---
_id: '14301'
abstract:
- lang: eng
text: DNA has become a prime material for assembling complex three-dimensional objects
that promise utility in various areas of application. However, achieving user-defined
goals with DNA objects has been hampered by the difficulty to prepare them at
arbitrary concentrations and in user-defined solution conditions. Here, we describe
a method that solves this problem. The method is based on poly(ethylene glycol)-induced
depletion of species with high molecular weight. We demonstrate that our method
is applicable to a wide spectrum of DNA shapes and that it achieves excellent
recovery yields of target objects up to 97 %, while providing efficient separation
from non-integrated DNA strands. DNA objects may be prepared at concentrations
up to the limit of solubility, including the possibility for bringing DNA objects
into a solid phase. Due to the fidelity and simplicity of our method we anticipate
that it will help to catalyze the development of new types of applications that
use self-assembled DNA objects.
article_processing_charge: No
article_type: original
author:
- first_name: Evi
full_name: Stahl, Evi
last_name: Stahl
- first_name: Thomas
full_name: Martin, Thomas
last_name: Martin
- first_name: Florian M
full_name: Praetorius, Florian M
id: dfec9381-4341-11ee-8fd8-faa02bba7d62
last_name: Praetorius
- first_name: Hendrik
full_name: Dietz, Hendrik
last_name: Dietz
citation:
ama: Stahl E, Martin T, Praetorius FM, Dietz H. Facile and scalable preparation
of pure and dense DNA origami solutions. Angewandte Chemie International Edition.
2014;126(47):12949-12954. doi:10.1002/ange.201405991
apa: Stahl, E., Martin, T., Praetorius, F. M., & Dietz, H. (2014). Facile and
scalable preparation of pure and dense DNA origami solutions. Angewandte Chemie
International Edition. Wiley. https://doi.org/10.1002/ange.201405991
chicago: Stahl, Evi, Thomas Martin, Florian M Praetorius, and Hendrik Dietz. “Facile
and Scalable Preparation of Pure and Dense DNA Origami Solutions.” Angewandte
Chemie International Edition. Wiley, 2014. https://doi.org/10.1002/ange.201405991.
ieee: E. Stahl, T. Martin, F. M. Praetorius, and H. Dietz, “Facile and scalable
preparation of pure and dense DNA origami solutions,” Angewandte Chemie International
Edition, vol. 126, no. 47. Wiley, pp. 12949–12954, 2014.
ista: Stahl E, Martin T, Praetorius FM, Dietz H. 2014. Facile and scalable preparation
of pure and dense DNA origami solutions. Angewandte Chemie International Edition.
126(47), 12949–12954.
mla: Stahl, Evi, et al. “Facile and Scalable Preparation of Pure and Dense DNA Origami
Solutions.” Angewandte Chemie International Edition, vol. 126, no. 47,
Wiley, 2014, pp. 12949–54, doi:10.1002/ange.201405991.
short: E. Stahl, T. Martin, F.M. Praetorius, H. Dietz, Angewandte Chemie International
Edition 126 (2014) 12949–12954.
date_created: 2023-09-06T12:51:14Z
date_published: 2014-11-17T00:00:00Z
date_updated: 2023-11-07T12:14:30Z
day: '17'
doi: 10.1002/ange.201405991
extern: '1'
external_id:
pmid:
- '25346175'
intvolume: ' 126'
issue: '47'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1002/ange.201405991
month: '11'
oa: 1
oa_version: Published Version
page: 12949-12954
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: Facile and scalable preparation of pure and dense DNA origami solutions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 126
year: '2014'
...
---
_id: '9050'
abstract:
- lang: eng
text: Self-propelled particles can exhibit surprising non-equilibrium behaviors,
and how they interact with obstacles or boundaries remains an important open problem.
Here we show that chemically propelled micro-rods can be captured, with little
change in their speed, into close orbits around solid spheres resting on or near
a horizontal plane. We show that this interaction between sphere and particle
is short-range, occurring even for spheres smaller than the particle length, and
for a variety of sphere materials. We consider a simple model, based on lubrication
theory, of a force- and torque-free swimmer driven by a surface slip (the phoretic
propulsion mechanism) and moving near a solid surface. The model demonstrates
capture, or movement towards the surface, and yields speeds independent of distance.
This study reveals the crucial aspects of activity–driven interactions of self-propelled
particles with passive objects, and brings into question the use of colloidal
tracers as probes of active matter.
article_number: '1784'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Daisuke
full_name: Takagi, Daisuke
last_name: Takagi
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
- first_name: Adam B.
full_name: Braunschweig, Adam B.
last_name: Braunschweig
- first_name: Michael J.
full_name: Shelley, Michael J.
last_name: Shelley
- first_name: Jun
full_name: Zhang, Jun
last_name: Zhang
citation:
ama: Takagi D, Palacci JA, Braunschweig AB, Shelley MJ, Zhang J. Hydrodynamic capture
of microswimmers into sphere-bound orbits. Soft Matter. 2014;10(11). doi:10.1039/c3sm52815d
apa: Takagi, D., Palacci, J. A., Braunschweig, A. B., Shelley, M. J., & Zhang,
J. (2014). Hydrodynamic capture of microswimmers into sphere-bound orbits. Soft
Matter. Royal Society of Chemistry . https://doi.org/10.1039/c3sm52815d
chicago: Takagi, Daisuke, Jérémie A Palacci, Adam B. Braunschweig, Michael J. Shelley,
and Jun Zhang. “Hydrodynamic Capture of Microswimmers into Sphere-Bound Orbits.”
Soft Matter. Royal Society of Chemistry , 2014. https://doi.org/10.1039/c3sm52815d.
ieee: D. Takagi, J. A. Palacci, A. B. Braunschweig, M. J. Shelley, and J. Zhang,
“Hydrodynamic capture of microswimmers into sphere-bound orbits,” Soft Matter,
vol. 10, no. 11. Royal Society of Chemistry , 2014.
ista: Takagi D, Palacci JA, Braunschweig AB, Shelley MJ, Zhang J. 2014. Hydrodynamic
capture of microswimmers into sphere-bound orbits. Soft Matter. 10(11), 1784.
mla: Takagi, Daisuke, et al. “Hydrodynamic Capture of Microswimmers into Sphere-Bound
Orbits.” Soft Matter, vol. 10, no. 11, 1784, Royal Society of Chemistry
, 2014, doi:10.1039/c3sm52815d.
short: D. Takagi, J.A. Palacci, A.B. Braunschweig, M.J. Shelley, J. Zhang, Soft
Matter 10 (2014).
date_created: 2021-02-01T13:43:31Z
date_published: 2014-03-21T00:00:00Z
date_updated: 2023-02-23T13:47:35Z
day: '21'
doi: 10.1039/c3sm52815d
extern: '1'
external_id:
arxiv:
- '1309.5662'
pmid:
- '24800268'
intvolume: ' 10'
issue: '11'
keyword:
- General Chemistry
- Condensed Matter Physics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1309.5662
month: '03'
oa: 1
oa_version: Preprint
pmid: 1
publication: Soft Matter
publication_identifier:
eissn:
- 1744-6848
issn:
- 1744-683X
publication_status: published
publisher: 'Royal Society of Chemistry '
quality_controlled: '1'
scopus_import: '1'
status: public
title: Hydrodynamic capture of microswimmers into sphere-bound orbits
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 10
year: '2014'
...
---
_id: '9166'
abstract:
- lang: eng
text: Light-activated self-propelled colloids are synthesized and their active motion
is studied using optical microscopy. We propose a versatile route using different
photoactive materials, and demonstrate a multiwavelength activation and propulsion.
Thanks to the photoelectrochemical properties of two semiconductor materials (α-Fe2O3
and TiO2), a light with an energy higher than the bandgap triggers the reaction
of decomposition of hydrogen peroxide and produces a chemical cloud around the
particle. It induces a phoretic attraction with neighbouring colloids as well
as an osmotic self-propulsion of the particle on the substrate. We use these mechanisms
to form colloidal cargos as well as self-propelled particles where the light-activated
component is embedded into a dielectric sphere. The particles are self-propelled
along a direction otherwise randomized by thermal fluctuations, and exhibit a
persistent random walk. For sufficient surface density, the particles spontaneously
form ‘living crystals’ which are mobile, break apart and reform. Steering the
particle with an external magnetic field, we show that the formation of the dense
phase results from the collisions heads-on of the particles. This effect is intrinsically
non-equilibrium and a novel principle of organization for systems without detailed
balance. Engineering families of particles self-propelled by different wavelength
demonstrate a good understanding of both the physics and the chemistry behind
the system and points to a general route for designing new families of self-propelled
particles.
article_number: '20130372'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
- first_name: S.
full_name: Sacanna, S.
last_name: Sacanna
- first_name: S.-H.
full_name: Kim, S.-H.
last_name: Kim
- first_name: G.-R.
full_name: Yi, G.-R.
last_name: Yi
- first_name: D. J.
full_name: Pine, D. J.
last_name: Pine
- first_name: P. M.
full_name: Chaikin, P. M.
last_name: Chaikin
citation:
ama: 'Palacci JA, Sacanna S, Kim S-H, Yi G-R, Pine DJ, Chaikin PM. Light-activated
self-propelled colloids. Philosophical Transactions of the Royal Society A:
Mathematical, Physical and Engineering Sciences. 2014;372(2029). doi:10.1098/rsta.2013.0372'
apa: 'Palacci, J. A., Sacanna, S., Kim, S.-H., Yi, G.-R., Pine, D. J., & Chaikin,
P. M. (2014). Light-activated self-propelled colloids. Philosophical Transactions
of the Royal Society A: Mathematical, Physical and Engineering Sciences. The
Royal Society. https://doi.org/10.1098/rsta.2013.0372'
chicago: 'Palacci, Jérémie A, S. Sacanna, S.-H. Kim, G.-R. Yi, D. J. Pine, and P.
