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Open-Source Workflows for Reproducible Molecular Simulation.

Record Type:	Electronic resources : Monograph/item
Title/Author:	Open-Source Workflows for Reproducible Molecular Simulation./
Author:	Fothergill, Jenny W.
Description:	1 online resource (326 pages)
Notes:	Source: Dissertations Abstracts International, Volume: 84-03, Section: B.
Contained By:	Dissertations Abstracts International84-03B.
Subject:	Computational chemistry. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=29259508click for full text (PQDT)
ISBN:	9798351435428

Open-Source Workflows for Reproducible Molecular Simulation.
Fothergill, Jenny W.

Open-Source Workflows for Reproducible Molecular Simulation. - 1 online resource (326 pages)

Source: Dissertations Abstracts International, Volume: 84-03, Section: B.

Thesis (Ph.D.)--Boise State University, 2022.

Includes bibliographical references

We apply molecular simulation to predict the equilibrium structure of organic molecular aggregates and how these structures determine material properties, with a focus on software engineering practices for ensuring correctness.Because simulations are implemented in software, there is potential for authentic scientific reproducibility in such work: An entire experimental apparatus (codebase) can be given to another investigator who should be able to use the same processes to find the same answers. Yet in practice, there are many barriers which stand in the way of reproducible molecular simulations that we address through automation, generalization, and software packaging. Collaboration on and application of the Molecular Simulation and Design Framework (MoSDeF) features prominently.We present structural investigations of organic molecule aggregates and the development of infrastructure and workflows that help manage, initialize, and analyze molecular simulation results through the following scientific applications (1)A screening study wherein we validate self-assembled poly-3-hexylthiophene (P3HT) morphologies show the same state dependency as in prior work, and (2) A multi-university collaborative reproducibility study where we examine modeling choices that give rise to differences between simulation engines. In aggregate, we reinforce the need for pipelines and practices emphasizing transferability, reproducibility, useability, and extensibility in molecular simulation.

Electronic reproduction.
Ann Arbor, Mich. :
ProQuest,
2023

Mode of access: World Wide Web

ISBN: 9798351435428Subjects--Topical Terms:

3350019
Computational chemistry.
Subjects--Index Terms:

Molecular simulationIndex Terms--Genre/Form:

542853
Electronic books.

Open-Source Workflows for Reproducible Molecular Simulation.
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245 1 0 $a Open-Source Workflows for Reproducible Molecular Simulation.
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500 $a Source: Dissertations Abstracts International, Volume: 84-03, Section: B.
500 $a Advisor: Jankowski, Eric; King, Matthew D.
502 $a Thesis (Ph.D.)--Boise State University, 2022.
504 $a Includes bibliographical references
520 $a We apply molecular simulation to predict the equilibrium structure of organic molecular aggregates and how these structures determine material properties, with a focus on software engineering practices for ensuring correctness.Because simulations are implemented in software, there is potential for authentic scientific reproducibility in such work: An entire experimental apparatus (codebase) can be given to another investigator who should be able to use the same processes to find the same answers. Yet in practice, there are many barriers which stand in the way of reproducible molecular simulations that we address through automation, generalization, and software packaging. Collaboration on and application of the Molecular Simulation and Design Framework (MoSDeF) features prominently.We present structural investigations of organic molecule aggregates and the development of infrastructure and workflows that help manage, initialize, and analyze molecular simulation results through the following scientific applications (1)A screening study wherein we validate self-assembled poly-3-hexylthiophene (P3HT) morphologies show the same state dependency as in prior work, and (2) A multi-university collaborative reproducibility study where we examine modeling choices that give rise to differences between simulation engines. In aggregate, we reinforce the need for pipelines and practices emphasizing transferability, reproducibility, useability, and extensibility in molecular simulation.
533 $a Electronic reproduction. $b Ann Arbor, Mich. : $c ProQuest, $d 2023
538 $a Mode of access: World Wide Web
650 4 $a Computational chemistry. $3 3350019
650 4 $a Materials science. $3 543314
653 $a Molecular simulation
653 $a Organic photovoltaics
653 $a Reproducibility
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773 0 $t Dissertations Abstracts International $g 84-03B.
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