Physical Sciences and Mathematics Commons^™

Host-Pathogen Co-Evolution With Various Transmission Modes Of Infection And Density-Dependent Dynamics, Bita Ghodsi

Electronic Thesis and Dissertation Repository

Pathogens can be transmitted both vertically (from the parent to the offspring) and horizontally. Here, I model the co-evolution of pathogens and their hosts allowing for vertical and horizontal transmission and density-dependent host population growth. My analysis uses evolutionary game theory. I use computational methods to find that increasing vertical transmission does not always result in more benign disease outcomes. Instead, it can lead to higher pathogen-induced mortality. Furthermore, more benign outcomes evolve more readily when horizontal transmission is more profitable for the pathogen, and overall virulence increases as horizontal transmission becomes more profitable. The results also indicate that vertical …

Understanding Protein Deep Learning Models Through Explainability, Zahra Fazel

Electronic Thesis and Dissertation Repository

This thesis investigates the application of Explainable Artificial Intelligence (XAI) techniques to deep learning models in the field of protein analysis, specifically targeting protein language models and protein interaction site prediction models. Despite the increasing adoption of these sophisticated deep learning models in bioinformatics, their intrinsic complexity often results in a black-box nature, obscuring the understanding of their decision-making processes.

This research represents a thorough effort to integrate explanation methods within this context. We analyze the resulting interpretations using biological-specific statistical tests to enhance the transparency and interpretability of the models. This work evaluates the efficacy of current XAI methods …

Quantum Field Theory And The Limits Of Reductionism, Emily Adlam

Mathematics, Physics, and Computer Science Faculty Articles and Research

I suggest that the current situation in quantum field theory (QFT) provides some reason to question the universal validity of ontological reductionism. I argue that the renormalization group flow is reversible except at fixed points, which makes the relation between large and small distance scales quite symmetric in QFT, opening up at least the technical possibility of a non-reductionist approach to QFT. I suggest that some conceptual problems encountered within QFT may potentially be mitigated by moving to an alternative picture in which it is no longer the case that the large supervenes on the small. Finally, I explore some …

The Bicomplex Tensor Product And A Bicomplex Choi Theorem, Daniel Alpay, Antonino De Martino, Kamal Diki, Mihaela Vajiac

Mathematics, Physics, and Computer Science Faculty Articles and Research

In this paper we extend the concept of tensor product to the bicomplex case and use it to prove the bicomplex counterpart of the classical Choi theorem in the theory of complex matrices and operators. The concept of hyperbolic tensor product is also discussed, and we link these results to the theory of quantum channels in the bicomplex and hyperbolic case.

An Online Nanoinformatics Platform Empowering Computational Modeling Of Nanomaterials By Nanostructure Annotations And Machine Learning Toolkits., Tong Wang, Daniel P Russo, Philip Demokritou, Xuelian Jia, Heng Huang, Xinyu Yang, Hao Zhu

College of Science & Mathematics Departmental Research

Modern nanotechnology has generated numerous datasets from in vitro and in vivo studies on nanomaterials, with some available on nanoinformatics portals. However, these existing databases lack the digital data and tools suitable for machine learning studies. Here, we report a nanoinformatics platform that accurately annotates nanostructures into machine-readable data files and provides modeling toolkits. This platform, accessible to the public at https://vinas-toolbox.com/, has annotated nanostructures of 14 material types. The associated nanodescriptor data and assay test results are appropriate for modeling purposes. The modeling toolkits enable data standardization, data visualization, and machine learning model development to predict properties and bioactivities …

Molecular Docking, Pharmacological Profiling, And Molecular Dynamics Simulation Of Potential Antihyperuricemic Agent From Secondary Metabolites Of Dillenia Philippinensis Rolfe (Dilleniaceae), Louie Rince C. Suyo, John P. Paulin, Nicole Clarence Louise L. Gapaz, Markus Brent S. Arevalo, Vince Tyrell P. Yongco, Librado A. Santiago

