---
_id: '877'
abstract:
- lang: eng
text: "Sequence analysis of protein and mitochondrially encoded tRNA genes shows
that substitutions\r\nproducing pathogenic effects in humans are often found in
normal, healthy individuals from other species.\r\nAnalysis of stability of protein
and tRNA structures shows that the disease-causing effects of pathogenic\r\nmutations
can be neutralized by other, compensatory substitutions that restore the structural
stability of the\r\nmolecule. Further study of such substitutions will, hopefully,
lead to new methods for curing genetic dis-\r\neases that may be based on the
correction of molecule stability as a whole instead of reversing an individual\r\npathogenic
mutation."
article_processing_charge: No
article_type: original
author:
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Kondrashov F. The analysis of monomer sequences in protein and tRNA and the
manifestation of the compensation of pathogenic deviations in their evolution.
Biofizika. 2005;50(3):389-395.
apa: Kondrashov, F. (2005). The analysis of monomer sequences in protein and tRNA
and the manifestation of the compensation of pathogenic deviations in their evolution.
Biofizika. Pleiades Publishing.
chicago: Kondrashov, Fyodor. “The Analysis of Monomer Sequences in Protein and TRNA
and the Manifestation of the Compensation of Pathogenic Deviations in Their Evolution.”
Biofizika. Pleiades Publishing, 2005.
ieee: F. Kondrashov, “The analysis of monomer sequences in protein and tRNA and
the manifestation of the compensation of pathogenic deviations in their evolution,”
Biofizika, vol. 50, no. 3. Pleiades Publishing, pp. 389–395, 2005.
ista: Kondrashov F. 2005. The analysis of monomer sequences in protein and tRNA
and the manifestation of the compensation of pathogenic deviations in their evolution.
Biofizika. 50(3), 389–395.
mla: Kondrashov, Fyodor. “The Analysis of Monomer Sequences in Protein and TRNA
and the Manifestation of the Compensation of Pathogenic Deviations in Their Evolution.”
Biofizika, vol. 50, no. 3, Pleiades Publishing, 2005, pp. 389–95.
short: F. Kondrashov, Biofizika 50 (2005) 389–395.
date_created: 2018-12-11T11:48:58Z
date_published: 2005-05-01T00:00:00Z
date_updated: 2021-01-12T08:21:01Z
day: '01'
extern: '1'
external_id:
pmid:
- '15977826'
intvolume: ' 50'
issue: '3'
language:
- iso: eng
main_file_link:
- url: http://pleiades.online/abstract/biophys/5/biophys0349_abstract.pdf
month: '05'
oa_version: None
page: 389 - 395
pmid: 1
publication: Biofizika
publication_status: published
publisher: Pleiades Publishing
publist_id: '6769'
quality_controlled: '1'
status: public
title: The analysis of monomer sequences in protein and tRNA and the manifestation
of the compensation of pathogenic deviations in their evolution
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 50
year: '2005'
...
---
_id: '878'
abstract:
- lang: eng
text: |
Negative trade-offs are thought to be a pervasive phenomenon and to inhibit evolution at all levels. New evidence shows that at the molecular level, there may be no trade-offs preventing the emergence of an enzyme with multiple functions.
author:
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Kondrashov F. In search of the limits of evolution. Nature Genetics.
2005;37(1):9-10. doi:10.1038/ng0105-9
apa: Kondrashov, F. (2005). In search of the limits of evolution. Nature Genetics.
Nature Publishing Group. https://doi.org/10.1038/ng0105-9
chicago: Kondrashov, Fyodor. “In Search of the Limits of Evolution.” Nature Genetics.
Nature Publishing Group, 2005. https://doi.org/10.1038/ng0105-9.
ieee: F. Kondrashov, “In search of the limits of evolution,” Nature Genetics,
vol. 37, no. 1. Nature Publishing Group, pp. 9–10, 2005.
ista: Kondrashov F. 2005. In search of the limits of evolution. Nature Genetics.
37(1), 9–10.
mla: Kondrashov, Fyodor. “In Search of the Limits of Evolution.” Nature Genetics,
vol. 37, no. 1, Nature Publishing Group, 2005, pp. 9–10, doi:10.1038/ng0105-9.
short: F. Kondrashov, Nature Genetics 37 (2005) 9–10.
date_created: 2018-12-11T11:48:59Z
date_published: 2005-01-01T00:00:00Z
date_updated: 2021-01-12T08:21:02Z
day: '01'
doi: 10.1038/ng0105-9
extern: 1
intvolume: ' 37'
issue: '1'
month: '01'
page: 9 - 10
publication: Nature Genetics
publication_status: published
publisher: Nature Publishing Group
publist_id: '6770'
quality_controlled: 0
status: public
title: In search of the limits of evolution
type: journal_article
volume: 37
year: '2005'
...
---
_id: '880'
abstract:
- lang: eng
text: Here, I describe a case of loss of the D-arm by mitochondrial cysteine tRNA
in the nine-banded armadillo (Dasypus novemcinctus) convergent with mt tRNASer(AGY).
Such evolution sheds light on the relationship between structure and function
of tRNA molecules and its impact on the patterns of molecular evolution.
article_processing_charge: No
author:
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Kondrashov F. The convergent evolution of the secondary structure of mitochondrial
cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus. Biofizika.
2005;50(3):396-403.
apa: Kondrashov, F. (2005). The convergent evolution of the secondary structure
of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus.
Biofizika. Pleiades Publishing.
chicago: Kondrashov, Fyodor. “The Convergent Evolution of the Secondary Structure
of Mitochondrial Cysteine TRNA in the Nine-Banded Armadillo Dasypus Novemcinctus.”
Biofizika. Pleiades Publishing, 2005.
ieee: F. Kondrashov, “The convergent evolution of the secondary structure of mitochondrial
cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus,” Biofizika,
vol. 50, no. 3. Pleiades Publishing, pp. 396–403, 2005.
ista: Kondrashov F. 2005. The convergent evolution of the secondary structure of
mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus.
Biofizika. 50(3), 396–403.
mla: Kondrashov, Fyodor. “The Convergent Evolution of the Secondary Structure of
Mitochondrial Cysteine TRNA in the Nine-Banded Armadillo Dasypus Novemcinctus.”
Biofizika, vol. 50, no. 3, Pleiades Publishing, 2005, pp. 396–403.
short: F. Kondrashov, Biofizika 50 (2005) 396–403.
date_created: 2018-12-11T11:48:59Z
date_published: 2005-05-01T00:00:00Z
date_updated: 2021-01-12T08:21:07Z
day: '01'
extern: '1'
external_id:
pmid:
- '15977827'
intvolume: ' 50'
issue: '3'
language:
- iso: eng
main_file_link:
- url: http://pleiades.online/abstract/biophys/5/biophys0356_abstract.pdf
month: '05'
oa_version: None
page: 396 - 403
pmid: 1
publication: Biofizika
publication_status: published
publisher: Pleiades Publishing
publist_id: '6768'
quality_controlled: '1'
status: public
title: The convergent evolution of the secondary structure of mitochondrial cysteine
tRNA in the nine-banded armadillo Dasypus novemcinctus
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 50
year: '2005'
...
