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Molecular dynamics (MD) is a powerful approach for modelling molecular systems, but it remains computationally intensive on spatial and time scales of many macromolecular systems of biological interest. To explore the opportunities offered…

Biomolecules · Quantitative Biology 2025-08-07 Mhd Hussein Murtada , Z. Faidon Brotzakis , Michele Vendruscolo

Molecular Dynamics (MD) simulation is a powerful tool for understanding the dynamics and structure of matter. Since the resolution of MD is atomic-scale, achieving long time-scale simulations with femtosecond integration is very expensive.…

Machine Learning · Computer Science 2022-04-27 Zijie Li , Kazem Meidani , Prakarsh Yadav , Amir Barati Farimani

Molecular dynamics (MD) simulation predicts the trajectory of atoms by solving Newton's equation of motion with a numeric integrator. Due to physical constraints, the time step of the integrator need to be small to maintain sufficient…

Computational Physics · Physics 2021-12-22 Tianze Zheng , Weihao Gao , Chong Wang

Efficient molecular dynamics (MD) simulation is vital for understanding atomic-scale processes in materials science and biophysics. Traditional density functional theory (DFT) methods are computationally expensive, which limits the…

Machine Learning · Computer Science 2025-10-03 Hung Le , Sherif Abbas , Minh Hoang Nguyen , Van Dai Do , Huu Hiep Nguyen , Dung Nguyen

Large Language Models (LLMs) have made great strides in areas such as language processing and computer vision. Despite the emergence of diverse techniques to improve few-shot learning capacity, current LLMs fall short in handling the…

Biomolecules · Quantitative Biology 2024-05-14 Xianggen Liu , Yan Guo , Haoran Li , Jin Liu , Shudong Huang , Bowen Ke , Jiancheng Lv

In this work, a novel multifidelity machine learning (ML) model, the gradient-enhanced multifidelity neural networks (GEMFNNs), is proposed. This model is a multifidelity version of gradient-enhanced neural networks (GENNs) as it uses both…

Machine Learning · Computer Science 2021-03-24 Jethro Nagawkar , Leifur Leifsson

Neural network potentials (NNPs) enable large-scale molecular dynamics (MD) simulations of systems containing >10,000 atoms with the accuracy comparable to ab initio methods and play a crucial role in material studies. Although NNPs are…

Molecular dynamics (MD) is a powerful and popular tool for understanding the dynamical evolution of materials at the nano and mesoscopic scales. There are various flavors of MD ranging from the high fidelity albeit computationally expensive…

Computational Physics · Physics 2020-04-02 Rohit Batra , Subramanian Sankaranarayanan

Machine learning (ML) offers considerable promise for the design of new molecules and materials. In real-world applications, the design problem is often domain-specific, and suffers from insufficient data, particularly labeled data, for ML…

Chemical Physics · Physics 2025-02-04 Ming Han , Ge Sun , Juan J. de Pablo

Long-range correlations are essential across numerous machine learning tasks, especially for data embedded in Euclidean space, where the relative positions and orientations of distant components are often critical for accurate predictions.…

Machine Learning · Computer Science 2025-09-30 J. Thorben Frank , Stefan Chmiela , Klaus-Robert Müller , Oliver T. Unke

Machine learning force fields show great promise in enabling more accurate molecular dynamics simulations compared to manually derived ones. Much of the progress in recent years was driven by exploiting prior knowledge about physical…

Machine Learning · Computer Science 2025-09-11 Andreas Burger , Luca Thiede , Alán Aspuru-Guzik , Nandita Vijaykumar

Molecular knowledge resides within three different modalities of information sources: molecular structures, biomedical documents, and knowledge bases. Effective incorporation of molecular knowledge from these modalities holds paramount…

Biomolecules · Quantitative Biology 2023-07-24 Yizhen Luo , Kai Yang , Massimo Hong , Xing Yi Liu , Zaiqing Nie

Metallic spin glass systems, such as dilute magnetic alloys, are characterized by randomly distributed local moments coupled to each other through a long-range electron-mediated effective interaction. We present a scalable machine learning…

Disordered Systems and Neural Networks · Physics 2023-11-29 Menglin Shi , Sheng Zhang , Gia-Wei Chern

We present a complete set of chemo-structural descriptors to significantly extend the applicability of machine-learning (ML) in material screening and mapping energy landscape for multicomponent systems. These new descriptors allow…

Materials Science · Physics 2018-08-08 Kamal Choudhary , Brian DeCost , Francesca Tavazza

Graph based molecular representation learning is essential for accurately predicting molecular properties in drug discovery and materials science; however, it faces significant challenges due to the intricate relationships among molecules…

Computational Engineering, Finance, and Science · Computer Science 2025-05-28 Zhengyang Zhou , Yunrui Li , Pengyu Hong , Hao Xu

We introduce AceFF, a pre-trained machine learning interatomic potential (MLIP) optimized for small molecule drug discovery. While MLIPs have emerged as efficient alternatives to Density Functional Theory (DFT), generalizability across…

Accurately modeling chemical reactions at the atomistic level requires high-level electronic structure theory due to the presence of unpaired electrons and the need to properly describe bond breaking and making energetics. Commonly used…

In general-purpose particle detectors, the particle-flow algorithm may be used to reconstruct a comprehensive particle-level view of the event by combining information from the calorimeters and the trackers, significantly improving the…

Data Analysis, Statistics and Probability · Physics 2021-06-10 Joosep Pata , Javier Duarte , Jean-Roch Vlimant , Maurizio Pierini , Maria Spiropulu

Our current understanding of the structure and dynamics of aqueous interfaces at the molecular level has grown substantially in the last few decades due to the continuous development of surface-specific spectroscopies, such as vibrational…

Chemical Physics · Physics 2023-09-27 Yair Litman , Jinggang Lan , Yuki Nagata , David M. Wilkins

Looking back at seven decades of highly extensive application in the semiconductor industry, silicon and its native oxide SiO$_2$ are still at the heart of several technological developments. Recently, the fabrication of ultra-thin oxide…