---
_id: '1827'
abstract:
- lang: eng
text: Bow-tie or hourglass structure is a common architectural feature found in
many biological systems. A bow-tie in a multi-layered structure occurs when intermediate
layers have much fewer components than the input and output layers. Examples include
metabolism where a handful of building blocks mediate between multiple input nutrients
and multiple output biomass components, and signaling networks where information
from numerous receptor types passes through a small set of signaling pathways
to regulate multiple output genes. Little is known, however, about how bow-tie
architectures evolve. Here, we address the evolution of bow-tie architectures
using simulations of multi-layered systems evolving to fulfill a given input-output
goal. We find that bow-ties spontaneously evolve when the information in the evolutionary
goal can be compressed. Mathematically speaking, bow-ties evolve when the rank
of the input-output matrix describing the evolutionary goal is deficient. The
maximal compression possible (the rank of the goal) determines the size of the
narrowest part of the network—that is the bow-tie. A further requirement is that
a process is active to reduce the number of links in the network, such as product-rule
mutations, otherwise a non-bow-tie solution is found in the evolutionary simulations.
This offers a mechanism to understand a common architectural principle of biological
systems, and a way to quantitate the effective rank of the goals under which they
evolved.
article_processing_charge: No
author:
- first_name: Tamar
full_name: Friedlander, Tamar
id: 36A5845C-F248-11E8-B48F-1D18A9856A87
last_name: Friedlander
- first_name: Avraham
full_name: Mayo, Avraham
last_name: Mayo
- first_name: Tsvi
full_name: Tlusty, Tsvi
last_name: Tlusty
- first_name: Uri
full_name: Alon, Uri
last_name: Alon
citation:
ama: Friedlander T, Mayo A, Tlusty T, Alon U. Evolution of bow-tie architectures
in biology. PLoS Computational Biology. 2015;11(3). doi:10.1371/journal.pcbi.1004055
apa: Friedlander, T., Mayo, A., Tlusty, T., & Alon, U. (2015). Evolution of
bow-tie architectures in biology. PLoS Computational Biology. Public Library
of Science. https://doi.org/10.1371/journal.pcbi.1004055
chicago: Friedlander, Tamar, Avraham Mayo, Tsvi Tlusty, and Uri Alon. “Evolution
of Bow-Tie Architectures in Biology.” PLoS Computational Biology. Public
Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004055.
ieee: T. Friedlander, A. Mayo, T. Tlusty, and U. Alon, “Evolution of bow-tie architectures
in biology,” PLoS Computational Biology, vol. 11, no. 3. Public Library
of Science, 2015.
ista: Friedlander T, Mayo A, Tlusty T, Alon U. 2015. Evolution of bow-tie architectures
in biology. PLoS Computational Biology. 11(3).
mla: Friedlander, Tamar, et al. “Evolution of Bow-Tie Architectures in Biology.”
PLoS Computational Biology, vol. 11, no. 3, Public Library of Science,
2015, doi:10.1371/journal.pcbi.1004055.
short: T. Friedlander, A. Mayo, T. Tlusty, U. Alon, PLoS Computational Biology 11
(2015).
date_created: 2018-12-11T11:54:14Z
date_published: 2015-03-23T00:00:00Z
date_updated: 2023-02-23T14:07:51Z
day: '23'
ddc:
- '576'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1004055
ec_funded: 1
file:
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checksum: b8aa66f450ff8de393014b87ec7d2efb
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:39Z
date_updated: 2020-07-14T12:45:17Z
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file_name: IST-2016-452-v1+1_journal.pcbi.1004055.pdf
file_size: 1811647
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file_date_updated: 2020-07-14T12:45:17Z
has_accepted_license: '1'
intvolume: ' 11'
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: PLoS Computational Biology
publication_status: published
publisher: Public Library of Science
publist_id: '5278'
pubrep_id: '452'
quality_controlled: '1'
related_material:
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scopus_import: 1
status: public
title: Evolution of bow-tie architectures in biology
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2015'
...
