Evidence map›Paper›PMID 25404761›Full record

ArticleChemical physics letters2014

A Multi-Scale Method for Dynamics Simulation in Continuum Solvent Models I: Finite-Difference Algorithm for Navier-Stokes Equation.

Li Xiao, Qin Cai, Zhilin Li, Hongkai Zhao, Ray Luo

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Chemical physics letters, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.

0numbers the graph read from it
0cells of the map it votes in
8citing 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

8 citing papers in PubMed.

  1. Improved Poisson-Boltzmann Methods for High-Performance Computing.Journal of chemical theory and computation · 2019
    Article
  2. An efficient second-order poisson-boltzmann method.Journal of computational chemistry · 2019
    Article
  3. Article
  4. Article
  5. A Continuum Poisson-Boltzmann Model for Membrane Channel Proteins.Journal of chemical theory and computation · 2017
    Article
  6. Article
  7. Article
  8. 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.

Li XiaoDepartment of Biomedical Engineering, University of California, Irvine, CA 92697 ; Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697.
Qin CaiDepartment of Biomedical Engineering, University of California, Irvine, CA 92697 ; Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697.
Zhilin LiDepartment of Mathematics, North Carolina State University, Raleigh, NC 27695.
Hongkai ZhaoDepartment of Mathematics, University of California, Irvine, CA 92697.
Ray LuoDepartment of Biomedical Engineering, University of California, Irvine, CA 92697 ; Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697 ; Department of Chemical Engineering and Materials Science, University of California, Irvine, CA 92697.

Funding

AMBER force field consortium: a coherent biomolecular simulation platformR01GM079383 · NIGMS · UNIVERSITY OF CALIFORNIA AT DAVIS · PI CIEPLAK, PIOTR, DUAN, YONG · 2007 to 2017
$4.7M
AMBER/PBSA: An Open-Source Computer Program for Accurate and Scalable Solvation Analysis ofBiomoleculesR01GM093040 · NIGMS · UNIVERSITY OF CALIFORNIA-IRVINE · PI LUO, RAY · 2010 to 2018
$2.2M
Mechanistic mixture models of mechanics of morphogenesis with murine measurementR01GM096195 · NIGMS · NORTH CAROLINA STATE UNIVERSITY RALEIGH · PI LUBKIN, SHARON R · 2010 to 2013
$1.4M
NIGMS NIH HHS R01 GM079383NIGMS NIH HHS R01 GM093040NIGMS NIH HHS R01 GM096195
6 · The paper itself

Abstract

A multi-scale framework is proposed for more realistic molecular dynamics simulations in continuum solvent models by coupling a molecular mechanics treatment of solute with a fluid mechanics treatment of solvent. This article reports our initial efforts to formulate the physical concepts necessary for coupling the two mechanics and develop a 3D numerical algorithm to simulate the solvent fluid via the Navier-Stokes equation. The numerical algorithm was validated with multiple test cases. The validation shows that the algorithm is effective and stable, with observed accuracy consistent with our design.

Identifiers

PMID25404761
PMCPMC4231827

What OpenQuestion holds

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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.