Molecules


Lext(p,n~345~355)
Lext(p,n~345~355~PLUS~MINUS)

Lext(p,n~345~346~347~348~349~350~351~352~353~354~355)

Lext p n 345 346 347 348 349 350 351 352 353 354 355

Pit(s~p~e,l1,l2,l3,l4,l5,l6,l7,l8,l9,l10)

Pit s p e l1 l2 l3 l4 l5 l6 l7 l8 l9 l10

End(l1,l2,l3,l4,l5,l6,l7,l8,l9,l10)

Lint(n~345~346~347~348~349~350~351~352~353~354~355)

Lint n 345 346 347 348 349 350 351 352 353 354 355

mRNA()

mRNA

GFP()

GFP

Trash()

Trash

I()

I

Timer()

Timer

Species

Lext(p,n~345)

Lext p n 345

Lext(p,n~346)

Lext p n 346

Lext(p,n~347)

Lext p n 347

Lext(p,n~348)

Lext p n 348

Lext(p,n~349)

Lext p n 349

Lext(p,n~350)

Lext p n 350

Lext(p,n~351)

Lext p n 351

Lext(p,n~352)

Lext p n 352

Lext(p,n~353)

Lext p n 353

Lext(p,n~354)

Lext p n 354

Lext(p,n~355)

Lext p n 355

Pit(s~p,l1,l2,l3,l4,l5,l6,l7,l8,l9,l10)

Pit s p l1 l2 l3 l4 l5 l6 l7 l8 l9 l10

mRNA()

mRNA

GFP()

GFP

I()

I

Timer()

Timer

Observables

Lext Lext(p,n)

Lext p n

Pit Pit(s~p)

Pit s p ?l1 ?l2 ?l3 ?l4 ?l5 ?l6 ?l7 ?l8 ?l9 ?l10

Endo Pit(s~e)

Pit s e ?l1 ?l2 ?l3 ?l4 ?l5 ?l6 ?l7 ?l8 ?l9 ?l10

Molecules Pit0 Pit()
Molecules Pit1 Lext(p!1,n).Pit(l1!1,l2,l3,l4,l5,l6,l7,l8,l9,l10)
Molecules Pit2 Lext(p!2,n).Lext(p!1,n).Pit(l1!1,l2!2,l3,l4,l5,l6,l7,l8,l9,l10)
Molecules Pit3 Lext(p!3,n).Lext(p!2,n).Lext(p!1,n).Pit(l1!1,l2!2,l3!3,l4,l5,l6,l7,l8,l9,l10)
Molecules Pit4 Lext(p!4,n).Lext(p!3,n).Lext(p!2,n).Lext(p!1,n).Pit(l1!1,l2!2,l3!3,l4!4,l5,l6,l7,l8,l9,l10)
Molecules Pit5 Lext(p!5,n).Lext(p!4,n).Lext(p!3,n).Lext(p!2,n).Lext(p!1,n).Pit(l1!1,l2!2,l3!3,l4!4,l5!5,l6,l7,l8,l9,l10)
Molecules Pit6 Lext(p!6,n).Lext(p!5,n).Lext(p!4,n).Lext(p!3,n).Lext(p!2,n).Lext(p!1,n).Pit(l1!1,l2!2,l3!3,l4!4,l5!5,l6!6,l7,l8,l9,l10)
Molecules Pit7 Lext(p!7,n).Lext(p!6,n).Lext(p!5,n).Lext(p!4,n).Lext(p!3,n).Lext(p!2,n).Lext(p!1,n).Pit(l1!1,l2!2,l3!3,l4!4,l5!5,l6!6,l7!7,l8,l9,l10)
Molecules Pit8 Lext(p!8,n).Lext(p!7,n).Lext(p!6,n).Lext(p!5,n).Lext(p!4,n).Lext(p!3,n).Lext(p!2,n).Lext(p!1,n).Pit(l1!1,l2!2,l3!3,l4!4,l5!5,l6!6,l7!7,l8!8,l9,l10)
Molecules Pit9 Lext(p!9,n).Lext(p!8,n).Lext(p!7,n).Lext(p!6,n).Lext(p!5,n).Lext(p!4,n).Lext(p!3,n).Lext(p!2,n).Lext(p!1,n).Pit(l1!1,l2!2,l3!3,l4!4,l5!5,l6!6,l7!7,l8!8,l9!9,l10)
Molecules Pit10 Lext(p!10,n).Lext(p!9,n).Lext(p!8,n).Lext(p!7,n).Lext(p!6,n).Lext(p!5,n).Lext(p!4,n).Lext(p!3,n).Lext(p!2,n).Lext(p!1,n).Pit(l1!1,l2!2,l3!3,l4!4,l5!5,l6!6,l7!7,l8!8,l9!9,l10!10)

