We present our response to the commentary piece by Makri {\it et al.} [arXiv:2410.08239], which raises critiques of our work [Nat. Commun. 15, 8087 (2024)]. In our paper, we considered various settings of open-quantum system dynamics, including non-commuting, non-diagonalizable system-bath coupling, and bosonic/spin/fermionic baths. For these, we showed a direct and explicit relationship between the discrete-time memory kernel (
K) of the generalized quantum master equation (GQME) and the discrete-time influence functions (
I) of the path integrals. As an application of this, we showed one can construct
K without projection-free dynamics inputs that conventional methods require, and we also presented a quantum sensing protocol that characterizes the bath spectral density from reduced system dynamics. As the Comment focused on the relationship between (
K) and
I in one specific setup (i.e., commuting, diagonalizable system-bath coupling with a bosonic bath), we focus on that aspect in this response. In summary, we could not find a set of equations that explicitly connect
I and
K from Makri's 2020 paper [J. Chem. Theory Comput. 16, 4038 (2020)]. Furthermore, while our analysis is specific to the choice of discretization of path-integral and GQME, we have not found issues with the GQME discretization employed. As per critiques on citations, in our paper, we note that we had acknowledged Makri's driven SMatPI work and Wang and Cai's tree-based SMatPI work for the number of Dyck paths needed for the computation of the memory kernel.
The transfer tensor method (TTM) [Cerrillo and Cao, Phys. Rev. Lett. 112, 110401 (2014)] can be considered a discrete-time formulation of the Nakajima-Zwanzig quantum master equation (NZ-QME) for modeling non-Markovian quantum dynamics. A recent paper [Makri, J. Chem. Theory Comput. 21, 5037 (2025)] raised concerns regarding the consistency of the TTM discretization, particularly a spurious term at the initial time t = 0. This work presents a detailed analysis of the discretization structure of the TTM, clarifying the origin of the initial-time correction and establishing a consistent relationship between the TTM discrete-time memory kernel KN and the continuous-time NZ-QME kernel K(NΔt). This relationship is validated numerically using the spin-boson model, demonstrating convergence of reconstructed memory kernels and accurate dynamical evolution as Δt → 0. While the TTM provides a consistent discretization, we note that alternative schemes are also viable, such as the midpoint derivative/midpoint integral scheme proposed in Makri's work. The relative performance of various schemes for either computing accurate K(NΔt) from exact dynamics or obtaining accurate dynamics from exact K(NΔt) warrants further investigation.
This preprint presents a self-contained and mathematically explicit reconstruction of the Gorini-Kossakowski-Sudarshan-Lindblad (GKSL) master equation starting from exact microscopic unitary dynamics through the Nakajima-Zwanzig projection operator formalism. Beginning with the exact non-local generalized master equation, we systematically analyze the hierarchy of approximations required for the emergence of a Markovian quantum dynamical semigroup. The Born (weak-coupling), Markov (time-localization), and secular approximations are derived and interpreted as successive information-reduction steps, each associated with clearly identifiable mathematical assumptions and physical consequences. Particular attention is devoted to the role of secularization in transforming the Redfield generator into a completely positive GKSL structure. To provide a concrete worked example, the formalism is applied to a damped two-level system coupled to a bosonic thermal reservoir, where the Redfield and GKSL equations are derived explicitly and compared at the microscopic level. Beyond the derivation itself, the work develops a systematic map of validity limits and failure regimes. The breakdown of the Born, Markov, secular, factorization, and stationarity assumptions is analyzed in terms of environmental correlation times, spectral-density structure, non-Markovian memory effects, information backflow, and loss of semigroup behavior. The resulting framework clarifies the precise operational domain in which GKSL dynamics can be regarded as a physically reliable effective description and provides a rigorous foundation for applications involving entropy-production theorems, quantum thermodynamics, and open-system information theory.