Advanced Theory and Simulations最新文献

{"title":"Machine Learning-Guided Discovery of Natural MDM2 Inhibitors: A Multistage In Silico Pipeline from Screening to ADMET Profiling","authors":"Bishal Budha, Mohamed Mohyeldin, Ali Raza Ayub, Madan Khanal, Arjun Acharya","doi":"10.1002/adts.202501502","DOIUrl":"https://doi.org/10.1002/adts.202501502","url":null,"abstract":"Tumor protein p53 (TP53) and mouse double minute two homolog (MDM2) regulate each other via an autoregulatory feedback loop that is frequently disrupted by MDM2 overexpression or mutation, a hallmark in sarcomas, glioblastomas, and breast carcinomas. In the absence of FDA-approved MDM2 inhibitors, a multi-stage in silico strategy is applied to identify novel candidates from COCONUT, a comprehensive natural product library. Using experimentally validated ChEMBL data, 40 machine-learning models are trained and evaluated; the best RandomForestClassifier selects 116 compounds from approximately 700,000 after sequential PAINS, Brenk, and Lipinski filtering. Docking-based screening prioritizes two leads with binding energies of <span data-altimg=\"/cms/asset/eca4fbde-6496-4321-807f-d4463d600bc3/adts70246-math-0001.png\"></span><mjx-container ctxtmenu_counter=\"9\" ctxtmenu_oldtabindex=\"1\" jax=\"CHTML\" role=\"application\" sre-explorer- style=\"font-size: 103%; position: relative;\" tabindex=\"0\"><mjx-math aria-hidden=\"true\" location=\"graphic/adts70246-math-0001.png\"><mjx-semantics><mjx-mrow data-semantic-annotation=\"clearspeak:simple\" data-semantic-children=\"1\" data-semantic-content=\"0\" data-semantic- data-semantic-role=\"negative\" data-semantic-speech=\"negative 10.0\" data-semantic-type=\"prefixop\"><mjx-mo data-semantic- data-semantic-operator=\"prefixop,−\" data-semantic-parent=\"2\" data-semantic-role=\"subtraction\" data-semantic-type=\"operator\" rspace=\"1\" style=\"margin-left: 0.056em;\"><mjx-c></mjx-c></mjx-mo><mjx-mn data-semantic-annotation=\"clearspeak:simple\" data-semantic-font=\"normal\" data-semantic- data-semantic-parent=\"2\" data-semantic-role=\"float\" data-semantic-type=\"number\"><mjx-c></mjx-c><mjx-c></mjx-c><mjx-c></mjx-c><mjx-c></mjx-c></mjx-mn></mjx-mrow></mjx-semantics></mjx-math><mjx-assistive-mml display=\"inline\" unselectable=\"on\"><math altimg=\"urn:x-wiley:25130390:media:adts70246:adts70246-math-0001\" display=\"inline\" location=\"graphic/adts70246-math-0001.png\" xmlns=\"http://www.w3.org/1998/Math/MathML\"><semantics><mrow data-semantic-=\"\" data-semantic-annotation=\"clearspeak:simple\" data-semantic-children=\"1\" data-semantic-content=\"0\" data-semantic-role=\"negative\" data-semantic-speech=\"negative 10.0\" data-semantic-type=\"prefixop\"><mo data-semantic-=\"\" data-semantic-operator=\"prefixop,−\" data-semantic-parent=\"2\" data-semantic-role=\"subtraction\" data-semantic-type=\"operator\">−</mo><mn data-semantic-=\"\" data-semantic-annotation=\"clearspeak:simple\" data-semantic-font=\"normal\" data-semantic-parent=\"2\" data-semantic-role=\"float\" data-semantic-type=\"number\">10.0</mn></mrow>$-10.0$</annotation></semantics></math></mjx-assistive-mml></mjx-container> <span data-altimg=\"/cms/asset/cd493ee6-fa3c-4b4a-906c-6907f4111a9b/adts70246-math-0002.png\"></span><mjx-container ctxtmenu_counter=\"10\" ctxtmenu_oldtabindex=\"1\" jax=\"CHTML\" role=\"application\" sre-explorer- style=\"font-size: 103%; position: relative;\" tabindex=\"0\"><mjx-math aria-hidden=\"true\" location=\"graphic/adts70246-math","PeriodicalId":7219,"journal":{"name":"Advanced Theory and Simulations","volume":"52 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145651004","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}

