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Mathematical modeling, analysis, and simulation of the COVID-19 pandemic with explicit and implicit behavioral changes 具有显性和隐性行为变化的新冠肺炎大流行的数学建模、分析和模拟
Q2 Mathematics Pub Date : 2020-01-01 DOI: 10.1515/cmb-2020-0113
Comfort Ohajunwa, Kirthi Kumar, P. Seshaiyer
Abstract As COVID-19 cases continue to rise globally, many researchers have developed mathematical models to help capture the dynamics of the spread of COVID-19. Specifically, the compartmental SEIR model and its variations have been widely employed. These models differ in the type of compartments included, nature of the transmission rates, seasonality, and several other factors. Yet, while the spread of COVID-19 is largely attributed to a wide range of social behaviors in the population, several of these SEIR models do not account for such behaviors. In this project, we consider novel SEIR-based models that incorporate various behaviors. We created a baseline model and explored incorporating both explicit and implicit behavioral changes. Furthermore, using the Next Generation Matrix method, we derive a basic reproduction number, which indicates the estimated number of secondary cases by a single infected individual. Numerical simulations for the various models we made were performed and user-friendly graphical user interfaces were created. In the future, we plan to expand our project to account for the use of face masks, age-based behaviors and transmission rates, and mixing patterns.
随着COVID-19病例在全球范围内持续上升,许多研究人员开发了数学模型来帮助捕捉COVID-19的传播动态。具体来说,分区SEIR模型及其变体已被广泛应用。这些模型在包括的隔间类型、传播率的性质、季节性和其他几个因素方面有所不同。然而,尽管COVID-19的传播在很大程度上归因于人群中广泛的社会行为,但其中一些SEIR模型并未考虑到这些行为。在这个项目中,我们考虑了包含各种行为的基于seir的新型模型。我们创建了一个基线模型,并探索将显性和隐性行为变化结合起来。此外,使用下一代矩阵方法,我们得到了一个基本的繁殖数,它表示单个感染个体的估计继发病例数。对我们制作的各种模型进行了数值模拟,并创建了用户友好的图形用户界面。在未来,我们计划扩展我们的项目,以考虑口罩的使用,基于年龄的行为和传播率,以及混合模式。
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引用次数: 7
Pharmacokinetics and Pharmacodynamics Models of Tumor Growth and Anticancer Effects in Discrete Time 肿瘤生长和抗癌作用的离散时间药代动力学和药效学模型
Q2 Mathematics Pub Date : 2020-01-01 DOI: 10.1515/cmb-2020-0105
F. Atici, Ngoc Nguyen, Kamala Dadashova, S. E. Pedersen, G. Koch
Abstract We study the h-discrete and h-discrete fractional representation of a pharmacokinetics-pharmacodynamics (PK-PD) model describing tumor growth and anticancer effects in continuous time considering a time scale h𝕅0, where h > 0. Since the measurements of the drug concentration in plasma were taken hourly, we consider h = 1/24 and obtain the model in discrete time (i.e. hourly). We then continue with fractionalizing the h-discrete nabla operator in the h-discrete model to obtain the model as a system of nabla h-fractional difference equations. In order to solve the fractional h-discrete system analytically we state and prove some theorems in the theory of discrete fractional calculus. After estimating and getting confidence intervals of the model parameters, we compare residual squared sum values of the models in one table. Our study shows that the new introduced models provide fitting as good as the existing models in continuous time.
我们研究了连续时间内描述肿瘤生长和抗癌作用的药代动力学-药效学(PK-PD)模型的h离散和h离散分数表示,考虑时间尺度h𝕅0,其中h > 0。由于血浆中药物浓度的测量是每小时进行一次,我们考虑h = 1/24,并以离散时间(即每小时)获得模型。然后,我们继续对h离散模型中的h离散nabla算子进行分数化,以得到作为nabla h分数阶差分方程系统的模型。为了解析解分数阶h离散系统,叙述并证明了离散分数阶微积分理论中的一些定理。在估计和得到模型参数的置信区间后,我们将模型的残差平方和值放在一张表中进行比较。研究表明,在连续时间条件下,新模型的拟合效果与现有模型一样好。
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引用次数: 14
A reaction-diffusion system to better comprehend the unlockdown: Application of SEIR-type model with diffusion to the spatial spread of COVID-19 in France 更好理解解锁的反应扩散系统:带扩散的SEIR型模型在法国新冠肺炎空间传播中的应用
Q2 Mathematics Pub Date : 2020-01-01 DOI: 10.1515/cmb-2020-0104
Y. Mammeri
Abstract We wondered that if a reaction-diffusion model considering only the mean daily movement of susceptible, exposed and asymptomatic individuals was enough to describe the spread of the COVID-19 virus. The model was calibrated using data on the confirmed infection and death from France as well as their initial spatial distribution. First, the system of partial differential equations is studied, then the basic reproduction number, 𝒭0 is derived. Second, numerical simulations, based on a combination of level-set and finite differences, shown the spatial spread of COVID-19 from March 16 to June 16. Finally, scenarios of unlockdown are compared according to variation of distancing, or partially spatial lockdown.