---
_id: '882'
abstract:
- lang: eng
text: Some mutations in human mitochondrial tRNAs are severely pathogenic. The available
computational methods have a poor record of predicting the impact of a tRNA mutation
on the phenotype and fitness. Here patterns of evolution at tRNA sites that harbor
pathogenic mutations and at sites that harbor phenotypically cryptic polymorphisms
were compared. Mutations that are pathogenic to humans occupy more conservative
sites, are only rarely fixed in closely related species, and, when located in
stem structures, often disrupt Watson-Crick pairing and display signs of compensatory
evolution. These observations make it possible to classify ∼90% of all known pathogenic
mutations as deleterious together with only ∼30% of polymorphisms. These polymorphisms
segregate at frequencies that are more than two times lower than frequencies of
polymorphisms classified as benign, indicating that at least ∼30% of known polymorphisms
in mitochondrial tRNAs affect fitness negatively.
acknowledgement: |
The author thanks P. Andolfatto, D. Bachtrog, N. Esipova, S. Makeev, A. Kondrashov, V. Ramensky, V. Tumanyan and P. Vlasov for a critical reading of the manuscript. The author is an NSF Graduate Research Fellow. This work was supported by a Contract of the Russian Ministry of Science and Education (02.434.11.1008) and a grant on Molecular and Cellular Biology from RAS.
author:
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Kondrashov F. Prediction of pathogenic mutations in mitochondrially encoded
human tRNAs. Human Molecular Genetics. 2005;14(16):2415-2419. doi:10.1093/hmg/ddi243
apa: Kondrashov, F. (2005). Prediction of pathogenic mutations in mitochondrially
encoded human tRNAs. Human Molecular Genetics. Oxford University Press.
https://doi.org/10.1093/hmg/ddi243
chicago: Kondrashov, Fyodor. “Prediction of Pathogenic Mutations in Mitochondrially
Encoded Human TRNAs.” Human Molecular Genetics. Oxford University Press,
2005. https://doi.org/10.1093/hmg/ddi243.
ieee: F. Kondrashov, “Prediction of pathogenic mutations in mitochondrially encoded
human tRNAs,” Human Molecular Genetics, vol. 14, no. 16. Oxford University
Press, pp. 2415–2419, 2005.
ista: Kondrashov F. 2005. Prediction of pathogenic mutations in mitochondrially
encoded human tRNAs. Human Molecular Genetics. 14(16), 2415–2419.
mla: Kondrashov, Fyodor. “Prediction of Pathogenic Mutations in Mitochondrially
Encoded Human TRNAs.” Human Molecular Genetics, vol. 14, no. 16, Oxford
University Press, 2005, pp. 2415–19, doi:10.1093/hmg/ddi243.
short: F. Kondrashov, Human Molecular Genetics 14 (2005) 2415–2419.
date_created: 2018-12-11T11:49:00Z
date_published: 2005-08-15T00:00:00Z
date_updated: 2021-01-12T08:21:10Z
day: '15'
doi: 10.1093/hmg/ddi243
extern: 1
intvolume: ' 14'
issue: '16'
month: '08'
page: 2415 - 2419
publication: Human Molecular Genetics
publication_status: published
publisher: Oxford University Press
publist_id: '6767'
quality_controlled: 0
status: public
title: Prediction of pathogenic mutations in mitochondrially encoded human tRNAs
type: journal_article
volume: 14
year: '2005'
...
---
_id: '893'
abstract:
- lang: eng
text: Amino acid composition of proteins varies substantially between taxa and,
thus, can evolve. For example, proteins from organisms with (G+C)-rich (or (A+T)-rich)
genomes contain more (or fewer) amino acids encoded by (G+C)-rich codons. However,
no universal trends in ongoing changes of amino acid frequencies have been reported.
We compared sets of orthologous proteins encoded by triplets of closely related
genomes from 15 taxa representing all three domains of life (Bacteria, Archaea
and Eukaryota), and used phylogenies to polarize amino acid substitutions. Cys,
Met, His, Ser and Phe accrue in at least 14 taxa, whereas Pro, Ala, Glu and Gly
are consistently lost. The same nine amino acids are currently accrued or lost
in human proteins, as shown by analysis of non-synonymous single-nucleotide polymorphisms.
All amino acids with declining frequencies are thought to be among the first incorporated
into the genetic code; conversely, all amino acids with increasing frequencies,
except Ser, were probably recruited late. Thus, expansion of initially under-represented
amino acids, which began over 3,400 million years ago, apparently continues to
this day.
acknowledgement: S.S. and I.A.A. were supported by the Genome Canada Foundation.
author:
- first_name: Ingo
full_name: Jordan, Ingo K
last_name: Jordan
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Ivan
full_name: Adzhubeǐ, Ivan A
last_name: Adzhubeǐ
- first_name: Yuri
full_name: Wolf, Yuri I
last_name: Wolf
- first_name: Eugene
full_name: Koonin, Eugene V
last_name: Koonin
- first_name: Alexey
full_name: Kondrashov, Alexey S
last_name: Kondrashov
- first_name: Shamil
full_name: Sunyaev, Shamil R
last_name: Sunyaev
citation:
ama: Jordan I, Kondrashov F, Adzhubeǐ I, et al. A universal trend of amino acid
gain and loss in protein evolution. Nature. 2005;433(7026):633-638. doi:10.1038/nature03306
apa: Jordan, I., Kondrashov, F., Adzhubeǐ, I., Wolf, Y., Koonin, E., Kondrashov,
A., & Sunyaev, S. (2005). A universal trend of amino acid gain and loss in
protein evolution. Nature. Nature Publishing Group. https://doi.org/10.1038/nature03306
chicago: Jordan, Ingo, Fyodor Kondrashov, Ivan Adzhubeǐ, Yuri Wolf, Eugene Koonin,
Alexey Kondrashov, and Shamil Sunyaev. “A Universal Trend of Amino Acid Gain and
Loss in Protein Evolution.” Nature. Nature Publishing Group, 2005. https://doi.org/10.1038/nature03306.
ieee: I. Jordan et al., “A universal trend of amino acid gain and loss in
protein evolution,” Nature, vol. 433, no. 7026. Nature Publishing Group,
pp. 633–638, 2005.
ista: Jordan I, Kondrashov F, Adzhubeǐ I, Wolf Y, Koonin E, Kondrashov A, Sunyaev
S. 2005. A universal trend of amino acid gain and loss in protein evolution. Nature.
433(7026), 633–638.
mla: Jordan, Ingo, et al. “A Universal Trend of Amino Acid Gain and Loss in Protein
Evolution.” Nature, vol. 433, no. 7026, Nature Publishing Group, 2005,
pp. 633–38, doi:10.1038/nature03306.
short: I. Jordan, F. Kondrashov, I. Adzhubeǐ, Y. Wolf, E. Koonin, A. Kondrashov,
S. Sunyaev, Nature 433 (2005) 633–638.
date_created: 2018-12-11T11:49:03Z
date_published: 2005-02-10T00:00:00Z
date_updated: 2021-01-12T08:21:23Z
day: '10'
doi: 10.1038/nature03306
extern: 1
intvolume: ' 433'
issue: '7026'
month: '02'
page: 633 - 638
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '6757'
quality_controlled: 0
status: public
title: A universal trend of amino acid gain and loss in protein evolution
type: journal_article
volume: 433
year: '2005'
...
---
_id: '8028'
abstract:
- lang: eng
text: 'Transmission of signals within the brain is essential for cognitive function,
but it is not clear how neural circuits support reliable and accurate signal propagation
over a sufficiently large dynamic range. Two modes of propagation have been studied:
synfire chains, in which synchronous activity travels through feedforward layers
of a neuronal network, and the propagation of fluctuations in firing rate across
these layers. In both cases, a sufficient amount of noise, which was added to
previous models from an external source, had to be included to support stable
propagation. Sparse, randomly connected networks of spiking model neurons can
generate chaotic patterns of activity. We investigate whether this activity, which
is a more realistic noise source, is sufficient to allow for signal transmission.
We find that, for rate-coded signals but not for synfire chains, such networks
support robust and accurate signal reproduction through up to six layers if appropriate
adjustments are made in synaptic strengths. We investigate the factors affecting
transmission and show that multiple signals can propagate simultaneously along
different pathways. Using this feature, we show how different types of logic gates
can arise within the architecture of the random network through the strengthening
of specific synapses.'
article_processing_charge: No
article_type: original
author:
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
- first_name: L. F.
full_name: Abbott, L. F.
last_name: Abbott
citation:
ama: Vogels TP, Abbott LF. Signal propagation and logic gating in networks of integrate-and-fire
neurons. Journal of Neuroscience. 2005;25(46):10786-10795. doi:10.1523/jneurosci.3508-05.2005
apa: Vogels, T. P., & Abbott, L. F. (2005). Signal propagation and logic gating
in networks of integrate-and-fire neurons. Journal of Neuroscience. Society
for Neuroscience. https://doi.org/10.1523/jneurosci.3508-05.2005
chicago: Vogels, Tim P, and L. F. Abbott. “Signal Propagation and Logic Gating in
Networks of Integrate-and-Fire Neurons.” Journal of Neuroscience. Society
for Neuroscience, 2005. https://doi.org/10.1523/jneurosci.3508-05.2005.
ieee: T. P. Vogels and L. F. Abbott, “Signal propagation and logic gating in networks
of integrate-and-fire neurons,” Journal of Neuroscience, vol. 25, no. 46.
