Ayanava Basak, Syamal K Dana, Nandadulal Bairagi, Ulrike Feudel
Climate change and anthropogenic impacts have a significant effect on natural ecosystems. As a response, tipping phenomena, i.e., abrupt qualitative changes in the dynamics of ecosystems, like transitions between alternative stable states, can be observed. We study such critical transitions, caused by an interplay between B-tipping, the rate of change of environmental forcing, and a rate-dependent basin boundary crossing. Instead of a slow trend of environmental change, we focus on pulses of variation in the carrying capacity in a simple ecological model, the spruce budworm model, and show how one pulse of environmental change can lead to tracking the current stable state or to tipping to an alternative state depending on the strength and the duration of the pulse. Moreover, we demonstrate that applying a second pulse after the first one, which can track the desired state, can lead to tipping, although its rate is slow and does not even cross the critical threshold. We explain this unexpected behavior in terms of the interacting timescales, the intrinsic ecological timescale, the rate of environmental change, and the movement of the basin boundaries separating the basins of attraction of the two alternative states.
{"title":"When do multiple pulses of environmental variation trigger tipping in an ecological system?","authors":"Ayanava Basak, Syamal K Dana, Nandadulal Bairagi, Ulrike Feudel","doi":"10.1063/5.0205410","DOIUrl":"https://doi.org/10.1063/5.0205410","url":null,"abstract":"<p><p>Climate change and anthropogenic impacts have a significant effect on natural ecosystems. As a response, tipping phenomena, i.e., abrupt qualitative changes in the dynamics of ecosystems, like transitions between alternative stable states, can be observed. We study such critical transitions, caused by an interplay between B-tipping, the rate of change of environmental forcing, and a rate-dependent basin boundary crossing. Instead of a slow trend of environmental change, we focus on pulses of variation in the carrying capacity in a simple ecological model, the spruce budworm model, and show how one pulse of environmental change can lead to tracking the current stable state or to tipping to an alternative state depending on the strength and the duration of the pulse. Moreover, we demonstrate that applying a second pulse after the first one, which can track the desired state, can lead to tipping, although its rate is slow and does not even cross the critical threshold. We explain this unexpected behavior in terms of the interacting timescales, the intrinsic ecological timescale, the rate of environmental change, and the movement of the basin boundaries separating the basins of attraction of the two alternative states.</p>","PeriodicalId":9974,"journal":{"name":"Chaos","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142124984","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
R S Martin, C M Greve, C E Huerta, A S Wong, J W Koo, D Q Eckhardt
This work presents a heuristic for the selection of a time delay based on optimizing the global maximum of mutual information in orthonormal coordinates for embedding a dynamical system. This criterion is demonstrated to be more robust compared to methods that utilize a local minimum, as the global maximum is guaranteed to exist in the proposed coordinate system for any dynamical system. By contrast, methods using local minima can be ill-posed as a local minimum can be difficult to identify in the presence of noise or may simply not exist. The performance of the global maximum and local minimum methods are compared in the context of causality detection using convergent cross mapping using both a noisy Lorenz system and experimental data from an oscillating plasma source. The proposed heuristic for time lag selection is shown to be more consistent in the presence of noise and closer to an optimal uniform time lag selection.
