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SSRN 2024年

作者： Nguyen, Thi-Thu-Ha Vu, Duc Quang Doan, Ngoc Phu Thi Khanh Chi, Huynh Li, Peixin Van Binh, Doan An, Yimeng Tuan Dung, Pham Hoang, Tuan A. Thai Son, Mai Laboratory of Environmental Sciences and Climate Change Institute for Computational Science and Artificial Intelligence Van Lang University Ho Chi Minh City70000 Viet Nam Faculty of Environment School of Technology Van Lang University Ho Chi Minh City70000 Viet Nam Department of Computer Science and Information System Thai Nguyen University of Education Viet Nam School of Electronics Electrical Engineering and Computer Science Queen’s University Belfast United Kingdom College of Economics and Management Nanjing University of Aeronautics and Astronautics China Master program in Water Technology Reuse and Management Faculty of Engineering Vietnamese-German University Binh Duong Province Ben Cat Town820000 Viet Nam

The Mekong River Basin (MRB) is one of the highest biodiversity areas in the world and is the vital source of livelihoods for more than 60 millions of people over six countries in Southeast Asia. However, it is suffering from a severe sediment starvation problem caused by climate change and human activities, particularly dam constructions. Understanding long-term sediment changes thus plays a crucial role for management and contingency plans. Current sediment concentration data in the MRB are extremely sporadic, making it a non-trivial task to analyze them. This paper focuses on the sediment reconstruction to provide long-term reliable suspended sediment concentration (SSC) data using Machine Learning (ML) perspectives. In particular, a novel semi-supervised ML model, which can effectively deal with data sparsity, is introduced to predict/reconstruct missing sediment data. The key idea of this approach is to exploit abundant available hydroclimate data to reduce training overfitting rather than solely relying on sediment concentration data, thus enhancing the accuracy of the employed ML models. Extensive experiments on data obtained from 1979 to 2019 at the three main stations (i.e., Chiang Saen, Nong Khai, and Mukdahan) are conducted to demonstrate the performances of the proposed method compared to other state-of-the-art supervised techniques and traditional simulation methods commonly used in previous sediment forecasting/reconstruction studies. To the best of our knowledge, this approach is the first semi-supervised method to reconstruct sediment data in the field. Though this study focuses on the MRB, sediment sparsity is a very common problem in other river systems worldwide. Thus, this method can be widely applied for them for more effective sediment reconstruction/prediction in general. © 2024, The Authors. All rights reserved.

关键词： Biodiversity

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Algal biomass based bio-refineries: Concurrent pre-treatment strategies and perspectives for sustainable feedstock

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Biomass and Bioenergy 2024年 187卷

作者： Shashikumar, Uday Ranjan, Kumar Rakesh Sharma, Ankit Naina Subramanian, Balaji Tsai, Pei-Chien Lin, Yuan-Chung Lay, Chyi-How Wang, Chin-Tsan Biswas, Shelly Ponnusamy, Vinoth Kumar Department of Medicinal and Applied Chemistry Kaohsiung Medical University Kaohsiung City 807 Taiwan Department of Chemistry Amity Institute of Applied Sciences Amity University Uttar Pradesh Noida201303 India Department of Mechanical Engineering SRM Institute of Science and Technology Kattankulathur Tamil Nadu Chennai603203 India Institute of Environmental Engineering National Sun Yat-Sen University Taiwan Master Program of Green Energy Science and Technology Feng Chia University Taiwan Department of Mechanical and Electro-Mechanical Engineering National I-Lan University I Lan Taiwan Department of Space Engineering and Rocketry Birla Institute of Technology Mesra Jharkhand Ranchi835215 India 807 Kaohsiung City Taiwan 807 Kaohsiung City Taiwan Department of Computational Biology Institute of Bioinformatics Saveetha School of Engineering Saveetha Institute of Medical and Technical Sciences Tamil Nadu Chennai602105 India Institute of Aquatic Science and Technology National Kaohsiung University of Science and Technology Kaohsiung City81157 Taiwan Department of Food Science National Pingtung University of Science and Technology Pingtung91201 Taiwan

