full_name: Strüber, Michael
last_name: Strüber
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Marlene
full_name: Bartos, Marlene
last_name: Bartos
citation:
ama: Strüber M, Jonas PM, Bartos M. Strength and duration of perisomatic GABAergic
inhibition depend on distance between synaptically connected cells. PNAS.
2015;112(4):1220-1225. doi:10.1073/pnas.1412996112
apa: Strüber, M., Jonas, P. M., & Bartos, M. (2015). Strength and duration of
perisomatic GABAergic inhibition depend on distance between synaptically connected
cells. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1412996112
chicago: Strüber, Michael, Peter M Jonas, and Marlene Bartos. “Strength and Duration
of Perisomatic GABAergic Inhibition Depend on Distance between Synaptically Connected
Cells.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1412996112.
ieee: M. Strüber, P. M. Jonas, and M. Bartos, “Strength and duration of perisomatic
GABAergic inhibition depend on distance between synaptically connected cells,”
PNAS, vol. 112, no. 4. National Academy of Sciences, pp. 1220–1225, 2015.
ista: Strüber M, Jonas PM, Bartos M. 2015. Strength and duration of perisomatic
GABAergic inhibition depend on distance between synaptically connected cells.
PNAS. 112(4), 1220–1225.
mla: Strüber, Michael, et al. “Strength and Duration of Perisomatic GABAergic Inhibition
Depend on Distance between Synaptically Connected Cells.” PNAS, vol. 112,
no. 4, National Academy of Sciences, 2015, pp. 1220–25, doi:10.1073/pnas.1412996112.
short: M. Strüber, P.M. Jonas, M. Bartos, PNAS 112 (2015) 1220–1225.
date_created: 2018-12-11T11:53:02Z
date_published: 2015-01-27T00:00:00Z
date_updated: 2021-01-12T06:52:01Z
day: '27'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1073/pnas.1412996112
ec_funded: 1
external_id:
pmid:
- '25583495'
file:
- access_level: open_access
checksum: 6703309a1f58493cf5a704211fb6ebed
content_type: application/pdf
creator: dernst
date_created: 2019-01-17T07:52:40Z
date_updated: 2020-07-14T12:45:07Z
file_id: '5838'
file_name: 2015_PNAS_Strueber.pdf
file_size: 1280860
relation: main_file
file_date_updated: 2020-07-14T12:45:07Z
has_accepted_license: '1'
intvolume: ' 112'
issue: '4'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 1220 - 1225
pmid: 1
project:
- _id: 25C26B1E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P24909-B24
name: Mechanisms of transmitter release at GABAergic synapses
- _id: 25C0F108-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '268548'
name: Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '5552'
quality_controlled: '1'
scopus_import: 1
status: public
title: Strength and duration of perisomatic GABAergic inhibition depend on distance
between synaptically connected cells
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2015'
...
---
_id: '1311'
abstract:
- lang: eng
text: In this paper, we develop an energy method to study finite speed of propagation
and waiting time phenomena for the stochastic porous media equation with linear
multiplicative noise in up to three spatial dimensions. Based on a novel iteration
technique and on stochastic counterparts of weighted integral estimates used in
the deterministic setting, we formulate a sufficient criterion on the growth of
initial data which locally guarantees a waiting time phenomenon to occur almost
surely. Up to a logarithmic factor, this criterion coincides with the optimal
criterion known from the deterministic setting. Our technique can be modified
to prove finite speed of propagation as well.
acknowledgement: The first author has been supported by the Lithuanian-Swiss co- operation
program under the project agreement No. CH-SMM-01/0.
author:
- first_name: Julian L
full_name: Julian Fischer
id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87
last_name: Fischer
orcid: 0000-0002-0479-558X
- first_name: Günther
full_name: Grün, Günther
last_name: Grün
citation:
ama: 'Fischer JL, Grün G. Finite speed of propagation and waiting times for the
stochastic porous medium equation: A unifying approach. SIAM Journal on Mathematical
Analysis. 2015;47(1):825-854. doi:10.1137/140960578'
apa: 'Fischer, J. L., & Grün, G. (2015). Finite speed of propagation and waiting
times for the stochastic porous medium equation: A unifying approach. SIAM
Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics
. https://doi.org/10.1137/140960578'
chicago: 'Fischer, Julian L, and Günther Grün. “Finite Speed of Propagation and
Waiting Times for the Stochastic Porous Medium Equation: A Unifying Approach.”
SIAM Journal on Mathematical Analysis. Society for Industrial and Applied
Mathematics , 2015. https://doi.org/10.1137/140960578.'
ieee: 'J. L. Fischer and G. Grün, “Finite speed of propagation and waiting times
for the stochastic porous medium equation: A unifying approach,” SIAM Journal
on Mathematical Analysis, vol. 47, no. 1. Society for Industrial and Applied
Mathematics , pp. 825–854, 2015.'
ista: 'Fischer JL, Grün G. 2015. Finite speed of propagation and waiting times for
the stochastic porous medium equation: A unifying approach. SIAM Journal on Mathematical
Analysis. 47(1), 825–854.'
mla: 'Fischer, Julian L., and Günther Grün. “Finite Speed of Propagation and Waiting
Times for the Stochastic Porous Medium Equation: A Unifying Approach.” SIAM
Journal on Mathematical Analysis, vol. 47, no. 1, Society for Industrial and
Applied Mathematics , 2015, pp. 825–54, doi:10.1137/140960578.'
short: J.L. Fischer, G. Grün, SIAM Journal on Mathematical Analysis 47 (2015) 825–854.
date_created: 2018-12-11T11:51:18Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2021-01-12T06:49:48Z
day: '01'
doi: 10.1137/140960578
extern: 1
intvolume: ' 47'
issue: '1'
month: '01'
page: 825 - 854
publication: SIAM Journal on Mathematical Analysis
publication_status: published
publisher: 'Society for Industrial and Applied Mathematics '
publist_id: '5958'
quality_controlled: 0
status: public
title: 'Finite speed of propagation and waiting times for the stochastic porous medium
equation: A unifying approach'
type: journal_article
volume: 47
year: '2015'
...
---
_id: '1313'
abstract:
- lang: eng
text: We present an algorithm for the derivation of lower bounds on support propagation
for a certain class of nonlinear parabolic equations. We proceed by combining
the ideas in some recent papers by the author with the algorithmic construction
of entropies due to Jüngel and Matthes, reducing the problem to a quantifier elimination
problem. Due to its complexity, the quantifier elimination problem cannot be solved
by present exact algorithms. However, by tackling the quantifier elimination problem
numerically, in the case of the thin-film equation we are able to improve recent
results by the author in the regime of strong slippage n ∈ (1, 2). For certain
second-order doubly nonlinear parabolic equations, we are able to extend the known
lower bounds on free boundary propagation to the case of irregular oscillatory
initial data. Finally, we apply our method to a sixth-order quantum drift-diffusion
equation, resulting in an upper bound on the time which it takes for the support
to reach every point in the domain.
acknowledgement: This research was supported by the Lithuanian-Swiss cooperation program
under the project agreement No. CH-SMM-01/0.
author:
- first_name: Julian L
full_name: Julian Fischer
id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87
last_name: Fischer
orcid: 0000-0002-0479-558X
citation:
ama: 'Fischer JL. Estimates on front propagation for nonlinear higher-order parabolic
equations: An algorithmic approach. Interfaces and Free Boundaries. 2015;17(1):1-20.
doi:10.4171/IFB/331'
apa: 'Fischer, J. L. (2015). Estimates on front propagation for nonlinear higher-order
parabolic equations: An algorithmic approach. Interfaces and Free Boundaries.
European Mathematical Society Publishing House. https://doi.org/10.4171/IFB/331'
chicago: 'Fischer, Julian L. “Estimates on Front Propagation for Nonlinear Higher-Order
Parabolic Equations: An Algorithmic Approach.” Interfaces and Free Boundaries.