M. Chaikin. “Light-Activated Self-Propelled Colloids.” Philosophical Transactions
of the Royal Society A: Mathematical, Physical and Engineering Sciences. The
Royal Society, 2014. https://doi.org/10.1098/rsta.2013.0372.'
ieee: 'J. A. Palacci, S. Sacanna, S.-H. Kim, G.-R. Yi, D. J. Pine, and P. M. Chaikin,
“Light-activated self-propelled colloids,” Philosophical Transactions of the
Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 372,
no. 2029. The Royal Society, 2014.'
ista: 'Palacci JA, Sacanna S, Kim S-H, Yi G-R, Pine DJ, Chaikin PM. 2014. Light-activated
self-propelled colloids. Philosophical Transactions of the Royal Society A: Mathematical,
Physical and Engineering Sciences. 372(2029), 20130372.'
mla: 'Palacci, Jérémie A., et al. “Light-Activated Self-Propelled Colloids.” Philosophical
Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences,
vol. 372, no. 2029, 20130372, The Royal Society, 2014, doi:10.1098/rsta.2013.0372.'
short: 'J.A. Palacci, S. Sacanna, S.-H. Kim, G.-R. Yi, D.J. Pine, P.M. Chaikin,
Philosophical Transactions of the Royal Society A: Mathematical, Physical and
Engineering Sciences 372 (2014).'
date_created: 2021-02-18T14:31:11Z
date_published: 2014-11-28T00:00:00Z
date_updated: 2021-02-22T10:44:16Z
day: '28'
doi: 10.1098/rsta.2013.0372
extern: '1'
external_id:
arxiv:
- '1410.7278'
pmid:
- '25332383'
intvolume: ' 372'
issue: '2029'
keyword:
- General Engineering
- General Physics and Astronomy
- General Mathematics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1098/rsta.2013.0372
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: 'Philosophical Transactions of the Royal Society A: Mathematical, Physical
and Engineering Sciences'
publication_identifier:
eissn:
- 1471-2962
issn:
- 1364-503X
publication_status: published
publisher: The Royal Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Light-activated self-propelled colloids
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 372
year: '2014'
...
---
_id: '925'
abstract:
- lang: eng
text: The morphological stability of biological tubes is crucial for the efficient
circulation of fluids and gases. Failure of this stability causes irregularly
shaped tubes found in multiple pathological conditions. Here, we report that Drosophila
mutants of the ESCRT III component Shrub/Vps32 exhibit a strikingly elongated
sinusoidal tube phenotype. This is caused by excessive apical membrane synthesis
accompanied by the ectopic accumulation and overactivation of Crumbs in swollen
endosomes. Furthermore, we demonstrate that the apical extracellular matrix (aECM)
of the tracheal tube is a viscoelastic material coupled with the apical membrane.
We present a simple mechanical model in which aECM elasticity, apical membrane
growth, and their interaction are three vital parameters determining the stability
of biological tubes. Our findings demonstrate a mechanical role for the extracellular
matrix and suggest that the interaction of the apical membrane and an elastic
aECM determines the final morphology of biological tubes independent of cell shape.
acknowledgement: We thank F. Gao, R.E. Ward, S. Luschnig, T. Okajima, M. Affolter,
D. Bilder, E. Knust, T. Tanaka, A. Nakamura, C. Samakovlis, K. Saigo, M. Furuse,
the Bloomington Stock Center, Drosophila Genetic Resource Center in Kyoto, Japan,
and the Developmental Studies Hybridoma Bank for generously providing antibodies
and fly stocks; H. Wada for UAS-3×TagRFP fly and dye injection; Y.H. Zhang for plasmid
and protocol for CBP preparation; and J. Prost and J.F. Joanny for their support
for the project and discussion. We also thank T. Shibata, Y. Morishita, T. Kondo,
and G. Sheng for critically reading the manuscript. This work was supported by a
Grant-in-Aid for Scientific Research on Innovative Areas from MEXT Japan to S.H.
and the RIKEN Foreign Postdoctoral Researcher Program to B.D.
article_processing_charge: No
author:
- first_name: Bo
full_name: Dong, Bo
last_name: Dong
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Shigeo
full_name: Hayashi, Shigeo
last_name: Hayashi
citation:
ama: Dong B, Hannezo EB, Hayashi S. Balance between apical membrane growth and luminal
matrix resistance determines epithelial tubule shape. Cell Reports. 2014;7(4):941-950.
doi:10.1016/j.celrep.2014.03.066
apa: Dong, B., Hannezo, E. B., & Hayashi, S. (2014). Balance between apical
membrane growth and luminal matrix resistance determines epithelial tubule shape.
Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2014.03.066
chicago: Dong, Bo, Edouard B Hannezo, and Shigeo Hayashi. “Balance between Apical
Membrane Growth and Luminal Matrix Resistance Determines Epithelial Tubule Shape.”
Cell Reports. Cell Press, 2014. https://doi.org/10.1016/j.celrep.2014.03.066.
ieee: B. Dong, E. B. Hannezo, and S. Hayashi, “Balance between apical membrane growth
and luminal matrix resistance determines epithelial tubule shape,” Cell Reports,
vol. 7, no. 4. Cell Press, pp. 941–950, 2014.
ista: Dong B, Hannezo EB, Hayashi S. 2014. Balance between apical membrane growth
and luminal matrix resistance determines epithelial tubule shape. Cell Reports.
7(4), 941–950.
mla: Dong, Bo, et al. “Balance between Apical Membrane Growth and Luminal Matrix
Resistance Determines Epithelial Tubule Shape.” Cell Reports, vol. 7, no.
4, Cell Press, 2014, pp. 941–50, doi:10.1016/j.celrep.2014.03.066.
short: B. Dong, E.B. Hannezo, S. Hayashi, Cell Reports 7 (2014) 941–950.
date_created: 2018-12-11T11:49:14Z
date_published: 2014-05-22T00:00:00Z
date_updated: 2021-01-12T08:21:57Z
day: '22'
doi: 10.1016/j.celrep.2014.03.066
extern: '1'
intvolume: ' 7'
issue: '4'
language:
- iso: eng
month: '05'
oa_version: None
page: 941 - 950
publication: Cell Reports
publication_status: published
publisher: Cell Press
publist_id: '6515'
status: public
title: Balance between apical membrane growth and luminal matrix resistance determines
epithelial tubule shape
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2014'
...
---
_id: '926'
abstract:
- lang: eng
text: 'The regulation of cell growth in animal tissues is a question of critical
importance: most tissues contain different types of cells in interconversion and
the fraction of each type has to be controlled in a precise way, by mechanisms
that remain unclear. Here, we provide a theoretical framework for the homeostasis
of stem-cell-containing epithelial tissues using mechanical equations, which describe
the size of the tissue and kinetic equations, which describe the interconversions
of the cell populations. We show that several features, such as the evolution
of stem cell fractions during intestinal development, the shape of a developing
intestinal wall, as well as the increase in the proliferative compartment in cancer
initiation, can be studied and understood from generic modelling which does not
rely on a particular regulatory mechanism. Finally, inspired by recent experiments,
we propose a model where cell division rates are regulated by the mechanical stresses
in the epithelial sheet. We show that pressure-controlled growth can, in addition
to the previous features, also explain with few parameters the formation of stem
cell compartments as well as the morphologies observed when a colonic crypt becomes
cancerous. We also discuss optimal strategies of wound healing, in connection
with experiments on the cornea.'
acknowledgement: We thank Jens Elgeti and Silvia Fre for fruitful discussions.
article_processing_charge: No
author:
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Jacques
full_name: Prost, Jacques
last_name: Prost
- first_name: Jean
full_name: Joanny, Jean
last_name: Joanny
citation:
ama: Hannezo EB, Prost J, Joanny J. Growth homeostatic regulation and stem cell
dynamics in tissues. Journal of the Royal Society Interface. 2014;11(93).
doi:10.1098/rsif.2013.0895
apa: Hannezo, E. B., Prost, J., & Joanny, J. (2014). Growth homeostatic regulation
and stem cell dynamics in tissues. Journal of the Royal Society Interface.
Royal Society of London. https://doi.org/10.1098/rsif.2013.0895
chicago: Hannezo, Edouard B, Jacques Prost, and Jean Joanny. “Growth Homeostatic
Regulation and Stem Cell Dynamics in Tissues.” Journal of the Royal Society
Interface. Royal Society of London, 2014. https://doi.org/10.1098/rsif.2013.0895.
ieee: E. B. Hannezo, J. Prost, and J. Joanny, “Growth homeostatic regulation and
stem cell dynamics in tissues,” Journal of the Royal Society Interface,
vol. 11, no. 93. Royal Society of London, 2014.
ista: Hannezo EB, Prost J, Joanny J. 2014. Growth homeostatic regulation and stem
cell dynamics in tissues. Journal of the Royal Society Interface. 11(93).
mla: Hannezo, Edouard B., et al. “Growth Homeostatic Regulation and Stem Cell Dynamics
in Tissues.” Journal of the Royal Society Interface, vol. 11, no. 93, Royal
Society of London, 2014, doi:10.1098/rsif.2013.0895.
short: E.B. Hannezo, J. Prost, J. Joanny, Journal of the Royal Society Interface
11 (2014).
date_created: 2018-12-11T11:49:14Z
date_published: 2014-04-06T00:00:00Z
date_updated: 2021-01-12T08:21:57Z
day: '06'
doi: 10.1098/rsif.2013.0895
extern: '1'
intvolume: ' 11'
issue: '93'
language:
- iso: eng
month: '04'
oa_version: None
publication: Journal of the Royal Society Interface
publication_status: published
publisher: Royal Society of London
publist_id: '6516'
status: public
title: Growth homeostatic regulation and stem cell dynamics in tissues
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2014'
...