---
_id: '1809'
abstract:
- lang: eng
text: 'Background: Indirect genetic effects (IGEs) occur when genes expressed in
one individual alter the expression of traits in social partners. Previous studies
focused on the evolutionary consequences and evolutionary dynamics of IGEs, using
equilibrium solutions to predict phenotypes in subsequent generations. However,
whether or not such steady states may be reached may depend on the dynamics of
interactions themselves. Results: In our study, we focus on the dynamics of social
interactions and indirect genetic effects and investigate how they modify phenotypes
over time. Unlike previous IGE studies, we do not analyse evolutionary dynamics;
rather we consider within-individual phenotypic changes, also referred to as phenotypic
plasticity. We analyse iterative interactions, when individuals interact in a
series of discontinuous events, and investigate the stability of steady state
solutions and the dependence on model parameters, such as population size, strength,
and the nature of interactions. We show that for interactions where a feedback
loop occurs, the possible parameter space of interaction strength is fairly limited,
affecting the evolutionary consequences of IGEs. We discuss the implications of
our results for current IGE model predictions and their limitations.'
author:
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
- first_name: Reinmar
full_name: Hager, Reinmar
last_name: Hager
citation:
ama: Trubenova B, Novak S, Hager R. Indirect genetic effects and the dynamics of
social interactions. PLoS One. 2015;10(5). doi:10.1371/journal.pone.0126907
apa: Trubenova, B., Novak, S., & Hager, R. (2015). Indirect genetic effects
and the dynamics of social interactions. PLoS One. Public Library of Science.
https://doi.org/10.1371/journal.pone.0126907
chicago: Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Indirect Genetic
Effects and the Dynamics of Social Interactions.” PLoS One. Public Library
of Science, 2015. https://doi.org/10.1371/journal.pone.0126907.
ieee: B. Trubenova, S. Novak, and R. Hager, “Indirect genetic effects and the dynamics
of social interactions,” PLoS One, vol. 10, no. 5. Public Library of Science,
2015.
ista: Trubenova B, Novak S, Hager R. 2015. Indirect genetic effects and the dynamics
of social interactions. PLoS One. 10(5).
mla: Trubenova, Barbora, et al. “Indirect Genetic Effects and the Dynamics of Social
Interactions.” PLoS One, vol. 10, no. 5, Public Library of Science, 2015,
doi:10.1371/journal.pone.0126907.
short: B. Trubenova, S. Novak, R. Hager, PLoS One 10 (2015).
date_created: 2018-12-11T11:54:07Z
date_published: 2015-05-18T00:00:00Z
date_updated: 2023-02-23T14:07:48Z
day: '18'
ddc:
- '570'
- '576'
department:
- _id: NiBa
doi: 10.1371/journal.pone.0126907
file:
- access_level: open_access
checksum: d3a4a58ef4bd3b3e2f32b7fd7af4a743
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:07Z
date_updated: 2020-07-14T12:45:17Z
file_id: '4730'
file_name: IST-2016-453-v1+1_journal.pone.0126907.pdf
file_size: 2748982
relation: main_file
file_date_updated: 2020-07-14T12:45:17Z
has_accepted_license: '1'
intvolume: ' 10'
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '5299'
pubrep_id: '453'
quality_controlled: '1'
related_material:
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- id: '9715'
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- id: '9772'
relation: research_data
status: public
scopus_import: 1
status: public
title: Indirect genetic effects and the dynamics of social interactions
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2015'
...
---
_id: '9772'
article_processing_charge: No
author:
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
- first_name: Reinmar
full_name: Hager, Reinmar
last_name: Hager
citation:
ama: Trubenova B, Novak S, Hager R. Description of the agent based simulations.
2015. doi:10.1371/journal.pone.0126907.s003
apa: Trubenova, B., Novak, S., & Hager, R. (2015). Description of the agent
based simulations. Public Library of Science. https://doi.org/10.1371/journal.pone.0126907.s003
chicago: Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Description of
the Agent Based Simulations.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0126907.s003.
ieee: B. Trubenova, S. Novak, and R. Hager, “Description of the agent based simulations.”
Public Library of Science, 2015.
ista: Trubenova B, Novak S, Hager R. 2015. Description of the agent based simulations,
Public Library of Science, 10.1371/journal.pone.0126907.s003.
mla: Trubenova, Barbora, et al. Description of the Agent Based Simulations.
Public Library of Science, 2015, doi:10.1371/journal.pone.0126907.s003.
short: B. Trubenova, S. Novak, R. Hager, (2015).
date_created: 2021-08-05T12:55:20Z
date_published: 2015-05-18T00:00:00Z
date_updated: 2023-02-23T10:15:25Z
day: '18'
department:
- _id: NiBa
doi: 10.1371/journal.pone.0126907.s003
month: '05'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1809'
relation: used_in_publication
status: public
status: public
title: Description of the agent based simulations
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2015'
...
