CKineticsDB─一种可扩展和公平的数据管理框架和数据中心,用于在异质催化中进行多尺度建模
Siddhant M Lambor1, Sashank Kasiraju1, Dionisios G Vlachos1,2
1RAPID Manufacturing Institute, Delaware Energy Institute, University of Delaware, Newark, Delaware 19716, United States.
Journal of chemical information and modeling
|July 12, 2023
概括
现在可以访问异质催化物的计算研究数据. 化学动力学数据库 (CKineticsDB) 确保数据可重复性和可重复使用性,用于多尺度建模工作流程.
科学领域:
- 计算化学是一种计算化学.
- 材料科学是一种材料科学.
- 化学工程是化学工程的组成部分.
背景情况:
- 异质催化物的计算研究数据因后勤限制而面临可访问性挑战.
- 可复制性和可重复使用性是计算研究的关键优势,但数据碎片化阻碍了进步.
- 标准化的数据组织,来源和可访问性对于开发集成的多尺度建模工具至关重要.
研究的目的:
- 开发一个数据中心,CKineticsDB,符合FAIR原则,用于管理异质催化中的计算研究数据.
- 创建一个集中存储库,解决阻碍数据可访问性和可重复使用性的后勤限制.
- 通过统一的数据组织和易于访问,促进多尺度建模工作流程的集成.
主要方法:
- 开发了CKineticsDB,一个使用MongoDB后端进行扩展的数据中心,以及基于引用的数据模型来最大限度地减少冗余.
- 创建了一个用于数据处理,质量评估和基于催化剂和模拟参数的选择性数据检索的Python软件程序.
- 确保符合FAIR (可查找,可访问,可互操作,可重复使用) 科学数据管理的指导原则.
主要成果:
- CKineticsDB集中了来自各种理论尺度 (ab initio,热化学,微动力学) 的异质催化数据.
- 该数据库评估数据质量,保留精选的模拟信息,并能够准确地再生已发布的结果.
- 基于特定的催化剂和模拟参数实现了优化存储和选择性数据检索.
结论:
- 通过提供可访问的,符合FAIR的数据,CCKineticsDB加速了新反应途径,动力分析和催化发现的发展.
- 该平台支持数据驱动的应用程序,并增强了多尺度建模工作流程的集成.
- CKineticsDB克服了数据可访问性的障碍,促进了计算催化研究中的可复制性和可重复使用性.
相关概念视频
Catalysis
27.1K
The presence of a catalyst affects the rate of a chemical reaction. A catalyst is a substance that can increase the reaction rate without being consumed during the process. A basic comprehension of a catalysts’ role during chemical reactions can be understood from the concept of reaction mechanisms and energy diagrams.
27.1K
Introduction to Mechanisms of Enzyme Catalysis
8.3K
For many years, scientists thought that enzyme-substrate binding took place in a simple "lock-and-key" fashion. This model stated that the enzyme and substrate fit together perfectly in one instantaneous step. However, current research supports a more refined view scientists call induced fit. The induced-fit model expands upon the lock-and-key model by describing a more dynamic interaction between enzyme and substrate. As the enzyme and substrate come together, their interaction causes...
8.3K
Model Approaches for Pharmacokinetic Data: Distributed Parameter Models
96
Pharmacokinetic models are mathematical constructs that represent and predict the time course of drug concentrations in the body, providing meaningful pharmacokinetic parameters. These models are categorized into compartment, physiological, and distributed parameter models.
The distributed parameter models are specifically designed to account for variations and differences in some drug classes. This model is particularly useful for assessing regional concentrations of anticancer or...
The distributed parameter models are specifically designed to account for variations and differences in some drug classes. This model is particularly useful for assessing regional concentrations of anticancer or...
96
Introduction to Enzyme Kinetics
20.2K
Enzyme kinetics studies the rates of biochemical reactions. Scientists monitor the reaction rates for a particular enzymatic reaction at various substrate concentrations. Additional trials with inhibitors or other molecules that affect the reaction rate may also be performed.
The experimenter can then plot the initial reaction rate or velocity (Vo) of a given trial against the substrate concentration ([S]) to obtain a graph of the reaction properties. For many enzymatic reactions involving a...
The experimenter can then plot the initial reaction rate or velocity (Vo) of a given trial against the substrate concentration ([S]) to obtain a graph of the reaction properties. For many enzymatic reactions involving a...
20.2K
Coupled Reactions
7.9K
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....
7.9K


