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

From: Mathematical model of the Tat-Rev regulation of HIV-1 replication in an activated cell predicts the existence of oscillatory dynamics in the synthesis of viral components

Subsystem number Parameter notation Units Reference value Reference
1 k t r a n s c r , i n i Transcription initiation/(min genome) 0.25 (for non-activated cell) [64, 65]
    25 (for activated cell)  
  LTR _ prom _ HIV1 elements/nucleus 1 assigned
2 k d e l a y 1/min 1 assigned
  λ   0.99 estimated
3 k a s s , T a t _ T A R elements/(nucleus min) 0.0017 [45]
  k d i s , T A T _ T A R 1/min 1  
  k a n t i t e r m 1/min 60 assigned
4 k t r a n s c r , e l o n g , i , i = 1 , . . . , n D N A u n i t 1/min 5.33 derived
  n D N A u n i t dimensionless 20 assigned
5 k t r a n s c r , t e r m 1/min 60 assigned
6 k m o d i f 1/min 60 assigned
7 k s p l i c i n g , 94 1/min 0.0415 [38, 48, 49]
8 k s p l i c i n g , 42 1/min 0.0415  
  δ 4 , T a t dimensionless 0.115 Estimated from [83]
  δ 4 , R e v dimensionless 0.115  
9 k t r a n s p , 2 k b - m R N A _ X x x , X x x { T a t , R e v } 1/min 0.0767 [27]
10 k t r a n s l , i n i , X x x , X x x { T a t , R e v } 1/min 10 assigned
  k t r a n s l , e l o n g , i , X x x { T a t , R e v } 1/min 18 derived
  k t r a n s l , t e r m , n X x x + 1 , X x x { T a t , R e v } 1/min 60 assigned
  n X x x , X x x { T a t , R e v } dimensionless 20 assigned
11 k t r a n s p , p r o t _ X x x , X x x { T a t , R e v } 1/min 0.347 [54]
12 k a s s , R e v _ ( i ) _ X _ n u c , i = 1 , . . . , n R e v , X { 9 , 4 }  
  copy/(nucleus min) 0.59  
  k a s s , R e v _ ( i ) _ X _ c y t , i = 1 , . . . , n R e v , X { 9 , 4 }    
  [28]    
  k d i s , R e v _ ( i ) _ X _ n u c , i = 1 , . . . , n R e v , X { 9 , 4 } 1/min 8.4  
  k d i s , R e v _ ( i ) _ X _ c y t , i = 1 , . . . , n R e v , X { 9 , 4 }    
13 k t r a n s p , X , 1 , X { 9 , 4 } 1/min 0 [82]
  k t r a n s p , X , i , i = 2 , . . . , n R e v , X , X { 9 , 4 } 1/min 0.0767 [27]
  γ i , i = 1 , . . . , n R e v , X dimensionless 12 Quantified following the recycling in the nuclear pore hypothesis
12,13 n R e v , X , X { 9 , 4 } dimensionless 12 [28, 52, 53]
14 k d e g r , X k b - m R N A _ y y y , X { 9 , 4 } , y y y { n u c , c y t }    
  k d e g r , 2 k b _ m R N A _ T a t _ y y y , y y y { n u c , c y t } 1/min 0.0029 [58]
  k d e g r , 2 k b _ m R N A _ Re v _ y y y , y y y { n u c , c y t }    
  k d e g r , p r o t - X x x _ n u c , X x x { T a t , R e v } 1/min 0.000722  
  [60]    
  k d e g r , p r o t - X x x _ c y t , X x x { T a t , R e v } 1/min 0.00289  
Auxiliary parameters r t r a n s c r , e l o n g nts/min 2400 [38, 40]
  r t r a n s c l , e l o n g nts/min 1800 [55, 56]
  Nucl_9 kb-RNA nucl 9000 [25]
  Nucl_2 kb-mRNA nucl 2000