{"title":"A robust time-delay selection criterion applied to convergent cross mapping.","authors":"R S Martin, C M Greve, C E Huerta, A S Wong, J W Koo, D Q Eckhardt","doi":"10.1063/5.0209028","DOIUrl":"https://doi.org/10.1063/5.0209028","url":null,"abstract":"<p><p>This work presents a heuristic for the selection of a time delay based on optimizing the global maximum of mutual information in orthonormal coordinates for embedding a dynamical system. This criterion is demonstrated to be more robust compared to methods that utilize a local minimum, as the global maximum is guaranteed to exist in the proposed coordinate system for any dynamical system. By contrast, methods using local minima can be ill-posed as a local minimum can be difficult to identify in the presence of noise or may simply not exist. The performance of the global maximum and local minimum methods are compared in the context of causality detection using convergent cross mapping using both a noisy Lorenz system and experimental data from an oscillating plasma source. The proposed heuristic for time lag selection is shown to be more consistent in the presence of noise and closer to an optimal uniform time lag selection.</p>","PeriodicalId":9974,"journal":{"name":"Chaos","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142131983","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Enrique C Gabrick, Eduardo L Brugnago, Ana L R de Moraes, Paulo R Protachevicz, Sidney T da Silva, Fernando S Borges, Iberê L Caldas, Antonio M Batista, Jürgen Kurths
In this work, effects of constant and time-dependent vaccination rates on the Susceptible-Exposed-Infected-Recovered-Susceptible (SEIRS) seasonal model are studied. Computing the Lyapunov exponent, we show that typical complex structures, such as shrimps, emerge for given combinations of a constant vaccination rate and another model parameter. In some specific cases, the constant vaccination does not act as a chaotic suppressor and chaotic bands can exist for high levels of vaccination (e.g., >0.95). Moreover, we obtain linear and non-linear relationships between one control parameter and constant vaccination to establish a disease-free solution. We also verify that the total infected number does not change whether the dynamics is chaotic or periodic. The introduction of a time-dependent vaccine is made by the inclusion of a periodic function with a defined amplitude and frequency. For this case, we investigate the effects of different amplitudes and frequencies on chaotic attractors, yielding low, medium, and high seasonality degrees of contacts. Depending on the parameters of the time-dependent vaccination function, chaotic structures can be controlled and become periodic structures. For a given set of parameters, these structures are accessed mostly via crisis and, in some cases, via period-doubling. After that, we investigate how the time-dependent vaccine acts in bi-stable dynamics when chaotic and periodic attractors coexist. We identify that this kind of vaccination acts as a control by destroying almost all the periodic basins. We explain this by the fact that chaotic attractors exhibit more desirable characteristics for epidemics than periodic ones in a bi-stable state.
{"title":"Control, bi-stability, and preference for chaos in time-dependent vaccination campaign.","authors":"Enrique C Gabrick, Eduardo L Brugnago, Ana L R de Moraes, Paulo R Protachevicz, Sidney T da Silva, Fernando S Borges, Iberê L Caldas, Antonio M Batista, Jürgen Kurths","doi":"10.1063/5.0221150","DOIUrl":"https://doi.org/10.1063/5.0221150","url":null,"abstract":"<p><p>In this work, effects of constant and time-dependent vaccination rates on the Susceptible-Exposed-Infected-Recovered-Susceptible (SEIRS) seasonal model are studied. Computing the Lyapunov exponent, we show that typical complex structures, such as shrimps, emerge for given combinations of a constant vaccination rate and another model parameter. In some specific cases, the constant vaccination does not act as a chaotic suppressor and chaotic bands can exist for high levels of vaccination (e.g., >0.95). Moreover, we obtain linear and non-linear relationships between one control parameter and constant vaccination to establish a disease-free solution. We also verify that the total infected number does not change whether the dynamics is chaotic or periodic. The introduction of a time-dependent vaccine is made by the inclusion of a periodic function with a defined amplitude and frequency. For this case, we investigate the effects of different amplitudes and frequencies on chaotic attractors, yielding low, medium, and high seasonality degrees of contacts. Depending on the parameters of the time-dependent vaccination function, chaotic structures can be controlled and become periodic structures. For a given set of parameters, these structures are accessed mostly via crisis and, in some cases, via period-doubling. After that, we investigate how the time-dependent vaccine acts in bi-stable dynamics when chaotic and periodic attractors coexist. We identify that this kind of vaccination acts as a control by destroying almost all the periodic basins. We explain this by the fact that chaotic attractors exhibit more desirable characteristics for epidemics than periodic ones in a bi-stable state.</p>","PeriodicalId":9974,"journal":{"name":"Chaos","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142281127","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Eugene Tan, Shannon Algar, Débora Corrêa, Michael Small, Thomas Stemler, David Walker
