优化反应坐标用于分析增强采样.
Julian Widmer1, Cassiano Langini1, Andreas Vitalis1
1University of Zurich, Department of Biochemistry, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
The Journal of chemical physics
|July 5, 2023
概括
无监督反应坐标测定有助于分析复杂的生物模拟. 这种方法从增强的采样数据中准确地重建平衡性质和运动速率.
科学领域:
- 计算生物学 计算生物学
- 生物物理学的生物物理.
- 分子动力学分子动力学
背景情况:
- 原子模拟提供了高分辨率的生物学见解,但需要对相关时间尺度进行增强的采样.
- 分析加速模拟数据需要统计学上正确的重量和缩来进行解释.
研究的目的:
- 评估一种用于确定最佳反应坐标 (RCs) 的新型无监督方法.
- 证明这些RCs对生物系统中增强采样数据的分析和重权重的有用性.
主要方法:
- 无监督RC测定在增强型采样模拟中的应用.
- 使用优化RCs对模拟轨迹进行统计重量调整.
- 结果与平衡模拟和其他分析方法 (马尔科夫状态模型,SAPPHIRE) 的比较.
主要成果:
- 优化的RC有效地从模型系统的增强样本取样轨迹中重建平衡性质.
- 再加权RC的运动速率常数和自由能量概况与平衡模拟值密切匹配.
- 该方法已成功应用于一个更复杂的系统:三脱离原体,揭示RC的优点和局限性.
结论:
- 对反应坐标的无监督确定是分析和重量化分子模拟中增强采样数据的强大工具.
- 这种方法与已知方法 (如马尔科夫状态模型和SAPPHIRE分析) 提供了协同作用的潜力.
- 这些发现凸显了该方法能够从原子模拟中改进对复杂生物过程的解释的能力.
相关概念视频
Measuring Reaction Rates
25.4K
Polarimetry finds application in chemical kinetics to measure the concentration and reaction kinetics of optically active substances during a chemical reaction. Optically active substances have the capability of rotating the plane of polarization of linearly polarized light passing through them—a feature called optical rotation. Optical activity is attributed to the molecular structure of substances. Normal monochromatic light is unpolarized and possesses oscillations of the electrical...
25.4K
Quantitative Aspects of Drug-Receptor Interaction
1.0K
The receptor occupancy theory connects a drug's response to the number of occupied receptors. With higher drug concentrations, more receptors are occupied, leading to increased responses. The formation of drug-receptor complexes involves association and dissociation rates, which reach equilibrium when the forward and backward reactions are equal. The equilibrium association constant (Ka) and its inverse, the equilibrium dissociation constant (Kd), indicate drug affinity. Higher Ka and lower...
1.0K
Energy Diagrams, Transition States, and Intermediates
16.7K
Free-energy diagrams, or reaction coordinate diagrams, are graphs showing the energy changes that occur during a chemical reaction. The reaction coordinate represented on the horizontal axis shows how far the reaction has progressed structurally. Positions along the x-axis close to the reactants have structures resembling the reactants, while positions close to the products resemble the products. Peaks on the energy diagram represent stable structures with measurable lifetimes, while...
16.7K
Standard Entropy Change for a Reaction
20.6K
Entropy is a state function, so the standard entropy change for a chemical reaction (ΔS°rxn) can be calculated from the difference in standard entropy between the products and the reactants.
20.6K
The Integrated Rate Law: The Dependence of Concentration on Time
35.5K
While the differential rate law relates the rate and concentrations of reactants, a second form of rate law called the integrated rate law relates concentrations of reactants and time. Integrated rate laws can be used to determine the amount of reactant or product present after a period of time or to estimate the time required for a reaction to proceed to a certain extent. For example, an integrated rate law helps determine the length of time a radioactive material must be stored for its...
35.5K


