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SSRN 2022年

作者： Mereness, Jared A. Benoit, Danielle S.W. Piraino, Lindsay R. Chen, Chiao Yun Moyston, Tracey DeLouise, Lisa A. Ovitt, Catherine E. Department of Biomedical Engineering University of Rochester RochesterNY United States Department of Dermatology University of Rochester RochesterNY United States Department of Biomedical Genetics University of Rochester RochesterNY United States Materials Science Program University of Rochester RochesterNY United States Department of Chemical Engineering University of Rochester RochesterNY United States Center for Musculoskeletal Research University of Rochester RochesterNY United States Knight Campus Bioengineering Department University of Oregon EugeneOR United States

Salivary gland dysfunction resulting in xerostomia occurs in the majority of head and neck cancer patients treated with radiation therapy. Progress in determining the mechanism of radiation damage and methods for prevention has been hampered by the lack of in vitro salivary gland models. We recently developed a salivary gland tissue mimetic (SGm), comprised of salivary gland tissue clusters encapsulated in matrix metalloproteinase (MMP)–degradable poly(ethylene glycol) hydrogels within arrays of ~320 Om diameter spherical cavities molded in PDMS. The SGm provides a functional and physiologically relevant salivary gland model well suited to high-throughput drug screening for radioprotective compounds. However, the utility of the SGm would significantly benefit from improved retention of acinar phenotype and function over longer culture durations. We hypothesize that tuning biochemical cues presented within the PEG hydrogel matrix will improve maintenance of acinar cell phenotype and function by mimicking the natural extracellular matrix microenvironment of the intact gland. Hydrogels formed using slower-degrading MMP-sensitive peptide crosslinkers showed >2-fold increase in sphere number formed at 48 hr, increased expression of acinar cell markers, and more robust response to calcium stimulation by the secretory agonist, carbachol, with reduced SGm tissue cluster disruption and outgrowth during prolonged culture. The incorporation of adhesive peptides containing RGD or IKVAV improved calcium flux response to secretory agonists at 14 days of culture. Tuning the hydrogel matrix improved cell aggregation, and promoted acinar cell phenotype, and stability of the SGm in long-term culture. Furthermore, combining this matrix with optimized media conditions synergistically improved retention of acinar cells in SGm. © 2022, The Authors. All rights reserved.

关键词： Polyethylene glycols

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Protocol to explain support vector machine predictions via exact Shapley value computation

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STAR Protocols 2024年第2期5卷 103010页

作者： Mastropietro, Andrea Bajorath, Jürgen Deparment of Computer Control and Management Engineering “Antonio Ruberti” Sapienza University of Rome Via Ariosto 25 Rome 00185 Italy Department of Life Science Informatics and Data Science B-IT LIMES Program Unit Chemical Biology and Medicinal Chemistry Rheinische Friedrich-Wilhelms-Universität Friedrich-Hirzebruch-Allee 5/6 Bonn 53115 Germany Lamarr Institute for Machine Learning and Artificial Intelligence Friedrich-Hirzebruch-Allee 5/6 Bonn 53115 Germany

Shapley values from cooperative game theory are adapted for explaining machine learning predictions. For large feature sets used in machine learning, Shapley values are approximated. We present a protocol for two techniques for explaining support vector machine predictions with exact Shapley value computation. We detail the application of these algorithms and provide ready-to-use Python scripts and custom code. The final output of the protocol includes quantitative feature analysis and mapping of important features for visualization. For complete details on the use and execution of this protocol, please refer to Feldmann and Bajorath¹ and Mastropietro et al.² © 2024 The Author(s)

关键词： Bioinformatics Chemistry Computer sciences

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Incorporating Simultaneous Effect of Initial Concentration and Sorbent Dose into Removal Prediction Model Using Glyphosate Experimental Data and Theoretical Analysis

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SSRN 2022年

作者： Esmaeilian, Anahita Dionysiou, Dionysios D. O’Shea, Kevin E. Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street MiamiFL33199 United States Institute of Environment Florida International University Modesto A. Maidique Campus 11200 SW 8th Street MiamiFL33199 United States Environmental Engineering and Science Program Department of Chemical and Environmental Engineering University of Cincinnati CincinnatiOH45221 United States

