Frontiers in Physics最新文献

{"title":"Free energy calculations in biomolecule-nanomaterial interactions","authors":"Hongze Fu, Yinbang Zhu, Qu Chen","doi":"10.3389/fphy.2024.1469515","DOIUrl":"https://doi.org/10.3389/fphy.2024.1469515","url":null,"abstract":"In computational chemistry and molecular modeling, the interactions between biomolecules (BMs) and nanomaterials (NMs) play a crucial role in various physical and biological processes, and have significant implications in material discovery and development. While there is extensive literature on free energy calculations for drug-target interactions, reviews specifically addressing BM-NM interactions are relatively scarce. This manuscript aims to fill in this gap by presenting a comprehensive overview of the most widely used and well-established methods for free energy calculations. It provides a detailed analysis of the advantages and limitations of these methods and discusses their applicability to BM-NM systems. This work is intended to offer insights into free energy calculations and serve as a guide for future research in this field.","PeriodicalId":12507,"journal":{"name":"Frontiers in Physics","volume":"211 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142255607","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A kinetic study of fusion burn waves in compressed deuterium–tritium and proton–boron plasmas","authors":"Michael J. Lavell, Ayden J. Kish, Andrew T. Sexton, Eugene S. Evans, Ibrahim Mohammad, Sara Gomez-Ramirez, William Scullin, Marcus Borscz, Sergey Pikuz, Thomas A. Mehlhorn, Max Tabak, Greg Ainsworth, Adam B. Sefkow","doi":"10.3389/fphy.2024.1440037","DOIUrl":"https://doi.org/10.3389/fphy.2024.1440037","url":null,"abstract":"We present particle-in-cell simulations with Monte Carlo collisions of fusion burn waves in compressed deuterium–tritium and proton–boron plasmas. We study the energy balance in the one-dimensional expansion of a hot-spot by simulating Coulomb collisions, fusion reactions, and bremsstrahlung emission with a Monte Carlo model and inverse bremsstrahlung absorption using a new PIC model. This allows us to self-consistently capture the alpha particle heating and radiative losses in the expanding hot-spot and surrounding cold fuel. After verifying our model in a code-to-code comparison with both kinetic and fluid codes for the case of a deuterium–tritium hot-spot, we simulate the expansion of a proton–boron hot-spot initialized at 200 keV and 1,000 g/<jats:inline-formula><mml:math xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"><mml:msup><mml:mrow><mml:mtext>cm</mml:mtext></mml:mrow><mml:mrow><mml:mn>3</mml:mn></mml:mrow></mml:msup></mml:math></jats:inline-formula>. Our model predicts that energy radiated by the hot-spot is recaptured by the surrounding high-density opaque fuel reducing the expansion work done by the propagating burn wave. As a result, we find the net fusion energy produced over the course of $20$∼ps is twice the initial hot-spot energy independent of whether radiation physics is included.","PeriodicalId":12507,"journal":{"name":"Frontiers in Physics","volume":"10 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142269019","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"State estimation for Markovian jump Hopfield neural networks with mixed time delays","authors":"Lili Guo, Wanhui Huang","doi":"10.3389/fphy.2024.1447788","DOIUrl":"https://doi.org/10.3389/fphy.2024.1447788","url":null,"abstract":"Markovian jump Hopfield NNs (MJHNNs) have received considerable attention due to their potential for application in various areas. This paper deals with the issue of state estimation concerning a category of MJHNNs with discrete and distributed delays. Both time-invariant and time-variant discrete delay cases are taken into account. The objective is to design full-order state estimators such that the filtering error systems exhibit exponential stability in the mean-square sense. Two sufficient conditions on the mean-square exponential stability of MJHNNs are established utilizing augmented Lyapunov–Krasovskii functionals, the Wirtinger–based integral inequality, the Bessel-Legendre inequality, and the convex combination inequality. Then, linear matrix inequalities-based design methods for the required estimators are developed through eliminating nonlinear coupling terms. The feasibility of these linear matrix inequalities can be readily verified via available Matlab software, thus enabling numerically tractable implementation of the proposed design methods. Finally, two numerical examples with simulations are provided to demonstrate the applicability