{"title":"Erratum to selecting embedding delays: An overview of embedding techniques and a new method using persistent homology [Chaos: Interdiscip. J. Nonlin. Sci. 33(3), 24 (2023)].","authors":"Eugene Tan, Shannon Algar, Débora Corrêa, Michael Small, Thomas Stemler, David Walker","doi":"10.1063/5.0233347","DOIUrl":"https://doi.org/10.1063/5.0233347","url":null,"abstract":"","PeriodicalId":9974,"journal":{"name":"Chaos","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142281129","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Muyun Mou, Yu Guo, Fanming Luo, Yang Yu, Jiang Zhang
Complex systems, characterized by intricate interactions among numerous entities, give rise to emergent behaviors whose data-driven modeling and control are of utmost significance, especially when there is abundant observational data but the intervention cost is high. Traditional methods rely on precise dynamical models or require extensive intervention data, often falling short in real-world applications. To bridge this gap, we consider a specific setting of the complex systems control problem: how to control complex systems through a few online interactions on some intervenable nodes when abundant observational data from natural evolution is available. We introduce a two-stage model predictive complex system control framework, comprising an offline pre-training phase that leverages rich observational data to capture spontaneous evolutionary dynamics and an online fine-tuning phase that uses a variant of model predictive control to implement intervention actions. To address the high-dimensional nature of the state-action space in complex systems, we propose a novel approach employing action-extended graph neural networks to model the Markov decision process of complex systems and design a hierarchical action space for learning intervention actions. This approach performs well in three complex system control environments: Boids, Kuramoto, and Susceptible-Infectious-Susceptible (SIS) metapopulation. It offers accelerated convergence, robust generalization, and reduced intervention costs compared to the baseline algorithm. This work provides valuable insights into controlling complex systems with high-dimensional state-action spaces and limited intervention data, presenting promising applications for real-world challenges.
{"title":"Model predictive complex system control from observational and interventional data.","authors":"Muyun Mou, Yu Guo, Fanming Luo, Yang Yu, Jiang Zhang","doi":"10.1063/5.0195208","DOIUrl":"https://doi.org/10.1063/5.0195208","url":null,"abstract":"<p><p>Complex systems, characterized by intricate interactions among numerous entities, give rise to emergent behaviors whose data-driven modeling and control are of utmost significance, especially when there is abundant observational data but the intervention cost is high. Traditional methods rely on precise dynamical models or require extensive intervention data, often falling short in real-world applications. To bridge this gap, we consider a specific setting of the complex systems control problem: how to control complex systems through a few online interactions on some intervenable nodes when abundant observational data from natural evolution is available. We introduce a two-stage model predictive complex system control framework, comprising an offline pre-training phase that leverages rich observational data to capture spontaneous evolutionary dynamics and an online fine-tuning phase that uses a variant of model predictive control to implement intervention actions. To address the high-dimensional nature of the state-action space in complex systems, we propose a novel approach employing action-extended graph neural networks to model the Markov decision process of complex systems and design a hierarchical action space for learning intervention actions. This approach performs well in three complex system control environments: Boids, Kuramoto, and Susceptible-Infectious-Susceptible (SIS) metapopulation. It offers accelerated convergence, robust generalization, and reduced intervention costs compared to the baseline algorithm. This work provides valuable insights into controlling complex systems with high-dimensional state-action spaces and limited intervention data, presenting promising applications for real-world challenges.</p>","PeriodicalId":9974,"journal":{"name":"Chaos","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142281134","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The Koopman operator framework holds promise for spectral analysis of nonlinear dynamical systems based on linear operators. Eigenvalues and eigenfunctions of the Koopman operator, the so-called Koopman eigenvalues and Koopman eigenfunctions, respectively, mirror global properties of the system's flow. In this paper, we perform the Koopman analysis of the singularly perturbed van der Pol system. First, we show the spectral signature depending on singular perturbation: how two Koopman principal eigenvalues are ordered and what distinct shapes emerge in their associated Koopman eigenfunctions. Second, we discuss the singular limit of the Koopman operator, which is derived through the concatenation of Koopman operators for the fast and slow subsystems. From the spectral properties of the Koopman operator for the singularly perturbed system and the singular limit, we suggest that the Koopman eigenfunctions inherit geometric properties of the singularly perturbed system. These results are applicable to general planar singularly perturbed systems with stable limit cycles.