---
_id: '927'
abstract:
- lang: eng
text: Morphogenesis during embryo development requires the coordination of mechanical
forces to generate the macroscopic shapes of organs. We propose a minimal theoretical
model, based on cell adhesion and actomyosin contractility, which describes the
various shapes of epithelial cells and the bending and buckling of epithelial
sheets, as well as the relative stability of cellular tubes and spheres. We show
that, to understand these processes, a full 3D description of the cells is needed,
but that simple scaling laws can still be derived. The morphologies observed in
vivo can be understood as stable points of mechanical equations and the transitions
between them are either continuous or discontinuous. We then focus on epithelial
sheet bending, a ubiquitous morphogenetic process. We calculate the curvature
of an epithelium as a function of actin belt tension as well as of cell-cell and
and cell-substrate tension. The model allows for a comparison of the relative
stabilities of spherical or cylindrical cellular structures (acini or tubes).
Finally, we propose a unique type of buckling instability of epithelia, driven
by a flattening of individual cell shapes, and discuss experimental tests to verify
our predictions.
article_processing_charge: No
author:
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Jacques
full_name: Prost, Jacques
last_name: Prost
- first_name: Jean
full_name: Joanny, Jean
last_name: Joanny
citation:
ama: Hannezo EB, Prost J, Joanny J. Theory of epithelial sheet morphology in three
dimensions. PNAS. 2014;111(1):27-32. doi:10.1073/pnas.1312076111
apa: Hannezo, E. B., Prost, J., & Joanny, J. (2014). Theory of epithelial sheet
morphology in three dimensions. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1312076111
chicago: Hannezo, Edouard B, Jacques Prost, and Jean Joanny. “Theory of Epithelial
Sheet Morphology in Three Dimensions.” PNAS. National Academy of Sciences,
2014. https://doi.org/10.1073/pnas.1312076111.
ieee: E. B. Hannezo, J. Prost, and J. Joanny, “Theory of epithelial sheet morphology
in three dimensions,” PNAS, vol. 111, no. 1. National Academy of Sciences,
pp. 27–32, 2014.
ista: Hannezo EB, Prost J, Joanny J. 2014. Theory of epithelial sheet morphology
in three dimensions. PNAS. 111(1), 27–32.
mla: Hannezo, Edouard B., et al. “Theory of Epithelial Sheet Morphology in Three
Dimensions.” PNAS, vol. 111, no. 1, National Academy of Sciences, 2014,
pp. 27–32, doi:10.1073/pnas.1312076111.
short: E.B. Hannezo, J. Prost, J. Joanny, PNAS 111 (2014) 27–32.
date_created: 2018-12-11T11:49:14Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T08:21:58Z
day: '01'
doi: 10.1073/pnas.1312076111
extern: '1'
intvolume: ' 111'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 27 - 32
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '6517'
status: public
title: Theory of epithelial sheet morphology in three dimensions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 111
year: '2014'
...
---
_id: '9458'
abstract:
- lang: eng
text: Dnmt1 epigenetically propagates symmetrical CG methylation in many eukaryotes.
Their genomes are typically depleted of CG dinucleotides because of imperfect
repair of deaminated methylcytosines. Here, we extensively survey diverse species
lacking Dnmt1 and show that, surprisingly, symmetrical CG methylation is nonetheless
frequently present and catalyzed by a different DNA methyltransferase family,
Dnmt5. Numerous Dnmt5-containing organisms that diverged more than a billion years
ago exhibit clustered methylation, specifically in nucleosome linkers. Clustered
methylation occurs at unprecedented densities and directly disfavors nucleosomes,
contributing to nucleosome positioning between clusters. Dense methylation is
enabled by a regime of genomic sequence evolution that enriches CG dinucleotides
and drives the highest CG frequencies known. Species with linker methylation have
small, transcriptionally active nuclei that approach the physical limits of chromatin
compaction. These features constitute a previously unappreciated genome architecture,
in which dense methylation influences nucleosome positions, likely facilitating
nuclear processes under extreme spatial constraints.
article_processing_charge: No
article_type: original
author:
- first_name: Jason T.
full_name: Huff, Jason T.
last_name: Huff
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Huff JT, Zilberman D. Dnmt1-independent CG methylation contributes to nucleosome
positioning in diverse eukaryotes. Cell. 2014;156(6):1286-1297. doi:10.1016/j.cell.2014.01.029
apa: Huff, J. T., & Zilberman, D. (2014). Dnmt1-independent CG methylation contributes
to nucleosome positioning in diverse eukaryotes. Cell. Elsevier. https://doi.org/10.1016/j.cell.2014.01.029
chicago: Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation
Contributes to Nucleosome Positioning in Diverse Eukaryotes.” Cell. Elsevier,
2014. https://doi.org/10.1016/j.cell.2014.01.029.
ieee: J. T. Huff and D. Zilberman, “Dnmt1-independent CG methylation contributes
to nucleosome positioning in diverse eukaryotes,” Cell, vol. 156, no. 6.
Elsevier, pp. 1286–1297, 2014.
ista: Huff JT, Zilberman D. 2014. Dnmt1-independent CG methylation contributes to
nucleosome positioning in diverse eukaryotes. Cell. 156(6), 1286–1297.
mla: Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes
to Nucleosome Positioning in Diverse Eukaryotes.” Cell, vol. 156, no. 6,
Elsevier, 2014, pp. 1286–97, doi:10.1016/j.cell.2014.01.029.
short: J.T. Huff, D. Zilberman, Cell 156 (2014) 1286–1297.
date_created: 2021-06-04T12:00:16Z
date_published: 2014-03-13T00:00:00Z
date_updated: 2021-12-14T08:22:36Z
day: '13'
department:
- _id: DaZi
doi: 10.1016/j.cell.2014.01.029
extern: '1'
external_id:
pmid:
- '24630728'
intvolume: ' 156'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cell.2014.01.029
month: '03'
oa: 1
oa_version: Published Version
page: 1286-1297
pmid: 1
publication: Cell
publication_identifier:
eissn:
- 1097-4172
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse
eukaryotes
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 156
year: '2014'
...
---
_id: '9479'
abstract:
- lang: eng
text: Centromeres mediate chromosome segregation and are defined by the centromere-specific
histone H3 variant (CenH3)/centromere protein A (CENP-A). Removal of CenH3 from
centromeres is a general property of terminally differentiated cells, and the
persistence of CenH3 increases the risk of diseases such as cancer. However, active
mechanisms of centromere disassembly are unknown. Nondividing Arabidopsis pollen
vegetative cells, which transport engulfed sperm by extended tip growth, undergo
loss of CenH3; centromeric heterochromatin decondensation; and bulk activation
of silent rRNA genes, accompanied by their translocation into the nucleolus. Here,
we show that these processes are blocked by mutations in the evolutionarily conserved
AAA-ATPase molecular chaperone, CDC48A, homologous to yeast Cdc48 and human p97
proteins, both of which are implicated in ubiquitin/small ubiquitin-like modifier
(SUMO)-targeted protein degradation. We demonstrate that CDC48A physically associates
with its heterodimeric cofactor UFD1-NPL4, known to bind ubiquitin and SUMO, as
well as with SUMO1-modified CenH3 and mutations in NPL4 phenocopy cdc48a mutations.
In WT vegetative cell nuclei, genetically unlinked ribosomal DNA (rDNA) loci are
uniquely clustered together within the nucleolus and all major rRNA gene variants,
including those rDNA variants silenced in leaves, are transcribed. In cdc48a mutant
vegetative cell nuclei, however, these rDNA loci frequently colocalized with condensed
centromeric heterochromatin at the external periphery of the nucleolus. Our results
indicate that the CDC48ANPL4 complex actively removes sumoylated CenH3 from centromeres
and disrupts centromeric heterochromatin to release bulk rRNA genes into the nucleolus
for ribosome production, which fuels single nucleus-driven pollen tube growth
and is essential for plant reproduction.
article_processing_charge: No
article_type: original
author:
- first_name: Zsuzsanna
full_name: Mérai, Zsuzsanna
last_name: Mérai
- first_name: Nina
full_name: Chumak, Nina
last_name: Chumak
- first_name: Marcelina
full_name: García-Aguilar, Marcelina
last_name: García-Aguilar
- first_name: Tzung-Fu
full_name: Hsieh, Tzung-Fu
last_name: Hsieh
- first_name: Toshiro
full_name: Nishimura, Toshiro
last_name: Nishimura
- first_name: Vera K.
full_name: Schoft, Vera K.
last_name: Schoft
- first_name: János
full_name: Bindics, János
last_name: Bindics
- first_name: Lucyna
full_name: Ślusarz, Lucyna
last_name: Ślusarz
- first_name: Stéphanie
full_name: Arnoux, Stéphanie
last_name: Arnoux
- first_name: Susanne
full_name: Opravil, Susanne
last_name: Opravil
- first_name: Karl
full_name: Mechtler, Karl
last_name: Mechtler
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Hisashi
full_name: Tamaru, Hisashi
last_name: Tamaru
citation:
ama: Mérai Z, Chumak N, García-Aguilar M, et al. The AAA-ATPase molecular chaperone
Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and
activates ribosomal RNA genes. Proceedings of the National Academy of Sciences.
2014;111(45):16166-16171. doi:10.1073/pnas.1418564111
apa: Mérai, Z., Chumak, N., García-Aguilar, M., Hsieh, T.-F., Nishimura, T., Schoft,
V. K., … Tamaru, H. (2014). The AAA-ATPase molecular chaperone Cdc48/p97 disassembles
sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA
genes. Proceedings of the National Academy of Sciences. National Academy
of Sciences. https://doi.org/10.1073/pnas.1418564111
chicago: Mérai, Zsuzsanna, Nina Chumak, Marcelina García-Aguilar, Tzung-Fu Hsieh,
Toshiro Nishimura, Vera K. Schoft, János Bindics, et al. “The AAA-ATPase Molecular
Chaperone Cdc48/P97 Disassembles Sumoylated Centromeres, Decondenses Heterochromatin,
and Activates Ribosomal RNA Genes.” Proceedings of the National Academy of
Sciences. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1418564111.
ieee: Z. Mérai et al., “The AAA-ATPase molecular chaperone Cdc48/p97 disassembles
sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA
genes,” Proceedings of the National Academy of Sciences, vol. 111, no.