The quest for viable and scalable biofuel sources has been at the forefront of scientific innovation for the past three decades. Due to its rich chemical constituents, microalgal biomass has emerged as a pivotal sustainable and scalable feedstock for biorefineries. This comprehensive review critically analyzes the different types of microalgae feedstock, concurrent extraction technologies, bio-pre-treatment procedures, and the key chemical and physical parameters influencing lipid formation and algal biofuel production. We propose a novel approach of photo-initiated culturing of algal biomass using photobioreactors (PBRs) to address the limitations of concurrent space and time-related constraints. The innovative photo bio-refinery strategy presented herein aims to enhance sustainability factors while minimizing emissions, catering to the needs of futuristic non-electric vehicles. A comparative quality analysis of microalgae-derived biofuel against conventional fossil fuels and other biofuels is conducted, considering chemical, environmental, economic, and social perspectives. Furthermore, we elucidate the efficacy of bio-pre-treatment strategies such as dehydration, hydrothermal liquefaction, pyrolysis, and gasification in optimizing biofuel production. The proposed photo biorefineries exhibit the potential to yield a diverse range of value-added products, including biodiesel, biogases, bio-fertilizers, bio-pesticides, bio-alcohols, dyes, proteins, carotenoids, and drug vitals. This review provides a comprehensive framework for the development of sustainable and efficient microalgae-based biorefineries, paving the way for a greener and more economically viable future in the biofuel industry. © 2024 Elsevier Ltd

关键词： Feedstocks

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Theoretical study on adsorption and reaction of polymeric formic acid on the Cu(111) surface

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Physical Review Materials 2021年第7期5卷 075801-075801页

作者： Septia Eka Marsha Putra Fahdzi Muttaqien Yuji Hamamoto Kouji Inagaki Akitoshi Shiotari Jun Yoshinobu Yoshitada Morikawa Ikutaro Hamada Department of Precision Engineering Graduate School of Engineering Osaka University 2-1 Yamada-oka Suita Osaka 565-0871 Japan Department of Engineering Physics Institut Teknologi Sumatera Jalan Terusan Ryacudu Way Hui Jati Agung South Lampung 35365 Indonesia Instrumentation and Computational Physics Research Group Faculty of Mathematics and Natural Sciences Institut Teknologi Bandung Jalan Ganesha 10 Bandung West Java 40132 Indonesia Master Program in Computational Science Faculty of Mathematics and Natural Sciences Institut Teknologi Bandung Jalan Ganesha 10 Bandung West Java 40132 Indonesia Elements Strategy Initiative for Catalysts and Batteries (ESICB) Kyoto University Goryo-Ohara Nishikyou-ku Katsura Kyoto 615-8245 Japan Department of Advanced Materials Science The University of Tokyo 5-1-5 Kashiwanoha Kashiwa Chiba 277-8561 Japan The Institute for Solid State Physics The University of Tokyo 5-1-5 Kashiwanoha Kashiwa Chiba 277-8581 Japan Research Center for Precision Engineering Graduate School of Engineering Osaka University 2-1 Yamada-oka Suita Osaka 565-0871 Japan

We investigate the polymeric adsorption of formic acid (HCOOH) on the Cu(111) surface by means of density functional theory. We present structural models for the polymeric form of HCOOH on Cu(111) and characterize their stability, electronic, and vibrational properties. Based on the energetics and dynamics, as well as simulated scanning tunneling microscopy and atomic force microscopy images, we propose that the α polymorph is likely to be formed on the Cu(111) surface and can explain the experimental findings. We also study the initial step of the catalytic dehydrogenation of HCOOH and find that the O-H bond dissociation at the edge of the polymer is facilitated, rather than that forming hydrogen bonding, agreeing well with the experiments.

