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Scalable agent-based simulations

707d0934f77fc31048f004103e10c57f?s=47 Greg Goltsov
February 13, 2013

Scalable agent-based simulations

A talk I gave at the end of my Nuffield project a few years back. I've been working on scientifically sound blood clotting simulation with a nice 3d visualisation on top.

707d0934f77fc31048f004103e10c57f?s=128

Greg Goltsov

February 13, 2013
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Transcript

  1. Scalable agent-based simulations: a blood clotting demonstrator Results of the

    8 week Nuffield project Gregory Goltsov
  2. What is blood clotting

  3. What is hemostasis

  4. Physical modelling of clot formation Xu Z, Lioi J, Mu

    J, Kamocka MM, Liu X, Chen DZ, Rosen ED, & Alber M (2010). A multiscale model of venous thrombus formation with surface-mediated control of blood coagulation cascade. Biophysical journal, 98 (9), 1723-32 PMID: 20441735
  5. Physical modelling of clot formation Xu Z, Lioi J, Mu

    J, Kamocka MM, Liu X, Chen DZ, Rosen ED, & Alber M (2010). A multiscale model of venous thrombus formation with surface-mediated control of blood coagulation cascade. Biophysical journal, 98 (9), 1723-32 PMID: 20441735
  6. Pathology Thromboembolism Formation in a blood vessel of a clot

    (thrombus) that breaks loose and is carried by the blood stream to plug another vessel. Pulmonary embolism Blockage of the main artery of the lung.
  7. Pathology Thromboembolism Formation in a blood vessel of a clot

    (thrombus) that breaks loose and is carried by the blood stream to plug another vessel. Pulmonary embolism Blockage of the main artery of the lung. Aspirin
  8. Aspirin Everyone aged over 45 should consider a small daily

    dose of aspirin to help protect themselves against heart disease and cancer “
  9. Clotting modelling: ODEs

  10. Clotting modelling: ODEs Great attention to uid dynamics

  11. Clotting modelling: ODEs Great attention to uid dynamics Not so

    much to internal representation of platelet
  12. Clotting modelling: ODEs Great attention to uid dynamics Not so

    much to internal representation of platelet Probabilistic representation of space
  13. Platelet

  14. Vs

  15. None
  16. None
  17. Clotting modelling: agents

  18. Clotting modelling: agents Agent-based simulation — platelets are agents.

  19. Clotting modelling: agents Agent-based simulation — platelets are agents. Each

    individual platelet has its own behaviour.
  20. Clotting modelling: agents Agent-based simulation — platelets are agents. Each

    individual platelet has its own behaviour. Explicit account of space — allows for near-neighbour interactions.
  21. None
  22. None
  23. What’s been done

  24. None
  25. TUNA TECHNOLOGY UNDERPINNING N A N O T E C

    H ASSEMBLERS
  26. TUNA TECHNOLOGY UNDERPINNING N A N O T E C

    H ASSEMBLERS
  27. TUNA TECHNOLOGY UNDERPINNING N A N O T E C

    H ASSEMBLERS CoSMoS C O M P L E X S Y S T E M S MODELLING & SIMULATION
  28. TUNA TECHNOLOGY UNDERPINNING N A N O T E C

    H ASSEMBLERS CoSMoS C O M P L E X S Y S T E M S MODELLING & SIMULATION +
  29. TUNA TECHNOLOGY UNDERPINNING N A N O T E C

    H ASSEMBLERS CoSMoS C O M P L E X S Y S T E M S MODELLING & SIMULATION + CrISp CENTRE FOR RESEARCH IN SYSTEMS PATHOLOGY
  30. What is inside of each platelet?

  31. Hybrid functional Petri net of platelet activation TXA2ext TP receptors

    PLC PIP2 PIP3 IP3R calcium receptor Ca2+ in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc
  32. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc Hybrid functional Petri net of platelet activation
  33. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc Hybrid functional Petri net of platelet activation
  34. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc Hybrid functional Petri net of platelet activation
  35. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc Hybrid functional Petri net of platelet activation
  36. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc Hybrid functional Petri net of platelet activation
  37. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc Hybrid functional Petri net of platelet activation
  38. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc Hybrid functional Petri net of platelet activation
  39. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc Hybrid functional Petri net of platelet activation
  40. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc Hybrid functional Petri net of platelet activation
  41. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc Hybrid functional Petri net of platelet activation
  42. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc Hybrid functional Petri net of platelet activation
  43. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc Hybrid functional Petri net of platelet activation
  44. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc Hybrid functional Petri net of platelet activation
  45. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc
  46. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc
  47. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc
  48. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc AA
  49. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc AA
  50. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc AA COX1
  51. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc AA COX1
  52. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc AA TXA2int COX1
  53. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc AA TXA2int COX1
  54. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc AA TXA2ext TXA2int COX1
  55. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc AA TXA2ext TXA2int COX1
  56. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc AA TXA2ext TXA2int ASA COX1
  57. COX1 AA TXA2int TR1 TR2 TXA2ext TR4 COX1inact TR3 ASA

    acytCOX1 TR5
  58. COX1 AA TXA2int TR1 TR2 TXA2ext TR4 COX1inact TR3 ASA

    acytCOX1 TR5 Model
  59. COX1 AA TXA2int TR1 TR2 TXA2ext TR4 COX1inact TR3 ASA

    acytCOX1 TR5 Model
  60. COX1 AA TXA2int TR1 TR2 TXA2ext TR4 COX1inact TR3 ASA

    acytCOX1 TR5 Model // Place(name, initial_concentration) NodePtr txa2_ext (new Place("TXA2_ext" NodePtr aa (new Place("AA" NodePtr cox1 (new Place("COX1" NodePtr txa2_int (new Place("TXA2_int" // Transition(name, substrate, product, NodePtr tr1 (new Transition("TR1", tr1_e NodePtr tr2 (new Transition("TR2", tr2_e NodePtr tr3 (new Transition("TR3", tr3_e DSL D O M A I N - S P E C I F I C LANGUAGE
  61. Visualisation

  62. Visualisation +

  63. Visualisation interactive +

  64. Visualisation interactive +tweakable

  65. Visualisation interactive +tweakable

  66. Demo

  67. EMITTED TXA2 ~20 cells WOUND VESSEL WALL TUNA model

  68. WOUND VESSEL WALL New model EMITTED TXA2

  69. WOUND VESSEL WALL New model EMITTED TXA2

  70. WOUND VESSEL WALL New model EMITTED TXA2

  71. WOUND VESSEL WALL New model AMPLIFIED ACTIVATION EMITTED TXA2

  72. ~5 cells WOUND VESSEL WALL New model AMPLIFIED ACTIVATION EMITTED

    TXA2
  73. Future work

  74. Future work Applications

  75. Improvements

  76. Improvements: Physics Realistic uid dynamics model for the blood ow.

  77. Improvements: DSL Editor Epsilon editor for easy pathway creation and

    integration.
  78. { } MODELLING SIMULATION VISUALISATION

  79. CrISp CENTRE FOR RESEARCH IN SYSTEMS PATHOLOGY { } MODELLING

    SIMULATION VISUALISATION
  80. CrISp CENTRE FOR RESEARCH IN SYSTEMS PATHOLOGY { } MODELLING

    SIMULATION VISUALISATION DR UG T EST ING, PHARMACOKINE TICS, PHARMACODYNAMI CS, DRUG D IS TRI BUT ION, DRUG INTER AC TION
  81. Thank you! Special thanks to Supervisor Dr Adam Sampson Prof

    James Bown GREGORY@GOLTSOV.INFO WWW.GREGORY.GOLTSOV.INFO