Article
Materials Science, Multidisciplinary
Farzana Kousar, Jenny Malmstrom, Simon Swift, Jacqueline Ross, Janesha Perera, Stephen C. Moratti
Summary: A novel polymer nano-coating has been developed to prevent protein and material adsorption on the surface of stainless steel, exhibiting excellent anti-biofouling properties. The coating can be easily applied and shows significant inhibition against various proteins and bacterial adhesion.
ACS APPLIED POLYMER MATERIALS
(2021)
Article
Biochemistry & Molecular Biology
Van-Sieu Luc, Chien-Cheng Lin, Shao-Yu Wang, Hsiu-Pen Lin, Bor-Ran Li, Ying-Nien Chou, Chia-Chih Chang
Summary: In this study, a new type of antifouling material called poly(amine oxide) (PAO) has been evaluated as an alternative to overcome nonspecific foulant adsorption and impart comparable biocompatibility. The results show that the cross-linked PAO-modified surface can efficiently inhibit biofouling, suggesting its potential application in biomedical devices.
Article
Engineering, Environmental
Chunlu Jiang, Fengdie Yue, Chang Li, Shijia Zhou, Liugen Zheng
Summary: This study investigates the removal of Cu2+ from polluted water using modified lobster shell biochar. The results show that the modified biochar has a higher Cu2+ adsorption capacity due to the increased number of nitrogen-containing groups. The initial concentration of Cu2+ has the greatest impact on its removal, while the interaction between pH and initial concentration is also significant.
JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING
(2022)
Review
Biochemistry & Molecular Biology
Mario Bonomini, Luca Piscitani, Lorenzo Di Liberato, Vittorio Sirolli
Summary: The properties of the membrane in hemodialyzers play a crucial role in the success and quality of dialysis therapy. Biocompatibility is essential to minimize uremic complications and improve patient outcomes, making the development of more biocompatible membranes a priority.
Article
Engineering, Environmental
Lin Feng, Qingge Feng, Qihua Liang, Yuan Qi, Fanghong Qin, Kao Chen, Xiaoxiao Huang, Junyi Liu, Zhuoyan Huang
Summary: Amine-modified silica aerogel was synthesized as an efficient and environmentally friendly adsorbent for removing nanoparticles. Doping with 3-aminopropyltriethoxysilanes enhanced the adsorption capacity, making it 19 times more efficient than unmodified aerogel. The study provides a reliable adsorption approach for nanoparticle removal and investigates the intricate adsorption mechanism.
JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING
(2023)
Article
Nanoscience & Nanotechnology
Li Zhou, Quan Li Li, Hai Ming Wong
Summary: The novel dual-bioactive peptide constructed by grafting a dentotropic moiety onto an antimicrobial peptide has beneficial functions on tooth surfaces, including inhibiting bacterial adhesion, killing planktonic bacteria, destroying biofilms, protecting teeth, and inducing self-healing regeneration. Molecular dynamics simulations elucidate the main adsorption and mineralization mechanisms, which contribute to its promising potential for preventing dental caries and inducing in situ self-healing remineralization for decayed teeth.
ACS APPLIED MATERIALS & INTERFACES
(2021)
Review
Biochemistry & Molecular Biology
Yijie Liu, Xiaoling Lu, Meilun Chen, Zheng Wei, Guangnan Peng, Jie Yang, Chunhua Tang, Peng Yu
Summary: Peptides and peptide aptamers have shown promise in various biomedical applications due to their unique properties and versatile functionalities. This review discusses screening strategies, synthesis methods, and modification techniques for these molecules, as well as their diverse biomedical applications. A comprehensive understanding of these aspects will aid in the development of novel peptide-based therapeutics and diagnostic tools.
Article
Environmental Sciences
Hang Yang, Zimao Ding, Yilingyun Zou, Yangxiya Liu, Yi Zhang, Shibin Xia
Summary: In this study, second pyrolysis oil-based drill cutting ash (OBDCA-sp) was modified and used as a novel adsorbent to remove tetracycline (TC) from aqueous solutions. The modified OBDCA-sp showed a maximum adsorption capacity when modified with CTAB, and the adsorption process followed the Freundlich model. The experiments also demonstrated the reusability of OBDCA-sp.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2022)
Article
Chemistry, Physical
Virginia Alessandra Gobbo, Mari Lallukka, Francesca Gamna, Mirko Prato, Alessandra Vitale, Sara Ferraris, Ziba Najmi, Andrea Cochis, Lia Rimondini, Jonathan Massera, Silvia Spriano
Summary: This research focuses on developing a protocol to attach nisin, an antimicrobial peptide, to a nanotextured titanium alloy surface. The coated surface shows high surface energy, suitable for tissue integration, and releases nisin over a period longer than 1 day. The antibacterial properties were confirmed by reduced metabolic activity and viable adhered colonies of Staphylococcus aureus. This study demonstrates the potential of using chemically treated titanium surfaces coupled with nisin for bioactive and antibacterial tissue integration.
