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Numerical modelling of the transition of infected cells and virions between two lymph nodes in a stochastic model of HIV-1 infection 在HIV-1感染的随机模型中感染细胞和病毒粒子在两个淋巴结间转移的数值模拟
IF 0.6 4区 数学 Q2 Mathematics Pub Date : 2021-11-01 DOI: 10.1515/rnam-2021-0024
N. Pertsev, V. Topchii, K. Loginov
Abstract The paper is focused on stochastic modelling of the process of transition of infected cells and virions of HIV-1 infection between two lymph nodes. The model is based on the following assumptions: (1) the duration of transition of infected cells and virions between two lymph nodes is set using a time-dependent function, (2) infected cells produce virions in the process of transition between two lymph nodes, (3) infected cells and virions may die when moving between two lymph nodes. The methods of the theory of branching random processes are used to study analytically the model variables. An algorithm for statistical modelling of the number of infected cells and virions in the second lymph node is presented. The results of computational experiments studying the distribution law of the number of virions produced by one infected cell depending on the duration of movement between two lymph nodes are presented.
摘要本文研究了HIV-1感染细胞和病毒粒子在两个淋巴结间转移过程的随机模型。该模型基于以下假设:(1)感染细胞和病毒粒子在两个淋巴结之间转移的持续时间使用时间依赖函数设定;(2)感染细胞在两个淋巴结之间转移的过程中产生病毒粒子;(3)感染细胞和病毒粒子在两个淋巴结之间移动时可能死亡。利用分支随机过程理论的方法对模型变量进行了解析研究。提出了一种用于统计第二淋巴结感染细胞和病毒粒子数量的算法。本文介绍了一个感染细胞产生的病毒粒子数量随两个淋巴结间运动时间的分布规律的计算实验结果。
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引用次数: 1
Numerical evaluation of the effectiveness of coronary revascularization 冠状动脉血运重建有效性的数值评估
IF 0.6 4区 数学 Q2 Mathematics Pub Date : 2021-11-01 DOI: 10.1515/rnam-2021-0025
S. Simakov, T. Gamilov, F. Liang, D. Gognieva, Mariam K. Gappoeva, P. Kopylov
Abstract In the present paper we construct the model of coronary flow which utilizes the patient’s CT data on both large CA and perfusion. We reconstruct large coronary vessels based on the CT data and extrude possibly invisible vessels from the branches of the left coronary artery so that every terminal point supply every of standardized zone of myocardium. We apply a previously developed and validated 1D model of haemodynamics. Utilizing the patient-specific CTP data for modifying outflow terminal resistance at rest and under stress conditions is the major novelty of the present work. From our results it follows that acceptable values of fractional flow reserve (FFR) after the stenotic treatment may produce false negative output. Therefore healthy FFR values may be observed after ineffective revascularization. We also conclude that microvascular perfusion impairment plays significant role in correct computational estimation of haemodynamic indices before stenotic treatment. The advantage of the presented approach is the availability of transmural perfusion ratio assessment in everyday practice.
摘要在本文中,我们构建了冠状动脉血流模型,该模型利用了患者在大CA和灌注方面的CT数据。我们根据CT数据重建大的冠状动脉血管,并从左冠状动脉的分支中挤出可能不可见的血管,使每个终点都能提供心肌的每个标准区。我们应用了先前开发和验证的血液动力学1D模型。利用患者特异性CTP数据来修改静息和应激条件下的流出端阻力是本工作的主要新颖之处。根据我们的结果,狭窄治疗后血流储备分数(FFR)的可接受值可能会产生假阴性输出。因此,在无效的血运重建后可以观察到健康的FFR值。我们还得出结论,微血管灌注损伤在狭窄治疗前血流动力学指标的正确计算估计中起着重要作用。所提出的方法的优点是在日常实践中可以进行跨壁灌注比率评估。
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引用次数: 6
Herd immunity levels and multi-strain influenza epidemics in Russia: a modelling study 俄罗斯群体免疫水平和多株流感流行:一项模型研究
IF 0.6 4区 数学 Q2 Mathematics Pub Date : 2021-11-01 DOI: 10.1515/rnam-2021-0023
V. Leonenko
Abstract In the present paper, we consider a compartmental epidemic model which simulates the co-circulation of three influenza strains, A(H1N1)pdm09, A(H3N2), and B, in a population with the history of exposure to these virus strains. A strain-specific incidence data for the model input was generated using long-term weekly ARI incidence and virologic testing data. The algorithm for model calibration was developed as a combination of simulated annealing and BFGS optimization methods. Two simulations were carried out, assuming the absence and the presence of protected individuals in the population, with 2017– 2018 and 2018–2019 epidemic seasons in Moscow as a case study. It was shown that strain-specific immune levels defined by virologic studies might be used in the model to obtain plausible incidence curves. However, different output parameter values, such as fractions of individuals exposed to particular virus strain in the previous epidemic season, can correspond to similar incidence trajectories, which complicates the assessment of herd immunity levels based on the model calibration. The results of the study will be used in the research of the interplay between the immunity formation dynamics and the circulation of influenza strains in Russian cities.
