\(\newcommand{\p}[1]{\frac{\partial }{\partial #1}}\) \(\newcommand{\pp}[2]{\frac{\partial #1}{\partial #2}}\) \(\newcommand{\dd}[2]{\frac{d #1}{d #2}}\) \(\newcommand{\h}{\frac{1}{2}}\) \(\newcommand{\op}[1]{\operatorname{#1}}\)

8.7.3.19. Viruses¶

To turn plankton type jv into a virus, set isvirus(jv) to 1 and set v_absorp(js,jv) to the absorption rate for any susceptible plankton type js. Set isinfect(js,jv) to the number of the infected type js turns into when infected by jv. For other parameters, see Table 8.57.

8.7.3.19.1. Dynamic equations¶

Denote with \(S\) the biomass of the susceptible plankton type, with \(I\) that of the infected type and with \(V\) that of the virus type. Viral dynamics adds the following tendencies to the model equations:

\[\begin{split}\partial_t S &= -\frac{\epsilon\varphi}{Q_{\mathrm{V}}} S V \\ \partial_t I &= +\frac{\epsilon\varphi}{Q_{\mathrm{V}}} S V +\frac{\epsilon\varphi}{Q_{\mathrm{S}}} S V -\frac{1}{\eta} I \\ \partial_t V &= +\beta \frac{Q_{\mathrm{V}}}{Q_{\mathrm{S}}} \frac{1}{\eta} I -\frac{\varphi}{Q_{\mathrm{S}}} S V \\ \partial_t\op{DOM} &= \alpha (1-\beta \frac{Q_{\mathrm{V}}}{Q_{\mathrm{S}}}) \frac{1}{\eta} I +(1 - \epsilon) \frac{\varphi}{Q_{\mathrm{S}}} S V \\ \partial_t\op{POM} &= (1-\alpha) (1-\beta \frac{Q_{\mathrm{V}}}{Q_{\mathrm{S}}}) \frac{1}{\eta} I \\\end{split}\]

\(Q_{\mathrm{S}}\) is the carbon quota of the susceptible type as used in allometric trait generation. The other parameters are listed in Table 8.57.

8.7.3.19.2. Runtime parameters¶

Table 8.57 Darwin virus parameters¶
	Name	Type	Description
	isvirus(jv)	INTEGER	1: plankton type jv is a virus
	isinfect(js,jv)	INTEGER	>0: type jv infects type js to become type isinfect(js,jv)
\(Q_{\mathrm{V}}\)	v_quota(jv)	_RL	virus carbon quota [mmol C/viron]
\(\varphi\)	v_absorp(js,jv)	_RL	specific virus absorption rate [\(m^3/s/\)individual]
\(\epsilon\)	v_abeff(js,jv)	_RL	absorption efficiency
\(\eta\)	v_latent(js,jv)	_RL	latency period [s]
\(\beta\)	v_burst(js,jv)	_RL	burst size [#virons]
\(\alpha\)	v_dompomfrac(js,jv)	_RL	fraction if burst going to DOM

So far only fixed elemential ratios are supported.