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Per- and polyfluoroalkyl substances (PFAS) contamination has posed a significant environmental and public health challenge due to their ubiquitous nature. Adsorption has emerged as a promising remediation technique, yet optimizing adsorption efficiency remains complex due to the diverse physicochemical properties of PFAS and the wide range of adsorbent materials. Traditional modeling approaches, such as response surface methodology (RSM), struggled to capture nonlinear interactions, while standalone machine learning (ML) models required extensive datasets. This study addressed these limitations by developing hybrid RSM-ML models to improve the prediction and optimization of PFAS adsorption. A comprehensive dataset was constructed using experimental adsorption data, integrating key parameters such as pH, pHpzc, surface area, temperature, and PFAS molecular properties. RSM was employed to model adsorption behavior, while gradient boosting (GB), random forest (RF), and extreme gradient boosting (XGB) were used to enhance predictive performance. Hybrid models—linear, RMSE-based, multiplicative, and meta-learning—were developed and evaluated. The meta-learning HOP-RSM-GB model achieved near-perfect accuracy (R² = 1.00, RMSE = 10.59), outperforming all other models. Surface plots revealed that low pH and high pHpzc maximized the adsorption while increasing log Kow consistently enhanced PFAS adsorption. These findings establish hybrid RSM-ML modeling as a powerful framework for optimizing PFAS remediation strategies. The integration of statistical and machine learning approaches significantly improves predictive accuracy, reduces experimental costs, and provides deeper insights into adsorption mechanisms. This study underscores the importance of data-driven approaches in environmental engineering and highlights future opportunities for integrating ML-driven modeling with experimental adsorption research. 

Adenylate kinases (AKs) have evolved AMP-binding and lid domains that are encoded as continuous polypeptides embedded at different locations within the discontinuous polypeptide encoding the core domain. A prior study showed that AK homologues of different stabilities consistently retain cellular activity following circular permutation that splits a region with high energetic frustration within the AMP-binding domain into discontinuous fragments. Herein, we show that mesophilic and thermophilic AKs having this topological restructuring retain activity and substrate-binding characteristics of the parental AK. While permutation decreased the activity of both AK homologues at physiological temperatures, the catalytic activity of the thermophilic AK increased upon permutation when assayed >30 °C below the melting temperature of the native AK. The thermostabilities of the permuted AKs were uniformly lower than those of native AKs, and they exhibited multiphasic unfolding transitions, unlike the native AKs, which presented cooperative thermal unfolding. In addition, proteolytic digestion revealed that permutation destabilized each AK in differing manners, and mass spectrometry suggested that the new termini within the AMP-binding domain were responsible for the increased proteolysis sensitivity. These findings illustrate how changes in contact order can be used to tune enzyme activity and alter folding dynamics in multidomain enzymes. 

Motivation Annotations of biochemical models provide details of chemical species, documentation of chemical reactions, and other essential information. Unfortunately, the vast majority of biochemical models have few, if any, annotations, or the annotations provide insufficient detail to understand the limitations of the model. The quality and quantity of annotations can be improved by developing tools that recommend annotations. For example, recommender tools have been developed for annotations of genes. Although annotating genes is conceptually similar to annotating biochemical models, there are important technical differences that make it difficult to directly apply this prior work. Results We present AMAS, a system that predicts annotations for elements of models represented in the Systems Biology Markup Language (SBML) community standard. We provide a general framework for predicting model annotations for a query element based on a database of annotated reference elements and a match score function that calculates the similarity between the query element and reference elements. The framework is instantiated to specific element types (e.g., species, reactions) by specifying the reference database (e.g., ChEBI for species) and the match score function (e.g., string similarity). We analyze the computational efficiency and prediction quality of AMAS for species and reactions in BiGG and BioModels and find that it has sub-second response times and accuracy between 80% and 95% depending on specifics of what is predicted. We have incorporated AMAS into an open-source, pip-installable Python package that can run as a command-line tool that predicts and adds annotations to species and reactions to an SBML model. Availability Our project is hosted at https://github.com/sys-bio/AMAS, where we provide examples, documentation, and source code files. Our source code is licensed under the MIT open-source license. 

Abstract Modern high-resolution microscopes are commonly used to study specimens that have dense and aperiodic spatial structure. Extracting meaningful information from images obtained from such microscopes remains a formidable challenge. Fourier analysis is commonly used to analyze the structure of such images. However, the Fourier transform fundamentally suffers from severe phase noise when applied to aperiodic images. Here, we report the development of an algorithm based on nonconvex optimization that directly uncovers the fundamental motifs present in a real-space image. Apart from being quantitatively superior to traditional Fourier analysis, we show that this algorithm also uncovers phase sensitive information about the underlying motif structure. We demonstrate its usefulness by studying scanning tunneling microscopy images of a Co-doped iron arsenide superconductor and prove that the application of the algorithm allows for the complete recovery of quasiparticle interference in this material.