摘要在本文中,我们考虑了一个分区流行病模型,该模型模拟了三种流感毒株,a(H1N1)pdm09、a(H3N2)和B,在有接触这些病毒株历史的人群中的共同循环。使用长期每周ARI发病率和病毒学检测数据生成模型输入的菌株特异性发病率数据。模型校准算法是将模拟退火和BFGS优化方法相结合而开发的。假设人群中不存在和存在受保护的个体,进行了两次模拟,以莫斯科的2017-2018年和2018-2019年疫情季节为例进行了研究。研究表明,病毒学研究定义的菌株特异性免疫水平可用于该模型,以获得合理的发病率曲线。然而,不同的输出参数值,例如在上一个流行季节暴露于特定病毒株的个体的分数,可能对应于相似的发病轨迹,这使基于模型校准的群体免疫水平评估变得复杂。这项研究的结果将用于研究免疫形成动力学与俄罗斯城市流感毒株传播之间的相互作用。
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引用次数: 2
Two-scale haemodynamic modelling for patients with Fontan circulation Fontan循环患者的双尺度血流动力学模型
IF 0.6 4区 数学 Q2 Mathematics Pub Date : 2021-11-01 DOI: 10.1515/rnam-2021-0022
T. Dobroserdova, Y. Vassilevski, S. Simakov, T. Gamilov, A. Svobodov, L. Yurpolskaya
Abstract Palliation of congenital single ventricle heart defects suggests multi-stage surgical interventions that divert blood flow from the inferior and superior vena cava directly to the right and left pulmonary arteries, skipping the right ventricle. Such system with cavopulmonary anastomoses and single left ventricle is called Fontan circulation, and the region of reconnection is called the total cavopulmonary connection (TCPC). Computational blood flow models allow clinicians to predict the results of the Fontan operation, to choose an optimal configuration of TCPC and thus to reduce negative postoperative consequences. We propose a two-scale (1D3D) haemodynamic model of systemic circulation for a patient who has underwent Fontan surgical operation. We use CT and 4D flow MRI data to personalize the model. The model is tuned to patient’s data and is able to represent measured time-averaged flow rates at the inlets and outlets of TCPC, as well as pressure in TCPC for the patient in horizontal position.We demonstrate that changing to quiescent standing position leads to other patterns of blood flow in regional (TCPC) and global haemodynamics. This confirms clinical data on exercise intolerance of Fontan patients.
摘要缓解先天性单心室心脏缺陷需要多阶段的手术干预,将下腔静脉和上腔静脉的血流直接转移到左右肺动脉,跳过右心室。这种具有腔肺吻合和单个左心室的系统被称为Fontan循环,重新连接的区域被称为全腔肺连接(TCPC)。计算血流模型使临床医生能够预测Fontan手术的结果,选择TCPC的最佳配置,从而减少术后的负面后果。我们为一名接受Fontan手术的患者提出了一个系统循环的双尺度(1D3D)血液动力学模型。我们使用CT和4D流MRI数据对模型进行个性化设置。该模型根据患者的数据进行了调整,能够表示TCPC入口和出口处测量的时间平均流速,以及处于水平位置的患者的TCPC中的压力。我们证明,改变为静止站立姿势会导致区域(TCPC)和全球血流动力学的其他模式。这证实了Fontan患者运动不耐受的临床数据。
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引用次数: 1
Frontiers in mathematical modelling of the lipid metabolism under normal conditions and its alterations in heart diseases 正常情况下脂质代谢的数学模型及其在心脏病中的变化的前沿
IF 0.6 4区 数学 Q2 Mathematics Pub Date : 2021-11-01 DOI: 10.1515/rnam-2021-0021
G. Bocharov, D. Grebennikov, R. Savinkov
Abstract Pathophysiology of ischemic heart disease is a complex phenomenon determined by the interaction of multiple processes including the inflammatory, immunological, infectious, mechanical, biochemical and epigenetic ones. A predictive clinically relevant modelling of the entire trajectory of the human organism, from the initial alterations in lipid metabolism through to atherosclerotic plaque formation and finally to the pathologic state of the ischemic heart disease, is an open insufficiently explored problem. In the present review, we consider the existing mathematical frameworks which are used to describe, analyze and predict the dynamics of various processes related to cardiovascular diseases at the molecular, cellular, tissue, and holistic human organism level. The mechanistic, statistical and machine learning models are discussed in detail with special focus on the underlying assumptions and their clinical relevance. All together, they provide a solid computational platform for further expansion and tailoring for practical applications.