Society for Neuroscience, pp. 10786–10795, 2005.
ista: Vogels TP, Abbott LF. 2005. Signal propagation and logic gating in networks
of integrate-and-fire neurons. Journal of Neuroscience. 25(46), 10786–10795.
mla: Vogels, Tim P., and L. F. Abbott. “Signal Propagation and Logic Gating in Networks
of Integrate-and-Fire Neurons.” Journal of Neuroscience, vol. 25, no. 46,
Society for Neuroscience, 2005, pp. 10786–95, doi:10.1523/jneurosci.3508-05.2005.
short: T.P. Vogels, L.F. Abbott, Journal of Neuroscience 25 (2005) 10786–10795.
date_created: 2020-06-25T13:12:33Z
date_published: 2005-11-16T00:00:00Z
date_updated: 2021-01-12T08:16:37Z
day: '16'
doi: 10.1523/jneurosci.3508-05.2005
extern: '1'
external_id:
pmid:
- '16291952'
intvolume: ' 25'
issue: '46'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6725859/
month: '11'
oa: 1
oa_version: Published Version
page: 10786-10795
pmid: 1
publication: Journal of Neuroscience
publication_identifier:
issn:
- 0270-6474
- 1529-2401
publication_status: published
publisher: Society for Neuroscience
quality_controlled: '1'
status: public
title: Signal propagation and logic gating in networks of integrate-and-fire neurons
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 25
year: '2005'
...
---
_id: '8029'
abstract:
- lang: eng
text: 'Neural network modeling is often concerned with stimulus-driven responses,
but most of the activity in the brain is internally generated. Here, we review
network models of internally generated activity, focusing on three types of network
dynamics: (a) sustained responses to transient stimuli, which provide a model
of working memory; (b) oscillatory network activity; and (c) chaotic activity,
which models complex patterns of background spiking in cortical and other circuits.
We also review propagation of stimulus-driven activity through spontaneously active
networks. Exploring these aspects of neural network dynamics is critical for understanding
how neural circuits produce cognitive function.'
article_processing_charge: No
article_type: review
author:
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
- first_name: Kanaka
full_name: Rajan, Kanaka
last_name: Rajan
- first_name: L.F.
full_name: Abbott, L.F.
last_name: Abbott
citation:
ama: Vogels TP, Rajan K, Abbott LF. Neural network dynamics. Annual Review of
Neuroscience. 2005;28(1):357-376. doi:10.1146/annurev.neuro.28.061604.135637
apa: Vogels, T. P., Rajan, K., & Abbott, L. F. (2005). Neural network dynamics.
Annual Review of Neuroscience. Annual Reviews. https://doi.org/10.1146/annurev.neuro.28.061604.135637
chicago: Vogels, Tim P, Kanaka Rajan, and L.F. Abbott. “Neural Network Dynamics.”
Annual Review of Neuroscience. Annual Reviews, 2005. https://doi.org/10.1146/annurev.neuro.28.061604.135637.
ieee: T. P. Vogels, K. Rajan, and L. F. Abbott, “Neural network dynamics,” Annual
Review of Neuroscience, vol. 28, no. 1. Annual Reviews, pp. 357–376, 2005.
ista: Vogels TP, Rajan K, Abbott LF. 2005. Neural network dynamics. Annual Review
of Neuroscience. 28(1), 357–376.
mla: Vogels, Tim P., et al. “Neural Network Dynamics.” Annual Review of Neuroscience,
vol. 28, no. 1, Annual Reviews, 2005, pp. 357–76, doi:10.1146/annurev.neuro.28.061604.135637.
short: T.P. Vogels, K. Rajan, L.F. Abbott, Annual Review of Neuroscience 28 (2005)
357–376.
date_created: 2020-06-25T13:13:11Z
date_published: 2005-07-21T00:00:00Z
date_updated: 2021-01-12T08:16:37Z
day: '21'
doi: 10.1146/annurev.neuro.28.061604.135637
extern: '1'
external_id:
pmid:
- '16022600'
intvolume: ' 28'
issue: '1'
language:
- iso: eng
month: '07'
oa_version: None
page: 357-376
pmid: 1
publication: Annual Review of Neuroscience
publication_identifier:
issn:
- 0147-006X
- 1545-4126
publication_status: published
publisher: Annual Reviews
quality_controlled: '1'
status: public
title: Neural network dynamics
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 28
year: '2005'
...
---
_id: '1740'
abstract:
- lang: eng
text: 'A systematic study of the morphology of self-organized islands in the InAs/GaAs(0
0 1) and Ge/Si(0 0 1) systems is presented, based on high-resolution scanning
tunneling microscopy measurements. We demonstrate that in both cases two main
island families coexist: smaller pyramids bound by one type of shallow facets
and larger multifaceted domes. Their structure and facet orientation are precisely
determined, thus solving a highly debated argument in the case of InAs/GaAs(0
0 1). The comparison between the two material systems reveals the existence of
striking similarities that extend even to the nature of island precursors and
to the islands that form when depositing InGaAs or GeSi alloys. The implications
of these observations on a possible universal description of the Stranski-Krastanow
growth mode are discussed with respect to recent theoretical results.'
author:
- first_name: Giovanni
full_name: Costantini, Giovanni
last_name: Costantini
- first_name: Armando
full_name: Rastelli, Armando
last_name: Rastelli
- first_name: Carlos
full_name: Manzano, Carlos
last_name: Manzano
- first_name: P
full_name: Acosta-Diaz, P
last_name: Acosta Diaz
- first_name: Georgios
full_name: Georgios Katsaros
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
- first_name: Rudeeson
full_name: Songmuang, Rudeeson
last_name: Songmuang
- first_name: Oliver
full_name: Schmidt, Oliver G
last_name: Schmidt
- first_name: Hans
full_name: Von Känel, Hans
last_name: Von Känel
- first_name: Klaus
full_name: Kern, Klaus
last_name: Kern
citation:
ama: Costantini G, Rastelli A, Manzano C, et al. Pyramids and domes in the InAs/GaAs
(0 0 1) and Ge/Si (0 0 1) systems. Journal of Crystal Growth. 2005;278(1-4):38-45.
doi:10.1016/j.jcrysgro.2004.12.047
apa: Costantini, G., Rastelli, A., Manzano, C., Acosta Diaz, P., Katsaros, G., Songmuang,
R., … Kern, K. (2005). Pyramids and domes in the InAs/GaAs (0 0 1) and Ge/Si (0
0 1) systems. Journal of Crystal Growth. Elsevier. https://doi.org/10.1016/j.jcrysgro.2004.12.047
chicago: Costantini, Giovanni, Armando Rastelli, Carlos Manzano, P Acosta Diaz,
Georgios Katsaros, Rudeeson Songmuang, Oliver Schmidt, Hans Von Känel, and Klaus
Kern. “Pyramids and Domes in the InAs/GaAs (0 0 1) and Ge/Si (0 0 1) Systems.”
Journal of Crystal Growth. Elsevier, 2005. https://doi.org/10.1016/j.jcrysgro.2004.12.047.
ieee: G. Costantini et al., “Pyramids and domes in the InAs/GaAs (0 0 1)
and Ge/Si (0 0 1) systems,” Journal of Crystal Growth, vol. 278, no. 1–4.
Elsevier, pp. 38–45, 2005.
ista: Costantini G, Rastelli A, Manzano C, Acosta Diaz P, Katsaros G, Songmuang
R, Schmidt O, Von Känel H, Kern K. 2005. Pyramids and domes in the InAs/GaAs (0
0 1) and Ge/Si (0 0 1) systems. Journal of Crystal Growth. 278(1–4), 38–45.
mla: Costantini, Giovanni, et al. “Pyramids and Domes in the InAs/GaAs (0 0 1) and
Ge/Si (0 0 1) Systems.” Journal of Crystal Growth, vol. 278, no. 1–4, Elsevier,
2005, pp. 38–45, doi:10.1016/j.jcrysgro.2004.12.047.
short: G. Costantini, A. Rastelli, C. Manzano, P. Acosta Diaz, G. Katsaros, R. Songmuang,
O. Schmidt, H. Von Känel, K. Kern, Journal of Crystal Growth 278 (2005) 38–45.
date_created: 2018-12-11T11:53:45Z
date_published: 2005-05-01T00:00:00Z
date_updated: 2021-01-12T06:52:54Z
day: '01'
doi: 10.1016/j.jcrysgro.2004.12.047
extern: 1
intvolume: ' 278'
issue: 1-4
month: '05'
page: 38 - 45
publication: Journal of Crystal Growth
publication_status: published
publisher: Elsevier
publist_id: '5384'
quality_controlled: 0
status: public
title: Pyramids and domes in the InAs/GaAs (0 0 1) and Ge/Si (0 0 1) systems
type: journal_article
volume: 278
year: '2005'
...
