---
_id: '770'
abstract:
- lang: eng
text: 'Dynamic memory reclamation is arguably the biggest open problem in concurrent
data structure design: All known solutions induce high overhead, or must be customized
to the specific data structure by the programmer, or both. This paper presents
StackTrack, the first concurrent memory reclamation scheme that can be applied
automatically by a compiler, while maintaining efficiency. StackTrack eliminates
most of the expensive bookkeeping required for memory reclamation by leveraging
the power of hardware transactional memory (HTM) in a new way: it tracks thread
variables dynamically, and in an atomic fashion. This effectively makes all memory
references visible without having threads pay the overhead of writing out this
information. Our empirical results show that this new approach matches or outperforms
prior, non-automated, techniques.'
acknowledgement: "Dan Alistarh - Part of this work was performed while the
\ author was a Postdoctoral\r\nAssociate a MIT CSAIL, supported in part by NSF
grant CCF-1217921,\r\nDoE ASCR grant ER26116/DE-SC0008923, and by grants from the
Oracle\r\nand Intel corporations.\r\nPatrick Eugester - Supported in part by DARPA
grant N11AP20014 and NSF grant CNS-\r\n1117065.\r\nMaurice Herlihy - Supported by
NSF grant 1301924.\r\nNir Shavit - Supported in part by NSF grants CCF-1217921 and
CCF-1301926, DoE\r\nASCR grant ER26116/DE-SC0008923, and by grants from the Oracle
and\r\nIntel corporations."
article_processing_charge: No
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Patrick
full_name: Eugster, Patrick
last_name: Eugster
- first_name: Maurice
full_name: Herlihy, Maurice
last_name: Herlihy
- first_name: Alexander
full_name: Matveev, Alexander
last_name: Matveev
- first_name: Nir
full_name: Shavit, Nir
last_name: Shavit
citation:
ama: 'Alistarh D-A, Eugster P, Herlihy M, Matveev A, Shavit N. StackTrack: An automated
transactional approach to concurrent memory reclamation. In: ACM; 2014. doi:10.1145/2592798.2592808'
apa: 'Alistarh, D.-A., Eugster, P., Herlihy, M., Matveev, A., & Shavit, N. (2014).
StackTrack: An automated transactional approach to concurrent memory reclamation.
Presented at the EuroSys: European Conference on Computer Systems, ACM. https://doi.org/10.1145/2592798.2592808'
chicago: 'Alistarh, Dan-Adrian, Patrick Eugster, Maurice Herlihy, Alexander Matveev,
and Nir Shavit. “StackTrack: An Automated Transactional Approach to Concurrent
Memory Reclamation.” ACM, 2014. https://doi.org/10.1145/2592798.2592808.'
ieee: 'D.-A. Alistarh, P. Eugster, M. Herlihy, A. Matveev, and N. Shavit, “StackTrack:
An automated transactional approach to concurrent memory reclamation,” presented
at the EuroSys: European Conference on Computer Systems, 2014.'
ista: 'Alistarh D-A, Eugster P, Herlihy M, Matveev A, Shavit N. 2014. StackTrack:
An automated transactional approach to concurrent memory reclamation. EuroSys:
European Conference on Computer Systems.'
mla: 'Alistarh, Dan-Adrian, et al. StackTrack: An Automated Transactional Approach
to Concurrent Memory Reclamation. ACM, 2014, doi:10.1145/2592798.2592808.'
short: D.-A. Alistarh, P. Eugster, M. Herlihy, A. Matveev, N. Shavit, in:, ACM,
2014.
conference:
name: 'EuroSys: European Conference on Computer Systems'
date_created: 2018-12-11T11:48:24Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2023-02-23T13:14:25Z
day: '01'
doi: 10.1145/2592798.2592808
extern: '1'
language:
- iso: eng
month: '01'
oa_version: None
publication_status: published
publisher: ACM
publist_id: '6888'
status: public
title: 'StackTrack: An automated transactional approach to concurrent memory reclamation'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '771'
abstract:
- lang: eng
text: 'We consider the following natural problem: n failure-prone servers, communicating
synchronously through message passing, must assign themselves one-to-one to n
distinct items. Existing literature suggests two possible approaches to this problem.
First, model it as an instance of tight renaming in synchronous message-passing
systems; for deterministic solutions, a tight bound of ©(logn) communication rounds
is known. Second, model the scenario as an instance of randomized load-balancing,
for which elegant sub-logarithmic solutions exist. However, careful examination
reveals that known load-balancing schemes do not apply to our scenario, because
they either do not tolerate faults or do not ensure one-to-one allocation. It
is thus natural to ask if sublogarithmic solutions exist for this apparently simple
but intriguing problem. In this paper, we combine the two approaches to provide
a new randomized solution for tight renaming, which terminates in O (log log n)
communication rounds with high probability, against a strong adaptive adversary.
Our solution, called Balls-into-Leaves, combines the deterministic approach with
a new randomized scheme to obtain perfectly balanced allocations. The algorithm
arranges the items as leaves of a tree, and participants repeatedly perform random
choices among the leaves. The algorithm exchanges information in each round to
split the participants into progressively smaller groups whose random choices
do not conflict. We then extend the algorithm to terminate early in O(log log)
rounds w.h.p., where is the actual number of failures. These results imply an
exponential separation between deterministic and randomized algorithms for the
tight renaming problem in message-passing systems.'
acknowledgement: "Dan Alistarh was partially supported by the SNF Post-\r\ndoctoral
Fellows Program, NSF grant CCF-1217921, DoE\r\nASCR grant ER26116/DE-SC0008923,
and by grants from\r\nthe Oracle and Intel corporations.\r\nOksana Denysyuk and
Lu ́ıs Rodrigues were partially supported by Funda ̧c ̃ao para a Ciˆencia e Tecnologia
(FCT) via\r\nthe project PEPITA (PTDC/EEI-SCR/2776/2012) and via\r\nthe INESC-ID
multi-annual funding through the PIDDAC\r\nProgram fund grant, under project PEst-OE/EEI/LA0021/\r\n2013.\r\nNir
Shavit was supported in part by NSF grants CCF-1217921 and CCF-1301926, DoE ASCR
grant ER26116/DE-SC0008923, and by grants from the Oracle and Intel corporations."
article_processing_charge: No
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Oksana
full_name: Denysyuk, Oksana
last_name: Denysyuk
- first_name: Luís
full_name: Rodrígues, Luís
last_name: Rodrígues
- first_name: Nir
full_name: Shavit, Nir
last_name: Shavit
citation:
ama: 'Alistarh D-A, Denysyuk O, Rodrígues L, Shavit N. Balls-into-Leaves: Sub-logarithmic
renaming in synchronous message-passing systems. In: ACM; 2014:232-241. doi:10.1145/2611462.2611499'
apa: 'Alistarh, D.-A., Denysyuk, O., Rodrígues, L., & Shavit, N. (2014). Balls-into-Leaves:
Sub-logarithmic renaming in synchronous message-passing systems (pp. 232–241).
Presented at the PODC: Principles of Distributed Computing, ACM. https://doi.org/10.1145/2611462.2611499'
chicago: 'Alistarh, Dan-Adrian, Oksana Denysyuk, Luís Rodrígues, and Nir Shavit.
“Balls-into-Leaves: Sub-Logarithmic Renaming in Synchronous Message-Passing Systems,”
232–41. ACM, 2014. https://doi.org/10.1145/2611462.2611499.'
ieee: 'D.-A. Alistarh, O. Denysyuk, L. Rodrígues, and N. Shavit, “Balls-into-Leaves:
Sub-logarithmic renaming in synchronous message-passing systems,” presented at
the PODC: Principles of Distributed Computing, 2014, pp. 232–241.'
ista: 'Alistarh D-A, Denysyuk O, Rodrígues L, Shavit N. 2014. Balls-into-Leaves:
Sub-logarithmic renaming in synchronous message-passing systems. PODC: Principles
of Distributed Computing, 232–241.'
mla: 'Alistarh, Dan-Adrian, et al. Balls-into-Leaves: Sub-Logarithmic Renaming
in Synchronous Message-Passing Systems. ACM, 2014, pp. 232–41, doi:10.1145/2611462.2611499.'
short: D.-A. Alistarh, O. Denysyuk, L. Rodrígues, N. Shavit, in:, ACM, 2014, pp.
