对分子过渡率的指导估计
Andrew R Mitchell1, Grant M Rotskoff1
1Department of Chemistry, Stanford University, Stanford, California 94305, United States.
Journal of chemical theory and computation
|October 18, 2024
概括
这项研究使用基于物理的机器学习来准确计算复杂物理系统的提交函数. 这种方法可以精确预测分子动力学中的过渡速率.
科学领域:
- 计算物理 计算物理
- 机器学习 机器学习
- 化学动力学 化学动力学
背景情况:
- 提交函数量化了物理系统中超稳态之间的过渡概率.
- 参数化高维提交函数在计算上具有挑战性.
- 基于物理的机器学习为解决复杂微分方程提供了一个有前途的方法.
研究的目的:
- 为了利用半组方法来学习提交函数.
- 评估学习的提交函数对预测动态量 (如过渡率) 的有用性.
- 为了提高提交函数计算的准确性和计算范围.
主要方法:
- 使用半组方法与神经网络相结合,学习提交函数.
- 为了提高准确性,重构目标函数.
- 实施适应性采样策略,以实现高效的计算.
- 应用Hill关系来从提交函数中推导过渡率.
主要成果:
- 通过对象函数重构和自适应采样,实现了提交函数的高度准确的表示.
- 证明了学习过的提交函数能够预测动态量的能力.
- 通过应用希尔关系,成功地获得了分子系统的准确过渡率.
结论:
- 基于物理的机器学习,特别是半组方法,为计算高维提交函数提供了有效的方法.
- 改进的目标函数和抽样策略提高了犯人计算的准确性.
- 衍生出的提交函数准确地预测了分子系统中的过渡速率,推进了化学动力学的研究.
更多相关视频
09:04Studying Ribonucleotide Incorporation: Strand-specific Detection of Ribonucleotides in the Yeast Genome and Measuring Ribonucleotide-induced Mutagenesis
Published on: July 26, 2018
7.7K
05:56Exploring Caspase Mutations and Post-Translational Modification by Molecular Modeling Approaches
Published on: October 13, 2022
1.3K
相关概念视频
UV–Vis Spectroscopy: Molecular Electronic Transitions
1.4K
In Ultraviolet–Visible (UV–Vis) spectroscopy, the absorption of electromagnetic radiation is used to probe the electronic structure of molecules. This technique provides insights into molecular electronic transitions, particularly the movement of electrons between different molecular orbitals. Radiation is absorbed if the energy of the electromagnetic radiation passing through the molecule is precisely equal to the energy difference between the excited and ground states. During this...
1.4K
Measuring Reaction Rates
24.7K
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...
24.7K
Cooperative Allosteric Transitions
7.9K
Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
7.9K
Temperature Dependence on Reaction Rate
81.2K
The Collision Theory
Atoms, molecules, or ions must collide before they can react with each other. Atoms must be close together to form chemical bonds. This premise is the basis for a theory that explains many observations regarding chemical kinetics, including factors affecting reaction rates.
The collision theory is based on the postulates that (i) the reaction rate is proportional to the rate of reactant collisions, (ii) the reacting species collide in an orientation allowing contact between...
Atoms, molecules, or ions must collide before they can react with each other. Atoms must be close together to form chemical bonds. This premise is the basis for a theory that explains many observations regarding chemical kinetics, including factors affecting reaction rates.
The collision theory is based on the postulates that (i) the reaction rate is proportional to the rate of reactant collisions, (ii) the reacting species collide in an orientation allowing contact between...
81.2K
Calculating Standard Free Energy Changes
20.7K
The free energy change for a reaction that occurs under the standard conditions of 1 bar pressure and at 298 K is called the standard free energy change. Since free energy is a state function, its value depends only on the conditions of the initial and final states of the system. A convenient and common approach to the calculation of free energy changes for physical and chemical reactions is by use of widely available compilations of standard state thermodynamic data. One method involves the...
20.7K
EDTA: Conditional Formation Constant
771
Each EDTA molecule has six binding sites: four carboxyl groups and two amino groups. The fully protonated form of EDTA is represented as H6Y2+. However, it can exist in different forms, H5Y+, H4Y, H3Y−, H2Y2−, and HY3−, depending on the pH of the solution. In very basic solutions with pH > 10.17, the fully deprotonated form, Y4−, is the predominant species that readily complexes with metal ions in a 1:1 ratio.
For the equilibrium reaction of the metal with the...
For the equilibrium reaction of the metal with the...
771
