Advanced Theory and Simulations最新文献

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A Topology‐Based Site‐to‐Site Jump Detection Method to Unlock Correlated Transport Mechanism in Superionic Conductors 一种基于拓扑的点对点跳跃检测方法解锁超离子导体的相关传输机制
IF 3.3 4区 工程技术
Advanced Theory and Simulations Pub Date : 2025-07-07 DOI: 10.1002/adts.202500703
Bing He, Shaoying Hu, Zheyi Zou, Bowei Pu, Zhicong Lai, Shen Li, Zhikang Xie, Yingqi Cao, Siqi Shi
{"title":"A Topology‐Based Site‐to‐Site Jump Detection Method to Unlock Correlated Transport Mechanism in Superionic Conductors","authors":"Bing He, Shaoying Hu, Zheyi Zou, Bowei Pu, Zhicong Lai, Shen Li, Zhikang Xie, Yingqi Cao, Siqi Shi","doi":"10.1002/adts.202500703","DOIUrl":"https://doi.org/10.1002/adts.202500703","url":null,"abstract":"Atomic trajectories from molecular dynamics (MD) simulations are used to study multi‐ion correlated transport mechanism in superionic conductors (SICs). However, it remains challenging to assess the extent of correlated migration in these materials. Here, a topology‐based method is developed to detect site‐to‐site jumps of mobile ions and analyze correlations between jumps. The host lattice of SICs is partitioned into non‐overlapping polyhedra, with mobile ions assigned to these polyhedral site regions. Such a process discretizes the MD trajectories, enabling the extraction of the sequences and timings of jumps. Through appropriate spatial and temporal criteria, correlated jumps can be identified accurately in a straightforward way. Following this, two representative SICs, and , are assembled to demonstrate its potential utility and applications. Both materials exhibit correlated transport mechanism, with the former primarily featuring two‐ion jumps and the latter involving jumps of more than two ions. This method, extendable to other SICs with rigid frameworks, can assist in designing new descriptors for ionic conductivity and accelerate the discovery of SICs.","PeriodicalId":7219,"journal":{"name":"Advanced Theory and Simulations","volume":"47 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144577873","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
C3 Substituted Naphthalimide Derivatives as Promising TADF Emitters: Effect of Donor Strength Revealed by Computational Studies (Adv. Theory Simul. 7/2025) C3取代萘酰亚胺衍生物作为有前途的TADF发射体:计算研究揭示的施主强度的影响(ad . Theory Simul. 7/2025)
IF 2.9 4区 工程技术
Advanced Theory and Simulations Pub Date : 2025-07-07 DOI: 10.1002/adts.202570013
Chetan Saini, K. R. Justin Thomas
{"title":"C3 Substituted Naphthalimide Derivatives as Promising TADF Emitters: Effect of Donor Strength Revealed by Computational Studies (Adv. Theory Simul. 7/2025)","authors":"Chetan Saini,&nbsp;K. R. Justin Thomas","doi":"10.1002/adts.202570013","DOIUrl":"https://doi.org/10.1002/adts.202570013","url":null,"abstract":"<p>In article 2401571, Chetan Saini and K. R. Justin Thomas demonstrate the use of Density Functional Theory (DFT) in screening high-performance Thermally Activated Delayed Fluorescence (TADF) molecules. The background features a cluster of candidate molecules undergoing computational evaluation. A magnifier highlights the most efficient molecule identified through DFT analysis.\u0000\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":7219,"journal":{"name":"Advanced Theory and Simulations","volume":"8 7","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/adts.202570013","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144573794","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
DFT‐Guided Design of Hydroxytyrosol‐Encapsulated Nanocages: Comparative Insights into Boron Nitride Versus Carbon Fullerenes for Targeted Drug Delivery and Therapeutic Applications DFT引导下羟基酪醇包封纳米笼的设计:氮化硼与碳富勒烯在靶向药物传递和治疗应用中的比较见解
IF 3.3 4区 工程技术
Advanced Theory and Simulations Pub Date : 2025-07-05 DOI: 10.1002/adts.202500582
A. Khosravi, Mohammad T. Baei, S. Zahra Sayyed‐Alangi, E. Tazikeh Lemeski