232–241.
conference:
name: 'PODC: Principles of Distributed Computing'
date_created: 2018-12-11T11:48:25Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2023-02-23T13:14:49Z
day: '01'
doi: 10.1145/2611462.2611499
extern: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 232 - 241
publication_status: published
publisher: ACM
publist_id: '6884'
status: public
title: 'Balls-into-Leaves: Sub-logarithmic renaming in synchronous message-passing
systems'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '772'
abstract:
- lang: eng
text: Lock-free concurrent algorithms guarantee that some concurrent operation will
always make progress in a finite number of steps. Yet programmers prefer to treat
concurrent code as if it were wait-free, guaranteeing that all operations always
make progress. Unfortunately, designing wait-free algorithms is generally a very
complex task, and the resulting algorithms are not always efficient. While obtaining
efficient wait-free algorithms has been a long-time goal for the theory community,
most non-blocking commercial code is only lock-free. This paper suggests a simple
solution to this problem. We show that, for a large class of lock-free algorithms,
under scheduling conditions which approximate those found in commercial hardware
architectures, lock-free algorithms behave as if they are wait-free. In other
words, programmers can keep on designing simple lock-free algorithms instead of
complex wait-free ones, and in practice, they will get wait-free progress. Our
main contribution is a new way of analyzing a general class of lock-free algorithms
under a stochastic scheduler. Our analysis relates the individual performance
of processes with the global performance of the system using Markov chain lifting
between a complex per-process chain and a simpler system progress chain. We show
that lock-free algorithms are not only wait-free with probability 1, but that
in fact a general subset of lock-free algorithms can be closely bounded in terms
of the average number of steps required until an operation completes. To the best
of our knowledge, this is the first attempt to analyze progress conditions, typically
stated in relation to a worst case adversary, in a stochastic model capturing
their expected asymptotic behavior.
acknowledgement: "Dan Alistarh - Part of this work was performed while the author
was a Postdoctoral Associate at MIT CSAIL, where he was supported by SNF\r\nPostdoctoral
Fellows Program, NSF grant CCF-1217921, DoE\r\nASCR grant ER26116/DE-SC0008923,
and by grants from the Oracle and Intel corporations.\r\nKeron Censor-Hillel - Shalon
Fellow\r\nNir Shavit - This work was supported in part by NSF grants CCF-1217921
and\r\nCCF-1301926, DoE ASCR grant ER26116/DE-SC0008923, and\r\nby grants from the
Oracle and Intel corporations."
article_processing_charge: No
arxiv: 1
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Keren
full_name: Censor Hillel, Keren
last_name: Censor Hillel
- first_name: Nir
full_name: Shavit, Nir
last_name: Shavit
citation:
ama: 'Alistarh D-A, Censor Hillel K, Shavit N. Are lock-free concurrent algorithms
practically wait-free? In: ACM; 2014:714-723. doi:10.1145/2591796.2591836'
apa: 'Alistarh, D.-A., Censor Hillel, K., & Shavit, N. (2014). Are lock-free
concurrent algorithms practically wait-free? (pp. 714–723). Presented at the STOC:
Symposium on Theory of Computing, ACM. https://doi.org/10.1145/2591796.2591836'
chicago: Alistarh, Dan-Adrian, Keren Censor Hillel, and Nir Shavit. “Are Lock-Free
Concurrent Algorithms Practically Wait-Free?,” 714–23. ACM, 2014. https://doi.org/10.1145/2591796.2591836.
ieee: 'D.-A. Alistarh, K. Censor Hillel, and N. Shavit, “Are lock-free concurrent
algorithms practically wait-free?,” presented at the STOC: Symposium on Theory
of Computing, 2014, pp. 714–723.'
ista: 'Alistarh D-A, Censor Hillel K, Shavit N. 2014. Are lock-free concurrent algorithms
practically wait-free? STOC: Symposium on Theory of Computing, 714–723.'
mla: Alistarh, Dan-Adrian, et al. Are Lock-Free Concurrent Algorithms Practically
Wait-Free? ACM, 2014, pp. 714–23, doi:10.1145/2591796.2591836.
short: D.-A. Alistarh, K. Censor Hillel, N. Shavit, in:, ACM, 2014, pp. 714–723.
conference:
name: 'STOC: Symposium on Theory of Computing'
date_created: 2018-12-11T11:48:25Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2023-02-23T13:15:13Z
day: '01'
doi: 10.1145/2591796.2591836
extern: '1'
external_id:
arxiv:
- '1311.3200'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1311.3200
month: '01'
oa: 1
oa_version: Preprint
page: 714 - 723
publication_status: published
publisher: ACM
publist_id: '6885'
status: public
title: Are lock-free concurrent algorithms practically wait-free?
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '773'
abstract:
- lang: eng
text: "We describe a new randomized consensus protocol with expected message complexity
O(n2log2n) when fewer than n/2 processes may fail by crashing. This is an almost-linear
improvement over the best previously known protocol, and within logarithmic factors
of a known Ω(n2) message lower bound. The protocol further ensures that no process
sends more than O(n log3n) messages in expectation, which is again within logarithmic
factors of optimal.We also present a generalization of the algorithm to an arbitrary
number of failures t, which uses expected O(nt + t2log2t) total messages. Our
protocol uses messages of size O(log n), and can therefore scale to large networks.\r\n\r\nWe
consider the problem of consensus in the challenging classic model. In this model,
the adversary is adaptive; it can choose which processors crash at any point during
the course of the algorithm. Further, communication is via asynchronous message
passing: there is no known upper bound on the time to send a message from one
processor to another, and all messages and coin flips are seen by the adversary.\r\n\r\nOur
approach is to build a message-efficient, resilient mechanism for aggregating
individual processor votes, implementing the message-passing equivalent of a weak
shared coin. Roughly, in our protocol, a processor first announces its votes to
small groups, then propagates them to increasingly larger groups as it generates
more and more votes. To bound the number of messages that an individual process
might have to send or receive, the protocol progressively increases the weight
of generated votes. The main technical challenge is bounding the impact of votes
that are still “in flight” (generated, but not fully propagated) on the final
outcome of the shared coin, especially since such votes might have different weights.
We achieve this by leveraging the structure of the algorithm, and a technical
argument based on martingale concentration bounds. Overall, we show that it is
possible to build an efficient message-passing implementation of a shared coin,
and in the process (almost-optimally) solve the classic consensus problem in the
asynchronous message-passing model."
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: James
full_name: Aspnes, James
last_name: Aspnes
- first_name: Valerie
full_name: King, Valerie
last_name: King
- first_name: Jared
full_name: Saia, Jared
last_name: Saia
citation:
ama: 'Alistarh D-A, Aspnes J, King V, Saia J. Communication-efficient randomized
consensus. In: Kuhn F, ed. Vol 8784. Springer; 2014:61-75. doi:10.1007/978-3-662-45174-8_5'
apa: 'Alistarh, D.-A., Aspnes, J., King, V., & Saia, J. (2014). Communication-efficient
randomized consensus. In F. Kuhn (Ed.) (Vol. 8784, pp. 61–75). Presented at the
DISC: Distributed Computing, Austin, USA: Springer. https://doi.org/10.1007/978-3-662-45174-8_5'
chicago: Alistarh, Dan-Adrian, James Aspnes, Valerie King, and Jared Saia. “Communication-Efficient
Randomized Consensus.” edited by Fabian Kuhn, 8784:61–75. Springer, 2014. https://doi.org/10.1007/978-3-662-45174-8_5.
ieee: 'D.-A. Alistarh, J. Aspnes, V. King, and J. Saia, “Communication-efficient
randomized consensus,” presented at the DISC: Distributed Computing, Austin, USA,
2014, vol. 8784, pp. 61–75.'
ista: 'Alistarh D-A, Aspnes J, King V, Saia J. 2014. Communication-efficient randomized
consensus. DISC: Distributed Computing, LNCS, vol. 8784, 61–75.'
mla: Alistarh, Dan-Adrian, et al. Communication-Efficient Randomized Consensus.
Edited by Fabian Kuhn, vol. 8784, Springer, 2014, pp. 61–75, doi:10.1007/978-3-662-45174-8_5.
short: D.-A. Alistarh, J. Aspnes, V. King, J. Saia, in:, F. Kuhn (Ed.), Springer,
2014, pp. 61–75.
conference:
end_date: 2014-10-15
location: Austin, USA
name: 'DISC: Distributed Computing'
start_date: 2014-10-12
date_created: 2018-12-11T11:48:25Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2023-02-23T13:15:36Z
day: '01'
doi: 10.1007/978-3-662-45174-8_5
editor:
- first_name: Fabian
full_name: Kuhn, Fabian
last_name: Kuhn
extern: '1'
intvolume: ' 8784'
language:
- iso: eng
month: '01'
oa_version: None
page: 61 - 75
publication_status: published
publisher: Springer
publist_id: '6881'
status: public
title: Communication-efficient randomized consensus
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8784
year: '2014'
...
---
_id: '774'
abstract:
- lang: eng
text: Lock-free concurrent algorithms guarantee that some concurrent operation will
always make progress in a finite number of steps. Yet programmers would prefer
to treat concurrent code as if it were wait-free, guaranteeing that all operations
always make progress. Unfortunately, designing wait-free algorithms is in general
a complex undertaking, and the resulting algorithms are not always efficient,
so most non-blocking commercial code is only lock-free, and the design of efficient
wait-free algorithms has been left to the academic community. In [2], we suggest
a solution to this problem. We show that, for a large class of lock-free algorithms,
under scheduling conditions which approximate those found in commercial hardware
architectures, lock-free algorithms behave as if they are wait-free. In other
words, programmers can keep on designing simple lock-free algorithms instead of
complex wait-free ones, and in practice, they will get wait-free progress. Our
main contribution is a new way of analyzing a general class of lock-free algorithms
under a stochastic scheduler. Our analysis relates the individual performance
of processes with the global performance of the system using Markov chain lifting
between a complex per-process chain and a simpler system progress chain. We show
that lock-free algorithms are not only wait-free with probability 1, but that
in fact a broad subset of lock-free algorithms can be closely bounded in terms
of the average number of steps required until an operation completes.
acknowledgement: "Dan Alistarh - Part of this work was performed while the
\ author was a\r\nPostdoctoral Associate at MIT CSAIL, where he was supported
\ by SNF Postdoctoral Fellows Program, NSF grant\r\nCCF-1217921, DoE ASCR
grant ER26116/DE-SC0008923,\r\nand by grants from the Oracle and Intel corporations.\r\nKeren
Censor-Hille - Shalon Fellow\r\nNir Shavit - This work was supported in part
\ by NSF grants CCF-1217921 and CCF-1301926, DoE ASCR grant ER26116/DE-\r\nSC0008923,
and by grants from the Oracle and Intel corporations."