Karbala International Journal of Modern Science

Crystal accumulation in the joints due to increased serum uric acid (sUA) may lead to an inflammatory condition called gout. Increased sUA is caused by the excessive reabsorption of the urate anion transporter-1 (URAT-1). Therefore, URAT-1 inhibition will promote uric acid excretion and reduce the risk of having gout. Dillenia philippinensis Rolfe, often known as katmon, is an endemic plant in the Philippines with bioactive compounds associated with several therapeutic benefits. The present study represents the first scientific inquiry into the antihyperuricemic potential of compounds isolated from D. philippinensis. This study aimed to assess the interaction of URAT-1 with …

Osculating Curves, Sepideh Bahrami

Electronic Thesis and Dissertation Repository

Consider a complex analytic curve $X$ in $\mathbb{C}^2$, along with a specific point $p \in X$. The primary concern arises in approximating geometrically the curve $X$ precisely at the point $p$. Analogously, in introductory calculus, students learn to compute the tangent line to the graph of a function $y=f(x)$ at a given point $p=(x_*,f(x_*))$ by utilizing the derivative of $f$ at $x_*$.

For analytical convenience, we assume a local representation of the curve $X$ using a power series expansion. This representation centers the point $p$ at the origin $(0,0) \in \mathbb{C}^2$. Thus, our mathematical input becomes a Taylor series:

\[ …

Coal Mines In Light Of The Provisions Of The Proposed Regulation Of The European Parliament And Of The Council On The Reduction Of Methane Emissions In The Energy Sector, Amending Regulation (Eu) 2019/942, Magdalena Zięba, Jacek Skiba, Piotr Kalisz, Regina Kościarz, Adam Smoliński

Journal of Sustainable Mining

In December 2021, the European Commission presented a draft Regulation of the European Parliament and of the Council on the reduction of methane emissions in the energy sector and amending Regulation (EU) 2019/942. The article summarizes the proposed EU rules on methane emissions from coal mines. In addition, it summarizes the figures of anthropogenic methane emissions for the European Union countries from the three main emission sources: agriculture, waste and the energy sector. The volumes of methane emissions from EU and Polish coal mines are also presented and divided into underground and surface mines, as well as active mines, abandoned …

Exploring The Efficiency Of Nitrogenated Carbon Quantum Dots/Tio2 S-Scheme Heterojunction In Photodegradation Of Ciprofloxacin In Aqueous Environments, Yilmaz Ateş, Zafer Eroğlu, Özkan Açişli, Önder Meti̇n, Semra Karaca

Turkish Journal of Chemistry

The usability of polyvinyl chloride-based quaternary triethanol ammonium chloride anionite (PVC-TEAC) as a potential extractant for tungstate was investigated to recover tungstate from Gabal Qash Amir, Egypt, assaying 70.91% WO3. Structure elucidation for PVC-TEAC anionite was successfully carried out using several techniques. Experimental measurements, such as pH, agitation time, initial tungsten concentration, anionite dose, co-ions, temperature, and eluting agents, have been optimized. It was found that PVC-TEAC anionite has a maximum capacity of 63 mg per gram. From the distribution isotherm modeling, Langmuir’s model fits the experimental results better than Freundlich’s, with a theoretical value of 61.728 mg g–1. According …

Synthesis And Characterization Of New Hexahydroquinoline Derivatives, Evaluation Of Their Cytotoxicity, Intracellular Ros Production And Inhibitory Effects On Inflammatory Mediators, Ezgi̇ Pehli̇vanlar, Deni̇z Arca Çakir, Sonia Sanajou, Hülya Tezel Yalçin, Terken Baydar, Pinar Erkekoğlu, Hani̇fe Avci, Rahi̇me Şi̇mşek

Turkish Journal of Chemistry

Inflammation is a response to injury and infection in the organism. It can be categorized as acute and chronic inflammation. Chronic inflammation is the underlying cause of many diseases such as Alzheimer's, diabetes, rheumatoid arthritis, atherosclerosis and cardiovascular diseases. Recent studies have proven the anti-inflammatory properties of 1,4-dihydropyridines (1,4-DHPs) and its derivatives, which have many biological properties including calcium channel blockers. The structures of the synthesized compounds were elucidated by IR, 1H-NMR, 13C-NMR and HRMS methods. The cytotoxic properties of the compounds were determined by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) method in 3T3 cell line. Among the 15 compounds, the three compounds …