45. National Academy of Sciences, pp. 16166–16171, 2014.
ista: Mérai Z, Chumak N, García-Aguilar M, Hsieh T-F, Nishimura T, Schoft VK, Bindics
J, Ślusarz L, Arnoux S, Opravil S, Mechtler K, Zilberman D, Fischer RL, Tamaru
H. 2014. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated
centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. Proceedings
of the National Academy of Sciences. 111(45), 16166–16171.
mla: Mérai, Zsuzsanna, et al. “The AAA-ATPase Molecular Chaperone Cdc48/P97 Disassembles
Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA
Genes.” Proceedings of the National Academy of Sciences, vol. 111, no.
45, National Academy of Sciences, 2014, pp. 16166–71, doi:10.1073/pnas.1418564111.
short: Z. Mérai, N. Chumak, M. García-Aguilar, T.-F. Hsieh, T. Nishimura, V.K. Schoft,
J. Bindics, L. Ślusarz, S. Arnoux, S. Opravil, K. Mechtler, D. Zilberman, R.L.
Fischer, H. Tamaru, Proceedings of the National Academy of Sciences 111 (2014)
16166–16171.
date_created: 2021-06-07T07:23:43Z
date_published: 2014-11-11T00:00:00Z
date_updated: 2021-12-14T08:23:26Z
day: '11'
department:
- _id: DaZi
doi: 10.1073/pnas.1418564111
extern: '1'
external_id:
pmid:
- '25344531'
intvolume: ' 111'
issue: '45'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1418564111
month: '11'
oa: 1
oa_version: Published Version
page: 16166-16171
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres,
decondenses heterochromatin, and activates ribosomal RNA genes
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 111
year: '2014'
...
---
_id: '9519'
abstract:
- lang: eng
text: Transposons are selfish genetic sequences that can increase their copy number
and inflict substantial damage on their hosts. To combat these genomic parasites,
plants have evolved multiple pathways to identify and silence transposons by methylating
their DNA. Plants have also evolved mechanisms to limit the collateral damage
from the antitransposon machinery. In this review, we examine recent developments
that have elucidated many of the molecular workings of these pathways. We also
highlight the evidence that the methylation and demethylation pathways interact,
indicating that plants have a highly sophisticated, integrated system of transposon
defense that has an important role in the regulation of gene expression.
article_processing_charge: No
article_type: review
author:
- first_name: M. Yvonne
full_name: Kim, M. Yvonne
last_name: Kim
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Kim MY, Zilberman D. DNA methylation as a system of plant genomic immunity.
Trends in Plant Science. 2014;19(5):320-326. doi:10.1016/j.tplants.2014.01.014
apa: Kim, M. Y., & Zilberman, D. (2014). DNA methylation as a system of plant
genomic immunity. Trends in Plant Science. Elsevier. https://doi.org/10.1016/j.tplants.2014.01.014
chicago: Kim, M. Yvonne, and Daniel Zilberman. “DNA Methylation as a System of Plant
Genomic Immunity.” Trends in Plant Science. Elsevier, 2014. https://doi.org/10.1016/j.tplants.2014.01.014.
ieee: M. Y. Kim and D. Zilberman, “DNA methylation as a system of plant genomic
immunity,” Trends in Plant Science, vol. 19, no. 5. Elsevier, pp. 320–326,
2014.
ista: Kim MY, Zilberman D. 2014. DNA methylation as a system of plant genomic immunity.
Trends in Plant Science. 19(5), 320–326.
mla: Kim, M. Yvonne, and Daniel Zilberman. “DNA Methylation as a System of Plant
Genomic Immunity.” Trends in Plant Science, vol. 19, no. 5, Elsevier, 2014,
pp. 320–26, doi:10.1016/j.tplants.2014.01.014.
short: M.Y. Kim, D. Zilberman, Trends in Plant Science 19 (2014) 320–326.
date_created: 2021-06-07T14:38:09Z
date_published: 2014-05-04T00:00:00Z
date_updated: 2021-12-14T08:24:48Z
day: '04'
department:
- _id: DaZi
doi: 10.1016/j.tplants.2014.01.014
extern: '1'
external_id:
pmid:
- '24618094 '
intvolume: ' 19'
issue: '5'
language:
- iso: eng
month: '05'
oa_version: None
page: 320-326
pmid: 1
publication: Trends in Plant Science
publication_identifier:
eissn:
- 1878-4372
issn:
- 1360-1385
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA methylation as a system of plant genomic immunity
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 19
year: '2014'
...
---
_id: '9594'
abstract:
- lang: eng
text: Let d≥3 be a fixed integer. We give an asympotic formula for the expected
number of spanning trees in a uniformly random d-regular graph with n vertices.
(The asymptotics are as n→∞, restricted to even n if d is odd.) We also obtain
the asymptotic distribution of the number of spanning trees in a uniformly random
cubic graph, and conjecture that the corresponding result holds for arbitrary
(fixed) d. Numerical evidence is presented which supports our conjecture.
article_number: P1.45
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Catherine
full_name: Greenhill, Catherine
last_name: Greenhill
- first_name: Matthew Alan
full_name: Kwan, Matthew Alan
id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
last_name: Kwan
orcid: 0000-0002-4003-7567
- first_name: David
full_name: Wind, David
last_name: Wind
citation:
ama: Greenhill C, Kwan MA, Wind D. On the number of spanning trees in random regular
graphs. The Electronic Journal of Combinatorics. 2014;21(1). doi:10.37236/3752
apa: Greenhill, C., Kwan, M. A., & Wind, D. (2014). On the number of spanning
trees in random regular graphs. The Electronic Journal of Combinatorics.
The Electronic Journal of Combinatorics. https://doi.org/10.37236/3752
chicago: Greenhill, Catherine, Matthew Alan Kwan, and David Wind. “On the Number
of Spanning Trees in Random Regular Graphs.” The Electronic Journal of Combinatorics.
The Electronic Journal of Combinatorics, 2014. https://doi.org/10.37236/3752.
ieee: C. Greenhill, M. A. Kwan, and D. Wind, “On the number of spanning trees in
random regular graphs,” The Electronic Journal of Combinatorics, vol. 21,
no. 1. The Electronic Journal of Combinatorics, 2014.
ista: Greenhill C, Kwan MA, Wind D. 2014. On the number of spanning trees in random
regular graphs. The Electronic Journal of Combinatorics. 21(1), P1.45.
mla: Greenhill, Catherine, et al. “On the Number of Spanning Trees in Random Regular
Graphs.” The Electronic Journal of Combinatorics, vol. 21, no. 1, P1.45,
The Electronic Journal of Combinatorics, 2014, doi:10.37236/3752.
short: C. Greenhill, M.A. Kwan, D. Wind, The Electronic Journal of Combinatorics
21 (2014).
date_created: 2021-06-23T06:29:35Z
date_published: 2014-02-28T00:00:00Z
date_updated: 2023-02-23T14:02:12Z
day: '28'
doi: 10.37236/3752
extern: '1'
external_id:
arxiv:
- '1309.6710'
intvolume: ' 21'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.37236/3752
month: '02'
oa: 1
oa_version: Published Version
publication: The Electronic Journal of Combinatorics
publication_identifier:
eissn:
- 1077-8926
publication_status: published
publisher: The Electronic Journal of Combinatorics
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the number of spanning trees in random regular graphs
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 21
year: '2014'
...
---
_id: '96'
abstract:
- lang: eng
text: Multielectron spin qubits are demonstrated, and performance examined by comparing
coherent exchange oscillations in coupled single-electron and multielectron quantum
dots, measured in the same device. Fast (>1 GHz) exchange oscillations with
a quality factor Q∼15 are found for the multielectron case, compared to Q∼2 for
the single-electron case, the latter consistent with experiments in the literature.
A model of dephasing that includes voltage and hyperfine noise is developed that
is in good agreement with both single- and multielectron data, though in both
cases additional exchange-independent dephasing is needed to obtain quantitative
agreement across a broad parameter range.
acknowledgement: The research is supported by the Intelligence Advanced Research Projects
Activity (IARPA), through the Army Research Office Grant No. W911NF-12-1-0354, the
DARPA QuEST Program, the Department of Energy, Office of Science, and the Danish
National Research Foundation.
article_number: '026801'
arxiv: 1
author:
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
- first_name: Ferdinand
full_name: Kuemmeth, Ferdinand
last_name: Kuemmeth
- first_name: Micah
full_name: Hanson, Micah
last_name: Hanson
- first_name: Arthur
full_name: Gossard, Arthur
last_name: Gossard
- first_name: Charles
full_name: Marcus, Charles
last_name: Marcus
citation:
ama: Higginbotham AP, Kuemmeth F, Hanson M, Gossard A, Marcus C. Coherent operations
and screening in multielectron spin qubits. APS Physics, Physical Review Letters.
2014;112(2). doi:10.1103/PhysRevLett.112.026801
apa: Higginbotham, A. P., Kuemmeth, F., Hanson, M., Gossard, A., & Marcus, C.
(2014). Coherent operations and screening in multielectron spin qubits. APS
Physics, Physical Review Letters. American Physiological Society. https://doi.org/10.1103/PhysRevLett.112.026801
chicago: Higginbotham, Andrew P, Ferdinand Kuemmeth, Micah Hanson, Arthur Gossard,
and Charles Marcus. “Coherent Operations and Screening in Multielectron Spin Qubits.”