article_processing_charge: No
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Keren
full_name: Censor Hille, Keren
last_name: Censor Hille
- first_name: Nir
full_name: Shavit, Nir
last_name: Shavit
citation:
ama: 'Alistarh D-A, Censor Hille K, Shavit N. Brief announcement: Are lock-free
concurrent algorithms practically wait-free? In: ACM; 2014:50-52. doi:10.1145/2611462.2611502'
apa: 'Alistarh, D.-A., Censor Hille, K., & Shavit, N. (2014). Brief announcement:
Are lock-free concurrent algorithms practically wait-free? (pp. 50–52). Presented
at the PODC: Principles of Distributed Computing, ACM. https://doi.org/10.1145/2611462.2611502'
chicago: 'Alistarh, Dan-Adrian, Keren Censor Hille, and Nir Shavit. “Brief Announcement:
Are Lock-Free Concurrent Algorithms Practically Wait-Free?,” 50–52. ACM, 2014.
https://doi.org/10.1145/2611462.2611502.'
ieee: 'D.-A. Alistarh, K. Censor Hille, and N. Shavit, “Brief announcement: Are
lock-free concurrent algorithms practically wait-free?,” presented at the PODC:
Principles of Distributed Computing, 2014, pp. 50–52.'
ista: 'Alistarh D-A, Censor Hille K, Shavit N. 2014. Brief announcement: Are lock-free
concurrent algorithms practically wait-free? PODC: Principles of Distributed Computing,
50–52.'
mla: 'Alistarh, Dan-Adrian, et al. Brief Announcement: Are Lock-Free Concurrent
Algorithms Practically Wait-Free? ACM, 2014, pp. 50–52, doi:10.1145/2611462.2611502.'
short: D.-A. Alistarh, K. Censor Hille, N. Shavit, in:, ACM, 2014, pp. 50–52.
conference:
name: 'PODC: Principles of Distributed Computing'
date_created: 2018-12-11T11:48:26Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2023-02-23T13:15:54Z
day: '01'
doi: 10.1145/2611462.2611502
extern: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 50 - 52
publication_status: published
publisher: ACM
publist_id: '6882'
status: public
title: 'Brief announcement: Are lock-free concurrent algorithms practically wait-free?'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '7743'
abstract:
- lang: eng
text: Experimental studies have demonstrated that environmental variation can create
genotype‐environment interactions (GEIs) in the traits involved in sexual selection.
Understanding the genetic architecture of phenotype across environments will require
statistical tests that can describe both changes in genetic variance and covariance
across environments. This chapter outlines the theoretical framework for the processes
of sexual selection in the wild, identifying key parameters in wild systems, and
highlighting the potential effects of the environment. It describes the proposed
approaches for the estimation of these key parameters in a quantitative genetic
framework within naturally occurring pedigreed populations. The chapter provides
a worked example for a range of analysis methods. It aims to provide an overview
of the analytical methods that can be used to model GEIs for traits involved in
sexual selection in naturally occurring pedigreed populations.
article_processing_charge: No
author:
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: Anna
full_name: Qvarnström, Anna
last_name: Qvarnström
citation:
ama: 'Robinson MR, Qvarnström A. Influence of the environment on the genetic architecture
of traits involved in sexual selection within wild populations. In: Hunt J, Hosken
D, eds. Genotype-by-Environment Interactions and Sexual Selection. Chichester,
UK: Wiley; 2014:137-168. doi:10.1002/9781118912591.ch6'
apa: 'Robinson, M. R., & Qvarnström, A. (2014). Influence of the environment
on the genetic architecture of traits involved in sexual selection within wild
populations. In J. Hunt & D. Hosken (Eds.), Genotype-by-Environment Interactions
and Sexual Selection (pp. 137–168). Chichester, UK: Wiley. https://doi.org/10.1002/9781118912591.ch6'
chicago: 'Robinson, Matthew Richard, and Anna Qvarnström. “Influence of the Environment
on the Genetic Architecture of Traits Involved in Sexual Selection within Wild
Populations.” In Genotype-by-Environment Interactions and Sexual Selection,
edited by John Hunt and David Hosken, 137–68. Chichester, UK: Wiley, 2014. https://doi.org/10.1002/9781118912591.ch6.'
ieee: 'M. R. Robinson and A. Qvarnström, “Influence of the environment on the genetic
architecture of traits involved in sexual selection within wild populations,”
in Genotype-by-Environment Interactions and Sexual Selection, J. Hunt and
D. Hosken, Eds. Chichester, UK: Wiley, 2014, pp. 137–168.'
ista: 'Robinson MR, Qvarnström A. 2014.Influence of the environment on the genetic
architecture of traits involved in sexual selection within wild populations. In:
Genotype-by-Environment Interactions and Sexual Selection. , 137–168.'
mla: Robinson, Matthew Richard, and Anna Qvarnström. “Influence of the Environment
on the Genetic Architecture of Traits Involved in Sexual Selection within Wild
Populations.” Genotype-by-Environment Interactions and Sexual Selection,
edited by John Hunt and David Hosken, Wiley, 2014, pp. 137–68, doi:10.1002/9781118912591.ch6.
short: M.R. Robinson, A. Qvarnström, in:, J. Hunt, D. Hosken (Eds.), Genotype-by-Environment
Interactions and Sexual Selection, Wiley, Chichester, UK, 2014, pp. 137–168.
date_created: 2020-04-30T10:58:39Z
date_published: 2014-08-29T00:00:00Z
date_updated: 2021-01-12T08:15:13Z
day: '29'
doi: 10.1002/9781118912591.ch6
editor:
- first_name: John
full_name: Hunt, John
last_name: Hunt
- first_name: David
full_name: Hosken, David
last_name: Hosken
extern: '1'
language:
- iso: eng
month: '08'
oa_version: None
page: 137-168
place: Chichester, UK
publication: Genotype-by-Environment Interactions and Sexual Selection
publication_identifier:
eisbn:
- '9781118912591'
isbn:
- '9780470671795'
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Influence of the environment on the genetic architecture of traits involved
in sexual selection within wild populations
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '7744'
article_processing_charge: No
article_type: original
author:
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: Naomi R.
full_name: Wray, Naomi R.
last_name: Wray
- first_name: Peter M.
full_name: Visscher, Peter M.
last_name: Visscher
citation:
ama: Robinson MR, Wray NR, Visscher PM. Explaining additional genetic variation
in complex traits. Trends in Genetics. 2014;30(4):124-132. doi:10.1016/j.tig.2014.02.003
apa: Robinson, M. R., Wray, N. R., & Visscher, P. M. (2014). Explaining additional
genetic variation in complex traits. Trends in Genetics. Elsevier. https://doi.org/10.1016/j.tig.2014.02.003
chicago: Robinson, Matthew Richard, Naomi R. Wray, and Peter M. Visscher. “Explaining
Additional Genetic Variation in Complex Traits.” Trends in Genetics. Elsevier,
2014. https://doi.org/10.1016/j.tig.2014.02.003.
ieee: M. R. Robinson, N. R. Wray, and P. M. Visscher, “Explaining additional genetic
variation in complex traits,” Trends in Genetics, vol. 30, no. 4. Elsevier,
pp. 124–132, 2014.
ista: Robinson MR, Wray NR, Visscher PM. 2014. Explaining additional genetic variation
in complex traits. Trends in Genetics. 30(4), 124–132.
mla: Robinson, Matthew Richard, et al. “Explaining Additional Genetic Variation
in Complex Traits.” Trends in Genetics, vol. 30, no. 4, Elsevier, 2014,
pp. 124–32, doi:10.1016/j.tig.2014.02.003.
short: M.R. Robinson, N.R. Wray, P.M. Visscher, Trends in Genetics 30 (2014) 124–132.
date_created: 2020-04-30T10:58:58Z
date_published: 2014-04-01T00:00:00Z
date_updated: 2021-01-12T08:15:14Z
day: '01'
doi: 10.1016/j.tig.2014.02.003
extern: '1'
intvolume: ' 30'
issue: '4'
language:
- iso: eng
month: '04'
oa_version: None
page: 124-132
publication: Trends in Genetics
publication_identifier:
issn:
- 0168-9525
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Explaining additional genetic variation in complex traits
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2014'
...
---
_id: '775'
abstract:
- lang: eng
text: 'The long-lived renaming problem appears in shared-memory systems where a
set of threads need to register and deregister frequently from the computation,
while concurrent operations scan the set of currently registered threads. Instances
of this problem show up in concurrent implementations of transactional memory,
flat combining, thread barriers, and memory reclamation schemes for lock-free
data structures. In this paper, we analyze a randomized solution for long-lived
renaming. The algorithmic technique we consider, called the Level Array, has previously
been used for hashing and one-shot (single-use) renaming. Our main contribution
is to prove that, in long-lived executions, where processes may register and deregister
polynomially many times, the technique guarantees constant steps on average and
O (log log n) steps with high probability for registering, unit cost for deregistering,
and O (n) steps for collect queries, where n is an upper bound on the number of
processes that may be active at any point in time. We also show that the algorithm
has the surprising property that it is self-healing: under reasonable assumptions
on the schedule, operations running while the data structure is in a degraded
state implicitly help the data structure re-balance itself. This subtle mechanism
obviates the need for expensive periodic rebuilding procedures. Our benchmarks
validate this approach, showing that, for typical use parameters, the average
number of steps a process takes to register is less than two and the worst-case
number of steps is bounded by six, even in executions with billions of operations.
