---
_id: '10128'
abstract:
- lang: eng
text: 'An extensive computational study of the conformational preferences of three
capped dipeptides: Ac-Xxx-Phe-NH2, Xxx = Gly, Ala, Val is reported. On the basis
of local second-order Møller–Plesset perturbation theory (LMP2) and DFT computations
we were able to identify the experimentally observed conformers as γL–γL(g−) and
β-turn I(g+) in Ac-Gly-Phe-NH2, and Ac-Ala-Phe-NH2, and as the closely related
γL(g+)–γL(g−) and β-turn I(a,g+) in Ac-Val-Phe-NH2. In contrast to the experimental
observation that peptides with bulky side chain have a propensity for β-turns,
we show that in Ac-Val-Phe-NH2 the minimum energy structure corresponds to the
experimentally non detected β-strand.'
acknowledgement: This work has been supported by the MZOŠ projects 098-0352851-2921
and 119-1191342-2959.
article_processing_charge: No
article_type: original
author:
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: T.
full_name: Hrenar, T.
last_name: Hrenar
- first_name: M.
full_name: Mališ, M.
last_name: Mališ
- first_name: N.
full_name: Došlić, N.
last_name: Došlić
citation:
ama: Šarić A, Hrenar T, Mališ M, Došlić N. Quantum mechanical study of secondary
structure formation in protected dipeptides. Physical Chemistry Chemical Physics.
2010;12(18):4678-4685. doi:10.1039/b923041f
apa: Šarić, A., Hrenar, T., Mališ, M., & Došlić, N. (2010). Quantum mechanical
study of secondary structure formation in protected dipeptides. Physical Chemistry
Chemical Physics. Royal Society of Chemistry . https://doi.org/10.1039/b923041f
chicago: Šarić, Anđela, T. Hrenar, M. Mališ, and N. Došlić. “Quantum Mechanical
Study of Secondary Structure Formation in Protected Dipeptides.” Physical Chemistry
Chemical Physics. Royal Society of Chemistry , 2010. https://doi.org/10.1039/b923041f.
ieee: A. Šarić, T. Hrenar, M. Mališ, and N. Došlić, “Quantum mechanical study of
secondary structure formation in protected dipeptides,” Physical Chemistry
Chemical Physics, vol. 12, no. 18. Royal Society of Chemistry , pp. 4678–4685,
2010.
ista: Šarić A, Hrenar T, Mališ M, Došlić N. 2010. Quantum mechanical study of secondary
structure formation in protected dipeptides. Physical Chemistry Chemical Physics.
12(18), 4678–4685.
mla: Šarić, Anđela, et al. “Quantum Mechanical Study of Secondary Structure Formation
in Protected Dipeptides.” Physical Chemistry Chemical Physics, vol. 12,
no. 18, Royal Society of Chemistry , 2010, pp. 4678–85, doi:10.1039/b923041f.
short: A. Šarić, T. Hrenar, M. Mališ, N. Došlić, Physical Chemistry Chemical Physics
12 (2010) 4678–4685.
date_created: 2021-10-12T08:44:34Z
date_published: 2010-03-16T00:00:00Z
date_updated: 2021-10-12T09:49:22Z
day: '16'
doi: 10.1039/b923041f
extern: '1'
external_id:
pmid:
- '20428547'
intvolume: ' 12'
issue: '18'
keyword:
- Physical and Theoretical Chemistry
- General Physics and Astronomy
language:
- iso: eng
main_file_link:
- url: https://europepmc.org/article/med/20428547
month: '03'
oa_version: None
page: 4678-4685
pmid: 1
publication: Physical Chemistry Chemical Physics
publication_identifier:
issn:
- 1463-9076
- 1463-9084
publication_status: published
publisher: 'Royal Society of Chemistry '
quality_controlled: '1'
status: public
title: Quantum mechanical study of secondary structure formation in protected dipeptides
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 12
year: '2010'
...
---
_id: '10127'
abstract:
- lang: eng
text: We use numerical simulations to show how noninteracting hard particles binding
to a deformable elastic shell may self-assemble into a variety of linear patterns.
This is a result of the nontrivial elastic response to deformations of shells.
The morphology of the patterns can be controlled by the mechanical properties
of the surface, and can be fine-tuned by varying the binding energy of the particles.
We also repeat our calculations for a fully flexible chain and find that the chain
conformations follow patterns similar to those formed by the nanoparticles under
analogous conditions. We propose a simple way of understanding and sorting the
different structures and relate it to the underlying shape transition of the shell.