European Mathematical Society Publishing House, 2015. https://doi.org/10.4171/IFB/331.'
ieee: 'J. L. Fischer, “Estimates on front propagation for nonlinear higher-order
parabolic equations: An algorithmic approach,” Interfaces and Free Boundaries,
vol. 17, no. 1. European Mathematical Society Publishing House, pp. 1–20, 2015.'
ista: 'Fischer JL. 2015. Estimates on front propagation for nonlinear higher-order
parabolic equations: An algorithmic approach. Interfaces and Free Boundaries.
17(1), 1–20.'
mla: 'Fischer, Julian L. “Estimates on Front Propagation for Nonlinear Higher-Order
Parabolic Equations: An Algorithmic Approach.” Interfaces and Free Boundaries,
vol. 17, no. 1, European Mathematical Society Publishing House, 2015, pp. 1–20,
doi:10.4171/IFB/331.'
short: J.L. Fischer, Interfaces and Free Boundaries 17 (2015) 1–20.
date_created: 2018-12-11T11:51:19Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2021-01-12T06:49:48Z
day: '01'
doi: 10.4171/IFB/331
extern: 1
intvolume: ' 17'
issue: '1'
month: '01'
page: 1 - 20
publication: Interfaces and Free Boundaries
publication_status: published
publisher: European Mathematical Society Publishing House
publist_id: '5956'
quality_controlled: 0
status: public
title: 'Estimates on front propagation for nonlinear higher-order parabolic equations:
An algorithmic approach'
type: journal_article
volume: 17
year: '2015'
...
---
_id: '1314'
abstract:
- lang: eng
text: 'We derive a posteriori estimates for the modeling error caused by the assumption
of perfect incompressibility in the incompressible Navier-Stokes equation: Real
fluids are never perfectly incompressible but always feature at least some low
amount of compressibility. Thus, their behavior is described by the compressible
Navier-Stokes equation, the pressure being a steep function of the density. We
rigorously estimate the difference between an approximate solution to the incompressible
Navier-Stokes equation and any weak solution to the compressible Navier-Stokes
equation in the sense of Lions (without assuming any additional regularity of
solutions). Heuristics and numerical results suggest that our error estimates
are of optimal order in the case of "well-behaved" flows and divergence-free
approximations of the velocity field. Thus, we expect our estimates to justify
the idealization of fluids as perfectly incompressible also in practical situations.'
acknowledgement: The research of the author was supported by the Lithuanian-Swiss
cooperation program under the project agreement CH-SMM-01/0.
author:
- first_name: Julian L
full_name: Fischer, Julian L
id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87
last_name: Fischer
orcid: 0000-0002-0479-558X
citation:
ama: Fischer JL. A posteriori modeling error estimates for the assumption of perfect
incompressibility in the Navier-Stokes equation. SIAM Journal on Numerical
Analysis. 2015;53(5):2178-2205. doi:10.1137/140966654
apa: Fischer, J. L. (2015). A posteriori modeling error estimates for the assumption
of perfect incompressibility in the Navier-Stokes equation. SIAM Journal on
Numerical Analysis. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/140966654
chicago: Fischer, Julian L. “A Posteriori Modeling Error Estimates for the Assumption
of Perfect Incompressibility in the Navier-Stokes Equation.” SIAM Journal on
Numerical Analysis. Society for Industrial and Applied Mathematics , 2015.
https://doi.org/10.1137/140966654.
ieee: J. L. Fischer, “A posteriori modeling error estimates for the assumption of
perfect incompressibility in the Navier-Stokes equation,” SIAM Journal on Numerical
Analysis, vol. 53, no. 5. Society for Industrial and Applied Mathematics ,
pp. 2178–2205, 2015.
ista: Fischer JL. 2015. A posteriori modeling error estimates for the assumption
of perfect incompressibility in the Navier-Stokes equation. SIAM Journal on Numerical
Analysis. 53(5), 2178–2205.
mla: Fischer, Julian L. “A Posteriori Modeling Error Estimates for the Assumption
of Perfect Incompressibility in the Navier-Stokes Equation.” SIAM Journal on
Numerical Analysis, vol. 53, no. 5, Society for Industrial and Applied Mathematics
, 2015, pp. 2178–205, doi:10.1137/140966654.
short: J.L. Fischer, SIAM Journal on Numerical Analysis 53 (2015) 2178–2205.
date_created: 2018-12-11T11:51:19Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2021-01-12T06:49:49Z
day: '01'
doi: 10.1137/140966654
extern: '1'
intvolume: ' 53'
issue: '5'
language:
- iso: eng
month: '01'
oa_version: None
page: 2178 - 2205
publication: SIAM Journal on Numerical Analysis
publication_status: published
publisher: 'Society for Industrial and Applied Mathematics '
publist_id: '5957'
quality_controlled: '1'
status: public
title: A posteriori modeling error estimates for the assumption of perfect incompressibility
in the Navier-Stokes equation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 53
year: '2015'
...
---
_id: '1316'
abstract:
- lang: eng
text: In the present work we introduce the notion of a renormalized solution for
reaction–diffusion systems with entropy-dissipating reactions. We establish the
global existence of renormalized solutions. In the case of integrable reaction
terms our notion of a renormalized solution reduces to the usual notion of a weak
solution. Our existence result in particular covers all reaction–diffusion systems
involving a single reversible reaction with mass-action kinetics and (possibly
species-dependent) Fick-law diffusion; more generally, it covers the case of systems
of reversible reactions with mass-action kinetics which satisfy the detailed balance
condition. For such equations the existence of any kind of solution in general
was an open problem, thereby motivating the study of renormalized solutions.
acknowledgement: This research was supported by the Lithuanian-Swiss cooperation program
under the project agreement No. CH-SMM-01/0.
author:
- first_name: Julian L
full_name: Julian Fischer
id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87
last_name: Fischer
orcid: 0000-0002-0479-558X
citation:
ama: Fischer JL. Global existence of renormalized solutions to entropy-dissipating
reaction–diffusion systems. Archive for Rational Mechanics and Analysis.
2015;218(1):553-587. doi:10.1007/s00205-015-0866-x
apa: Fischer, J. L. (2015). Global existence of renormalized solutions to entropy-dissipating
reaction–diffusion systems. Archive for Rational Mechanics and Analysis.
Springer. https://doi.org/10.1007/s00205-015-0866-x
chicago: Fischer, Julian L. “Global Existence of Renormalized Solutions to Entropy-Dissipating
Reaction–Diffusion Systems.” Archive for Rational Mechanics and Analysis.
Springer, 2015. https://doi.org/10.1007/s00205-015-0866-x.
ieee: J. L. Fischer, “Global existence of renormalized solutions to entropy-dissipating
reaction–diffusion systems,” Archive for Rational Mechanics and Analysis,
vol. 218, no. 1. Springer, pp. 553–587, 2015.
ista: Fischer JL. 2015. Global existence of renormalized solutions to entropy-dissipating
reaction–diffusion systems. Archive for Rational Mechanics and Analysis. 218(1),
553–587.
mla: Fischer, Julian L. “Global Existence of Renormalized Solutions to Entropy-Dissipating
Reaction–Diffusion Systems.” Archive for Rational Mechanics and Analysis,
vol. 218, no. 1, Springer, 2015, pp. 553–87, doi:10.1007/s00205-015-0866-x.
short: J.L. Fischer, Archive for Rational Mechanics and Analysis 218 (2015) 553–587.
date_created: 2018-12-11T11:51:20Z
date_published: 2015-10-01T00:00:00Z
date_updated: 2021-01-12T06:49:50Z
day: '01'
doi: 10.1007/s00205-015-0866-x
extern: 1
intvolume: ' 218'
issue: '1'
month: '10'
page: 553 - 587
publication: Archive for Rational Mechanics and Analysis
publication_status: published
publisher: Springer
publist_id: '5955'
quality_controlled: 0
status: public
title: Global existence of renormalized solutions to entropy-dissipating reaction–diffusion
systems
type: journal_article
volume: 218
year: '2015'
...
