Related papers: Bifunctional enzyme provides absolute concentratio…

Bifunctional enzymes, which catalyze both the forward and reverse steps of a substrate modification reaction, arise naturally in bacterial two-component signaling systems and metabolic regulation. Beyond their well-known role in conferring…

Substrate modification networks are ubiquitous in living, biochemical systems. A higher-level hypergraph "skeleton" captures key information about which substrates are transformed in the presence of modification-specific enzymes. Many…

Many reaction networks arising in applications are multistationary, that is, they have the capacity for more than one steady state; while some networks exhibit absolute concentration robustness (ACR), which means that some species…

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…

For reaction networks arising in systems biology, the capacity for two or more steady states, that is, multistationarity, is an important property that underlies biochemical switches. Another property receiving much attention recently is…

The nonlinearities found in molecular networks usually prevent mathematical analysis of network behaviour, which has largely been studied by numerical simulation. This can lead to difficult problems of parameter determination. However,…

In a reaction network, the concentration of a species with the property of dynamic absolute concentration robustness (dynamic ACR) converges to the same value independent of the overall initial values. This property endows a biochemical…

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…

Multistationarity, underlies biochemical switching and cellular decision-making. We study how multistationarity in the sequential n-site phosphorylation-dephosphorylation cycle is affected when only some species are open, meaning allowed to…

Mathematical and computational modelling of biochemical networks is often done in terms of either the concentrations of molecular species or the fluxes of biochemical reactions. When is mathematical modelling from either perspective…

Living systems contain intricate biochemical networks whose structure is closely related to their function and allows them to exhibit robust behavior in the presence of external stimuli. Such networks typically involve catalytic enzymes,…

Living organisms, ecosystems, and social systems are examples of complex systems in which robustness against inclusion of new elements is an essential feature. A recently proposed simple model has revealed a general mechanism by which such…

The functioning of many biochemical networks is often robust -- remarkably stable under changes in external conditions and internal reaction parameters. Much recent work on robustness and evolvability has focused on the structure of neutral…

Here we propose a generic mechanism - networked buffering - for generating robust traits in complex systems that requires two basic conditions to be satisfied: 1) agents are versatile enough to perform more than one single functional role…

Evolving biomolecular networks have to combine the stability against perturbations with flexibility allowing their constituents to assume new roles in the cell. Gene duplication followed by functional divergence of associated proteins is a…

The enzyme turnover rate is a fundamental parameter in enzyme kinetics, reflecting the catalytic efficiency of enzymes. However, enzyme turnover rates remain scarce across most organisms due to the high cost and complexity of experimental…

There is a crescent use of enzymes in multiple industries and sciences, ranging from materials and fuel synthesis to pharmaceutical and food production. Their applicability in this variety of fields depends not only on their biochemical…

Cellulases hold great promise for the production of biofuels and biochemicals. However, they are modular enzymes acting on a complex heterogeneous substrate. Because of this complexity, the computational prediction of their catalytic…

We study the evolution of a random weighted network with complex nonlinear dynamics at each node, whose activity may cease as a result of interactions with other nodes. Starting from a knowledge of the micro-level behaviour at each node, we…

Switch-like motifs are among the basic building blocks of biochemical networks. A common motif that can serve as an ultrasensitive switch consists of two enzymes acting antagonistically on a substrate, one making and the other removing a…