{"title":"DFT‐Guided Design of Hydroxytyrosol‐Encapsulated Nanocages: Comparative Insights into Boron Nitride Versus Carbon Fullerenes for Targeted Drug Delivery and Therapeutic Applications","authors":"A. Khosravi, Mohammad T. Baei, S. Zahra Sayyed‐Alangi, E. Tazikeh Lemeski","doi":"10.1002/adts.202500582","DOIUrl":"https://doi.org/10.1002/adts.202500582","url":null,"abstract":"Hydroxytyrosol (HT), a bioactive compound in olive oil, has therapeutic potential but is limited by low bioavailability and instability. This study explores fullerene‐like nanocages (B₁₂N₁₂, B₁₆N₁₆, C₂₄, C₃₂) as nanocarriers to enhance HT delivery. Using DFT, QTAIM, and molecular docking, interactions between HT and nanocages are analyzed. Boron nitride nanocages, particularly B₁₂N₁₂, show the strongest binding (Eads = −25.28 kcal mol<jats:sup>−1</jats:sup> in water) via Lewis acid‐base interactions, improving stability (ΔG = −11.90 kcal mol<jats:sup>−1</jats:sup>) and solubility. Carbon cages (C₂₄, C₃₂) exhibit weaker van der Waals interactions (Eads = −7.42 to −10.24 kcal mol<jats:sup>−1</jats:sup>), favoring controlled release. Electronic analyses reveal altered HT reactivity upon complexation. QTAIM confirms partially covalent B─O bonds in (BN)<jats:sub>n = 12, 16</jats:sub>‐HT systems, while carbon cages rely on dispersive forces. UV–vis spectra show redshifted peaks for BN‐HT complexes, indicating enhanced delocalization. Molecular docking demonstrates improved therapeutic effects of HT‐nanocage complexes. For instance, C₂₄‐HT strongly bound to COVID‐19 protease (E<jats:sub>Dc</jats:sub> = −3.86 kcal mol<jats:sup>−1</jats:sup>) and HER2 kinase (E<jats:sub>Dc</jats:sub> = −3.99 kcal mol<jats:sup>−1</jats:sup>), enhancing antiviral and anticancer activity. Similarly, B₁₆N₁₆‐HT effectively targets TNF‐α (E<jats:sub>Dc</jats:sub> = −3.70 kcal mol<jats:sup>−1</jats:sup>), showing superior anti‐inflammatory effects. These findings highlight nanocarriers' potential to overcome HT's limitations, enabling advanced biomedical applications.","PeriodicalId":7219,"journal":{"name":"Advanced Theory and Simulations","volume":"48 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144566100","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
Generalized Distribution Function of Relaxation Times with the Davidson‐Cole Model as a Kernel 以Davidson‐Cole模型为核的松弛时间广义分布函数
IF 3.3 4区 工程技术
Advanced Theory and Simulations Pub Date : 2025-07-05 DOI: 10.1002/adts.202500792
Anis Allagui, Ahmed Elwakil
{"title":"Generalized Distribution Function of Relaxation Times with the Davidson‐Cole Model as a Kernel","authors":"Anis Allagui, Ahmed Elwakil","doi":"10.1002/adts.202500792","DOIUrl":"https://doi.org/10.1002/adts.202500792","url":null,"abstract":"Many physical phenomena, such as the polarization of dielectrics and viscoelastic materials, or porous electrode/electrolyte interfaces cannot be modeled by a single relaxation time of the Debye type. To account for this fact, data analysis based on distribution functions of the Debye relaxation times (DFRT) is conventionally used. In this study, a generalized DFRT is proposed considering the Davidson‐Cole model as an elementary process instead of the standard Debye model. The distribution function can then be retrieved from the inverse of the generalized Stieltjes transform, expressed in terms of iterated Laplace transforms, applied on a given frequency function. Computable analytical expressions of the generalized DFRT are derived for some of the most known impedance (or admittance) models including the constant phase element, the Davidson‐Cole, Havriliak–Negami and the Kohlrausch–Williams–Watts models. The obtained distributions will be valuable to interpret and compare with inverted frequency‐domain data using numerical methods, in addition to the usual way of equivalent circuit modeling. The proposed theory and results can be easily translated to other physical systems that are known to exhibit local frequency dispersion features.","PeriodicalId":7219,"journal":{"name":"Advanced Theory and Simulations","volume":"8 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144566099","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
Numerical Investigation of Eco‐Friendly All‐Zinc Based Thin Film Solar Cells For Sustainable Photovoltaics 生态友好型全锌基薄膜太阳能电池的数值研究
IF 3.3 4区 工程技术
Advanced Theory and Simulations Pub Date : 2025-07-05 DOI: 10.1002/adts.202500157
K. Jenifer, Balaji Gururajan, Wei‐Sheng Liu, S. Parthiban
