The biochemical system logically processing biochemical signals using immune-specific and biocatalytic reactions was designed, and the generated output signals were analyzed by AFM and optical means. Different patterns of immune signals resulted in the formation of various interfacial structures followed by biocatalytic reactions activated by the next set of biochemical inputs. The developed ap...

Genome-scale metabolic networks can be reconstructed. The systemic biochemical properties of these networks can now be studied. Here, genome-scale reconstructed metabolic networks were analysed using singular value decomposition (SVD). All the individual biochemical conversions contained in a reconstructed metabolic network are described by a stoichiometric matrix (S). SVD of S led to the defin...

SUMMARY A-Cell is a tool for constructing models of complex and complicated biochemical reactions. An important feature of A-Cell is its graphical user interface for constructing biochemical reactions. In addition, it has a capability of importing previously constructed models, combining them, and constructing a comprehensive model. The simulation program for the model is automatically generate...

Systems biology is an emerging field that aims at obtaining a system-level understanding of biological processes. The modelling and simulation of networks of biochemical reactions have great and promising application potential but require reliable kinetic data. In order to support the systems biology community with such data we have developed SABIO-RK (System for the Analysis of Biochemical Pat...

Microbial cell factories based on renewable carbon sources are fundamental to a sustainable bio-economy. The economic feasibility of producer cells requires robust performance balancing growth and production. However, the inherent competition between these two objectives often leads to instability and reduces productivity. While algorithms exist to design metabolic network reduction strategies ...

In most contemporary life forms, the confinement of cell membranes provides localized concentration and protection for biomolecules, leading to efficient biochemical reactions. Similarly, confinement may have also played an important role for prebiotic compartmentalization in early life evolution when the cell membrane had not yet formed. It remains an open question how biochemical reactions de...

Natural Computing is concerned with human-designed computing inspired by nature as well as with computation taking place in nature. The latter strand of research investigates in terms of information processing, processes taking place in nature, and the computational nature of biochemical reactions is a research theme belonging here. Reaction systems are a formal framework for investigating proc...

Two primary biochemical reactions in seed ageing (lipid peroxidation and non-enzymatic protein glycosylation with reducing sugars) have been studied under different seed water contents and storage temperatures, and the role of the glassy state in retarding biochemical deterioration examined. The viability loss of Vigna radiata seeds during storage is associated with Maillard reactions; however,...

Processes in living cells are the result of interactions between biochemical compounds in highly complex biochemical networks. It is a major challenge in biology to understand causes and consequences of the specific design of these networks. A characteristic design feature of metabolic networks is the presence of hub metabolites such as ATP or NADH that are involved in a high number of reaction...