and less conservatism of the proposed stability criteria and estimators. Lastly, two numerical examples are given to demonstrate the applicability and reduced conservatism of the proposed stability criteria and estimator design methods. Future research could explore further refinement of these analysis and design results, and exporing their extention to more complex neural network models.","PeriodicalId":12507,"journal":{"name":"Frontiers in Physics","volume":"2 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142219667","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Automated size-specific dosimetry for chest posterior–anterior projection radiography","authors":"An Dedulle, Niki Fitousi, Nicholas Marshall, Hilde Bosmans","doi":"10.3389/fphy.2024.1441316","DOIUrl":"https://doi.org/10.3389/fphy.2024.1441316","url":null,"abstract":"IntroductionChest radiography is a frequently performed examination, and therefore, accurate patient dosimetry is important. One means of increasing dosimetric accuracy is through the use of size-specific dosimetry, and the aim of this work was to determine which patients would benefit from such a methodology applied in chest posterior–anterior (PA) projection radiography.MethodsA database of 44 voxel models was created from CT scans, representing adults with BMI from underweight, normal, overweight, and obese classes. Monte Carlo simulation was performed to generate dose conversion factors for each model. Correlation curves of the dose conversion factors with water equivalent diameter (WED) of the 44 voxel phantoms were obtained. A total of 8,536 chest PA examinations acquired between 2015 and 2019 using three X-ray systems were then retrospectively collected; 4,748 men (median age: 61 ± 21 years) and 3,788 women (median age: 60 ± 23 years). The WED of the patients was estimated from the ratio of detector air-kerma to incident air-kerma, using parameters in the DICOM header of the images. For all patients, a size-specific conversion factor was selected automatically using the relation between WED and dose conversion factor determined for the phantoms. The size-specific organ doses and effective doses were calculated based on these conversion factors, and then compared to the standard effective dose calculation with a paired test.ResultsThe lung doses ranged from 7 μGy to 96 μGy and had a good correlation with patient size in terms of WED (<jats:italic>p</jats:italic> &amp;lt; 0.01, R² between 0.52 and 0.77). The doses for thyroid ranged from 2 μGy to 42 μGy and correlated strongly with the patient size (p &amp;lt; 0.01, R² between 0.65 and 0.85). Breast doses ranged from 2 μGy to 13 μGy, and the correlation with the patient size was weak (<jats:italic>p</jats:italic> &amp;lt; 0.01, R<jats:sup>2</jats:sup> between 0.01 and 0.28). The size-specific effective dose ranged from 4 μSv to 42 μSv. The difference between the size-specific and standard effective dose ranged from −35% to 69% (<jats:italic>p</jats:italic> &amp;lt; 0.01), with differences exceeding ± 20% for 37% of the cases.DiscussionIn conclusion, the method presented in this study enables automated size-specific dosimetry, within the proposed maximum deviation of ± 20%, and should be considered for routine application.","PeriodicalId":12507,"journal":{"name":"Frontiers in Physics","volume":"15 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142227309","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Numerical simulation and theoretical analysis of pattern dynamics for the fractional-in-space Schnakenberg model","authors":"Ji-Lei Wang, Yu-Xing Han, Qing-Tong Chen, Zhi-Yuan Li, Ming-Jing Du, Yu-Lan Wang","doi":"10.3389/fphy.2024.1452077","DOIUrl":"https://doi.org/10.3389/fphy.2024.1452077","url":null,"abstract":"Effective exploration of the pattern dynamic behaviors of reaction–diffusion models is a popular but difficult topic. The Schnakenberg model is a famous reaction–diffusion system that has been widely used in many fields, such as physics, chemistry, and biology. Herein, we explore the stability, Turing instability, and weakly non-linear analysis of the Schnakenberg model; further, the pattern dynamics of the fractional-in-space Schnakenberg model was simulated numerically based on the Fourier spectral method. The patterns under different parameters, initial conditions, and perturbations are shown, including the target, bar, and dot patterns. It was found that the pattern not only splits and spreads from the bar to spot pattern but also forms a bar pattern from the broken connections of the dot pattern. The effects of the fractional Laplacian operator on