{"title":"Koopman analysis of the singularly perturbed van der Pol oscillator.","authors":"Natsuki Katayama, Yoshihiko Susuki","doi":"10.1063/5.0216779","DOIUrl":"https://doi.org/10.1063/5.0216779","url":null,"abstract":"<p><p>The Koopman operator framework holds promise for spectral analysis of nonlinear dynamical systems based on linear operators. Eigenvalues and eigenfunctions of the Koopman operator, the so-called Koopman eigenvalues and Koopman eigenfunctions, respectively, mirror global properties of the system's flow. In this paper, we perform the Koopman analysis of the singularly perturbed van der Pol system. First, we show the spectral signature depending on singular perturbation: how two Koopman principal eigenvalues are ordered and what distinct shapes emerge in their associated Koopman eigenfunctions. Second, we discuss the singular limit of the Koopman operator, which is derived through the concatenation of Koopman operators for the fast and slow subsystems. From the spectral properties of the Koopman operator for the singularly perturbed system and the singular limit, we suggest that the Koopman eigenfunctions inherit geometric properties of the singularly perturbed system. These results are applicable to general planar singularly perturbed systems with stable limit cycles.</p>","PeriodicalId":9974,"journal":{"name":"Chaos","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142307210","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
We proposed a neighbor selection mechanism based on memory and target payoff, where the target payoff is the maximum value of the group's average expected payoff. According to this mechanism, individuals prioritize selecting neighbors whose average payoffs in the last M rounds are close to the target payoff for strategy learning, aiming to maximize the group's expected payoff. Simulation results on the grid-based Prisoner's Dilemma and Snowdrift games demonstrate that this mechanism can significantly improve the group's payoff and cooperation level. Furthermore, the longer the memory length, the higher the group's payoff and cooperation level. Overall, the combination of memory and target payoff can lead to the emergence and persistence of cooperation in social dilemmas as individuals are motivated to cooperate based on both their past experiences and future goals. This interplay highlights the significance of taking into account numerous variables in comprehending and promoting cooperation within evolutionary frameworks.
我们提出了一种基于记忆和目标报酬的邻居选择机制,其中目标报酬是群体平均预期报酬的最大值。根据这一机制,个体会优先选择在过去 M 轮中平均报酬接近目标报酬的邻居进行策略学习,从而实现群体预期报酬的最大化。基于网格的囚徒困境和雪漂游戏的模拟结果表明,这种机制能显著提高群体的收益和合作水平。此外,记忆长度越长,小组的收益和合作水平就越高。总之,记忆和目标报酬的结合可以导致社会困境中合作的出现和持续,因为个体的合作动机是基于他们过去的经验和未来的目标。这种相互作用凸显了在进化框架内理解和促进合作时考虑众多变量的重要性。
{"title":"Memory and target payoff enhance cooperation in evolutionary social dilemmas.","authors":"Xinle Lin, Jianhe Li, Suohai Fan","doi":"10.1063/5.0220490","DOIUrl":"https://doi.org/10.1063/5.0220490","url":null,"abstract":"<p><p>We proposed a neighbor selection mechanism based on memory and target payoff, where the target payoff is the maximum value of the group's average expected payoff. According to this mechanism, individuals prioritize selecting neighbors whose average payoffs in the last M rounds are close to the target payoff for strategy learning, aiming to maximize the group's expected payoff. Simulation results on the grid-based Prisoner's Dilemma and Snowdrift games demonstrate that this mechanism can significantly improve the group's payoff and cooperation level. Furthermore, the longer the memory length, the higher the group's payoff and cooperation level. Overall, the combination of memory and target payoff can lead to the emergence and persistence of cooperation in social dilemmas as individuals are motivated to cooperate based on both their past experiences and future goals. This interplay highlights the significance of taking into account numerous variables in comprehending and promoting cooperation within evolutionary frameworks.</p>","PeriodicalId":9974,"journal":{"name":"Chaos","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141874275","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The general form of the Hamiltonian function serves as the foundation for the creation of a new four-dimensional chaotic system in this study. We discover that the external excitation parameter d, the internal parameter a, and all initial values have a transforming influence on the system property. Additionally, the corresponding fractional-order chaotic system in accordance with the constructed four-dimensional chaotic system is proposed. It is found that as the order q rises, the system transforms gradually from a dissipative system to a conservative system. Multiple coexisting attraction flows based on the Hamiltonian energy magnitude are present in this dual-property chaotic system. The complexity analysis shows that the system has a high level of complexity. NIST test indicates that the chaotic sequences produced by this dual-property chaotic system exhibit good pseudo-randomness. Finally, a Digital Signal Processing-based hardware platform confirms the physical realizability of the system.