We contrast this with other randomized implementations, whose worst-case behavior
we show to be unreliable, and with deterministic implementations, whose cost is
linear in n.'
article_processing_charge: No
arxiv: 1
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Justin
full_name: Kopinsky, Justin
last_name: Kopinsky
- first_name: Alexander
full_name: Matveev, Alexander
last_name: Matveev
- first_name: Nir
full_name: Shavit, Nir
last_name: Shavit
citation:
ama: 'Alistarh D-A, Kopinsky J, Matveev A, Shavit N. The levelarray: A fast, practical
long-lived renaming algorithm. In: IEEE; 2014:348-357. doi:10.1109/ICDCS.2014.43'
apa: 'Alistarh, D.-A., Kopinsky, J., Matveev, A., & Shavit, N. (2014). The levelarray:
A fast, practical long-lived renaming algorithm (pp. 348–357). Presented at the
ICDCS: International Conference on Distributed Computing Systems, IEEE. https://doi.org/10.1109/ICDCS.2014.43'
chicago: 'Alistarh, Dan-Adrian, Justin Kopinsky, Alexander Matveev, and Nir Shavit.
“The Levelarray: A Fast, Practical Long-Lived Renaming Algorithm,” 348–57. IEEE,
2014. https://doi.org/10.1109/ICDCS.2014.43.'
ieee: 'D.-A. Alistarh, J. Kopinsky, A. Matveev, and N. Shavit, “The levelarray:
A fast, practical long-lived renaming algorithm,” presented at the ICDCS: International
Conference on Distributed Computing Systems, 2014, pp. 348–357.'
ista: 'Alistarh D-A, Kopinsky J, Matveev A, Shavit N. 2014. The levelarray: A fast,
practical long-lived renaming algorithm. ICDCS: International Conference on Distributed
Computing Systems, 348–357.'
mla: 'Alistarh, Dan-Adrian, et al. The Levelarray: A Fast, Practical Long-Lived
Renaming Algorithm. IEEE, 2014, pp. 348–57, doi:10.1109/ICDCS.2014.43.'
short: D.-A. Alistarh, J. Kopinsky, A. Matveev, N. Shavit, in:, IEEE, 2014, pp.
348–357.
conference:
name: 'ICDCS: International Conference on Distributed Computing Systems'
date_created: 2018-12-11T11:48:26Z
date_published: 2014-08-29T00:00:00Z
date_updated: 2023-02-23T13:16:18Z
day: '29'
doi: 10.1109/ICDCS.2014.43
extern: '1'
external_id:
arxiv:
- '1405.5461'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1405.5461
month: '08'
oa: 1
oa_version: Preprint
page: 348 - 357
publication_status: published
publisher: IEEE
publist_id: '6883'
status: public
title: 'The levelarray: A fast, practical long-lived renaming algorithm'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '7768'
abstract:
- lang: eng
text: We investigate the vibrational modes of quasi-two-dimensional disordered colloidal
packings of hard colloidal spheres with short-range attractions as a function
of packing fraction. Certain properties of the vibrational density of states (vDOS)
are shown to correlate with the density and structure of the samples (i.e., in
sparsely versus densely packed samples). Specifically, a crossover from dense
glassy to sparse gel-like states is suggested by an excess of phonon modes at
low frequency and by a variation in the slope of the vDOS with frequency at low
frequency. This change in phonon mode distribution is demonstrated to arise largely
from localized vibrations that involve individual and/or small clusters of particles
with few local bonds. Conventional order parameters and void statistics did not
exhibit obvious gel-glass signatures as a function of volume fraction. These mode
behaviors and accompanying structural insights offer a potentially new set of
indicators for identification of glass-gel transitions and for assignment of gel-like
versus glass-like character to a disordered solid material.
article_number: '062305'
article_processing_charge: No
article_type: original
author:
- first_name: Matthew A.
full_name: Lohr, Matthew A.
last_name: Lohr
- first_name: Tim
full_name: Still, Tim
last_name: Still
- first_name: Raman
full_name: Ganti, Raman
last_name: Ganti
- first_name: Matthew D.
full_name: Gratale, Matthew D.
last_name: Gratale
- first_name: Zoey S.
full_name: Davidson, Zoey S.
last_name: Davidson
- first_name: Kevin B.
full_name: Aptowicz, Kevin B.
last_name: Aptowicz
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Daniel M.
full_name: Sussman, Daniel M.
last_name: Sussman
- first_name: A. G.
full_name: Yodh, A. G.
last_name: Yodh
citation:
ama: Lohr MA, Still T, Ganti R, et al. Vibrational and structural signatures of
the crossover between dense glassy and sparse gel-like attractive colloidal packings.
Physical Review E. 2014;90(6). doi:10.1103/physreve.90.062305
apa: Lohr, M. A., Still, T., Ganti, R., Gratale, M. D., Davidson, Z. S., Aptowicz,
K. B., … Yodh, A. G. (2014). Vibrational and structural signatures of the crossover
between dense glassy and sparse gel-like attractive colloidal packings. Physical
Review E. American Physical Society. https://doi.org/10.1103/physreve.90.062305
chicago: Lohr, Matthew A., Tim Still, Raman Ganti, Matthew D. Gratale, Zoey S. Davidson,
Kevin B. Aptowicz, Carl Peter Goodrich, Daniel M. Sussman, and A. G. Yodh. “Vibrational
and Structural Signatures of the Crossover between Dense Glassy and Sparse Gel-like
Attractive Colloidal Packings.” Physical Review E. American Physical Society,
2014. https://doi.org/10.1103/physreve.90.062305.
ieee: M. A. Lohr et al., “Vibrational and structural signatures of the crossover
between dense glassy and sparse gel-like attractive colloidal packings,” Physical
Review E, vol. 90, no. 6. American Physical Society, 2014.
ista: Lohr MA, Still T, Ganti R, Gratale MD, Davidson ZS, Aptowicz KB, Goodrich
CP, Sussman DM, Yodh AG. 2014. Vibrational and structural signatures of the crossover
between dense glassy and sparse gel-like attractive colloidal packings. Physical
Review E. 90(6), 062305.
mla: Lohr, Matthew A., et al. “Vibrational and Structural Signatures of the Crossover
between Dense Glassy and Sparse Gel-like Attractive Colloidal Packings.” Physical
Review E, vol. 90, no. 6, 062305, American Physical Society, 2014, doi:10.1103/physreve.90.062305.
short: M.A. Lohr, T. Still, R. Ganti, M.D. Gratale, Z.S. Davidson, K.B. Aptowicz,
C.P. Goodrich, D.M. Sussman, A.G. Yodh, Physical Review E 90 (2014).
date_created: 2020-04-30T11:41:54Z
date_published: 2014-12-05T00:00:00Z
date_updated: 2021-01-12T08:15:24Z
day: '05'
doi: 10.1103/physreve.90.062305
extern: '1'
intvolume: ' 90'
issue: '6'
language:
- iso: eng
month: '12'
oa_version: None
publication: Physical Review E
publication_identifier:
issn:
- 1539-3755
- 1550-2376
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Vibrational and structural signatures of the crossover between dense glassy
and sparse gel-like attractive colloidal packings
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 90
year: '2014'
...
---
_id: '7769'
abstract:
- lang: eng
text: 'Athermal packings of soft repulsive spheres exhibit a sharp jamming transition
in the thermodynamic limit. Upon further compression, various structural and mechanical
properties display clean power-law behavior over many decades in pressure. As
with any phase transition, the rounding of such behavior in finite systems close
to the transition plays an important role in understanding the nature of the transition
itself. The situation for jamming is surprisingly rich: the assumption that jammed
packings are isotropic is only strictly true in the large-size limit, and finite-size
has a profound effect on the very meaning of jamming. Here, we provide a comprehensive
numerical study of finite-size effects in sphere packings above the jamming transition,
focusing on stability as well as the scaling of the contact number and the elastic
response.'
article_number: '022138'
article_processing_charge: No
article_type: original
author:
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Simon
full_name: Dagois-Bohy, Simon
last_name: Dagois-Bohy
- first_name: Brian P.
full_name: Tighe, Brian P.
last_name: Tighe
- first_name: Martin
full_name: van Hecke, Martin
last_name: van Hecke
- first_name: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
- first_name: Sidney R.
full_name: Nagel, Sidney R.
last_name: Nagel
citation:
ama: 'Goodrich CP, Dagois-Bohy S, Tighe BP, van Hecke M, Liu AJ, Nagel SR. Jamming
in finite systems: Stability, anisotropy, fluctuations, and scaling. Physical
Review E. 2014;90(2). doi:10.1103/physreve.90.022138'
apa: 'Goodrich, C. P., Dagois-Bohy, S., Tighe, B. P., van Hecke, M., Liu, A. J.,
& Nagel, S. R. (2014). Jamming in finite systems: Stability, anisotropy, fluctuations,
and scaling. Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.90.022138'
chicago: 'Goodrich, Carl Peter, Simon Dagois-Bohy, Brian P. Tighe, Martin van Hecke,
Andrea J. Liu, and Sidney R. Nagel. “Jamming in Finite Systems: Stability, Anisotropy,
Fluctuations, and Scaling.” Physical Review E. American Physical Society,
2014. https://doi.org/10.1103/physreve.90.022138.'
ieee: 'C. P. Goodrich, S. Dagois-Bohy, B. P. Tighe, M. van Hecke, A. J. Liu, and
S. R. Nagel, “Jamming in finite systems: Stability, anisotropy, fluctuations,
and scaling,” Physical Review E, vol. 90, no. 2. American Physical Society,
2014.'
ista: 'Goodrich CP, Dagois-Bohy S, Tighe BP, van Hecke M, Liu AJ, Nagel SR. 2014.
