Genome-scale metabolic models provide a powerful means to harness information from genomes to deepen biological insights. With exponentially increasing sequencing capacity, there is an enormous need for automated reconstruction techniques that can provide more accurate models in a short time frame. Current methods for automated metabolic network reconstruction rely on gene and reaction annotati...

Metabolic pathways reflect an organism's chemical repertoire and hence their elucidation and design have been a primary goal in metabolic engineering. Various computational methods have been developed to design novel metabolic pathways while taking into account several prerequisites such as pathway stoichiometry, thermodynamics, host compatibility, and enzyme availability. The choice of the met...

Thermodynamic analysis of metabolic networks has recently generated increasing interest for its ability to add constraints on metabolic network operation, and to combine metabolic fluxes and metabolite measurements in a mechanistic manner. Concepts for the calculation of the change in Gibbs energy of biochemical reactions have long been established. However, a concept for incorporation of cross...

The metabolic network of a cell can be decomposed into discrete elementary modes that contribute, each with a certain probability, to the overall flux through the metabolism. These modes are cell function supporting, fundamental pathways that represent permissible ‘quantum’ states of the metabolism. For the case that cellular regulatory mechanisms for pathway fluxes evolved in an unbiased way, ...

Metabolic reactions of single-cell organisms are routinely observed to become dispensable or even incapable of carrying activity under certain circumstances. Yet, the mechanisms as well as the range of conditions and phenotypes associated with this behavior remain very poorly understood. Here we predict computationally and analytically that any organism evolving to maximize growth rate, ATP pro...

The modelling and analysis of signalling pathways in living organisms is one of the most challenging problems in systems biology that can be handled using the theory of chemical reaction networks (CRNs) obeying the mass-action law. In addition to being used to describe pure chemical reactions, such networks are also widely used to model the dynamics of intracellular processes, metabolic or cell...

In this paper, conventional SAPO-34 and Cerium Hierarchical SAPO-34 zeolites are synthesized using a hydrothermal method for methanol-to-propylene (MTP) reaction. The Ce-H-SAPO-34 catalyst shows a slightly larger crystal size, bimodal pore size distribution (microporous and mesoporous) and lower surface acidity compared to conventional SAPO-34 catalysts. According to these physicochemical prope...

Background: In prokaryotic genomes the number of transcriptional regulators is known to quadratically scale with the total number of protein-coding genes. Toolbox model of evolution was recently proposed to explain this scaling for metabolic enzymes and their regulators. According to its rules the metabolic network of an organism evolves by horizontal transfer of pathways from other species. Th...

The Artificial Reaction Network (ARN) is an Artificial Chemistry representation inspired by cell signaling networks. The ARN has previously been applied to the simulation of biological signaling pathways and to the control of limbed robots. In this paper we create multiple cell-like autonomous agents using ARN networks. It is shown that these agents can simulate some aspects of the behavior of ...