缺血性心脏病的病理生理是炎症、免疫、感染、机械、生化、表观遗传等多个过程共同作用的复杂现象。从最初的脂质代谢改变到动脉粥样硬化斑块形成,最后到缺血性心脏病的病理状态,人类机体整个轨迹的预测临床相关建模是一个尚未充分探索的开放性问题。在本综述中,我们考虑了现有的数学框架,用于描述,分析和预测在分子,细胞,组织和整体人体有机体水平上与心血管疾病相关的各种过程的动力学。详细讨论了机制、统计和机器学习模型,特别关注潜在的假设及其临床相关性。总之,它们为进一步扩展和裁剪实际应用提供了一个坚实的计算平台。
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引用次数: 0
A regularized isothermal phase-field model of two-phase solid–fluid mixture and its spatial dissipative discretization equations 固液两相混合物的正则化等温相场模型及其空间耗散离散化方程
IF 0.6 4区 数学 Q2 Mathematics Pub Date : 2021-08-01 DOI: 10.1515/rnam-2021-0017
V. Balashov
Abstract The present paper is devoted to a model describing a two-phase isothermal mixture, in which one of the phases obeys solid-like (namely, elastic) rheology. A fully Eulerian description is considered. To describe the stress–strain behaviour of the solid phase the elastic energy term is added to the Helmholtz free energy. The term depends on Almansi strain tensor. In its turn, the strain tensor is defined as the solution of the corresponding evolutionary equation. Considered model belongs to the phase field family. Formally it describes two-component mixture and uses mass densities of the components as order parameters. A distinctive feature of the considered model is its preliminary regularization according to the quasi-hydrodynamic framework. The dissipativity in total energy is proved when periodic boundary conditions are imposed. A spatial dissipative semi-discrete (continuous in time and discrete in space) scheme based on staggered grids is suggested. The theoretical results remain valid in the absence of the regularization. The results of a numerical study in a 2D setting are presented.
摘要本文致力于描述两相等温混合物的模型,其中一相服从固体状(即弹性)流变。考虑一个完全欧拉的描述。为了描述固相的应力-应变行为,在亥姆霍兹自由能中加入弹性能项。这一项取决于Almansi应变张量。反过来,应变张量被定义为相应演化方程的解。所考虑的模型属于相场族。形式上,它描述双组分混合物,并使用组分的质量密度作为序参数。所考虑的模型的一个显著特征是它根据准流体动力框架进行了初步正则化。在周期边界条件下,证明了总能量的耗散率。提出了一种基于交错网格的空间耗散半离散(时间连续,空间离散)方案。在没有正则化的情况下,理论结果仍然有效。本文给出了二维环境下的数值研究结果。
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引用次数: 1
Stability analysis of implicit semi-Lagrangian methods for numerical solution of non-hydrostatic atmospheric dynamics equations 非流体静力大气动力学方程数值解的隐式半拉格朗日方法的稳定性分析
IF 0.6 4区 数学 Q2 Mathematics Pub Date : 2021-08-01 DOI: 10.1515/rnam-2021-0020
V. Shashkin
Abstract The stability of implicit semi-Lagrangian schemes for time-integration of the non-hydrostatic atmosphere dynamics equations is analyzed in the present paper. The main reason for the instability of the considered class of schemes is the semi-Lagrangian advection of stratified thermodynamic variables coupled to the fixed point iteration method used to solve the implicit in time upstream trajectory computation problem. We identify two types of unstable modes and obtain stability conditions in terms of the scheme parameters. Stabilization of sound modes requires the use of a pressure reference profile and time off-centering. Gravity waves are stable only for an even number of fixed point method iterations. The maximum time step is determined by inverse buoyancy frequency in the case when the reference profile of the potential temperature is not used. Generally, applying time off-centering and reference profile to pressure variable is necessary for stability. Using reference profile for potential temperature and an even number of the iterations allows one to significantly increase the maximum time-step value.