Jamming in finite systems: Stability, anisotropy, fluctuations, and scaling. Physical
Review E. 90(2), 022138.'
mla: 'Goodrich, Carl Peter, et al. “Jamming in Finite Systems: Stability, Anisotropy,
Fluctuations, and Scaling.” Physical Review E, vol. 90, no. 2, 022138,
American Physical Society, 2014, doi:10.1103/physreve.90.022138.'
short: C.P. Goodrich, S. Dagois-Bohy, B.P. Tighe, M. van Hecke, A.J. Liu, S.R. Nagel,
Physical Review E 90 (2014).
date_created: 2020-04-30T11:42:09Z
date_published: 2014-08-27T00:00:00Z
date_updated: 2021-01-12T08:15:24Z
day: '27'
doi: 10.1103/physreve.90.022138
extern: '1'
intvolume: ' 90'
issue: '2'
language:
- iso: eng
month: '08'
oa_version: None
publication: Physical Review E
publication_identifier:
issn:
- 1539-3755
- 1550-2376
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: 'Jamming in finite systems: Stability, anisotropy, fluctuations, and scaling'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 90
year: '2014'
...
---
_id: '7770'
abstract:
- lang: eng
text: Packings of frictionless athermal particles that interact only when they overlap
experience a jamming transition as a function of packing density. Such packings
provide the foundation for the theory of jamming. This theory rests on the observation
that, despite the multitude of disordered configurations, the mechanical response
to linear order depends only on the distance to the transition. We investigate
the validity and utility of such measurements that invoke the harmonic approximation
and show that, despite particles coming in and out of contact, there is a well-defined
linear regime in the thermodynamic limit.
article_number: '022201'
article_processing_charge: No
article_type: original
author:
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
- first_name: Sidney R.
full_name: Nagel, Sidney R.
last_name: Nagel
citation:
ama: Goodrich CP, Liu AJ, Nagel SR. Contact nonlinearities and linear response in
jammed particulate packings. Physical Review E. 2014;90(2). doi:10.1103/physreve.90.022201
apa: Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2014). Contact nonlinearities
and linear response in jammed particulate packings. Physical Review E.
American Physical Society. https://doi.org/10.1103/physreve.90.022201
chicago: Goodrich, Carl Peter, Andrea J. Liu, and Sidney R. Nagel. “Contact Nonlinearities
and Linear Response in Jammed Particulate Packings.” Physical Review E.
American Physical Society, 2014. https://doi.org/10.1103/physreve.90.022201.
ieee: C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Contact nonlinearities and linear
response in jammed particulate packings,” Physical Review E, vol. 90, no.
2. American Physical Society, 2014.
ista: Goodrich CP, Liu AJ, Nagel SR. 2014. Contact nonlinearities and linear response
in jammed particulate packings. Physical Review E. 90(2), 022201.
mla: Goodrich, Carl Peter, et al. “Contact Nonlinearities and Linear Response in
Jammed Particulate Packings.” Physical Review E, vol. 90, no. 2, 022201,
American Physical Society, 2014, doi:10.1103/physreve.90.022201.
short: C.P. Goodrich, A.J. Liu, S.R. Nagel, Physical Review E 90 (2014).
date_created: 2020-04-30T11:42:24Z
date_published: 2014-08-04T00:00:00Z
date_updated: 2021-01-12T08:15:25Z
day: '04'
doi: 10.1103/physreve.90.022201
extern: '1'
intvolume: ' 90'
issue: '2'
language:
- iso: eng
month: '08'
oa_version: None
publication: Physical Review E
publication_identifier:
issn:
- 1539-3755
- 1550-2376
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Contact nonlinearities and linear response in jammed particulate packings
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 90
year: '2014'
...
---
_id: '7771'
abstract:
- lang: eng
text: 'In their Letter, Schreck, Bertrand, O''Hern and Shattuck [Phys. Rev. Lett.
107, 078301 (2011)] study nonlinearities in jammed particulate systems that arise
when contacts are altered. They conclude that there is "no harmonic regime in
the large system limit for all compressions" and "at jamming onset for any system
size." Their argument rests on the claim that for finite-range repulsive potentials,
of the form used in studies of jamming, the breaking or forming of a single contact
is sufficient to destroy the linear regime. We dispute these conclusions and argue
that linear response is both justified and essential for understanding the nature
of the jammed solid. '
article_number: '049801 '
article_processing_charge: No
article_type: letter_note
arxiv: 1
author:
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
- first_name: Sidney R.
full_name: Nagel, Sidney R.
last_name: Nagel
citation:
ama: Goodrich CP, Liu AJ, Nagel SR. Comment on “Repulsive contact interactions make
jammed particulate systems inherently nonharmonic.” Physical Review Letters.
2014;112(4). doi:10.1103/physrevlett.112.049801
apa: Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2014). Comment on “Repulsive
contact interactions make jammed particulate systems inherently nonharmonic.”
Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.112.049801
chicago: Goodrich, Carl Peter, Andrea J. Liu, and Sidney R. Nagel. “Comment on ‘Repulsive
Contact Interactions Make Jammed Particulate Systems Inherently Nonharmonic.’”
Physical Review Letters. American Physical Society, 2014. https://doi.org/10.1103/physrevlett.112.049801.
ieee: C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Comment on ‘Repulsive contact
interactions make jammed particulate systems inherently nonharmonic,’” Physical
Review Letters, vol. 112, no. 4. American Physical Society, 2014.
ista: Goodrich CP, Liu AJ, Nagel SR. 2014. Comment on “Repulsive contact interactions
make jammed particulate systems inherently nonharmonic”. Physical Review Letters.
112(4), 049801.
mla: Goodrich, Carl Peter, et al. “Comment on ‘Repulsive Contact Interactions Make
Jammed Particulate Systems Inherently Nonharmonic.’” Physical Review Letters,
vol. 112, no. 4, 049801, American Physical Society, 2014, doi:10.1103/physrevlett.112.049801.
short: C.P. Goodrich, A.J. Liu, S.R. Nagel, Physical Review Letters 112 (2014).
date_created: 2020-04-30T11:42:39Z
date_published: 2014-04-20T00:00:00Z
date_updated: 2021-01-12T08:15:26Z
day: '20'
doi: 10.1103/physrevlett.112.049801
extern: '1'
external_id:
arxiv:
- '1306.1285'
intvolume: ' 112'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1306.1285
month: '04'
oa: 1
oa_version: Preprint
publication: Physical Review Letters
publication_identifier:
issn:
- 0031-9007
- 1079-7114
publication_status: published
publisher: American Physical Society
status: public
title: Comment on “Repulsive contact interactions make jammed particulate systems
inherently nonharmonic”
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2014'
...
---
_id: '7772'
abstract:
- lang: eng
text: Particle tracking and displacement covariance matrix techniques are employed
to investigate the phonon dispersion relations of two-dimensional colloidal glasses
composed of soft, thermoresponsive microgel particles whose temperature-sensitive
size permits in situ variation of particle packing fraction. Bulk, B, and shear,
G, moduli of the colloidal glasses are extracted from the dispersion relations
as a function of packing fraction, and variation of the ratio G/B with packing
fraction is found to agree quantitatively with predictions for jammed packings
of frictional soft particles. In addition, G and B individually agree with numerical
predictions for frictional particles. This remarkable level of agreement enabled
us to extract an energy scale for the interparticle interaction from the individual
elastic constants and to derive an approximate estimate for the interparticle
friction coefficient.
article_number: '012301'
article_processing_charge: No
article_type: original
author:
- first_name: Tim
full_name: Still, Tim
last_name: Still
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Ke
full_name: Chen, Ke
last_name: Chen
- first_name: Peter J.
full_name: Yunker, Peter J.
last_name: Yunker
- first_name: Samuel
full_name: Schoenholz, Samuel
last_name: Schoenholz
- first_name: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
- first_name: A. G.
full_name: Yodh, A. G.
last_name: Yodh
citation:
ama: Still T, Goodrich CP, Chen K, et al. Phonon dispersion and elastic moduli of
two-dimensional disordered colloidal packings of soft particles with frictional
interactions. Physical Review E. 2014;89(1). doi:10.1103/physreve.89.012301
apa: Still, T., Goodrich, C. P., Chen, K., Yunker, P. J., Schoenholz, S., Liu, A.
J., & Yodh, A. G. (2014). Phonon dispersion and elastic moduli of two-dimensional
disordered colloidal packings of soft particles with frictional interactions.
Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.89.012301
chicago: Still, Tim, Carl Peter Goodrich, Ke Chen, Peter J. Yunker, Samuel Schoenholz,
Andrea J. Liu, and A. G. Yodh. “Phonon Dispersion and Elastic Moduli of Two-Dimensional
Disordered Colloidal Packings of Soft Particles with Frictional Interactions.”