{"title":"Complete Conversion and Fast Light From Double Quantum Dot-Metal Nanoparticle System Under the Orbital Angular Momentum Light","authors":"Mohanad Ahmed Abdulmahdi, Amin Habbeb Al-Khursan","doi":"10.1002/adts.202501150","DOIUrl":"https://doi.org/10.1002/adts.202501150","url":null,"abstract":"This work studies four-wave mixing (FWM) in a double quantum dot (DQD)-metal nanoparticle (MNP) system. Two control optical waves and a weak probe are applied. The probe is characterized by its orbital angular momentum (OAM) light optical properties. An analytical form of the probe and the generated FWM signal is obtained using spatial-temporal equations. A high second control field reduces efficiency, thereby increasing the FWM signal. At weak coupling DQD-MNP, the first coupling field increases the efficiency, and a near-complete conversion is attained. Such a result is unprecedented and arises from the DQD's properties, where the manipulation between DQD states is high and the DQD behaves as a whole system. Weak coupling gives high efficiency. Such a result refers to the direct effect of the controlling fields on the FWM conversion. The OAM number increases the probe and FWM fields. A fast light is obtained, and the group-velocity peak is shifted under a strong control field. While both complete conversion and fast light are observed at the earliest, other results are within the range reported in the literature. The results obtained are essential for many critical applications.","PeriodicalId":7219,"journal":{"name":"Advanced Theory and Simulations","volume":"12 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145613950","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}

{"title":"Performance Engineering of Cs2AuScI6 Double Halide Perovskite Solar Cell: A DFT and SCAPS-1D Approach to 31.82% Efficiency","authors":"Shuaib Mahmud, Md. Mainol Islam, Md. Mukter Hossain, Md. Mohi Uddin, Md. Ashraf Ali","doi":"10.1002/adts.202501693","DOIUrl":"https://doi.org/10.1002/adts.202501693","url":null,"abstract":"In response to pressing environmental priorities, the development of nontoxic and stable alternatives to lead-based Perovskite solar cells is critical. This study focuses on Cs₂AuScI₆, a lead-free Perovskite, as a promising photovoltaic material. Through density functional theory (DFT) calculations using Wien2k, a bandgap of 1.30 eV is revealed, with Au-<i>d</i> and Sc-<i>d</i> orbitals playing key roles in electronic properties and Au atoms dominating charge distribution. The material exhibits visible absorption peaks of the 10⁵ order, indicating its potential for solar applications. Conducted by DFT, 36 configurations combining various electron transport layers and hole transport layers (HTLs) are investigated. Copper Barium Tin Sulfide (CBTS) is identified as the optimal HTL due to its alignment with the absorber material. Five standout device architectures of ITO/WS₂/Cs₂AuScI₆/CBTS/Ni, ITO/ZnO/Cs₂AuScI₆/CBTS/Ni, ITO/TiO₂/Cs₂AuScI₆/CBTS/Ni, ITO/PCBM/Cs₂AuScI₆/CBTS/Ni, and ITO/IGZO/Cs₂AuScI₆/CBTS/Ni (Where ITO means Indium Tin Oxide) achieved exceptional power conversion efficiencies of 31.48%, 31.46%, 29.44%, 28.75%, and 31.82%, respectively, surpassing the 18.61% efficiency of the ITO/C₆₀/Cs₂AuScI₆/CBTS/Ni structure. The study further examines practical performance factors, including resistances, temperature effects, current–voltage (<i>J</i>–<i>V</i>) characteristics, and quantum efficiency, thereby enhancing its real-world applicability. These findings highlight the potential of Cs₂AuScI₆ as a nontoxic, inorganic alternative for perovskite solar technology, contributing to the sustainable development of photovoltaics.","PeriodicalId":7219,"journal":{"name":"Advanced Theory and Simulations","volume":"144 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145613952","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}

