Related papers: Identification of Parameters and Initial Values fo…
Signaling proteins are an important topic in drug development due to the increased importance of finding fast, accurate and cheap methods to evaluate new molecular targets involved in specific diseases. The complexity of the protein…
Chemical kinetic mechanisms can be represented by sets of elementary reactions that are easily translated into mathematical terms using physicochemical relationships. The schematic representation of reactions captures the interactions…
Reaction--diffusion mechanism are a robust paradigm that can be used to represent many biological and physical phenomena over multiple spatial scales. Applications include intracellular dynamics, the migration of cells and the patterns…
Zero-one reaction networks are pivotal to cellular signaling, and establishing the equivalence of such networks represents a foundational computational challenge in the realm of chemical reaction network research. Herein, we propose a…
We propose certain approach of solving two-dimensional non-stationary and stationary advection-diffusion-reaction boundary value problems through their reduction to the set of corresponding one-dimensional problems. This method leverages…
Finding optimal pathways in chemical reaction networks is essential for elucidating and designing chemical processes, with significant applications such as synthesis planning and metabolic pathway analysis. Such a chemical pathway-finding…
The aim of this paper is to discuss potential advances in PET kinetic models and direct reconstruction of kinetic parameters. As a prominent example we focus on a typical task in perfusion imaging and derive a system of…
We present a numerical scheme for solving a parameter estimation problem for a model of low-grade glioma growth. Our goal is to estimate the spatial distribution of tumor concentration, as well as the magnitude of anisotropic tumor…
In this paper we perform a formal asymptotic analysis on a kinetic model for reactive mixtures in order to derive a reaction-diffusion system of Maxwell-Stefan type. More specifically, we start from the kinetic model of simple reacting…
Signaling networks are designed to sense an environmental stimulus and adapt to it. We propose and study a minimal model of signaling network that can sense and respond to external stimuli of varying strength in an adaptive manner. The…
Open biochemical systems of interacting molecules are ubiquitous in life-related processes. However, established computational methodologies, like molecular dynamics, are still mostly constrained to closed systems and timescales too small…
In this paper we present a method for estimating unknown parameter that appear in a two dimensional nonlinear reaction-diffusion model of cancer invasion. This model considers that tumor-induced alteration of microenvironmental pH provides…
A simple reaction-diffusion-advection equation is proposed in a dichotomous tree network to discuss an optimal network. An optimal size ratio r is evaluated by the principle of maximization of total reaction rate. In the case of…
Inverse protein folding is challenging due to its inherent one-to-many mapping characteristic, where numerous possible amino acid sequences can fold into a single, identical protein backbone. This task involves not only identifying viable…
Computational systems biology has provided plenty of insights into cell biology. Early on, the focus was on reaction networks between molecular species. Spatial distribution only began to be considered mostly within the last decade.…
Inspired by the recent developments in modeling and analysis of reaction networks, we provide a geometric formulation of the reversible reaction networks under the influence of diffusion. Using the graph knowledge of the underlying reaction…
We develop a simple but rigorous model of protein-protein association kinetics based on diffusional association on free energy landscapes obtained by sampling configurations within and surrounding the native complex binding funnels. Guided…
We develop an immersed-boundary approach to modeling reaction-diffusion processes in dispersions of reactive spherical particles, from the diffusion-limited to the reaction-limited setting. We represent each reactive particle with a…
In this paper, we study the initial value problem for infinite dimensional fractional non-autonomous reaction-diffusion equations. Applying general time-splitting methods, we prove the existence of solutions globally defined in time using…
Sensitivity analysis of biochemical reactions aims at quantifying the dependence of the reaction dynamics on the reaction rates. The computation of the parameter sensitivities, however, poses many computational challenges when taking…