Lint Lint()

Lint n 345 346 347 348 349 350 351 352 353 354 ?355

mRNA mRNA

mRNA

GFP GFP

GFP

TimerCount Timer

Timer

Reaction Rules


degrade external lipoplex (washing)

Lext(p,n) -> Trash()

Lext p n degraded Trash synthesized

attach - external lipoplex attaches to clathrin-coated pit

Lext(p,n) + Pit(s~p,l1,l2,l3,l4,l5,l6,l7,l8,l9,l10) -> Lext(p!1,n).Pit(s~p,l1!1,l2,l3,l4,l5,l6,l7,l8,l9,l10) + Pit(s~p,l1,l2,l3,l4,l5,l6,l7,l8,l9,l10)

Lext p n ⬇ Pit s p l1 l2 l3 l4 l5 l6 l7 l8 l9 l10 Pit s p l1 l2 l3 l4 l5 l6 l7 l8 l9 l10 synthesized

Lext(p,n) + Lext(p!1,n).Pit(s~p,l1!1,l2,l3,l4,l5,l6,l7,l8,l9,l10) -> Lext(p!2,n).Lext(p!1,n).Pit(s~p,l1!1,l2!2,l3,l4,l5,l6,l7,l8,l9,l10)

Lext ⬇p n ⬇ Lext p n Pit s p l1 ⬇l2 l3 l4 l5 l6 l7 l8 l9 l10

Lext(p,n) + Lext(p!2,n).Lext(p!1,n).Pit(s~p,l1!1,l2!2,l3,l4,l5,l6,l7,l8,l9,l10) -> Lext(p!3,n).Lext(p!2,n).Lext(p!1,n).Pit(s~p,l1!1,l2!2,l3!3,l4,l5,l6,l7,l8,l9,l10)

Lext ⬇p n ⬇ Lext p n Lext p n Pit s p l1 l2 ⬇l3 l4 l5 l6 l7 l8 l9 l10

Lext(p,n) + Lext(p!3,n).Lext(p!2,n).Lext(p!1,n).Pit(s~p,l1!1,l2!2,l3!3,l4,l5,l6,l7,l8,l9,l10) -> Lext(p!4,n).Lext(p!3,n).Lext(p!2,n).Lext(p!1,n).Pit(s~p,l1!1,l2!2,l3!3,l4!4,l5,l6,l7,l8,l9,l10)

Lext ⬇p n ⬇ Lext p n Lext p n Lext p n Pit s p l1 l2 l3 ⬇l4 l5 l6 l7 l8 l9 l10

Lext(p,n) + Lext(p!4,n).Lext(p!3,n).Lext(p!2,n).Lext(p!1,n).Pit(s~p,l1!1,l2!2,l3!3,l4!4,l5,l6,l7,l8,l9,l10) -> Lext(p!5,n).Lext(p!4,n).Lext(p!3,n).Lext(p!2,n).Lext(p!1,n).Pit(s~p,l1!1,l2!2,l3!3,l4!4,l5!5,l6,l7,l8,l9,l10)

Lext ⬇p n ⬇ Lext p n Lext p n Lext p n Lext p n Pit s p l1 l2 l3 l4 ⬇l5 l6 l7 l8 l9 l10

Lext(p,n) + Lext(p!5,n).Lext(p!4,n).Lext(p!3,n).Lext(p!2,n).Lext(p!1,n).Pit(s~p,l1!1,l2!2,l3!3,l4!4,l5!5,l6,l7,l8,l9,l10) -> Lext(p!6,n).Lext(p!5,n).Lext(p!4,n).Lext(p!3,n).Lext(p!2,n).Lext(p!1,n).Pit(s~p,l1!1,l2!2,l3!3,l4!4,l5!5,l6!6,l7,l8,l9,l10)