APPLIED SURFACE SCIENCE
(2023)
Article
Chemistry, Analytical
Zhong Lai, Zhidan Liang, Lin Yan, Xiaoxia Qian, Haitao Jiang, Wendy Zhong
Summary: Protein conjugation is an effective method to add different functionalities to proteins, but identifying products, optimizing reaction conditions, and synthesizing desired molecules can be challenging. Therefore, quick and easy analytical methods are needed for reaction monitoring to guide this complex process.
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS
(2021)
Article
Chemistry, Multidisciplinary
Xing-Yu Liu, Xinjian Ji, Christian Heinis, Jerome Waser
Summary: We present a new method for modifying peptides using highly reactive hypervalent iodine reagents called ethynylbenziodoxolones (EBXs). These peptide-EBXs can be easily synthesized through solution- and solid-phase peptide synthesis (SPPS). They can be used to couple peptides to other peptides or proteins via reaction with Cys, resulting in thioalkynes in organic solvents or hypervalent iodine adducts in water buffer. Additionally, a photocatalytic decarboxylative coupling to the C-terminus of peptides was developed, leading to macrocyclic peptides with unprecedented crosslinking.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Review
Chemistry, Multidisciplinary
Hongfei Jiang, Wujun Chen, Jie Wang, Renshuai Zhang
Summary: Numerous strategies have been developed and applied in the field of biological chemistry to link desired chemical probes with target peptides and proteins. Site-specific modification of native amino acid residues provides novel biological tools for understanding the role of peptides and proteins. Selective N-terminal modification strategies, which have been extensively studied in the last decade, have the potential for applications in medicine, basic research, and applied materials science.
CHINESE CHEMICAL LETTERS
(2022)
Review
Genetics & Heredity
Boyan Shen, Zhaoming Chen, Chunyu Yu, Taoyu Chen, Minglei Shi, Tingting Li
Summary: Phase separation is a crucial mechanism for the compartmentalization of proteins in cells, with predictors currently biased towards IDR-containing proteins and overlooking those with low IDR content. Incorporating features like protein-protein interactions, post-translational modifications, and immunofluorescence images is essential for accurate phase separation prediction in future studies.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2021)
Article
Engineering, Environmental
Ana Caroline Reis Meira, Joao Vitor Gehlen Zago, Bruna Ghellere Tremarin, Daniela Zambelli Mezalira, Ana Cristina Trindade Cursino, Alesandro Bail, Rodrigo Leonardo de Oliveira Basso, Renata Mello Giona
Summary: A magnetic magnesium-aluminum layered double hydroxide (Mag-MgAl) was prepared and modified to enhance its adsorption capacity for antibiotics and dyes. The modification with surfactant sodium dodecyl sulfate (SDS) improved the adsorption of cationic contaminants, while the original adsorbent only removed anionic contaminants. The results suggest that the surface of the composite can be adjusted to modulate the behavior of the adsorbent toward organic contaminants.
JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING
(2023)
Article
Engineering, Environmental
V. G. Dileep Kumar, Sandhyawasini Kumari, K. R. Balaji, Afaq Ahmad Khan, C. R. Ravikumar, B. M. Basavaraja, M. S. Santosh, Sami Rtimi
Summary: This study investigates the effect of surface modifiers on the catalytic properties and degradation efficiency of a polymeric matrix (CuO/PVA) using three different surfactants: cationic (CTAB), anionic (SLS), and non-ionic (T80). The results show that surface modification significantly enhances the degradation ability of the polymeric CuO, with CTAB-assisted CuO exhibiting a 29% higher degradation rate compared to its unmodified counterpart. The surface characteristics of the catalyst, including particle size, band gap, and morphology, also play a crucial role in the degradation process.
CHEMICAL ENGINEERING JOURNAL
(2023)
Article
Physics, Applied
M. Chakraborty, M. Ziatdinov, O. Dyck, S. Jesse, A. D. White, Sergei V. Kalinin
JOURNAL OF APPLIED PHYSICS
(2020)
Article
Chemistry, Medicinal
Rainier Barrett, Andrew D. White
Summary: The research explored methods like active learning and meta-learning to reduce the number of experiments needed to build a predictive model. It was found that the meta-learning method Reptile improved the average accuracy across data sets, but combining meta-learning with active learning did not consistently offer benefits.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Chemistry, Multidisciplinary
Geemi P. Wellawatte, Aditi Seshadri, Andrew D. White
Summary: A major challenge in deep learning in chemistry is the lack of interpretability, which hinders the deployment of AI models. Counterfactuals provide a rationale for model predictions and insights into chemical structures. This work demonstrates a universal model-agnostic approach that can explain predictions of any black-box model.
Article
Chemistry, Multidisciplinary
Heta A. Gandhi, Andrew D. White
Summary: V2G utilizes existing EV battery resources as energy storage, with key factors being EV battery design and profitability incentives for owners. Through economic modeling, it was found that charging rate and efficiency are the most important factors affecting EV users' profits, while battery cost and degradation due to cycling have little impact.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2021)
Article
Multidisciplinary Sciences
Seren Hamsici, Andrew D. White, Handan Acar
Summary: The discovery of a new strategy for studying peptide intermolecular interactions, based on co-assembly of oppositely charged peptides, is presented in this study. Computational and experimental methods were used to analyze the free energy and amino acid contacts during co-assembly, and their correlation with the physical properties of the aggregates. The results indicate that opposite charges and the presence of a hydrophobic core play crucial roles in the assembly of peptide-based materials.