Glyphosate, the most used herbicide in the world, poses a serious threat to terrestrial and aquatic ecosystems. Magnetic nanosorbents composed of magnetite (Fe 3 O 4 ) cores coated with humic acid were synthesized, characterized, and used to investigate the removal of glyphosate (GLY) through adsorption. The spherical-type particles (average particle size = 9 nm), highly crystalline spinel structure of the iron core and surface morphology were unchanged before and after GLY adsorption. Adsorption fits with the pseudo second-order kinetic and Langmuir isotherm models. The humic acid coated magnetic nanomaterials (HA-MNP) exhibit a high maximum adsorption capacity for GLY, 30.4 mg g −1 . The result of thermodynamics study indicated the adsorption is endothermic and spontaneous. Removal efficiency increased with decreasing solution pH. Chloride ions exhibit no inhibition, while nitrate and phosphate compete with GLY adsorption to HA-MNP. Although multi-parameter models have been successfully applied to model adsorption processes, such studies often require large sets of experiments and complex mathematical representations to capture the interactive play of different variables. We observed excellent agreement between predicted and experimental results using a new approach employing dimensional analyses with the application of Buckingham’s π theorem for the combined concentration and dosing effects in the removal of GLY. In addition, error functions (r 2 =0.88) confirm the applicability of this model in the batch scale design independently of the sorbent dose and initial concentration. The accurate demonstration of this modeling approach for the adsorption of GLY on HA-MNP illustrates promise for predicting and optimizing adsorption treatment processes for different sorbents and target pollutants. © 2022, The Authors. All rights reserved.

关键词： Adsorption

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On sparse identification of complex dynamical systems: a study on discovering influential reactions in chemical reaction networks

arXiv

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arXiv 2020年

作者： Harirchi, Farshad Kim, Doohyun Khalil, Omar Liu, Sijia Elvati, Paolo Baranwal, Mayank Hero, Alfred Violi, Angela Department of Electrical Engineering and Computer Science University of Michigan Ann ArborMI48109–2125 United States Department of Mechanical Engineering University of Michigan Ann ArborMI48109–2125 United States Departments of Chemical Engineering Biomedical Engineering Macromolecular Science and Engineering Biophysics Program University of Michigan Ann ArborMI48109–2125 United States

A wide variety of real life complex networks are prohibitively large for modeling, analysis and control. Understanding the structure and dynamics of such networks entails creating a smaller representative network that preserves its relevant topological and dynamical properties. While modern machine learning methods have enabled identification of governing laws for complex dynamical systems, their inability to produce white-box models with sufficient physical interpretation renders such methods undesirable to domain experts. In this paper, we introduce a hybrid black-box, white-box approach for the sparse identification of the governing laws for complex, highly coupled dynamical systems with particular emphasis on finding the influential reactions in chemical reaction networks for combustion applications, using a data-driven sparse-learning technique. The proposed approach identifies a set of influential reactions using species concentrations and reaction rates, with minimal computational cost without requiring additional data or simulations. The new approach is applied to analyze the combustion chemistry of H2 and C3H8 in a constant-volume homogeneous reactor. The influential reactions determined by the sparse-learning method are consistent with the current kinetics knowledge of chemical mechanisms. Additionally, we show that a reduced version of the parent mechanism can be generated as a combination of the significantly reduced influential reactions identified at different times and conditions and that for both H2 and C3H8 fuel, the reduced mechanisms perform closely to the parent mechanisms as a function of the ignition delay time over a wide range of conditions. Our results demonstrate the potential of the sparse-learning approach as an effective and efficient tool for dynamical system analysis and reduction. The uniqueness of this approach as applied to combustion systems lies in the ability to identify influential reactions in specified conditions and times dur

关键词： Learning systems

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Toward Ambitious Multiscale Modeling of Nanocrystal Catalysts for Water Splitting

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ACS ENERGY LETTERS 2020年第6期5卷 2042-2044页

