Scillations observed at population level. To answer this question, stochastic simulations were obtained by using different pulse numbers of the upstream signal in different simulations. According to simulations in Figs. 6B and 6E, it was assumed that the pulse number of the upstream signal was equal to the p53 pulse number. Thus the fraction of cells with different pulse numbers of the upstream signal in Fig. 7A is the same as that of the p53 pulse numbers which was estimated from Fig. 3 in [9]. Simulations in Figs. 7B and 7C successfully realized the damped oscillations of p53 and MDM2 protein levels that were compatible to experimental observations [51]. The height of oscillations at population level is proportional to the dose of gamma radiation. Simulations suggested that a higher radiation dose induced a larger fraction of cells showing more pulses of p53 activity, which led to the higher expression levels of gene MDM2 at population level in Figure 7C.Modeling of Memory ReactionsFigure 3. Averaged bursting numbers under various conditions. The averaged bursting number per simulation based on different numbers of TF but a fixed number of RNAP with either constant lengths of memory windows in (A) or lengths following the exponential distributions in (B). Rate constant are the same as those in Figure 2. The averaged bursting number per simulation based on different numbers of RNAP but a fixed TF number with the binding rate of RNAP to DNA as k 0:021 in (C) or 
k 0:0021 in (D). The corresponding rate constant in Figure 2 is k 0:21 (solid line: mean; dash-line: mean+std). doi:10.1371/journal.pone.0052029.gDiscussionThis work proposed the concept of memory reaction to describe conditional chemical reactions that occur in 15481974 the path of memory events. The proposed memory-SSA represents an innovative strategy to use a reduced model to describe nonlinear dynamics. To demonstrate the power of the proposed theory, we developed a stochastic model of single-gene expression. Numerical simulations suggested that memory reactions for realizing gene activation/ inactivation windows play a major role in generating bursting dynamics of gene expression. The function of memory reactions has been further supported by realizing the oscillatory activities of the p53 core module in single cells. Simulations suggested that memory process is a key inhibitor mechanism to generate sustained oscillations of protein levels in single cells and damped oscillations in population of cells. These successful applications suggested that the proposed theory is an effective tool to realize conditional chemical reactions in a wide range of complex biological Epigenetic Reader Domain system. Time delay is 
a modeling technique to realize slow reactions or simplify multiple small step reactions [24,25]. It is emphasized that the difference between the delayed reaction and the proposed memory reaction is substantial. First, the firing of delayed reactions depends on the competition with other reactions in the system. However, the occurrence of memory reactions is conditional to the path of memory events, though simultaneouslyFigure 4. Simulated noise in protein abundance. Noise in protein abundance (sp =vpw) derived from stochastic simulations with different TF numbers (solid-line: lengths of memory windows are constant; dash-line: lengths of windows follow the exponential distributions; dash-dot line: theoretical prediction from a simpler stochastic model in [19]). doi:10.1371/journal.pone.0052029.gModeling of Me.Scillations observed at population level. To answer this question, stochastic simulations were obtained by using different pulse numbers of the upstream signal in different simulations. According to simulations in Figs. 6B and 6E, it was assumed that the pulse number of the upstream signal was equal to the p53 pulse number. Thus the fraction of cells with different pulse numbers of the upstream signal in Fig. 7A is the same as that of the p53 pulse numbers which was estimated from Fig. 3 in [9]. Simulations in Figs. 7B and 7C successfully realized the damped oscillations of p53 and MDM2 protein levels that were compatible to experimental observations [51]. The height of oscillations at population level is proportional to the dose of gamma radiation. Simulations suggested that a higher radiation dose induced a larger fraction of cells showing more pulses of p53 activity, which led to the higher expression levels of gene MDM2 at population level in Figure 7C.Modeling of Memory ReactionsFigure 3. Averaged bursting numbers under various conditions. The averaged bursting number per simulation based on different numbers of TF but a fixed number of RNAP with either constant lengths of memory windows in (A) or lengths following the exponential distributions in (B). Rate constant are the same as those in Figure 2. The averaged bursting number per simulation based on different numbers of RNAP but a fixed TF number with the binding rate of RNAP to DNA as k 0:021 in (C) or k 0:0021 in (D). The corresponding rate constant in Figure 2 is k 0:21 (solid line: mean; dash-line: mean+std). doi:10.1371/journal.pone.0052029.gDiscussionThis work proposed the concept of memory reaction to describe conditional chemical reactions that occur in 15481974 the path of memory events. The proposed memory-SSA represents an innovative strategy to use a reduced model to describe nonlinear dynamics. To demonstrate the power of the proposed theory, we developed a stochastic model of single-gene expression. Numerical simulations suggested that memory reactions for realizing gene activation/ inactivation windows play a major role in generating bursting dynamics of gene expression. The function of memory reactions has been further supported by realizing the oscillatory activities of the p53 core module in single cells. Simulations suggested that memory process is a key mechanism to generate sustained oscillations of protein levels in single cells and damped oscillations in population of cells. These successful applications suggested that the proposed theory is an effective tool to realize conditional chemical reactions in a wide range of complex biological system. Time delay is a modeling technique to realize slow reactions or simplify multiple small step reactions [24,25]. It is emphasized that the difference between the delayed reaction and the proposed memory reaction is substantial. First, the firing of delayed reactions depends on the competition with other reactions in the system. However, the occurrence of memory reactions is conditional to the path of memory events, though simultaneouslyFigure 4. Simulated noise in protein abundance. Noise in protein abundance (sp =vpw) derived from stochastic simulations with different TF numbers (solid-line: lengths of memory windows are constant; dash-line: lengths of windows follow the exponential distributions; dash-dot line: theoretical prediction from a simpler stochastic model in [19]). doi:10.1371/journal.pone.0052029.gModeling of Me.
