Informally, a chemical reaction network is “atomic” if each reaction may be interpreted as the rearrangement of indivisible units of matter. There are several reasonable definitions formalizing this idea. We investigate the computational complexity of deciding whether a given network is atomic according to each of these definitions. Our first definition, primitive atomic, which requires each re...

MOTIVATION Novel techniques are required to analyze computational models of intracellular processes as they increase steadily in size and complexity. The theory of chemical organizations has recently been introduced as such a technique that links the topology of biochemical reaction network models to their dynamical repertoire. The network is decomposed into algebraically closed and self-mainta...

In chemical reaction networks (CRNs) with stochastic semantics based on continuous-time Markov chains (CTMCs), the typically large populations of species cause combinatorially large state spaces. This makes the analysis very difficult in practice and represents the major bottleneck for the applicability of minimization techniques based, for instance, on lumpability. In this paper we present syn...

Organisms that can learn about their environment and modify their behaviour appropriately during their lifetime are more likely to survive and reproduce than organisms that do not. While associative learning - the ability to detect correlated features of the environment - has been studied extensively in nervous systems, where the underlying mechanisms are reasonably well understood, mechanisms ...

Inevitably, reading is one of the requirements to be undergone. To improve the performance and quality, someone needs to have something new every day. It will suggest you to have more inspirations, then. However, the needs of inspirations will make you searching for some sources. Even from the other people experience, internet, and many books. Books and internet are the recommended media to hel...

How do chemical reaction networks that process information evolve? This is not only a fundamental question in the study of the origin of life, but also in diverse fields like molecular computing, synthetic biology, and systems biology. Here, we study the evolution of chemical flip-flops by means of chemical organisation theory. Additionally, we compare evolved circuits with manually constructed...

s for talks The construction of an integrated metabolic and transcriptional regulatory network

We characterize the distributions of short cycles in a large metabolic network previously shown to have small world characteristics and a power law degree distribution. Compared with three classes of random networks, including Erdős-Rényi random graphs and synthetic small world networks of the same connectivity, both the metabolic network and models for the chemical reaction networks of planeta...

Complex networks like the scale-free model proposed by BarabasiAlbert are observed in many biological systems and the application of this topology to artificial neural network leads to interesting considerations. In this paper, we present a preliminary study on how to evolve neural networks with complex topologies. This approach is utilized in the problem of modeling a chemical process with the...

We define catalytic networks as chemical reaction networks with an essentially catalytic reaction pathway: one which is "on" in the presence of certain catalysts and "off" in their absence. We show that examples of catalytic networks include synthetic DNA molecular circuits that have been shown to perform signal amplification and molecular logic. Recall that a critical siphon is a subset of the...