---
_id: '13392'
abstract:
- lang: eng
text: The chemical behaviour of molecules can be significantly modified by confinement
to volumes comparable to the dimensions of the molecules. Although such confined
spaces can be found in various nanostructured materials, such as zeolites, nanoporous
organic frameworks and colloidal nanocrystal assemblies, the slow diffusion of
molecules in and out of these materials has greatly hampered studying the effect
of confinement on their physicochemical properties. Here, we show that this diffusion
limitation can be overcome by reversibly creating and destroying confined environments
by means of ultraviolet and visible light irradiation. We use colloidal nanocrystals
functionalized with light-responsive ligands that readily self-assemble and trap
various molecules from the surrounding bulk solution. Once trapped, these molecules
can undergo chemical reactions with increased rates and with stereoselectivities
significantly different from those in bulk solution. Illumination with visible
light disassembles these nanoflasks, releasing the product in solution and thereby
establishes a catalytic cycle. These dynamic nanoflasks can be useful for studying
chemical reactivities in confined environments and for synthesizing molecules
that are otherwise hard to achieve in bulk solution.
article_processing_charge: No
article_type: original
author:
- first_name: Hui
full_name: Zhao, Hui
last_name: Zhao
- first_name: Soumyo
full_name: Sen, Soumyo
last_name: Sen
- first_name: T.
full_name: Udayabhaskararao, T.
last_name: Udayabhaskararao
- first_name: Michał
full_name: Sawczyk, Michał
last_name: Sawczyk
- first_name: Kristina
full_name: Kučanda, Kristina
last_name: Kučanda
- first_name: Debasish
full_name: Manna, Debasish
last_name: Manna
- first_name: Pintu K.
full_name: Kundu, Pintu K.
last_name: Kundu
- first_name: Ji-Woong
full_name: Lee, Ji-Woong
last_name: Lee
- first_name: Petr
full_name: Král, Petr
last_name: Král
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Zhao H, Sen S, Udayabhaskararao T, et al. Reversible trapping and reaction
acceleration within dynamically self-assembling nanoflasks. Nature Nanotechnology.
2015;11:82-88. doi:10.1038/nnano.2015.256
apa: Zhao, H., Sen, S., Udayabhaskararao, T., Sawczyk, M., Kučanda, K., Manna, D.,
… Klajn, R. (2015). Reversible trapping and reaction acceleration within dynamically
self-assembling nanoflasks. Nature Nanotechnology. Springer Nature. https://doi.org/10.1038/nnano.2015.256
chicago: Zhao, Hui, Soumyo Sen, T. Udayabhaskararao, Michał Sawczyk, Kristina Kučanda,
Debasish Manna, Pintu K. Kundu, Ji-Woong Lee, Petr Král, and Rafal Klajn. “Reversible
Trapping and Reaction Acceleration within Dynamically Self-Assembling Nanoflasks.”
Nature Nanotechnology. Springer Nature, 2015. https://doi.org/10.1038/nnano.2015.256.
ieee: H. Zhao et al., “Reversible trapping and reaction acceleration within
dynamically self-assembling nanoflasks,” Nature Nanotechnology, vol. 11.
Springer Nature, pp. 82–88, 2015.
ista: Zhao H, Sen S, Udayabhaskararao T, Sawczyk M, Kučanda K, Manna D, Kundu PK,
Lee J-W, Král P, Klajn R. 2015. Reversible trapping and reaction acceleration
within dynamically self-assembling nanoflasks. Nature Nanotechnology. 11, 82–88.
mla: Zhao, Hui, et al. “Reversible Trapping and Reaction Acceleration within Dynamically
Self-Assembling Nanoflasks.” Nature Nanotechnology, vol. 11, Springer Nature,
2015, pp. 82–88, doi:10.1038/nnano.2015.256.
short: H. Zhao, S. Sen, T. Udayabhaskararao, M. Sawczyk, K. Kučanda, D. Manna, P.K.
Kundu, J.-W. Lee, P. Král, R. Klajn, Nature Nanotechnology 11 (2015) 82–88.
date_created: 2023-08-01T09:44:04Z
date_published: 2015-11-23T00:00:00Z
date_updated: 2023-08-07T12:55:46Z
day: '23'
doi: 10.1038/nnano.2015.256
extern: '1'
external_id:
pmid:
- '26595335'
intvolume: ' 11'
keyword:
- Electrical and Electronic Engineering
- Condensed Matter Physics
- General Materials Science
- Biomedical Engineering
- Atomic and Molecular Physics
- and Optics
- Bioengineering
language:
- iso: eng
month: '11'
oa_version: None
page: 82-88
pmid: 1
publication: Nature Nanotechnology
publication_identifier:
eissn:
- 1748-3395
issn:
- 1748-3387
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Reversible trapping and reaction acceleration within dynamically self-assembling
nanoflasks
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2015'
...
---
_id: '13393'
abstract:
- lang: eng
text: Precise control of the self-assembly of selected components within complex
mixtures is a challenging goal whose realization is important for fabricating
novel nanomaterials. Herein we show that by decorating the surfaces of metallic
nanoparticles with differently substituted azobenzenes, it is possible to modulate
the wavelength of light at which the self-assembly of these nanoparticles is induced.
Exposing a mixture of two types of nanoparticles, each functionalized with a different
azobenzene, to UV or blue light induces the selective self-assembly of only one
type of nanoparticles. Irradiation with the other wavelength triggers the disassembly
of the aggregates, and the simultaneous self-assembly of nanoparticles of the
other type. By placing both types of azobenzenes on the same nanoparticles, we
created unique materials (“frustrated” nanoparticles) whose self-assembly is induced
irrespective of the wavelength of the incident light.
article_processing_charge: No
article_type: original
author:
- first_name: Debasish
full_name: Manna, Debasish
last_name: Manna
- first_name: Thumu
full_name: Udayabhaskararao, Thumu
last_name: Udayabhaskararao
- first_name: Hui
full_name: Zhao, Hui
last_name: Zhao
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Manna D, Udayabhaskararao T, Zhao H, Klajn R. Orthogonal light-induced self-assembly
of nanoparticles using differently substituted azobenzenes. Angewandte Chemie
International Edition. 2015;54(42):12394-12397. doi:10.1002/anie.201502419
apa: Manna, D., Udayabhaskararao, T., Zhao, H., & Klajn, R. (2015). Orthogonal
light-induced self-assembly of nanoparticles using differently substituted azobenzenes.
Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201502419
chicago: Manna, Debasish, Thumu Udayabhaskararao, Hui Zhao, and Rafal Klajn. “Orthogonal
Light-Induced Self-Assembly of Nanoparticles Using Differently Substituted Azobenzenes.”
