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Detailed Simulations of Cell Biology with Smoldyn 2.1

Overview of attention for article published in PLoS Computational Biology, March 2010
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About this Attention Score

  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (95th percentile)
  • High Attention Score compared to outputs of the same age and source (83rd percentile)

Mentioned by

blogs
3 blogs
policy
1 policy source
twitter
3 X users
wikipedia
3 Wikipedia pages

Citations

dimensions_citation
285 Dimensions

Readers on

mendeley
257 Mendeley
citeulike
10 CiteULike
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Title
Detailed Simulations of Cell Biology with Smoldyn 2.1
Published in
PLoS Computational Biology, March 2010
DOI 10.1371/journal.pcbi.1000705
Pubmed ID
Authors

Steven S. Andrews, Nathan J. Addy, Roger Brent, Adam P. Arkin

Abstract

Most cellular processes depend on intracellular locations and random collisions of individual protein molecules. To model these processes, we developed algorithms to simulate the diffusion, membrane interactions, and reactions of individual molecules, and implemented these in the Smoldyn program. Compared to the popular MCell and ChemCell simulators, we found that Smoldyn was in many cases more accurate, more computationally efficient, and easier to use. Using Smoldyn, we modeled pheromone response system signaling among yeast cells of opposite mating type. This model showed that secreted Bar1 protease might help a cell identify the fittest mating partner by sharpening the pheromone concentration gradient. This model involved about 200,000 protein molecules, about 7000 cubic microns of volume, and about 75 minutes of simulated time; it took about 10 hours to run. Over the next several years, as faster computers become available, Smoldyn will allow researchers to model and explore systems the size of entire bacterial and smaller eukaryotic cells.

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 257 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 11 4%
Switzerland 3 1%
Spain 3 1%
Japan 3 1%
United Kingdom 2 <1%
Germany 1 <1%
Netherlands 1 <1%
Italy 1 <1%
Norway 1 <1%
Other 5 2%
Unknown 226 88%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 74 29%
Researcher 53 21%
Student > Master 29 11%
Professor 18 7%
Professor > Associate Professor 17 7%
Other 45 18%
Unknown 21 8%
Readers by discipline Count As %
Agricultural and Biological Sciences 93 36%
Biochemistry, Genetics and Molecular Biology 29 11%
Computer Science 26 10%
Engineering 20 8%
Physics and Astronomy 19 7%
Other 43 17%
Unknown 27 11%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 26. 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 08 September 2023.
All research outputs
#1,493,509
of 25,394,764 outputs
Outputs from PLoS Computational Biology
#1,261
of 8,964 outputs
Outputs of similar age
#4,962
of 102,851 outputs
Outputs of similar age from PLoS Computational Biology
#9
of 55 outputs
Altmetric has tracked 25,394,764 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 94th percentile: it's in the top 10% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 8,964 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 20.4. This one has done well, scoring higher than 85% 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 102,851 tracked outputs that were published within six weeks on either side of this one in any source. This one has done particularly well, scoring higher than 95% of its contemporaries.
We're also able to compare this research output to 55 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 83% of its contemporaries.