{"title":"Deep Learning Approach for Predicting Efficiency in Organic Photovoltaics from 2D Molecular Images of D/A Pairs","authors":"Khoukha Khoussa, Patrick Lévêque, Larbi Boubchir","doi":"10.1002/adts.202500822","DOIUrl":"https://doi.org/10.1002/adts.202500822","url":null,"abstract":"Organic Photovoltaic (OPV) Devices Have Emerged as a Promising Alternative to Conventional Solar Cells due to Their Flexibility, Lightweight Nature, and Potential for Low-cost Production. However, Optimizing OPV Performance Remains a Complex Challenge, Traditionally Requiring Extensive Experimental Trials or Computational Chemistry Approaches Based on Molecular Descriptors. To Accelerate the Development of High-efficiency OPVs, Artificial Intelligence (AI) Has Been Increasingly Utilized, Particularly Machine Learning Models That Rely on Chemical Descriptors. While these Methods Have Shown Success, They Are Often Limited by the Quality and Completeness of the Selected Descriptors, Potentially Overlooking Key Structural and Morphological Information. In this Work, We Propose a Novel Deep Learning Framework Leveraging Convolutional Neural Networks (CNNs) to Predict OPV Performance Directly from 2D Images of Donor and Acceptor Materials. By Employing a Customized Representation of Molecular Structures, Our Approach Captures Spatial and Hierarchical Patterns That Traditional Descriptors Based ML Models May Miss. We Compare Our Model's Predictive Capability to Conventional Machine Learning Techniques and Demonstrate Its Potential for Improving Prediction Accuracy and Generalization without Need to Add the Frontier Molecular Orbitals (FMOs) to Enhance Predictions. Our Findings Highlight the Power of Deep Learning in Accelerating the Discovery of Efficient Organic Photovoltaic Materials, Paving the Way for a Data-driven Approach to Materials Science and Device Optimization.","PeriodicalId":7219,"journal":{"name":"Advanced Theory and Simulations","volume":"203 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145613953","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}

{"title":"A Comparative Performance Analysis of Activation Functions for Cardiovascular Disease Detection Using ECG Images","authors":"Mrityunjay Chaubey, Abhay Kumar Pathak, Marisha, Manjari Gupta","doi":"10.1002/adts.202501567","DOIUrl":"https://doi.org/10.1002/adts.202501567","url":null,"abstract":"In recent years, artificial intelligence (AI) has become an automated tool for detecting cardiovascular diseases using ECG images. Activation functions are the core of neural network models, ranging from shallow to deep convolutional neural networks (CNN). In ECG image-based cardiovascular disease detection, activation functions enable the network to capture non-linear patterns like irregular heartbeats and subtle anomalies. The proposed CNN architecture in this paper comprised convolutional layers for feature extraction, followed by custom activation functions to introduce non-linearity and enhanced learning. These features are downsampled using max pooling and aggregated through global average pooling. Fully connected layers, with a suitable dropout regularization, map the features to the final classification output, which is probabilistically determined using a softmax activation function. This paper used a public dataset of ECG images of cardiac patients to analyze the significance of activation functions in predicting the four main cardiac abnormalities: irregular heartbeat, myocardial infarction, history of myocardial infarction, and normal person classes. We have analyzed 19 different activation functions for their detection performance on the same dataset. The detection performance is compared with the existing state-of-the-art studies. A set of activation functions is suggested for robust and accurate detection of cardiovascular disease using ECG images.","PeriodicalId":7219,"journal":{"name":"Advanced Theory and Simulations","volume":"115 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145613951","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}