Angewandte Chemie International Edition. Wiley, 2015. https://doi.org/10.1002/anie.201502419.
ieee: D. Manna, T. Udayabhaskararao, H. Zhao, and R. Klajn, “Orthogonal light-induced
self-assembly of nanoparticles using differently substituted azobenzenes,” Angewandte
Chemie International Edition, vol. 54, no. 42. Wiley, pp. 12394–12397, 2015.
ista: Manna D, Udayabhaskararao T, Zhao H, Klajn R. 2015. Orthogonal light-induced
self-assembly of nanoparticles using differently substituted azobenzenes. Angewandte
Chemie International Edition. 54(42), 12394–12397.
mla: Manna, Debasish, et al. “Orthogonal Light-Induced Self-Assembly of Nanoparticles
Using Differently Substituted Azobenzenes.” Angewandte Chemie International
Edition, vol. 54, no. 42, Wiley, 2015, pp. 12394–97, doi:10.1002/anie.201502419.
short: D. Manna, T. Udayabhaskararao, H. Zhao, R. Klajn, Angewandte Chemie International
Edition 54 (2015) 12394–12397.
date_created: 2023-08-01T09:44:19Z
date_published: 2015-10-01T00:00:00Z
date_updated: 2023-08-07T12:58:29Z
day: '01'
doi: 10.1002/anie.201502419
extern: '1'
external_id:
pmid:
- '25959725'
intvolume: ' 54'
issue: '42'
keyword:
- General Chemistry
- Catalysis
language:
- iso: eng
month: '10'
oa_version: None
page: 12394-12397
pmid: 1
publication: Angewandte Chemie International Edition
publication_identifier:
eissn:
- 1521-3773
issn:
- 1433-7851
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Orthogonal light-induced self-assembly of nanoparticles using differently substituted
azobenzenes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 54
year: '2015'
...
---
_id: '13394'
abstract:
- lang: eng
text: The ability to guide the assembly of nanosized objects reversibly with external
stimuli, in particular light, is of fundamental importance, and it contributes
to the development of applications as diverse as nanofabrication and controlled
drug delivery. However, all the systems described to date are based on nanoparticles
(NPs) that are inherently photoresponsive, which makes their preparation cumbersome
and can markedly hamper their performance. Here we describe a conceptually new
methodology to assemble NPs reversibly using light that does not require the particles
to be functionalized with light-responsive ligands. Our strategy is based on the
use of a photoswitchable medium that responds to light in such a way that it modulates
the interparticle interactions. NP assembly proceeds quantitatively and without
apparent fatigue, both in solution and in gels. Exposing the gels to light in
a spatially controlled manner allowed us to draw images that spontaneously disappeared
after a specific period of time.
article_processing_charge: No
article_type: original
author:
- first_name: Pintu K.
full_name: Kundu, Pintu K.
last_name: Kundu
- first_name: Dipak
full_name: Samanta, Dipak
last_name: Samanta
- first_name: Ron
full_name: Leizrowice, Ron
last_name: Leizrowice
- first_name: Baruch
full_name: Margulis, Baruch
last_name: Margulis
- first_name: Hui
full_name: Zhao, Hui
last_name: Zhao
- first_name: Martin
full_name: Börner, Martin
last_name: Börner
- first_name: T.
full_name: Udayabhaskararao, T.
last_name: Udayabhaskararao
- first_name: Debasish
full_name: Manna, Debasish
last_name: Manna
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Kundu PK, Samanta D, Leizrowice R, et al. Light-controlled self-assembly of
non-photoresponsive nanoparticles. Nature Chemistry. 2015;7:646-652. doi:10.1038/nchem.2303
apa: Kundu, P. K., Samanta, D., Leizrowice, R., Margulis, B., Zhao, H., Börner,
M., … Klajn, R. (2015). Light-controlled self-assembly of non-photoresponsive
nanoparticles. Nature Chemistry. Springer Nature. https://doi.org/10.1038/nchem.2303
chicago: Kundu, Pintu K., Dipak Samanta, Ron Leizrowice, Baruch Margulis, Hui Zhao,
Martin Börner, T. Udayabhaskararao, Debasish Manna, and Rafal Klajn. “Light-Controlled
Self-Assembly of Non-Photoresponsive Nanoparticles.” Nature Chemistry.
Springer Nature, 2015. https://doi.org/10.1038/nchem.2303.
ieee: P. K. Kundu et al., “Light-controlled self-assembly of non-photoresponsive
nanoparticles,” Nature Chemistry, vol. 7. Springer Nature, pp. 646–652,
2015.
ista: Kundu PK, Samanta D, Leizrowice R, Margulis B, Zhao H, Börner M, Udayabhaskararao
T, Manna D, Klajn R. 2015. Light-controlled self-assembly of non-photoresponsive
nanoparticles. Nature Chemistry. 7, 646–652.
mla: Kundu, Pintu K., et al. “Light-Controlled Self-Assembly of Non-Photoresponsive
Nanoparticles.” Nature Chemistry, vol. 7, Springer Nature, 2015, pp. 646–52,
doi:10.1038/nchem.2303.
short: P.K. Kundu, D. Samanta, R. Leizrowice, B. Margulis, H. Zhao, M. Börner, T.
Udayabhaskararao, D. Manna, R. Klajn, Nature Chemistry 7 (2015) 646–652.
date_created: 2023-08-01T09:44:33Z
date_published: 2015-07-20T00:00:00Z
date_updated: 2023-08-07T13:00:15Z
day: '20'
doi: 10.1038/nchem.2303
extern: '1'
external_id:
pmid:
- '26201741'
intvolume: ' 7'
keyword:
- General Chemical Engineering
- General Chemistry
language:
- iso: eng
month: '07'
oa_version: None
page: 646-652
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: Light-controlled self-assembly of non-photoresponsive nanoparticles
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2015'
...
---
_id: '13395'
abstract:
- lang: eng
text: Metallic nanoparticles co-functionalised with monolayers of UV- and CO2-sensitive
ligands were prepared and shown to respond to these two types of stimuli reversibly
and in an orthogonal fashion. The composition of the coating could be tailored
to yield nanoparticles capable of aggregating exclusively when both UV and CO2
were applied at the same time, analogously to the behaviour of an AND logic gate.
article_processing_charge: No
article_type: original
author:
- first_name: Ji-Woong
full_name: Lee, Ji-Woong
last_name: Lee
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Lee J-W, Klajn R. Dual-responsive nanoparticles that aggregate under the simultaneous
action of light and CO2. Chemical Communications. 2015;51(11):2036-2039.
doi:10.1039/c4cc08541h
apa: Lee, J.-W., & Klajn, R. (2015). Dual-responsive nanoparticles that aggregate
under the simultaneous action of light and CO2. Chemical Communications.
Royal Society of Chemistry. https://doi.org/10.1039/c4cc08541h
chicago: Lee, Ji-Woong, and Rafal Klajn. “Dual-Responsive Nanoparticles That Aggregate
under the Simultaneous Action of Light and CO2.” Chemical Communications.
Royal Society of Chemistry, 2015. https://doi.org/10.1039/c4cc08541h.
ieee: J.-W. Lee and R. Klajn, “Dual-responsive nanoparticles that aggregate under
the simultaneous action of light and CO2,” Chemical Communications, vol.
51, no. 11. Royal Society of Chemistry, pp. 2036–2039, 2015.
ista: Lee J-W, Klajn R. 2015. Dual-responsive nanoparticles that aggregate under
the simultaneous action of light and CO2. Chemical Communications. 51(11), 2036–2039.
mla: Lee, Ji-Woong, and Rafal Klajn. “Dual-Responsive Nanoparticles That Aggregate
under the Simultaneous Action of Light and CO2.” Chemical Communications,
vol. 51, no. 11, Royal Society of Chemistry, 2015, pp. 2036–39, doi:10.1039/c4cc08541h.
short: J.-W. Lee, R. Klajn, Chemical Communications 51 (2015) 2036–2039.
date_created: 2023-08-01T09:44:48Z
date_published: 2015-11-18T00:00:00Z
date_updated: 2023-08-07T13:01:53Z
day: '18'
doi: 10.1039/c4cc08541h
extern: '1'
external_id:
pmid:
- '25417754'
intvolume: ' 51'
issue: '11'
keyword:
- Materials Chemistry
- Metals and Alloys
- Surfaces
- Coatings and Films
- General Chemistry
- Ceramics and Composites
- Electronic
- Optical and Magnetic Materials
- Catalysis
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1039/C4CC08541H
month: '11'
oa: 1
oa_version: Published Version
page: 2036-2039
pmid: 1
publication: Chemical Communications
publication_identifier:
eissn:
- 1364-548X
issn:
- 1359-7345
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dual-responsive nanoparticles that aggregate under the simultaneous action
of light and CO2
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 51
year: '2015'
...
