Uch refractory states that exist only in a particular time period.

Uch refractory states that exist only in a particular time period. The key feature of the memory reaction is the exit strategy for determining the length of memory time period and for defining exit reactions for transferring memory species to the normal 22948146 species. There are two time periods that are Epigenetics associated with memory reactions, namely the waiting time for the firing of a memory reaction and the memory time period during which memory reactions are capable of firing. Although the waiting time of memory reaction still follows an exponential distribution, the length of a memory time period can be defined as a constant or a random variable following a particular distribution, such as the Gaussian or exponential distribution. By properly defining the length of memory time period, we have successfully realized the stochastic dynamics of biological networks that also have certain deterministic feature. Therefore, the proposed memory reaction represents a quantum step towards the development of sophisticated modeling methodologies to explore the regulatory mechanisms of complex biological systems. Although different modeling approaches have been proposed to realize noisy process in gene expression [58,59,60], recent experimental observations suggested that the expression dynamics has certain deterministic properties including the relatively constant heights and durations of expression bursts. These stochastic events may be regulated by complex networks that are still not fully understood; or the underlying mechanisms may be too complex to be represented by reduced mathematical models. These mechanisms may include the chromatin modification and chromatin looping formation, the spatio-temporal dynamics of protein movement, as well as the intrinsically cyclic association of transcriptional factors and their co-factors. It may not be practical to use competitive chemical reactions in the SSA or delay-SSA framework to represent these stochastic events with deterministic properties. To this end, the proposed memory reaction provides a powerful tool to describe the complex regulatory mechanisms by using reduced mathematical models. In addition, it is expected that memory reaction will be used as a mechanism to realize the robustness property of biological systems [61,62]. The gene activation and inactivation windows realized by memory reaction provided novel insight into the origin of the repeated pulses in the p53-MDM2 core module. In particular, the stable time periods of gene activation play a major role in generating bursting dynamics with constant width and height of protein activity oscillations. A striking simulation result is that the oscillatory upstream signal is the key stimulus to maintain oscillatory dynamics of the p53 core module. In contract, the feedback regulations Epigenetic Reader Domain between p53 and MDM2 are not sufficient to maintain the oscillations of the p53 activity. This result is well compatible with the recent experimental observations showing that p53 induction is mediated by the damage-activated regulators [50,63]. Since a number of important regulatory mechanisms were excluded from the proposed stochastic model, including protein spatial distributions, regulation of other proteins such as MDMX, and feedback regulations between the upstream signals, more sophisticated models are needed to provide accurate simulations and testable predictions.Modeling of Memory ReactionsSupporting InformationSupporting Information S1 A detailed description o.Uch refractory states that exist only in a particular time period. The key feature of the memory reaction is the exit strategy for determining the length of memory time period and for defining exit reactions for transferring memory species to the normal 22948146 species. There are two time periods that are associated with memory reactions, namely the waiting time for the firing of a memory reaction and the memory time period during which memory reactions are capable of firing. Although the waiting time of memory reaction still follows an exponential distribution, the length of a memory time period can be defined as a constant or a random variable following a particular distribution, such as the Gaussian or exponential distribution. By properly defining the length of memory time period, we have successfully realized the stochastic dynamics of biological networks that also have certain deterministic feature. Therefore, the proposed memory reaction represents a quantum step towards the development of sophisticated modeling methodologies to explore the regulatory mechanisms of complex biological systems. Although different modeling approaches have been proposed to realize noisy process in gene expression [58,59,60], recent experimental observations suggested that the expression dynamics has certain deterministic properties including the relatively constant heights and durations of expression bursts. These stochastic events may be regulated by complex networks that are still not fully understood; or the underlying mechanisms may be too complex to be represented by reduced mathematical models. These mechanisms may include the chromatin modification and chromatin looping formation, the spatio-temporal dynamics of protein movement, as well as the intrinsically cyclic association of transcriptional factors and their co-factors. It may not be practical to use competitive chemical reactions in the SSA or delay-SSA framework to represent these stochastic events with deterministic properties. To this end, the proposed memory reaction provides a powerful tool to describe the complex regulatory mechanisms by using reduced mathematical models. In addition, it is expected that memory reaction will be used as a mechanism to realize the robustness property of biological systems [61,62]. The gene activation and inactivation windows realized by memory reaction provided novel insight into the origin of the repeated pulses in the p53-MDM2 core module. In particular, the stable time periods of gene activation play a major role in generating bursting dynamics with constant width and height of protein activity oscillations. A striking simulation result is that the oscillatory upstream signal is the key stimulus to maintain oscillatory dynamics of the p53 core module. In contract, the feedback regulations between p53 and MDM2 are not sufficient to maintain the oscillations of the p53 activity. This result is well compatible with the recent experimental observations showing that p53 induction is mediated by the damage-activated regulators [50,63]. Since a number of important regulatory mechanisms were excluded from the proposed stochastic model, including protein spatial distributions, regulation of other proteins such as MDMX, and feedback regulations between the upstream signals, more sophisticated models are needed to provide accurate simulations and testable predictions.Modeling of Memory ReactionsSupporting InformationSupporting Information S1 A detailed description o.