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Enabling surface dependent diffusion in spatial simulations using Smoldyn

Overview of attention for article published in BMC Research Notes, December 2015
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  • Above-average Attention Score compared to outputs of the same age and source (62nd percentile)

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3 X users

Citations

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2 Dimensions

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7 Mendeley
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Title
Enabling surface dependent diffusion in spatial simulations using Smoldyn
Published in
BMC Research Notes, December 2015
DOI 10.1186/s13104-015-1723-6
Pubmed ID
Authors

Christine Seeliger, Nicolas Le Novère

Abstract

Spatial computer simulations are becoming more feasible and relevant for studies of signaling pathways due to technical advances in experimental techniques yielding better high resolution data. However, many common single particle simulation environments used in computational systems biology lack the functionality to easily implement spatially heterogeneous membrane environments. We introduce an extension to the single particle simulator Smoldyn that allows modeling of surface-dependent diffusion, without unnecessarily increasing molecular states or numbers, hence avoiding explosion of molecule and reaction definitions. We demonstrate the usefulness of this approach studying AMPA receptor diffusion at the postsynaptic density and its spatial trapping without introducing hypothetical scaffold elements or membrane barriers.

X Demographics

X Demographics

The data shown below were collected from the profiles of 3 X users who shared this research output. Click here to find out more about how the information was compiled.
Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 7 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Spain 1 14%
Unknown 6 86%

Demographic breakdown

Readers by professional status Count As %
Researcher 3 43%
Student > Bachelor 1 14%
Other 1 14%
Student > Master 1 14%
Unknown 1 14%
Readers by discipline Count As %
Agricultural and Biological Sciences 3 43%
Physics and Astronomy 1 14%
Materials Science 1 14%
Neuroscience 1 14%
Unknown 1 14%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 2. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 16 December 2015.
All research outputs
#13,451,339
of 22,834,308 outputs
Outputs from BMC Research Notes
#1,684
of 4,265 outputs
Outputs of similar age
#187,412
of 388,741 outputs
Outputs of similar age from BMC Research Notes
#56
of 148 outputs
Altmetric has tracked 22,834,308 research outputs across all sources so far. This one is in the 39th percentile – i.e., 39% of other outputs scored the same or lower than it.
So far Altmetric has tracked 4,265 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 5.5. This one has gotten more attention than average, scoring higher than 58% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 388,741 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 50% of its contemporaries.
We're also able to compare this research output to 148 others from the same source and published within six weeks on either side of this one. This one has gotten more attention than average, scoring higher than 62% of its contemporaries.