---
_id: '13396'
abstract:
- lang: eng
text: 'Photoswitching in densely packed azobenzene self-assembled monolayers (SAMs)
is strongly affected by steric constraints and excitonic coupling between neighboring
chromophores. Therefore, control of the chromophore density is essential for enhancing
and manipulating the photoisomerization yield. We systematically compare two methods
to achieve this goal: First, we assemble monocomponent azobenzene–alkanethiolate
SAMs on gold nanoparticles of varying size. Second, we form mixed SAMs of azobenzene–alkanethiolates
and “dummy” alkanethiolates on planar substrates. Both methods lead to a gradual
decrease of the chromophore density and enable efficient photoswitching with low-power
light sources. X-ray spectroscopy reveals that coadsorption from solution yields
mixtures with tunable composition. The orientation of the chromophores with respect
to the surface normal changes from a tilted to an upright position with increasing
azobenzene density. For both systems, optical spectroscopy reveals a pronounced
excitonic shift that increases with the chromophore density. In spite of exciting
the optical transition of the monomer, the main spectral change in mixed SAMs
occurs in the excitonic band. In addition, the photoisomerization yield decreases
only slightly by increasing the azobenzene–alkanethiolate density, and we observed
photoswitching even with minor dilutions. Unlike in solution, azobenzene in the
planar SAM can be switched back almost completely by optical excitation from the
cis to the original trans state within a short time scale. These observations
indicate cooperativity in the photoswitching process of mixed SAMs.'
article_processing_charge: No
article_type: original
author:
- first_name: Thomas
full_name: Moldt, Thomas
last_name: Moldt
- first_name: Daniel
full_name: Brete, Daniel
last_name: Brete
- first_name: Daniel
full_name: Przyrembel, Daniel
last_name: Przyrembel
- first_name: Sanjib
full_name: Das, Sanjib
last_name: Das
- first_name: Joel R.
full_name: Goldman, Joel R.
last_name: Goldman
- first_name: Pintu K.
full_name: Kundu, Pintu K.
last_name: Kundu
- first_name: Cornelius
full_name: Gahl, Cornelius
last_name: Gahl
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
- first_name: Martin
full_name: Weinelt, Martin
last_name: Weinelt
citation:
ama: Moldt T, Brete D, Przyrembel D, et al. Tailoring the properties of surface-immobilized
azobenzenes by monolayer dilution and surface curvature. Langmuir. 2015;31(3):1048-1057.
doi:10.1021/la504291n
apa: Moldt, T., Brete, D., Przyrembel, D., Das, S., Goldman, J. R., Kundu, P. K.,
… Weinelt, M. (2015). Tailoring the properties of surface-immobilized azobenzenes
by monolayer dilution and surface curvature. Langmuir. American Chemical
Society. https://doi.org/10.1021/la504291n
chicago: Moldt, Thomas, Daniel Brete, Daniel Przyrembel, Sanjib Das, Joel R. Goldman,
Pintu K. Kundu, Cornelius Gahl, Rafal Klajn, and Martin Weinelt. “Tailoring the
Properties of Surface-Immobilized Azobenzenes by Monolayer Dilution and Surface
Curvature.” Langmuir. American Chemical Society, 2015. https://doi.org/10.1021/la504291n.
ieee: T. Moldt et al., “Tailoring the properties of surface-immobilized azobenzenes
by monolayer dilution and surface curvature,” Langmuir, vol. 31, no. 3.
American Chemical Society, pp. 1048–1057, 2015.
ista: Moldt T, Brete D, Przyrembel D, Das S, Goldman JR, Kundu PK, Gahl C, Klajn
R, Weinelt M. 2015. Tailoring the properties of surface-immobilized azobenzenes
by monolayer dilution and surface curvature. Langmuir. 31(3), 1048–1057.
mla: Moldt, Thomas, et al. “Tailoring the Properties of Surface-Immobilized Azobenzenes
by Monolayer Dilution and Surface Curvature.” Langmuir, vol. 31, no. 3,
American Chemical Society, 2015, pp. 1048–57, doi:10.1021/la504291n.
short: T. Moldt, D. Brete, D. Przyrembel, S. Das, J.R. Goldman, P.K. Kundu, C. Gahl,
R. Klajn, M. Weinelt, Langmuir 31 (2015) 1048–1057.
date_created: 2023-08-01T09:45:02Z
date_published: 2015-01-27T00:00:00Z
date_updated: 2023-08-07T13:05:04Z
day: '27'
doi: 10.1021/la504291n
extern: '1'
external_id:
pmid:
- '25544061'
intvolume: ' 31'
issue: '3'
keyword:
- Electrochemistry
- Spectroscopy
- Surfaces and Interfaces
- Condensed Matter Physics
- General Materials Science
language:
- iso: eng
month: '01'
oa_version: None
page: 1048-1057
pmid: 1
publication: Langmuir
publication_identifier:
eissn:
- 1520-5827
issn:
- 0743-7463
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tailoring the properties of surface-immobilized azobenzenes by monolayer dilution
and surface curvature
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 31
year: '2015'
...
---
_id: '13397'
abstract:
- lang: eng
text: Self-assembly of inorganic nanoparticles has been studied extensively for
particles having different sizes and compositions. However, relatively little
attention has been devoted to how the shape and surface chemistry of magnetic
nanoparticles affects their self-assembly properties. Here, we undertook a combined
experiment–theory study aimed at better understanding of the self-assembly of
cubic magnetite (Fe3O4) particles. We demonstrated that, depending on the experimental
parameters, such as the direction of the magnetic field and nanoparticle density,
a variety of superstructures can be obtained, including one-dimensional filaments
and helices, as well as C-shaped assemblies described here for the first time.
Furthermore, we functionalized the surfaces of the magnetic nanocubes with light-sensitive
ligands. Using these modified nanoparticles, we were able to achieve orthogonal
control of self-assembly using a magnetic field and light.
article_processing_charge: No
article_type: original
author:
- first_name: Gurvinder
full_name: Singh, Gurvinder
last_name: Singh
- first_name: Henry
full_name: Chan, Henry
last_name: Chan
- first_name: T.
full_name: Udayabhaskararao, T.
last_name: Udayabhaskararao
- first_name: Elijah
full_name: Gelman, Elijah
last_name: Gelman
- first_name: Davide
full_name: Peddis, Davide
last_name: Peddis
- first_name: Artem
full_name: Baskin, Artem
last_name: Baskin
- first_name: Gregory
full_name: Leitus, Gregory
last_name: Leitus
- first_name: Petr
full_name: Král, Petr
last_name: Král
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Singh G, Chan H, Udayabhaskararao T, et al. Magnetic field-induced self-assembly
of iron oxide nanocubes. Faraday Discussions. 2015;181:403-421. doi:10.1039/c4fd00265b
apa: Singh, G., Chan, H., Udayabhaskararao, T., Gelman, E., Peddis, D., Baskin,
A., … Klajn, R. (2015). Magnetic field-induced self-assembly of iron oxide nanocubes.
Faraday Discussions. Royal Society of Chemistry. https://doi.org/10.1039/c4fd00265b
chicago: Singh, Gurvinder, Henry Chan, T. Udayabhaskararao, Elijah Gelman, Davide
Peddis, Artem Baskin, Gregory Leitus, Petr Král, and Rafal Klajn. “Magnetic Field-Induced
Self-Assembly of Iron Oxide Nanocubes.” Faraday Discussions. Royal Society
of Chemistry, 2015. https://doi.org/10.1039/c4fd00265b.
ieee: G. Singh et al., “Magnetic field-induced self-assembly of iron oxide
nanocubes,” Faraday Discussions, vol. 181. Royal Society of Chemistry,
pp. 403–421, 2015.
ista: Singh G, Chan H, Udayabhaskararao T, Gelman E, Peddis D, Baskin A, Leitus
G, Král P, Klajn R. 2015. Magnetic field-induced self-assembly of iron oxide nanocubes.