---
_id: '1741'
abstract:
- lang: eng
text: SiGe islands move laterally on a Si(001) substrate during in situ postgrowth
annealing. This surprising behavior is revealed by an analysis of the substrate
surface morphology after island removal using wet chemical etching. We explain
the island motion by asymmetric surface-mediated alloying. Material leaves one
side of the island by surface diffusion, and mixes with additional Si from the
surrounding surface as it redeposits on the other side. Thus the island moves
laterally while becoming larger and more dilute.
acknowledgement: The work was supported by the BMBF (03N8711)
author:
- first_name: Ulrich
full_name: Denker, Ulrich
last_name: Denker
- first_name: Armando
full_name: Rastelli, Armando
last_name: Rastelli
- first_name: Mathieu
full_name: Stoffel, Mathieu
last_name: Stoffel
- first_name: Jerry
full_name: Tersoff, Jerry
last_name: Tersoff
- first_name: Georgios
full_name: Georgios Katsaros
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
- first_name: Giovanni
full_name: Costantini, Giovanni
last_name: Costantini
- first_name: Klaus
full_name: Kern, Klaus
last_name: Kern
- first_name: Neng
full_name: Jin-Phillipp, Neng Y
last_name: Jin Phillipp
- first_name: David
full_name: Jesson, David E
last_name: Jesson
- first_name: Oliver
full_name: Schmidt, Oliver G
last_name: Schmidt
citation:
ama: Denker U, Rastelli A, Stoffel M, et al. Lateral motion of SiGe islands driven
by surface-mediated alloying. Physical Review Letters. 2005;94(21). doi:10.1103/PhysRevLett.94.216103
apa: Denker, U., Rastelli, A., Stoffel, M., Tersoff, J., Katsaros, G., Costantini,
G., … Schmidt, O. (2005). Lateral motion of SiGe islands driven by surface-mediated
alloying. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.94.216103
chicago: Denker, Ulrich, Armando Rastelli, Mathieu Stoffel, Jerry Tersoff, Georgios
Katsaros, Giovanni Costantini, Klaus Kern, Neng Jin Phillipp, David Jesson, and
Oliver Schmidt. “Lateral Motion of SiGe Islands Driven by Surface-Mediated Alloying.”
Physical Review Letters. American Physical Society, 2005. https://doi.org/10.1103/PhysRevLett.94.216103.
ieee: U. Denker et al., “Lateral motion of SiGe islands driven by surface-mediated
alloying,” Physical Review Letters, vol. 94, no. 21. American Physical
Society, 2005.
ista: Denker U, Rastelli A, Stoffel M, Tersoff J, Katsaros G, Costantini G, Kern
K, Jin Phillipp N, Jesson D, Schmidt O. 2005. Lateral motion of SiGe islands driven
by surface-mediated alloying. Physical Review Letters. 94(21).
mla: Denker, Ulrich, et al. “Lateral Motion of SiGe Islands Driven by Surface-Mediated
Alloying.” Physical Review Letters, vol. 94, no. 21, American Physical
Society, 2005, doi:10.1103/PhysRevLett.94.216103.
short: U. Denker, A. Rastelli, M. Stoffel, J. Tersoff, G. Katsaros, G. Costantini,
K. Kern, N. Jin Phillipp, D. Jesson, O. Schmidt, Physical Review Letters 94 (2005).
date_created: 2018-12-11T11:53:46Z
date_published: 2005-06-03T00:00:00Z
date_updated: 2021-01-12T06:52:54Z
day: '03'
doi: 10.1103/PhysRevLett.94.216103
extern: 1
intvolume: ' 94'
issue: '21'
month: '06'
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '5383'
quality_controlled: 0
status: public
title: Lateral motion of SiGe islands driven by surface-mediated alloying
type: journal_article
volume: 94
year: '2005'
...
---
_id: '1742'
abstract:
- lang: eng
text: The effects of substrate temperature, growth rate, and postgrowth annealing
on the composition of Ge islands grown on Si(001) were investigated with a combination
of selective wet chemical etching and atomic force microscopy. A simple kinetic
model comprising only surface diffusion processes can explain all the experimentally
observed compositional profiles for pyramid and dome islands grown in the 560-620°C
range. From this model three-dimensional compositional maps were extracted. By
performing annealing experiments a change in the composition of the domes was
observed. This could be explained as the result of the islands' movement induced
by alloying-driven energy minimization. Also in this case kinetically hindered
bulk diffusion processes are not needed to explain the experimental observations.
acknowledgement: G. K. acknowledges the financial support of DAAD (Deutscher Akademischer
Austausch Dienst)
author:
- first_name: Georgios
full_name: Georgios Katsaros
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
- first_name: Giovanni
full_name: Costantini, Giovanni
last_name: Costantini
- first_name: Mathieu
full_name: Stoffel, Mathieu
last_name: Stoffel
- first_name: Rubén
full_name: Esteban, Rubén
last_name: Esteban
- first_name: Alexander
full_name: Bittner, Alexander M
last_name: Bittner
- first_name: Armando
full_name: Rastelli, Armando
last_name: Rastelli
- first_name: Ulrich
full_name: Denker, Ulrich
last_name: Denker
- first_name: Oliver
full_name: Schmidt, Oliver G
last_name: Schmidt
- first_name: Klaus
full_name: Kern, Klaus
last_name: Kern
citation:
ama: Katsaros G, Costantini G, Stoffel M, et al. Kinetic origin of island intermixing
during the growth of Ge on Si (001). Physical Review B - Condensed Matter and
Materials Physics. 2005;72(19). doi:10.1103/PhysRevB.72.195320
apa: Katsaros, G., Costantini, G., Stoffel, M., Esteban, R., Bittner, A., Rastelli,
A., … Kern, K. (2005). Kinetic origin of island intermixing during the growth
of Ge on Si (001). Physical Review B - Condensed Matter and Materials Physics.
American Physical Society. https://doi.org/10.1103/PhysRevB.72.195320
chicago: Katsaros, Georgios, Giovanni Costantini, Mathieu Stoffel, Rubén Esteban,
Alexander Bittner, Armando Rastelli, Ulrich Denker, Oliver Schmidt, and Klaus
Kern. “Kinetic Origin of Island Intermixing during the Growth of Ge on Si (001).”
Physical Review B - Condensed Matter and Materials Physics. American Physical
Society, 2005. https://doi.org/10.1103/PhysRevB.72.195320.
ieee: G. Katsaros et al., “Kinetic origin of island intermixing during the
growth of Ge on Si (001),” Physical Review B - Condensed Matter and Materials
Physics, vol. 72, no. 19. American Physical Society, 2005.
ista: Katsaros G, Costantini G, Stoffel M, Esteban R, Bittner A, Rastelli A, Denker
U, Schmidt O, Kern K. 2005. Kinetic origin of island intermixing during the growth
of Ge on Si (001). Physical Review B - Condensed Matter and Materials Physics.
72(19).
mla: Katsaros, Georgios, et al. “Kinetic Origin of Island Intermixing during the
Growth of Ge on Si (001).” Physical Review B - Condensed Matter and Materials
Physics, vol. 72, no. 19, American Physical Society, 2005, doi:10.1103/PhysRevB.72.195320.
short: G. Katsaros, G. Costantini, M. Stoffel, R. Esteban, A. Bittner, A. Rastelli,
U. Denker, O. Schmidt, K. Kern, Physical Review B - Condensed Matter and Materials
Physics 72 (2005).
date_created: 2018-12-11T11:53:46Z
date_published: 2005-11-15T00:00:00Z
date_updated: 2021-01-12T06:52:55Z
day: '15'
doi: 10.1103/PhysRevB.72.195320
extern: 1
intvolume: ' 72'
issue: '19'
month: '11'
publication: Physical Review B - Condensed Matter and Materials Physics
publication_status: published
publisher: American Physical Society
publist_id: '5382'
quality_controlled: 0
status: public
title: Kinetic origin of island intermixing during the growth of Ge on Si (001)
type: journal_article
volume: 72
year: '2005'
...
