Advanced Theory and Simulations最新文献

筛选
英文 中文
Computational Design of High‐Efficiency ZrS2/Perovskite Tandem Solar Cell via Bandgap and Current Matching Optimization 基于带隙和电流匹配优化的高效ZrS2/钙钛矿串联太阳能电池计算设计
IF 3.3 4区 工程技术
Advanced Theory and Simulations Pub Date : 2025-09-30 DOI: 10.1002/adts.202501325
Nabin Kumar Shaw, Basudeba Maharana, Avijit Kumar, Shyamal Chatterjee
{"title":"Computational Design of High‐Efficiency ZrS2/Perovskite Tandem Solar Cell via Bandgap and Current Matching Optimization","authors":"Nabin Kumar Shaw, Basudeba Maharana, Avijit Kumar, Shyamal Chatterjee","doi":"10.1002/adts.202501325","DOIUrl":"https://doi.org/10.1002/adts.202501325","url":null,"abstract":"Zirconium disulphide (ZrS<jats:sub>2</jats:sub>) homojunction solar cells are proposed as a sustainable top sub‐cell for effective perovskite tandem solar cell (TSC) for higher efficiency, and enhanced spectral utilization with a potential for low‐cost fabrication. The simulation shows that the two terminal (2T) ZrS<jats:sub>2</jats:sub> and CH<jats:sub>3</jats:sub>NH<jats:sub>3</jats:sub>SnI<jats:sub>3</jats:sub> (Methylammonium tin iodide) based tandem solar cells may provide optimal efficiency up to 37.20%. SCAPS‐1D software has been utilized to investigate the dependence of various parameters such as thickness, doping densities, and defect densities on the photovoltaic properties of the standalone sub‐cells. Specifically, bandgap of the perovskite layers is varied between 1.18 and 1.36 eV to investigate its effect on the performance of the cell. The current matching criteria to be ≈ 19.33 mA cm<jats:sup>−2</jats:sup>, at each point of the investigation has been checked, to get the perfectly matched ZrS<jats:sub>2</jats:sub>/CH<jats:sub>3</jats:sub>NH<jats:sub>3</jats:sub>SnI<jats:sub>3</jats:sub> tandem solar cell. The quantum efficiency (QE) versus wavelength curve confirms that the top ZrS<jats:sub>2</jats:sub> sub‐cell absorbs the shorter wavelength whereas the perovskite bottom sub‐cell absorbs the longer wavelength photons, promising a better utilization of most of the incident photons. This work provides a numerical justification for the experimental realization of 2T tandem solar cells with ZrS<jats:sub>2</jats:sub> as a top sub‐cell in perovskite TSCs for higher efficiencies.","PeriodicalId":7219,"journal":{"name":"Advanced Theory and Simulations","volume":"93 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145195041","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Modeling of Hepatitis B Virus Transmission With Vaccination, Treatment, and Memory Effects 乙型肝炎病毒传播与疫苗接种、治疗和记忆效应的建模
IF 3.3 4区 工程技术
Advanced Theory and Simulations Pub Date : 2025-09-30 DOI: 10.1002/adts.202501358
Taruna Garg, Madhuchanda Rakshit, M. Manivel, Shyamsunder
{"title":"Modeling of Hepatitis B Virus Transmission With Vaccination, Treatment, and Memory Effects","authors":"Taruna Garg, Madhuchanda Rakshit, M. Manivel, Shyamsunder","doi":"10.1002/adts.202501358","DOIUrl":"https://doi.org/10.1002/adts.202501358","url":null,"abstract":"This study presents a comprehensive fractional-order compartmental model to analyze the transmission dynamics of the hepatitis B virus (HBV), incorporating the impacts of vaccination, treatment, and memory effects. Utilizing Caputo fractional derivatives, the model captures the hereditary and memory characteristics inherent in biological systems, offering a more realistic depiction of disease progression. The population is divided into various compartments, representing various stages of infection, immunity, treatment, and recovery. The model's mathematical rigor includes the derivation of the basic reproduction number &lt;span data-altimg=\"/cms/asset/0e80e9db-470d-49be-bc69-a0f7bca63224/adts70148-math-0001.png\"&gt;&lt;/span&gt;&lt;mjx-container ctxtmenu_counter=\"3\" ctxtmenu_oldtabindex=\"1\" jax=\"CHTML\" role=\"application\" sre-explorer- style=\"font-size: 103%; position: relative;\" tabindex=\"0\"&gt;&lt;mjx-math