相关论文: Tropical geometries and dynamics of biochemical ne…
A reaction network is a chemical system involving multiple reactions and chemical species. Stochastic models of such networks treat the system as a continuous time Markov chain on the number of molecules of each species with reactions as…
We discuss a novel analysis method for reaction network systems with polynomial or rational rate functions. This method is based on computing tropical equilibrations defined by the equality of at least two dominant monomials of opposite…
We present a numerical approximation technique for the analysis of continuous-time Markov chains that describe networks of biochemical reactions and play an important role in the stochastic modeling of biological systems. Our approach is…
We present an analytical model for describing complex dynamics of a hybrid system consisting of interacting classical and quantum resonant structures. Classical structures in our model correspond to plasmonic nano-resonators of different…
Astrochemical models can be greatly simplified, with obvious computational advantages, if the reaction networks for key species can be reduced to a bare minimum. In addition, if chemical equilibrium holds, then simple analytical solutions…
Molecular dynamics simulations are indispensable for exploring the behavior of atoms and molecules. Grounded in quantum mechanical principles, quantum molecular dynamics provides high predictive power but its computational cost is dominated…
We present a modification of the Hybrid Monte Carlo algorithm for tackling the critical slowing down of generating Markov chains of lattice gauge configurations towards the continuum limit. We propose a new method to exchange information…
Motivated by an ongoing collaboration with clinical oncologists and pathologists, we develop a hybrid partial differential equation--ordinary differential equation (PDE--ODE) framework that captures (i) competition between susceptible and…
Biochemical reaction networks frequently consist of species evolving on multiple timescales. Stochastic simulations of such networks are often computationally challenging and therefore various methods have been developed to obtain sensible…
The modern thermodynamics of discrete systems is based on graph theory, which provides both algebraic methods to define observables and a geometric intuition of their meaning and role. However, because chemical reactions are usually…
Biological mixtures, such as the cellular cytoplasm, are composed of a large number of different components. From this heterogeneity, ordered mesoscopic structures emerge, such as liquid phases with controlled composition. These structures…
We cast the metabolism of interacting cells within a statistical mechanics framework considering both, the actual phenotypic capacities of each cell and its interaction with its neighbors. Reaction fluxes will be the components of…
We study a simplification of the well-known Shigesada-Kawasaki-Teramoto model, which consists of two nonlinear reaction-diffusion equations with cross-diffusion. A complete set of Q-conditional (nonclassical) symmetries is derived using an…
A Topological examination of phospholipid dynamics in the Far from Equilibrium state has demonstrated that metabolically active cells use waste heat to generate spatially patterned membrane flows by forced convection and shear. This paper…
Stochastic models of chemical reaction networks are an important tool to describe and analyze noise effects in cell biology. When chemical species and reaction rates in a reaction system have different orders of magnitude, the associated…
Simplified stochastic models are widely used in the study of frequency-resolved noise propagation in biochemical reaction networks, a common measure being the coherence between random fluctuations in molecule number trajectories. Such…
We introduce a fully generalized quiescent chemical reactor system in arbitrary space $\vdim =1,2$ or 3, with $n\in\mathbb{N}$ chemical constituents $\alpha_{i}$, where the character of the numerical solution is strongly determined by the…
Partial equilibrium approximation (PEA) and quasi-steady-state approximation (QSSA) are two classical methods for reducing complex macroscopic chemical reactions into simple computable ones. Previous studies mainly focus on the accuracy of…
In this work we provide a complete model of semiclassical theories by including back-reaction and correlation into the picture. We specially aim at the interaction between light and a two-level atom, and we also illustrate it via the…
The asymmetric Hopfield model is used to simulate signaling dynamics in gene/transcription factor networks. The model allows for a direct mapping of a gene expression pattern into attractor states. We analyze different control strategies…