ArticleBMC research notes2015
Enabling surface dependent diffusion in spatial simulations using Smoldyn.
Article in BMC research notes, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
2 citing papers in PubMed.
- AMPA receptor trafficking and its role in heterosynaptic plasticity.Scientific reports · 2018Article
- Electrodiffusion phenomena in neuroscience: a neglected companion.Nature reviews. Neuroscience · 2017Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
backgroundSpatial 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.
resultsWe 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.
conclusionsWe 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.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.