Given the following PDE: $u_t(x,t)=u_{xx}(x,t)$, where the subindices are partial differentiation. Using the Fourier transform $(\mathcal{F})$ for the spatial frequency domain $(\omega)$, in the eq. gives:
$$\mathcal{F}\{u_t(x,t)\} = \mathcal{F}\{u_{xx}(x,t)\}$$ $$\Rightarrow \hat{u_t}(\omega,t)=-\omega^2\hat u(\omega,t) $$ $$\Rightarrow{d\over dt}\hat u=-\omega^2\hat u $$
and then solving the last ODE...
$$\hat u(\omega,t)=e^{-\omega^2t}\ \hat u(\omega,0) $$
Using now the inverse Fourier transform $(\mathcal F^{-1})$...
$$\mathcal F^{-1}\{\hat u(\omega,t)\}=\mathcal F^{-1}\{e^{-\omega^2t}\ \hat u(\omega,0)\} $$ $$\Rightarrow u(x,t)=\mathcal{F}^{-1}\{e^{-\omega^2t}\}*u(x,0) $$ $$\Rightarrow u(x,t)={1\over 2\sqrt{\pi t}}e^{-x^2\over 4t}*u(x,0) $$
where the simbol $*$ indicates the convolution operation in the space domain. Now my question is how to solve for boundary conditions? If we solve for Neumann conditions with boundaries for a function $u:[a,b]\times \Bbb R^+\to\Bbb R$:
$$u_x(a,t)=u_x(b,t)=0$$
partial differentiate the convolution...
$${\partial u\over \partial x}={\partial\over \partial x}\left( {1\over 2\sqrt{\pi t}}e^{-x^2\over 4t}*u(x,0)\right) $$
$$\Rightarrow {1\over 2\sqrt{\pi t}}e^{-x^2\over 4t}*u_x(x,0)= {-x\over \sqrt{\pi t}}e^{-x^2\over 4t}*u(x,0) $$
but then I don't know how to proceed. I now that using Fourier series, for the Dirichlet boundary conditions, the solutios is writen as a series of sines because for the domain $[0,L]$, $\sin(0)=\sin(n\pi x/L)=0$; and for the Neumann boundary conditions, the solution is writen as a series of cosines because $(\cos(n\pi x/L))'=\sin(n\pi x/L)$ and then the same as above is true. But How can I relationate the solutions using Fourier series with the solution using the convolution with the gaussian?
The usual Fourier transform is only defined for functions whose domain is the whole Euclidian space $\mathbb{R}^n$, so that method doesn't work when the domain of $u$ is $[a,b]$.
However, while the proof doesn't use Fourier transforms as far as I know, you can still write the solution as \begin{equation*} u(x,t) = {\int}_{\Omega} K(t,x,y)\ u(y,0)\ dy, \end{equation*} for a general domain $\Omega$. $K$ is called the heat kernel, and when $\Omega=\mathbb{R}$, it is indeed as you've written it : $$ K(t,x,y) = \frac{1}{2\sqrt{\pi t}} e^{-\frac{(x-y)^2}{4t}}. $$ As per Wikipedia,