{"title":"Numerical Investigation of Eco‐Friendly All‐Zinc Based Thin Film Solar Cells For Sustainable Photovoltaics","authors":"K. Jenifer, Balaji Gururajan, Wei‐Sheng Liu, S. Parthiban","doi":"10.1002/adts.202500157","DOIUrl":"https://doi.org/10.1002/adts.202500157","url":null,"abstract":"In this numerical study, the performance of thin‐film solar cells comprising entirely Zn‐based layers is evaluated using SCAPS‐1D. ZnSnN₂ is chosen as the absorber layer due to its abundance on earth, and it has good optoelectrical properties suitable for photovoltaic (PV) applications. Its narrow bandgap and high absorption coefficient further enhance its suitability for such devices. The buffer layers explored in this study include ZnN, ZnON, ZnS, and ZnOS, all containing zinc. Likewise, the window layers examined are AZO, GZO, and ZTO. Nickel and Aluminium are used as the front and back contacts. A comprehensive analysis of each layer's properties and potential defects is conducted to improve the solar cell efficiency. The optimized device structure is determined to be Ni/ZnSnN₂/ZnON/ZTO/Al, achieving an efficiency of ≈19% with a short‐circuit current density (Jsc) of 20.05 mA cm<jats:sup>−</jats:sup><jats:sup>2</jats:sup> and an open‐circuit voltage (Voc) of 1.1 V. These findings present a novel, eco‐friendly, scalable, and efficient thin film solar cell design unlike its predecessor fabricated with toxic and rare earth materials.","PeriodicalId":7219,"journal":{"name":"Advanced Theory and Simulations","volume":"89 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144566574","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
Mechanistic Study of β‐Glucogallin Extracted from Amla: DFT, Docking, and Molecular Dynamics Simulations Amla β - Glucogallin提取机理研究:DFT、对接和分子动力学模拟
IF 3.3 4区 工程技术
Advanced Theory and Simulations Pub Date : 2025-07-01 DOI: 10.1002/adts.202500422
Anaswara Uppumthara, Rohith Ramasamy, Alen Binu Abraham, Deepa kallumpurath, Rajadurai Vijay Solomon
{"title":"Mechanistic Study of β‐Glucogallin Extracted from Amla: DFT, Docking, and Molecular Dynamics Simulations","authors":"Anaswara Uppumthara, Rohith Ramasamy, Alen Binu Abraham, Deepa kallumpurath, Rajadurai Vijay Solomon","doi":"10.1002/adts.202500422","DOIUrl":"https://doi.org/10.1002/adts.202500422","url":null,"abstract":"Reactive oxygen species (ROS) have garnered significant interest due to their role in cellular signaling and potential to induce cell death. The search for effective antioxidants from natural sources continues, with recent focus on β‐glucogallin (BGG) from <jats:italic>Emblica officinalis</jats:italic> (amla). Despite BGG's seven OH groups, the specific group responsible for its antioxidant properties remains unclear. Comprehensive density functional theory (DFT) calculations are conducted, revealing the predominant involvement of the hydrogen atom transfer (HAT) mechanism. Specifically, the sixth OH group exhibits high HOO<jats:sup>•</jats:sup> radical scavenging activity, supported by its low bond dissociation value of 87.92 kcal mol<jats:sup>−1</jats:sup>. Molecular docking and dynamics simulations with monoamine oxidase (MAO) and xanthine oxidase (XO) shed light on BGG's binding modes and stability within proteins. These findings provide crucial insights into BGG's antioxidant action, aiding the development of antioxidant therapies in medicinal chemistry.","PeriodicalId":7219,"journal":{"name":"Advanced Theory and Simulations","volume":"41 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144520458","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
Continuum Percolation in Anisotropic Rectangles: The Role of Excluded Area and Average Connectivity at the Threshold 各向异性矩形的连续渗流:排除面积和阈值处平均连通性的作用
IF 3.3 4区 工程技术
Advanced Theory and Simulations Pub Date : 2025-06-27 DOI: 10.1002/adts.202500580
Danvendra Singh, Daivik Agrawal, Avik P. Chatterjee, Christian Kudisonga, Michael T. Heitzmann, Amit Rawal
