Let $u \in C^{1}(0,\infty) \times C^{1}[0,1]$ be a solution to heat equation (1) with inital boundaries (2),(3)
(1) $\partial_tu(t,x)-\partial_{xx}u(t,x)=0$, for all $(t,x) \in[0,\infty)\times[0,1]$
(2) $u(t,0)=u(t,1)=0,$ for $t \in[0,\infty]$
(3) $u(0,x)=u_{0}(x),$ for $x\in[0,1]$
Show that there exists constants $C_{1},C_{2}$ such that $$ \int_{0}^{1}u^2(t,x)dx \leq C_{1}e^{-tC_2}\;\text{ for all }t\geq0 $$
Thoughts
I want to get this into a form where I can apply Wirtinger's inequality for functions: I tried by multiplying the through by $u(t,x)$ and intergrating but I couldn't get it out that way, so I'm not sure how to solve this.
Let's assume your solution has the regularity required by the equation. A way to get an estimate of this form is as follows: Consider a shifted multiple of the fundamental solution $G$, $w(x,t)=MG(x,t+1)$. For large enough $M$, $w(x,0)=MG(x,1)\ge u_0$. These shifted and rescaled Gaussians are solutions to your equation in all of $[0,\infty)\times\mathbb{R}$. Therefore they are solutions on $[0,\infty)\times[0,1]$ (with boundary data equal $w(t,0)>0$ and $w(t,1)>0$). By the parabolic comparison principle, the solution to your equation will be below $w$ at all times, $u(x,t)\le w(x,t)$ and, for $x\in[0,1]$, $w(x,t)\le Ct^{-1/2}$ where $C=M/{\sqrt{4\pi}}$.
As a consequence, $$ \int\limits_0^1 u^2(x,t)\, dx\le C^2t^{-1} $$