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相关概念视频

Dimensional Analysis01:23

Dimensional Analysis

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Dimensional analysis is a powerful tool that is used in physics and engineering to understand and predict the behavior of physical systems. The basic idea behind dimensional analysis is to express physical quantities in terms of fundamental dimensions such as the mass, length, and time. Derived dimensions like the velocity, acceleration, and force are derived from the combinations of these fundamental dimensions.
Dimensional analysis allows us to analyze and compare physical quantities on a...
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Dimensionless Groups in Fluid Mechanics01:15

Dimensionless Groups in Fluid Mechanics

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Dimensionless groups in fluid mechanics provide simplified ratios that help analyze fluid behavior without relying on specific units. The Reynolds number (Re), which represents the ratio of inertial to viscous forces, distinguishes between laminar and turbulent flows, making it essential in the design of pipelines and aerodynamic surfaces. The Froude number (Fr), the ratio of inertial to gravitational forces, is particularly useful in predicting wave formation and hydraulic jumps in...
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Two-Dimensional (2D) NMR: Overview01:12

Two-Dimensional (2D) NMR: Overview

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The 1D NMR spectrum of large and complex molecules like natural products has complicated splitting patterns and overlapping signals, which can be easily interpreted using 2-dimensional (2D) NMR. Unlike 1D NMR, 2D NMR has two frequency axes that provide the coupling information between the nucleus A and nucleus B in a molecule. The process from which 2D spectra are obtained has four steps.
The first step is the preparation period, during which nucleus A is excited with a radiofrequency pulse....
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Problem Solving: Dimensional Analysis01:08

Problem Solving: Dimensional Analysis

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Every mathematical equation that connects separate distinct physical quantities must be dimensionally consistent, which implies it must abide by two rules. For this reason, the concept of dimension is crucial. The first rule is that an equation's expressions on either side of an equality must have the exact same dimension, i.e., quantities of the same dimension can be added or removed. The second rule stipulates that all popular mathematical functions, such as exponential, logarithmic, and...
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¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

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At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately 105 times per second. These two chair conformers are in equilibrium. The rapid ring flipping results in the interconversion of the axial proton to an equatorial proton and an equatorial to the axial proton. Such interconversions are too rapid and cannot be detected on the NMR timescale. Hence, the NMR spectrometer cannot distinguish between the...
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Collisions in Multiple Dimensions: Introduction01:05

Collisions in Multiple Dimensions: Introduction

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It is far more common for collisions to occur in two dimensions; that is, the initial velocity vectors are neither parallel nor antiparallel to each other. Let's see what complications arise from this. The first idea is that momentum is a vector. Like all vectors, it can be expressed as a sum of perpendicular components (usually, though not always, an x-component and a y-component, and a z-component if necessary). Thus, when the statement of conservation of momentum is written for a...
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用于分子动力学减小维度的自动编码器:集体变量维度,偏差和过渡状态.

Zineb Belkacemi1,2, Marc Bianciotto1, Hervé Minoux1

  • 1Integrated Drug Discovery, Molecular Design Sciences, Sanofi, Vitry-sur-Seine, France.

The Journal of chemical physics
|July 11, 2023
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概括

本研究使用自编码器学习的集体变量来描述热冲击蛋白90 (Hsp90) N端域动态. 从5D瓶中获得的2D集体变量有效地捕捉了Hsp90原始状态过渡.

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科学领域:

  • 生物化学 生物化学
  • 分子生物学分子生物学
  • 计算生物物理学的计算生物物理学

背景情况:

  • 热冲击蛋白90 (Hsp90) 是一个关键的分子伴侣.
  • Hsp90通过ATP水解来调节客户端蛋白的折叠和激活.
  • N端域 (NTD) 是 Hsp90.0 的活性位点.

研究的目的:

  • 描述Hsp90 NTD的动态行为.
  • 开发和应用自编码器学习的集体变量 (CVs) 用于Hsp90 NTD动态.
  • 在分子动力学模拟中研究CV的最佳维度.

主要方法:

  • 将实验性Hsp90 NTD结构集群到原生状态.
  • 无偏的分子动力学 (MD) 模拟来生成特定状态的数据集.
  • 训练具有不同架构和瓶尺寸 (k=1-10) 的自动编码器.
  • 适应性偏差力 兰格温动力学模拟使用学习的简历.

主要成果:

  • 通过额外的隐藏层,自动编码器的性能并没有显著提高.
  • 一个二维 (2D) 瓶提供了足够的信息,以代表国家.
  • 确定了一个最优的瓶尺寸为五个.
  • 从5D潜伏空间中选择2D简历,比直接学习2D简历的效果更好.
  • 使用偏向的自由能量动态观察到Hsp90原生状态之间的过渡.

结论:

  • 自动编码器学习的CV对于表征Hsp90 NTD动态是有效的.
  • 从更高维的潜空间中衍生出来的2D CV为观察状态转换提供了卓越的性能.
  • 这种方法推进了分子陪伴力学和构造性景观的研究.