Physical Review E. American Physical Society, 2014. https://doi.org/10.1103/physreve.89.012301.
ieee: T. Still et al., “Phonon dispersion and elastic moduli of two-dimensional
disordered colloidal packings of soft particles with frictional interactions,”
Physical Review E, vol. 89, no. 1. American Physical Society, 2014.
ista: Still T, Goodrich CP, Chen K, Yunker PJ, Schoenholz S, Liu AJ, Yodh AG. 2014.
Phonon dispersion and elastic moduli of two-dimensional disordered colloidal packings
of soft particles with frictional interactions. Physical Review E. 89(1), 012301.
mla: Still, Tim, et al. “Phonon Dispersion and Elastic Moduli of Two-Dimensional
Disordered Colloidal Packings of Soft Particles with Frictional Interactions.”
Physical Review E, vol. 89, no. 1, 012301, American Physical Society, 2014,
doi:10.1103/physreve.89.012301.
short: T. Still, C.P. Goodrich, K. Chen, P.J. Yunker, S. Schoenholz, A.J. Liu, A.G.
Yodh, Physical Review E 89 (2014).
date_created: 2020-04-30T11:43:02Z
date_published: 2014-01-03T00:00:00Z
date_updated: 2021-01-12T08:15:26Z
day: '03'
doi: 10.1103/physreve.89.012301
extern: '1'
intvolume: ' 89'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
publication: Physical Review E
publication_identifier:
issn:
- 1539-3755
- 1550-2376
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Phonon dispersion and elastic moduli of two-dimensional disordered colloidal
packings of soft particles with frictional interactions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 89
year: '2014'
...
---
_id: '7773'
abstract:
- lang: eng
text: 'For more than a century, physicists have described real solids in terms of
perturbations about perfect crystalline order1. Such an approach takes us only
so far: a glass, another ubiquitous form of rigid matter, cannot be described
in any meaningful sense as a defected crystal2. Is there an opposite extreme to
a crystal—a solid with complete disorder—that forms an alternative starting point
for understanding real materials? Here, we argue that the solid comprising particles
with finite-ranged interactions at the jamming transition3,4,5 constitutes such
a limit. It has been shown that the physics associated with this transition can
be extended to interactions that are long ranged6. We demonstrate that jamming
physics is not restricted to amorphous systems, but dominates the behaviour of
solids with surprisingly high order. Just as the free-electron and tight-binding
models represent two idealized cases from which to understand electronic structure1,
we identify two extreme limits of mechanical behaviour. Thus, the physics of jamming
can be set side by side with the physics of crystals to provide an organizing
structure for understanding the mechanical properties of solids over the entire
spectrum of disorder.'
article_processing_charge: No
article_type: original
author:
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
- first_name: Sidney R.
full_name: Nagel, Sidney R.
last_name: Nagel
citation:
ama: Goodrich CP, Liu AJ, Nagel SR. Solids between the mechanical extremes of order
and disorder. Nature Physics. 2014;10(8):578-581. doi:10.1038/nphys3006
apa: Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2014). Solids between the
mechanical extremes of order and disorder. Nature Physics. Springer Nature.
https://doi.org/10.1038/nphys3006
chicago: Goodrich, Carl Peter, Andrea J. Liu, and Sidney R. Nagel. “Solids between
the Mechanical Extremes of Order and Disorder.” Nature Physics. Springer
Nature, 2014. https://doi.org/10.1038/nphys3006.
ieee: C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Solids between the mechanical
extremes of order and disorder,” Nature Physics, vol. 10, no. 8. Springer
Nature, pp. 578–581, 2014.
ista: Goodrich CP, Liu AJ, Nagel SR. 2014. Solids between the mechanical extremes
of order and disorder. Nature Physics. 10(8), 578–581.
mla: Goodrich, Carl Peter, et al. “Solids between the Mechanical Extremes of Order
and Disorder.” Nature Physics, vol. 10, no. 8, Springer Nature, 2014, pp.
578–81, doi:10.1038/nphys3006.
short: C.P. Goodrich, A.J. Liu, S.R. Nagel, Nature Physics 10 (2014) 578–581.
date_created: 2020-04-30T11:43:29Z
date_published: 2014-07-06T00:00:00Z
date_updated: 2021-01-12T08:15:26Z
day: '06'
doi: 10.1038/nphys3006
extern: '1'
intvolume: ' 10'
issue: '8'
language:
- iso: eng
month: '07'
oa_version: None
page: 578-581
publication: Nature Physics
publication_identifier:
issn:
- 1745-2473
- 1745-2481
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Solids between the mechanical extremes of order and disorder
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2014'
...
---
_id: '8021'
abstract:
- lang: eng
text: 'Most excitatory inputs in the mammalian brain are made on dendritic spines,
rather than on dendritic shafts. Spines compartmentalize calcium, and this biochemical
isolation can underlie input-specific synaptic plasticity, providing a raison
d''etre for spines. However, recent results indicate that the spine can experience
a membrane potential different from that in the parent dendrite, as though the
spine neck electrically isolated the spine. Here we use two-photon calcium imaging
of mouse neocortical pyramidal neurons to analyze the correlation between the
morphologies of spines activated under minimal synaptic stimulation and the excitatory
postsynaptic potentials they generate. We find that excitatory postsynaptic potential
amplitudes are inversely correlated with spine neck lengths. Furthermore, a spike
timing-dependent plasticity protocol, in which two-photon glutamate uncaging over
a spine is paired with postsynaptic spikes, produces rapid shrinkage of the spine
neck and concomitant increases in the amplitude of the evoked spine potentials.
Using numerical simulations, we explore the parameter regimes for the spine neck
resistance and synaptic conductance changes necessary to explain our observations.
Our data, directly correlating synaptic and morphological plasticity, imply that
long-necked spines have small or negligible somatic voltage contributions, but
that, upon synaptic stimulation paired with postsynaptic activity, they can shorten
their necks and increase synaptic efficacy, thus changing the input/output gain
of pyramidal neurons. '
article_processing_charge: No
article_type: original
author:
- first_name: R.
full_name: Araya, R.
last_name: Araya
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
- first_name: R.
full_name: Yuste, R.
last_name: Yuste
citation:
ama: Araya R, Vogels TP, Yuste R. Activity-dependent dendritic spine neck changes
are correlated with synaptic strength. Proceedings of the National Academy
of Sciences. 2014;111(28):E2895-E2904. doi:10.1073/pnas.1321869111
apa: Araya, R., Vogels, T. P., & Yuste, R. (2014). Activity-dependent dendritic
spine neck changes are correlated with synaptic strength. Proceedings of the
National Academy of Sciences. Proceedings of the National Academy of Sciences.
https://doi.org/10.1073/pnas.1321869111
chicago: Araya, R., Tim P Vogels, and R. Yuste. “Activity-Dependent Dendritic Spine
Neck Changes Are Correlated with Synaptic Strength.” Proceedings of the National
Academy of Sciences. Proceedings of the National Academy of Sciences, 2014.
https://doi.org/10.1073/pnas.1321869111.
ieee: R. Araya, T. P. Vogels, and R. Yuste, “Activity-dependent dendritic spine
neck changes are correlated with synaptic strength,” Proceedings of the National
Academy of Sciences, vol. 111, no. 28. Proceedings of the National Academy
of Sciences, pp. E2895–E2904, 2014.
ista: Araya R, Vogels TP, Yuste R. 2014. Activity-dependent dendritic spine neck
changes are correlated with synaptic strength. Proceedings of the National Academy
of Sciences. 111(28), E2895–E2904.
mla: Araya, R., et al. “Activity-Dependent Dendritic Spine Neck Changes Are Correlated
with Synaptic Strength.” Proceedings of the National Academy of Sciences,
vol. 111, no. 28, Proceedings of the National Academy of Sciences, 2014, pp. E2895–904,
doi:10.1073/pnas.1321869111.
short: R. Araya, T.P. Vogels, R. Yuste, Proceedings of the National Academy of Sciences
111 (2014) E2895–E2904.
date_created: 2020-06-25T13:06:24Z
date_published: 2014-07-15T00:00:00Z
date_updated: 2021-01-12T08:16:34Z
day: '15'
doi: 10.1073/pnas.1321869111
extern: '1'
external_id:
pmid:
- '24982196'
intvolume: ' 111'
issue: '28'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4104910/
month: '07'
oa: 1
oa_version: Published Version
page: E2895-E2904
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
status: public
title: Activity-dependent dendritic spine neck changes are correlated with synaptic
strength
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 111
year: '2014'
...
---
_id: '8022'
abstract:
- lang: eng
text: Populations of neurons in motor cortex engage in complex transient dynamics
of large amplitude during the execution of limb movements. Traditional network
models with stochastically assigned synapses cannot reproduce this behavior. Here
we introduce a class of cortical architectures with strong and random excitatory
recurrence that is stabilized by intricate, fine-tuned inhibition, optimized from
a control theory perspective. Such networks transiently amplify specific activity
states and can be used to reliably execute multidimensional movement patterns.