Research And Practice Of Digital Institute And Its System Framework, Jianjun Yu, Yue Wang, Kongmin Wang, Zhuomin Shi

Bulletin of Chinese Academy of Sciences (Chinese Version)

In the era of the digital economy, digital scientific research and digital government are both crucial components, serving as application scenarios enabled by new information technologies. Currently, the new generation of information technologies, especially artificial intelligence and big data, is instrumental in modernizing governance at scientific research institutions within Chinese Academy of Sciences (CAS). They notably drive paradigm shifts in scientific activities and accelerate the digital transformation of these institutions. The digital system formed by the digital transformation of management processes in scientific activities at research institutes is defined as the digital institute. This study analyzes the impact of digital …

Natural Resource Factors Promoting Urban And Rural Integrated Development In The New Era: Target Selection And Policy Design, Zhimin Zhang, Guohua Yuan, Ruilin Liu

Bulletin of Chinese Academy of Sciences (Chinese Version)

Reconstructing the reverse flood of natural resource elements in rural and urban regional systems is the basic form of requirement for realizing urban-rural integration. Taking target selection-realistic obstacles-institutional demand-system construction as the logical main line, starting from the current situation of natural resource element allocation under the framework of urban-rural integrated development, it sorted out the problems existing in the urban-rural integrated development of natural resources such as asymmetrical property rights design, inconsistent bearing plans of various types, lack of natural resource revenue sharing mechanism, and poor asset flow channels and trading systems, with unified layout, power return, paid use, …

Developing Green Design, Leading Green And Low-Carbon Society, Yongxiang Lu

Bulletin of Chinese Academy of Sciences (Chinese Version)

Green design refers to a design principle and method that comprehensively considers energy and resource conservation, emission reduction, and environmental impact during the product manufacturing and operation process in the product design stage. It strives to reduce greenhouse gas emissions throughout the entire product lifecycle. In the era of information networks, green design is supported by big data, AI network collaborative design, network detection and monitoring, etc. It involves selecting energy-saving processes, green and low-carbon materials, and optimizing product geometry design and surface treatment to achieve efficient resource utilization and minimize waste. For example, selecting environmentally friendly materials through networked …

Challenges And Recommendations For Building Open Source Innovation Ecosystem For Large-Models In China, Xin Wen, Chao Zhang, Rui Guo, Kaihua Chen, Ze Feng, Qigang Zhu

Bulletin of Chinese Academy of Sciences (Chinese Version)

Addressing the current technological development issues that constrain the development of China’s large-scale model industry is needed to promote the continuous prosperity and development of the industry and enhance its international competitiveness. The study analyzes the significance of the open-source innovation ecosystem for the development of large-scale models in China. Based on reviewing the international experience of constructing the open-source innovation ecosystem, it further dissects the problems and challenges faced by the construction of the open-source innovation ecosystem for large-scale models in China and puts forward targeted suggestions. The study finds that the open-source innovation ecosystem for large-scale models in …

Research And Implications Of The Us Clean Energy Strategy, Lanchun Li, Qing Liu, Wei Chen, Yun Tang, Jun Chen

Bulletin of Chinese Academy of Sciences (Chinese Version)

As the world enters a new period of carbon neutrality, the US government is actively building a clean energy innovation ecosystem through both internal and external measures. Systematically tracking and in-depth analysis of the intent, structure, approach, and other characteristics of the new phase of the US clean energy strategy is of practical significance to Chinese energy revolution. The US focuses on the strategic objectives of science and technology innovation, energy security, and infrastructure, and has constructed an innovation ecology characterized by technology lists, planning blueprints, full-chain research, and innovative subjects from the perspective of whole-government coordination, cross-institutional decision-making, deep …

Effective Carbon Cost Constraints: Unity Of Environmental Effectiveness, Cost Effectiveness, And Incentive Effectiveness, Yongping Sun, Jingning Jiang, Xinyu Zhang

Bulletin of Chinese Academy of Sciences (Chinese Version)

