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A Multifaceted Study of Nematic Order Reconstruction in Microfluidic Channels 微流控通道中向列有序重构的多方面研究
IF 1.9 4区 数学 Q1 MATHEMATICS, APPLIED Pub Date : 2023-11-27 DOI: 10.1137/22m1490909
James Dalby, Yucen Han, Apala Majumdar, Lidia Mrad
SIAM Journal on Applied Mathematics, Volume 83, Issue 6, Page 2284-2309, December 2023.
Abstract. We study order reconstruction (OR) solutions in the Beris–Edwards framework for nematodynamics, for both passive and active nematic flows in a microfluidic channel. OR solutions exhibit polydomains and domain walls, and as such, are of physical interest. We show that OR solutions exist for passive flows with constant velocity and pressure, but only for specific boundary conditions. We prove the existence of unique, symmetric, and nonsingular nematic profiles for boundary conditions that do not allow for OR solutions. We compute asymptotic expansions for OR-type solutions for passive flows with nonconstant velocity and pressure, and active flows, which shed light on the internal structure of domain walls. The asymptotics are complemented by numerical studies that demonstrate the universality of OR-type structures in static and dynamic scenarios.
SIAM应用数学学报,83卷,第6期,2284-2309页,2023年12月。摘要。我们在Beris-Edwards框架下研究了微流控通道中被动和主动向列流的有序重建(OR)解。OR解决方案展示了多域和域壁,因此具有物理意义。我们证明了对于恒速恒压被动流动存在OR解,但仅适用于特定的边界条件。在不允许或解的边界条件下,证明了唯一、对称和非奇异向列型轮廓的存在性。我们计算了非恒定速度和压力的被动流动和主动流动的or型解的渐近展开式,从而揭示了区域壁面的内部结构。数值研究补充了渐近性,证明了or型结构在静态和动态情况下的普遍性。
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引用次数: 1
Prevalence of Multistationarity and Absolute Concentration Robustness in Reaction Networks 反应网络中多平稳性和绝对浓度鲁棒性的普遍性
IF 1.9 4区 数学 Q1 MATHEMATICS, APPLIED Pub Date : 2023-11-20 DOI: 10.1137/23m1549316
Badal Joshi, Nidhi Kaihnsa, Tung D. Nguyen, Anne Shiu
SIAM Journal on Applied Mathematics, Volume 83, Issue 6, Page 2260-2283, December 2023.
Abstract. For reaction networks arising in systems biology, the capacity for two or more steady states, that is, multistationarity, is an important property that underlies biochemical switches. Another property receiving much attention recently is absolute concentration robustness (ACR), which means that some species concentration is the same at all positive steady states. In this work, we investigate the prevalence of each property while paying close attention to when the properties occur together. Specifically, we consider a stochastic block framework for generating random networks and prove edge-probability thresholds at which, with high probability, multistationarity appears and ACR becomes rare. We also show that the small window in which both properties occur only appears in networks with many species. Taken together, our results confirm that, in random reversible networks, ACR and multistationarity together, or even ACR on its own, is highly atypical. Our proofs rely on two prior results, one pertaining to the prevalence of networks with deficiency zero and the other “lifting” multistationarity from small networks to larger ones.
SIAM应用数学杂志,83卷,第6期,2260-2283页,2023年12月。摘要。对于系统生物学中产生的反应网络,具有两个或多个稳定状态的能力,即多平稳性,是生化开关的重要特性。另一个最近受到广泛关注的性质是绝对浓度鲁棒性(ACR),这意味着某些物种的浓度在所有正稳态下都是相同的。在这项工作中,我们调查了每个属性的普遍性,同时密切关注这些属性何时一起出现。具体来说,我们考虑了一个随机块框架来生成随机网络,并证明了边缘概率阈值,在该阈值下,多平稳性在高概率下出现,并且ACR变得罕见。我们还表明,两种性质同时出现的小窗口只出现在有许多物种的网络中。综上所述,我们的结果证实,在随机可逆网络中,ACR和多平稳性一起,甚至单独的ACR,都是非典型的。我们的证明依赖于两个先前的结果,一个与缺乏性为零的网络的普遍性有关,另一个将多平稳性从小型网络“提升”到大型网络。
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引用次数: 2
Power-Engine-Load Form for Dynamic Absolute Concentration Robustness 动力-发动机负载形式的动态绝对集中稳健性
IF 1.9 4区 数学 Q1 MATHEMATICS, APPLIED Pub Date : 2023-11-20 DOI: 10.1137/22m1535450
Badal Joshi, Gheorghe Craciun
SIAM Journal on Applied Mathematics, Volume 83, Issue 6, Page 2237-2259, December 2023.