Similar to the experimental observations, these transients must be preceded by
a steady-state initialization phase from which the network relaxes back into the
background state by way of complex internal dynamics. In our networks, excitation
and inhibition are as tightly balanced as recently reported in experiments across
several brain areas, suggesting inhibitory control of complex excitatory recurrence
as a generic organizational principle in cortex.
article_processing_charge: No
article_type: original
author:
- first_name: Guillaume
full_name: Hennequin, Guillaume
last_name: Hennequin
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
- first_name: Wulfram
full_name: Gerstner, Wulfram
last_name: Gerstner
citation:
ama: Hennequin G, Vogels TP, Gerstner W. Optimal control of transient dynamics in
balanced networks supports generation of complex movements. Neuron. 2014;82(6):1394-1406.
doi:10.1016/j.neuron.2014.04.045
apa: Hennequin, G., Vogels, T. P., & Gerstner, W. (2014). Optimal control of
transient dynamics in balanced networks supports generation of complex movements.
Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2014.04.045
chicago: Hennequin, Guillaume, Tim P Vogels, and Wulfram Gerstner. “Optimal Control
of Transient Dynamics in Balanced Networks Supports Generation of Complex Movements.”
Neuron. Elsevier, 2014. https://doi.org/10.1016/j.neuron.2014.04.045.
ieee: G. Hennequin, T. P. Vogels, and W. Gerstner, “Optimal control of transient
dynamics in balanced networks supports generation of complex movements,” Neuron,
vol. 82, no. 6. Elsevier, pp. 1394–1406, 2014.
ista: Hennequin G, Vogels TP, Gerstner W. 2014. Optimal control of transient dynamics
in balanced networks supports generation of complex movements. Neuron. 82(6),
1394–1406.
mla: Hennequin, Guillaume, et al. “Optimal Control of Transient Dynamics in Balanced
Networks Supports Generation of Complex Movements.” Neuron, vol. 82, no.
6, Elsevier, 2014, pp. 1394–406, doi:10.1016/j.neuron.2014.04.045.
short: G. Hennequin, T.P. Vogels, W. Gerstner, Neuron 82 (2014) 1394–1406.
date_created: 2020-06-25T13:07:37Z
date_published: 2014-06-18T00:00:00Z
date_updated: 2021-01-12T08:16:35Z
day: '18'
doi: 10.1016/j.neuron.2014.04.045
extern: '1'
external_id:
pmid:
- '24945778'
intvolume: ' 82'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6364799/
month: '06'
oa: 1
oa_version: Submitted Version
page: 1394-1406
pmid: 1
publication: Neuron
publication_identifier:
issn:
- 0896-6273
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Optimal control of transient dynamics in balanced networks supports generation
of complex movements
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 82
year: '2014'
...
---
_id: '8023'
abstract:
- lang: eng
text: Uniform random sparse network architectures are ubiquitous in computational
neuroscience, but the implicit hypothesis that they are a good representation
of real neuronal networks has been met with skepticism. Here we used two experimental
data sets, a study of triplet connectivity statistics and a data set measuring
neuronal responses to channelrhodopsin stimuli, to evaluate the fidelity of thousands
of model networks. Network architectures comprised three neuron types (excitatory,
fast spiking, and nonfast spiking inhibitory) and were created from a set of rules
that govern the statistics of the resulting connection types. In a high-dimensional
parameter scan, we varied the degree distributions (i.e., how many cells each
neuron connects with) and the synaptic weight correlations of synapses from or
onto the same neuron. These variations converted initially uniform random and
homogeneously connected networks, in which every neuron sent and received equal
numbers of synapses with equal synaptic strength distributions, to highly heterogeneous
networks in which the number of synapses per neuron, as well as average synaptic
strength of synapses from or to a neuron were variable. By evaluating the impact
of each variable on the network structure and dynamics, and their similarity to
the experimental data, we could falsify the uniform random sparse connectivity
hypothesis for 7 of 36 connectivity parameters, but we also confirmed the hypothesis
in 8 cases. Twenty-one parameters had no substantial impact on the results of
the test protocols we used.
article_processing_charge: No
article_type: original
author:
- first_name: Christian
full_name: Tomm, Christian
last_name: Tomm
- first_name: Michael
full_name: Avermann, Michael
last_name: Avermann
- first_name: Carl
full_name: Petersen, Carl
last_name: Petersen
- first_name: Wulfram
full_name: Gerstner, Wulfram
last_name: Gerstner
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
citation:
ama: Tomm C, Avermann M, Petersen C, Gerstner W, Vogels TP. Connection-type-specific
biases make uniform random network models consistent with cortical recordings.
Journal of Neurophysiology. 2014;112(8):1801-1814. doi:10.1152/jn.00629.2013
apa: Tomm, C., Avermann, M., Petersen, C., Gerstner, W., & Vogels, T. P. (2014).
Connection-type-specific biases make uniform random network models consistent
with cortical recordings. Journal of Neurophysiology. American Physiological
Society. https://doi.org/10.1152/jn.00629.2013
chicago: Tomm, Christian, Michael Avermann, Carl Petersen, Wulfram Gerstner, and
Tim P Vogels. “Connection-Type-Specific Biases Make Uniform Random Network Models
Consistent with Cortical Recordings.” Journal of Neurophysiology. American
Physiological Society, 2014. https://doi.org/10.1152/jn.00629.2013.
ieee: C. Tomm, M. Avermann, C. Petersen, W. Gerstner, and T. P. Vogels, “Connection-type-specific
biases make uniform random network models consistent with cortical recordings,”
Journal of Neurophysiology, vol. 112, no. 8. American Physiological Society,
pp. 1801–1814, 2014.
ista: Tomm C, Avermann M, Petersen C, Gerstner W, Vogels TP. 2014. Connection-type-specific
biases make uniform random network models consistent with cortical recordings.
Journal of Neurophysiology. 112(8), 1801–1814.
mla: Tomm, Christian, et al. “Connection-Type-Specific Biases Make Uniform Random
Network Models Consistent with Cortical Recordings.” Journal of Neurophysiology,
vol. 112, no. 8, American Physiological Society, 2014, pp. 1801–14, doi:10.1152/jn.00629.2013.
short: C. Tomm, M. Avermann, C. Petersen, W. Gerstner, T.P. Vogels, Journal of Neurophysiology
112 (2014) 1801–1814.
date_created: 2020-06-25T13:08:30Z
date_published: 2014-10-15T00:00:00Z
date_updated: 2021-01-12T08:16:35Z
day: '15'
ddc:
- '570'
doi: 10.1152/jn.00629.2013
extern: '1'
external_id:
pmid:
- '24944218'
file:
- access_level: open_access
checksum: 7c06a086da6f924342650de6dc555c3f
content_type: application/pdf
creator: cziletti
date_created: 2020-07-16T10:12:13Z
date_updated: 2020-07-16T10:12:13Z
file_id: '8122'
file_name: 2014_JNeurophysiol_Tomm.pdf
file_size: 1632295
relation: main_file
success: 1
file_date_updated: 2020-07-16T10:12:13Z
has_accepted_license: '1'
intvolume: ' 112'
issue: '8'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/3.0/
month: '10'
oa: 1
oa_version: Published Version
page: 1801-1814
pmid: 1
publication: Journal of Neurophysiology
publication_identifier:
eissn:
- 1522-1598
issn:
- 0022-3077
publication_status: published
publisher: American Physiological Society
quality_controlled: '1'
status: public
title: Connection-type-specific biases make uniform random network models consistent
with cortical recordings
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 112
year: '2014'
...
---
_id: '8044'
abstract:
- lang: eng
text: Many questions concerning models in quantum mechanics require a detailed analysis
of the spectrum of the corresponding Hamiltonian, a linear operator on a suitable
Hilbert space. Of particular relevance for an understanding of the low-temperature
properties of a system is the structure of the excitation spectrum, which is the
part of the spectrum close to the spectral bottom. We present recent progress
on this question for bosonic many-body quantum systems with weak two-body interactions.
Such system are currently of great interest, due to their experimental realization
in ultra-cold atomic gases. We investigate the accuracy of the Bogoliubov approximations,
which predicts that the low-energy spectrum is made up of sums of elementary excitations,
with linear dispersion law at low momentum. The latter property is crucial for
the superfluid behavior the system.
article_processing_charge: No
author:
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: 'Seiringer R. Structure of the excitation spectrum for many-body quantum systems.
In: Proceeding of the International Congress of Mathematicans. Vol 3. International
Congress of Mathematicians; 2014:1175-1194.'
apa: 'Seiringer, R. (2014). Structure of the excitation spectrum for many-body quantum
systems. In Proceeding of the International Congress of Mathematicans (Vol.
3, pp. 1175–1194). Seoul, South Korea: International Congress of Mathematicians.'
chicago: Seiringer, Robert. “Structure of the Excitation Spectrum for Many-Body
Quantum Systems.” In Proceeding of the International Congress of Mathematicans,
3:1175–94. International Congress of Mathematicians, 2014.
ieee: R. Seiringer, “Structure of the excitation spectrum for many-body quantum
systems,” in Proceeding of the International Congress of Mathematicans,
Seoul, South Korea, 2014, vol. 3, pp. 1175–1194.
ista: 'Seiringer R. 2014. Structure of the excitation spectrum for many-body quantum
systems. Proceeding of the International Congress of Mathematicans. ICM: International
Congress of Mathematicans vol. 3, 1175–1194.'
mla: Seiringer, Robert. “Structure of the Excitation Spectrum for Many-Body Quantum
Systems.” Proceeding of the International Congress of Mathematicans, vol.
