相关论文: A Simple Comparison of Biochemical Systems Theory …
The Kappa biochemistry and the M{\O}D organic chemistry frameworks are amongst the most intensely developed applications of rewriting-based methods in the life sciences to date. A typical feature of these types of rewriting theories is the…
The paper analyses stochastic systems describing reacting molecular systems with a combination of two types of state spaces, a finite-dimensional, and an infinite dimenional part. As a typical situation consider the interaction of larger…
Multistability of mesoscopic, driven biochemical reaction systems has implications to a wide range of cellular processes. Using several simple models, we show that one class of bistable chemical systems has a deterministic counterpart in…
Biomolecular condensates are small droplets forming spontaneously in biological cells via phase separation. They play a role in many cellular processes, but it is unclear how cells control them. Cellular regulation often relies on…
Metabolic pathways describe chains of enzymatic reactions. Their modelling is a key point to understand living systems. An enzymatic reaction is an interaction between one or several metabolites (substrates) and an enzyme (simple protein or…
We define a subclass of Chemical Reaction Networks called Post-Translational Modification systems. Important biological examples of such systems include MAPK cascades and two-component systems which are well-studied experimentally as well…
Key insights in molecular biology, such as enzyme kinetics, protein allostery and gene regulation emerged from quantitative analysis based on time-scale separation, allowing internal complexity to be eliminated and resulting in the…
To develop and investigate detailed mathematical models of cellular metabolic processes is one of the primary challenges in systems biology. However, despite considerable advance in the topological analysis of metabolic networks, explicit…
A notion of biologic system or just a system implies a functional wholeness of comprising system components. Positive and negative feedback are the examples of how the idea to unite anatomical elements in the whole functional structure was…
Biological systems are often modeled as a system of ordinary differential equations (ODEs) with time-invariant parameters. However, cell signaling events or pharmacological interventions may alter the cellular state and induce multi-mode…
Stochastic thermodynamics provides a framework for describing small systems like colloids or biomolecules driven out of equilibrium but still in contact with a heat bath. Both, a first-law like energy balance involving exchanged heat and…
Chemical reaction networks describe interactions between biochemical species. Once an underlying reaction network is given for a biochemical system, the system dynamics can be modelled with various mathematical frameworks such as continuous…
Neural network (NN) model chemistries (MCs) promise to facilitate the accurate exploration of chemical space and simulation of large reactive systems. One important path to improving these models is to add layers of physical detail,…
Biochemical reaction networks in living cells usually involve reversible covalent modification of signaling molecules, such as protein phosphorylation. Under conditions of small molecule numbers, as is frequently the case in living cells,…
Liquid chromatography mass spectrometry (LC-MS)-based metabolomics and exposomics aim to measure detectable small molecules in biological samples. The results facilitate hypothesis-generating discovery of metabolic changes and disease…
To understand the fairness properties of the BBR congestion-control algorithm (CCA), previous research has analyzed BBR behavior with a variety of models. However, previous model-based work suffers from a trade-off between accuracy and…
Biomolecular condensates govern essential cellular processes yet elude description by traditional equilibrium models. This roadmap, distilled from structured discussions at a workshop and reflecting the consensus of its participants,…
Simple ideas, endowed from the mathematical theory of control, are used in order to analyze in general grounds the human immune system. The general principles are minimization of the pathogen load and economy of resources. They should…
Accurately determining and classifying the structure of complex networks is the focus of much current research. One class of network of particular interest are metabolic pathways, which have previously been studied from a graph theoretical…
Life has a special status, it even has its own science: biology. In many ways, the logic of life seems to differ from that of atoms, molecules, planets, or any other `inanimate object'. However, life is increasingly measured using…