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相关概念视频

Kinetic Molecular Theory: Molecular Velocities, Temperature, and Kinetic Energy03:07

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The kinetic molecular theory qualitatively explains the behaviors described by the various gas laws. The postulates of this theory may be applied in a more quantitative fashion to derive these individual laws.
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The word "gas" comes from the Flemish word meaning "chaos," first used to describe vapors by the chemist J. B. van Helmont. Consider a container filled with gas, with a continuous and random motion of molecules. During collisions, the velocity component parallel to the wall is unchanged, and the component perpendicular to the wall reverses direction but does not change in magnitude. If the molecule’s velocity changes in the x-direction, then its momentum is changed.
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The ideal-gas equation, which is empirical, describes the behavior of gases by establishing relationships between their macroscopic properties. For example, Charles’ law states that volume and temperature are directly related. Gases, therefore, expand when heated at constant pressure. Although gas laws explain how the macroscopic properties change relative to one another, it does not explain the rationale behind it.
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Generating Controlled, Dynamic Chemical Landscapes to Study Microbial Behavior
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想象一个分子动力学轨迹的能量景观.

Vilmos Neuman1,2, Patryk A Wesołowski2, Krzysztof K Bojarski3,4

  • 1Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom.

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PubMed
概括

我们开发了一个开源程序,使用断开连接图可视化分子动力学能量景观. 该工具有效地从模拟数据中直接识别构造路径和层次结构,而无需进行几何优化.

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科学领域:

  • 计算化学的计算化学
  • 生物物理学的生物物理.
  • 材料科学 材料科学 材料科学

背景情况:

  • 分子动力学 (MD) 模拟产生了大量的数据.
  • 想象MD探索的复杂的能源景观是一项挑战.
  • 解释形状变化和路径需要高效的分析工具.

研究的目的:

  • 引入一个开源程序,用于将MD轨迹转换为断开连接图.
  • 为了提供能源景观的简洁和可解释的可视化.
  • 为了使探索的构造空间在没有几何优化的情况下进行直接分析.

主要方法:

  • 将萨维茨基-戈莱平滑应用于每个的热力学痕迹 (潜在能量或度).
  • 识别局部极端作为最小值和过渡状态的代理.
  • 生成用于断开连接图构建的文件,兼容各种集合和模拟类型.

主要成果:

  • 在标准硬件上快速处理大型MD数据集 (10^4-10^5).
  • 产生能源景观拓学的近似表示.
  • 在选定的分辨率上捕捉访问的结构和路径,反映MD时间表.

结论:

  • 开发的程序提供了一种有效的方法来分析MD模拟数据.
  • 断开连接图提供了可解释的结构概要的构造层次结构.
  • 这种方法有助于从模拟中直接了解分子行为和景观组织.