Faraday Discussions. 181, 403–421.
mla: Singh, Gurvinder, et al. “Magnetic Field-Induced Self-Assembly of Iron Oxide
Nanocubes.” Faraday Discussions, vol. 181, Royal Society of Chemistry,
2015, pp. 403–21, doi:10.1039/c4fd00265b.
short: G. Singh, H. Chan, T. Udayabhaskararao, E. Gelman, D. Peddis, A. Baskin,
G. Leitus, P. Král, R. Klajn, Faraday Discussions 181 (2015) 403–421.
date_created: 2023-08-01T09:45:17Z
date_published: 2015-01-02T00:00:00Z
date_updated: 2023-08-07T13:06:23Z
day: '02'
doi: 10.1039/c4fd00265b
extern: '1'
external_id:
pmid:
- '25920522'
intvolume: ' 181'
keyword:
- Physical and Theoretical Chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1039/C4FD00265B
month: '01'
oa: 1
oa_version: Published Version
page: 403-421
pmid: 1
publication: Faraday Discussions
publication_identifier:
eissn:
- 1364-5498
issn:
- 1359-6640
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Magnetic field-induced self-assembly of iron oxide nanocubes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 181
year: '2015'
...
---
_id: '13398'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Yugang
full_name: Sun, Yugang
last_name: Sun
- first_name: Leonardo
full_name: Scarabelli, Leonardo
last_name: Scarabelli
- first_name: Nicholas
full_name: Kotov, Nicholas
last_name: Kotov
- first_name: Moritz
full_name: Tebbe, Moritz
last_name: Tebbe
- first_name: Xiao-Min
full_name: Lin, Xiao-Min
last_name: Lin
- first_name: Ward
full_name: Brullot, Ward
last_name: Brullot
- first_name: Lucio
full_name: Isa, Lucio
last_name: Isa
- first_name: Peter
full_name: Schurtenberger, Peter
last_name: Schurtenberger
- first_name: Helmuth
full_name: Moehwald, Helmuth
last_name: Moehwald
- first_name: Igor
full_name: Fedin, Igor
last_name: Fedin
- first_name: Orlin
full_name: Velev, Orlin
last_name: Velev
- first_name: Damien
full_name: Faivre, Damien
last_name: Faivre
- first_name: Christopher
full_name: Sorensen, Christopher
last_name: Sorensen
- first_name: Régine
full_name: Perzynski, Régine
last_name: Perzynski
- first_name: Munish
full_name: Chanana, Munish
last_name: Chanana
- first_name: Zhihai
full_name: Li, Zhihai
last_name: Li
- first_name: Fernando
full_name: Bresme, Fernando
last_name: Bresme
- first_name: Petr
full_name: Král, Petr
last_name: Král
- first_name: Emre
full_name: Firlar, Emre
last_name: Firlar
- first_name: David
full_name: Schiffrin, David
last_name: Schiffrin
- first_name: Joao Batista
full_name: Souza Junior, Joao Batista
last_name: Souza Junior
- first_name: Andreas
full_name: Fery, Andreas
last_name: Fery
- first_name: Elena
full_name: Shevchenko, Elena
last_name: Shevchenko
- first_name: Ozgur
full_name: Tarhan, Ozgur
last_name: Tarhan
- first_name: Armand Paul
full_name: Alivisatos, Armand Paul
last_name: Alivisatos
- first_name: Sabrina
full_name: Disch, Sabrina
last_name: Disch
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
- first_name: Suvojit
full_name: Ghosh, Suvojit
last_name: Ghosh
citation:
ama: 'Sun Y, Scarabelli L, Kotov N, et al. Field-assisted self-assembly process:
General discussion. Faraday Discussions. 2015;181:463-479. doi:10.1039/c5fd90041g'
apa: 'Sun, Y., Scarabelli, L., Kotov, N., Tebbe, M., Lin, X.-M., Brullot, W., …
Ghosh, S. (2015). Field-assisted self-assembly process: General discussion. Faraday
Discussions. Royal Society of Chemistry. https://doi.org/10.1039/c5fd90041g'
chicago: 'Sun, Yugang, Leonardo Scarabelli, Nicholas Kotov, Moritz Tebbe, Xiao-Min
Lin, Ward Brullot, Lucio Isa, et al. “Field-Assisted Self-Assembly Process: General
Discussion.” Faraday Discussions. Royal Society of Chemistry, 2015. https://doi.org/10.1039/c5fd90041g.'
ieee: 'Y. Sun et al., “Field-assisted self-assembly process: General discussion,”
Faraday Discussions, vol. 181. Royal Society of Chemistry, pp. 463–479,
2015.'
ista: 'Sun Y, Scarabelli L, Kotov N, Tebbe M, Lin X-M, Brullot W, Isa L, Schurtenberger
P, Moehwald H, Fedin I, Velev O, Faivre D, Sorensen C, Perzynski R, Chanana M,
Li Z, Bresme F, Král P, Firlar E, Schiffrin D, Souza Junior JB, Fery A, Shevchenko
E, Tarhan O, Alivisatos AP, Disch S, Klajn R, Ghosh S. 2015. Field-assisted self-assembly
process: General discussion. Faraday Discussions. 181, 463–479.'
mla: 'Sun, Yugang, et al. “Field-Assisted Self-Assembly Process: General Discussion.”
Faraday Discussions, vol. 181, Royal Society of Chemistry, 2015, pp. 463–79,
doi:10.1039/c5fd90041g.'
short: Y. Sun, L. Scarabelli, N. Kotov, M. Tebbe, X.-M. Lin, W. Brullot, L. Isa,
P. Schurtenberger, H. Moehwald, I. Fedin, O. Velev, D. Faivre, C. Sorensen, R.
Perzynski, M. Chanana, Z. Li, F. Bresme, P. Král, E. Firlar, D. Schiffrin, J.B.
Souza Junior, A. Fery, E. Shevchenko, O. Tarhan, A.P. Alivisatos, S. Disch, R.
Klajn, S. Ghosh, Faraday Discussions 181 (2015) 463–479.
date_created: 2023-08-01T09:45:29Z
date_published: 2015-07-07T00:00:00Z
date_updated: 2023-08-08T07:16:20Z
day: '07'
doi: 10.1039/c5fd90041g
extern: '1'
external_id:
pmid:
- '26149295'
intvolume: ' 181'
keyword:
- Physical and Theoretical Chemistry
language:
- iso: eng
month: '07'
oa_version: None
page: 463-479
pmid: 1
publication: Faraday Discussions
publication_identifier:
eissn:
- 1364-5498
issn:
- 1359-6640
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Field-assisted self-assembly process: General discussion'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 181
year: '2015'
...
---
_id: '1383'
abstract:
- lang: eng
text: In plants, vacuolar H+-ATPase (V-ATPase) activity acidifies both the trans-Golgi
network/early endosome (TGN/EE) and the vacuole. This dual V-ATPase function has
impeded our understanding of how the pH homeostasis within the plant TGN/EE controls
exo- and endocytosis. Here, we show that the weak V-ATPase mutant deetiolated3
(det3) displayed a pH increase in the TGN/EE, but not in the vacuole, strongly
impairing secretion and recycling of the brassinosteroid receptor and the cellulose
synthase complexes to the plasma membrane, in contrast to mutants lacking tonoplast-localized
V-ATPase activity only. The brassinosteroid insensitivity and the cellulose deficiency
defects in det3 were tightly correlated with reduced Golgi and TGN/EE motility.