{"title":"Multi‐Objective Optimization of a Novel Auxetic Tubular Re‐Entrant Structure (ATRS) Using 3D Printing and Statistical Design","authors":"Kang Du, Xiaopeng Huang, Xin Yao, Guansheng Qiu, Song Zhao, Zhi Huang","doi":"10.1002/adts.202501893","DOIUrl":"https://doi.org/10.1002/adts.202501893","url":null,"abstract":"This study presents, a comprehensive investigation into the failure behavior and parametric optimization of novel 3D‐printed Auxetic Tubular Re‐entrant Structures (ATRS), using an integrated experimental–numerical framework. Compression tests are performed on four ATRS designs featuring different unit cell angles, thicknesses, and widths to confirm simulation accuracy and evaluate mechanical performance. Excellent agreement is observed between experimental and simulation results, capturing both the initial linear response and the nonlinear buckling behavior. The simulations revealed exceptional auxetic responses and showed how geometric parameters govern stress localization and failure initiation. Reduced unit cell widths led to earlier buckling owing to a smaller load‐bearing area and increased soft mode activation, whereas larger angles raised buckling forces but triggered instability sooner. Also, energy absorption capacity rose significantly with increases in unit cell width, angle, and thickness, reaching as much as four times higher in thicker samples. According to Response Surface Methodology (RSM) and Analysis of Variance (ANOVA), thickness and width are the primary parameters influencing buckling force, stiffness, and energy absorption, with thickness having the greatest impact. These findings facilitate accurate predictive modeling of ATRS mechanical behavior driven by geometric design and offer new pathways for designing damage‐tolerant structures with tunable mechanical responses.","PeriodicalId":7219,"journal":{"name":"Advanced Theory and Simulations","volume":"172 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145610860","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}

{"title":"Electronic Structure and Topology‐Based Insights into Andrographolides as Potential CDK2 Inhibitors: Comprehensive DFT and Molecular Dynamics Investigation","authors":"Jibin K. Varughese, Jisna Jose, Abdullah F. AlAsmari, Mohammad Rashid Khan, Shamama Nishat, Nemat Ali, Thomas V. Mathew","doi":"10.1002/adts.202501807","DOIUrl":"https://doi.org/10.1002/adts.202501807","url":null,"abstract":"Andrographolide is a bicyclic diterpenoid lactone that has garnered considerable interest for its potential therapeutic applications, particularly in anticancer effects. Cyclin‐dependent kinases (CDKs), especially CDK2 and its regulatory subunits, are dysregulated in many human cancers, and emerging evidence suggests that CDK2 inhibition induces antitumor activity. This study provides a comprehensive analysis of the electronic structure and topology of three distinct andrographolide derivatives (AG‐OH, AG‐NO <jats:sub>2</jats:sub> , and AG‐Cl) to assess their efficacy as inhibitors of CDK2. Density functional theory (DFT) calculations are utilized to examine frontier molecular orbitals (FMOs), electrostatic potential (ESP) surfaces, and natural bond orbital (NBO) interactions, yielding detailed insights into their reactivity, electronic distributions, and intramolecular charge transfer properties. The reduced density gradient (RDG) and non‐covalent interaction analyses elucidated critical stabilization regions and interaction intensities among the derivatives. ADMET calculations demonstrated that all derivatives adhered to Lipinski's rule of five and exhibited advantageous pharmacokinetic characteristics, including moderate lipophilicity (Consensus LogP 2.58–4.06) and acceptable polarity (TPSA 86.99–132.81 Å <jats:sup>2</jats:sup> ), indicating their potential as CDK2 inhibitors. Molecular docking studies demonstrated robust binding affinities in the range −9.2–−10.2 kcal/mol, later validated by molecular dynamics (MD) simulations, where the RMSD remained stable approximately at 0.2 nm. Calculations of binding free energy using MM‐GBSA confirmed the strong and stable nature of the complex, with binding energy values ranging from −26.54 to −39.70 kcal/mol, exhibiting significantly favorable energetics. Our thorough computational analysis identifies andrographolides as potential CDK2 inhibitors, providing valuable insights for future experimental validation and potential development as anticancer agents.","PeriodicalId":7219,"journal":{"name":"Advanced Theory and Simulations","volume":"5 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145610862","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}