aria-hidden=\"true\" location=\"graphic/adts70148-math-0001.png\"&gt;&lt;mjx-semantics&gt;&lt;mjx-msub data-semantic-children=\"0,1\" data-semantic- data-semantic-role=\"latinletter\" data-semantic-speech=\"upper R 0\" data-semantic-type=\"subscript\"&gt;&lt;mjx-mi data-semantic-annotation=\"clearspeak:simple\" data-semantic-font=\"italic\" data-semantic- data-semantic-parent=\"2\" data-semantic-role=\"latinletter\" data-semantic-type=\"identifier\"&gt;&lt;mjx-c&gt;&lt;/mjx-c&gt;&lt;/mjx-mi&gt;&lt;mjx-script style=\"vertical-align: -0.15em;\"&gt;&lt;mjx-mn data-semantic-annotation=\"clearspeak:simple\" data-semantic-font=\"normal\" data-semantic- data-semantic-parent=\"2\" data-semantic-role=\"integer\" data-semantic-type=\"number\" size=\"s\"&gt;&lt;mjx-c&gt;&lt;/mjx-c&gt;&lt;/mjx-mn&gt;&lt;/mjx-script&gt;&lt;/mjx-msub&gt;&lt;/mjx-semantics&gt;&lt;/mjx-math&gt;&lt;mjx-assistive-mml display=\"inline\" unselectable=\"on\"&gt;&lt;math altimg=\"urn:x-wiley:25130390:media:adts70148:adts70148-math-0001\" display=\"inline\" location=\"graphic/adts70148-math-0001.png\" xmlns=\"http://www.w3.org/1998/Math/MathML\"&gt;&lt;semantics&gt;&lt;msub data-semantic-=\"\" data-semantic-children=\"0,1\" data-semantic-role=\"latinletter\" data-semantic-speech=\"upper R 0\" data-semantic-type=\"subscript\"&gt;&lt;mi data-semantic-=\"\" data-semantic-annotation=\"clearspeak:simple\" data-semantic-font=\"italic\" data-semantic-parent=\"2\" data-semantic-role=\"latinletter\" data-semantic-type=\"identifier\"&gt;R&lt;/mi&gt;&lt;mn data-semantic-=\"\" data-semantic-annotation=\"clearspeak:simple\" data-semantic-font=\"normal\" data-semantic-parent=\"2\" data-semantic-role=\"integer\" data-semantic-type=\"number\"&gt;0&lt;/mn&gt;&lt;/msub&gt;$R_0$&lt;/annotation&gt;&lt;/semantics&gt;&lt;/math&gt;&lt;/mjx-assistive-mml&gt;&lt;/mjx-container&gt;, existence and uniqueness, and Hyers–Ulam stability of solutions. Sensitivity analysis highlights the influence of vaccination rate, recruitment rate, and vaccine efficacy on &lt;span data-altimg=\"/cms/asset/55ae6f5a-9040-4c14-bf91-58a2c4644032/adts70148-math-0002.png\"&gt;&lt;/span&gt;&lt;mjx-container ctxtmenu_counter=\"4\" ctxtmenu_oldtabindex=\"1\" jax=\"CHTML\" role=\"application\" sre-explorer- style=\"font-size: 103%; position: relative;\" tabindex=\"0\"&gt;&lt;mjx-math aria-hidden=\"true\" location=\"graphic/adts70148-math-0002.png\"&gt;","PeriodicalId":7219,"journal":{"name":"Advanced Theory and Simulations","volume":"114 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145209722","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The Physical Model and Numerical Investigation of B‐Equations Based on Quintic Trigonometric B‐Spline Collocation Technique with Finite Difference and Crank‐Nicolson Schemes 基于有限差分和曲柄-尼科尔森格式的五次三角B样条配置技术的B -方程的物理模型和数值研究
IF 3.3 4区 工程技术
Advanced Theory and Simulations Pub Date : 2025-09-30 DOI: 10.1002/adts.202500537
Saumya Ranjan Jena, Itishree Sahu
{"title":"The Physical Model and Numerical Investigation of B‐Equations Based on Quintic Trigonometric B‐Spline Collocation Technique with Finite Difference and Crank‐Nicolson Schemes","authors":"Saumya Ranjan Jena, Itishree Sahu","doi":"10.1002/adts.202500537","DOIUrl":"https://doi.org/10.1002/adts.202500537","url":null,"abstract":"In order to construct physical models of B‐equations, such as nonlinear Camassa–Holm (CH), modified Camassa–Holm (MCH), Degasperis–Procesi (DP), and modified Degasperis–Procesi (MDP) equations that arise in shallow water waves, this paper provides a quintic trigonometric B‐spline function based on collocation and a finite difference scheme. For the spatial and temporal derivatives, discretization is accomplished using the trigonometric B‐spline function of degree five and the finite difference technique, respectively. The approximate results are contrasted with the analytical results and other published methods in the literature. Furthermore, it is demonstrated