Fish Biology

Following initialization, the simulation was conducted by combining LTRANS with our own MATLAB scripts, thus avoiding the complications of modifying LTRANS code for the purposes of this study, and making post-simulation data organization and analysis straightforward.

Using this software combination, the following processes were updated at appropriate time steps: growth, behavior, particle position, mortality, and recruitment. Model calculations followed this same order. First, size (total length , TTL) was updated for each particle. Second, when used, size-dependent particle behavior was determined for simulations involving non-passive particles. Third, particle position was updated as the interaction of advection, vertical turbulence and horizontal turbulence (and behavior when present), based on the hydrodynamic data read in from the Espresso flow fields. Fourth, mortality was estimated from the combination of natural mTrortality, transport out of model domain, or premature entrance into nursery areas (see below). Fifth, numbers of recruits was calculated, based on larval size, particle position and particle internal amounts. The first three processes (growth, behavior and particle position) were updated every 60 second; mortality and recruitment was assessed every 2 hours. Methods used to calculate each process are detailed below.

Growth

Behaviour

Mortality

Recruitment to nurseries

Last revised: 5/7/2015