{"title":"Continuum Percolation in Anisotropic Rectangles: The Role of Excluded Area and Average Connectivity at the Threshold","authors":"Danvendra Singh, Daivik Agrawal, Avik P. Chatterjee, Christian Kudisonga, Michael T. Heitzmann, Amit Rawal","doi":"10.1002/adts.202500580","DOIUrl":"https://doi.org/10.1002/adts.202500580","url":null,"abstract":"Percolation is a geometric phase transition in which formerly local clusters spontaneously form a system‐spanning cluster, also referred to as a percolating cluster, facilitating efficient charge transport in conductive materials. Here, a combinatorial approach is developed that integrates a theoretical framework with Monte Carlo simulations to investigate the percolation behavior of penetrable rectangles by systematically exploring the effects of aspect ratio and anisotropic orientation distributions. A theoretical model incorporating a modified expression for the average excluded area is proposed, with both the model and simulations providing rigorous validation and correcting the errors in the original work. With the aid of predictive modeling and simulations, the critical area fraction and bond number have been computed by considering the aspect ratio of rectangles with a specified degree of anisotropy. These results demonstrate that the bond number in isotropic networks remains within 3.6–4.5 across a wide aspect ratio range (1–1000), in strong agreement with established benchmarks reporting convergence to 3.6 for aspect ratios above 20. Using the predicted critical area fractions, the electrical conductivity trends of two‐dimensional (2D) conductive networks are modeled by fitting power‐law curves to the reported simulation and experimental results.","PeriodicalId":7219,"journal":{"name":"Advanced Theory and Simulations","volume":"26 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144503454","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
Making Physics‐Informed Neural Networks Theory‐Compliant: The Case of Fischer‐Tropsch Catalyst Modeling 使物理-知情神经网络理论-兼容:Fischer - Tropsch催化剂建模的情况
IF 3.3 4区 工程技术
Advanced Theory and Simulations Pub Date : 2025-06-27 DOI: 10.1002/adts.202500177
Tymofii Nikolaienko, Harshil Patel, Aniruddha Panda, Subodh Madhav Joshi, Stanislav Jaso, Kaushic Kalyanaraman
{"title":"Making Physics‐Informed Neural Networks Theory‐Compliant: The Case of Fischer‐Tropsch Catalyst Modeling","authors":"Tymofii Nikolaienko, Harshil Patel, Aniruddha Panda, Subodh Madhav Joshi, Stanislav Jaso, Kaushic Kalyanaraman","doi":"10.1002/adts.202500177","DOIUrl":"https://doi.org/10.1002/adts.202500177","url":null,"abstract":"Physics‐Informed Neural Networks (PINNs) accelerate equation solving by merging physics‐based theories with machine learning. Yet, their application in multi‐staged computational workflows unveils reliability issues. This is demonstrated for Fischer‐Tropsch synthesis modeling, by leveraging PINNs for source terms evaluation in the finite‐difference method solving the coupled reaction‐diffusion equations. Subtle inaccuracies of PINNs approximating the functions in close vicinity of their input variables' ranges boundaries, while not captured by traditional neural network assessment methods, are shown to induce unphysical ultimate solutions and convergence failures. A problem‐specific PINN architecture is proposed that has a correct asymptotic behavior and resolves the revealed issues. Combined with a tailored initial guess generation scheme, the proposed modifications are shown to recover the overall stability of the simulations while preserving the speed‐up brought by PINNs as the workflow component. The possible applications of the proposed hybrid solver are discussed in the context of chemical reactor simulations.","PeriodicalId":7219,"journal":{"name":"Advanced Theory and Simulations","volume":"17 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144500768","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 Stability, Physical Properties, and Molecular Dynamics in KSrZH6 (Z = Rh, Ir) for Hydrogen Storage Applications 储氢材料KSrZH6 (Z = Rh, Ir)的稳定性、物理性质和分子动力学第一性原理研究
IF 3.3 4区 工程技术
Advanced Theory and Simulations Pub Date : 2025-06-25 DOI: 10.1002/adts.202500622
Aya Chelh, Boutaina akenoun, Smahane Dahbi, Hamid Ez‐Zahraouy, E. A. Elghmaz, N.S. Abd EL‐Gawaad, Mohammed S. Abu‐Jafar, Asif Hosen