Lext ⬇p n ⬇ Lext p n Lext p n Lext p n Lext p n Lext p n Pit s p l1 l2 l3 l4 l5 ⬇l6 l7 l8 l9 l10

Lext(p,n) + Lext(p!6,n).Lext(p!5,n).Lext(p!4,n).Lext(p!3,n).Lext(p!2,n).Lext(p!1,n).Pit(s~p,l1!1,l2!2,l3!3,l4!4,l5!5,l6!6,l7,l8,l9,l10) -> Lext(p!7,n).Lext(p!6,n).Lext(p!5,n).Lext(p!4,n).Lext(p!3,n).Lext(p!2,n).Lext(p!1,n).Pit(s~p,l1!1,l2!2,l3!3,l4!4,l5!5,l6!6,l7!7,l8,l9,l10)

Lext ⬇p n ⬇ Lext p n Lext p n Lext p n Lext p n Lext p n Lext p n Pit s p l1 l2 l3 l4 l5 l6 ⬇l7 l8 l9 l10

Lext(p,n) + Lext(p!7,n).Lext(p!6,n).Lext(p!5,n).Lext(p!4,n).Lext(p!3,n).Lext(p!2,n).Lext(p!1,n).Pit(s~p,l1!1,l2!2,l3!3,l4!4,l5!5,l6!6,l7!7,l8,l9,l10) -> # Lext(p!8,n).Lext(p!7,n).Lext(p!6,n).Lext(p!5,n).Lext(p!4,n).Lext(p!3,n).Lext(p!2,n).Lext(p!1,n).Pit(s~p,l1!1,l2!2,l3!3,l4!4,l5!5,l6!6,l7!7,l8!8,l9,l10) kA
Lext(p,n) + Lext(p!8,n).Lext(p!7,n).Lext(p!6,n).Lext(p!5,n).Lext(p!4,n).Lext(p!3,n).Lext(p!2,n).Lext(p!1,n).Pit(s~p,l1!1,l2!2,l3!3,l4!4,l5!5,l6!6,l7!7,l8!8,l9,l10) -> # Lext(p!9,n).Lext(p!8,n).Lext(p!7,n).Lext(p!6,n).Lext(p!5,n).Lext(p!4,n).Lext(p!3,n).Lext(p!2,n).Lext(p!1,n).Pit(s~p,l1!1,l2!2,l3!3,l4!4,l5!5,l6!6,l7!7,l8!8,l9!9,l10) kA
Lext(p,n) + Lext(p!9,n).Lext(p!8,n).Lext(p!7,n).Lext(p!6,n).Lext(p!5,n).Lext(p!4,n).Lext(p!3,n).Lext(p!2,n).Lext(p!1,n).Pit(s~p,l1!1,l2!2,l3!3,l4!4,l5!5,l6!6,l7!7,l8!8,l9!9,l10) -> # Lext(p!10,n).Lext(p!9,n).Lext(p!8,n).Lext(p!7,n).Lext(p!6,n).Lext(p!5,n).Lext(p!4,n).Lext(p!3,n).Lext(p!2,n).Lext(p!1,n).Pit(s~p,l1!1,l2!2,l3!3,l4!4,l5!5,l6!6,l7!7,l8!8,l9!9,l10!10) kA
endocytosis - pit is converted to endosome

Lext(p!1,n).Pit(s~p,l1!1,l2,l3,l4,l5,l6,l7,l8,l9,l10) -> Lext(p!1,n).Pit(s~e,l1!1,l2,l3,l4,l5,l6,l7,l8,l9,l10)

Lext p n Pit s p e take all branches, once each, in any order⬇ l1 l2 l3 l4 l5 l6 l7 l8 l9 l10

Lext(p!2,n).Lext(p!1,n).Pit(s~p,l1!1,l2!2,l3,l4,l5,l6,l7,l8,l9,l10) -> Lext(p!2,n).Lext(p!1,n).Pit(s~e,l1!1,l2!2,l3,l4,l5,l6,l7,l8,l9,l10)