本研究以哈密顿函数的一般形式为基础,创建了一个新的四维混沌系统。我们发现外部激励参数 d、内部参数 a 以及所有初始值都会对系统性质产生转化影响。此外,还根据所构建的四维混沌系统提出了相应的分数阶混沌系统。研究发现,随着阶数 q 的增加,系统逐渐从耗散系统转变为保守系统。该双属性混沌系统中存在基于哈密顿能量大小的多种共存吸引流。复杂性分析表明,该系统具有很高的复杂性。NIST 测试表明,该双属性混沌系统产生的混沌序列具有良好的伪随机性。最后,基于数字信号处理的硬件平台证实了该系统的物理可实现性。
{"title":"A new four-dimensional chaotic system with rich transitional characteristics between dissipative and conservative.","authors":"Xu Sun, Xiangxin Leng, Bowen Tian, Baoxiang Du","doi":"10.1063/5.0205144","DOIUrl":"https://doi.org/10.1063/5.0205144","url":null,"abstract":"<p><p>The general form of the Hamiltonian function serves as the foundation for the creation of a new four-dimensional chaotic system in this study. We discover that the external excitation parameter d, the internal parameter a, and all initial values have a transforming influence on the system property. Additionally, the corresponding fractional-order chaotic system in accordance with the constructed four-dimensional chaotic system is proposed. It is found that as the order q rises, the system transforms gradually from a dissipative system to a conservative system. Multiple coexisting attraction flows based on the Hamiltonian energy magnitude are present in this dual-property chaotic system. The complexity analysis shows that the system has a high level of complexity. NIST test indicates that the chaotic sequences produced by this dual-property chaotic system exhibit good pseudo-randomness. Finally, a Digital Signal Processing-based hardware platform confirms the physical realizability of the system.</p>","PeriodicalId":9974,"journal":{"name":"Chaos","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141981835","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Human games are inherently diverse, involving more than mere identity interactions. The diversity of game tasks offers a more authentic explanation in the exploration of social dilemmas. Human behavior is also influenced by conformity, and prosociality is a crucial factor in addressing social dilemmas. This study proposes a generalized prisoner's dilemma model of task diversity that incorporates a conformity-driven interaction. Simulation findings indicate that the diversity of multi-tasks and the path dependence contribute to the flourishing of cooperation in games. Conformity-driven interactions also promote cooperation. However, this promotion effect does not increase linearly, and only appropriate task sizes and suitable proportions of conformity-driven interactions yield optimal results. From a broader group perspective, the interplay of network adaptation, task size, and conformity-driven interaction can form a structure of attractors or repellents.