Abstract. In a reaction network, the concentration of a species with the property of dynamic absolute concentration robustness (dynamic ACR) converges to the same value independent of the overall initial values. This property endows a biochemical network with output robustness and therefore is essential for its functioning in a highly variable environment. It is important to identify the structure of the dynamical system as well as the constraints required for dynamic ACR. We propose a power-engine-load form of dynamic ACR and obtain results regarding convergence to the ACR value based on this form.
SIAM应用数学学报,83卷,第6期,2237-2259页,2023年12月。摘要。在反应网络中,具有动态绝对浓度鲁棒性(dynamic绝对浓度鲁棒性,动态ACR)的物种的浓度收敛到与整体初始值无关的同一值。这一特性赋予生化网络输出鲁棒性,因此对其在高度可变的环境中发挥作用至关重要。确定动力系统的结构以及动态ACR所需的约束条件是很重要的。提出了一种动力-发动机-负荷形式的动态ACR,并在此基础上得到了ACR值收敛性的结果。
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引用次数: 0
Cell Polarity and Movement with Reaction-Diffusion and Moving Boundary: Rigorous Model Analysis and Robust Simulations 具有反应扩散和移动边界的细胞极性和运动:严格的模型分析和鲁棒模拟
IF 1.9 4区 数学 Q1 MATHEMATICS, APPLIED Pub Date : 2023-11-16 DOI: 10.1137/22m1506766
Shuang Liu, Li-Tien Cheng, Bo Li
SIAM Journal on Applied Mathematics, Ahead of Print.
Abstract. Cell polarity and movement are fundamental to many biological functions. Experimental and theoretical studies have indicated that interactions of certain proteins lead to the cell polarization which plays a key role in controlling the cell movement. We study the cell polarity and movement based on a class of biophysical models that consist of reaction-diffusion equations for different proteins and the dynamics of a moving cell boundary. Such a moving boundary is often simulated by a phase-field model. We first apply the matched asymptotic analysis to give a rigorous derivation of the sharp-interface model of the cell boundary from a phase-field model. We then develop a robust numerical approach that combines the level-set method to track the sharp boundary of a moving cell and accurate discretization techniques for solving the reaction-diffusion equations on the moving cell region. Our extensive numerical simulations predict the cell polarization under various kinds of stimuli and capture both the linear and the circular trajectories of a moving cell for a long period of time. In particular, we have identified some key parameters controlling different cell trajectories that are less accurately predicted by reduced models. Our work has linked different models and also developed tools that can be adapted for the challenging three-dimensional simulations.