Lext p n Lext p n Pit s p e take all branches, once each, in any order⬇ l1 l2 l3 l4 l5 l6 l7 l8 l9 l10

Lext(p!3,n).Lext(p!2,n).Lext(p!1,n).Pit(s~p,l1!1,l2!2,l3!3,l4,l5,l6,l7,l8,l9,l10) -> Lext(p!3,n).Lext(p!2,n).Lext(p!1,n).Pit(s~e,l1!1,l2!2,l3!3,l4,l5,l6,l7,l8,l9,l10)

Lext p n Lext p n Lext p n Pit s p e take all branches, once each, in any order⬇ l1 l2 l3 l4 l5 l6 l7 l8 l9 l10

Lext(p!4,n).Lext(p!3,n).Lext(p!2,n).Lext(p!1,n).Pit(s~p,l1!1,l2!2,l3!3,l4!4,l5,l6,l7,l8,l9,l10) -> Lext(p!4,n).Lext(p!3,n).Lext(p!2,n).Lext(p!1,n).Pit(s~e,l1!1,l2!2,l3!3,l4!4,l5,l6,l7,l8,l9,l10)

Lext p n Lext p n Lext p n Lext p n Pit s p e take all branches, once each, in any order⬇ l1 l2 l3 l4 l5 l6 l7 l8 l9 l10

Lext(p!5,n).Lext(p!4,n).Lext(p!3,n).Lext(p!2,n).Lext(p!1,n).Pit(s~p,l1!1,l2!2,l3!3,l4!4,l5!5,l6,l7,l8,l9,l10) -> Lext(p!5,n).Lext(p!4,n).Lext(p!3,n).Lext(p!2,n).Lext(p!1,n).Pit(s~e,l1!1,l2!2,l3!3,l4!4,l5!5,l6,l7,l8,l9,l10)

Lext p n Lext p n Lext p n Lext p n Lext p n Pit s p e take all branches, once each, in any order⬇ l1 l2 l3 l4 l5 l6 l7 l8 l9 l10

5 more endocytosis reactions needed
endosome degradation

Pit(s~e,l1,l2,l3,l4,l5,l6,l7,l8,l9,l10) -> Trash()

Pit s e l1 l2 l3 l4 l5 l6 l7 l8 l9 l10 degraded Trash synthesized

the following reactions hit combinatorial complexity, but would be OK if it were possible to use the state of the reactant in the product
!! lysis of endosome with 1 lipoplex - 11 reactions
Lext(p!1,n~?).Pit(s~e,l1!1,l2,l3,l4,l5,l6,l7,l8,l9,l10) -> Lint(n) kL

Lext(p!1,n~345).Pit(s~e,l1!1,l2,l3,l4,l5,l6,l7,l8,l9,l10) -> Lint(n~345)

Lext ⬆p n 345 degraded ⬆ Pit s e ⬆l1 l2 l3 l4 l5 l6 l7 l8 l9 l10 degraded Lint n 345 synthesized

Lext(p!1,n~346).Pit(s~e,l1!1,l2,l3,l4,l5,l6,l7,l8,l9,l10) -> Lint(n~346)

Lext ⬆p n 346 degraded ⬆ Pit s e ⬆l1 l2 l3 l4 l5 l6 l7 l8 l9 l10 degraded Lint n 346 synthesized

Lext(p!1,n~347).Pit(s~e,l1!1,l2,l3,l4,l5,l6,l7,l8,l9,l10) -> Lint(n~347)

Lext ⬆p n 347 degraded ⬆ Pit s e ⬆l1 l2 l3 l4 l5 l6 l7 l8 l9 l10 degraded Lint n 347 synthesized

Lext(p!1,n~348).Pit(s~e,l1!1,l2,l3,l4,l5,l6,l7,l8,l9,l10) -> Lint(n~348)

Lext ⬆p n 348 degraded ⬆ Pit s e ⬆l1 l2 l3 l4 l5 l6 l7 l8 l9 l10 degraded Lint n 348 synthesized