{"title":"First‐Principles Study of the Stability, Physical Properties, and Molecular Dynamics in KSrZH6 (Z = Rh, Ir) for Hydrogen Storage Applications","authors":"Aya Chelh, Boutaina akenoun, Smahane Dahbi, Hamid Ez‐Zahraouy, E. A. Elghmaz, N.S. Abd EL‐Gawaad, Mohammed S. Abu‐Jafar, Asif Hosen","doi":"10.1002/adts.202500622","DOIUrl":"https://doi.org/10.1002/adts.202500622","url":null,"abstract":"This study examines the structural, electronic, optical, elastic, thermodynamic, and hydrogen storage properties of KSrZH<jats:sub>6</jats:sub> (Z = Rh, Ir) utilizing density functional theory to explore their potential as hydrogen storage materials. The structural analysis confirms that all the studied materials crystallize in the cubic phase with space group 216 (). The phonon dispersion and ab initio molecular dynamics (AIMD) computations reveal dynamic and thermal stability for both compounds. In addition, the electronic structures exhibit indirect semiconducting properties, with an extensive hybridization near the Fermi level between 1s‐orbitals of hydrogen (H), and d‐orbitals of the transition metals (Rh and Ir). Furthermore, optical investigations reveal significant UV absorption, as well as a moderate refractive index and reflectivity, which can be useful in optoelectronic devices. All of the studied materials possess mechanical stability and show brittle properties. Among the compounds, KSrRhH<jats:sub>6</jats:sub> exhibits the highest gravimetric hydrogen storage capacity of 2.57 wt.%, while KSrIrH<jats:sub>6</jats:sub> shows a slightly lower value of 1.86 wt.%. The storage capacity decreases when the cationic atom Rh is substituted with Ir, attributed to variations in atomic radius. This comprehensive study underscores the promising potential of KSrZH<jats:sub>6</jats:sub> (Z = Rh, Ir) for both hydrogen storage and optoelectronic applications.","PeriodicalId":7219,"journal":{"name":"Advanced Theory and Simulations","volume":"17 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144478957","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
Packing and Ejection Dynamics of Polymers: Role of Confinement, Polymer Stiffness, and Activity 聚合物的堆积和抛射动力学:约束、聚合物刚度和活性的作用
IF 3.3 4区 工程技术
Advanced Theory and Simulations Pub Date : 2025-06-24 DOI: 10.1002/adts.202500420
Gokul Upadhyay, Rajeev Kapri, Anil Kumar Dasanna, Abhishek Chaudhuri
{"title":"Packing and Ejection Dynamics of Polymers: Role of Confinement, Polymer Stiffness, and Activity","authors":"Gokul Upadhyay, Rajeev Kapri, Anil Kumar Dasanna, Abhishek Chaudhuri","doi":"10.1002/adts.202500420","DOIUrl":"https://doi.org/10.1002/adts.202500420","url":null,"abstract":"The translocation of biopolymers, such as DNA and proteins, across cellular or nuclear membranes is essential for numerous biological processes. The translocation dynamics are influenced by the properties of the polymers, such as polymer stiffness, and the geometry of the capsid. This study aims to investigate the impact of polymer stiffness, activity, and different capsid geometries on the packing and ejection dynamics of both passive and active polymers. Langevin dynamics simulations are employed for a systematic investigation. It is observed that flexible polymers exhibit packing times that are faster than those of their semi‐flexible counterparts. Interestingly, for large polymers compared to the capsid size, sphere facilitates faster packing, and unpacking compared to ellipsoid, mimicking the cell nucleus and suggesting a geometrical advantage for biopolymer translocation. In summary, it is observed that increasing activity accelerates both the packing and ejection processes for both flexible and semi‐flexible polymers. However, the effect is significantly more pronounced for semi‐flexible polymers, highlighting the crucial role of polymer flexibility in these dynamics. These findings deepen the understanding of the intricate interplay between polymer flexibility, capsid geometry, and activity, providing valuable insight into the dynamics of polymer packing and ejection processes.","PeriodicalId":7219,"journal":{"name":"Advanced Theory and Simulations","volume":"20 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144478959","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
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