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Use $T={\xi }^0$ and ${\xi }^i={\partial }^i\lambda$, and define the physical background Hubble parameter by $H=\dot{a}/(\bar{N}a)$. At first order, the spacetime metric components are $\delta g_{00}=-2{\bar{N}}^2\Phi$, $\delta g_{0i}=a^2{B}_{,i}$ and $\delta g_{ij}=-2a^2(\Psi {\delta }_{ij}+E_{,ij})$. Apply the given passive cosmological gauge transformation component by component. The temporal component changes by $2\bar{N}\dot{\bar{N}}T+2{\bar{N}}^2\dot{T}$; the mixed component changes by ${\bar{N}}^2{T}_{,i}-a^2{\dot{\lambda }}_{,i}$; and the spatial component changes by $-2a\dot{a}T{\delta }_{ij}-2a^2{\lambda }_{,ij}$. HenceThese are the scalar gauge transformations with a background lapse in the paper's sign convention.

Starting in synchronous gauge, preserving both $\Phi =0$ and $B=0$ requiresThe first equation integrates to $\bar{N}T=C(\mathbf{x})$; substituting in the second and integrating givesThe arbitrary lower integration limit is absorbed into $D$. Thus specifying synchronous lapse and shift does not fix the origins of the freely falling clocks or all spatial coordinate labels. This is the residual gauge freedom in synchronous gauge.

During cosmic inflation, choosing these clocks remains arbitrary. For example, the $C$ mode shifts the spatial potential by $HC$ and the density perturbation by $3HC(\bar{\rho }+\bar{P})$. In the de Sitter approximation, $H$ varies little, so a nearly constant metric perturbation can contain a pure coordinate contribution. An inflaton fluctuation or density contrast in synchronous gauge therefore cannot be declared physical solely from its time behavior. Use a uniform-density curvature perturbation or an appropriate field-based gauge-invariant variable, or fix a physical initial slicing. The exact de Sitter case has no evolving homogeneous density clock, which makes density-defined slicing degenerate.

During the standard hot Big Bang, a cold-matter rest frame supplies a convenient additional condition: imposing zero cold-matter velocity removes the nontrivial spatially varying time-shift mode. Before that condition is imposed, the pure-gauge density contrast for constant $w$ is $3H(1+w)C$, which decays as $t^{-1}$ in either radiation or matter domination. In conformal time this is proportional to ${\tau }^{-2}$ during radiation domination and ${\tau }^{-3}$ during matter domination. It can be confused with an independent decaying physical mode unless gauge freedom is fixed. The $D$ mode is a time-independent spatial relabeling and must likewise be fixed by a coordinate or initial-metric convention.

Finally, a scalar density transforms by evaluating the homogeneous scalar at the shifted time:To reach Newtonian gauge from synchronous quantities, impose $\tilde{E}=\tilde{B}=0$. For the nonhomogeneous scalar modes, chooseUsing background stress-energy conservation, $\dot{\bar{\rho }}=-3\bar{N}H(\bar{\rho }+\bar{P})$, gives the synchronous-to-Newtonian density transformation with a lapse:The expression includes the lapse factors because dots refer to the arbitrary time coordinate, not automatically to proper time.

Retain the homogeneous lapse function $\bar{N}(t)$, and define the physical Hubble parameter $H=\dot{a}/(\bar{N}a)$. At first order the scalar metric perturbations give $\delta g_{00}=-2{\bar{N}}^2\Phi$, $\delta g_{0i}=a^2{B}_{,i}$, and $\delta g_{ij}=-2a^2(\Psi {\delta }_{ij}+E_{,ij})$. Applying the passive coordinate displacement component by component gives the scalar gauge transformations with a background lapseFor example the $0i$ transformation is $\delta {\tilde{g}}_{0i}=a^2{\partial }_{i}B-a^2{\partial }_i\dot{\lambda }+{\bar{N}}^2{\partial }_i{\xi }^0$. The spatial isotropic part acquires $-2a\dot{a}{\xi }^0{\delta }_{ij}$, explaining the positive sign in the transformation of $\Psi$.

Preserving synchronous gauge requires both transformed $\Phi$ and $B$ to remain zero. The first condition is ${\partial }_t(\bar{N}{\xi }^0)=0$, and the second is $\dot{\lambda }={\bar{N}}^2{\xi }^0/a^2$. Integrating them givesThus fixing the lapse function and shift vector perturbations does not exhaust the scalar coordinate freedom. The functions $C,D$ describe residual synchronous-gauge freedom; an integration-origin change in the integral is absorbed into $D$.

To move from synchronous gauge to Newtonian gauge, choose $\lambda =-E_S$ to set $\tilde{E}=0$. Requiring $\tilde{B}=0$ then givesA scalar energy density transforms as $\delta {\rho }_N=\delta {\rho }_S-\dot{\bar{\rho }}{\xi }^0$. Dividing by the background energy density, which changes the contrast only at second order if perturbed in that denominator, yields the synchronous-to-Newtonian density transformation with a lapseThe last form uses background stress-energy conservation, $\dot{\bar{\rho }}=-3\bar{N}H(\bar{\rho }+\bar{P})$. With cosmic time $\bar{N}=1$ this is ${\delta }_N={\delta }_S-3(1+w)a^{2}H{\dot{E}}_S$; with conformal time $\bar{N}=a$ it is ${\delta }_N={\delta }_S-3(1+w)\mathcal{H}{E}_S^{\prime }$, where $\mathcal{H}=a^{\prime }/a$. Keeping these clock conventions distinct is essential to the factors of $a$.