Thus, our results provide strong evidence that acidification of the TGN/EE, but
not of the vacuole, is indispensable for functional secretion and recycling in
plants.
article_number: '15094'
article_processing_charge: No
article_type: original
author:
- first_name: Luo
full_name: Yu, Luo
last_name: Yu
- first_name: Stefan
full_name: Scholl, Stefan
last_name: Scholl
- first_name: Anett
full_name: Doering, Anett
last_name: Doering
- first_name: Zhang
full_name: Yi, Zhang
last_name: Yi
- first_name: Niloufer
full_name: Irani, Niloufer
last_name: Irani
- first_name: Simone
full_name: Di Rubbo, Simone
last_name: Di Rubbo
- first_name: Lutz
full_name: Neumetzler, Lutz
last_name: Neumetzler
- first_name: Praveen
full_name: Krishnamoorthy, Praveen
last_name: Krishnamoorthy
- first_name: Isabelle
full_name: Van Houtte, Isabelle
last_name: Van Houtte
- first_name: Evelien
full_name: Mylle, Evelien
last_name: Mylle
- first_name: Volker
full_name: Bischoff, Volker
last_name: Bischoff
- first_name: Samantha
full_name: Vernhettes, Samantha
last_name: Vernhettes
- first_name: Johan
full_name: Winne, Johan
last_name: Winne
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: York
full_name: Stierhof, York
last_name: Stierhof
- first_name: Karin
full_name: Schumacher, Karin
last_name: Schumacher
- first_name: Staffan
full_name: Persson, Staffan
last_name: Persson
- first_name: Eugenia
full_name: Russinova, Eugenia
last_name: Russinova
citation:
ama: Yu L, Scholl S, Doering A, et al. V-ATPase activity in the TGN/EE is required
for exocytosis and recycling in Arabidopsis. Nature Plants. 2015;1(7).
doi:10.1038/nplants.2015.94
apa: Yu, L., Scholl, S., Doering, A., Yi, Z., Irani, N., Di Rubbo, S., … Russinova,
E. (2015). V-ATPase activity in the TGN/EE is required for exocytosis and recycling
in Arabidopsis. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/nplants.2015.94
chicago: Yu, Luo, Stefan Scholl, Anett Doering, Zhang Yi, Niloufer Irani, Simone
Di Rubbo, Lutz Neumetzler, et al. “V-ATPase Activity in the TGN/EE Is Required
for Exocytosis and Recycling in Arabidopsis.” Nature Plants. Nature Publishing
Group, 2015. https://doi.org/10.1038/nplants.2015.94.
ieee: L. Yu et al., “V-ATPase activity in the TGN/EE is required for exocytosis
and recycling in Arabidopsis,” Nature Plants, vol. 1, no. 7. Nature Publishing
Group, 2015.
ista: Yu L, Scholl S, Doering A, Yi Z, Irani N, Di Rubbo S, Neumetzler L, Krishnamoorthy
P, Van Houtte I, Mylle E, Bischoff V, Vernhettes S, Winne J, Friml J, Stierhof
Y, Schumacher K, Persson S, Russinova E. 2015. V-ATPase activity in the TGN/EE
is required for exocytosis and recycling in Arabidopsis. Nature Plants. 1(7),
15094.
mla: Yu, Luo, et al. “V-ATPase Activity in the TGN/EE Is Required for Exocytosis
and Recycling in Arabidopsis.” Nature Plants, vol. 1, no. 7, 15094, Nature
Publishing Group, 2015, doi:10.1038/nplants.2015.94.
short: L. Yu, S. Scholl, A. Doering, Z. Yi, N. Irani, S. Di Rubbo, L. Neumetzler,
P. Krishnamoorthy, I. Van Houtte, E. Mylle, V. Bischoff, S. Vernhettes, J. Winne,
J. Friml, Y. Stierhof, K. Schumacher, S. Persson, E. Russinova, Nature Plants
1 (2015).
date_created: 2018-12-11T11:51:42Z
date_published: 2015-07-06T00:00:00Z
date_updated: 2021-01-12T06:50:18Z
day: '06'
department:
- _id: JiFr
doi: 10.1038/nplants.2015.94
external_id:
pmid:
- '27250258'
intvolume: ' 1'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4905525/
month: '07'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: Nature Plants
publication_status: published
publisher: Nature Publishing Group
publist_id: '5827'
quality_controlled: '1'
scopus_import: 1
status: public
title: V-ATPase activity in the TGN/EE is required for exocytosis and recycling in
Arabidopsis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2015'
...
---
_id: '1399'
abstract:
- lang: eng
text: This thesis is concerned with the computation and approximation of intrinsic
volumes. Given a smooth body M and a certain digital approximation of it, we develop
algorithms to approximate various intrinsic volumes of M using only measurements
taken from its digital approximations. The crucial idea behind our novel algorithms
is to link the recent theory of persistent homology to the theory of intrinsic
volumes via the Crofton formula from integral geometry and, in particular, via
Euler characteristic computations. Our main contributions are a multigrid convergent
digital algorithm to compute the first intrinsic volume of a solid body in R^n
as well as an appropriate integration pipeline to approximate integral-geometric
integrals defined over the Grassmannian manifold.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Florian
full_name: Pausinger, Florian
id: 2A77D7A2-F248-11E8-B48F-1D18A9856A87
last_name: Pausinger
orcid: 0000-0002-8379-3768
citation:
ama: Pausinger F. On the approximation of intrinsic volumes. 2015.
apa: Pausinger, F. (2015). On the approximation of intrinsic volumes. Institute
of Science and Technology Austria.
chicago: Pausinger, Florian. “On the Approximation of Intrinsic Volumes.” Institute
of Science and Technology Austria, 2015.
ieee: F. Pausinger, “On the approximation of intrinsic volumes,” Institute of Science
and Technology Austria, 2015.
ista: Pausinger F. 2015. On the approximation of intrinsic volumes. Institute of
Science and Technology Austria.
mla: Pausinger, Florian. On the Approximation of Intrinsic Volumes. Institute
of Science and Technology Austria, 2015.
short: F. Pausinger, On the Approximation of Intrinsic Volumes, Institute of Science
and Technology Austria, 2015.
date_created: 2018-12-11T11:51:48Z
date_published: 2015-06-01T00:00:00Z
date_updated: 2023-09-07T11:41:25Z
day: '01'
degree_awarded: PhD
department:
- _id: HeEd
language:
- iso: eng
month: '06'
oa_version: None
page: '144'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '5808'
related_material:
record:
- id: '1662'
relation: part_of_dissertation
status: public
- id: '1792'
relation: part_of_dissertation
status: public
- id: '2255'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
title: On the approximation of intrinsic volumes
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2015'
...
---
_id: '1400'
abstract:
- lang: eng
text: Cancer results from an uncontrolled growth of abnormal cells. Sequentially
accumulated genetic and epigenetic alterations decrease cell death and increase
cell replication. We used mathematical models to quantify the effect of driver
gene mutations. The recently developed targeted therapies can lead to dramatic
regressions. However, in solid cancers, clinical responses are often short-lived
because resistant cancer cells evolve. We estimated that approximately 50 different
mutations can confer resistance to a typical targeted therapeutic agent. We find
that resistant cells are likely to be present in expanded subclones before the
start of the treatment. The dominant strategy to prevent the evolution of resistance
is combination therapy. Our analytical results suggest that in most patients,
dual therapy, but not monotherapy, can result in long-term disease control. However,
long-term control can only occur if there are no possible mutations in the genome
that can cause cross-resistance to both drugs. Furthermore, we showed that simultaneous
therapy with two drugs is much more likely to result in long-term disease control
than sequential therapy with the same drugs. To improve our understanding of the
underlying subclonal evolution we reconstruct the evolutionary history of a patient's
cancer from next-generation sequencing data of spatially-distinct DNA samples.
