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Let $\Omega$ be a bounded and regular open subset $\Omega$ of $\mathbb{R}^N$ and $u:[0,\infty)\times \Omega\to \mathbb{R}$ be a smooth function (for example a smooth solution to a PDE). Thus the function $w=\min(0,u)$ has weak time derivative given by $w_t=u_t.1_{\{u \leq 0 \}}$. Does the following "weak differentiation under the integral sign" holds? $$\frac{d}{dt}\int_\Omega w(t,x)dx=\int_\Omega \frac{\partial}{\partial t}w(t,x)dx,$$ for almost all $t\geq 0$.

We know that differentiation under the integral sign holds for $u$ because it is smooth. But I am wondering if it also holds for a function like $w=\min(0,u)$ which only has a weak derivative.

My guess is that since $w$ has a weak derivative in time (real line), then it must be differentiable for almost all $t\geq 0$ (which is not necessarily true in higher dimension, for example differentiation with respect to space $x$). So $\int_\Omega w(t,x)dx$ must also be differentiable for almost all $t\geq 0$ and so we can use some kind of dominated convergence theorem.

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Yes, it does hold, and the only necessary information about $w$ is that it's weakly differentiable. $\newcommand{\pl}{\partial}$

The fact that $w$ has a weak derivative $\pl_t w$ means $$ \int_0^\infty \int_\Omega \pl_t \Phi(t,x) w(t,x) + \Phi(t,x) \pl_t w(t,x) \, dx dt = 0 \quad \text{for } \Phi \in C_c^\infty((0,\infty) \times \Omega). $$ Specializing to $\Phi$ of the form $\Phi(t,x) = \varphi(t)\eta(x)$ with $\varphi \in C_c^\infty(0,\infty)$ and $\eta \in C_c^\infty(\Omega)$, we have $$ \int_0^\infty \int_\Omega (\pl_t \varphi(t,x) w(t,x) + \varphi(t,x) \pl_t w(t,x)) \eta(x) \, dx dt = 0 \quad \text{for all } \varphi, \ \eta. $$ One can choose a sequence of $\eta$'s approximating the function constantly equal $1$ on $\Omega$. If only $w$ and $\pl_t w$ are integrable (in your case, this translates to an integrability condition for $u$ and $\pl_t u$), Lebesgue's dominated convergence theorem implies in the limit that $$ \int_0^\infty \int_\Omega \pl_t \varphi(t,x) w(t,x) + \varphi(t,x) \pl_t w(t,x) \, dx dt = 0 \quad \text{for } \varphi \in C_c^\infty(0,\infty). $$ The above can be rewritten as $$ \int_0^\infty \pl_t \varphi(t,x) \left( \int_\Omega w(t,x) \, dx \right) + \varphi(t,x) \left( \int_\Omega \pl_t w(t,x) \, dx \right) dt = 0 \quad \text{for } \varphi \in C_c^\infty(0,\infty), $$ which is nothing else but the statement that $$ \pl_t \left( \int_\Omega w(t,x) \, dx \right) = \int_\Omega \pl_t w(t,x) \, dx $$ weakly.

If you want to have a.e. pointwise differentiability, just recall that any weakly differentiable function on the line is almost everywhere differentiable (its pointwise derivative coinciding with its weak derivative).