Article
Engineering, Chemical
Mehrad Ansari, Heta A. Gandhi, David G. Foster, Andrew D. White
Summary: Computational fluid dynamics (CFD) analysis is widely used in chemical engineering. In this study, active learning (AL) and symbolic regression (SR) are combined to obtain symbolic equations for system variables from CFD simulations. This scalable approach is applicable for any desired number of CFD design parameters.
Article
Chemistry, Physical
Sam Cox, Andrew D. White
Summary: We propose a formulation of molecular dynamics that can generate only symmetric configurations, which is implemented for all 2D planar and 3D space groups. An atlas of 2D Lennard-Jones crystals under all planar groups is created using symmetric molecular dynamics.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Medicinal
Mehrad Ansari, Andrew D. White
Summary: We propose three deep learning sequence-based prediction models for peptide properties, achieving comparable results to state-of-the-art models. Our sequence-based solubility predictor, MahLooL, outperforms current methods for short peptides. These models are implemented as a static website, providing accessible and reproducible predictions without the need for third-party servers or cloud computing.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Review
Chemistry, Physical
Geemi P. Wellawatte, Heta A. Gandhi, Aditi Seshadri, Andrew D. White
Summary: Chemists are skeptical about using deep learning (DL) for decision making due to lack of interpretability in black-box models. Explainable artificial intelligence (XAI) addresses this issue by providing tools to interpret DL models and predictions. This article reviews XAI principles in chemistry, introduces emerging methods, and focuses on our group's methods and their applications in predicting solubility, blood-brain barrier permeability, and scent of molecules. XAI methods like chemical counterfactuals and descriptor explanations can explain DL predictions and provide insights into structure-property relationships. The two-step process of developing a black-box model and explaining predictions can uncover structure-property relationships.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Editorial Material
Chemistry, Multidisciplinary
Andrew D. White
Summary: Large language models like GPT-4 are getting closer to human-level proficiency in various expert domains. GPT-4 can perform complex tasks in chemistry solely based on English instructions, potentially revolutionizing the field.
NATURE REVIEWS CHEMISTRY
(2023)
Review
Chemistry, Multidisciplinary
Alston Lo, Robert Pollice, Akshatkumar Nigam, Andrew D. White, Mario Krenn, Alan Aspuru-Guzik
Summary: String-based molecular representations are important in cheminformatics, and SELFIES is a robust representation that has been improved and extended. The updated version of selfies library, version 2.1.1, is described in this paper.
Article
Physics, Fluids & Plasmas
Mehrad Ansari, David Soriano-Panos, Gourab Ghoshal, Andrew D. White
Summary: Mathematical modeling is important in predicting disease outbreaks and inferring the origin of diseases. However, current models are sensitive to noisy and incomplete data. To address these issues, a maximum entropy framework is proposed to provide calibrated infection origin probabilities and robustness to noise.
Article
Computer Science, Artificial Intelligence
Wei Zhu, Jiebo Luo, Andrew D. White
Summary: This research introduces federated heterogeneous molecular learning to address the heterogeneity and sharing concerns in chemistry research. Experimental validation on existing datasets demonstrates the advantages of the proposed method.
Article
Computer Science, Artificial Intelligence
Rainier Barrett, Mehrad Ansari, Gourab Ghoshal, Andrew D. White
Summary: In this paper, a MaxEnt-based approach for inferring input parameters of simulators is proposed, which is suitable for sparse data and approximately correct models. This method can fit new data by making the smallest change in the latent joint distribution without relying on likelihood or model derivatives, and it is insensitive to prior strength. The assumption that data is fit in expectation is required, making it applicable to scenarios with few data points, and it improves algorithm efficiency through sample reweighting.
MACHINE LEARNING-SCIENCE AND TECHNOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Ziyue Yang, Maghesree Chakraborty, Andrew D. White
Summary: The study utilizes graph neural networks (GNNs) for NMR chemical shift prediction, accurately capturing important chemical shift phenomena such as hydrogen bonding-induced downfield shift and shifts of organic molecules. These GNN models do not require feature engineering, only data training, yet are as accurate as previous empirical protein NMR models.
Article
Engineering, Biomedical
Lin-Lin Luo, Jie Xu, Bing-Qiao Wang, Chen Chen, Xi Chen, Qiu-Mei Hu, Yu-Qiu Wang, Wan-Yun Zhang, Wan-Xiang Jiang, Xin-Ting Li, Hu Zhou, Xiao Xiao, Kai Zhao, Sen Lin
Summary: A novel AAV serotype, AAVYC5, introduced in this study, showed more efficient transduction into multiple retinal layers compared to AAV2, and enabled successful delivery of anti-angiogenic molecules in mice and non-human primates.
