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In the limit (taurightarrow0), (2.5) reduces to the neural master equation of Buice et al. [17, 20].
The probability distribution is taken to evolve according to a master equation of the form [20 23] (1).
The master equation of the SQDs' subsystem is given by ∂ t ρ = - i [ H ″, ρ ] + ς S Q D, (14).
This produces a flow out of the state n at rate α, proportional to (p_{n}(t)), hence a term in the master equation of the form (-alpha nP_{n}(t)).
Taking this, and assuming the typical experimental case in which the lattice spacing a is comparable to the wavelength of scattered photons,, the dynamics of the many-body density operator ρ follows a master equation of the form,.
This implies that when approximatingthe neural master equation of Buice et al. [46, 54] by a Langevin equation in the form of Equation 5.1 with σ ~ 1 N, where N is the system size, the resulting Hamiltonian differs from that obtained directly from the master equation and can thus generate a poor estimate of the extinction time.
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(A rigorous analysis of the convergence of solutions of a chemical master equation to solutions of the corresponding Langevin equation in the mean-field limit has been carried out by Kurtz [48].) It is important to note that the Langevin equation (12) takes the form of an Ito rather than Stratonovich stochastic differential equation (SDE).
The goal of this section is to develop a master equation for the rate of coalescence.
The total electronic energy of folding, ΔEfolding, is just one part of the folding free energy, ΔGfolding, obtained using the master equation for the computation of the folding free energy from a fully unfolded reference structure [19].
The master
The framework yields a stochastic master equation for the probabilities of DNA microstates.
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