SIAM应用数学杂志,出版前。摘要。细胞极性和运动是许多生物功能的基础。实验和理论研究表明,某些蛋白质的相互作用导致细胞极化,并在控制细胞运动中起着关键作用。我们研究细胞极性和运动基于一类生物物理模型,包括不同蛋白质的反应-扩散方程和移动细胞边界的动力学。这种移动边界通常用相场模型来模拟。我们首先应用匹配渐近分析从相场模型推导出细胞边界的锐界面模型。然后,我们开发了一种鲁棒的数值方法,该方法结合了水平集方法来跟踪移动细胞的尖锐边界和精确的离散化技术来求解移动细胞区域上的反应扩散方程。我们广泛的数值模拟预测了各种刺激下的细胞极化,并捕获了长时间运动细胞的线性和圆形轨迹。特别是,我们已经确定了一些控制不同细胞轨迹的关键参数,这些参数通过简化模型预测的准确性较低。我们的工作将不同的模型联系起来,并开发了能够适应具有挑战性的三维模拟的工具。
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引用次数: 0
Global Dynamics and Pattern Formation in a Diffusive Population-Toxicant Model with Negative Toxicant-Taxis 具有负毒性趋向性的扩散种群-毒性模型的全局动力学和模式形成
IF 1.9 4区 数学 Q1 MATHEMATICS, APPLIED Pub Date : 2023-11-15 DOI: 10.1137/22m1510881
Xiumei Deng, Qihua Huang, Zhi-An Wang
SIAM Journal on Applied Mathematics, Volume 83, Issue 6, Page 2212-2236, December 2023.
Abstract. Because of the significance of remediating contaminated ecosystems, many mathematical models have been developed to describe the interactions between populations and toxicants in polluted aquatic environments. These models typically neglect the consequences of toxicant-induced behavioral changes on population dynamics. Taking into account that individuals may flee from areas with high toxicant concentrations to areas with low toxicant concentrations in order to improve their chances of survival, growth, and reproduction, we develop a diffusive population-toxicant model with toxicant-taxis. We establish the global well-posedness of our model and prove the global stability of spatially homogeneous toxicant-only steady states and population-toxicant coexistence steady states under some conditions. We find conditions under which stable spatially inhomogeneous steady states become unstable to trigger spatial pattern formations as the toxicant-taxis is strong. We also identify a narrow parameter regime in which toxicant-only and population-toxicant coexistence steady states are bistable. Numerical simulations are performed to illustrate that spatial aggregation and segregation patterns between the population and the toxicant will typically emerge. Our study highlights the important effects of toxicant-induced movement responses on the spatial distributions of populations in polluted aquatic environments.
应用数学学报,83卷,第6期,2212-2236页,2023年12月。摘要。由于修复被污染的生态系统的重要性,许多数学模型已经被开发来描述在被污染的水生环境中种群与毒物之间的相互作用。这些模型通常忽略了毒物引起的行为变化对种群动态的影响。考虑到个体可能会从高毒性浓度地区逃到低毒性浓度地区,以提高其生存、生长和繁殖的机会,我们开发了一个具有毒性趋向性的扩散种群-毒性模型。建立了模型的全局适定性,证明了在一定条件下空间均质毒物稳态和种群毒物共存稳态的全局稳定性。我们发现,当毒性趋向性很强时,稳定的空间非均匀稳态变得不稳定,从而触发空间格局的形成。我们还确定了一个狭窄的参数制度,其中毒物和种群毒物共存稳定状态是双稳态的。数值模拟表明,种群和毒物之间的空间聚集和隔离模式将典型地出现。我们的研究强调了毒物诱导的运动反应对受污染水生环境中种群空间分布的重要影响。
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引用次数: 0
Detecting and Resetting Tipping Points to Create More HIV Post-Treatment Controllers with Bifurcation and Sensitivity Analysis 用分岔和敏感性分析检测和重置引爆点以创建更多的HIV治疗后控制器
IF 1.9 4区 数学 Q1 MATHEMATICS, APPLIED Pub Date : 2023-11-15 DOI: 10.1137/22m1485255
Wenjing Zhang, Leif A. Ellingson
SIAM Journal on Applied Mathematics, Ahead of Print.
Abstract. The existence of HIV post-treatment controllers (PTCs) offers hope for an HIV functional cure, and understanding the critical mechanisms determining PTC represents a key step toward this goal. Here, we have studied these mechanisms by analyzing an established mathematical model for HIV viral dynamics. In mathematical models, critical mechanisms are represented by parameters that affect the tipping points to induce qualitatively different dynamics, and in cases with multiple stability, the initial conditions of the system also play a role in determining the fate of the solution. As such, for the tipping points in parameter space, we developed and implemented a sensitivity analysis of the threshold conditions of the associated bifurcations to identify the critical mechanisms for this model. Our results suggest that the infected cell death rate and the saturation parameter for cytotoxic T lymphocyte proliferation significantly affect post-treatment control. For the case with multiple stability, in state space of initial conditions, we first investigated the saddle-type equilibrium point to identify its stable manifold, which delimits trapping regions associated to the high and low viral set points. The identified stable manifold serves as a guide for the loads of immune cells and HIV virus at the time of therapy termination to achieve post-treatment control.
