scholarly journals Quantifying Epigenetic Stability with Minimum Action Paths

2020 ◽  
Author(s):  
Amogh Sood ◽  
Bin Zhang
Keyword(s):  
Histone Modifications ◽  
Transition Probability ◽  
Model Parameters ◽  
The Stability ◽  
Probable Path ◽  
Most Probable Path ◽  
Discrete Stochastic Models ◽  
Stochastic Reaction ◽  
Stochastic Reaction Networks ◽  
Number Of Particles

Chromatin can adopt multiple stable, heritable states with distinct histone modifications and varying levels of gene expression. Insight on the stability and maintenance of such epigenetic states can be gained by mathematical modeling of stochastic reaction networks for histone modifications. Analytical results for the kinetic networks are particularly valuable. Compared to computationally demanding numerical simulations, they often are more convenient at evaluating the robustness of conclusions with respect to model parameters. In this communication, we developed a second-quantization based approach that can be used to analyze discrete stochastic models with a fixed, finite number of particles using a representation of the SU (2) algebra. We applied the approach to a kinetic model of chromatin states that captures the feedback between nucleosomes and the enzymes conferring histone modifications. Using a path integral expression for the transition probability, we computed the epigenetic landscape that helps to identify the emergence of bistability and the most probable path connecting the two steady states. We anticipate the generalizability of the approach will make it useful for studying more complicated models that couple epigenetic modifications with transcription factors and chromatin structure.

scholarly journals An efficient and unbiased method for sensitivity analysis of stochastic reaction networks

2014 ◽  
Vol 11 (101) ◽  
pp. 20140979 ◽  
Author(s):  
Ankit Gupta ◽  
Mustafa Khammash
Keyword(s):  
Finite Difference ◽  
Finite Difference Methods ◽  
Parameter Sensitivity ◽  
Reaction Networks ◽  
Model Parameters ◽  
Exact Representation ◽  
Computationally Efficient ◽  
Sensitivity Estimation ◽  
Stochastic Reaction ◽  
Stochastic Reaction Networks

We consider the problem of estimating parameter sensitivity for Markovian models of reaction networks. Sensitivity values measure the responsiveness of an output with respect to the model parameters. They help in analysing the network, understanding its robustness properties and identifying the important reactions for a specific output. Sensitivity values are commonly estimated using methods that perform finite-difference computations along with Monte Carlo simulations of the reaction dynamics. These methods are computationally efficient and easy to implement, but they produce a biased estimate which can be unreliable for certain applications. Moreover, the size of the bias is generally unknown and hence the accuracy of these methods cannot be easily determined. There also exist unbiased schemes for sensitivity estimation but these schemes can be computationally infeasible, even for very simple networks. Our goal in this paper is to present a new method for sensitivity estimation, which combines the computational efficiency of finite-difference methods with the accuracy of unbiased schemes. Our method is easy to implement and it relies on an exact representation of parameter sensitivity that we recently proved elsewhere. Through examples, we demonstrate that the proposed method can outperform the existing methods, both biased and unbiased, in many situations.

scholarly journals Dynamics of the rumor-spreading model with hesitation mechanism in heterogenous networks and bilingual environment

2020 ◽  
Vol 2020 (1) ◽  
Author(s):  
Shuai Yang ◽  
Haijun Jiang ◽  
Cheng Hu ◽  
Juan Yu ◽  
Jiarong Li
Keyword(s):  
Lyapunov Method ◽  
Reproduction Number ◽  
Model Parameters ◽  
Rumor Spreading ◽  
Spreading Model ◽  
Reductio Ad Absurdum ◽  
The Stability ◽  
The Impact ◽  
Theoretical Results ◽  
The Basic Reproduction Number

Abstract In this paper, a novel rumor-spreading model is proposed under bilingual environment and heterogenous networks, which considers that exposures may be converted to spreaders or stiflers at a set rate. Firstly, the nonnegativity and boundedness of the solution for rumor-spreading model are proved by reductio ad absurdum. Secondly, both the basic reproduction number and the stability of the rumor-free equilibrium are systematically discussed. Whereafter, the global stability of rumor-prevailing equilibrium is explored by utilizing Lyapunov method and LaSalle’s invariance principle. Finally, the sensitivity analysis and the numerical simulation are respectively presented to analyze the impact of model parameters and illustrate the validity of theoretical results.

