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解析计算(生物)材料建模的前景。

Unfolding the prospects of computational (bio)materials modeling.

机构信息

Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands.

Laboratory of Molecular Modeling, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland.

出版信息

J Chem Phys. 2020 Sep 14;153(10):100901. doi: 10.1063/5.0019773.

Abstract

In this perspective communication, we briefly sketch the current state of computational (bio)material research and discuss possible solutions for the four challenges that have been increasingly identified within this community: (i) the desire to develop a unified framework for testing the consistency of implementation and physical accuracy for newly developed methodologies, (ii) the selection of a standard format that can deal with the diversity of simulation data and at the same time simplifies data storage, data exchange, and data reproduction, (iii) how to deal with the generation, storage, and analysis of massive data, and (iv) the benefits of efficient "core" engines. Expressed viewpoints are the result of discussions between computational stakeholders during a Lorentz center workshop with the prosaic title Workshop on Multi-scale Modeling and are aimed at (i) improving validation, reporting and reproducibility of computational results, (ii) improving data migration between simulation packages and with analysis tools, (iii) popularizing the use of coarse-grained and multi-scale computational tools among non-experts and opening up these modern computational developments to an extended user community.

摘要

在本次观点交流中,我们简要概述了当前计算(生物)材料研究的现状,并讨论了该领域中日益凸显的四项挑战的可能解决方案:(i) 希望为新开发的方法建立一个统一的框架,以测试其实现和物理准确性的一致性;(ii) 选择一种标准格式,以处理模拟数据的多样性,同时简化数据存储、数据交换和数据再现;(iii) 如何处理大规模数据的生成、存储和分析;(iv) 高效“核心”引擎的优势。这些观点是在洛伦兹中心(Lorentz center)举办的一次题为“多尺度建模研讨会”的会议上,计算利益相关者讨论的结果,旨在(i) 提高计算结果的验证、报告和可重复性;(ii) 改善模拟包之间以及与分析工具的数据迁移;(iii) 在非专家中推广使用粗粒化和多尺度计算工具,并将这些现代计算发展开放给更广泛的用户群体。

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