关键词： Adsorption Chemical bonding Chemical kinetics, dynamics & catalysis Electronic structure Surface & interfacial phenomena Surfaces Density functional theory First-principles calculations

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Simultaneous biomonitoring of volatile organic compounds’ metabolites in human urine samples using a novel in-syringe based fast urinary metabolites extraction (FaUMEx) technique coupled with UHPLC-MS/MS analysis

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Chemosphere 2023年第1期329卷 138667页

作者： Gurrani, Swapnil Prakasham, Karthikeyan Huang, Po-Chin Wu, Ming-Tsang Wu, Chia-Fang Lin, Yu-Chia Tsai, Bongee Krishnan, Anbarasu Tsai, Pei-Chien Ponnusamy, Vinoth Kumar Kaohsiung City807 Taiwan Miaoli County 35053 Taiwan Department of Medical Research China Medical University Hospital China Medical University Taichung City Taiwan Kaohsiung City807 Taiwan Department of Public Health Kaohsiung Medical University Kaohsiung City Taiwan International Master Program of Translational Medicine College of Engineering and Science National United University Miaoli Taiwan Corporation No.392 Yucheng Rd. Zuoying District. Kaohsiung City813 Taiwan Department of Computational Biology Institute of Bioinformatics Saveetha School of Engineering Saveetha Institute of Medical and Technical Sciences Saveetha University Chennai602105 India Kaohsiung City807 Taiwan Kaohsiung City807 Taiwan

Assessing the impact of human exposure to environmental toxicants is often crucial to biomonitoring the exposed dose. In this work, we report a novel fast urinary metabolites extraction (FaUMEx) technique coupled with UHPLC-MS/MS analysis for the highly sensitive and simultaneous biomonitoring of the five major urinary metabolites (thiodiglycolic acid, s-phenylmercapturic acid, t,t-muconic acid, mandelic acid, and phenyl glyoxylic acid) of common volatile organic compounds' (VOCs) exposure (vinyl chloride, benzene, styrene, and ethylbenzene) in human. FaUMEx technique comprises of two-steps, liquid-liquid microextraction was performed first in an extraction syringe using 1 mL of methanol (pH 3) as an extraction solvent and then, the extractant was passed through a clean-up syringe (pre-packed-with various sorbents including 500 mg anhydrous MgSO4, 50 mg C18, and 50 mg SiO2) to obtain the high order of matrice clean-up and preconcentration efficiency. The developed method displayed excellent linearity, and the correlation coefficients were >0.998 for all the target metabolites with detection and quantification limits of 0.02–0.24 ng mL−1 and 0.05–0.72 ng mL−1, respectively. Furthermore, the matrix effects were © 2023 Elsevier Ltd

关键词： Metabolites

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Prediction of the Binding Mechanism of a Selective DNA Methyltransferase 3A Inhibitor by Molecular Simulation

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SSRN 2023年

作者： Kudo, Genki Hirao, Takumi Harada, Ryuhei Hirokawa, Takatsugu Shigeta, Yasuteru Yoshino, Ryunosuke Physics Department Graduate School of Pure and Applied Sciences University of Tsukuba 1-1-1 Tennodai Ibaraki Tsukuba305-8571 Japan Master’s Program in Medical Sciences Graduate School of Comprehensive Human Sciences University of Tsukuba Ibaraki Tsukuba305-8575 Japan Division of Biomedical Science Faculty of Medicine University of Tsukuba 1-1-1 Tennodai Ibaraki Tsukuba305-8575 Japan Center for Computational Sciences University of Tsukuba 1-1-1 Tennodai Ibaraki Tsukuba305-8577 Japan Transborder Medical Research Center University of Tsukuba 1-1-1 Tennodai Ibaraki Tsukuba305-8575 Japan Japan

DNA methylation is an epigenetic mechanism that introduces a methyl group at the C5 position of cytosine. This reaction is catalyzed by DNA methyltransferases (DNMTs) and is essential for the regulation of gene transcription. The DNMT1 and DNMT3A or -3B family proteins are known targets for the inhibition of DNA hypermethylation in cancer cells. A selective non-nucleoside DNMT3A inhibitor that mimics S-adenosyl-l-methionine and deoxycytidine has been developed;however, its selectivity mechanism is unclear because the structure of the inhibitor–protein complex has not yet been determined. Therefore, we performed docking and molecular dynamics simulations to predict the structure of the complex formed by the association between DNMT3A and the selective inhibitor. Through our simulations, binding free energy decomposition analysis, structural isoform comparison, and residue scanning revealed that Arg688 of DNMT3A is involved in the interaction with this inhibitor, as seen by its significant contribution to the binding free energy. The presence of Asn1192 at the corresponding residues in DNMT1 results in a loss of affinity for the inhibitor, suggesting that the interactions mediated by Arg688 in DNMT3A are essential for selectivity. Our study findings can be applied in the design of DNMT-selective inhibitors and methylation-specific drug optimization procedures. © 2023, The Authors. All rights reserved.

