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  1. Free, publicly-accessible full text available October 1, 2024
  2. Abstract

    Protein engineering is an emerging field in biotechnology that has the potential to revolutionize various areas, such as antibody design, drug discovery, food security, ecology, and more. However, the mutational space involved is too vast to be handled through experimental means alone. Leveraging accumulative protein databases, machine learning (ML) models, particularly those based on natural language processing (NLP), have considerably expedited protein engineering. Moreover, advances in topological data analysis (TDA) and artificial intelligence-based protein structure prediction, such as AlphaFold2, have made more powerful structure-based ML-assisted protein engineering strategies possible. This review aims to offer a comprehensive, systematic, and indispensable set of methodological components, including TDA and NLP, for protein engineering and to facilitate their future development.

  3. Free, publicly-accessible full text available July 10, 2024
  4. Free, publicly-accessible full text available June 7, 2024
  5. Free, publicly-accessible full text available June 1, 2024
  6. Abstract

    Virtual screening (VS) is a critical technique in understanding biomolecular interactions, particularly in drug design and discovery. However, the accuracy of current VS models heavily relies on three-dimensional (3D) structures obtained through molecular docking, which is often unreliable due to the low accuracy. To address this issue, we introduce a sequence-based virtual screening (SVS) as another generation of VS models that utilize advanced natural language processing (NLP) algorithms and optimized deepK-embedding strategies to encode biomolecular interactions without relying on 3D structure-based docking. We demonstrate that SVS outperforms state-of-the-art performance for four regression datasets involving protein-ligand binding, protein-protein, protein-nucleic acid binding, and ligand inhibition of protein-protein interactions and five classification datasets for protein-protein interactions in five biological species. SVS has the potential to transform current practices in drug discovery and protein engineering.

  7. The pioneering work of William F. Vinen (also known as Joe Vinen) on thermal counterflow turbulence in superfluid helium-4 largely inaugurated the research on quantum turbulence. Despite decades of research on this topic, there are still open questions remaining to be solved. One such question is related to the anomalous increase in the vortex-line density L(t) during the decay of counterflow turbulence, which is often termed as the “bump” on the L(t) curve. In 2016, Vinen and colleagues developed a theoretical model to explain this puzzling phenomenon (JETP Letters, 103, 648-652 (2016)). However, he realized in the last a few years of his life that this theory must be at least inadequate. In remembrance of Joe, we discuss in this paper his latest thoughts on counterflow turbulence and its decay. We also briefly outline our recent experimental and numerical work on this topic.
    Free, publicly-accessible full text available March 22, 2024
  8. Abstract

    The motion of quantized vortices is responsible for many intriguing phenomena in diverse quantum-fluid systems. Having a theoretical model to reliably predict the vortex motion therefore promises a broad significance. But a grand challenge in developing such a model is to evaluate the dissipative force caused by thermal quasiparticles in the quantum fluids scattering off the vortex cores. Various models have been proposed, but it remains unclear which model describes reality due to the lack of comparative experimental data. Here we report a visualization study of quantized vortex rings propagating in superfluid helium. By examining how the vortex rings spontaneously decay, we provide decisive data to identify the model that best reproduces observations. This study helps to eliminate ambiguities about the dissipative force acting on vortices, which could have implications for research in various quantum-fluid systems that also involve similar forces, such as superfluid neutron stars and gravity-mapped holographic superfluids.

  9. Free, publicly-accessible full text available January 1, 2024
  10. Free, publicly-accessible full text available January 1, 2024