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Nanoparticle (NP)-protein complexes exhibit the correct identity of NP in biological media. Therefore, protein-NP interactions should be closely explored to understand and to modulate the nature of NPs in medical implementations. This…

Understanding how protein mutations affect protein-nucleic acid binding is critical for unraveling disease mechanisms and advancing therapies. Current experimental approaches are laborious, and computational methods remain limited in…

Quantitative Methods · Quantitative Biology 2025-05-30 Xiang Liu , Junjie Wee , Guo-Wei Wei

Nanoparticles (NPs) demonstrate considerable potential in medical applications, including targeted drug delivery and diagnostic probes. However, their efficacy depends on their ability to navigate through the complex biological environments…

Soft Condensed Matter · Physics 2025-10-10 Beatrice Cipriani , Hender Lopez

The revolution in materials in the past century was built on a knowledge of the atomic arrangements and the structure-property relationship. The sine qua non for obtaining quantitative structural information is single crystal…

Computational Physics · Physics 2023-12-27 Gabe Guo , Judah Goldfeder , Ling Lan , Aniv Ray , Albert Hanming Yang , Boyuan Chen , Simon JL Billinge , Hod Lipson

The article proposes a conceptual approach for evaluating the impact of engineered nanoparticles (NPs) on the functionality of small biomolecules. The developed machine learning (ML) model is based on in-silico 13C NMR spectroscopy chemical…

Other Quantitative Biology · Quantitative Biology 2026-03-23 Mariya L Ivanova , Michael Nichols , Nicola Russo , Gueorgui Mihaylov , Konstantin Nikolic

Machine learning (ML) provides a broad spectrum of tools and architectures that enable the transformation of data from simulations and experiments into useful and explainable science, thereby augmenting domain knowledge. Furthermore,…

Plasma Physics · Physics 2024-09-05 Farbod Faraji , Maryam Reza

A nanoparticle (NP) immersed in biological media rapidly forms a corona of adsorbed proteins, which later controls the eventual fate of the particle and the route through which adverse outcomes may occur. The composition and timescale for…

Soft Condensed Matter · Physics 2021-11-03 I. Rouse , V. Lobaskin

Machine learning (ML) empowers biomedical systems with the capability to optimize their performance through modeling of the available data extremely well, without using strong assumptions about the modeled system. Especially in nano-scale…

This study introduces a pioneering machine learning (ML)-based approach for predicting the impact of nanoparticle (NP) carriers on the functionality of attached small biomolecules. It was hypothesised that NP interactions induce measurable…

Quantitative Methods · Quantitative Biology 2026-03-23 Mariya L. Ivanova , Michael Nicholls , Nicola Russo , Gueorgui Mihaylov , Konstantin Nikolic

Machine learning (ML) is transforming all areas of science. The complex and time-consuming calculations in molecular simulations are particularly suitable for a machine learning revolution and have already been profoundly impacted by the…

Chemical Physics · Physics 2019-11-11 Frank Noé , Alexandre Tkatchenko , Klaus-Robert Müller , Cecilia Clementi

In cancer therapeutics, protein-metal binding mechanisms critically govern the pharmacokinetics and targeting efficacy of drugs, thereby fundamentally shaping the rational design of anticancer metallodrugs. While conventional laboratory…

In recent years, Artificial Intelligence techniques have proved to be very successful when applied to problems in physical sciences. Here we apply an unsupervised Machine Learning (ML) algorithm called Principal Component Analysis (PCA) as…

Materials Science · Physics 2021-05-26 T. Tula , G. Möller , J. Quintanilla , S. R. Giblin , A. D. Hillier , E. E. McCabe , S. Ramos , D. S. Barker , S. Gibson

Recent advancements in machine learning (ML) are transforming the field of structural biology. For example, AlphaFold, a groundbreaking neural network for protein structure prediction, has been widely adopted by researchers. The…

RNAs play crucial and versatile roles in biological processes. Computational prediction approaches can help to understand RNA structures and their stabilizing factors, thus providing information on their functions, and facilitating the…

Biological Physics · Physics 2020-09-04 Bin Huang , Yuanyang Du , Shuai Zhang , Wenfei Li , Jun Wang , Jian Zhang

Many aspects of the study of protein folding and dynamics have been affected by the recent advances in machine learning. Methods for the prediction of protein structures from their sequences are now heavily based on machine learning tools.…

Biological Physics · Physics 2019-11-25 Frank Noé , Gianni De Fabritiis , Cecilia Clementi

The Gene or DNA sequence in every cell does not control genetic properties on its own; Rather, this is done through translation of DNA into protein and subsequent formation of a certain 3D structure. The biological function of a protein is…

Computational Engineering, Finance, and Science · Computer Science 2019-05-30 Leila Khalatbari , Mohammad Reza Kangavari , Saeid Hosseini , Hongzhi Yin , Ngai-Man Cheung

Nuclear materials are often demanded to function for extended time in extreme environments, including high radiation fluxes and transmutation, high temperature and temperature gradients, stresses, and corrosive coolants. They also have a…

Materials Science · Physics 2022-11-18 Dane Morgan , Ghanshyam Pilania , Adrien Couet , Blas P. Uberuaga , Cheng Sun , Ju Li

Protein structure determination has long been one of the primary challenges of structural biology, to which deep machine learning (ML)-based approaches have increasingly been applied. However, these ML models generally do not incorporate…

Biological Physics · Physics 2025-11-14 Tom Pan , Evan Dramko , Mitchell D. Miller , Anastasios Kyrillidis , George N. Phillips

A protein's function depends critically on its conformational ensemble, a collection of energy weighted structures whose balance depends on temperature and environment. Though recent deep learning (DL) methods have substantially advanced…

Biomolecules · Quantitative Biology 2026-01-09 Myeongsang Lee , Lauren L. Porter

Proteins are complex biomolecules that play a central role in various biological processes, making them critical targets for breakthroughs in molecular biology, medical research, and drug discovery. Deciphering their intricate, hierarchical…

Machine Learning · Computer Science 2025-05-09 Viet Thanh Duy Nguyen , Truong-Son Hy
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