---
_id: '9773'
article_processing_charge: No
author:
- first_name: Tamar
full_name: Friedlander, Tamar
id: 36A5845C-F248-11E8-B48F-1D18A9856A87
last_name: Friedlander
- first_name: Avraham E.
full_name: Mayo, Avraham E.
last_name: Mayo
- first_name: Tsvi
full_name: Tlusty, Tsvi
last_name: Tlusty
- first_name: Uri
full_name: Alon, Uri
last_name: Alon
citation:
ama: Friedlander T, Mayo AE, Tlusty T, Alon U. Evolutionary simulation code. 2015.
doi:10.1371/journal.pcbi.1004055.s002
apa: Friedlander, T., Mayo, A. E., Tlusty, T., & Alon, U. (2015). Evolutionary
simulation code. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004055.s002
chicago: Friedlander, Tamar, Avraham E. Mayo, Tsvi Tlusty, and Uri Alon. “Evolutionary
Simulation Code.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004055.s002.
ieee: T. Friedlander, A. E. Mayo, T. Tlusty, and U. Alon, “Evolutionary simulation
code.” Public Library of Science, 2015.
ista: Friedlander T, Mayo AE, Tlusty T, Alon U. 2015. Evolutionary simulation code,
Public Library of Science, 10.1371/journal.pcbi.1004055.s002.
mla: Friedlander, Tamar, et al. Evolutionary Simulation Code. Public Library
of Science, 2015, doi:10.1371/journal.pcbi.1004055.s002.
short: T. Friedlander, A.E. Mayo, T. Tlusty, U. Alon, (2015).
date_created: 2021-08-05T12:58:07Z
date_published: 2015-03-23T00:00:00Z
date_updated: 2023-02-23T10:16:13Z
day: '23'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1004055.s002
month: '03'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1827'
relation: used_in_publication
status: public
status: public
title: Evolutionary simulation code
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2015'
...
---
_id: '981'
abstract:
- lang: eng
text: The tunability of topological surface states and controllable opening of the
Dirac gap are of fundamental and practical interest in the field of topological
materials. In the newly discovered topological crystalline insulators (TCIs),
theory predicts that the Dirac node is protected by a crystalline symmetry and
that the surface state electrons can acquire a mass if this symmetry is broken.
Recent studies have detected signatures of a spontaneously generated Dirac gap
in TCIs; however, the mechanism of mass formation remains elusive. In this work,
we present scanning tunnelling microscopy (STM) measurements of the TCI Pb 1â'x
Sn x Se for a wide range of alloy compositions spanning the topological and non-topological
regimes. The STM topographies reveal a symmetry-breaking distortion on the surface,
which imparts mass to the otherwise massless Dirac electrons-a mechanism analogous
to the long sought-after Higgs mechanism in particle physics. Interestingly, the
measured Dirac gap decreases on approaching the trivial phase, whereas the magnitude
of the distortion remains nearly constant. Our data and calculations reveal that
the penetration depth of Dirac surface states controls the magnitude of the Dirac
mass. At the limit of the critical composition, the penetration depth is predicted
to go to infinity, resulting in zero mass, consistent with our measurements. Finally,
we discover the existence of surface states in the non-topological regime, which
have the characteristics of gapped, double-branched Dirac fermions and could be
exploited in realizing superconductivity in these materials.
acknowledgement: We thank R. Buczko, C. Chamon, J. C. Seamus Davis, M. El-Batanouny,
A. Mesaros, Y. Ran and A. Soumyanarayanan for useful conversations and G. McMahon
for help with EDS measurements. V.M. gratefully acknowledges funding from the US
Department of Energy, Scanned Probe Division under Award Number DE-FG02-12ER46880
for the support of I.Z., Y.O., W.Z. and D.W. for this project. Work at Massachusetts
Institute of Technology is supported by US Department of Energy, Office of Basic
Energy Sciences, Division of Materials Sciences and Engineering under Award DE-SC0010526
(L.F.), and NSF-DMR-1104498 (M.S.). H.L. acknowledges the Singapore National Research
Foundation for support under NRF Award No. NRF-NRFF2013-03. Y.O. was partly supported
by JSPS KAKENHI Grant Numbers 26707016 and 00707656. The work at Northeastern University
is supported by the US Department of Energy grant number DE-FG02-07ER46352, and
benefited from Northeastern University’s Advanced Scientific Computation Center
(ASCC), theory support at the Advanced Light Source, Berkeley and the allocation
of supercomputer time at the NERSC through DOE grant number DE-AC02-05CH11231. Work
at Princeton University is supported by the US National Science Foundation Grant,
NSF-DMR-1006492. F.C. acknowledges the support provided by MOST-Taiwan under project
number NSC-102-2119-M-002-004.
