降低神经网络对反应分子系统产生潜力的成本
Krystof Brezina1, Hubert Beck1, Ondrej Marsalek1
1Charles University, Faculty of Mathematics and Physics, Ke Karlovu 3, 121 16, Prague 2, Czech Republic.
Journal of chemical theory and computation
|September 25, 2023
概括
这项研究介绍了过渡管采样,这是一种创新的方法,用于创建机器学习潜力的高效培训集. 这种方法通过优化几何选择来显著降低分子模拟的计算成本.
科学领域:
- 计算化学的计算化学
- 材料科学 材料科学 材料科学
- 分子动力学分子动力学
背景情况:
- 机器学习潜力 (MLP) 具有先进的分子模拟.
- 为MLP构建强大的训练集在计算上是昂贵的,通常需要广泛的初始计算.
- 需要全面的几何覆盖范围限制了MLP对复杂系统的适用性.
研究的目的:
- 开发一种计算效率高的方法,用于为MLP生成训练集.
- 为了减轻与训练集生成的参考ab initio模拟相关的高成本.
- 为了实现对具有复杂潜在能量景观的系统进行精确的分子模拟.
主要方法:
- 引入过渡管采样,以在过渡路径周围生成相关几何形状.
- 利用稀疏的局部正常模式扩展用于热几何生成.
- 采用一个积极的学习协议,以有效地选择几何形状,创建一个专注的训练集.
主要成果:
- 开发的方法产生了训练集,捕捉了必要的过渡路径几何,没有昂贵的参考轨迹.
- 经过这种方法培训的MLP的表现与经过完全ab initio数据培训的MLP相提并论.
- 这种方法提供了显著的计算加速,这是ML潜力的特征.
结论:
- 过渡管采样有效地减少了MLP的训练集生成的计算负担.
- 该方法产生了准确的ML潜力,适用于经典和路径积分模拟.
- 这种技术提高了将ML潜能应用于各种分子系统的实用性和效率.
相关概念视频
Negative Regulator Molecules
35.4K
Positive regulators allow a cell to advance through cell cycle checkpoints. Negative regulators have an equally important role as they terminate a cell’s progression through the cell cycle—or pause it—until the cell meets specific criteria.
35.4K
The Nernst Equation
41.2K
Nonstandard Reaction Conditions
The interconnection between standard cell potentials and various thermodynamic parameters such as the standard free energy change ΔG° and equilibrium constant K has been previously explored. For example, a redox reaction involving zinc(II) and tin(II) ions at 1 M concentration with Eºcell = +0.291 V and ΔG° = −56.2 kJ is spontaneous.
The interconnection between standard cell potentials and various thermodynamic parameters such as the standard free energy change ΔG° and equilibrium constant K has been previously explored. For example, a redox reaction involving zinc(II) and tin(II) ions at 1 M concentration with Eºcell = +0.291 V and ΔG° = −56.2 kJ is spontaneous.
41.2K
Thermodynamic Potentials
870
Thermodynamic potentials are state functions that are extremely useful in analyzing a thermodynamic system. They have dimensions of energy. The four important thermodynamic potentials are internal energy, enthalpy, Helmholtz free energy, and Gibbs free energy. These thermodynamic potentials can be expressed using two of the following variables: pressure, volume, temperature, and entropy. These two variables are expressed as the rate of change of the thermodynamic potential with respect to other...
870
Coupled Reactions
7.8K
Cellular processes such as building and breaking down complex molecules occur through stepwise chemical reactions. Some of these chemical reactions are spontaneous and release energy, whereas others require energy to proceed. Cells often couple the energy-releasing reaction with the energy-requiring one to carry out important cell functions.
Energy in adenosine triphosphate or ATP molecules is easily accessible to do work. ATP powers the majority of energy-requiring cellular reactions....
Energy in adenosine triphosphate or ATP molecules is easily accessible to do work. ATP powers the majority of energy-requiring cellular reactions....
7.8K
Phase I Reactions: Reductive Reactions
222
Phase I biotransformation reductive reactions are chemical processes that modify drugs by introducing or revealing polar functional groups via reduction. Enzymes called reductases catalyze these reactions, playing a pivotal role in drug metabolism by transforming lipophilic drugs into more polar, water-soluble metabolites for easy excretion. An essential type of reductive reaction is the carbonyl group reduction, where aldehydes and ketones are reduced to alcohols. An example is the...
222
Propagation of Action Potentials
5.9K
The propagation of an action potential refers to the process by which a nerve impulse, or "action potential," travels along a neuron.
Neurons (nerve cells) have a resting membrane potential, with a slightly negative charge inside compared to outside. This is maintained by ion channels, such as sodium (Na+) and potassium (K+) channels, which control the flow of ions. When a stimulus, like a touch or a signal from another neuron, triggers the neuron, sodium channels open, allowing sodium ions to...
Neurons (nerve cells) have a resting membrane potential, with a slightly negative charge inside compared to outside. This is maintained by ion channels, such as sodium (Na+) and potassium (K+) channels, which control the flow of ions. When a stimulus, like a touch or a signal from another neuron, triggers the neuron, sodium channels open, allowing sodium ions to...
5.9K