SIAM应用数学杂志,出版前。摘要。HIV治疗后控制器(PTC)的存在为HIV功能性治愈提供了希望,而了解决定PTC的关键机制是实现这一目标的关键一步。在这里,我们通过分析建立的HIV病毒动力学数学模型来研究这些机制。在数学模型中,关键机制是由影响临界点的参数来表示的,以诱导质量不同的动力学,并且在具有多重稳定性的情况下,系统的初始条件也在决定解的命运中起作用。因此,对于参数空间中的临界点,我们开发并实施了相关分支阈值条件的敏感性分析,以确定该模型的关键机制。我们的结果表明,感染细胞的死亡率和细胞毒性T淋巴细胞增殖的饱和参数显著影响治疗后的控制。对于具有多重稳定性的情况,在初始条件的状态空间中,我们首先研究了鞍型平衡点,以确定其稳定流形,该流形划分了与高、低病毒设定点相关的捕获区域。鉴定的稳定流形在治疗结束时为免疫细胞和HIV病毒的负荷提供指导,以实现治疗后的控制。
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引用次数: 0
Sliding-Mode Theory Under Feedback Constraints and the Problem of Epidemic Control 反馈约束下的滑模理论与流行病控制问题
4区 数学 Q1 MATHEMATICS, APPLIED Pub Date : 2023-11-15 DOI: 10.1137/22m1535309
Mauro Bisiacco, Gianluigi Pillonetto
One of the most important branches of nonlinear control theory of dynamical systems is the so-called sliding mode. Its aim is the design of a (nonlinear) feedback law that brings and maintains the state trajectory of a dynamic system on a given sliding surface. Here, dynamics become completely independent of the model parameters and can be tuned accordingly to the desired target. In this paper we study this problem when the feedback law is subject to strong structural constraints. In particular, we assume that the control input may take values only over two bounded and disjoint sets. Such sets could be also not perfectly known a priori. An example is a control input allowed to switch only between two values. Under these peculiarities, we derive the necessary and sufficient conditions that guarantee sliding-mode control effectiveness for a class of time-varying continuous-time linear systems that includes all the stationary state-space linear models. Our analysis covers several scientific fields. It is only apparently confined to the linear setting and also allows one study an important set of nonlinear models. We describe fundamental examples related to epidemiology where the control input is the level of contact rate among people and the sliding surface permits to control the number of infected. We prove the global convergence of epidemic sliding-mode control schemes applied to two popular dynamical systems used in epidemiology, i.e., SEIR and SAIR, and based on the introduction of severe restrictions like lockdowns. Results obtained in the literature regarding control of many other epidemiological models are also generalized by casting them within a general sliding-mode theory.