我们想知道,仅考虑易感、暴露和无症状个体的平均每日运动量的反应-扩散模型是否足以描述COVID-19病毒的传播。该模型使用来自法国的确诊感染和死亡数据及其初始空间分布进行校准。首先对偏微分方程组进行了研究,然后推导出了偏微分方程组的基本再现数𝒭0。其次,基于水平集和有限差分相结合的数值模拟显示了3月16日至6月16日COVID-19的空间传播。最后,根据距离的变化,或部分空间封锁,比较了解除封锁的情景。
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引用次数: 31
On Linear Growth in COVID-19 Cases 新冠肺炎病例线性增长研究
Q2 Mathematics Pub Date : 2020-01-01 DOI: 10.1101/2020.06.19.20135640
M. Grinfeld, P. Mulheran
Abstract We present an elementary model of COVID-19 propagation that makes explicit the connection between testing strategies and rates of transmission and the linear growth in new cases observed in many parts of the world.
摘要我们提出了新冠肺炎传播的基本模型,该模型明确了检测策略和传播率与世界许多地区观察到的新病例线性增长之间的联系。
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引用次数: 2
The Weighted Gaussian Curvature Derivative of a Space-Filling Diagram 空间填充图的加权高斯曲率导数
Q2 Mathematics Pub Date : 2019-08-19 DOI: 10.1515/cmb-2020-0101
A. Akopyan, H. Edelsbrunner
Abstract The morphometric approach [11, 14] writes the solvation free energy as a linear combination of weighted versions of the volume, area, mean curvature, and Gaussian curvature of the space-filling diagram. We give a formula for the derivative of the weighted Gaussian curvature. Together with the derivatives of the weighted volume in [7], the weighted area in [4], and the weighted mean curvature in [1], this yields the derivative of the morphometric expression of solvation free energy.
摘要形态计量方法[11,14]将溶剂化自由能写成空间填充图的体积、面积、平均曲率和高斯曲率的加权版本的线性组合。我们给出了加权高斯曲率导数的一个公式。与[7]中的加权体积、[4]中的加权面积和[1]中的加权平均曲率的导数一起,这产生了溶剂化自由能的形态计量表达式的导数。
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引用次数: 4
The Weighted Mean Curvature Derivative of a Space-Filling Diagram 空间填充图的加权平均曲率导数
Q2 Mathematics Pub Date : 2019-08-19 DOI: 10.1515/cmb-2020-0100
A. Akopyan, H. Edelsbrunner
Abstract Representing an atom by a solid sphere in 3-dimensional Euclidean space, we get the space-filling diagram of a molecule by taking the union. Molecular dynamics simulates its motion subject to bonds and other forces, including the solvation free energy. The morphometric approach [12, 17] writes the latter as a linear combination of weighted versions of the volume, area, mean curvature, and Gaussian curvature of the space-filling diagram. We give a formula for the derivative of the weighted mean curvature. Together with the derivatives of the weighted volume in [7], the weighted area in [3], and the weighted Gaussian curvature [1], this yields the derivative of the morphometric expression of the solvation free energy.