关键词： Molecular dynamics

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computational modeling of inclusion complex between aromatic amine and calixarene analogs using Semiempiric Quantum Method (SQM)

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Journal of Physics: Conference Series 2021年第1期1869卷

作者： A L Ivansyah Master Program in Computational Science Faculty of Mathematics and Natural Sciences Institut Teknologi Bandung Jl. Ganesha No. 10 Bandung Indonesia Analytical Chemistry Research Group Department of Chemistry Faculty of Mathematics and Natural Sciences Institut Teknologi Bandung Jl. Ganesha No. 10 Bandung Indonesia

PM3 Semiempiric Quantum calculation has been done in this research by using Gaussian 2009 Rev. D 01 software package to explore the capability of Calixarene and its analogs for aromatic amine extraction. The Calixarene analogs used in this research are Calixpyrrole, Calixpyridine, Thiacalixarene, Heterocalixaromatic, Calixcarbazole and Calixnaphtalene; and the aromatic amine used in this research are Aniline, 4-Chloroaniline, Toluene-2,4-diamine, 2-Naphty lamině, 4,4'-Mety lenbis(2-chloroaniline), 4,4'-Metylendianiline, N-Nitrosodiphenylamine, Benzidine, 2-Aminobiphenyl, 2-Amino-1-methyl-6-phenylimidazo[4,5-b] Pyridine, 3-Trifluoromethylaniline, p-Phenylendiamine, o-Toluidin, 4-Chloro-o-toluidin. The most suitable host molecule of calixarene analogs for extraction of aromatic amine compounds are Calixnaphthalene and Calixpyridine because all of aromatic amine compounds form inclusion complex with them spontaneously shown by negative value of binding energy.

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Molecular docking study of inclusion complex between aromatic amine and Calixarene analogs

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Journal of Physics: Conference Series 2021年第1期1869卷

A molecular docking was performed in this research by using ArgusLab version 4.0.1. It was used to explore the capability of Calixarene analogs for aromatic amine extraction. There are 6 Calixarene analogs used in this research, i.e. Calixpyrrole, Calixpyridine, Thiacalixarene, Heterocalixaromatic, Calixcarbazole and Calixnaphtalene; and the aromatic amine used in this research are Aniline, 4-Chloroaniline, Toluene-2,4-diamine, 2-Naphtylamine, 4,4'-Metylenbis(2-chloroaniline), 4,4'-Metylendianiline, N-Nitrosodiphenylamine, Benzidine, 2-Aminobiphenyl, 2-Amino-1-methyl-6-phenylimidazo [4,5-b] Pyridine, 3-Trifluoromethylaniline, p-Phenylendiamine, o-Toluidin, 4-Chloro-o-toluidin. In this molecular docking simulation, the guest molecule of aromatic amine compounds were treated as ligand and host molecule of calixarene and its analogs were treated as binding site. This molecular docking simulation used AScore scoring function, binding sitebox size for host molecule with grid size of 0.4 Å, GA docking engine with flexible ligand, 50 population sizes, 1000 max generations, 5 elitisms, 0.2 mutation rate, and 0.8 crossover rate. Calixcarbazole and Calixnaphthelene is the best host molecule for aromatic amines extraction because the inclusion complexes formed between them have negative value of binding energy.