Model and Stability of the Traffic Flow Consisting of Heterogeneous Drivers

2015 ◽  
Vol 10 (3) ◽  
Author(s):  
Da Yang ◽  
Liling Zhu ◽  
Yun Pu
Keyword(s):  
Traffic Flow ◽  
Heterogeneous Traffic ◽  
Model Parameters ◽  
Optimal Velocity ◽  
Stability Functions ◽  
Car Following Model ◽  
Traffic Wave ◽  
The Stability ◽  
Different Characteristics ◽  
Stationary Velocity

Although traffic flow has attracted a great amount of attention in past decades, few of the studies focused on heterogeneous traffic flow consisting of different types of drivers or vehicles. This paper attempts to investigate the model and stability analysis of the heterogeneous traffic flow, including drivers with different characteristics. The two critical characteristics of drivers, sensitivity and cautiousness, are taken into account, which produce four types of drivers: the sensitive and cautious driver (S-C), the sensitive and incautious driver (S-IC), the insensitive and cautious driver (IS-C), and the insensitive and incautious driver (IS-IC). The homogeneous optimal velocity car-following model is developed into a heterogeneous form to describe the heterogeneous traffic flow, including the four types of drivers. The stability criterion of the heterogeneous traffic flow is derived, which shows that the proportions of the four types of drivers and their stability functions only relating to model parameters are two critical factors to affect the stability. Numerical simulations are also conducted to verify the derived stability condition and further explore the influences of the driver characteristics on the heterogeneous traffic flow. The simulations reveal that the IS-IC drivers are always the most unstable drivers, the S-C drivers are always the most stable drivers, and the stability effects of the IS-C and the S-IC drivers depend on the stationary velocity. The simulations also indicate that a wider extent of the driver heterogeneity can attenuate the traffic wave.

Stability of a Rigid Body With an Oscillating Particle: An Application of MACSYMA

1985 ◽  
Vol 52 (3) ◽  
pp. 686-692 ◽  
Author(s):  
L. A. Month ◽  
R. H. Rand
Keyword(s):  
Angular Velocity ◽  
Rigid Body ◽  
Classical Problem ◽  
Moment Of Inertia ◽  
Model Parameters ◽  
Stability Chart ◽  
The Stability ◽  
Transition Curves ◽  
Minimum Moment ◽  
Small Angular Velocity

This problem is a generalization of the classical problem of the stability of a spinning rigid body. We obtain the stability chart by using: (i) the computer algebra system MACSYMA in conjunction with a perturbation method, and (ii) numerical integration based on Floquet theory. We show that the form of the stability chart is different for each of the three cases in which the spin axis is the minimum, maximum, or middle principal moment of inertia axis. In particular, a rotation with arbitrarily small angular velocity about the maximum moment of inertia axis can be made unstable by appropriately choosing the model parameters. In contrast, a rotation about the minimum moment of inertia axis is always stable for a sufficiently small angular velocity. The MACSYMA program, which we used to obtain the transition curves, is included in the Appendix.

scholarly journals A Theoretical Model for the Transmission Dynamics of the Buruli Ulcer with Saturated Treatment

2014 ◽  
Vol 2014 ◽  
pp. 1-14 ◽  
Author(s):  
Ebenezer Bonyah ◽  
Isaac Dontwi ◽  
Farai Nyabadza
Keyword(s):  
Human Population ◽  
Reproduction Number ◽  
Buruli Ulcer ◽  
Coupled System ◽  
Model Parameters ◽  
The Public ◽  
Treatment Function ◽  
Medical Facilities ◽  
The Stability ◽  
Saturated Treatment

The management of the Buruli ulcer (BU) in Africa is often accompanied by limited resources, delays in treatment, and macilent capacity in medical facilities. These challenges limit the number of infected individuals that access medical facilities. While most of the mathematical models with treatment assume a treatment function proportional to the number of infected individuals, in settings with such limitations, this assumption may not be valid. To capture these challenges, a mathematical model of the Buruli ulcer with a saturated treatment function is developed and studied. The model is a coupled system of two submodels for the human population and the environment. We examine the stability of the submodels and carry out numerical simulations. The model analysis is carried out in terms of the reproduction number of the submodel of environmental dynamics. The dynamics of the human population submodel, are found to occur at the steady states of the submodel of environmental dynamics. Sensitivity analysis is carried out on the model parameters and it is observed that the BU epidemic is driven by the dynamics of the environment. The model suggests that more effort should be focused on environmental management. The paper is concluded by discussing the public implications of the results.

scholarly journals Accelerated Sensitivity Analysis in High-Dimensional Stochastic Reaction Networks

PLoS ONE ◽  
2015 ◽  
Vol 10 (7) ◽  
pp. e0130825 ◽  
Author(s):  
Georgios Arampatzis ◽  
Markos A. Katsoulakis ◽  
Yannis Pantazis
Keyword(s):  
Sensitivity Analysis ◽  
Reaction Networks ◽  
High Dimensional ◽  
Stochastic Reaction ◽  
Stochastic Reaction Networks
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