that the method is unconditionally stable with the von Neumann method and accurate to convergence with order . Four representative examples are provided to show the benefit of the suggested method. For some current physical difficulties, the suggested procedure is considered to be a very reliable alternative.","PeriodicalId":7219,"journal":{"name":"Advanced Theory and Simulations","volume":"3 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145195024","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Thallium Nitride Nanosensors for Selective Detection of CO2, CO, NO, and BF3 Gases: Insights from Ab Initio Molecular Dynamics 用于选择性检测CO2, CO, NO和BF3气体的氮化铊纳米传感器:从头开始分子动力学的见解
IF 3.3 4区 工程技术
Advanced Theory and Simulations Pub Date : 2025-09-30 DOI: 10.1002/adts.202501198
Mandar Jatkar, Arpan Shah, Shubha Hegde, Tejas B G
{"title":"Thallium Nitride Nanosensors for Selective Detection of CO2, CO, NO, and BF3 Gases: Insights from Ab Initio Molecular Dynamics","authors":"Mandar Jatkar, Arpan Shah, Shubha Hegde, Tejas B G","doi":"10.1002/adts.202501198","DOIUrl":"https://doi.org/10.1002/adts.202501198","url":null,"abstract":"This study investigates the electronic properties of Thallium Nitride Nanoribbons (ThNNRs) in bare, pristine, and functionalized forms using density functional theory (DFT). The influence of nanoribbon width on structural stability and electronic characteristics is also examined. Bare ThNNRs exhibit metallic behavior with a zero bandgap, whereas pristine ThNNRs display semiconducting behavior, with their bandgap decreasing as the ribbon width increases. Functionalization with sensing molecules such as BF<jats:sub>3</jats:sub>, NO<jats:sub>2</jats:sub>, and CO<jats:sub>2</jats:sub> significantly alters the electronic response. In particular, NO<jats:sub>2</jats:sub>‐ and CO<jats:sub>2</jats:sub>‐functionalized ThNNRs undergo a semiconductor‐to‐metallic phase transition with increasing width. Sensitivity analysis reveals that sensitivity decreases with temperature, indicating an inverse relationship. Recovery time analysis shows that ThNNRs–BF<jats:sub>3</jats:sub> and ThNNRs–CO<jats:sub>2</jats:sub> configurations are minimally affected by temperature. In contrast, ThNNRs–NO<jats:sub>2</jats:sub> exhibits strong temperature dependence, with recovery times peaking at 34.13 s at 500 K. These findings demonstrate the tunable electronic properties of ThNNRs and underscore their potential in nanoelectronics and chemical sensing applications.","PeriodicalId":7219,"journal":{"name":"Advanced Theory and Simulations","volume":"12 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145195062","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Comparison of Voronoi Tessellation‐Derived and Molecular Dynamics‐Derived Atomistic Models of Polycrystalline Titania: A Computational Study of Structures, Band Structures, and Mechanical Properties 多晶二氧化钛的Voronoi镶嵌模型和分子动力学模型的比较:结构、带结构和力学性能的计算研究
IF 3.3 4区 工程技术
Advanced Theory and Simulations Pub Date : 2025-09-30 DOI: 10.1002/adts.202501245
Takuma Okamoto, Keisuke Kameda, Hao Wang, Manabu Ihara, Sergei Manzhos
{"title":"Comparison of Voronoi Tessellation‐Derived and Molecular Dynamics‐Derived Atomistic Models of Polycrystalline Titania: A Computational Study of Structures, Band Structures, and Mechanical Properties","authors":"Takuma Okamoto, Keisuke Kameda, Hao Wang, Manabu Ihara, Sergei Manzhos","doi":"10.1002/adts.202501245","DOIUrl":"https://doi.org/10.1002/adts.202501245","url":null,"abstract":"Grain boundaries (GB) affect properties of polycrystalline ceramics, including mechanical and electronic properties. While often individual postulated GBs are considered in atomistic models, a distribution of GBs present in real ceramics should be accounted for. An often‐used method to build polycrystalline models is geometry‐based Voronoi tessellation. With it, random grain orientations generally obtain in atomistic models of GBs with non‐physically