author:
- first_name: Ilija
full_name: Zeljkovic, Ilija
last_name: Zeljkovic
- first_name: Yoshinori
full_name: Okada, Yoshinori
last_name: Okada
- first_name: Maksym
full_name: Maksym Serbyn
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Raman
full_name: Sankar, Raman
last_name: Sankar
- first_name: Daniel
full_name: Walkup, Daniel
last_name: Walkup
- first_name: Wenwen
full_name: Zhou, Wenwen
last_name: Zhou
- first_name: Junwei
full_name: Liu, Junwei
last_name: Liu
- first_name: Guoqing
full_name: Chang, Guoqing
last_name: Chang
- first_name: Yungjui
full_name: Wang, Yungjui
last_name: Wang
- first_name: Md
full_name: Hasan, Md Z
last_name: Hasan
- first_name: Fangcheng
full_name: Chou, Fangcheng
last_name: Chou
- first_name: Hsin
full_name: Lin, Hsin
last_name: Lin
- first_name: Arun
full_name: Bansil, Arun
last_name: Bansil
- first_name: Liang
full_name: Fu, Liang
last_name: Fu
- first_name: Vidya
full_name: Madhavan, Vidya
last_name: Madhavan
citation:
ama: Zeljkovic I, Okada Y, Serbyn M, et al. Dirac mass generation from crystal symmetry
breaking on the surfaces of topological crystalline insulators. Nature Materials.
2015;14(3):318-324. doi:10.1038/nmat4215
apa: Zeljkovic, I., Okada, Y., Serbyn, M., Sankar, R., Walkup, D., Zhou, W., … Madhavan,
V. (2015). Dirac mass generation from crystal symmetry breaking on the surfaces
of topological crystalline insulators. Nature Materials. Nature Publishing
Group. https://doi.org/10.1038/nmat4215
chicago: Zeljkovic, Ilija, Yoshinori Okada, Maksym Serbyn, Raman Sankar, Daniel
Walkup, Wenwen Zhou, Junwei Liu, et al. “Dirac Mass Generation from Crystal Symmetry
Breaking on the Surfaces of Topological Crystalline Insulators.” Nature Materials.
Nature Publishing Group, 2015. https://doi.org/10.1038/nmat4215.
ieee: I. Zeljkovic et al., “Dirac mass generation from crystal symmetry breaking
on the surfaces of topological crystalline insulators,” Nature Materials,
vol. 14, no. 3. Nature Publishing Group, pp. 318–324, 2015.
ista: Zeljkovic I, Okada Y, Serbyn M, Sankar R, Walkup D, Zhou W, Liu J, Chang G,
Wang Y, Hasan M, Chou F, Lin H, Bansil A, Fu L, Madhavan V. 2015. Dirac mass generation
from crystal symmetry breaking on the surfaces of topological crystalline insulators.
Nature Materials. 14(3), 318–324.
mla: Zeljkovic, Ilija, et al. “Dirac Mass Generation from Crystal Symmetry Breaking
on the Surfaces of Topological Crystalline Insulators.” Nature Materials,
vol. 14, no. 3, Nature Publishing Group, 2015, pp. 318–24, doi:10.1038/nmat4215.
short: I. Zeljkovic, Y. Okada, M. Serbyn, R. Sankar, D. Walkup, W. Zhou, J. Liu,
G. Chang, Y. Wang, M. Hasan, F. Chou, H. Lin, A. Bansil, L. Fu, V. Madhavan, Nature
Materials 14 (2015) 318–324.
date_created: 2018-12-11T11:49:31Z
date_published: 2015-03-01T00:00:00Z
date_updated: 2021-01-12T08:22:24Z
day: '01'
doi: 10.1038/nmat4215
extern: 1
intvolume: ' 14'
issue: '3'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1403.4906
month: '03'
oa: 1
page: 318 - 324
publication: Nature Materials
publication_status: published
publisher: Nature Publishing Group
publist_id: '6419'
quality_controlled: 0
status: public
title: Dirac mass generation from crystal symmetry breaking on the surfaces of topological
crystalline insulators
type: journal_article
volume: 14
year: '2015'
...