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Simulation of Semi-Autogenous Grinding (SAG) Mill using Circular-Disks-based Model

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Journal of Physics: Conference Series 2018年第1期1090卷 012009-012009页

作者： Sari, R Widartiningsih, P M Martoprawiro, M A Hendrajaya, L Viridi, S Master Program in Computational Science Faculty of Mathematics and Natural Sciences Institut Teknologi Bandung Jalan Ganesha 10 Bandung 40132 Indonesia Master Program in Physics Faculty of Mathematics and Natural Sciences Institut Teknologi Bandung Jalan Ganesha 10 Bandung 40132 Indonesia Chemistry Department Faculty of Mathematics and Natural Sciences Institut Teknologi Bandung Jalan Ganesha 10 Bandung 40132 Indonesia Physics Department Faculty of Mathematics and Natural Sciences Institut Teknologi Bandung Jalan Ganesha 10 Bandung 40132 Indonesia

System of semi-autogenous grinding (SAG) mill is modeled in this work based on circular-disk objects, which represents not only the ground materials but also the mill liners. Interaction between these objects is through linear spring dash-pot force, which is solved numerically in soft-sphere scheme using molecular dynamics (MD) method. There is also force due to earth gravity. For ground materials a grain consists of several smaller grains, which are attached through some adhesive force. As the ground materials are smashed to the mill liners, when they reach maximum compression, they will be shattered into the smaller grains. Shattering process happens in a special materials motion known as cataracting mode. Friction is not considered in this work due to its complexity.

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computational investigation of interaction between β-cyclodextrin and hydroxychloroquine

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AIP Conference Proceedings 2021年第1期2349卷

作者： Atthar L. Ivansyah 1Master Program in Computational Science Faculty of Mathematics and Natural Sciences Institut Teknologi Bandung Jalan Ganesha No. 10 Bandung West Java 40132 Indonesia 2Analytical Chemistry Research Group Department of Chemistry Faculty of Mathematics and Natural Sciences Institut Teknologi Bandung Jalan Ganesha No. 10 Bandung West Java 40132 Indonesia

There was an outbreak with symptoms similar to SARS caused by the SARS-CoV-2 virus in the People’s Republic of China at the end of 2019. The rapid spread of the virus, even in Indonesia, led to a pandemic status being given by the WHO. The use of current medications before a vaccine is identified and ready for help is one alternative to reducing COVID-19 patients. As a candidate for anti-COVID-19 drugs, Hydroxychloroquine has been extensively studied and has now reached the clinical trial stage. Hydroxychloroquine’s solubility in water, however, is so limited that it affects its low human body bioavailability. The development of a stable inclusion complex with β-cyclodextrin is one way to increase Hydroxychloroquine’s solubility in water. This research investigated the interaction between β-cyclodextrin and Hydroxychloroquine through molecular docking analysis and a semiempirical quantum process. The results of the semiempirical quantum method and the study of molecular docking suggest that β-cyclodextrin and Hydroxychloroquine are a stable inclusion complex. Hydroxychloroquine’s solubility in aqueous solution can also be increased by forming an inclusion complex with β-cyclodextrin.

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Theoretical investigation of interaction between hydroxypropyl-β-cyclodextrin and hydroxychloroquine

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AIP Conference Proceedings 2021年第1期2349卷

At the end of 2019, there was an outbreak with symptoms similar to SARS in the People’s Republic of China caused by the SARS-CoV-2 virus. The massive spread of the virus, including in Indonesia, caused the WHO to issue a pandemic status. One alternative to reducing COVID-19 patients is to use existing drugs until a vaccine is found and ready for use. Currently, hydroxychloroquine has been widely researched as a candidate for anti-COVID-19 medicines, which has now entered the clinical trial stage. However, the solubility of hydroxychloroquine in water is so small that it impacts its low bioavailability in the human body. One way to increase hydroxychloroquine’s solubility in water is through the formation of a stable inclusion complex with hydroxypropyl-β-cyclodextrin. In this research, a molecular docking study and semiempirical quantum method were conducted to investigate the interaction between hydroxypropyl-β-cyclodextrin and hydroxychloroquine. The molecular docking study results and semiempirical quantum method show that hydroxypropyl-β-cyclodextrin and hydroxychloroquine form stable inclusion complex. The solubility of hydroxychloroquine in aqueous solution can be enhanced by forming an inclusion complex with hydroxypropyl-β-cyclodextrin.

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