The carbon market serves as a crucial policy tool in the pursuit of carbon peaking and carbon neutrality goals. It holds significant importance in driving the innovation of green and low-carbon technologies in China, facilitating the realization of nationally determined contributions, and bolstering China’s global leadership in climate action. The core function of the carbon market is carbon pricing, which can only be effective and achieve various objectives like carbon emissions reduction and sustainable development when carbon costs are reasonably constrained. Environmental effectiveness, cost effectiveness, and incentive effectiveness are three important dimensions to evaluate the effectiveness of the carbon market, …

Technology Governance And Governance Technology: From Perspective Of Regulatory Research On Blockchain Digital Assets, Yikai Wu, Guoan Li

Bulletin of Chinese Academy of Sciences (Chinese Version)

The Outline of the 14th Five-Year Plan takes blockchain as one of the key industries of the digital economy, and a number of ministries and commissions have also made clear deployments to accelerate the innovative application of blockchain, promote the digital transformation of the industry, and promote the high-quality development of the economy and society in the policy documents related to the informatization of the industry. The regulation and governance of blockchain digital assets cannot be separated from the understanding and analysis of blockchain technology itself, and observing the development mechanism of blockchain digital assets from the scientific and technological …

Large-Scale Experimental Platform For Dynamic Simulation Of Mountain Hazards (Leads), Gongdan Zhou, Peng Cui, Hongwei Wu, Yong You, Wei Zhong, Dongri Song, Chuiyi Zhou, Hongwei Shen, Mingsheng Shang, Xuerui Zhang

Bulletin of Chinese Academy of Sciences (Chinese Version)

Mountain hazards involve complex multiphase media composed of granular materials and fluids. The challenges related to scale effects and similarity issues in physical modelling of these hazards are key problems in both fundamental research on dynamics of granular materials and applied research in disaster prevention and mitigation. Supported by the Chinese Academy of Sciences’ key scientific infrastructure construction project at the field station network, the National Dongchuan Debris Flow Observation and Research Station in Jiangjia Gully, Dongchuan District, Kunming City completed the construction of the large-scale experimental platform on dynamic simulation of mountain hazards (LEADS) in 2024. This platform is …

International Development Strategy And Analysis Of Science And Technology Trends In Carbon Capture, Utilization, And Storage (Ccus), Aning Qin, Yuling Sun

Bulletin of Chinese Academy of Sciences (Chinese Version)

In the context of carbon neutrality, carbon capture, utilization, and storage (CCUS) technology has emerged as a critical focus for policymakers worldwide. Recognized as a critical tool for combating climate change and achieving carbon neutrality, CCUS has gained widespread endorsement from major nations and international organizations. Through methods such as bibliometrics, text clustering, and comprehensive research involving foreign official institutions and authoritative websites, this study delves into the technology strategy and development trends of CCUS. It is found that various countries，including the United States, Europe, and Japan, have sequentially rolled out CCUS strategies, elevating CCUS to a pivotal national strategic …

A Coarse-Grained Molecular Dynamics Study Of Gas Hydrate Formation And Dissociation, Meisam Adibifard

LSU Doctoral Dissertations

The study of gas hydrates has increased significantly over the last two decades because of their potential application in energy storage, production and transportation, water desalination, refrigeration, gas separation, etc. There is a significant interest in commercially developing natural gas hydrates because the energy content of methane hydrate reservoirs (MHRs) is at least twice that of all conventional fossil fuels combined. Additionally, due to the higher storage capacity of hydrates, it is proposed to sequester CO₂ in the form of CO₂ hydrate, thereby reducing the amount of greenhouse gases. Hence, hydrates offer a dual solution to two of …

Challenges And Practices Of Deep Learning Model Reengineering: A Case Study On Computer Vision, Wenxin Jiang, Vishnu Banna, Naveen Vivek, Abhinav Goel, Nicholas Synovic, George K. Thiruvathukal, James C. Davis

Computer Science: Faculty Publications and Other Works

Many engineering organizations are reimplementing and extending deep neural networks from the research community. We describe this process as deep learning model reengineering. Deep learning model reengineering — reusing, replicating, adapting, and enhancing state-of-the-art deep learning approaches — is challenging for reasons including under-documented reference models, changing requirements, and the cost of implementation and testing.

