Table 1 Summary of the model parameters used for numerical simulations of HIV-1 replication.

$k_{transcr,ini}$

Transcription initiation/(min genome)

0.25 (for non-activated cell)

[64, 65]

25 (for activated cell)

$LTR\text{\_}prom\text{\_}HIV1$

elements/nucleus

1

assigned

$k_{delay}$

1/min

1

assigned

λ

0.99

estimated

$k_{ass,Tat\text{\_}TAR}$

elements/(nucleus min)

0.0017

[45]

$k_{dis,TAT\text{\_}TAR}$

1/min

1

$k_{antiterm}$

1/min

60

assigned

$k_{transcr,elong,i},i=1,...,n_{DNAunit}$

1/min

5.33

derived

$n_{DNAunit}$

dimensionless

20

assigned

$k_{transcr,term}$

1/min

60

assigned

$k_{modif}$

1/min

60

assigned

$k_{splicing,94}$

1/min

0.0415

[38, 48, 49]

$k_{splicing,42}$

1/min

0.0415

${\delta }_{4,Tat}$

dimensionless

0.115

Estimated from [83]

${\delta }_{4,Rev}$

dimensionless

0.115

$\begin{array}{c}{k}_{transp,2kb-mRNA\text{\_}Xxx},\\ Xxx\in \left\{Tat,Rev\right\}\end{array}$

1/min

0.0767

[27]

$k_{transl,ini,Xxx},Xxx\in \left\{Tat,Rev\right\}$

1/min

10

assigned

$k_{transl,elong,i},Xxx\in \left\{Tat,Rev\right\}$

1/min

18

derived

$k_{transl,term,n_{Xxx}+1},Xxx\in \left\{Tat,Rev\right\}$

1/min

60

assigned

$n_{Xxx},Xxx\in \left\{Tat,Rev\right\}$

dimensionless

20

assigned

$k_{transp,prot\text{\_}Xxx},Xxx\in \left\{Tat,Rev\right\}$

1/min

0.347

[54]

$\begin{array}{c}{k}_{ass,Rev\text{\_}\left(i\right)\text{\_}X\text{\_}nuc},\\ i=1,...,n_{Rev},X\in \left\{9,4\right\}\end{array}$

copy/(nucleus min)

0.59

$\begin{array}{c}{k}_{ass,Rev\text{\_}\left(i\right)\text{\_}X\text{\_}cyt},\\ i=1,...,n_{Rev},X\in \left\{9,4\right\}\end{array}$

[28]

$\begin{array}{c}{k}_{dis,Rev\text{\_}\left(i\right)\text{\_}X\text{\_}nuc},\\ i=1,...,n_{Rev},X\in \left\{9,4\right\}\end{array}$

1/min

8.4

$\begin{array}{c}{k}_{dis,Rev\text{\_}\left(i\right)\text{\_}X\text{\_}cyt},\\ i=1,...,n_{Rev},X\in \left\{9,4\right\}\end{array}$

$k_{transp,X,1},X\in \left\{9,4\right\}$

1/min

0

[82]

$\begin{array}{c}{k}_{transp,X,i},\\ i=2,...,n_{Rev,X},X\in \left\{9,4\right\}\end{array}$

1/min

0.0767

[27]

${\gamma }_i,i=1,...,n_{Rev,X}$

dimensionless

12

Quantified following the recycling in the nuclear pore hypothesis

$n_{Rev,X},X\in \left\{9,4\right\}$

dimensionless

12

[28, 52, 53]

$k_{degr,Xkb-mRNA\text{\_}yyy},X\in \left\{9,4\right\}$,

$yyy\in \left\{nuc,cyt\right\}$

$\begin{array}{c}{k}_{degr,2kb\text{\_}mRNA\text{\_}Tat\text{\_}yyy},\\ yyy\in \left\{nuc,cyt\right\}\end{array}$

1/min

0.0029

[58]

$\begin{array}{c}{k}_{degr,2kb\text{\_}mRNA\text{\_}\mathsf{\text{Re}}v\text{\_}yyy},\\ yyy\in \left\{nuc,cyt\right\}\end{array}$

$\begin{array}{c}{k}_{degr,prot-Xxx\text{\_}nuc},\\ Xxx\in \left\{Tat,Rev\right\}\end{array}$

1/min

0.000722

[60]

$k_{degr,prot-Xxx\text{\_}cyt},Xxx\in \left\{Tat,Rev\right\}$

1/min

0.00289

Auxiliary

parameters

$r_{transcr,elong}$

nts/min

2400

[38, 40]

$r_{transcl,elong}$

nts/min

1800

[55, 56]

Nucl_9 kb-RNA

nucl

9000

[25]

Nucl_2 kb-mRNA

nucl

2000