ترغب بنشر مسار تعليمي؟ اضغط هنا

A Fokker-Planck approach to the study of robustness in gene expression

50   0   0.0 ( 0 )
 نشر من قبل Maxime Herda
 تاريخ النشر 2020
  مجال البحث الهندسة المعلوماتية
والبحث باللغة English




اسأل ChatGPT حول البحث

We study several Fokker-Planck equations arising from a stochastic chemical kinetic system modeling a gene regulatory network in biology. The densities solving the Fokker-Planck equations describe the joint distribution of the messenger RNA and micro RNA content in a cell. We provide theoretical and numerical evidences that the robustness of the gene expression is increased in the presence of micro RNA. At the mathematical level, increased robustness shows in a smaller coefficient of variation of the marginal density of the messenger RNA in the presence of micro RNA. These results follow from explicit formulas for solutions. Moreover, thanks to dimensional analyses and numerical simulations we provide qualitative insight into the role of each parameter in the model. As the increase of gene expression level comes from the underlying stochasticity in the models, we eventually discuss the choice of noise in our models and its influence on our results.

قيم البحث

اقرأ أيضاً

We propose an equilibrium-driven deformation algorithm (EDDA) to simulate the inbetweening transformations starting from an initial image to an equilibrium image, which covers images varying from a greyscale type to a colorful type on plane or manifo ld. The algorithm is based on Fokker-Planck dynamics on manifold, which automatically cooperates positivity, unconditional stability, mass conservation law, exponentially convergence and also the manifold structure suggested by dataset. The thresholding scheme is adapted for the sharp interface dynamics and is used to achieve the finite time convergence. Using EDDA, three challenging examples, (I) facial aging process, (II) coronavirus disease 2019 (COVID-19) invading/treatment process, and (III) continental evolution process are conducted efficiently.
We consider the Vlasov-Fokker-Planck equation with random electric field where the random field is parametrized by countably many infinite random variables due to uncertainty. At the theoretical level, with suitable assumption on the anisotropy of th e randomness, adopting the technique employed in elliptic PDEs [Cohen, DeVore, 2015], we prove the best N approximation in the random space breaks the dimension curse and the convergence rate is faster than the Monte Carlo method. For the numerical method, based on the adaptive sparse polynomial interpolation (ASPI) method introduced in [Chkifa, Cohen, Schwab, 2014], we develop a residual-based adaptive sparse polynomial interpolation (RASPI) method which is more efficient for multi-scale linear kinetic equation, when using numerical schemes that are time-dependent and implicit. Numerical experiments show that the numerical error of the RASPI decays faster than the Monte-Carlo method and is also dimension independent.
In the last years, tens of thousands gene expression profiles for cells of several organisms have been monitored. Gene expression is a complex transcriptional process where mRNA molecules are translated into proteins, which control most of the cell f unctions. In this process, the correlation among genes is crucial to determine the specific functions of genes. Here, we propose a novel multi-dimensional stochastic approach to deal with the gene correlation phenomena. Interestingly, our stochastic framework suggests that the study of the gene correlation requires only one theoretical assumption -Markov property- and the experimental transition probability, which characterizes the gene correlation system. Finally, a gene expression experiment is proposed for future applications of the model.
Fractional Fokker-Planck equation plays an important role in describing anomalous dynamics. To the best of our knowledge, the existing discussions mainly focus on this kind of equation involving one diffusion operator. In this paper, we first derive the fractional Fokker-Planck equation with two-scale diffusion from the Levy process framework, and then the fully discrete scheme is built by using the $L_{1}$ scheme for time discretization and finite element method for space. With the help of the sharp regularity estimate of the solution, we optimally get the spatial and temporal error estimates. Finally, we validate the effectiveness of the provided algorithm by extensive numerical experiments.
78 - N. Loy , M. Zanella 2019
In this work we consider an extension of a recently proposed structure preserving numerical scheme for nonlinear Fokker-Planck-type equations to the case of nonconstant full diffusion matrices. While in existing works the schemes are formulated in a one-dimensional setting, here we consider exclusively the two-dimensional case. We prove that the proposed schemes preserve fundamental structural properties like nonnegativity of the solution without restriction on the size of the mesh and entropy dissipation. Moreover, all the methods presented here are at least second order accurate in the transient regimes and arbitrarily high order for large times in the hypothesis in which the flux vanishes at the stationary state. Suitable numerical tests will confirm the theoretical results.
التعليقات
جاري جلب التعليقات جاري جلب التعليقات
سجل دخول لتتمكن من متابعة معايير البحث التي قمت باختيارها
mircosoft-partner

هل ترغب بارسال اشعارات عن اخر التحديثات في شمرا-اكاديميا