作者： Pavone, Michele Toroker, Maytal Caspary Department of Chemical Sciences University of Naples Federico II Comp. Univ. M. S. Angelo Via Cintia 21 Naples 80126 Italy Department of Materials Science and Engineering Technion - Israel Institute of Technology Haifa 3200003 Israel The Nancy and Stephen Grand Technion Energy Program Technion - Israel Institute of Technology Haifa 3200003 Israel

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Stability and electronic properties of edges of SnS2

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Physical Review B 2020年第15期102卷 155306-155306页

作者： Tao Yan Pratap M. Rao N. Aaron Deskins Materials Science and Engineering program Worcester Polytechnic Institute Worcester Massachusetts 01609 USA Department of Mechanical Engineering Worcester Polytechnic Institute Worcester Massachusetts 01609 USA Department of Chemical Engineering Worcester Polytechnic Institute Worcester Massachusetts 01609 USA

Because of its two-dimensional structure and semiconducting properties, tin disulfide (SnS2) is of interest for many applications, such as photocatalysis, photovoltaics, sensing, and electronics. While the atomic and electronic structure of bulk and monolayer SnS2 have been studied, much less is known about the edges of layers. Such edges could have a major influence on the performance of SnS2. This paper reports on density functional theory (DFT) simulations of the atomic and electronic structure of the edges of SnS2. We modeled several different edge terminations at various S coverages and orientations, as well as performed thermodynamic analysis of edge terminations. Our results show that edges with 0% and 50% S atoms are most stable and that higher S coverage are unstable. We directly link edge stability with environmental temperature and pressure, which will guide the experimental synthesis of SnS2 materials. We found all the edges to be semiconducting, unlike other metal chalcogenides, and that the band gap energy decreased with increasing S coverage. Semiconducting edges could lead to lower charge recombination rates and better photocatalytic performance. Our calculations also show that edges may have direct or indirect band gaps, depending on the edge termination. Finally, we examined the reactivity of edges through hydrogen dissociation and found edges to be more reactive than basal planes. Our work provides important details on the nature of SnS2 edges and how these edges influence the electrical and chemical features of SnS2.

关键词： Dichalcogenides Surfaces Density functional theory

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Graphene Nanoribbons/Manganese Oxide Nanocomposite Modified Electrode for Detection of Antimicrobial Drug Nitrofurantoin

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Journal of Nanomaterials 2023年第1期2023卷

作者： Nagarajan, Ramila D. Magesh, Vasanth Sundramoorthy, Ashok K. Murugan, Preethika Atchudan, Raji Ganapathy, Dhanraj Arya, Sandeep Mahmoud Karami, Abdulnasser Govindasamy, Mani Department of Chemistry V.V.Vanniaperumal College for Women Tamil Nadu Virudhunagar626001 India Centre for Nano-Biosensors Department of Prosthodontics Saveetha Dental College and Hospitals Saveetha Institute of Medical and Technical Sciences Poonamallee High Road Velappanchavadi Tamil Nadu Chennai600077 India Augsburg University Am Technologiezentrum 8 Augsburg86159 Germany School of Chemical Engineering Yeungnam University Gyeongsan38541 Korea Republic of Department of Physics University of Jammu Jammu and Kashmir Jammu180006 India Department of Chemistry College of Science King Saud University Riyadh11451 Saudi Arabia International PhD Program in Innovative Technology of Biomedical Engineering and Medical Devices Ming Chi University of Technology New Taipei City243303 Taiwan