---
_id: '1743'
abstract:
- lang: eng
text: Laterally aligned multilayer GeSiSi islands grown on a patterned Si (001)
substrate are disclosed by selective etching of Si in a KOH solution. This procedure
allows us to visualize the vertical alignment of the islands in a three-dimensional
perspective. Our technique reveals that partly coalesced double islands in the
initial layer do not merge together, but instead gradually reproduce into well-separated
double islands in upper layers. We attribute this effect to very thin spacer layers,
which efficiently transfer the strain modulation of each island through the spacer
layer to the surface. The etching rate of Si is reduced in tensile strained regions,
which helps to preserve sufficient Si between the stacked islands to form a periodic
array of freestanding and vertically modulated heterostructure pillars.
acknowledgement: This work was supported by the BMBF (03N8711) and the EU NOE SANDiE
author:
- first_name: Zheyang
full_name: Zhong, Zheyang
last_name: Zhong
- first_name: Georgios
full_name: Georgios Katsaros
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
- first_name: Mathieu
full_name: Stoffel, Mathieu
last_name: Stoffel
- first_name: Giovanni
full_name: Costantini, Giovanni
last_name: Costantini
- first_name: Klaus
full_name: Kern, Klaus
last_name: Kern
- first_name: Oliver
full_name: Schmidt, Oliver G
last_name: Schmidt
- first_name: Neng
full_name: Jin-Phillipp, Neng Y
last_name: Jin Phillipp
- first_name: Günther
full_name: Bauer, Günther
last_name: Bauer
citation:
ama: Zhong Z, Katsaros G, Stoffel M, et al. Periodic pillar structures by Si etching
of multilayer GeSi/Si islands. Applied Physics Letters. 2005;87(26):1-3.
doi:10.1063/1.2150278
apa: Zhong, Z., Katsaros, G., Stoffel, M., Costantini, G., Kern, K., Schmidt, O.,
… Bauer, G. (2005). Periodic pillar structures by Si etching of multilayer GeSi/Si
islands. Applied Physics Letters. American Institute of Physics. https://doi.org/10.1063/1.2150278
chicago: Zhong, Zheyang, Georgios Katsaros, Mathieu Stoffel, Giovanni Costantini,
Klaus Kern, Oliver Schmidt, Neng Jin Phillipp, and Günther Bauer. “Periodic Pillar
Structures by Si Etching of Multilayer GeSi/Si Islands.” Applied Physics Letters.
American Institute of Physics, 2005. https://doi.org/10.1063/1.2150278.
ieee: Z. Zhong et al., “Periodic pillar structures by Si etching of multilayer
GeSi/Si islands,” Applied Physics Letters, vol. 87, no. 26. American Institute
of Physics, pp. 1–3, 2005.
ista: Zhong Z, Katsaros G, Stoffel M, Costantini G, Kern K, Schmidt O, Jin Phillipp
N, Bauer G. 2005. Periodic pillar structures by Si etching of multilayer GeSi/Si
islands. Applied Physics Letters. 87(26), 1–3.
mla: Zhong, Zheyang, et al. “Periodic Pillar Structures by Si Etching of Multilayer
GeSi/Si Islands.” Applied Physics Letters, vol. 87, no. 26, American Institute
of Physics, 2005, pp. 1–3, doi:10.1063/1.2150278.
short: Z. Zhong, G. Katsaros, M. Stoffel, G. Costantini, K. Kern, O. Schmidt, N.
Jin Phillipp, G. Bauer, Applied Physics Letters 87 (2005) 1–3.
date_created: 2018-12-11T11:53:46Z
date_published: 2005-01-01T00:00:00Z
date_updated: 2021-01-12T06:52:55Z
day: '01'
doi: 10.1063/1.2150278
extern: 1
intvolume: ' 87'
issue: '26'
month: '01'
page: 1 - 3
publication: Applied Physics Letters
publication_status: published
publisher: American Institute of Physics
publist_id: '5381'
quality_controlled: 0
status: public
title: Periodic pillar structures by Si etching of multilayer GeSi/Si islands
type: journal_article
volume: 87
year: '2005'
...
---
_id: '1744'
abstract:
- lang: eng
text: This paper presents optical duobinary and dicode signalling, as alternatives
to the binary format, in order to improve the transmission performance in the
presense of non-linear effects in a dense wavelength division multiplex (WDM)
optical system. Duobinary signalling is applied to an optical system to explore
the reduction of stimulated Brillouin scattering (SBS) effects. Duobinary signalling
suppresses the SBS effects, and an eye-opening improvement of 0.25 to 1.2 dB is
achieved relative to binary transmission over a range of input power levels. An
experimental study demonstrates that duobinary modulation suppresses the four
wave mixing (FWM) products of a dense WDM system by a maximum of 3 dB. The suppression
is maintained over a range of channel spacings. An investigation of the impact
of fibre dispersion on FWM products under binary, duobinary and dicode modulation
in a dense WDM system is then performed, with interchannel spacing and optical
power variation. This leads to the development of a set of guidelines for the
application areas, in which it is appropriate to use duobinary or dicode modulation
in WDM systems as a means of mitigating the impact of FWM.
acknowledgement: IET
author:
- first_name: Georgios
full_name: Georgios Katsaros
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
- first_name: Izzat
full_name: Darwazeh, Izzat Z
last_name: Darwazeh
- first_name: Phil
full_name: Lane, Phil M
last_name: Lane
citation:
ama: Katsaros G, Darwazeh I, Lane P. Non linear transmission effects in duobinary
and dicode optical systems. IEE Proceedings - Optoelectronics. 2005;152(6):344-352.
doi:10.1049/ip-opt:20045067
apa: Katsaros, G., Darwazeh, I., & Lane, P. (2005). Non linear transmission
effects in duobinary and dicode optical systems. IEE Proceedings - Optoelectronics.
Institute of Electrical Engineers. https://doi.org/10.1049/ip-opt:20045067
chicago: Katsaros, Georgios, Izzat Darwazeh, and Phil Lane. “Non Linear Transmission
Effects in Duobinary and Dicode Optical Systems.” IEE Proceedings - Optoelectronics.
Institute of Electrical Engineers, 2005. https://doi.org/10.1049/ip-opt:20045067.
ieee: G. Katsaros, I. Darwazeh, and P. Lane, “Non linear transmission effects in
duobinary and dicode optical systems,” IEE Proceedings - Optoelectronics,
vol. 152, no. 6. Institute of Electrical Engineers, pp. 344–352, 2005.
ista: Katsaros G, Darwazeh I, Lane P. 2005. Non linear transmission effects in duobinary
and dicode optical systems. IEE Proceedings - Optoelectronics. 152(6), 344–352.
mla: Katsaros, Georgios, et al. “Non Linear Transmission Effects in Duobinary and
Dicode Optical Systems.” IEE Proceedings - Optoelectronics, vol. 152, no.
6, Institute of Electrical Engineers, 2005, pp. 344–52, doi:10.1049/ip-opt:20045067.
short: G. Katsaros, I. Darwazeh, P. Lane, IEE Proceedings - Optoelectronics 152
(2005) 344–352.
date_created: 2018-12-11T11:53:46Z
date_published: 2005-12-01T00:00:00Z
date_updated: 2021-01-12T06:52:55Z
day: '01'
doi: 10.1049/ip-opt:20045067
extern: 1
intvolume: ' 152'
issue: '6'
month: '12'
page: 344 - 352
publication: IEE Proceedings - Optoelectronics
publication_status: published
publisher: Institute of Electrical Engineers
publist_id: '5380'
quality_controlled: 0
status: public
title: Non linear transmission effects in duobinary and dicode optical systems
type: journal_article
volume: 152
year: '2005'
...
---
_id: '1795'
abstract:
- lang: eng
text: 'Background: Murine leukemia virus (MLV) vector particles can be pseudotyped
with a truncated variant of the human immunodeficiency virus type 1 (HIV-1) envelope
protein (Env) and selectively target gene transfer to human cells expressing both
CD4 and an appropriate co-receptor. Vector transduction mimics the HIV-1 entry
process and is therefore a safe tool to study HIV-1 entry. Results: Using FLY
cells, which express the MLV gag and pol genes, we generated stable producer cell
lines that express the HIV-1 envelope gene and a retroviral vector genome encoding
the green fluorescent protein (GFP). The BH10 or 89.6 P HIV-1 Env was expressed
from a bicistronic vector which allowed the rapid selection of stable cell lines.