Preparation Of A Chiral Hyperbranched Polymer Based On Cinchona Alkaloids And Investigation Of Its Catalytic Activity In Asymmetric Reactions, Rafiqul Islam, Mohammad Shahid Ullah, Abdus Salam, Shinichi Itsuno

Turkish Journal of Chemistry

Cinchona alkaloid-derived sulfonamides and ester dimers containing chiral hyperbranched polymers have been successfully synthesized and applied as catalysts in asymmetric reactions. Several hyperbranched polymers derived from cinchona alkaloids, incorporating sulfonamides and esters, were synthesized through Mizoroki–Heck coupling polymerization. These polymers were subsequently applied in enantioselective Michael addition reactions. As the prepared polymers are not soluble in frequently used organic solvents, they act as efficient catalysts in the enantioselective reaction of β-ketoesters to nitroolefins, achieving up to 99% enantioselectivity with good yields. The insoluble property allows them to better satisfy “green chemistry” requirements and be used several times without losing the …

Synthesis, Characterization, And Physico-Chemical Aspects Of A New Pvc-Based Quaternary Triethanol Ammonium Chloride Anionite For Tungsten Recovery, Bahig Atia

Turkish Journal of Chemistry

The usability of polyvinyl chloride-based quaternary triethanol ammonium chloride anionite (PVC-TEAC) as a potential extractant for tungstate was investigated to recover tungstate from Gabal Qash Amir, Egypt, assaying 70.91% WO3. Structure elucidation for PVC-TEAC anionite was successfully carried out using several techniques. Experimental measurements, such as pH, agitation time, initial tungsten concentration, anionite dose, co-ions, temperature, and eluting agents, have been optimized. It was found that PVC-TEAC anionite has a maximum capacity of 63 mg per gram. From the distribution isotherm modeling, Langmuir’s model fits the experimental results better than Freundlich’s, with a theoretical value of 61.728 mg g–1. According …

Liquefaction Optimization Of Grape Pulp Using Response Surface Methodology For Biopolyol Production And Bio-Based Polyurethane Foam Synthesis, Furkan Çolakoğlu, Emre Akdoğan, Murat Erdem

Turkish Journal of Chemistry

Both environmental and economic disadvantages of using petroleum-based products have been forcing researchers to work on environmentally friendly, sustainable, and economical alternatives. The purpose of this study is to optimize the solvothermal liquefaction process of grape pomace using response surface methodology coupled with a central composite design. After investigating the physicochemical properties of the liquified products (biopolyol) in detail, a bio-based rigid polyurethane foam (RPUF) was synthesized and characterized. The hydroxyl and acid numbers and viscosity values of all the biopolyols were analyzed. According to variance analysis results (%95 confidence range), both the reaction temperature and catalyst loading were determined …

New Imidazolidindionedioximes And Their Pt(Ii) Complexes: Synthesis And Investigation Of Their Antitumoral Activities On Breast Cancer Cells, Emrah Karahan, Tuğba Gençoğlu Katmerli̇kaya, Emel Önal, Aydan Dağ, Ayşe Gül Gürek, Vefa Ahsen

Turkish Journal of Chemistry

Breast cancer is one of the most common types of cancer worldwide and has the most lethality ratio for females among all cancers. Although current cancer therapeutics have made considerable advancements, there is still room for improvement in terms of efficacy. Many anticancer drugs have a risk of causing serious adverse effects due to their non-specific cytotoxic effects on both tumor and healthy cells. New therapeutics might have a greater ability to kill cancer cells, reduce the volume of tumors, and improve overall therapy response rates. Herein, we report the efficient synthesis and characterization of three amphi vic-dioximes and their …

Synthesis Of 3-Methyl-3-Buten-1-Ol By Supercritical Co2 In Coordination With Hzsm-5 Catalyzed Formaldehyde-Isobutene Prins Reaction, Hang Yuan, Gui-Ping Cao, Hui Lv

