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Predicting the structure of multi-protein complexes is a grand challenge in biochemistry, with major implications for basic science and drug discovery. Computational structure prediction methods generally leverage pre-defined structural…

Biomolecules · Quantitative Biology 2021-01-26 Stephan Eismann , Raphael J. L. Townshend , Nathaniel Thomas , Milind Jagota , Bowen Jing , Ron O. Dror

Identifying pathogens in complex samples such as blood, urine, and wastewater is critical to detect infection and inform optimal treatment. Surface-enhanced Raman spectroscopy (SERS) and machine learning (ML) can distinguish among multiple…

Targeted protein degradation (TPD) induced by small molecules has emerged as a rapidly evolving modality in drug discovery, targeting proteins traditionally considered "undruggable". Proteolysis-targeting chimeras (PROTACs) and molecular…

Biomolecules · Quantitative Biology 2025-02-27 Fanglei Xue , Meihan Zhang , Shuqi Li , Xinyu Gao , James A. Wohlschlegel , Wenbing Huang , Yi Yang , Weixian Deng

Accurate detection and analysis of traces of persistent organic pollutants in water is important in many areas, including environmental monitoring and food quality control, due to their long environmental stability and potential…

Machine Learning · Computer Science 2024-02-02 Vishnu Jayaprakash , Jae Bem You , Chiranjeevi Kanike , Jinfeng Liu , Christopher McCallum , Xuehua Zhang

Surface-enhanced Raman spectroscopy (SERS) is a potential fast and inexpensive method of analyte quantification, which can be combined with deep learning to discover biomarker-disease relationships. This study aims to address present…

Quantitative Methods · Quantitative Biology 2024-11-14 Jihan K. Zaki , Jakub Tomasik , Jade A. McCune , Sabine Bahn , Pietro Liò , Oren A. Scherman

Supervised deep learning approaches can artificially increase the resolution of microscopy images by learning a mapping between two image resolutions or modalities. However, such methods often require a large set of hard-to-get…

Image and Video Processing · Electrical Eng. & Systems 2024-11-20 Marzieh Gheisari , Auguste Genovesio

Leveraging scanning tunneling microscopy (STM) for atomic-scale fabrication has led to many advancements such as the creation of atomic electron-spin qubit structures on surfaces. However, the time-consuming and tedious nature of this…

Mesoscale and Nanoscale Physics · Physics 2024-10-18 Angéline Lafleur , Soo-hyon Phark

Table structure recognition (TSR) aims to parse the inherent structure of a table from its input image. The `"split-and-merge" paradigm is a pivotal approach to parse table structure, where the table separation line detection is crucial.…

Computer Vision and Pattern Recognition · Computer Science 2024-05-21 Chunxia Qin , Zhenrong Zhang , Pengfei Hu , Chenyu Liu , Jiefeng Ma , Jun Du

Atomistic structures of materials offer valuable insights into their functionality. Determining these structures remains a fundamental challenge in materials science, especially for systems with defects. While both experimental and…

Materials Science · Physics 2025-01-16 Haili Jia , Yiming Chen , Gi-Hyeok Lee , Jacob Smith , Miaofang Chi , Wanli Yang , Maria K. Y. Chan

The automatic recognition of tabular data in document images presents a significant challenge due to the diverse range of table styles and complex structures. Tables offer valuable content representation, enhancing the predictive…

Computer Vision and Pattern Recognition · Computer Science 2024-04-22 Avinash Anand , Raj Jaiswal , Pijush Bhuyan , Mohit Gupta , Siddhesh Bangar , Md. Modassir Imam , Rajiv Ratn Shah , Shin'ichi Satoh

Even after more than four decades of rapid-pace advances, the adoption of Surface-Enhanced Raman Scattering (SERS) remains limited, due to the difficulties in fabrication of effective and affordable nanostructured surfaces or templates.…

Spectroscopic techniques are essential tools for determining the structure of molecules. Different spectroscopic techniques, such as Nuclear magnetic resonance (NMR), Infrared spectroscopy, and Mass Spectrometry, provide insight into the…

Chemical Physics · Physics 2024-10-30 Marvin Alberts , Oliver Schilter , Federico Zipoli , Nina Hartrampf , Teodoro Laino

Surface enhanced Raman scattering (SERS) in nanoscale hotspots has been placed great hopes upon for identification of minimum chemical traces and in-situ investigation of single molecule structures and dynamics. However, previous work…

Optics · Physics 2016-09-19 Jing Long , Hui Yi , Hongquan Li , Tian Yang

Artificial Neural Networks (ANN) are already heavily involved in methods and applications for frequent tasks in the field of computational chemistry such as representation of potential energy surfaces (PES) and spectroscopic predictions.…

Chemical Physics · Physics 2022-12-23 Silvan Käser , Luis Itza Vazquez-Salazar , Markus Meuwly , Kai Töpfer

Functional groups and moieties are chemical descriptors of biomolecules that can be used to interpret their properties and functions, leading to the understanding of chemical or biological mechanisms. These chemical building blocks, or…

Biomolecules · Quantitative Biology 2021-11-08 Yasemin Yesiltepe , Ryan S. Renslow , Thomas O. Metz

Vibrational spectroscopy is a key technique to elucidate microscopic structure and dynamics. Without the aid of theoretical approaches, it is however, often difficult to understand such spectra at a microscopic level. Ab initio molecular…

Chemical Physics · Physics 2023-03-14 Philipp Schienbein

Table Structure Recognition (TSR) is a widely discussed task aiming at transforming unstructured table images into structured formats, such as HTML sequences, to make text-only models, such as ChatGPT, that can further process these tables.…

Computer Vision and Pattern Recognition · Computer Science 2024-01-11 Bin Xiao , Murat Simsek , Burak Kantarci , Ala Abu Alkheir

In drug discovery, knowledge of the graph structure of chemical compounds is essential. Many thousands of scientific articles in chemistry and pharmaceutical sciences have investigated chemical compounds, but in cases the details of the…

Machine Learning · Statistics 2020-09-16 Martijn Oldenhof , Adam Arany , Yves Moreau , Jaak Simm

We present an innovative fabrication method to achieve bottom-up in situ surface-overstructured Au nanoislands (NIs) with tunable grades of surface coverage, elongation, and branching, directly on micro-optical fibers for sensing…

Infrared and Raman spectroscopy are widely used for the characterization of gases, liquids, and solids, as the spectra contain a wealth of information concerning in particular the dynamics of these systems. Atomic scale simulations can be…

Mesoscale and Nanoscale Physics · Physics 2024-08-15 Nan Xu , Petter Rosander , Christian Schäfer , Eric Lindgren , Nicklas Österbacka , Mandi Fang , Wei Chen , Yi He , Zheyong Fan , Paul Erhart