Related papers: Partial equilibrium approximations in Apoptosis
In this paper we introduce a formalism that allows to describe the response of a part of a biochemical system in terms of renewal equations. In particular, we examine under which conditions the interactions between the different parts of a…
The evaluation of the probability of union of a large number of independent events requires several combinations involving the factorial and the use of high performance computers with several hours of processing. Bounds and simplifications…
In feedback flow control, one of the challenges is to develop mathematical models that describe the fluid physics relevant to the task at hand, while neglecting irrelevant details of the flow in order to remain computationally tractable. A…
The trend to equilibrium for reaction-diffusion systems modelling chemical reaction networks is investigated, in the case when reaction processes happen on subsets of the domain. We prove the convergence to equilibrium by directly showing…
This work concerns the exponential stabilization of underactuated linear homogeneous systems of m parabolic partial differential equations (PDEs) in cascade (reaction-diffusion systems), where only the first state is controlled either…
The process of protein synthesis in biological systems resembles a one dimensional driven lattice gas in which the particles have spatial extent, covering more than one lattice site. We expand the well studied Totally Asymmetric Exclusion…
The Quantum Approximate Optimization Algorithm (QAOA) is a promising variational algorithm for solving combinatorial optimization problems on near-term devices. However, as the number of layers in a QAOA circuit increases, which is…
Fluid models are a popular formalism in the quantitative modeling of biochemical systems and analytical performance models. The main idea is to approximate a large-scale Markov chain by a compact set of ordinary differential equations…
Entropic measures like Shannon entropy (SE), its quantum mechanical analogue von Neumann entropy, and Kullback-Leibler divergence (KL) are key components in many tools used in physics, information theory, machine learning (ML) and quantum…
The theory of quasi-Lie systems, i.e. systems of first order ordinary differential equations which can be related via a generalised flow to Lie systems, is extended to systems of partial differential equations and its applications to…
The influence of nonequilibrium initial values of the order parameter on its evolution at a critical point is described using a renormalization group approach of the field theory. The dynamic critical exponent $\theta'$ of the short time…
In this work, we investigate the numerical approximation of the second order non-autonomous semilnear parabolic partial differential equation (PDE) using the finite element method. To the best of our knowledge, only the linear case is…
The equation of state (EOS) of a low-density porous substance plasma is proposed in the form of continuous media EOS containing, as a pressure control parameter, the degree of plasma homogenization, which is function of the initial porous…
Simulations of the dynamics generated by partial differential equations (PDEs) provide approximate, numerical solutions to initial value problems. Such simulations are ubiquitous in scientific computing, but the correctness of the results…
Performance analysis based on modelling consists of two major steps: model construction and model analysis. Formal modelling techniques significantly aid model construction but can exacerbate model analysis. In particular, here we consider…
To investigate whether treating cancer patients with erythropoiesis-stimulating agents (ESAs) would increase the mortality risk, Bennett et al. [Journal of the American Medical Association 299 (2008) 914--924] conducted a meta-analysis with…
We address the problem of evaluating the transfer entropy (TE) produced by biochemical reactions from experimentally measured data. Although these reactions are generally non-linear and non-stationary processes making it challenging to…
In this work, we derive particle schemes, based on micro-macro decomposition, for linear kinetic equations in the diffusion limit. Due to the particle approximation of the micro part, a splitting between the transport and the collision part…
In parallel iterative applications, computational efficiency is essential for addressing large problems. Load imbalance is one of the major performance degradation factors of parallel applications. Therefore, distributing, cleverly, and as…
We present two approaches for describing chemical reactions taking place in fluid phase. The first method mirrors the usual derivation of the hydrodynamic equations of motion by relating conserved---or to account for chemical reactions,…