Finally, we discuss the implications of our results.
acknowledgement: This work was supported by the National Science Foundation under
Career Grant No. DMR-0846426. We thank Josep C. Pàmies for helpful discussions.
article_processing_charge: No
article_type: original
author:
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Angelo
full_name: Cacciuto, Angelo
last_name: Cacciuto
citation:
ama: Šarić A, Cacciuto A. Particle self-assembly on soft elastic shells. Soft
Matter. 2010;7(5):1874-1878. doi:10.1039/c0sm01143f
apa: Šarić, A., & Cacciuto, A. (2010). Particle self-assembly on soft elastic
shells. Soft Matter. Royal Society of Chemistry (RSC). https://doi.org/10.1039/c0sm01143f
chicago: Šarić, Anđela, and Angelo Cacciuto. “Particle Self-Assembly on Soft Elastic
Shells.” Soft Matter. Royal Society of Chemistry (RSC), 2010. https://doi.org/10.1039/c0sm01143f.
ieee: A. Šarić and A. Cacciuto, “Particle self-assembly on soft elastic shells,”
Soft Matter, vol. 7, no. 5. Royal Society of Chemistry (RSC), pp. 1874–1878,
2010.
ista: Šarić A, Cacciuto A. 2010. Particle self-assembly on soft elastic shells.
Soft Matter. 7(5), 1874–1878.
mla: Šarić, Anđela, and Angelo Cacciuto. “Particle Self-Assembly on Soft Elastic
Shells.” Soft Matter, vol. 7, no. 5, Royal Society of Chemistry (RSC),
2010, pp. 1874–78, doi:10.1039/c0sm01143f.
short: A. Šarić, A. Cacciuto, Soft Matter 7 (2010) 1874–1878.
date_created: 2021-10-12T08:34:23Z
date_published: 2010-12-23T00:00:00Z
date_updated: 2021-10-12T09:49:27Z
day: '23'
doi: 10.1039/c0sm01143f
extern: '1'
external_id:
arxiv:
- '1010.2453'
intvolume: ' 7'
issue: '5'
keyword:
- condensed matter physics
- general chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1010.2453
month: '12'
oa: 1
oa_version: Preprint
page: 1874-1878
publication: Soft Matter
publication_identifier:
issn:
- 1744-683X
- 1744-6848
publication_status: published
publisher: Royal Society of Chemistry (RSC)
quality_controlled: '1'
status: public
title: Particle self-assembly on soft elastic shells
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 7
year: '2010'
...
---
_id: '10390'
abstract:
- lang: eng
text: 'We use numerical simulations to study the phase behavior of a system of purely
repulsive soft dumbbells as a function of size ratio of the two components and
their relative degree of deformability. We find a plethora of different phases,
which includes most of the mesophases observed in self-assembly of block copolymers
but also crystalline structures formed by asymmetric, hard binary mixtures. Our
results detail the phenomenological behavior of these systems when softness is
introduced in terms of two different classes of interparticle interactions: (a)
the elastic Hertz potential, which has a finite energy cost for complete overlap
of any two components, and (b) a generic power-law repulsion with tunable exponent.
We discuss how simple geometric arguments can be used to account for the large
structural variety observed in these systems and detail the similarities and differences
in the phase behavior for the two classes of potentials under consideration.'
acknowledgement: This work was supported by the National Science Foundation under
CAREER Grant No. DMR-0846426 and partly by Columbia University.
article_processing_charge: No
article_type: original
author:
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Behnaz
full_name: Bozorgui, Behnaz
last_name: Bozorgui
- first_name: Angelo
full_name: Cacciuto, Angelo
last_name: Cacciuto
citation:
ama: Šarić A, Bozorgui B, Cacciuto A. Packing of soft asymmetric dumbbells. The
Journal of Physical Chemistry B. 2010;115(22):7182-7189. doi:10.1021/jp107545w
apa: Šarić, A., Bozorgui, B., & Cacciuto, A. (2010). Packing of soft asymmetric
dumbbells. The Journal of Physical Chemistry B. American Chemical Society.
https://doi.org/10.1021/jp107545w
chicago: Šarić, Anđela, Behnaz Bozorgui, and Angelo Cacciuto. “Packing of Soft Asymmetric
Dumbbells.” The Journal of Physical Chemistry B. American Chemical Society,
2010. https://doi.org/10.1021/jp107545w.
ieee: A. Šarić, B. Bozorgui, and A. Cacciuto, “Packing of soft asymmetric dumbbells,”
The Journal of Physical Chemistry B, vol. 115, no. 22. American Chemical
Society, pp. 7182–7189, 2010.
ista: Šarić A, Bozorgui B, Cacciuto A. 2010. Packing of soft asymmetric dumbbells.
