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An experiment often consists of more than a single step. In this case, measurements at each step give rise to uncertainty. Because the measurements occur in successive steps, the uncertainty in one step necessarily contributes to that in the subsequent step. As we perform statistical analysis on these types of experiments, we must learn to account for the propagation of uncertainty from one step to the next. The propagation of uncertainty depends on the type of arithmetic operation performed on...
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MD-BAX:用于输入依赖噪声的分子动力学模拟的通用贝叶斯设计框架.

Tianhong Tan1,2, Ting-Yeh Chen1, Jacob R Breese1

  • 1Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio 43210, USA.

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我们开发了MD-贝叶斯算法执行 (BAX),这是一个自动化框架,可以有效指导分子动力学 (MD) 模拟. MD-BAX通过基于不确定性的战略选择参数来识别系统属性,提高复杂分子建模的计算效率.

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科学领域:

  • 计算化学是一种计算化学.
  • 统计力学就是统计力学.
  • 聚合物科学 聚合物科学

背景情况:

  • 分子动力学 (MD) 模拟对于理解分子行为至关重要,但在计算上昂贵.
  • 探索广的参数空间是具有挑战性的,因为噪音和昂贵的模拟结果.
  • 现有的贝叶斯优化方法专注于单个最佳条件,而不是更广泛的系统属性.

研究的目的:

  • 介绍MD-贝叶斯算法执行 (BAX),用于高效的MD模拟设计的自动化框架.
  • 能够识别更广泛的系统属性,如相位过渡和水平集.
  • 提高绘制分子结构,环境和行为之间的关系的效率.

主要方法:

  • MD-BAX利用BAX的收购策略来引导模拟活动向有意义的功能.
  • 采用高斯过程替代模型,从MD轨迹统计数据中估计的输入依赖噪声.
  • 包含不确定性估计,以战略性选择下一个模拟参数.

主要成果:

  • MD-BAX有效地引导模拟,以确定更广泛的系统属性,而不仅仅是最佳条件.
  • 包括轨道衍生噪声在内,可以改善不确定性校准,从而获得更可靠的指导.
  • 在一个案例研究中,成功地绘制了聚合物结构,溶剂质量和结构性行为之间的关系.

结论:

  • MD-BAX是MD模拟的BAX框架的一个域信息化专业化.
  • 该框架有效地从基于轨迹的随机输出中推断出关键系统行为.
  • 广泛适用于需要从模拟中推断系统属性的分子建模问题.