ATP oscillation caused by Gradual Entry of Substrates within Mitochondria

The gradual entry of the substrate into enzyme solution causes the oscillatory reaction. We proved this by using dialysis membrane as a means of gradual entry of substrates 7. It was considered that a suitable combination of permeation rate through membrane of the substrate and rate constants for catalytic reaction regulates the oscillation. It was suggested that such oscillatory reactions also should occur in actual living organisms. On the basis of this suggestion, we explored the oscillatory reaction within mitochondria, because many reactions in mitochondria also occur in the mediation of membrane. We found that the gradual entry of pyruvate together with ADP caused the oscillations of both NADH and ATP within mitochondria. Likewise, the gradual entry of NAD+ and malate together with ADP caused the oscillations of NADH and of ATP. At the same time, pH oscillation within mitochondria was also observed. Besides the experiment with mitochondria, we also investigated oscillations of NADH and the other intermediates using dialysis membrane both in the citric acid cycle and in the respiratory chain. Putting these together, we concluded that the oscillatory reactions caused by the gradual entry of pyruvate occur continuously both in the citric acid cycle and in the respiratory chain and is taken over finally by the reaction of ATP synthase in the oxidative phosphorylation, inducing the oscillation of ATP. Furthermore, it was found that oscillations occurred without going through the citric acid cycle when NAD+ and malate were used instead of pyruvate.

Belousov-Zhabotinsky type reactions: the non-linear behavior of chemical systems

Chemical oscillators are open systems characterized by periodic variations of some reaction species concentration due to complex physico-chemical phenomena that may cause bistability, rise of limit cycle attractors, birth of spiral waves and Turing patterns and finally deterministic chaos. Specifically, the Belousov-Zhabotinsky reaction is a noteworthy example of non-linear behavior of chemical systems occurring in homogenous media. This reaction can take place in several variants and may offer an overview on chemical oscillators, owing to its simplicity of mathematical handling and several more complex deriving phenomena. This work provides an overview of Belousov-Zhabotinsky-type reactions, focusing on modeling under different operating conditions, from the most simple to the most widely applicable models presented during the years. In particular, the stability of simplified models as a function of bifurcation parameters is studied as causes of several complex behaviors. Rise of waves and fronts is mathematically explained as well as birth and evolution issues of the chaotic ODEs system describing the Györgyi-Field model of the Belousov-Zhabotinsky reaction. This review provides not only the general information about oscillatory reactions, but also provides the mathematical solutions in order to be used in future biochemical reactions and reactor designs.

APPLICABILITY OF BRAY-LIEBHAFSKY REACTION FOR CHEMICAL COMPUTING

The first discovered homogeneous oscillatory reaction was the Bray-Liebhafsky (BL) one, described in a paper published exactly 100 years ago. However, the applicability of oscillatory reactions in chemical computing was recently discovered. Here we intend to expose the native computing concept applied to intermittent states of the BL reaction, because we believe that this particular state may have some advantages. For this purpose, numerical simulations will be used based on the known model. Sequences of perturbations will be introduced by adding iodate (IO3-) and hydrogen peroxide (H2O2), separately, as well as in various combinations with one another. It will be shown that dynamic states obtained after perturbations with same species depend very much on the sequence in which these species were used in perturbations. Additionally, it will be shown that obtained dynamic states shift the system from chaotic intermittent dynamic state to different complex periodic states. Hence, the applicability of the BL reaction system in chemical computing was demonstrated.

THE MINOR INFLUENCE OF CALCIUM DOPED PHOSPHATE TUNGSTEN BRONZE ON THE BRIGGS-RAUSCHER REACTION DYNAMICS

The Briggs-Rauscher (BR) oscillatory reaction is the oxidation of malonic acid in the presence of hydrogen peroxide and iodate in the acidic environment, which is catalyzed by ions of manganese. This reaction is very sensitive to the presence of additives. In this paper, the BR reaction has been used to investigate the phosphate tungsten bronze as well as calcium doped tungsten bronze, obtained by thermal treatment. The addition (0.01-0.08 g) of phosphate tungsten bronze and calcium doped phosphate tungsten bronze has a different effect on the dynamics of the Briggs-Rauscher reaction. In the case of the addition of phosphate tungsten bronze in the Briggs-Rauscher reaction, the linear dependence of the length of the oscillatory period on the mass of the added bronze was obtained, while in the case of addition of calcium doped phosphate tungsten bronze, the oscillatory period does not significantly change with an increase of added mass. The mechanism of calcium doped and undoped phosphate tungsten bronze action in BR reaction is probably adsorptive, and it will be the subject of future work. Keywords: oscillatory reactions, Briggs-Rauscher reaction, phosphate tungsten bronze, calcium doped phosphate tungsten bronze, thermal treatment.

Synchrony and pattern formation of coupled genetic oscillators on a chip of artificial cells

Understanding how biochemical networks lead to large-scale nonequilibrium self-organization and pattern formation in life is a major challenge, with important implications for the design of programmable synthetic systems. Here, we assembled cell-free genetic oscillators in a spatially distributed system of on-chip DNA compartments as artificial cells, and measured reaction–diffusion dynamics at the single-cell level up to the multicell scale. Using a cell-free gene network we programmed molecular interactions that control the frequency of oscillations, population variability, and dynamical stability. We observed frequency entrainment, synchronized oscillatory reactions and pattern formation in space, as manifestation of collective behavior. The transition to synchrony occurs as the local coupling between compartments strengthens. Spatiotemporal oscillations are induced either by a concentration gradient of a diffusible signal, or by spontaneous symmetry breaking close to a transition from oscillatory to nonoscillatory dynamics. This work offers design principles for programmable biochemical reactions with potential applications to autonomous sensing, distributed computing, and biomedical diagnostics.