high Miller index grain surfaces. Recently, models of polycrystalline rutile TiO<jats:sub>2</jats:sub> were constructed with molecular dynamics (MD) using computational heat treatment, a procedurally nature‐like approach resulting in a distribution of GBs dominated by low‐index surfaces. It is important to understand the similarities and differences in GB‐affected properties with MD‐ and Voronoi tessellation‐based models for informed selection of an appropriate model for specific applications. Such a comparison is presented. Structural properties and the effect of grainy structures on mechanical properties and band structure are compared. High‐index surfaces prevalent in Voronoi structures lead to the formation of amorphous interlayers, and fracture stress is lower than with MD‐based structures. Band structures of GBs are analyzed in large‐scale electronic structure calculations. It is found that while low‐index surfaces do not result in trap states, high‐index surfaces and amorphous interlayers may introduce such states.","PeriodicalId":7219,"journal":{"name":"Advanced Theory and Simulations","volume":"71 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145195023","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
QSAR‐Based Machine Learning Reveals a Repurposed Dual‐Function G4 Ligand against Ensitrelvir‐Resistant SARS‐CoV‐2 Main Protease 基于QSAR的机器学习揭示了一种针对Ensitrelvir - Resistant SARS - CoV - 2主蛋白酶的双重功能G4配体
IF 3.3 4区 工程技术
Advanced Theory and Simulations Pub Date : 2025-09-28 DOI: 10.1002/adts.202501079
Napat Prompat, Panik Nadee, Aekkaraj Nualla‐ong
{"title":"QSAR‐Based Machine Learning Reveals a Repurposed Dual‐Function G4 Ligand against Ensitrelvir‐Resistant SARS‐CoV‐2 Main Protease","authors":"Napat Prompat, Panik Nadee, Aekkaraj Nualla‐ong","doi":"10.1002/adts.202501079","DOIUrl":"https://doi.org/10.1002/adts.202501079","url":null,"abstract":"The emergence of drug‐resistant SARS‐CoV‐2 variants necessitates novel antiviral strategies targeting conserved viral components. This study integrates machine learning‐based quantitative structure‐activity relationship modeling and comprehensive computational approaches to identify dual‐function inhibitors against the main protease and RNA G‐quadruplex structures of SARS‐CoV‐2. A Random Forest classifier trained on 890 curated compounds achieves superior predictive performance (AUC = 0.9458) using CDK fingerprints, enabling virtual screening of 4,564 G‐quadruplex ligands from the G4LDB. Molecular docking reveals lead compound G4L2574 exhibits stronger binding affinity (−12.11 kcal mol<jats:sup>−1</jats:sup>) to the M49I mutant Mpro than clinical inhibitor ensitrelvir (−8.92 kcal mol<jats:sup>−1</jats:sup>), with molecular dynamics simulations demonstrating enhanced complex stability and persistent hydrogen bonding. MM/PBSA calculations confirm favorable binding free energy (−40.54 kcal mol<jats:sup>−1</jats:sup>) for G4L2574‐M49I, driven by robust electrostatic interactions. Structural analysis shows the M49I mutation induced steric hindrance compromising ensitrelvir binding, while G4L2574 maintained critical interactions with catalytic residues His41 and Cys145. Additionally, G4L2574 demonstrates superior RNA G‐quadruplex binding (−11.73 kcal mol<jats:sup>−1</jats:sup>) than RNA G‐quadruplex stabilizing ligand TMPyP4. This dual‐targeting mechanism, validated through machine learning and MD simulations, presents a promising strategy to circumvent resistance mutations while leveraging conserved viral replication targets. The integrated computational pipeline establishes a framework for rapid identification of broad‐spectrum antivirals against evolving coronaviruses.","PeriodicalId":7219,"journal":{"name":"Advanced Theory and Simulations","volume":"96 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145182813","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
First‐Principles Study of the Spintronic Potential of the Rare‐Earth‐Based Half‐Heusler Compound FeCeBi 稀土基半Heusler化合物FeCeBi自旋电子势的第一性原理研究