APS Physics, Physical Review Letters. American Physiological Society, 2014.
https://doi.org/10.1103/PhysRevLett.112.026801.
ieee: A. P. Higginbotham, F. Kuemmeth, M. Hanson, A. Gossard, and C. Marcus, “Coherent
operations and screening in multielectron spin qubits,” APS Physics, Physical
Review Letters, vol. 112, no. 2. American Physiological Society, 2014.
ista: Higginbotham AP, Kuemmeth F, Hanson M, Gossard A, Marcus C. 2014. Coherent
operations and screening in multielectron spin qubits. APS Physics, Physical Review
Letters. 112(2), 026801.
mla: Higginbotham, Andrew P., et al. “Coherent Operations and Screening in Multielectron
Spin Qubits.” APS Physics, Physical Review Letters, vol. 112, no. 2, 026801,
American Physiological Society, 2014, doi:10.1103/PhysRevLett.112.026801.
short: A.P. Higginbotham, F. Kuemmeth, M. Hanson, A. Gossard, C. Marcus, APS Physics,
Physical Review Letters 112 (2014).
date_created: 2018-12-11T11:44:36Z
date_published: 2014-01-14T00:00:00Z
date_updated: 2021-01-12T08:22:14Z
day: '14'
doi: 10.1103/PhysRevLett.112.026801
extern: '1'
external_id:
arxiv:
- '1306.2720'
intvolume: ' 112'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1306.2720
month: '01'
oa: 1
oa_version: Preprint
publication: APS Physics, Physical Review Letters
publication_status: published
publisher: American Physiological Society
publist_id: '7958'
quality_controlled: '1'
status: public
title: Coherent operations and screening in multielectron spin qubits
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2014'
...
---
_id: '9655'
abstract:
- lang: eng
text: Correlative microscopy incorporates the specificity of fluorescent protein
labeling into high-resolution electron micrographs. Several approaches exist for
correlative microscopy, most of which have used the green fluorescent protein
(GFP) as the label for light microscopy. Here we use chemical tagging and synthetic
fluorophores instead, in order to achieve protein-specific labeling, and to perform
multicolor imaging. We show that synthetic fluorophores preserve their post-embedding
fluorescence in the presence of uranyl acetate. Post-embedding fluorescence is
of such quality that the specimen can be prepared with identical protocols for
scanning electron microscopy (SEM) and transmission electron microscopy (TEM);
this is particularly valuable when singular or otherwise difficult samples are
examined. We show that synthetic fluorophores give bright, well-resolved signals
in super-resolution light microscopy, enabling us to superimpose light microscopic
images with a precision of up to 25 nm in the x–y plane on electron micrographs.
To exemplify the preservation quality of our new method we visualize the molecular
arrangement of cadherins in adherens junctions of mouse epithelial cells.
article_processing_charge: No
article_type: original
author:
- first_name: Mario
full_name: Perkovic, Mario
last_name: Perkovic
- first_name: Michael
full_name: Kunz, Michael
last_name: Kunz
- first_name: Ulrike
full_name: Endesfelder, Ulrike
last_name: Endesfelder
- first_name: Stefanie
full_name: Bunse, Stefanie
last_name: Bunse
- first_name: Christoph
full_name: Wigge, Christoph
last_name: Wigge
- first_name: Zhou
full_name: Yu, Zhou
last_name: Yu
- first_name: Victor-Valentin
full_name: Hodirnau, Victor-Valentin
id: 3661B498-F248-11E8-B48F-1D18A9856A87
last_name: Hodirnau
- first_name: Margot P.
full_name: Scheffer, Margot P.
last_name: Scheffer
- first_name: Anja
full_name: Seybert, Anja
last_name: Seybert
- first_name: Sebastian
full_name: Malkusch, Sebastian
last_name: Malkusch
- first_name: Erin M.
full_name: Schuman, Erin M.
last_name: Schuman
- first_name: Mike
full_name: Heilemann, Mike
last_name: Heilemann
- first_name: Achilleas S.
full_name: Frangakis, Achilleas S.
last_name: Frangakis
citation:
ama: Perkovic M, Kunz M, Endesfelder U, et al. Correlative light- and electron microscopy
with chemical tags. Journal of Structural Biology. 2014;186(2):205-213.
doi:10.1016/j.jsb.2014.03.018
apa: Perkovic, M., Kunz, M., Endesfelder, U., Bunse, S., Wigge, C., Yu, Z., … Frangakis,
A. S. (2014). Correlative light- and electron microscopy with chemical tags. Journal
of Structural Biology. Elsevier. https://doi.org/10.1016/j.jsb.2014.03.018
chicago: Perkovic, Mario, Michael Kunz, Ulrike Endesfelder, Stefanie Bunse, Christoph
Wigge, Zhou Yu, Victor-Valentin Hodirnau, et al. “Correlative Light- and Electron
Microscopy with Chemical Tags.” Journal of Structural Biology. Elsevier,
2014. https://doi.org/10.1016/j.jsb.2014.03.018.
ieee: M. Perkovic et al., “Correlative light- and electron microscopy with
chemical tags,” Journal of Structural Biology, vol. 186, no. 2. Elsevier,
pp. 205–213, 2014.
ista: Perkovic M, Kunz M, Endesfelder U, Bunse S, Wigge C, Yu Z, Hodirnau V-V, Scheffer
MP, Seybert A, Malkusch S, Schuman EM, Heilemann M, Frangakis AS. 2014. Correlative
light- and electron microscopy with chemical tags. Journal of Structural Biology.
186(2), 205–213.
mla: Perkovic, Mario, et al. “Correlative Light- and Electron Microscopy with Chemical
Tags.” Journal of Structural Biology, vol. 186, no. 2, Elsevier, 2014,
pp. 205–13, doi:10.1016/j.jsb.2014.03.018.
short: M. Perkovic, M. Kunz, U. Endesfelder, S. Bunse, C. Wigge, Z. Yu, V.-V. Hodirnau,
M.P. Scheffer, A. Seybert, S. Malkusch, E.M. Schuman, M. Heilemann, A.S. Frangakis,
Journal of Structural Biology 186 (2014) 205–213.
date_created: 2021-07-14T09:05:42Z
date_published: 2014-05-01T00:00:00Z
date_updated: 2021-07-22T08:26:32Z
day: '01'
ddc:
- '570'
doi: 10.1016/j.jsb.2014.03.018
extern: '1'
external_id:
pmid:
- '24698954'
file:
- access_level: open_access
checksum: a322991b43cdc5935c99db88d285aa3a
content_type: application/pdf
creator: asandaue
date_created: 2021-07-22T08:06:34Z
date_updated: 2021-07-22T08:06:34Z
file_id: '9701'
file_name: 2014_JournalOfStructuralBiology_Perkovic.pdf
file_size: 3454628
relation: main_file
success: 1
file_date_updated: 2021-07-22T08:06:34Z
has_accepted_license: '1'
intvolume: ' 186'
issue: '2'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/3.0/
month: '05'
oa: 1
oa_version: Published Version
page: 205-213
pmid: 1
publication: Journal of Structural Biology
publication_identifier:
issn:
- 1047-8477
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Correlative light- and electron microscopy with chemical tags
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND
3.0)
short: CC BY-NC-ND (3.0)
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 186
year: '2014'
...
---
_id: '9662'
abstract:
- lang: eng
text: Fractionation of isotopes among distinct molecules or phases is a quantum
effect which is often exploited to obtain insights on reaction mechanisms, biochemical,
geochemical, and atmospheric phenomena. Accurate evaluation of isotope ratios
in atomistic simulations is challenging, because one needs to perform a thermodynamic
integration with respect to the isotope mass, along with time-consuming path integral
calculations. By re-formulating the problem as a particle exchange in the ring
polymer partition function, we derive new estimators giving direct access to the
differential partitioning of isotopes, which can simplify the calculations by
avoiding thermodynamic integration. We demonstrate the efficiency of these estimators
by applying them to investigate the isotope fractionation ratios in the gas-phase
Zundel cation, and in a few simple hydrocarbons.
article_number: '244112'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Michele
full_name: Ceriotti, Michele
last_name: Ceriotti
citation:
ama: Cheng B, Ceriotti M. Direct path integral estimators for isotope fractionation
ratios. The Journal of Chemical Physics. 2014;141(24). doi:10.1063/1.4904293
apa: Cheng, B., & Ceriotti, M. (2014). Direct path integral estimators for isotope
fractionation ratios. The Journal of Chemical Physics. AIP Publishing.
https://doi.org/10.1063/1.4904293
chicago: Cheng, Bingqing, and Michele Ceriotti. “Direct Path Integral Estimators
for Isotope Fractionation Ratios.” The Journal of Chemical Physics. AIP
Publishing, 2014. https://doi.org/10.1063/1.4904293.
ieee: B. Cheng and M. Ceriotti, “Direct path integral estimators for isotope fractionation
ratios,” The Journal of Chemical Physics, vol. 141, no. 24. AIP Publishing,
2014.
ista: Cheng B, Ceriotti M. 2014. Direct path integral estimators for isotope fractionation
ratios. The Journal of Chemical Physics. 141(24), 244112.
mla: Cheng, Bingqing, and Michele Ceriotti. “Direct Path Integral Estimators for
Isotope Fractionation Ratios.” The Journal of Chemical Physics, vol. 141,
no. 24, 244112, AIP Publishing, 2014, doi:10.1063/1.4904293.
short: B. Cheng, M. Ceriotti, The Journal of Chemical Physics 141 (2014).
date_created: 2021-07-15T09:22:49Z
date_published: 2014-12-28T00:00:00Z
date_updated: 2021-08-09T12:32:24Z
day: '28'
doi: 10.1063/1.4904293
extern: '1'
external_id:
arxiv:
- '1412.1308'
pmid:
- '25554138'
intvolume: ' 141'
issue: '24'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1412.1308
month: '12'
oa: 1
oa_version: Preprint
pmid: 1
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Direct path integral estimators for isotope fractionation ratios
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 141
year: '2014'
...