动态系统的非线性控制理论的一个最重要的分支是所谓的滑模。它的目的是设计一个(非线性)反馈律,在给定的滑动表面上带来并保持动态系统的状态轨迹。在这里,动力学变得完全独立于模型参数,并且可以根据期望的目标进行相应的调整。本文研究了反馈律受强结构约束时的这一问题。特别地,我们假设控制输入只能取两个有界且不相交的集合上的值。这些集合也可能不是完全先验的。一个例子是只允许在两个值之间切换的控件输入。在这些特性下,我们得到了一类包含所有稳态空间线性模型的时变连续线性系统滑模控制有效性的充分必要条件。我们的分析涵盖了几个科学领域。它显然只局限于线性设置,也允许研究一组重要的非线性模型。我们描述了与流行病学相关的基本例子,其中控制输入是人与人之间的接触率水平,滑动表面允许控制感染人数。我们证明了流行病滑模控制方案的全球收敛性,应用于流行病学中常用的两种动态系统,即SEIR和SAIR,并基于引入严格的限制,如封锁。文献中关于控制许多其他流行病学模型的结果也通过将它们置于一般滑模理论中而得到推广。
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引用次数: 0
Fast Solver for Diffusive Transport Times on Dynamic Intracellular Networks 动态胞内网络上扩散传输时间的快速求解器
4区 数学 Q1 MATHEMATICS, APPLIED Pub Date : 2023-11-14 DOI: 10.1137/22m1509308
Lachlan Elam, Mónica C. Quiñones-Frías, Ying Zhang, Avital A. Rodal, Thomas G. Fai
. The transport of particles in cells is influenced by the properties of intracellular networks they traverse while searching for localized target regions or reaction partners. Moreover, given the rapid turnover in many intracellular structures, it is crucial to understand how temporal changes in the network structure affect diffusive transport. In this work, we use network theory to characterize complex intracellular biological environments across scales. We develop both a coarse-grained model and an efficient computational method to compute the mean first passage times for simulating a particle diffusing along two-dimensional planar networks extracted from fluorescence microscopy imaging. We first benchmark this methodology in the context of synthetic networks, and subsequently apply it to live-cell data from endoplasmic reticulum tubular networks.
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引用次数: 0
On Spatial Cohesiveness of Second-Order Self-Propelled Swarming Systems 二阶自走群系统的空间内聚性研究
4区 数学 Q1 MATHEMATICS, APPLIED Pub Date : 2023-11-09 DOI: 10.1137/23m1553388
Constantine Medynets, Irina Popovici
The study of emergent behavior of swarms is of great interest for applied sciences. One of the most fundamental questions for self-organizing swarms is whether the swarms disperse or remain in a spatially cohesive configuration. In this paper we study dissipativity properties and spatial cohesiveness of the swarm of self-propelled particles governed by the model , where , , and is a symmetric positive semidefinite matrix. The self-propulsion term is assumed to be continuously differentiable and to grow faster than , that is, as . We establish that the velocity and acceleration of the particles are ultimately bounded. We show that when is trivial, the positions of the particles are also ultimately bounded. For systems with , we show that, while the system might infinitely drift away from its initial location, the particles remain within a bounded distance from the generalized center of mass of the system, which geometrically coincides with the weighted average of agent positions. The weights are determined by the coefficients of the projection matrix onto . We also discuss the ultimate boundedness for systems with bounded coupling, including the Morse potential systems, and systems governed by power-law potentials with strong repulsion properties. We show that the former systems are ultimately bounded in the velocity-acceleration domain, whereas the models based on the power-law potentials are not.
蜂群涌现行为的研究是应用科学研究的热点。自组织群体的一个最基本的问题是群体是分散还是保持在一个空间内聚的结构中。本文研究了受该模型支配的自走粒子群的耗散性和空间内聚性,其中,为对称正半定矩阵。假设自推进项是连续可微的,并且增长速度快于,即。我们确定粒子的速度和加速度最终是有界的。我们证明当是平凡的,粒子的位置最终也是有界的。对于具有的系统,我们表明,当系统可能无限地远离其初始位置时,粒子保持在距离系统广义质心的有限距离内,该距离在几何上与代理位置的加权平均值一致。权值由投影矩阵的系数决定。我们还讨论了有界耦合系统的最终有界性,包括莫尔斯势系统和具有强斥力的幂律势控制的系统。我们证明了前一种系统最终在速度-加速度域中是有界的,而基于幂律势的模型则不是。
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引用次数: 2
Wearable Data Assimilation to Estimate the Circadian Phase 可穿戴数据同化以估计昼夜节律阶段
4区 数学 Q1 MATHEMATICS, APPLIED Pub Date : 2023-11-09 DOI: 10.1137/22m1509680
Dae Wook Kim, Minki P. Lee, Daniel B. Forger
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引用次数: 0
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SIAM Journal on Applied Mathematics
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