IF 3.3 4区 工程技术
Advanced Theory and Simulations Pub Date : 2025-09-27 DOI: 10.1002/adts.202501337
L. Boughlima, A. Jabar, L. Bahmad, L. B. Drissi, R. Ahl Laamara, A. Benyoussef
{"title":"First‐Principles Study of the Spintronic Potential of the Rare‐Earth‐Based Half‐Heusler Compound FeCeBi","authors":"L. Boughlima, A. Jabar, L. Bahmad, L. B. Drissi, R. Ahl Laamara, A. Benyoussef","doi":"10.1002/adts.202501337","DOIUrl":"https://doi.org/10.1002/adts.202501337","url":null,"abstract":"Systematic theoretical research of the half‐Heusler compound FeCeBi is carried out using first‐principles calculations on density functional theory (DFT) here. Three candidate crystal structures are studied, of which it is found that the ground‐state most stable configuration is the α‐phase in the ferromagnetic (FM) state. Electronic band structure computations verify that FeCeBi is an ideal half‐metal with a semiconducting gap in the spin‐up channel and metallic behavior in the spin‐down channel, and hence, it is highly promising for spintronic devices. Elastic properties such as elastic constants (C<jats:sub>11</jats:sub>, C<jats:sub>12</jats:sub>, and C<jats:sub>44</jats:sub>) confirmed mechanical stability based on Born–Huang criteria. Other mechanical indicators, such as the ratio B/G and Poisson's ratio, indicate a good balance of ductility and stiffness. Additionally, the electronic structure is determined to be structurally deformed sensitive; when compressed, the bandgap expands, while it reduces with dilatation. This tunability makes it easy to adapt FeCeBi to specific applications. Optical study reveals spin‐dependent effects, further confirming the compound's asymmetric half‐metallic character. Generally, the results demonstrate that FeCeBi is a very suitable material candidate for future spintronic and multifunctional device technologies.","PeriodicalId":7219,"journal":{"name":"Advanced Theory and Simulations","volume":"10 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145153775","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
On The Continuous Statistical Maxwell Distribution for Obtaining the Risk in Economy 关于获取经济风险的连续统计麦克斯韦分布
IF 3.3 4区 工程技术
Advanced Theory and Simulations Pub Date : 2025-09-24 DOI: 10.1002/adts.202501474
Malik Zaka Ullah, Monairah Alansari, Mir Asma, Abdullah K. Alzahrani
{"title":"On The Continuous Statistical Maxwell Distribution for Obtaining the Risk in Economy","authors":"Malik Zaka Ullah, Monairah Alansari, Mir Asma, Abdullah K. Alzahrani","doi":"10.1002/adts.202501474","DOIUrl":"https://doi.org/10.1002/adts.202501474","url":null,"abstract":"This paper introduces an approach to financial risk quantification by utilizing the Maxwell distribution as a foundation for deriving closed-form expressions of two essential risk measures: expected shortfall and value at risk. In contrast to classic solvers that predominantly depend on normality assumptions, the framework integrates these Maxwell-based formulations within a GARCH model structure, providing a theoretically grounded and computationally efficient alternative for risk assessment. The proposed methodology is empirically evaluated through forecasting on actual stock market data, demonstrating its practical effectiveness and robustness in capturing tail risk dynamics. This novelty stems from the fact that, unlike the Gaussian distribution, which systematically underestimates tail events due to its thin-tailed nature, the Maxwell distribution naturally accommodates heavier right tails and yields closed-form expressions for both VaR and ES. This provides a new analytical alternative for risk modeling beyond classical Gaussian-based frameworks.","PeriodicalId":7219,"journal":{"name":"Advanced Theory and Simulations","volume":"26 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145127332","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Investigation of the Behaviors of Some Newly Designed Ligands in the Epstein Barr EBNA1/DNA Binding Domain by MD Simulations and Binding Free Energy Calculations 一些新设计的配体在Epstein Barr EBNA1/DNA结合域中的行为的MD模拟和结合自由能计算