The Journal of Physical Chemistry B. 115(22), 7182–7189.
mla: Šarić, Anđela, et al. “Packing of Soft Asymmetric Dumbbells.” The Journal
of Physical Chemistry B, vol. 115, no. 22, American Chemical Society, 2010,
pp. 7182–89, doi:10.1021/jp107545w.
short: A. Šarić, B. Bozorgui, A. Cacciuto, The Journal of Physical Chemistry B 115
(2010) 7182–7189.
date_created: 2021-11-29T15:13:17Z
date_published: 2010-10-15T00:00:00Z
date_updated: 2021-11-29T16:20:29Z
day: '15'
doi: 10.1021/jp107545w
extern: '1'
external_id:
arxiv:
- '1010.2458'
pmid:
- '20949934'
intvolume: ' 115'
issue: '22'
keyword:
- materials chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1010.2458
month: '10'
oa: 1
oa_version: Preprint
page: 7182-7189
pmid: 1
publication: The Journal of Physical Chemistry B
publication_identifier:
eissn:
- 1520-5207
issn:
- 1520-6106
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Packing of soft asymmetric dumbbells
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 115
year: '2010'
...
---
_id: '10391'
abstract:
- lang: eng
text: We use numerical simulations to show how a fully flexible filament binding
to a deformable cylindrical surface may acquire a macroscopic persistence length
and a helical conformation. This is a result of the nontrivial elastic response
to deformations of elastic sheets. We find that the filament’s helical pitch is
completely determined by the mechanical properties of the surface, and can be
easily tuned by varying the surface stretching rigidity. We propose simple scaling
arguments to understand the physical mechanism behind this phenomenon and present
a phase diagram indicating under what conditions one should expect a fully flexible
chain to behave as a helical semiflexible filament. Finally, we discuss the implications
of our results.
acknowledgement: This work was supported by the National Science Foundation under
Career Grant No. DMR-0846426.
article_number: '226101'
article_processing_charge: No
article_type: original
author:
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Josep C.
full_name: Pàmies, Josep C.
last_name: Pàmies
- first_name: Angelo
full_name: Cacciuto, Angelo
last_name: Cacciuto
citation:
ama: Šarić A, Pàmies JC, Cacciuto A. Effective elasticity of a flexible filament
bound to a deformable cylindrical surface. Physical Review Letters. 2010;104(22).
doi:10.1103/physrevlett.104.226101
apa: Šarić, A., Pàmies, J. C., & Cacciuto, A. (2010). Effective elasticity of
a flexible filament bound to a deformable cylindrical surface. Physical Review
Letters. American Physical Society. https://doi.org/10.1103/physrevlett.104.226101
chicago: Šarić, Anđela, Josep C. Pàmies, and Angelo Cacciuto. “Effective Elasticity
of a Flexible Filament Bound to a Deformable Cylindrical Surface.” Physical
Review Letters. American Physical Society, 2010. https://doi.org/10.1103/physrevlett.104.226101.
ieee: A. Šarić, J. C. Pàmies, and A. Cacciuto, “Effective elasticity of a flexible
filament bound to a deformable cylindrical surface,” Physical Review Letters,
vol. 104, no. 22. American Physical Society, 2010.
ista: Šarić A, Pàmies JC, Cacciuto A. 2010. Effective elasticity of a flexible filament
bound to a deformable cylindrical surface. Physical Review Letters. 104(22), 226101.
mla: Šarić, Anđela, et al. “Effective Elasticity of a Flexible Filament Bound to
a Deformable Cylindrical Surface.” Physical Review Letters, vol. 104, no.
22, 226101, American Physical Society, 2010, doi:10.1103/physrevlett.104.226101.
short: A. Šarić, J.C. Pàmies, A. Cacciuto, Physical Review Letters 104 (2010).
date_created: 2021-11-29T15:14:33Z
date_published: 2010-06-03T00:00:00Z
date_updated: 2021-11-30T08:11:19Z
day: '03'
doi: 10.1103/physrevlett.104.226101
extern: '1'
external_id:
arxiv:
- '1005.2429'
pmid:
- '20867183'
intvolume: ' 104'
issue: '22'
keyword:
- general physics and astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1005.2429
month: '06'
oa: 1
oa_version: Preprint
pmid: 1
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Effective elasticity of a flexible filament bound to a deformable cylindrical
surface
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 104
year: '2010'
...