---
_id: '9686'
abstract:
- lang: eng
text: It is well known that ultrasonic vibration can soften metals, and this phenomenon
has been widely exploited in industrial applications concerning metal forming
and bonding. Recent experiments show that the simultaneous application of oscillatory
stresses from audible to ultrasonic frequency ranges can lead to not only softening
but also significant dislocation annihilation and subgrain formation in metal
samples from the nano- to macro-size range. These findings indicate that the existing
understanding of ultrasound softening – that the vibrations either impose additional
stress waves to augment the quasi-static applied load, or cause heating of the
metal, whereas the metal’s intrinsic deformation resistance or mechanism remains
unaltered – is far from complete. To understand the softening and the associated
enhanced subgrain formation and dislocation annihilation, a new simulator based
on the dynamics of dislocation-density functions is employed. This new simulator
considers the flux, production and annihilation, as well as the Taylor and elastic
interactions between dislocation densities. Softening during vibrations as well
as enhanced cell formation is predicted. The simulations reveal the main mechanism
for subcell formation under oscillatory loadings to be the enhanced elimination
of statistically stored dislocations (SSDs) by the oscillatory stress, leaving
behind geometrically necessary dislocations with low Schmid factors which then
form the subgrain walls. The oscillatory stress helps the depletion of the SSDs,
because the chance for them to meet up and annihilate is increased with reversals
of dislocation motions. This is the first simulation effort to successfully predict
the cell formation phenomenon under vibratory loadings.
article_processing_charge: No
article_type: original
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: H.S.
full_name: Leung, H.S.
last_name: Leung
- first_name: A.H.W.
full_name: Ngan, A.H.W.
last_name: Ngan
citation:
ama: Cheng B, Leung HS, Ngan AHW. Strength of metals under vibrations – dislocation-density-function
dynamics simulations. Philosophical Magazine. 2014;95(16-18):1845-1865.
doi:10.1080/14786435.2014.897008
apa: Cheng, B., Leung, H. S., & Ngan, A. H. W. (2014). Strength of metals under
vibrations – dislocation-density-function dynamics simulations. Philosophical
Magazine. Taylor & Francis. https://doi.org/10.1080/14786435.2014.897008
chicago: Cheng, Bingqing, H.S. Leung, and A.H.W. Ngan. “Strength of Metals under
Vibrations – Dislocation-Density-Function Dynamics Simulations.” Philosophical
Magazine. Taylor & Francis, 2014. https://doi.org/10.1080/14786435.2014.897008.
ieee: B. Cheng, H. S. Leung, and A. H. W. Ngan, “Strength of metals under vibrations
– dislocation-density-function dynamics simulations,” Philosophical Magazine,
vol. 95, no. 16–18. Taylor & Francis, pp. 1845–1865, 2014.
ista: Cheng B, Leung HS, Ngan AHW. 2014. Strength of metals under vibrations – dislocation-density-function
dynamics simulations. Philosophical Magazine. 95(16–18), 1845–1865.
mla: Cheng, Bingqing, et al. “Strength of Metals under Vibrations – Dislocation-Density-Function
Dynamics Simulations.” Philosophical Magazine, vol. 95, no. 16–18, Taylor
& Francis, 2014, pp. 1845–65, doi:10.1080/14786435.2014.897008.
short: B. Cheng, H.S. Leung, A.H.W. Ngan, Philosophical Magazine 95 (2014) 1845–1865.
date_created: 2021-07-19T09:27:15Z
date_published: 2014-06-23T00:00:00Z
date_updated: 2023-02-23T14:04:59Z
day: '23'
doi: 10.1080/14786435.2014.897008
extern: '1'
intvolume: ' 95'
issue: 16-18
language:
- iso: eng
month: '06'
oa_version: None
page: 1845-1865
publication: Philosophical Magazine
publication_identifier:
eissn:
- 1478-6443
issn:
- 1478-6435
publication_status: published
publisher: Taylor & Francis
quality_controlled: '1'
scopus_import: '1'
status: public
title: Strength of metals under vibrations – dislocation-density-function dynamics
simulations
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 95
year: '2014'
...
---
_id: '10382'
abstract:
- lang: eng
text: 'Protein oligomers have been implicated as toxic agents in a wide range of
amyloid-related diseases. However, it has remained unsolved whether the oligomers
are a necessary step in the formation of amyloid fibrils or just a dangerous byproduct.
Analogously, it has not been resolved if the amyloid nucleation process is a classical
one-step nucleation process or a two-step process involving prenucleation clusters.
We use coarse-grained computer simulations to study the effect of nonspecific
attractions between peptides on the primary nucleation process underlying amyloid
fibrillization. We find that, for peptides that do not attract, the classical
one-step nucleation mechanism is possible but only at nonphysiologically high
peptide concentrations. At low peptide concentrations, which mimic the physiologically
relevant regime, attractive interpeptide interactions are essential for fibril
formation. Nucleation then inevitably takes place through a two-step mechanism
involving prefibrillar oligomers. We show that oligomers not only help peptides
meet each other but also, create an environment that facilitates the conversion
of monomers into the β-sheet–rich form characteristic of fibrils. Nucleation typically
does not proceed through the most prevalent oligomers but through an oligomer
size that is only observed in rare fluctuations, which is why such aggregates
might be hard to capture experimentally. Finally, we find that the nucleation
of amyloid fibrils cannot be described by classical nucleation theory: in the
two-step mechanism, the critical nucleus size increases with increases in both
concentration and interpeptide interactions, which is in direct contrast with
predictions from classical nucleation theory.'
acknowledgement: We thank Michele Vendruscolo, Iskra Staneva, and William M. Jacobs,
for helpful discussions. A.Š. acknowledges support from the Human Frontier Science
Program and Emmanuel College. Y.C.C. and D.F. are supported by Engineering and Physical
Sciences Research Council Programme Grant EP/I001352/1. T.P.J.K. acknowledges the
Frances and Augustus Newman Foundation, the European Research Council, and the Biotechnology
and Biological Sciences Research Council. D.F. acknowledges European Research Council
Advanced Grant 227758.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Yassmine C.
full_name: Chebaro, Yassmine C.
last_name: Chebaro
- first_name: Tuomas P. J.
full_name: Knowles, Tuomas P. J.
last_name: Knowles
- first_name: Daan
full_name: Frenkel, Daan
last_name: Frenkel
citation:
ama: Šarić A, Chebaro YC, Knowles TPJ, Frenkel D. Crucial role of nonspecific interactions
in amyloid nucleation. Proceedings of the National Academy of Sciences.
2014;111(50):17869-17874. doi:10.1073/pnas.1410159111
apa: Šarić, A., Chebaro, Y. C., Knowles, T. P. J., & Frenkel, D. (2014). Crucial
role of nonspecific interactions in amyloid nucleation. Proceedings of the
National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1410159111
chicago: Šarić, Anđela, Yassmine C. Chebaro, Tuomas P. J. Knowles, and Daan Frenkel.
“Crucial Role of Nonspecific Interactions in Amyloid Nucleation.” Proceedings
of the National Academy of Sciences. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1410159111.
ieee: A. Šarić, Y. C. Chebaro, T. P. J. Knowles, and D. Frenkel, “Crucial role of
nonspecific interactions in amyloid nucleation,” Proceedings of the National
Academy of Sciences, vol. 111, no. 50. National Academy of Sciences, pp. 17869–17874,
2014.
ista: Šarić A, Chebaro YC, Knowles TPJ, Frenkel D. 2014. Crucial role of nonspecific
interactions in amyloid nucleation. Proceedings of the National Academy of Sciences.
111(50), 17869–17874.
mla: Šarić, Anđela, et al. “Crucial Role of Nonspecific Interactions in Amyloid
Nucleation.” Proceedings of the National Academy of Sciences, vol. 111,
no. 50, National Academy of Sciences, 2014, pp. 17869–74, doi:10.1073/pnas.1410159111.
short: A. Šarić, Y.C. Chebaro, T.P.J. Knowles, D. Frenkel, Proceedings of the National
Academy of Sciences 111 (2014) 17869–17874.
date_created: 2021-11-29T13:09:53Z
date_published: 2014-12-01T00:00:00Z
date_updated: 2021-11-29T13:29:05Z
day: '01'
doi: 10.1073/pnas.1410159111
extern: '1'
external_id:
arxiv:
- '1412.0897'
pmid:
- '25453085'
intvolume: ' 111'
issue: '50'
keyword:
- multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.pnas.org/content/111/50/17869
month: '12'
oa: 1
oa_version: Published Version
page: 17869-17874
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Crucial role of nonspecific interactions in amyloid nucleation
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 111
year: '2014'
...
---
_id: '10383'
abstract:
- lang: eng
text: We use numerical simulations to compute the equation of state of a suspension
of spherical self-propelled nanoparticles in two and three dimensions. We study
in detail the effect of excluded volume interactions and confinement as a function
of the system's temperature, concentration, and strength of the propulsion. We
find a striking nonmonotonic dependence of the pressure on the temperature and
provide simple scaling arguments to predict and explain the occurrence of such
anomalous behavior. We explicitly show how our results have important implications
for the effective forces on passive components suspended in a bath of active particles.
article_number: '052303'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: S. A.
full_name: Mallory, S. A.
last_name: Mallory
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: C.
full_name: Valeriani, C.
last_name: Valeriani
- first_name: A.
full_name: Cacciuto, A.
last_name: Cacciuto
citation:
ama: Mallory SA, Šarić A, Valeriani C, Cacciuto A. Anomalous thermomechanical properties
of a self-propelled colloidal fluid. Physical Review E. 2014;89(5). doi:10.1103/physreve.89.052303
apa: Mallory, S. A., Šarić, A., Valeriani, C., & Cacciuto, A. (2014). Anomalous
thermomechanical properties of a self-propelled colloidal fluid. Physical Review
E. American Physical Society. https://doi.org/10.1103/physreve.89.052303
chicago: Mallory, S. A., Anđela Šarić, C. Valeriani, and A. Cacciuto. “Anomalous
Thermomechanical Properties of a Self-Propelled Colloidal Fluid.” Physical
Review E. American Physical Society, 2014. https://doi.org/10.1103/physreve.89.052303.
ieee: S. A. Mallory, A. Šarić, C. Valeriani, and A. Cacciuto, “Anomalous thermomechanical
properties of a self-propelled colloidal fluid,” Physical Review E, vol.
