相关论文: Stability conditions of chemical networks in a lin…
Understanding the emergent behavior of chemical reaction networks (CRNs) is a fundamental aspect of biology and its origin from inanimate matter. A closed CRN monotonically tends to thermal equilibrium, but when it is opened to external…
Chemical reaction networks (CRNs) are foundational models for describing complex biochemical processes. We study noncompetitive CRNs, a class of networks whose static states are rate-independent, and that can implement ReLU neural networks.…
Computational techniques are required for narrowing down the vast space of possibilities to plausible prebiotic scenarios, since precise information on the molecular composition, the dominant reaction chemistry, and the conditions for that…
Linear stability of synchronized states in networks of delay-coupled oscillators depends on the type of interaction, the network and oscillator properties. For inert oscillator response, found ubiquitously from biology to engineering,…
We introduce a method that can be used to evolve the topology of a network in a way that preserves both the network's spectral as well as local structure. This method is quite versatile in the sense that it can be used to evolve a network's…
Quantifying the eigenvalue spectra of large random matrices allows one to understand the factors that contribute to the stability of dynamical systems with many interacting components. This work explores the effect that the interaction…
We consider how to generate chemical reaction networks (CRNs) from functional specifications. We propose a two-stage approach that combines synthesis by satisfiability modulo theories and Markov chain Monte Carlo based optimisation. First,…
Detailed balance of a chemical reaction network can be defined in several different ways. Here we investigate the relationship among four types of detailed balance conditions: deterministic, stochastic, local, and zero-order local detailed…
Inspired by Anderson et al. [J. R. Soc. Interface, 2014] we study the long-term behavior of discrete chemical reaction networks (CRNs). In particular, using techniques from both Petri net theory and CRN theory, we provide a powerful…
Recent experimental and computational evidence suggests that several dynamical properties may characterize the operating point of functioning neural networks: critical branching, neutral stability, and production of a wide range of firing…
We propose a novel measure valued process which models the behaviour of chemical reaction networks in spatially heterogeneous systems. It models reaction dynamics between different molecular species and continuous movement of molecules in…
A large variety of dynamical processes that take place on networks can be expressed in terms of the spectral properties of some linear operator which reflects how the dynamical rules depend on the network topology. Often such spectral…
Robustness of biochemical systems has become one of the central questions in Systems Biology, although it is notoriously difficult to formally capture its multifaceted nature. Maintenance of normal system function depends not only on the…
"Every object that biology studies is a system of systems." (Fran\c{c}ois Jacob, 1974). Most networks feature intricate architectures originating from tinkering, a repetitive use of existing components where structures are not invented but…
Cascades on random networks are typically analyzed by assuming they map onto percolation processes and then are solved using generating function formulations. This approach assumes that the network is infinite and weakly connected, yet…
The recent discovery of universal principles underlying many complex networks occurring across a wide range of length scales in the biological world has spurred physicists in trying to understand such features using techniques from…
Can a micron sized sack of interacting molecules autonomously learn an internal model of a complex and fluctuating environment? We draw insights from control theory, machine learning theory, chemical reaction network theory, and statistical…
This article characterizes certain small multistationary chemical reaction networks. We consider the set of fully open networks, those for which all chemical species participate in inflow and outflow, containing one non-flow (reversible 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…
It has been known for nearly a decade that deterministically modeled reaction networks that are weakly reversible and consist of a single linkage class have trajectories that are bounded from both above and below by positive constants (so…