Photoisomerization of conjugated systems is a common pathway for photomechanical energy conversion in biological chromophores. Such reactions are mediated by conical intersections (CIs)--points of degeneracy between different potential energy surfaces, which efficiently funnel population between electronic states. There are many examples of a chromophore's local environment playing an important role in determining the outcome of its photoisomerization reaction. To model such systems, we have employed the ab initio multiple spawning (AIMS) method for quantum dynamics on hybrid QM/MM potential energy surfaces. Studies of ethylene and p-coumaric acid photoisomerization suggest that electrostatic effects from the environment can play a dominant role in determining the outcome of these reactions. These reactions occur on ultrafast timescales, to which traditional transition state theories (TSTs) do not necessarily apply. To quantify the rates of such non-TST reactions, we have applied non-linear dimensionality reduction techniques to dynamical simulation data. Such techniques permit definition of simple, 1-dimensional reaction paths directly from dynamical simulation, without recourse to TST. These simple reaction path models help to elucidate the role of conical intersection topography in determining rates of interstate population transfer. [The dissertation citations contained here are published with the permission of ProQuest LLC. Further reproduction is prohibited without permission. Copies of dissertations may be obtained by Telephone (800) 1-800-521-0600. Web page: http://www.proquest.com.bibliotheek.ehb.be/en-US/products/dissertations/individuals.shtml.]