A codon-usage-optimized synthetic env gene permitted high, Rev-independent Env
expression. Vectors generated by these producer cells displayed different sensitivity
to entry inhibitors. Conclusion: These data illustrate that MLV/HIV-1 vectors
are a valuable screening system for entry inhibitors or neutralizing antisera
generated by vaccines.'
author:
- first_name: Sandra
full_name: Sandra Siegert
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
- first_name: Sonja
full_name: Thaler, Sonja
last_name: Thaler
- first_name: Ralf
full_name: Wagner, Ralf
last_name: Wagner
- first_name: Barbara
full_name: Schnierle, Barbara S
last_name: Schnierle
citation:
ama: Siegert S, Thaler S, Wagner R, Schnierle B. Assessment of HIV-1 entry inhibitors
by MLV/HIV-1 pseudotyped vectors. AIDS Research and Therapy. 2005;2(1).
doi:10.1186/1742-6405-2-7
apa: Siegert, S., Thaler, S., Wagner, R., & Schnierle, B. (2005). Assessment
of HIV-1 entry inhibitors by MLV/HIV-1 pseudotyped vectors. AIDS Research and
Therapy. BioMed Central. https://doi.org/10.1186/1742-6405-2-7
chicago: Siegert, Sandra, Sonja Thaler, Ralf Wagner, and Barbara Schnierle. “Assessment
of HIV-1 Entry Inhibitors by MLV/HIV-1 Pseudotyped Vectors.” AIDS Research
and Therapy. BioMed Central, 2005. https://doi.org/10.1186/1742-6405-2-7.
ieee: S. Siegert, S. Thaler, R. Wagner, and B. Schnierle, “Assessment of HIV-1 entry
inhibitors by MLV/HIV-1 pseudotyped vectors,” AIDS Research and Therapy,
vol. 2, no. 1. BioMed Central, 2005.
ista: Siegert S, Thaler S, Wagner R, Schnierle B. 2005. Assessment of HIV-1 entry
inhibitors by MLV/HIV-1 pseudotyped vectors. AIDS Research and Therapy. 2(1).
mla: Siegert, Sandra, et al. “Assessment of HIV-1 Entry Inhibitors by MLV/HIV-1
Pseudotyped Vectors.” AIDS Research and Therapy, vol. 2, no. 1, BioMed
Central, 2005, doi:10.1186/1742-6405-2-7.
short: S. Siegert, S. Thaler, R. Wagner, B. Schnierle, AIDS Research and Therapy
2 (2005).
date_created: 2018-12-11T11:54:03Z
date_published: 2005-09-12T00:00:00Z
date_updated: 2021-01-12T06:53:15Z
day: '12'
doi: 10.1186/1742-6405-2-7
extern: 1
intvolume: ' 2'
issue: '1'
month: '09'
publication: AIDS Research and Therapy
publication_status: published
publisher: BioMed Central
publist_id: '5315'
quality_controlled: 0
status: public
title: Assessment of HIV-1 entry inhibitors by MLV/HIV-1 pseudotyped vectors
type: journal_article
volume: 2
year: '2005'
...
---
_id: '1962'
abstract:
- lang: eng
text: |2-
Complex I of respiratory chains plays a central role in bioenergetics and is implicated in many human neurodegenerative diseases. An understanding of its mechanism requires a knowledge of the organization of redox centers. The arrangement of iron-sulfur clusters in the hydrophilic domain of complex I from Thermus thermophilus has been determined with the use of x-ray crystallography. One binuclear and six tetranuclear clusters are arranged, maximally 14 angstroms apart, in an 84-angstrom-long electron transfer chain. The binuclear cluster N1a and the tetranuclear cluster N7 are not in this pathway. Cluster N1a may play a role in the prevention of oxidative damage. The structure provides a framework for the interpretation of the large amounts of data accumulated on complex I.
acknowledgement: This work was funded by the Medical Research Council.
author:
- first_name: Philip
full_name: 'Hinchliffe, Philip '
last_name: Hinchliffe
- first_name: Leonid A
full_name: Leonid Sazanov
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: 'Hinchliffe P, Sazanov LA. Biochemistry: Organization of iron-sulfur clusters
in respiratory complex I. Science. 2005;309(5735):771-774. doi:10.1126/science.1113988'
apa: 'Hinchliffe, P., & Sazanov, L. A. (2005). Biochemistry: Organization of
iron-sulfur clusters in respiratory complex I. Science. American Association
for the Advancement of Science. https://doi.org/10.1126/science.1113988'
chicago: 'Hinchliffe, Philip, and Leonid A Sazanov. “Biochemistry: Organization
of Iron-Sulfur Clusters in Respiratory Complex I.” Science. American Association
for the Advancement of Science, 2005. https://doi.org/10.1126/science.1113988.'
ieee: 'P. Hinchliffe and L. A. Sazanov, “Biochemistry: Organization of iron-sulfur
clusters in respiratory complex I,” Science, vol. 309, no. 5735. American
Association for the Advancement of Science, pp. 771–774, 2005.'
ista: 'Hinchliffe P, Sazanov LA. 2005. Biochemistry: Organization of iron-sulfur
clusters in respiratory complex I. Science. 309(5735), 771–774.'
mla: 'Hinchliffe, Philip, and Leonid A. Sazanov. “Biochemistry: Organization of
Iron-Sulfur Clusters in Respiratory Complex I.” Science, vol. 309, no.
5735, American Association for the Advancement of Science, 2005, pp. 771–74, doi:10.1126/science.1113988.'
short: P. Hinchliffe, L.A. Sazanov, Science 309 (2005) 771–774.
date_created: 2018-12-11T11:54:56Z
date_published: 2005-07-29T00:00:00Z
date_updated: 2021-01-12T06:54:22Z
day: '29'
doi: 10.1126/science.1113988
extern: 1
intvolume: ' 309'
issue: '5735'
month: '07'
page: 771 - 774
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '5122'
quality_controlled: 0
status: public
title: 'Biochemistry: Organization of iron-sulfur clusters in respiratory complex
I'
type: journal_article
volume: 309
year: '2005'
...
---
_id: '13431'
abstract:
- lang: eng
text: 'Hydrogel stamps can microstructure solid surfaces, i.e., modify the surface
topology of metals, glasses, and crystals. It is demonstrated that stamps soaked
in an appropriate etchant can remove material with micrometer-scale precision.
The Figure shows an array of concentric circles etched in glass using the immersion
wet stamping process described (scale bar: 500 μm).'
article_processing_charge: No
article_type: original
author:
- first_name: S. K.
full_name: Smoukov, S. K.
last_name: Smoukov
- first_name: K. J. M.
full_name: Bishop, K. J. M.
last_name: Bishop
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
- first_name: C. J.
full_name: Campbell, C. J.
last_name: Campbell
- first_name: B. A.
full_name: Grzybowski, B. A.
last_name: Grzybowski
citation:
ama: Smoukov SK, Bishop KJM, Klajn R, Campbell CJ, Grzybowski BA. Cutting into solids
with micropatterned gels. Advanced Materials. 2005;17(11):1361-1365. doi:10.1002/adma.200402086
apa: Smoukov, S. K., Bishop, K. J. M., Klajn, R., Campbell, C. J., & Grzybowski,
B. A. (2005). Cutting into solids with micropatterned gels. Advanced Materials.
Wiley. https://doi.org/10.1002/adma.200402086
chicago: Smoukov, S. K., K. J. M. Bishop, Rafal Klajn, C. J. Campbell, and B. A.
Grzybowski. “Cutting into Solids with Micropatterned Gels.” Advanced Materials.
Wiley, 2005. https://doi.org/10.1002/adma.200402086.
ieee: S. K. Smoukov, K. J. M. Bishop, R. Klajn, C. J. Campbell, and B. A. Grzybowski,
“Cutting into solids with micropatterned gels,” Advanced Materials, vol.