---
_id: '1042'
abstract:
- lang: eng
text: Recent years have seen tremendous progress in the field of cold and ultracold
molecules. A central goal in the field is currently the realization of stable
rovibronic ground-state molecular samples in the regime of quantum degeneracy,
e.g. in the form of molecular Bose-Einstein condensates, molecular degenerate
Fermi gases, or, when an optical lattice is present, molecular Mott-insulator
phases. However, molecular samples are not readily cooled to the extremely low
temperatures at which quantum degeneracy occurs. In particular, laser cooling,
the \'workhorse\' for the field of atomic quantum gases, is generally not applicable
to molecular samples. Here we take an important step beyond previous work1 and
provide details on the realization of an ultracold quantum gas of ground-state
dimer molecules trapped in an optical lattice as recently reported in Ref. 2.
We demonstrate full control over all internal and external quantum degrees of
freedom for the ground-state molecules by deterministically preparing the molecules
in a single quantum state, i.e. in a specific hyperfine sublevel of the rovibronic
ground state, while the molecules are trapped in the motional ground state of
the individual lattice wells. We circumvent the problem of cooling by associating
weakly-bound molecules out of a zero-temperature atomic Mott-insulator state and
by transferring these to the absolute ground state in a four-photon STIRAP process.
Our preparation procedure directly leads to a long-lived, lattice-trapped molecular
many-body state, which we expect to form the platform for many of the envisioned
future experiments with molecular quantum gases, e.g. on precision molecular spectroscopy,
quantum information science, and dipolar quantum systems.
article_processing_charge: No
author:
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Manfred
full_name: Mark, Manfred
last_name: Mark
- first_name: Elmar
full_name: Haller, Elmar
last_name: Haller
- first_name: Mattias
full_name: Gustavsson, Mattias
last_name: Gustavsson
- first_name: Russell
full_name: Hart, Russell
last_name: Hart
- first_name: Hanns
full_name: Nägerl, Hanns
last_name: Nägerl
citation:
ama: 'Danzl JG, Mark M, Haller E, Gustavsson M, Hart R, Nägerl H. Production of
a quantum gas of rovibronic ground-state molecules in an optical lattice. In:
World Scientific Publishing; 2010:256-269. doi:10.1142/9789814282345_0024'
apa: 'Danzl, J. G., Mark, M., Haller, E., Gustavsson, M., Hart, R., & Nägerl,
H. (2010). Production of a quantum gas of rovibronic ground-state molecules in
an optical lattice (pp. 256–269). Presented at the ICOLS: International Conference
on Laser Spectroscopy, World Scientific Publishing. https://doi.org/10.1142/9789814282345_0024'
chicago: Danzl, Johann G, Manfred Mark, Elmar Haller, Mattias Gustavsson, Russell
Hart, and Hanns Nägerl. “Production of a Quantum Gas of Rovibronic Ground-State
Molecules in an Optical Lattice,” 256–69. World Scientific Publishing, 2010. https://doi.org/10.1142/9789814282345_0024.
ieee: 'J. G. Danzl, M. Mark, E. Haller, M. Gustavsson, R. Hart, and H. Nägerl, “Production
of a quantum gas of rovibronic ground-state molecules in an optical lattice,”
presented at the ICOLS: International Conference on Laser Spectroscopy, 2010,
pp. 256–269.'
ista: 'Danzl JG, Mark M, Haller E, Gustavsson M, Hart R, Nägerl H. 2010. Production
of a quantum gas of rovibronic ground-state molecules in an optical lattice. ICOLS:
International Conference on Laser Spectroscopy, 256–269.'
mla: Danzl, Johann G., et al. Production of a Quantum Gas of Rovibronic Ground-State
Molecules in an Optical Lattice. World Scientific Publishing, 2010, pp. 256–69,
doi:10.1142/9789814282345_0024.
short: J.G. Danzl, M. Mark, E. Haller, M. Gustavsson, R. Hart, H. Nägerl, in:, World
Scientific Publishing, 2010, pp. 256–269.
conference:
name: 'ICOLS: International Conference on Laser Spectroscopy'
date_created: 2018-12-11T11:49:50Z
date_published: 2010-01-01T00:00:00Z
date_updated: 2021-01-12T06:47:52Z
day: '01'
doi: 10.1142/9789814282345_0024
extern: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 256 - 269
publication_status: published
publisher: World Scientific Publishing
publist_id: '6346'
status: public
title: Production of a quantum gas of rovibronic ground-state molecules in an optical
lattice
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2010'
...