在三维欧几里得空间中用实心球表示原子,通过取并得到分子的空间填充图。分子动力学模拟其受化学键和其他力(包括溶剂化自由能)影响的运动。形态计量学方法[12,17]将后者写为空间填充图的体积、面积、平均曲率和高斯曲率的加权版本的线性组合。我们给出了加权平均曲率导数的公式。再加上加权体积[7]的导数,加权面积[3]的导数,加权高斯曲率[1]的导数,就得到了溶剂化自由能的形态计量表达式的导数。
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引用次数: 4
A simple algorithm to compute link polynomials defined by using skein relations 利用skein关系计算链路多项式的一种简单算法
Q2 Mathematics Pub Date : 2019-08-10 DOI: 10.1515/cmb-2020-0102
Xuezhi Zhao
Abstract We give a simple and practical algorithm to compute the link polynomials, which are defined according to the skein relations. Our method is based on a new total order on the set of all braid representatives. As by-product a new complete link invariant are obtained.
摘要给出了一种简单实用的计算链路多项式的算法,该算法是根据串线关系定义的。我们的方法是基于所有辫子代表集合上的一个新的总顺序。作为副产物,得到了一个新的完全连杆不变量。
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引用次数: 0
Improving RNA secondary structure prediction via state inference with deep recurrent neural networks 基于深度递归神经网络状态推理的RNA二级结构预测改进
Q2 Mathematics Pub Date : 2019-06-26 DOI: 10.1515/cmb-2020-0002
Devin Willmott, D. Murrugarra, Q. Ye
Abstract The problem of determining which nucleotides of an RNA sequence are paired or unpaired in the secondary structure of an RNA, which we call RNA state inference, can be studied by different machine learning techniques. Successful state inference of RNA sequences can be used to generate auxiliary information for data-directed RNA secondary structure prediction. Typical tools for state inference, such as hidden Markov models, exhibit poor performance in RNA state inference, owing in part to their inability to recognize nonlocal dependencies. Bidirectional long short-term memory (LSTM) neural networks have emerged as a powerful tool that can model global nonlinear sequence dependencies and have achieved state-of-the-art performances on many different classification problems. This paper presents a practical approach to RNA secondary structure inference centered around a deep learning method for state inference. State predictions from a deep bidirectional LSTM are used to generate synthetic SHAPE data that can be incorporated into RNA secondary structure prediction via the Nearest Neighbor Thermodynamic Model (NNTM). This method produces predicted secondary structures for a diverse test set of 16S ribosomal RNA that are, on average, 25 percentage points more accurate than undirected MFE structures. Accuracy is highly dependent on the success of our state inference method, and investigating the global features of our state predictions reveals that accuracy of both our state inference and structure inference methods are highly dependent on the similarity of pairing patterns of the sequence to the training dataset. Availability of a large training dataset is critical to the success of this approach. Code available at https://github.com/dwillmott/rna-state-inf.
摘要可以通过不同的机器学习技术来研究确定RNA序列的哪些核苷酸在RNA的二级结构中成对或不成对的问题,我们称之为RNA状态推断。RNA序列的成功状态推断可用于生成用于数据导向的RNA二级结构预测的辅助信息。用于状态推理的典型工具,如隐马尔可夫模型,在RNA状态推理中表现出较差的性能,部分原因是它们无法识别非局部依赖性。双向长短期记忆(LSTM)神经网络已成为一种强大的工具,可以对全局非线性序列相关性进行建模,并在许多不同的分类问题上取得了最先进的性能。本文围绕状态推理的深度学习方法,提出了一种实用的RNA二级结构推理方法。来自深度双向LSTM的状态预测用于生成合成的SHAPE数据,该数据可以通过最近邻热力学模型(NNTM)纳入RNA二级结构预测。这种方法为不同的16S核糖体RNA测试集产生预测的二级结构,平均比无向MFE结构准确25个百分点。准确性在很大程度上取决于我们的状态推理方法的成功,研究我们的状态预测的全局特征表明,我们的状态推断和结构推断方法的准确性都高度依赖于序列的配对模式与训练数据集的相似性。大型训练数据集的可用性对该方法的成功至关重要。代码可在https://github.com/dwillmott/rna-state-inf.