17, no. 11. Wiley, pp. 1361–1365, 2005.
ista: Smoukov SK, Bishop KJM, Klajn R, Campbell CJ, Grzybowski BA. 2005. Cutting
into solids with micropatterned gels. Advanced Materials. 17(11), 1361–1365.
mla: Smoukov, S. K., et al. “Cutting into Solids with Micropatterned Gels.” Advanced
Materials, vol. 17, no. 11, Wiley, 2005, pp. 1361–65, doi:10.1002/adma.200402086.
short: S.K. Smoukov, K.J.M. Bishop, R. Klajn, C.J. Campbell, B.A. Grzybowski, Advanced
Materials 17 (2005) 1361–1365.
date_created: 2023-08-01T10:38:01Z
date_published: 2005-06-24T00:00:00Z
date_updated: 2023-08-08T11:53:16Z
day: '24'
doi: 10.1002/adma.200402086
extern: '1'
external_id:
pmid:
- '34412440'
intvolume: ' 17'
issue: '11'
keyword:
- Mechanical Engineering
- Mechanics of Materials
- General Materials Science
language:
- iso: eng
month: '06'
oa_version: None
page: 1361-1365
pmid: 1
publication: Advanced Materials
publication_identifier:
eissn:
- 1521-4095
issn:
- 0935-9648
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cutting into solids with micropatterned gels
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2005'
...
---
_id: '13432'
abstract:
- lang: eng
text: A new experimental technique is described that uses reaction−diffusion phenomena
as a means of one-step microfabrication of complex, multilevel surface reliefs.
Thin films of dry gelatin doped with potassium hexacyanoferrate are chemically
micropatterned with a solution of silver nitrate delivered from an agarose stamp.
Precipitation reaction between the two salts causes the surface to deform. The
mechanism of surface deformation is shown to involve a sequence of reactions,
diffusion, and gel swelling/contraction. This mechanism is established experimentally
and provides a basis of a theoretical lattice-gas model that allows prediction
surface topographies emerging from arbitrary geometries of the stamped features.
The usefulness of the technique is demonstrated by using it to rapidly prepare
two types of mold for passive microfluidic mixers.
article_processing_charge: No
article_type: original
author:
- first_name: Christopher J.
full_name: Campbell, Christopher J.
last_name: Campbell
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
- first_name: Marcin
full_name: Fialkowski, Marcin
last_name: Fialkowski
- first_name: Bartosz A.
full_name: Grzybowski, Bartosz A.
last_name: Grzybowski
citation:
ama: Campbell CJ, Klajn R, Fialkowski M, Grzybowski BA. One-step multilevel microfabrication
by reaction−diffusion. Langmuir. 2005;21(1):418-423. doi:10.1021/la0487747
apa: Campbell, C. J., Klajn, R., Fialkowski, M., & Grzybowski, B. A. (2005).
One-step multilevel microfabrication by reaction−diffusion. Langmuir. American
Chemical Society. https://doi.org/10.1021/la0487747
chicago: Campbell, Christopher J., Rafal Klajn, Marcin Fialkowski, and Bartosz A.
Grzybowski. “One-Step Multilevel Microfabrication by Reaction−diffusion.” Langmuir.
American Chemical Society, 2005. https://doi.org/10.1021/la0487747.
ieee: C. J. Campbell, R. Klajn, M. Fialkowski, and B. A. Grzybowski, “One-step multilevel
microfabrication by reaction−diffusion,” Langmuir, vol. 21, no. 1. American
Chemical Society, pp. 418–423, 2005.
ista: Campbell CJ, Klajn R, Fialkowski M, Grzybowski BA. 2005. One-step multilevel
microfabrication by reaction−diffusion. Langmuir. 21(1), 418–423.
mla: Campbell, Christopher J., et al. “One-Step Multilevel Microfabrication by Reaction−diffusion.”
Langmuir, vol. 21, no. 1, American Chemical Society, 2005, pp. 418–23,
doi:10.1021/la0487747.
short: C.J. Campbell, R. Klajn, M. Fialkowski, B.A. Grzybowski, Langmuir 21 (2005)
418–423.
date_created: 2023-08-01T10:38:29Z
date_published: 2005-01-21T00:00:00Z
date_updated: 2023-08-08T12:15:48Z
day: '21'
doi: 10.1021/la0487747
extern: '1'
external_id:
pmid:
- '15620333'
intvolume: ' 21'
issue: '1'
keyword:
- Electrochemistry
- Spectroscopy
- Surfaces and Interfaces
- Condensed Matter Physics
- General Materials Science
language:
- iso: eng
month: '01'
oa_version: None
page: 418-423
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: One-step multilevel microfabrication by reaction−diffusion
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 21
year: '2005'
...
---
_id: '13433'
abstract:
- lang: eng
text: Self-assembled monolayers (SAMs) of alkane thiols on gold and other metals
are versatile constructs with which to study interfacial phenomena and reactions
at surfaces. Surface properties of SAMs - e.g., wettability, stability in diverse
environments, propensity to interact with or to resist adsorption of macromolecules
-- depend on and can be controlled flexibly by the properties of the functional
(head) groups in the w position of the alkyl chain. SAMs provide a basis for many
important scientific and technological applications, ranging from micropatterning
methods, through sensing, to biological recognition. Despite their importance,
the literature on SAMs and the synthesis of molecules that constitute them remains
scattered and often conflicting. The purpose of this Review is (i) to summarize
the applications and physical properties of SAMs and (ii) to systematize the strategies
of synthesis of ω-functionalized alkane thiols. Generic retrosynthetic scheme
is developed that allows efficient synthetic planning. Issues related to the selection
of appropriate protecting groups and the ways of introduction of the thiol functionality
are discussed in detail, and illustrated with examples of syntheses of several
complex alkane thiols.
article_processing_charge: No
article_type: original
author:
- first_name: Dariusz
full_name: Witt, Dariusz
last_name: Witt
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
- first_name: Piotr
full_name: Barski, Piotr
last_name: Barski
- first_name: Bartosz
full_name: Grzybowski, Bartosz
last_name: Grzybowski
citation:
ama: Witt D, Klajn R, Barski P, Grzybowski B. Applications, properties and synthesis
of w-functionalized n-alkanethiols and disulfides - the building blocks of self-assembled
monolayers. Current Organic Chemistry. 2005;8(18):1763-1797. doi:10.2174/1385272043369421
apa: Witt, D., Klajn, R., Barski, P., & Grzybowski, B. (2005). Applications,
properties and synthesis of w-functionalized n-alkanethiols and disulfides - the
building blocks of self-assembled monolayers. Current Organic Chemistry.
Bentham Science. https://doi.org/10.2174/1385272043369421
chicago: Witt, Dariusz, Rafal Klajn, Piotr Barski, and Bartosz Grzybowski. “Applications,
Properties and Synthesis of w-Functionalized n-Alkanethiols and Disulfides - the
Building Blocks of Self-Assembled Monolayers.” Current Organic Chemistry.
Bentham Science, 2005. https://doi.org/10.2174/1385272043369421.
ieee: D. Witt, R. Klajn, P. Barski, and B. Grzybowski, “Applications, properties
and synthesis of w-functionalized n-alkanethiols and disulfides - the building
blocks of self-assembled monolayers,” Current Organic Chemistry, vol. 8,
no. 18. Bentham Science, pp. 1763–1797, 2005.
ista: Witt D, Klajn R, Barski P, Grzybowski B. 2005. Applications, properties and
synthesis of w-functionalized n-alkanethiols and disulfides - the building blocks
of self-assembled monolayers. Current Organic Chemistry. 8(18), 1763–1797.
mla: Witt, Dariusz, et al. “Applications, Properties and Synthesis of w-Functionalized
n-Alkanethiols and Disulfides - the Building Blocks of Self-Assembled Monolayers.”
Current Organic Chemistry, vol. 8, no. 18, Bentham Science, 2005, pp. 1763–97,
doi:10.2174/1385272043369421.
short: D. Witt, R. Klajn, P. Barski, B. Grzybowski, Current Organic Chemistry 8
(2005) 1763–1797.
date_created: 2023-08-01T10:38:58Z
date_published: 2005-12-01T00:00:00Z
date_updated: 2023-08-08T12:39:52Z
day: '01'
doi: 10.2174/1385272043369421
extern: '1'
intvolume: ' 8'
issue: '18'
keyword:
- Organic Chemistry
language:
- iso: eng
month: '12'
oa_version: None
page: 1763-1797
publication: Current Organic Chemistry
publication_identifier:
eissn:
- 1875-5348
issn:
- 1385-2728
publication_status: published
publisher: Bentham Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Applications, properties and synthesis of w-functionalized n-alkanethiols and
disulfides - the building blocks of self-assembled monolayers
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2005'
...