The design and development of a new kind of cost-effective electrode material with excellent selectivity and stability are still a great challenge in the field of electrochemical sensors. Recently, researchers have paid more attention to the electrochemical reduction of nitro compounds due to their hazardous nature. Nitro compounds play a vital role in various industrial applications. However, the direct discharge of nitro compounds to the environment as industrial wastewater is harmful. In this study, a nanocomposite made of 1D graphene nanoribbons decorated with manganese dioxide (GNR-MnO2) was prepared to fabricate an electrochemical transducer for the determination of nitrofurantoin (NFT) in biofluids. First, 1D GNR was prepared by unzipping of multiwalled carbon nanotubes. Second, the GNR was decorated with MnO2 by the hydrothermal reduction method. As-prepared GNR-MnO2 nanocomposite was comprehensively characterized by field emission scanning electron microscopy with EDX, XRD, UV-visible, electrochemical impedance spectroscopy, and cyclic voltammetry. Moreover, GNR-MnO2-coated glassy carbon electrode (GCE) exhibited good electrocatalytic activity toward NFT. The electroreduction of NFT was found at -0.40 V which was 50 mV lower than bare GCE. GNR-MnO2 nanocomposite modified GCE showed a well-defined linear reduction peak current for NFT from 10 nM to 1,000 μM. The selectivity of the sensor was also analyzed in the presence of other nitro compounds which confirmed that NFT can be selectively detected at -0.4 V. The GNR-MnO2 modified electrode was also able to separate reduction peaks of other nitro compounds. In addition, the detection of NFT was carried out in human urine samples with a good recovery of 99.60%-98.60%. © 2023 Ramila D. Nagarajan et al.

关键词： Scanning electron microscopy

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Enhancing Stability and Performance in Perovskite Solar Cells Through Rationally Designed Phenanthro[9,10-D]Imidazole Derivatives for Tailored Interfacial engineering

SSRN

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SSRN 2024年

作者： Sun, Shih-Sheng Ramanujam, Rajarathinam Shi, Zhong-En Lung, Chien-Yu Li, Sie-Rong Wei, William Wu Wang, Chi-Chun Chen, Chih Ping Institute of Chemistry Academia Sinica Nankang Taipei11529 Taiwan Taiwan International Graduate Program Sustainable Chemical Science and Technology Academia Sinica Nankang Taipei11529 Taiwan Department of Applied Chemistry National Yang Ming Chiao Tung University Hsinchu30050 Taiwan Department of Materials Engineering Organic Electronics Research Center Ming Chi University of Technology 84 Gunjuan Road Taishan New Taipei City24301 Taiwan Taipei Fuhsing Private School 262 Section 1 Dun-Hua South Road Taipei Taiwan College of Engineering Center for Sustainability and Energy Technologies Chang Gung University Taoyuan City33302 Taiwan

Interfacial engineering techniques play a significant role in the development of perovskite solar cells (PSCs). In inverted PSCs, nickel oxide (NiOx) is commonly used as a hole transport material (HTM). The poor interactions at the NiOx/CH3NH3PbI3 (MAPbI3) interface contributed to the low stability and power conversion efficiency (PCE) in devices. To address this issue, dopant-free ultrathin interfacial layers (IFLs) have been introduced between the NiOx and perovskite. These IFLs enhance the chemical interaction between the NiOx and perovskite interfaces and result in improved device performance. Herein, T-shape phenanthro[9,10-d]imidazole derivatives, SR-1 and SR-2, were designed and synthesized. The SR-molecules were employed as IFL materials in p-i-n devices with a device configuration of ITO/NiOx/IFL/MAPbI3/PCBM/BCP/Ag. Notably, the IFLs serve multiple functions: modifying the energy levels of NiOx, improving the surface roughness and crystallinity of MAPbI3, passivating defects, enhancing charge extraction, and reducing trap density at the NiOx/MAPbI3 interface. As a result, the PCEs of both devices with SR-1 and SR-2 IFLs outperformed that of the pristine device. The best performance of 20.3% efficiency with nearly negligible hysteresis was achieved from the device with SR-1. The devices with SR-molecules achieved remarkable thermal stability under ambient air conditions and continuous heating at 60 °C with 50-60% relative humidity. © 2024, The Authors. All rights reserved.

