Evidence map›Paper›PMID 31031417›Full record

ArticleJournal of computational physics2019

A hybrid smoothed dissipative particle dynamics (SDPD) spatial stochastic simulation algorithm (sSSA) for advection-diffusion-reaction problems.

Drawert Brian, Jacob Bruno, Li Zhen, Yi Tau-Mu, Petzold Linda

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In one paragraph

Article in Journal of computational physics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

5 authors.

Drawert Brian *Department of Computer Science, University of North Carolina at Asheville, Asheville, North Carolina, 28804, USA.
Jacob Bruno *Department of Mechanical Engineering, University of California-Santa Barbara, Santa Barbara, California, 93106, USA.
Li ZhenDivision of Applied Mathematics, Brown University, Providence, Rhode Island 02912, USA.
Yi Tau-MuDepartment of Molecular, Cellular, and Developmental Biology, University of California-Santa Barbara, Santa Barbara, California 93106, USA.
Petzold LindaDepartment of Mechanical Engineering, University of California-Santa Barbara, Santa Barbara, California, 93106, USA.

Funding

StochSS: A Next-Generation Toolkit for Simulation-Driven Biological DiscoveryR01EB014877 · NIBIB · UNIVERSITY OF CALIFORNIA SANTA BARBARA · PI PETZOLD, LINDA R. · 2012 to 2022
$3.9M
Bridging the Gap Between Molecular and Mechanical Control of Cell MorphogenesisR01GM113241 · NIGMS · UNIVERSITY OF CALIFORNIA SANTA BARBARA · PI CAMPAS, OTGER · 2014 to 2018
$1.7M
NIBIB NIH HHS R01 EB014877NIGMS NIH HHS R01 GM113241
6 · The paper itself

Abstract

We have developed a new algorithm which merges discrete stochastic simulation, using the spatial stochastic simulation algorithm (sSSA), with the particle based fluid dynamics simulation framework of smoothed dissipative particle dynamics (SDPD). This hybrid algorithm enables discrete stochastic simulation of spatially resolved chemically reacting systems on a mesh-free dynamic domain with a Lagrangian frame of reference. SDPD combines two popular mesoscopic techniques: smoothed particle hydrodynamics and dissipative particle dynamics (DPD), linking the macroscopic and mesoscopic hydrodynamics effects of these two methods. We have implemented discrete stochastic simulation using the reaction-diffusion master equations (RDME) formalism, and deterministic reaction-diffusion equations based on the SDPD method. We validate the new method by comparing our results to four canonical models, and demonstrate the versatility of our method by simulating a flow containing a chemical gradient past a yeast cell in a microfluidics chamber.

Indexed as

Discrete Stochastic SimulationParticle Based Fluid DynamicsReaction-Diffusion Master Equation

Identifiers

PMID31031417
PMCPMC6481948

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Registered trials

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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.