{"title":"The effect of multi-tasks mechanism on cooperation in evolutionary game.","authors":"Jiarui Fan, Haifeng Du, Guangyu Li, Xiaochen He","doi":"10.1063/5.0210787","DOIUrl":"https://doi.org/10.1063/5.0210787","url":null,"abstract":"<p><p>Human games are inherently diverse, involving more than mere identity interactions. The diversity of game tasks offers a more authentic explanation in the exploration of social dilemmas. Human behavior is also influenced by conformity, and prosociality is a crucial factor in addressing social dilemmas. This study proposes a generalized prisoner's dilemma model of task diversity that incorporates a conformity-driven interaction. Simulation findings indicate that the diversity of multi-tasks and the path dependence contribute to the flourishing of cooperation in games. Conformity-driven interactions also promote cooperation. However, this promotion effect does not increase linearly, and only appropriate task sizes and suitable proportions of conformity-driven interactions yield optimal results. From a broader group perspective, the interplay of network adaptation, task size, and conformity-driven interaction can form a structure of attractors or repellents.</p>","PeriodicalId":9974,"journal":{"name":"Chaos","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141874326","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Wang Sang Koon, Houman Owhadi, Molei Tao, Tomohiro Yanao
We study the metastability, internal frequencies, activation mechanism, energy transfer, and the collective base-flipping in a mesoscopic DNA via resonance with specific electric fields. Our new mesoscopic DNA model takes into account not only the issues of helicity and the coupling of an electric field with the base dipole moments, but also includes environmental effects, such as fluid viscosity and thermal noise. Also, all the parameter values are chosen to best represent the typical values for the opening and closing dynamics of a DNA. Our study shows that while the mesoscopic DNA is metastable and robust to environmental effects, it is vulnerable to certain frequencies that could be targeted by specific THz fields for triggering its collective base-flipping dynamics and causing large amplitude separation of base pairs. Based on applying the Freidlin-Wentzell method of stochastic averaging and the newly developed theory of resonant enhancement to our mesoscopic DNA model, our semi-analytic estimates show that the required fields should be THz fields with frequencies around 0.28 THz and with amplitudes in the order of 450 kV/cm. These estimates compare well with the experimental data of Titova et al., which have demonstrated that they could affect the function of DNA in human skin tissues by THz pulses with frequencies around 0.5 THz and with a peak electric field at 220 kV/cm. Moreover, our estimates also conform to a number of other experimental results, which appeared in the last couple years.
我们研究了介观 DNA 通过与特定电场共振的蜕变性、内部频率、活化机制、能量转移和集体碱基翻转。我们的新介观 DNA 模型不仅考虑了螺旋度和电场与碱基偶极矩的耦合问题,还包括环境效应,如流体粘度和热噪声。此外,所有参数值的选择都是为了最好地代表 DNA 打开和关闭动态的典型值。我们的研究表明,虽然介观 DNA 对环境影响具有稳态和稳健性,但它很容易受到某些频率的影响,而特定的太赫兹场可能会触发其集体碱基翻转动力学,并导致碱基对的大振幅分离。根据弗里德林-文采尔随机平均法和新开发的共振增强理论对我们的介观 DNA 模型的应用,我们的半分析估计表明,所需的场应该是频率在 0.28 THz 左右、振幅在 450 kV/cm 左右的 THz 场。这些估计值与 Titova 等人的实验数据相差无几,后者证明,频率约为 0.5 THz、峰值电场为 220 kV/cm 的 THz 脉冲可以影响人体皮肤组织中 DNA 的功能。此外,我们的估算也符合最近几年出现的其他一些实验结果。
{"title":"Can specific THz fields induce collective base-flipping in DNA? A stochastic averaging and resonant enhancement investigation based on a new mesoscopic model.","authors":"Wang Sang Koon, Houman Owhadi, Molei Tao, Tomohiro Yanao","doi":"10.1063/5.0208609","DOIUrl":"https://doi.org/10.1063/5.0208609","url":null,"abstract":"<p><p>We study the metastability, internal frequencies, activation mechanism, energy transfer, and the collective base-flipping in a mesoscopic DNA via resonance with specific electric fields. Our new mesoscopic DNA model takes into account not only the issues of helicity and the coupling of an electric field with the base dipole moments, but also includes environmental effects, such as fluid viscosity and thermal noise. Also, all the parameter values are chosen to best represent the typical values for the opening and closing dynamics of a DNA. Our study shows that while the mesoscopic DNA is metastable and robust to environmental effects, it is vulnerable to certain frequencies that could be targeted by specific THz fields for triggering its collective base-flipping dynamics and causing large amplitude separation of base pairs. Based on applying the Freidlin-Wentzell method of stochastic averaging and the newly developed theory of resonant enhancement to our mesoscopic DNA model, our semi-analytic estimates show that the required fields should be THz fields with frequencies around 0.28 THz and with amplitudes in the order of 450 kV/cm. These estimates compare well with the experimental data of Titova et al., which have demonstrated that they could affect the function of DNA in human skin tissues by THz pulses with frequencies around 0.5 THz and with a peak electric field at 220 kV/cm. Moreover, our estimates also conform to a number of other experimental results, which appeared in the last couple years.</p>","PeriodicalId":9974,"journal":{"name":"Chaos","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142035393","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}