LaTeX macros gobble the trailing space, unless we escape it with '\ '.
D &\equiv P_0 - P && \text{the number of dead (unfolded) proteins} \\
\kappa &\equiv -\frac{1}{P} \deriv{t}{P} && \text{the unfolding rate}
\end{align}
-\nomenclature{$\equiv$}{Defined as (\ie equivalent to)}
+\nomenclature{$\equiv$}{Defined as (\ie\ equivalent to)}
The proteins are under constant loading because
\begin{equation}
\deriv{t}{F} = \deriv{x}{F}\deriv{t}{x} = kv\;,