Turkish Journal of Chemistry

The reaction solvent and catalyst play an essential role in the Prins reaction for the synthesis of 3-methyl-3-buten-1-ol (MBO) from formaldehyde and isobutene. The reactivity of the solid base catalyzed Prins condensation reaction by formaldehyde and isobutene in supercritical CO2 was investigated using CsH2PO4 modified HZSM-5. We finds that the alkaline sites of the alkali-loaded catalyst can extract the α-H on isobutene to generate olefin carbon negative ions, while the supercritical CO2 with weak Lewis acidity can activate formaldehyde to carbon positive ions, which can combine more easily with the carbon negative isobutene to react, thus improving the reactivity of …

Magnetic Solid-Phase Extraction Technique Based On Fe3o4@Coppy-Pth Nanocomposite For Extraction Of Cobalt, Chromium, And Nickel Prior To Determination By Micro-Sample Injection System-Flame Atomic Absorption Spectrometry In Alcoholic And Nonalcoholic Beverages, Meli̇ke Küçüksakalli, Qamar Salamat, Buket Ti̇reli̇, Şükrü Gökhan Elçi̇

Turkish Journal of Chemistry

A novel Fe3O4@coPPy-PTH nanocomposite-based sorbent was prepared via in-situ oxidative polymerization using Fe3O4 nanoparticles with spherical and flower-like morphologies of thiophene and pyrrole as the feedstocks. The synthesized nanocomposite utilized sensitive extraction and determination of the metal ions Co(II), Cr(III), and Ni(II) without a chelating agent, followed by a micro-sample injection system-flame atomic absorption spectrometer (MIS-FAAS). The composition and morphology of Fe3O4@coPPy-PTH nanocomposite were characterized by advanced spectroscopic and imaging techniques like SEM and FT-IR. SEM observations showed the size of Fe3O4 nanoparticles changed from 30 nm to 120 nm in diameter after the copolymer (PPy-PTH) coating. The Fe3O4@coPPy-PTH nanocomposite …

Β-Ketoenamine-Linked Covalent Organic Framework For Efficient Iodine Capture, Onur Büyükçakir

Turkish Journal of Chemistry

Exploring the materials that effectively capture radioactive iodine is crucial in managing nuclear waste produced from nuclear power plants. Herein, a β-ketoenamine-linked covalent organic framework (bCOF) was reported as an effective adsorbent to capture iodine from both vapor and solution. bCOF's high porosity and heteroatom-rich skeleton offer a notable iodine vapor uptake capacity of up to 2.51 g g-1 at 75 oC under ambient pressure. Furthermore, after five consecutive adsorption-desorption cycles, the bCOF demonstrates a high reusability performance with a significant iodine vapor capacity retention. The adsorption mechanism was also investigated using various ex-situ structural characterization techniques, and these mechanistic …

Lacoo3 Is A Promising Catalyst For Dry Reforming Of Benzene Used As A Surrogate Of Biomass Tar, Başar Çağlar, Deni̇z Üner

Turkish Journal of Chemistry

Tar build-up is one of the bottlenecks of biomass gasification process. Dry reforming of tar is an alternative solution if oxygen chemical potential on the catalyst surface is at sufficient levels. For this purpose, an oxygen donor perovskite, LaCoO3, was used as a catalyst for dry reforming of tar. To circumvent the complexity of the tar and its constituents, benzene molecule was chosen as a model compound. Dry reforming of benzene vapour on the LaCoO3 catalyst was investigated at temperatures of 600, 700, 800 °C, at the CO2/C6H6 ratios of 3, 6, 12 and at space velocities of 14000 and …

Identification Of Blood At Simulated Crime Scenes Using Silver Nanoparticles With Sers, Uğur Köroğlu, Necdet Sağlam, Uğur Tamer, Ramazan Akcan, İsmai̇l Hakki Boyaci, Eylül Evran

Turkish Journal of Chemistry

Analysis of substances and samples obtained from the crime scene are very important in solving forensic cases. In order to determine the variables involved in a crime and to expedite the investigation process, especially the rapid analysis of body fluids in a small quantity and within an environment containing diverse components is necessary. For this reason, it is of great importance to analyse biological fluids with rapid, non-chemical contamination, non-destructive, low-cost and accurate techniques. In recent years, with advancements in laser technology, spectroscopic methods have been introduced as an analytical technique in forensic medicine and chemical studies. This study focuses …