3, International Congress of Mathematicians, 2014, pp. 1175–94.
short: R. Seiringer, in:, Proceeding of the International Congress of Mathematicans,
International Congress of Mathematicians, 2014, pp. 1175–1194.
conference:
end_date: 2014-08-21
location: Seoul, South Korea
name: 'ICM: International Congress of Mathematicans'
start_date: 2014-08-13
date_created: 2020-06-29T07:59:35Z
date_published: 2014-08-01T00:00:00Z
date_updated: 2023-10-17T11:12:33Z
day: '01'
department:
- _id: RoSe
intvolume: ' 3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.icm2014.org/en/vod/proceedings.html
month: '08'
oa: 1
oa_version: Published Version
page: 1175-1194
publication: Proceeding of the International Congress of Mathematicans
publication_identifier:
isbn:
- '9788961058063'
publication_status: published
publisher: International Congress of Mathematicians
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structure of the excitation spectrum for many-body quantum systems
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2014'
...
---
_id: '809'
abstract:
- lang: eng
text: The assembly of HIV-1 is mediated by oligomerization of the major structural
polyprotein, Gag, into a hexameric protein lattice at the plasma membrane of the
infected cell. This leads to budding and release of progeny immature virus particles.
Subsequent proteolytic cleavage of Gag triggers rearrangement of the particles
to form mature infectious virions. Obtaining a structural model of the assembled
lattice of Gag within immature virus particles is necessary to understand the
interactions that mediate assembly of HIV-1 particles in the infected cell, and
to describe the substrate that is subsequently cleaved by the viral protease.
An 8-Å resolution structure of an immature virus-like tubular array assembled
from a Gag-derived protein of the related retrovirus Mason-Pfizer monkey virus
(M-PMV) has previously been reported, and a model for the arrangement of the HIV-1
capsid (CA) domains has been generated based on homology to this structure. Here
we have assembled tubular arrays of a HIV-1 Gag-derived protein with an immature-like
arrangement of the C-terminal CA domains and have solved their structure by using
hybrid cryo-EM and tomography analysis. The structure reveals the arrangement
of the C-terminal domain of CA within an immature-like HIV-1 Gag lattice, and
provides, to our knowledge, the first high-resolution view of the region immediately
downstream of CA, which is essential for assembly, and is significantly different
from the respective region in M-PMV. Our results reveal a hollow column of density
for this region in HIV-1 that is compatible with the presence of a six-helix bundle
at this position.
acknowledgement: 'The authors thank Leonardo Trabuco for help with running MDFF, Maria
Anders for preparing amprenavir-inhibited virus, Marie-Christine Vaney for help
with X-ray data processing and structure refinement, Ahmed Haouz and Patrick Weber
(robotized crystallization facility Proteopole, Institut Pasteur) for help in crystal
screening, and the European Molecular Biology Laboratory (EMBL) Information Technology
Services Unit and Frank Thommen for technical support. This study was supported
by Deutsche Forschungsgemeinschaft Grants BR 3635/2-1 (to J.A.G.B.) and KR 906/7-1
(to H.-G.K.) and a Federation of European Biochemical Societies long-term fellowship
(to T.A.M.B.). The laboratory of J.A.G.B. acknowledges financial support from EMBL
and the Chica und Heinz Schaller Stiftung. '
author:
- first_name: Tanmay
full_name: Bharata, Tanmay A
last_name: Bharata
- first_name: Luis
full_name: Menendez, Luis R
last_name: Menendez
- first_name: Wim
full_name: Hagena, Wim J
last_name: Hagena
- first_name: Vanda
full_name: Luxd, Vanda
last_name: Luxd
- first_name: Sebastien
full_name: Igonete, Sebastien
last_name: Igonete
- first_name: Martin
full_name: Schorba, Martin
last_name: Schorba
- first_name: Florian
full_name: Florian Schur
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Hans
full_name: Kraüsslich, Hans Georg
last_name: Kraüsslich
- first_name: John
full_name: Briggsa, John A
last_name: Briggsa
citation:
ama: Bharata T, Menendez L, Hagena W, et al. Cryo electron microscopy of tubular
arrays of HIV-1 Gag resolves structures essential for immature virus assembly.
PNAS. 2014;111(22):8233-8238. doi:10.1073/pnas.1401455111
apa: Bharata, T., Menendez, L., Hagena, W., Luxd, V., Igonete, S., Schorba, M.,
… Briggsa, J. (2014). Cryo electron microscopy of tubular arrays of HIV-1 Gag
resolves structures essential for immature virus assembly. PNAS. National
Academy of Sciences. https://doi.org/10.1073/pnas.1401455111
chicago: Bharata, Tanmay, Luis Menendez, Wim Hagena, Vanda Luxd, Sebastien Igonete,
Martin Schorba, Florian KM Schur, Hans Kraüsslich, and John Briggsa. “Cryo Electron
Microscopy of Tubular Arrays of HIV-1 Gag Resolves Structures Essential for Immature
Virus Assembly.” PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1401455111.
ieee: T. Bharata et al., “Cryo electron microscopy of tubular arrays of HIV-1
Gag resolves structures essential for immature virus assembly,” PNAS, vol.
111, no. 22. National Academy of Sciences, pp. 8233–8238, 2014.
ista: Bharata T, Menendez L, Hagena W, Luxd V, Igonete S, Schorba M, Schur FK, Kraüsslich
H, Briggsa J. 2014. Cryo electron microscopy of tubular arrays of HIV-1 Gag resolves
structures essential for immature virus assembly. PNAS. 111(22), 8233–8238.
mla: Bharata, Tanmay, et al. “Cryo Electron Microscopy of Tubular Arrays of HIV-1
Gag Resolves Structures Essential for Immature Virus Assembly.” PNAS, vol.
111, no. 22, National Academy of Sciences, 2014, pp. 8233–38, doi:10.1073/pnas.1401455111.
short: T. Bharata, L. Menendez, W. Hagena, V. Luxd, S. Igonete, M. Schorba, F.K.
Schur, H. Kraüsslich, J. Briggsa, PNAS 111 (2014) 8233–8238.
date_created: 2018-12-11T11:48:37Z
date_published: 2014-06-03T00:00:00Z
date_updated: 2021-01-12T08:16:50Z
day: '03'
doi: 10.1073/pnas.1401455111
extern: 1
intvolume: ' 111'
issue: '22'
month: '06'
page: 8233 - 8238
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '6838'
quality_controlled: 0
status: public
title: Cryo electron microscopy of tubular arrays of HIV-1 Gag resolves structures
essential for immature virus assembly
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
volume: 111
year: '2014'
...
---
_id: '1507'
abstract:
- lang: eng
text: The Wigner-Dyson-Gaudin-Mehta conjecture asserts that the local eigenvalue
statistics of large real and complex Hermitian matrices with independent, identically
distributed entries are universal in a sense that they depend only on the symmetry
class of the matrix and otherwise are independent of the details of the distribution.
We present the recent solution to this half-century old conjecture. We explain
how stochastic tools, such as the Dyson Brownian motion, and PDE ideas, such as
De Giorgi-Nash-Moser regularity theory, were combined in the solution. We also
show related results for log-gases that represent a universal model for strongly
correlated systems. Finally, in the spirit of Wigner’s original vision, we discuss
the extensions of these universality results to more realistic physical systems
such as random band matrices.
acknowledgement: The author is partially supported by SFB-TR 12 Grant of the German
Research Council.
article_processing_charge: No
author:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
citation:
ama: 'Erdös L. Random matrices, log-gases and Hölder regularity. In: Proceedings
of the International Congress of Mathematicians. Vol 3. International Congress
of Mathematicians; 2014:214-236.'
apa: 'Erdös, L. (2014). Random matrices, log-gases and Hölder regularity. In Proceedings
of the International Congress of Mathematicians (Vol. 3, pp. 214–236). Seoul,
Korea: International Congress of Mathematicians.'
chicago: Erdös, László. “Random Matrices, Log-Gases and Hölder Regularity.” In Proceedings
of the International Congress of Mathematicians, 3:214–36. International Congress
of Mathematicians, 2014.
ieee: L. Erdös, “Random matrices, log-gases and Hölder regularity,” in Proceedings
of the International Congress of Mathematicians, Seoul, Korea, 2014, vol.
3, pp. 214–236.
ista: 'Erdös L. 2014. Random matrices, log-gases and Hölder regularity. Proceedings
of the International Congress of Mathematicians. ICM: International Congress of
Mathematicians vol. 3, 214–236.'
mla: Erdös, László. “Random Matrices, Log-Gases and Hölder Regularity.” Proceedings
of the International Congress of Mathematicians, vol. 3, International Congress
of Mathematicians, 2014, pp. 214–36.
short: L. Erdös, in:, Proceedings of the International Congress of Mathematicians,
International Congress of Mathematicians, 2014, pp. 214–236.
conference:
end_date: 2014-08-21
location: Seoul, Korea
name: 'ICM: International Congress of Mathematicians'
start_date: 2014-08-13
date_created: 2018-12-11T11:52:25Z
date_published: 2014-08-01T00:00:00Z
date_updated: 2023-10-17T11:12:55Z
day: '01'
department:
- _id: LaEr
ec_funded: 1
intvolume: ' 3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1407.5752
month: '08'
oa: 1
oa_version: Submitted Version
page: 214 - 236
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Proceedings of the International Congress of Mathematicians
publication_status: published
publisher: International Congress of Mathematicians
publist_id: '5670'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Random matrices, log-gases and Hölder regularity
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2014'
...