Using a quantitative measure of genetic relatedness, we found that pancreatic
cancers and their metastases demonstrated a higher level of relatedness than that
expected for any two cells randomly taken from a normal tissue. This minimal amount
of genetic divergence among advanced lesions indicates that genetic heterogeneity,
when quantitatively defined, is not a fundamental feature of the natural history
of untreated pancreatic cancers. Our newly developed, phylogenomic tool Treeomics
finds evidence for seeding patterns of metastases and can directly be used to
discover rules governing the evolution of solid malignancies to transform cancer
into a more predictable disease.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Johannes
full_name: Reiter, Johannes
id: 4A918E98-F248-11E8-B48F-1D18A9856A87
last_name: Reiter
orcid: 0000-0002-0170-7353
citation:
ama: Reiter J. The subclonal evolution of cancer. 2015.
apa: Reiter, J. (2015). The subclonal evolution of cancer. Institute of Science
and Technology Austria.
chicago: Reiter, Johannes. “The Subclonal Evolution of Cancer.” Institute of Science
and Technology Austria, 2015.
ieee: J. Reiter, “The subclonal evolution of cancer,” Institute of Science and Technology
Austria, 2015.
ista: Reiter J. 2015. The subclonal evolution of cancer. Institute of Science and
Technology Austria.
mla: Reiter, Johannes. The Subclonal Evolution of Cancer. Institute of Science
and Technology Austria, 2015.
short: J. Reiter, The Subclonal Evolution of Cancer, Institute of Science and Technology
Austria, 2015.
date_created: 2018-12-11T11:51:48Z
date_published: 2015-04-01T00:00:00Z
date_updated: 2023-09-07T11:40:44Z
day: '01'
degree_awarded: PhD
department:
- _id: KrCh
language:
- iso: eng
month: '04'
oa_version: None
page: '183'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '5807'
related_material:
record:
- id: '1709'
relation: part_of_dissertation
status: public
- id: '2000'
relation: part_of_dissertation
status: public
- id: '2247'
relation: part_of_dissertation
status: public
- id: '2816'
relation: part_of_dissertation
status: public
- id: '2858'
relation: part_of_dissertation
status: public
- id: '3157'
relation: part_of_dissertation
status: public
- id: '3260'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
title: The subclonal evolution of cancer
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2015'
...
---
_id: '1401'
abstract:
- lang: eng
text: 'The human ability to recognize objects in complex scenes has driven research
in the computer vision field over couple of decades. This thesis focuses on the
object recognition task in images. That is, given the image, we want the computer
system to be able to predict the class of the object that appears in the image.
A recent successful attempt to bridge semantic understanding of the image perceived
by humans and by computers uses attribute-based models. Attributes are semantic
properties of the objects shared across different categories, which humans and
computers can decide on. To explore the attribute-based models we take a statistical
machine learning approach, and address two key learning challenges in view of
object recognition task: learning augmented attributes as mid-level discriminative
feature representation, and learning with attributes as privileged information.
Our main contributions are parametric and non-parametric models and algorithms
to solve these frameworks. In the parametric approach, we explore an autoencoder
model combined with the large margin nearest neighbor principle for mid-level
feature learning, and linear support vector machines for learning with privileged
information. In the non-parametric approach, we propose a supervised Indian Buffet
Process for automatic augmentation of semantic attributes, and explore the Gaussian
Processes classification framework for learning with privileged information. A
thorough experimental analysis shows the effectiveness of the proposed models
in both parametric and non-parametric views.'
acknowledgement: "I would like to thank my supervisor, Christoph Lampert, for guidance
throughout my studies and for patience in transforming me into a scientist, and
my thesis committee, Chris Wojtan and Horst Bischof, for their help and advice.
\r\n\r\nI would like to thank Elisabeth Hacker who perfectly assisted all my administrative
needs and was always nice and friendly to me, and the campus team for making the
IST Austria campus my second home. \r\nI was honored to collaborate with brilliant
researchers and to learn from their experience. Undoubtedly, I learned most of all
from Novi Quadrianto: brainstorming our projects and getting exciting results was
the most enjoyable part of my work – thank you! I am also grateful to David Knowles,
Zoubin Ghahramani, Daniel Hernández-Lobato, Kristian Kersting and Anastasia Pentina
for the fantastic projects we worked on together, and to Kristen Grauman and Adriana
Kovashka for the exceptional experience working with user studies. I would like
to thank my colleagues at IST Austria and my office mates who shared their happy
moods, scientific breakthroughs and thought-provoking conversations with me: Chao,
Filip, Rustem, Asya, Sameh, Alex, Vlad, Mayu, Neel, Csaba, Thomas, Vladimir, Cristina,
Alex Z., Avro, Amelie and Emilie, Andreas H. and Andreas E., Chris, Lena, Michael,
Ali and Ipek, Vera, Igor, Katia. Special thanks to Morten for the countless games
of table soccer we played together and the tournaments we teamed up for: we will
definitely win next time:) A very warm hug to Asya for always being so inspiring
and supportive to me, and for helping me to increase the proportion of female computer
scientists in our group. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Viktoriia
full_name: Sharmanska, Viktoriia
id: 2EA6D09E-F248-11E8-B48F-1D18A9856A87
last_name: Sharmanska
orcid: 0000-0003-0192-9308
citation:
ama: 'Sharmanska V. Learning with attributes for object recognition: Parametric
and non-parametrics views. 2015. doi:10.15479/at:ista:1401'
apa: 'Sharmanska, V. (2015). Learning with attributes for object recognition:
Parametric and non-parametrics views. Institute of Science and Technology
Austria. https://doi.org/10.15479/at:ista:1401'
chicago: 'Sharmanska, Viktoriia. “Learning with Attributes for Object Recognition:
Parametric and Non-Parametrics Views.” Institute of Science and Technology Austria,
2015. https://doi.org/10.15479/at:ista:1401.'
ieee: 'V. Sharmanska, “Learning with attributes for object recognition: Parametric
and non-parametrics views,” Institute of Science and Technology Austria, 2015.'
ista: 'Sharmanska V. 2015. Learning with attributes for object recognition: Parametric
and non-parametrics views. Institute of Science and Technology Austria.'
mla: 'Sharmanska, Viktoriia. Learning with Attributes for Object Recognition:
Parametric and Non-Parametrics Views. Institute of Science and Technology
Austria, 2015, doi:10.15479/at:ista:1401.'
short: 'V. Sharmanska, Learning with Attributes for Object Recognition: Parametric
and Non-Parametrics Views, Institute of Science and Technology Austria, 2015.'
date_created: 2018-12-11T11:51:48Z
date_published: 2015-04-01T00:00:00Z
date_updated: 2023-09-07T11:40:11Z
day: '01'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: ChLa
- _id: GradSch
doi: 10.15479/at:ista:1401
file:
- access_level: open_access
checksum: 3605b402bb6934e09ae4cf672c84baf7
content_type: application/pdf
creator: dernst
date_created: 2021-02-22T11:33:17Z
date_updated: 2021-02-22T11:33:17Z
file_id: '9177'
file_name: 2015_Thesis_Sharmanska.pdf
file_size: 7964342
relation: main_file
success: 1
- access_level: closed
checksum: e37593b3ee75bf3180629df2d6ca8f4e
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-16T14:40:45Z
date_updated: 2021-11-17T13:47:24Z
file_id: '10297'
file_name: 2015_Thesis_Sharmanska_pdfa.pdf
file_size: 7372241
relation: main_file
file_date_updated: 2021-11-17T13:47:24Z
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- url: http://users.sussex.ac.uk/~nq28/viktoriia/Thesis_Sharmanska.pdf
month: '04'
oa: 1
oa_version: Published Version
page: '144'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '5806'
status: public
supervisor:
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
title: 'Learning with attributes for object recognition: Parametric and non-parametrics
views'
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2015'
...