Lext(p!1,n~349).Pit(s~e,l1!1,l2,l3,l4,l5,l6,l7,l8,l9,l10) -> Lint(n~349)

Lext ⬆p n 349 degraded ⬆ Pit s e ⬆l1 l2 l3 l4 l5 l6 l7 l8 l9 l10 degraded Lint n 349 synthesized

Lext(p!1,n~350).Pit(s~e,l1!1,l2,l3,l4,l5,l6,l7,l8,l9,l10) -> Lint(n~350)

Lext ⬆p n 350 degraded ⬆ Pit s e ⬆l1 l2 l3 l4 l5 l6 l7 l8 l9 l10 degraded Lint n 350 synthesized

Lext(p!1,n~351).Pit(s~e,l1!1,l2,l3,l4,l5,l6,l7,l8,l9,l10) -> Lint(n~351)

Lext ⬆p n 351 degraded ⬆ Pit s e ⬆l1 l2 l3 l4 l5 l6 l7 l8 l9 l10 degraded Lint n 351 synthesized

Lext(p!1,n~352).Pit(s~e,l1!1,l2,l3,l4,l5,l6,l7,l8,l9,l10) -> Lint(n~352)

Lext ⬆p n 352 degraded ⬆ Pit s e ⬆l1 l2 l3 l4 l5 l6 l7 l8 l9 l10 degraded Lint n 352 synthesized

Lext(p!1,n~353).Pit(s~e,l1!1,l2,l3,l4,l5,l6,l7,l8,l9,l10) -> Lint(n~353)

Lext ⬆p n 353 degraded ⬆ Pit s e ⬆l1 l2 l3 l4 l5 l6 l7 l8 l9 l10 degraded Lint n 353 synthesized

Lext(p!1,n~354).Pit(s~e,l1!1,l2,l3,l4,l5,l6,l7,l8,l9,l10) -> Lint(n~354)

Lext ⬆p n 354 degraded ⬆ Pit s e ⬆l1 l2 l3 l4 l5 l6 l7 l8 l9 l10 degraded Lint n 354 synthesized

Lext(p!1,n~355).Pit(s~e,l1!1,l2,l3,l4,l5,l6,l7,l8,l9,l10) -> Lint(n~355)

Lext ⬆p n 355 degraded ⬆ Pit s e ⬆l1 l2 l3 l4 l5 l6 l7 l8 l9 l10 degraded Lint n 355 synthesized

!! lysis of endosome with 2 lipoplexes - 11^2 reactions

Lext(p!2,n~345).Lext(p!1,n~345).Pit(s~e,l1!1,l2!2,l3,l4,l5,l6,l7,l8,l9,l10) -> Lint(n~345) + Lint(n~345)

Lext ⬆p n 345 degraded ⬆ Lext ⬆p n 345 degraded ⬆ Pit s e ⬆l1 ⬆l2 l3 l4 l5 l6 l7 l8 l9 l10 degraded Lint n 345 synthesized Lint n 345 synthesized

lysis of endosome with 10 lipoplexes - 11^10 reactions
lipoplex degradation

Lint() -> Trash()

Lint n 345 346 347 348 349 350 351 352 353 354 ?355 degraded Trash synthesized

!! unpacking of lipoplex - 11 reactions with sum of 345 to 355 elements
Lint(n) -> n*mRNA kU
Lint(n~345) -> 345*mRNA kU

Lint(n~345) -> mRNA() + mRNA() + mRNA() + mRNA() + mRNA()

Lint n 345 degraded mRNA synthesized mRNA synthesized mRNA synthesized mRNA synthesized mRNA synthesized

Lint(n~346) -> mRNA() + mRNA() + mRNA() + mRNA() + mRNA()

Lint n 346 degraded mRNA synthesized mRNA synthesized mRNA synthesized mRNA synthesized mRNA synthesized

mRNA degradation

mRNA() -> Trash()

mRNA degraded Trash synthesized

translation

mRNA() -> mRNA() + GFP()

mRNA GFP synthesized

GFP degradation

GFP() -> Trash()

GFP degraded Trash synthesized

I() -> I() + Timer()

I Timer synthesized