{"title":"Thermal Conductivity Modulation in Carbon Nanotubes via Silicon Nanowire Encapsulation Investigated Using Neuroevolution Potential","authors":"Wei Zhang, Tinghong Gao, Yutao Liu, Guofa Shen, Bei Wang, Zhongzhong Zhu, Jin Huang, Shipeng Zhang, Shuang Li","doi":"10.1002/adts.202501834","DOIUrl":"https://doi.org/10.1002/adts.202501834","url":null,"abstract":"One‐dimensional van der Waals heterostructures based on single‐walled carbon nanotubes (SWCNT) have recently attracted increasing attention because of their structural flexibility and tunable thermal transport properties. Therefore, this study proposes a silicon nanowire (SiNW) encapsulation approach to construct a SiNW@CNT composite and systematically investigate its thermal transport behavior. Using an efficient neuroevolution potential model, we developed a high‐precision machine learning potential tailored for the SiNW@CNT structure. Using homogeneous non‐equilibrium molecular dynamics, equilibrium molecular dynamics, and heterogeneous nonequilibrium molecular dynamics simulations combined with spectral heat flux analysis, we found that SiNW encapsulation markedly reduces the thermal conductivity of SWCNT. The reduction in thermal conductivity becomes more pronounced as the SiNW filling ratio increases. At the maximum filling ratio, SiNW@CNT exhibits a thermal conductivity approximately 50% that of hollow SWCNTs. This reduction is attributed to SiNW encapsulation, which enhances phonon scattering within the SWCNT, shortens the phonon mean free path and lifetimes, and decreases overall thermal transport efficiency. In addition, as the system size increases, the thermal conductivity difference between SWCNT and SiNW@CNT widens, highlighting a clear size dependence and a transition from ballistic to diffusive transport. These findings provide a crucial theoretical basis for designing novel nanocomposites with tunable thermal conductivity.","PeriodicalId":7219,"journal":{"name":"Advanced Theory and Simulations","volume":"104 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145610858","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}

{"title":"Unveiling the Photovoltaic Potential of Rhombohedral RbGeX 3 (X = Cl, Br, I) Perovskites Via Combined DFT and SCAPS‐1D Study","authors":"Piyush Kumar Dash, Palash Banerjee, Anupriya Nyayban, Subhasis Panda","doi":"10.1002/adts.202501477","DOIUrl":"https://doi.org/10.1002/adts.202501477","url":null,"abstract":"In pursuit of efficient, non‐toxic all‐inorganic perovskite solar cells (PSCs), we have investigated the rhombohedral phase of the rubidium germanium halide perovskites (X = Cl, Br, I) using density functional theory (DFT). The band structures and partial density of states are computed using PBE and TB‐mBJ functionals, both with and without spin‐orbit coupling (SOC), to accurately estimate the bandgaps. Optical properties, including the dielectric function, absorption coefficient, and refractive index, are evaluated within the PBE framework. Among the halides, is identified as the most promising absorber material, exhibiting the narrowest bandgap (0.96 eV with TB‐mBJ + SOC) and superior optical absorption characteristics. SCAPS‐1D simulations are carried out using DFT‐derived input parameters including bandgap, effective density of states, and carrier mobilities. Device performance is optimized by exploring various inorganic hole and electron transport layers (HTL/ETL). The influence of the absorber layer (AL) thickness, doping levels, defect densities at AL, ETL/AL, and AL/HTL interfaces, back contact materials, as well as series and shunt resistance is examined. The optimized all‐inorganic, non‐toxic device structure FTO///CuI/Au achieves a power conversion efficiency (PCE) of 25.76% with a fill factor (FF) of 79.81%.","PeriodicalId":7219,"journal":{"name":"Advanced Theory and Simulations","volume":"7 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145610859","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}