相关论文: Tropical geometries and dynamics of biochemical ne…
The Michaelis-Menten equation has played a central role in our understanding of biochemical processes. It has long been understood how this equation approximates the dynamics of irreversible enzymatic reactions. However, a similar…
The paper presents a computational stochastic model of virtual cells irradiation, based on Quasi-Markov Chain Monte Carlo method and using biophysical input. The model is based on a stochastic tree of probabilities for each cell of the…
Stochasticity plays a fundamental role in various biochemical processes, such as cell regulatory networks and enzyme cascades. Isothermal, well-mixed systems can be modelled as Markov processes, typically simulated using the Gillespie…
The macroscopic behavior of the solution of a coupled system of partial differential equations arising in the modeling of reaction-diffusion processes in periodic porous media is analyzed. Our mathematical model can be used for studying…
In this letter, we demonstrate that oscillations and excitable behavior can be imparted to a chemical network by coupling the network to an active hydrogel. We discuss two mechanisms by which the mechanical response of the gel to the…
Model reduction techniques have been widely used to study the collective behavior of globally coupled oscillators. However, most approaches assume that there are infinitely many oscillators. Here we propose a new ansatz, based on the…
We discuss the symbolic dynamics of biochemical networks with separate timescales. We show that symbolic dynamics of monomolecular reaction networks with separated rate constants can be described by deterministic, acyclic automata with a…
This article presents a continuous model for hierarchical networks based on a combination of mathematically derived models of receptive fields and biologically inspired computations. Based on a functional model of complex cells in terms of…
Multichannel quantum defect theory (MQDT) has been widely applied to resonant and non-resonant scattering in a variety of atomic collision processes. In recent years, the method has been applied to cold collisions with considerable success,…
We developed a general theoretical approach and a user-ready computer code that permit to study the dynamics of collisional energy transfer and ro-vibrational energy exchange in complex molecule-molecule collisions. The method is a mixture…
In unsupervised classification, Hidden Markov Models (HMM) are used to account for a neighborhood structure between observations. The emission distributions are often supposed to belong to some parametric family. In this paper, a…
Models of biochemical networks are frequently high-dimensional and complex. Reduction methods that preserve important dynamical properties are therefore essential in their study. Interactions between the nodes in such networks are…
In this paper, we provide a graphic formulation of non-isothermal reaction systems and show that a non-isothermal detailed balanced network system converges (locally) asymptotically to the unique equilibrium within the invariant manifold…
Extracting the Hamiltonian of interacting quantum-information processing systems is a keystone problem in the realization of complex phenomena and large-scale quantum computers. The remarkable growth of the field increasingly requires…
Systems biology and whole-cell modelling are demanding increasingly comprehensive mathematical models of cellular biochemistry. These models require the development of simplified models of specific processes which capture essential…
Analyzing qualitative behaviors of biochemical reactions using its associated network structure has proven useful in diverse branches of biology. As an extension of our previous work, we introduce a graph-based framework to calculate steady…
Mathematical analysis of mass action models of large complex chemical systems is typically only possible if the models are reduced. The most common reduction technique is based on quasi-steady state assumptions. To increase the accuracy of…
We introduce a model for describing the dynamics of large numbers of interacting cells. The fundamental dynamical variables in the model are sub-cellular elements, which interact with each other through phenomenological intra- and…
In this paper we consider the 2-component reaction-diffusion model that was recently obtained by a systematic reduction of the 3-component Gilad et al. model for dryland ecosystem dynamics. The nonlinear structure of this model is more…
We investigate multicellular sender receiver systems embedded in hydrogel beads, where diffusible signals mediate interactions among heterogeneous cells. Such systems are modeled by PDE ODE couplings that combine three dimensional diffusion…