关键词： Thermodynamic stability

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A Comprehensive Study on the Degradation Process of Medical-Grade Polydioxanone at Low pH

SSRN

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SSRN 2024年

作者： Lelkes, Krisztina Dodzi Jezbera, Daniel Svoboda, Roman Podzimek, Štěpán Loskot, Jan Nalezinková, Martina Voda, Petr Duda, Piotr Fučíková, Alena Myslivcová Hosszú, Tomáš Alferi, Dino Bezrouk, Aleš Department of Medical Biophysics Faculty of Medicine in Hradec Králové Charles University Hradec Králové500 03 Czech Republic Department of Physics Faculty of Science University of Hradec Králové Rokitanského 62 Hradec Králové500 03 Czech Republic Department of Physical Chemistry Faculty of Chemical Technology University of Pardubice Studentská 573 Pardubice532 10 Czech Republic Institute of Chemistry and Technology of Macromolecular Materials Faculty of Chemical Technology University of Pardubice Studentská 573 Pardubice532 10 Czech Republic Department of Biology Faculty of Science University of Hradec Králové Rokitanského 62 Hradec Králové500 03 Czech Republic Institute of Biomedical Engineering University of Silesia in Katowice Będzińska 39 Sosnowiec41-205 Poland Department of Neurosurgery University Hospital Hradec Králové Sokolská 581 Hradec Králové500 05 Czech Republic

Polydioxanone (PPDX) has gained significant attention as a biocompatible and absorbable polymer used in various medical applications, such as sutures and tissue scaffolds. This research presents a thorough investigation into the degradation mechanisms of medical-grade polydioxanone under low pH conditions, simulating physiological environments where the polymer may encounter acidic surroundings during its intended applications, e.g., esophagus and stomach surgery. It mainly focuses on the dependence of the PPDX degradation rate on various pH values (1.0, 1.2, 1.67, 3.78, 7.0, and 7.4) of the test environment, which is a substantial knowledge for successful gastrointestinal treatment. The PPDX suture samples were degraded in the test environments for up to 6 weeks and analyzed using size exclusion chromatography, differential scanning calorimetry, Raman spectroscopy, scanning electron microscopy, X-ray microtomography, and mechanical property measurements. The results show that the PPDX degradation is significantly accelerated at pH below 1.67. Correlations of the molecular weight, crystallinity, glass transition temperature, Young’s modulus, shear modulus, tensile strength, and the 1733 cm−1 Raman peak shoulder area indicate that the degradation mechanism does not change with increasing acidity. Molecular weight, crystallinity, and Young’s modulus are shown to be the most suitable parameters for characterizing general PPDX polymer degradation. On the other hand, measurements of tensile strength, shear modulus, and the 1733 cm−1 Raman peak shoulder area were found to be the most suitable parameters for characterizing the PPDX filament’s macroscopic integrity. Raman spectroscopy is of particular interest in this regard due to its rapidity and practically no requirements on the sample preparation or form. © 2024, The Authors. All rights reserved.

关键词： Differential scanning calorimetry

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Front Cover: Potassium Carbonate as a Low-Cost and Highly Active Solid Base Catalyst for Low-Temperature Methanolysis of Polycarbonate (ChemSusChem 2/2025)

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ChemSusChem 2025年第2期18卷

作者： Tzu-Ming Lin Philip Anggo Krisbiantoro Miyu Sato Yu-Chia Chang Eduardo C. Atayde Dr. Weisheng Liao Prof. Yuichi Kamiya Dr. Ryoichi Otomo Prof. Kevin C.-W. Wu Department of Chemical Engineering National Taiwan University Taipei 10617 Taiwan Molecular Science and Technology Program Taiwan International Graduate Program Academia Sinica Taipei 11529 Taiwan International Graduate Program of Molecular Science and Technology National Taiwan University Taipei 10617 Taiwan Graduate School of Environmental Science Hokkaido University Nishi 5 Kita 10 Kita-ku Sapporo 060-0810 Japan Department of Chemistry National Tsing Hua University Hsinchu 30013 Taiwan Faculty of Environmental Earth Science Hokkaido University Nishi 5 Kita 10 Kita-ku Sapporo Japan Department of Chemical Engineering and Materials Science Yuan Ze University Chung-Li Taoyuan Taiwan Department of Chemical Engineering Chung Yuan Christian University Taoyuan City 320 Taiwan

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