Machine learning heralding a new development phase in molecular dynamics simulations

Prašnikar, Eva (author), Ljubič, Martin (author), Perdih, Andrej (author), Borišek, Jure (author)

Molecular dynamics (MD) simulations are a key computational chemistry technique that provide dynamic insight into the underlying atomic-level processes in the system under study. These insights not only improve our understanding of the molecular world, but also aid in the design of experiments and targeted interventions. Currently, MD is associated with several limitations, the most important of which are: insufficient sampling, inadequate accuracy of the atomistic models, and challenges with proper analysis and interpretation of the obtained trajectories. Although numerous efforts have been made to address these limitations, more effective solutions are still needed. The recent development of artificial intelligence, particularly machine learning (ML), offers exciting opportunities to address the challenges of MD. In this review we aim to familiarize readers with the basics of MD while highlighting its limitations. The main focus is on exploring the integration of deep learning with MD simulations. The advancements made by ML are systematically outlined, including the development of ML-based force fields, techniques for improved conformational space sampling, and innovative methods for trajectory analysis. Additionally, the challenges and implications associated with the integration of ML and artificial intelligence are discussed. While the potential of ML-MD fusion is clearly established, further applications are needed to confirm its superiority over traditional methods. This comprehensive overview of the new perspectives of MD, which ML has opened up, serves as a gentle introduction to the exciting phase of MD development.

• Language: English
• Keywords: molecular dynamics simulations, machine learning, deep learning, artificial intelligence
• Work type: Article
• Typology: 1.02 - Review Article
• Organization: FFA - Faculty of Pharmacy
• Publication status: Published
• Publication version: Version of Record
• Year: 2024
• Number of pages: 36 str.
• Numbering: Vol. 57, iss. 4, art. 102
• PID: 20.500.12556/RUL-156153
• UDC: 544
• ISSN on article: 1573-7462
• DOI: 10.1007/s10462-024-10731-4
• COBISS.SI-ID: 191433731
• Publication date in RUL: 10.05.2024

PRAŠNIKAR, Eva, LJUBIČ, Martin, PERDIH, Andrej and BORIŠEK, Jure, 2024, Machine learning heralding a new development phase in molecular dynamics simulations. Artificial intelligence review [online]. 2024. Vol. 57, no. 4,  102. [Accessed 8 April 2025]. DOI 10.1007/s10462-024-10731-4. Retrieved from: https://repozitorij.uni-lj.si/IzpisGradiva.php?lang=eng&id=156153

Record is a part of a journal

• Title: Artificial intelligence review
• Shortened title: Artif. intell. rev.
• Publisher: Springer Nature
• ISSN: 1573-7462
• COBISS.SI-ID: 513123865

Licences

• License: CC BY 4.0, Creative Commons Attribution 4.0 International
• Link: http://creativecommons.org/licenses/by/4.0/
• Description: This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.

Secondary language

• Language: Slovenian
• Keywords: fizikalna kemija, molekularna dinamika, strojno učenje, simulacije