IF 3.3 4区 工程技术
Advanced Theory and Simulations Pub Date : 2025-09-23 DOI: 10.1002/adts.202500371
Selami Ercan
{"title":"Investigation of the Behaviors of Some Newly Designed Ligands in the Epstein Barr EBNA1/DNA Binding Domain by MD Simulations and Binding Free Energy Calculations","authors":"Selami Ercan","doi":"10.1002/adts.202500371","DOIUrl":"https://doi.org/10.1002/adts.202500371","url":null,"abstract":"The Epstein-Barr nuclear antigen 1 requires DNA binding to function. Since no Food and Drug Administration-approved drugs exist to combat with Ebstein-Barr virus, the study aims to investigate the binding properties of formerly designed ligands in dynamic environment. Thus, in addition to five ligands, study includes molecular dynamics studies of apo-protein and DNA-protein complex. The RMSD plots of ligand-protein complexes revealed that while systems are reached stable states the extended loops of protein are more flexible in ligand-protein complexes than in DNA-protein complex. Among the ligands, <b>B288</b> showed best binding properties with a binding free energy value of −58.63 kcal mol<sup>−1</sup> which is followed by B183 with the value of −58.24 kcal mol<sup>−1</sup>. It is defined that designed ligands B175, B183, and B288 are more favorable in blocking DNA-protein binding than Z067 and Z108 ligands obtained from ZINC15 database. The study revealed that the binding of DNA to the EBNA1 antigen can be prevented by targeting the studied binding site of protein. Moreover, the molecular dynamics studies demonstrated the extended loop of protein which wraps up DNA closely is distorted by the ligands, which may also hamper binding of DNA to protein.","PeriodicalId":7219,"journal":{"name":"Advanced Theory and Simulations","volume":"12 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145117186","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Fast Atomistic Spin Dynamics (FASD): A Scalable Approach for Time-Dependent Magnetic Phenomena in Nanostructures 快速原子自旋动力学(FASD):纳米结构中随时间变化的磁现象的可扩展方法
IF 3.3 4区 工程技术
Advanced Theory and Simulations Pub Date : 2025-09-23 DOI: 10.1002/adts.202500272
J. Murillo-Polo, J. Mazo-Zuluaga, E. A. Velásquez, J. Mejía-López
{"title":"Fast Atomistic Spin Dynamics (FASD): A Scalable Approach for Time-Dependent Magnetic Phenomena in Nanostructures","authors":"J. Murillo-Polo, J. Mazo-Zuluaga, E. A. Velásquez, J. Mejía-López","doi":"10.1002/adts.202500272","DOIUrl":"https://doi.org/10.1002/adts.202500272","url":null,"abstract":"A methodology to perform Atomistic Spin Dynamics (ASD) calculations on magnetic nanometric structures in highly reduced times compared with standard approaches is proposed. To this aim, a scaling technique (ST) is implemented within the ASD framework by determining the appropriate time scaling factor, an approach referred to as Fast Atomistic Spin Dynamics (FASD). The quality of the FASD scheme is demonstrated by comparisons with micromagnetic simulations of well-known domain wall (DW) motion phenomena. After establishing its reliability, the FASD approach is applied to study DW motion in diameter-modulated ferromagnetic nanowires. The results offer two main advantages: (i) they enable the use of the FASD tool to perform simulation studies of time-dependent magnetic phenomena in systems consisting of many atoms in reduced times, and (ii) they reveal novel behaviors and phenomena related to DW movement in diameter-modulated samples of current technological interest.","PeriodicalId":7219,"journal":{"name":"Advanced Theory and Simulations","volume":"80 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145117182","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
相关产品
×
本文献相关产品
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:604180095
Book学术官方微信