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引用次数: 12
Thermal Response in Cellulose Iβ Based on Molecular Dynamics 基于分子动力学的纤维素Iβ的热响应
Q2 Mathematics Pub Date : 2019-01-01 DOI: 10.1515/cmb-2019-0007
Xuewei Jiang, Yu Chen, Yue Yuan, Lu Zheng
Abstract The structural details of cellulose I β were discussed according to molecular dynamics simulations with the GLYCAM-06 force field. The simulation outcomes were in agreement with previous experimental data, including structural parameters and hydrogen bond pattern at 298 K. We found a new conformation of cellulose Iβ existed at the intermediate temperature that is between the low and high temperatures. Partial chain rotations along the backbone direction were found and conformations of hydroxymethyl groups that alternated from tg to either gt or gg were observed when the temperature increased from 298 K to 400 K. In addition, the gg conformation is preferred than gt. For the structure adopted at high temperature of 500 K, major chains were twisted and two chains detached from each plain. In contrast to the observation under intermediate temperature, the population of hydroxymethyl groups in gt exceeded that in gg conformation at high temperature. In addition, three patterns of hydrogen bonding were identified at low, intermediate and high temperatures in the simulations. The provided structural information indicated the transitions occurred around 350 K and 450 K, considered as the transitional temperatures of cellulose Iβ in this work.
摘要利用GLYCAM-06力场进行分子动力学模拟,讨论了纤维素Iβ的结构细节。模拟结果与先前的实验数据一致,包括298K下的结构参数和氢键模式。我们发现纤维素Iβ在介于低温和高温之间的中间温度下存在一种新的构象。当温度从298K增加到400K时,发现了沿主链方向的部分链旋转,并观察到羟甲基从tg到gt或gg交替的构象。此外,gg构象比gt更优选。对于在500K的高温下采用的结构,主链扭曲,每个平面上有两条链分离。与在中等温度下的观察相反,在高温下,gt中的羟甲基基团的数量超过了gg构象中的羟基。此外,在模拟中,在低温、中温和高温下确定了三种氢键模式。所提供的结构信息表明,转变发生在350K和450K左右,在本工作中被认为是纤维素Iβ的转变温度。
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引用次数: 3
Using computational approaches to study dengue virus capsid assembly 利用计算方法研究登革热病毒衣壳组装
Q2 Mathematics Pub Date : 2019-01-01 DOI: 10.1515/cmb-2019-0005
G. S. Salas, A. E. L. Hernandez, Jiadi He, C. Karki, Yixin Xie, Shengjie Sun, Yuejiao Xian, Lin Li
Abstract Dengue viral capsid plays a significant role in viral life cycle of dengue, especially in vial genome protection and virus-cell fusion. Revealing mechanisms of the viral capsid protein assembly may lead to the discovery of anti-viral drugs that inhibit the assembly of the viral capsid. The E and M-proteins are arranged into heterotetramers, which consists of two copies of E and M-protein. The heterotetramers are assembled into a highly ordered capsid. While many investigations of the interactions between E and M-proteins have been performed, there are very few studies on the interactions between the heterotetramers and their roles in capsid assembly. Utilizing a series of computational approaches, this study focuses on the assembly mechanism of the heterotetramers. Our electrostatic analyses lead to the identification of four binding modes between each two dengue heterotetramers that repeat periodically throughout the virus capsid. Among these four binding modes, heterotetramers in binding modes I, II and IV are attractive. But in the binding mode III the heterotetramers repel each other, making mode III a suitable target for drug design. Furthermore, MD simulations were performed following by salt bridges analysis. This study demonstrates that using computational approaches is a promising direction to study the dengue virus.
摘要登革热病毒衣壳在登革热病毒生命周期中起着重要作用,尤其是在小瓶基因组保护和病毒细胞融合方面。揭示病毒衣壳蛋白组装的机制可能导致发现抑制病毒衣壳组装的抗病毒药物。E和M蛋白排列成异四聚体,由E和M蛋白质的两个拷贝组成。异源四聚体被组装成高度有序的衣壳。虽然已经对E和M蛋白之间的相互作用进行了许多研究,但对异源四聚体之间的相互关系及其在衣壳组装中的作用的研究很少。利用一系列的计算方法,本研究集中于异源四聚体的组装机制。我们的静电分析确定了每两种登革热异四聚体之间的四种结合模式,这些模式在整个病毒衣壳中周期性重复。在这四种结合模式中,结合模式I、II和IV中的异四聚体是有吸引力的。但在结合模式III中,异四聚体相互排斥,使模式III成为药物设计的合适靶点。此外,在盐桥分析之后进行了MD模拟。这项研究表明,使用计算方法是研究登革热病毒的一个很有前途的方向。
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引用次数: 10
期刊
Computational and Mathematical Biophysics
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