the pattern are also shown. In most cases, the diffusion rate of the fractional model was higher than that of the integer model. By comparing with different methods in literature, it was found that the simulated patterns were consistent with the results obtained with other numerical methods in literature, indicating that the Fourier spectral method can be used to effectively explore the dynamic behaviors of the fractional Schnakenberg model. Some novel pattern dynamics behaviors of the fractional-in-space Schnakenberg model are also demonstrated.","PeriodicalId":12507,"journal":{"name":"Frontiers in Physics","volume":"103 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142219668","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analytical solution of steady reconnection outflows in a time-varying three-dimensional reconnection model with generalized spatiotemporal distributions","authors":"Y. L. Chen, Y. Wang, F. S. Wei, X. S. Feng, Z. L. Zhou, B. Y. Wang, P. B. Zuo, C. W. Jiang, Y. X. Gu, L. D. Wang, X. J. Song, X. J. Xu","doi":"10.3389/fphy.2024.1439949","DOIUrl":"https://doi.org/10.3389/fphy.2024.1439949","url":null,"abstract":"Magnetic reconnection is a fundamental mechanism for energy conversion in the realms of space physics, astrophysics, and plasma physics. Over the past few decades, obtaining analytical solutions for three-dimensional (3D) magnetic reconnection has remained a challenging endeavor. Due to the complexity and nonlinearity of the equations, analytical solutions can only be obtained when specific spatiotemporal distributions of magnetic fields or plasma flows are provided. Particularly, the evolution of reconnection flows in time-dependent 3D reconnection has not been analytically discussed. Additionally, quasi-steady magnetic reconnection persisting for several hours can be observed in the turbulent solar wind, which raises an important question: can steady reconnection flows theoretically exist in a time-dependent 3D magnetic reconnection model? In this study, a generalized analytical model for time-dependent kinematic 3D magnetic reconnection has been constructed. In the framework of pure analytical approach, it is firstly demonstrated that steady reconnection outflows can theoretically exist within a time-varying magnetic field. We have also analytically discussed the possibility of the existence of quasi-steady reconnection flows in 3D magnetic reconnection for turbulent magnetic fields in the solar wind. These findings broaden our understanding of the stability and necessary conditions for time-dependent 3D magnetic reconnection, offering new insights into quasi-steady reconnection phenomena in real cosmic environments.","PeriodicalId":12507,"journal":{"name":"Frontiers in Physics","volume":"60 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142219669","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bayesian optimization of proton generation in terawatt laser–CH2 cluster interactions within a plasma channel","authors":"Artem Kim, Mordechai Botton, Arie Zigler","doi":"10.3389/fphy.2024.1424755","DOIUrl":"https://doi.org/10.3389/fphy.2024.1424755","url":null,"abstract":"Improving the energy efficiency in generating high-energy proton or boron ions is crucial for advancing the feasibility of neutronless laser-based proton–boron (p-B<jats:sup>11</jats:sup>) fusion reactions. The primary objective of this work is to optimize the fusion energy efficiency of a proposed advanced p-B<jats:sup>11</jats:sup> fusion scheme. In the proposed scheme, an ultrashort laser pulse is guided by a plasma channel filled with carbon–hydrogen (CH<jats:sub>2</jats:sub>) clusters. The MeV protons are generated by the Coulomb explosion (CE) of the cluster, which, therefore, interact with surrounding boron to produce alpha particles. To evaluate the fusion energy efficiency under various conditions, 2D particle-in-cell (PIC) simulations are used, supplemented with analytical calculations and estimations. The Bayesian optimization (BO) algorithm is utilized to optimize the key interaction parameters. The BO approach allows us to identify optimal cluster and laser parameters that would have higher fusion energy efficiency.","PeriodicalId":12507,"journal":{"name":"Frontiers in Physics","volume":"170 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142219670","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"eXplainable artificial intelligence applied to algorithms for disruption prediction in tokamak devices","authors":"L. Bonalumi, E. Aymerich, E. Alessi, B. Cannas, A. Fanni, E. Lazzaro, S. Nowak, F. Pisano, G. Sias, C. Sozzi","doi":"10.3389/fphy.2024.1359656","DOIUrl":"https://doi.org/10.3389/fphy.2024.1359656","url":null,"abstract":"Introduction: This work explores the use of eXplainable artificial intelligence (XAI) to analyze a convolutional neural network (CNN) trained for disruption prediction in tokamak devices and fed with inputs composed of different physical quantities.Methods: This work focuses on a reduced dataset containing disruptions that follow patterns which are distinguishable based on their impact on the electron temperature profile. Our objective is to demonstrate that the CNN, without explicit training for these specific mechanisms, has implicitly learned to differentiate between these two disruption paths. With this purpose, two XAI algorithms have been implemented: occlusion and saliency maps.Results: The main outcome of this paper comes from the temperature profile analysis, which evaluates whether the CNN prioritizes the outer and inner regions.Discussion: The result of this investigation reveals a consistent shift in the CNN’s output sensitivity depending on whether the inner or outer part of the temperature profile is perturbed, reflecting the underlying physical phenomena occurring in the plasma.","PeriodicalId":12507,"journal":{"name":"Frontiers in Physics","volume":"290 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142219674","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evolution and governance of online public opinion during COVID-19: a hybrid approach using communication visualization, SIR modeling, and simulation validation","authors":"Lin Ren, Jiehua Zhang, Zhongyue Su, Fujun Lai, Deping Xiong","doi":"10.3389/fphy.2024.1462089","DOIUrl":"https://doi.org/10.3389/fphy.2024.1462089","url":null,"abstract":"IntroductionThis study investigates the mechanisms of public opinion dissemination and governance strategies during public health events, using a two-stage SIR model informed by the Information Cascade Theory.MethodsThe research employs Gephi visual analysis to identify principal nodes of public opinion and combines model simulations with dynamic propagation analysis to verify the model's precision and applicability.ResultsThe findings reveal that pivotal information nodes significantly accelerate the spread of public opinion, while ordinary nodes contribute to the natural attenuation of public discourse due to their strong spontaneous recovery capabilities. The simulation analysis further identifies the optimal timing for government intervention, particularly during the initial and peak phases of public opinion dissemination.DiscussionBased on the results, the study recommends strategies to strengthen the management of key opinion nodes, enhance public information literacy, optimize policy implementation, and utilize simulation tools to assist in public opinion management. These recommendations offer valuable theoretical and practical insights for managing public opinion during public health events.","PeriodicalId":12507,"journal":{"name":"Frontiers in Physics","volume":"78 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142219675","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"New method for the investigation of mode coupling in graded-index polymer photonic crystal fibers using the Langevin stochastic differential equation","authors":"Svetislav Savović, Alexandar Djordjevich, Konstantinos Aidinis, Chen Chen, Rui Min","doi":"10.3389/fphy.2024.1479206","DOIUrl":"https://doi.org/10.3389/fphy.2024.1479206","url":null,"abstract":"The mode coupling in a graded-index polymer photonic crystal fiber (GI PPCF) with a solid core has been investigated using the Langevin equation. Based on the computer-simulated Langevin force, the Langevin equation is numerically integrated. The numerical solutions of the Langevin equation align with those of the time-independent power flow equation (TI PFE). We showed that by solving the Langevin equation, which is a stochastic differential equation, one can successfully treat a mode coupling in GI PPCFs, which is an intrinsically stochastic process. We demonstrated that, in terms of effectiveness, the Langevin equation is preferable compared to the TI PFE. The GI PPCF achieves the equilibrium mode distribution (EMD) at a coupling length that is even shorter than the conventional GI plastic optical fiber (POF). The application of multimode GI PCFs in communications and optical fiber sensor systems will benefit from these findings.","PeriodicalId":12507,"journal":{"name":"Frontiers in Physics","volume":"5 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142219673","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}