89, no. 5. American Physical Society, 2014.
ista: Mallory SA, Šarić A, Valeriani C, Cacciuto A. 2014. Anomalous thermomechanical
properties of a self-propelled colloidal fluid. Physical Review E. 89(5), 052303.
mla: Mallory, S. A., et al. “Anomalous Thermomechanical Properties of a Self-Propelled
Colloidal Fluid.” Physical Review E, vol. 89, no. 5, 052303, American Physical
Society, 2014, doi:10.1103/physreve.89.052303.
short: S.A. Mallory, A. Šarić, C. Valeriani, A. Cacciuto, Physical Review E 89 (2014).
date_created: 2021-11-29T13:10:33Z
date_published: 2014-05-06T00:00:00Z
date_updated: 2021-11-29T13:29:01Z
day: '06'
doi: 10.1103/physreve.89.052303
extern: '1'
external_id:
arxiv:
- '1310.0826'
pmid:
- '25353796'
intvolume: ' 89'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1310.0826
month: '05'
oa: 1
oa_version: Preprint
pmid: 1
publication: Physical Review E
publication_identifier:
eissn:
- 1550-2376
issn:
- 1539-3755
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Anomalous thermomechanical properties of a self-propelled colloidal fluid
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 89
year: '2014'
...
---
_id: '1058'
abstract:
- lang: eng
text: Diffraction-unlimited far-field super-resolution fluorescence (nanoscopy)
methods typically rely on transiently transferring fluorophores between two states,
whereby this transfer is usually laid out as a switch. However, depending on whether
this is induced in a spatially controlled manner using a pattern of light (coordinate-targeted)
or stochastically on a single-molecule basis, specific requirements on the fluorophores
are imposed. Therefore, the fluorophores are usually utilized just for one class
of methods only. In this study we demonstrate that the reversibly switchable fluorescent
protein Dreiklang enables live-cell recordings in both spatially controlled and
stochastic modes. We show that the Dreiklang chromophore entails three different
light-induced switching mechanisms, namely a reversible photochemical one, off-switching
by stimulated emission, and a reversible transfer to a long-lived dark state from
the S1 state, all of which can be utilized to overcome the diffraction barrier.
We also find that for the single-molecule- based stochastic GSDIM approach (ground-state
depletion followed by individual molecule return), Dreiklang provides a larger
number of on-off localization events as compared to its progenitor Citrine. Altogether,
Dreiklang is a versatile probe for essentially all popular forms of live-cell
fluorescence nanoscopy.
article_processing_charge: No
author:
- first_name: Nickels
full_name: Jensen, Nickels
last_name: Jensen
- 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: Katrin
full_name: Willig, Katrin
last_name: Willig
- first_name: Flavie
full_name: Lavoie Cardinal, Flavie
last_name: Lavoie Cardinal
- first_name: Tanja
full_name: Brakemann, Tanja
last_name: Brakemann
- first_name: Stefan
full_name: Hell, Stefan
last_name: Hell
- first_name: Stefan
full_name: Jakobs, Stefan
last_name: Jakobs
citation:
ama: Jensen N, Danzl JG, Willig K, et al. Coordinate-targeted and coordinate-stochastic
super-resolution microscopy with the reversibly switchable fluorescent protein
dreiklang. ChemPhysChem. 2014;15(4):756-762. doi:10.1002/cphc.201301034
apa: Jensen, N., Danzl, J. G., Willig, K., Lavoie Cardinal, F., Brakemann, T., Hell,
S., & Jakobs, S. (2014). Coordinate-targeted and coordinate-stochastic super-resolution
microscopy with the reversibly switchable fluorescent protein dreiklang. ChemPhysChem.
Wiley-Blackwell. https://doi.org/10.1002/cphc.201301034
chicago: Jensen, Nickels, Johann G Danzl, Katrin Willig, Flavie Lavoie Cardinal,
Tanja Brakemann, Stefan Hell, and Stefan Jakobs. “Coordinate-Targeted and Coordinate-Stochastic
Super-Resolution Microscopy with the Reversibly Switchable Fluorescent Protein
Dreiklang.” ChemPhysChem. Wiley-Blackwell, 2014. https://doi.org/10.1002/cphc.201301034.
ieee: N. Jensen et al., “Coordinate-targeted and coordinate-stochastic super-resolution
microscopy with the reversibly switchable fluorescent protein dreiklang,” ChemPhysChem,
vol. 15, no. 4. Wiley-Blackwell, pp. 756–762, 2014.
ista: Jensen N, Danzl JG, Willig K, Lavoie Cardinal F, Brakemann T, Hell S, Jakobs
S. 2014. Coordinate-targeted and coordinate-stochastic super-resolution microscopy
with the reversibly switchable fluorescent protein dreiklang. ChemPhysChem. 15(4),
756–762.
mla: Jensen, Nickels, et al. “Coordinate-Targeted and Coordinate-Stochastic Super-Resolution
Microscopy with the Reversibly Switchable Fluorescent Protein Dreiklang.” ChemPhysChem,
vol. 15, no. 4, Wiley-Blackwell, 2014, pp. 756–62, doi:10.1002/cphc.201301034.
short: N. Jensen, J.G. Danzl, K. Willig, F. Lavoie Cardinal, T. Brakemann, S. Hell,
S. Jakobs, ChemPhysChem 15 (2014) 756–762.
date_created: 2018-12-11T11:49:55Z
date_published: 2014-03-17T00:00:00Z
date_updated: 2021-01-12T06:47:58Z
day: '17'
doi: 10.1002/cphc.201301034
extern: '1'
intvolume: ' 15'
issue: '4'
language:
- iso: eng
month: '03'
oa_version: None
page: 756 - 762
publication: ChemPhysChem
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6332'
status: public
title: Coordinate-targeted and coordinate-stochastic super-resolution microscopy with
the reversibly switchable fluorescent protein dreiklang
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2014'
...
---
_id: '118'
abstract:
- lang: eng
text: While the penetration of objects into granular media is well-studied, there
is little understanding of how objects settle in gravities, geff, different from
that of Earth - a scenario potentially relevant to the geomorphology of planets
and asteroids and also to their exploration using man-made devices. By conducting
experiments in an accelerating frame, we explore geff ranging from 0.4 g to 1.2
g. Surprisingly, we find that the rest depth is independent of geff and also that
the time required for the object to come to rest scales like geff-1/2. With discrete
element modeling simulations, we reproduce the experimental results and extend
the range of geff to objects as small as asteroids and as large as Jupiter. Our
results shed light on the initial stage of sedimentation into dry granular media
across a range of celestial bodies and also have implications for the design of
man-made, extraterrestrial vehicles and structures. Key Points The settling depth
in granular media is independent of gravity The settling time scales like g-1/2
Layering driven by granular sedimentation should be similar.
acknowledgement: 'The Spanish MINECO project FIS2011-26675, the PIUNA program (U.
Navarra), and the Project 29942WL (Fonds de Solidarité Prioritaire France-Cuba)
have partially supported this research. '
author:
- first_name: Ernesto
full_name: Altshuler, Ernesto
last_name: Altshuler
- first_name: H
full_name: Torres, H
last_name: Torres
- first_name: A
full_name: González_Pita, A
last_name: González_Pita
- first_name: Colina G
full_name: Sánchez, Colina G
last_name: Sánchez
- first_name: Carlos
full_name: Pérez Penichet, Carlos
last_name: Pérez Penichet
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
- first_name: Rauól
full_name: Hidalgo, Rauól
last_name: Hidalgo
citation:
ama: Altshuler E, Torres H, González_Pita A, et al. Settling into dry granular media
in different gravities. Geophysical Research Letters. 2014;41(9):3032-3037.
doi:10.1002/2014GL059229
apa: Altshuler, E., Torres, H., González_Pita, A., Sánchez, C. G., Pérez Penichet,
C., Waitukaitis, S. R., & Hidalgo, R. (2014). Settling into dry granular media
in different gravities. Geophysical Research Letters. Wiley-Blackwell.
https://doi.org/10.1002/2014GL059229
chicago: Altshuler, Ernesto, H Torres, A González_Pita, Colina G Sánchez, Carlos
Pérez Penichet, Scott R Waitukaitis, and Rauól Hidalgo. “Settling into Dry Granular
Media in Different Gravities.” Geophysical Research Letters. Wiley-Blackwell,
2014. https://doi.org/10.1002/2014GL059229.
ieee: E. Altshuler et al., “Settling into dry granular media in different
gravities,” Geophysical Research Letters, vol. 41, no. 9. Wiley-Blackwell,
pp. 3032–3037, 2014.
ista: Altshuler E, Torres H, González_Pita A, Sánchez CG, Pérez Penichet C, Waitukaitis
SR, Hidalgo R. 2014. Settling into dry granular media in different gravities.
Geophysical Research Letters. 41(9), 3032–3037.
mla: Altshuler, Ernesto, et al. “Settling into Dry Granular Media in Different Gravities.”
Geophysical Research Letters, vol. 41, no. 9, Wiley-Blackwell, 2014, pp.
3032–37, doi:10.1002/2014GL059229.
short: E. Altshuler, H. Torres, A. González_Pita, C.G. Sánchez, C. Pérez Penichet,
S.R. Waitukaitis, R. Hidalgo, Geophysical Research Letters 41 (2014) 3032–3037.
date_created: 2018-12-11T11:44:43Z
date_published: 2014-05-16T00:00:00Z
date_updated: 2021-01-12T06:48:53Z
day: '16'
doi: 10.1002/2014GL059229
extern: '1'
intvolume: ' 41'
issue: '9'
language:
- iso: eng
month: '05'
oa_version: None
page: 3032 - 3037
publication: Geophysical Research Letters
publication_status: published
publisher: Wiley-Blackwell
publist_id: '7936'
quality_controlled: '1'
status: public
title: Settling into dry granular media in different gravities
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 41
year: '2014'
...