---
_id: '1444'
abstract:
- lang: eng
text: The paper surveys the mirror symmetry conjectures of Hausel-Thaddeus and Hausel-Rodriguez-Villegas
concerning the equality of certain Hodge numbers of SL(n, ℂ) vs. PGL(n, ℂ) flat
connections and character varieties for curves, respectively. Several new results
and conjectures and their relations to works of Hitchin, Gothen, Garsia-Haiman
and Earl-Kirwan are explained. These use the representation theory of finite groups
of Lie-type via the arithmetic of character varieties and lead to an unexpected
conjecture for a Hard Lefschetz theorem for their cohomology.
alternative_title:
- Progress in Mathematics
author:
- first_name: Tamas
full_name: Tamas Hausel
id: 4A0666D8-F248-11E8-B48F-1D18A9856A87
last_name: Hausel
citation:
ama: 'Hausel T. Mirror symmetry and Langlands duality in the non-Abelian Hodge theory
of a curve. In: Geometric Methods in Algebra and Number Theory. Vol 235.
Springer; 2005:193-217. doi:10.1007/0-8176-4417-2_9'
apa: Hausel, T. (2005). Mirror symmetry and Langlands duality in the non-Abelian
Hodge theory of a curve. In Geometric Methods in Algebra and Number Theory
(Vol. 235, pp. 193–217). Springer. https://doi.org/10.1007/0-8176-4417-2_9
chicago: Hausel, Tamás. “Mirror Symmetry and Langlands Duality in the Non-Abelian
Hodge Theory of a Curve.” In Geometric Methods in Algebra and Number Theory,
235:193–217. Springer, 2005. https://doi.org/10.1007/0-8176-4417-2_9.
ieee: T. Hausel, “Mirror symmetry and Langlands duality in the non-Abelian Hodge
theory of a curve,” in Geometric Methods in Algebra and Number Theory,
vol. 235, Springer, 2005, pp. 193–217.
ista: 'Hausel T. 2005.Mirror symmetry and Langlands duality in the non-Abelian Hodge
theory of a curve. In: Geometric Methods in Algebra and Number Theory. Progress
in Mathematics, vol. 235, 193–217.'
mla: Hausel, Tamás. “Mirror Symmetry and Langlands Duality in the Non-Abelian Hodge
Theory of a Curve.” Geometric Methods in Algebra and Number Theory, vol.
235, Springer, 2005, pp. 193–217, doi:10.1007/0-8176-4417-2_9.
short: T. Hausel, in:, Geometric Methods in Algebra and Number Theory, Springer,
2005, pp. 193–217.
date_created: 2018-12-11T11:52:03Z
date_published: 2005-01-01T00:00:00Z
date_updated: 2021-01-12T06:50:47Z
day: '01'
doi: 10.1007/0-8176-4417-2_9
extern: 1
intvolume: ' 235'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/math/0406380
month: '01'
oa: 1
page: 193 - 217
publication: Geometric Methods in Algebra and Number Theory
publication_status: published
publisher: Springer
publist_id: '5752'
quality_controlled: 0
status: public
title: Mirror symmetry and Langlands duality in the non-Abelian Hodge theory of a
curve
type: book_chapter
volume: 235
year: '2005'
...
---
_id: '1447'
abstract:
- lang: eng
text: Building on a recent paper [8], here we argue that the combinatorics of matroids
are intimately related to the geometry and topology of toric hyperkähler varieties.
We show that just like toric varieties occupy a central role in Stanley’s proof
for the necessity of McMullen’s conjecture (or g-inequalities) about the classification
of face vectors of simplicial polytopes, the topology of toric hyperkähler varieties
leads to new restrictions on face vectors of matroid complexes. Namely in this
paper we will give two proofs that the injectivity part of the Hard Lefschetz
theorem survives for toric hyperkähler varieties. We explain how this implies
the g-inequalities for rationally representable matroids. We show how the geometrical
intuition in the first proof, coupled with results of Chari [3], leads to a proof
of the g-inequalities for general matroid complexes, which is a recent result
of Swartz [20]. The geometrical idea in the second proof will show that a pure
O-sequence should satisfy the g-inequalities, thus showing that our result is
in fact a consequence of a long-standing conjecture of Stanley.
acknowledgement: Financial support wa s provided by a Miller Research Fellowship at
the University of California at Berkeley , and by NSF grants DMS- 0072675 and DMS-0305505.
author:
- first_name: Tamas
full_name: Tamas Hausel
id: 4A0666D8-F248-11E8-B48F-1D18A9856A87
last_name: Hausel
citation:
ama: Hausel T. Quaternionic geometry of matroids. Open Mathematics. 2005;3(1):26-38.
doi:10.2478/BF02475653
apa: Hausel, T. (2005). Quaternionic geometry of matroids. Open Mathematics.
Central European Science Journals. https://doi.org/10.2478/BF02475653
chicago: Hausel, Tamás. “Quaternionic Geometry of Matroids.” Open Mathematics.
Central European Science Journals, 2005. https://doi.org/10.2478/BF02475653.
ieee: T. Hausel, “Quaternionic geometry of matroids,” Open Mathematics, vol.
3, no. 1. Central European Science Journals, pp. 26–38, 2005.
ista: Hausel T. 2005. Quaternionic geometry of matroids. Open Mathematics. 3(1),
26–38.
mla: Hausel, Tamás. “Quaternionic Geometry of Matroids.” Open Mathematics,
vol. 3, no. 1, Central European Science Journals, 2005, pp. 26–38, doi:10.2478/BF02475653.
short: T. Hausel, Open Mathematics 3 (2005) 26–38.
date_created: 2018-12-11T11:52:05Z
date_published: 2005-03-01T00:00:00Z
date_updated: 2021-01-12T06:50:49Z
day: '01'
doi: 10.2478/BF02475653
extern: 1
intvolume: ' 3'
issue: '1'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/math/0308146
month: '03'
oa: 1
page: 26 - 38
publication: Open Mathematics
publication_status: published
publisher: Central European Science Journals
publist_id: '5749'
quality_controlled: 0
status: public
title: Quaternionic geometry of matroids
type: journal_article
volume: 3
year: '2005'
...
---
_id: '1463'
abstract:
- lang: eng
text: We study an integration theory in circle equivariant cohomology in order to
prove a theorem relating the cohomology ring of a hyperkähler quotient to the
cohomology ring of the quotient by a maximal abelian subgroup, analogous to a
theorem of Martin for symplectic quotients. We discuss applications of this theorem
to quiver varieties, and compute as an example the ordinary and equivariant cohomology
rings of a hyperpolygon space.
acknowledgement: ' Financial support was provided in part by NSF Grants DMS-0072675
and DMS-0305505.'
author:
- first_name: Tamas
full_name: Tamas Hausel
id: 4A0666D8-F248-11E8-B48F-1D18A9856A87
last_name: Hausel
- first_name: Nicholas
full_name: Proudfoot, Nicholas J
last_name: Proudfoot
citation:
ama: Hausel T, Proudfoot N. Abelianization for hyperkähler quotients. Topology.
2005;44(1):231-248. doi:10.1016/j.top.2004.04.002
apa: Hausel, T., & Proudfoot, N. (2005). Abelianization for hyperkähler quotients.
Topology. Elsevier. https://doi.org/10.1016/j.top.2004.04.002
chicago: Hausel, Tamás, and Nicholas Proudfoot. “Abelianization for Hyperkähler
Quotients.” Topology. Elsevier, 2005. https://doi.org/10.1016/j.top.2004.04.002.
ieee: T. Hausel and N. Proudfoot, “Abelianization for hyperkähler quotients,” Topology,
vol. 44, no. 1. Elsevier, pp. 231–248, 2005.
ista: Hausel T, Proudfoot N. 2005. Abelianization for hyperkähler quotients. Topology.
44(1), 231–248.
mla: Hausel, Tamás, and Nicholas Proudfoot. “Abelianization for Hyperkähler Quotients.”
Topology, vol. 44, no. 1, Elsevier, 2005, pp. 231–48, doi:10.1016/j.top.2004.04.002.
short: T. Hausel, N. Proudfoot, Topology 44 (2005) 231–248.
date_created: 2018-12-11T11:52:10Z
date_published: 2005-01-01T00:00:00Z
date_updated: 2021-01-12T06:50:55Z
day: '01'
doi: 10.1016/j.top.2004.04.002
extern: 1
intvolume: ' 44'
issue: '1'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/math/0310141
month: '01'
oa: 1
page: 231 - 248
publication: Topology
publication_status: published
publisher: Elsevier
publist_id: '5735'
quality_controlled: 0
status: public
title: Abelianization for hyperkähler quotients
type: journal_article
volume: 44
year: '2005'
...