  High resolution observations of Young Stellar Object (YSO) jets show them to
be composed of many small-scale knots or clumps. In this paper we report
results of 3-D numerical simulations designed to study how such clumps interact
and create morphologies and kinematic patterns seen in emission line
observations. Our simulations focus on clump scale dynamics by imposing
velocity differences between spherical, over-dense regions which then lead to
the formation of bow shocks as faster clumps overtake slower material. We show
that much of the spatial structure apparent in emission line images of jets
arises from the dynamics and interactions of these bow shocks. Our simulations
show a variety of time-dependent features, including bright knots associated
with Mach stems where the shocks intersect, a "frothy" emission structure that
arises from the presence of the Non-linear Thin Shell Instability (NTSI) along
the surfaces of the bow shocks, and the merging and fragmentation of clumps.
Our simulations use a new non-equilibrium cooling method to produce synthetic
emission maps in H$\alpha$ and [S II]. These are directly compared with
multi-epoch Hubble Space Telescope (HST) observations of Herbig-Haro (HH) jets.
We find excellent agreement between features seen in the simulations and the
observations in terms of both proper motion and morphologies. Thus we conclude
that YSO jets may be dominated by heterogeneous structures and that
interactions between these structures and the shocks they produce can account
for many details of YSO jet evolution.