本文分析了非静力大气动力学方程时间积分的隐式半拉格朗日格式的稳定性。所考虑的一类方案不稳定的主要原因是分层热力学变量的半拉格朗日平流与用于解决隐式时间上游轨迹计算问题的不动点迭代方法相耦合。我们识别了两种类型的不稳定模式,并根据方案参数获得了稳定条件。声音模式的稳定需要使用压力参考剖面和时间偏离中心。重力波只对偶数次的不动点方法迭代是稳定的。在不使用潜在温度的参考剖面的情况下,最大时间步长由反浮力频率确定。一般来说,将偏心时间和参考剖面应用于压力变量对于稳定性是必要的。使用潜在温度的参考轮廓和偶数次迭代允许显著增加最大时间步长值。
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引用次数: 0
The suite of Taylor–Galerkin class schemes for ice transport on sphere implemented by the INMOST package 由INMOST包实现的球上冰传输的Taylor-Galerkin类方案集
IF 0.6 4区 数学 Q2 Mathematics Pub Date : 2021-08-01 DOI: 10.1515/rnam-2021-0019
Sergey S. Petrov, N. Iakovlev
Abstract Realizations of the numerical solution of the scalar transport equation on the sphere, written in divergent form, are presented. Various temporal discretizations are considered: the one-step Taylor–Galerkin method (TG2), the two-step Taylor–Galerkin method of the second (TTG2), third (TTG3), and fourth (TTG4) orders. The standard Finite-Element Galerkin method with linear basis functions on a triangle is applied as spatial discretization. The flux correction technique (FCT) is implemented. Test runs are carried out with different initial profiles: a function from C∞ (Gaussian profile) and a discontinuous function (slotted cylinder). The profiles are advected by reversible, nondivergent velocity fields, therefore the initial distribution coincides with the final one. The case of a divergent velocity field is also considered to test the conservation and positivity properties of the schemes. It is demonstrated that TG2, TTG3, and TTG4 schemes with FCT applied give the best result for small Courant numbers, and TTG2, TTG4 are preferable in case of large Courant number. However, TTG2+FCT scheme has the worst stability. The use of FCT increases the integral errors, but ensures that the solution is positive with high accuracy. The implemented schemes are included in the dynamic core of a new sea ice model developed using the INMOST package. The acceleration of the parallel program and solution convergence with spatial resolution are demonstrated.
摘要给出了用发散形式写成的球上标量输运方程数值解的实现。考虑了各种时间离散化:一阶Taylor–Galerkin方法(TG2)、二阶(TTG2)、三阶(TTG3)和四阶(TTG4)的两阶Taylor–Gallerkin方法。将三角形上具有线性基函数的标准有限元伽辽金方法应用于空间离散化。实现了通量校正技术(FCT)。使用不同的初始轮廓进行了试运行:一个来自C∞的函数(高斯轮廓)和一个不连续函数(开槽圆柱体)。剖面被可逆的非分散速度场平推,因此初始分布与最终分布一致。还考虑了发散速度场的情况来检验方案的守恒性和正性。结果表明,应用FCT的TG2、TTG3和TTG4方案对于小Courant数给出了最好的结果,而对于大Courant数,TTG2、TTG4是优选的。然而,TTG2+FCT方案的稳定性最差。FCT的使用增加了积分误差,但确保了高精度的正解。所实施的方案包含在使用INMOST软件包开发的新海冰模型的动态核心中。证明了并行程序的加速性和解在空间分辨率下的收敛性。
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引用次数: 1
New correlative randomized algorithms for statistical modelling of radiation transfer in stochastic medium 随机介质辐射传递统计建模的新相关随机化算法
IF 0.6 4区 数学 Q2 Mathematics Pub Date : 2021-08-01 DOI: 10.1515/rnam-2021-0018
G. Mikhailov, I. N. Medvedev
Abstract Correlative randomized algorithms are constructed by simple randomization of the algorithm of maximum cross-section (equalization, delta tracking) with the use of a one-dimensional distribution and the correlation function or only correlation length of a random medium. The value of the used correlation length can be adjusted using simple test studies. The calculations carried out confirmed the practical effectiveness of the new algorithms.
摘要相关随机化算法是通过使用一维分布和随机介质的相关函数或仅相关长度对最大截面算法(均衡、delta跟踪)进行简单随机化而构建的。可以使用简单的测试研究来调整所使用的相关长度的值。所进行的计算证实了新算法的实际有效性。
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引用次数: 2
Model reduction for Smoluchowski equations with particle transfer 具有粒子转移的Smoluchowski方程的模型约简
IF 0.6 4区 数学 Q2 Mathematics Pub Date : 2021-06-01 DOI: 10.1515/rnam-2021-0015
I. Timokhin, S. Matveev, E. Tyrtyshnikov, A. Smirnov
Abstract In this paper we consider the problem of modelling a system of aggregating particles, that are being transported with stationary velocities dependent on masses of the particles in one-dimensional case. A numerical method based on the ideas of POD (Proper Orthogonal Decomposition) is constructed, and its capacity to speed up the solution up to 40 times is demonstrated.
摘要在本文中,我们考虑了聚集粒子系统的建模问题,在一维情况下,聚集粒子以取决于粒子质量的静止速度传输。构造了一种基于POD(适当正交分解)思想的数值方法,并证明了其将求解速度提高到40倍的能力。
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引用次数: 1
期刊
Russian Journal of Numerical Analysis and Mathematical Modelling
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