---
_id: '11855'
abstract:
- lang: eng
text: 'The decremental single-source shortest paths (SSSP) problem concerns maintaining
the distances between a given source node s to every node in an n-node m-edge
graph G undergoing edge deletions. While its static counterpart can be easily
solved in near-linear time, this decremental problem is much more challenging
even in the undirected unweighted case. In this case, the classic O(mn) total
update time of Even and Shiloach (JACM 1981) has been the fastest known algorithm
for three decades. With the loss of a (1 + ε)-approximation factor, the running
time was recently improved to O(n 2+o(1) ) by Bernstein and Roditty (SODA 2011),
and more recently to O(n 1.8+o(1) + m 1+o(1) ) by Henzinger, Krinninger, and Nanongkai
(SODA 2014). In this paper, we finally bring the running time of this case down
to near-linear: We give a (1 + ε)-approximation algorithm with O(m 1+o(1) ) total
update time, thus obtaining near-linear time. Moreover, we obtain O(m 1+o(1) log
W) time for the weighted case, where the edge weights are integers from 1 to W.
The only prior work on weighted graphs in o(mn log W) time is the O(mn 0.986 log
W)-time algorithm by Henzinger, Krinninger, and Nanongkai (STOC 2014) which works
for the general weighted directed case. In contrast to the previous results which
rely on maintaining a sparse emulator, our algorithm relies on maintaining a so-called
sparse (d, ε)-hop set introduced by Cohen (JACM 2000) in the PRAM literature.
A (d, ε)-hop set of a graph G = (V, E) is a set E'' of weighted edges such that
the distance between any pair of nodes in G can be (1 + ε)-approximated by their
d-hop distance (given by a path containing at most d edges) on G''=(V, E∪E'').
Our algorithm can maintain an (n o(1) , ε)-hop set of near-linear size in near-linear
time under edge deletions. It is the first of its kind to the best of our knowledge.
To maintain the distances on this hop set, we develop a monotone bounded-hop Even-Shiloach
tree. It results from extending and combining the monotone Even-Shiloach tree
of Henzinger, Krinninger, and Nanongkai (FOCS 2013) with the bounded-hop SSSP
technique of Bernstein (STOC 2013). These two new tools might be of independent
interest.'
article_processing_charge: No
arxiv: 1
author:
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Sebastian
full_name: Krinninger, Sebastian
last_name: Krinninger
- first_name: Danupon
full_name: Nanongkai, Danupon
last_name: Nanongkai
citation:
ama: 'Henzinger MH, Krinninger S, Nanongkai D. Decremental single-source shortest
paths on undirected graphs in near-linear total update time. In: 55th Annual
Symposium on Foundations of Computer Science. Institute of Electrical and
Electronics Engineers; 2014:146-155. doi:10.1109/focs.2014.24'
apa: 'Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2014). Decremental
single-source shortest paths on undirected graphs in near-linear total update
time. In 55th Annual Symposium on Foundations of Computer Science (pp.
146–155). Philadelphia, PA, United States: Institute of Electrical and Electronics
Engineers. https://doi.org/10.1109/focs.2014.24'
chicago: Henzinger, Monika H, Sebastian Krinninger, and Danupon Nanongkai. “Decremental
Single-Source Shortest Paths on Undirected Graphs in near-Linear Total Update
Time.” In 55th Annual Symposium on Foundations of Computer Science, 146–55.
Institute of Electrical and Electronics Engineers, 2014. https://doi.org/10.1109/focs.2014.24.
ieee: M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Decremental single-source
shortest paths on undirected graphs in near-linear total update time,” in 55th
Annual Symposium on Foundations of Computer Science, Philadelphia, PA, United
States, 2014, pp. 146–155.
ista: 'Henzinger MH, Krinninger S, Nanongkai D. 2014. Decremental single-source
shortest paths on undirected graphs in near-linear total update time. 55th Annual
Symposium on Foundations of Computer Science. FOCS: Annual Symposium on Foundations
of Computer Science, 146–155.'
mla: Henzinger, Monika H., et al. “Decremental Single-Source Shortest Paths on Undirected
Graphs in near-Linear Total Update Time.” 55th Annual Symposium on Foundations
of Computer Science, Institute of Electrical and Electronics Engineers, 2014,
pp. 146–55, doi:10.1109/focs.2014.24.
short: M.H. Henzinger, S. Krinninger, D. Nanongkai, in:, 55th Annual Symposium on
Foundations of Computer Science, Institute of Electrical and Electronics Engineers,
2014, pp. 146–155.
conference:
end_date: 2014-10-21
location: Philadelphia, PA, United States
name: 'FOCS: Annual Symposium on Foundations of Computer Science'
start_date: 2014-10-18
date_created: 2022-08-16T08:14:33Z
date_published: 2014-10-01T00:00:00Z
date_updated: 2023-02-21T16:27:34Z
day: '01'
doi: 10.1109/focs.2014.24
extern: '1'
external_id:
arxiv:
- '1402.0054'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1402.0054
month: '10'
oa: 1
oa_version: Preprint
page: 146-155
publication: 55th Annual Symposium on Foundations of Computer Science
publication_identifier:
eisbn:
- 978-1-4799-6517-5
issn:
- 0272-5428
publication_status: published
publisher: Institute of Electrical and Electronics Engineers
quality_controlled: '1'
related_material:
record:
- id: '11768'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Decremental single-source shortest paths on undirected graphs in near-linear
total update time
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '11870'
abstract:
- lang: eng
text: "We consider dynamic algorithms for maintaining Single-Source Reachability
(SSR) and approximate Single-Source Shortest Paths (SSSP) on n-node m-edge directed
graphs under edge deletions (decremental algorithms). The previous fastest algorithm
for SSR and SSSP goes back three decades to Even and Shiloach (JACM 1981); it
has O(1) query time and O(mn) total update time (i.e., linear amortized update
time if all edges are deleted). This algorithm serves as a building block for
several other dynamic algorithms. The question whether its total update time can
be improved is a major, long standing, open problem.\r\n\r\nIn this paper, we
answer this question affirmatively. We obtain a randomized algorithm which, in
a simplified form, achieves an Õ(mn0.984) expected total update time for SSR and
(1 + ε)-approximate SSSP, where Õ(·) hides poly log n. We also extend our algorithm
to achieve roughly the same running time for Strongly Connected Components (SCC),
improving the algorithm of Roditty and Zwick (FOCS 2002), and an algorithm that
improves the Õ (mn log W)-time algorithm of Bernstein (STOC 2013) for approximating
SSSP on weighted directed graphs, where the edge weights are integers from 1 to
W. All our algorithms have constant query time in the worst case."
article_number: 674 - 683
article_processing_charge: No
arxiv: 1
author:
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Sebastian
full_name: Krinninger, Sebastian
last_name: Krinninger
- first_name: Danupon
full_name: Nanongkai, Danupon
last_name: Nanongkai
citation:
ama: 'Henzinger MH, Krinninger S, Nanongkai D. Sublinear-time decremental algorithms
for single-source reachability and shortest paths on directed graphs. In: 46th
Annual ACM Symposium on Theory of Computing. Association for Computing Machinery;
2014. doi:10.1145/2591796.2591869'
apa: 'Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2014). Sublinear-time
decremental algorithms for single-source reachability and shortest paths on directed
graphs. In 46th Annual ACM Symposium on Theory of Computing. New York,
NY, United States: Association for Computing Machinery. https://doi.org/10.1145/2591796.2591869'
chicago: Henzinger, Monika H, Sebastian Krinninger, and Danupon Nanongkai. “Sublinear-Time
Decremental Algorithms for Single-Source Reachability and Shortest Paths on Directed
Graphs.” In 46th Annual ACM Symposium on Theory of Computing. Association
for Computing Machinery, 2014. https://doi.org/10.1145/2591796.2591869.
ieee: M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Sublinear-time decremental
algorithms for single-source reachability and shortest paths on directed graphs,”
in 46th Annual ACM Symposium on Theory of Computing, New York, NY, United
States, 2014.
ista: 'Henzinger MH, Krinninger S, Nanongkai D. 2014. Sublinear-time decremental
algorithms for single-source reachability and shortest paths on directed graphs.
46th Annual ACM Symposium on Theory of Computing. STOC: Symposium on Theory of
Computing, 674–683.'
mla: Henzinger, Monika H., et al. “Sublinear-Time Decremental Algorithms for Single-Source
Reachability and Shortest Paths on Directed Graphs.” 46th Annual ACM Symposium
on Theory of Computing, 674–683, Association for Computing Machinery, 2014,
doi:10.1145/2591796.2591869.
short: M.H. Henzinger, S. Krinninger, D. Nanongkai, in:, 46th Annual ACM Symposium
on Theory of Computing, Association for Computing Machinery, 2014.
conference:
end_date: 2014-06-03
location: New York, NY, United States
name: 'STOC: Symposium on Theory of Computing'
start_date: 2014-05-31
date_created: 2022-08-16T09:41:57Z
date_published: 2014-05-01T00:00:00Z
date_updated: 2023-02-17T11:18:52Z
day: '01'
doi: 10.1145/2591796.2591869
extern: '1'
external_id:
arxiv:
- '1504.07959'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1504.07959
month: '05'
oa: 1
oa_version: Preprint
publication: 46th Annual ACM Symposium on Theory of Computing
publication_identifier:
isbn:
- 978-145032710-7
issn:
- 0737-8017
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sublinear-time decremental algorithms for single-source reachability and shortest
paths on directed graphs
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...