Configurable bio-transport system simulator

• US 6,381,562 B2
• Filed: 07/13/1999
• Issued: 04/30/2002
• Est. Priority Date: 07/13/1998
• Status: Expired due to Term

• Current Assignee: John A. Keane
• Original Assignee: John A. Keane
• Inventors: Keane, John A.
• Primary Examiner(s): Choi, Kyle J.
• Application Number:
  US09/353,301
• Publication Number:
  US 20020002447A1
• Time in Patent Office: 1,022 Days
• Field of Search: 703/11, 703/9, 703/2, 434/126, 434/262, 434/268, 434/272
• US Class Current: 703/11
• CPC Class Codes: B82Y 10/00 Nanotechnology for information processing, storage or transmission, e.g. quantum computing or single electron logic
• CPC Class Codes: G06N 3/002 Biomolecular computers, i.e. using biomolecules, proteins, cells using DNA G06N3/123; using neurons G06N3/061

Abstract

A method of simulating a bio-transport system comprising: (a) characterizing one or more elements to represent a bio-transport system of an organism or a portion thereof; (b) constructing one or more mathematical representations that model one or more bio-transport dynamics for each element based on the characterization of the elements to form a configured simulation model; (c) initializing the configured simulation model; (d) executing the configured simulation model to obtain bio-transport dynamics data for one or more elements; and (e) outputting information to a user based on at least a portion of the bio-transport dynamics data.

Claims

1. A method of simulating a bio-transport system comprising:

characterizing a plurality of elements to represent a bio-transport system of at least a portion of an organism;

configuring a simulation model by constructing a plurality of mathematical representations that model bio-transport dynamics for each element based on the characterization of said elements, wherein said bio-transport dynamics include at least;

flow of a fluid in said bio-transport system, the flow at a particular element being modeled by a first mathematical representation which at least conserves momentum and conserves energy of essentially all of said elements; and

concentration of at least one entity within said fluid, the concentration of said entity at a particular element being modeled by a second mathematical representation which is a function of flow as determined by said first mathematical representation, and of concentration of said entity in essentially all of said elements;

initializing the configured simulation model;

executing said configured simulation model to obtain bio-transport dynamics data for one or more elements, wherein bio-transport dynamics data comprises at least flow data of said fluid at a particular element, and concentration data of said entity in said fluid at a particular element; and

outputting information to a user based on at least a portion of said bio-transport dynamics data.

2. The method of claim 1, wherein characterizing one or more elements is performed using data obtained from imaging equipment.

3. The method of claim 1, further comprising:

exchanging bio-transport dynamics data between one or more organ models.

4. The method of claim 3, wherein bio-transport dynamics data is exchanged between two or more organ models via said configured simulation model.

5. The method of claim 4, wherein one or more organ models are interfaced to said configured simulation model via a telecommunication link.

6. The method of claim 1, wherein an element is characterized to represent at least a portion an organ.

7. The method of claim 1, wherein said bio-transport system is a subsystem of an organ and said configured simulation model is an object in an organ model modeling said organ.

8. The method of claim 1, wherein said bio-transport system is a subsystem of a cell and said simulation model is an object in a cell simulation model modeling said cell.

9. The method of claim 1, wherein additional bio-transport dynamics are selected from the group consisting of heat transport in the fluid, external dynamic and mechanical effects on the fluid, effects at a distance, and combinations of two or more thereof.

10. The method of claim 9, wherein effects at a distance are simulated using a relations processing engine.

11. The method of claim 9, wherein heat transport in the fluid at a particular element is modeled by a third mathematical representation which is a function of flow as determined by said first mathematical representation, and of heat transport in essentially all of said elements, and wherein external dynamical and mechanical effects on the fluid at a particular element is modeled by a fourth mathematical representation which is a function of flow as determined by said first mathematical representation, and of external dynamical and mechanical effects on the fluid in essentially all of said elements.

12. The method of claim 1, wherein at least one element is characterized as having a condition of state.

13. The method of claim 1, wherein a plurality of elements are characterized to model multilevel branching.

14. The method of claim 1, wherein initializing said simulation model comprises entering prime mover data and/or input/output conditions of said bio-transport system.

15. The method of claim 14, wherein prime mover data represents a function of time and state.

16. The method of claim 15, wherein said flow is a function of an element'"'"'s position relative to said prime mover and the state condition of said prime mover.

17. The method of claim 1, wherein each element is an object in object-oriented programming environment.

18. The method of claim 1, wherein said bio-transport system is a circulatory system.

19. The method of claim 1, wherein said information is used for diagnostic purposes.

20. The method of claim 1, wherein said information is used for determining drug dissemination in a circulatory system as a function of time and position within a circulatory system.

21. The method of claim 1, wherein said configured simulation model incorporates conditions of state relationships in an overall set of relationships to be solved during execution of the configured simulation model.

22. The method of claim 1, wherein the mathematical relationships of one or more bio-transport dynamics are interrelated such that the output of one relationship is used as the input to at least another relationship.

23. The method of claim 1, wherein said configured simulation model comprises at least two simulation models.

24. The method of claim 1, wherein said bio-transport system has a prime mover which generated head, and wherein the flow at said particular element is based upon the sum of the fluid flow pressure drops through each element equals said head of said prime mover.

25. The method of claim 1, wherein said fluid is blood and said entity comprises at least one of plasma, blood cells, a clot, a chemical element, a chemical compound, a product of the immune system, a parasite, or a biological.

26. The method of claim 1, wherein said chemical compound is at least one of a drug, protein, amino acid, hormone or enzyme, said biologicals is at least one of a virus or bactterium, and said product of the immune system is at least one of a macrophage or a t cell.

27. The method of claim 1, wherein said second mathematical relationship is based on at least one of said mass transportation of said entity, chemical/biological interactions of said enetity, or a combination thereof.

28. The method of claim 27, wherein said second mathematical relationship considers changes in mass brought about by said chemical/biological interactions.

29. The method of claim 1, wherein a particular bio-transport dynamic at a particular element is a function of said particular bio-transport dynamic at essentially all of the elements.

30. A method of simulating a transport system comprising:

providing a constructed simulation model comprising;

a plurality of elements characterized to represent at least a portion of a bio-transport system;

at least one model having one or more mathematical representations of one or more bio-transport dynamics for each element, said mathematical representations being constructed based on the characterization of said elements, wherein said bio-transport dynamics include at least;

flow of a fluid in said bio-transport system, the flow at a particular element being modeled by a first mathematical representation which at least conserves energy of essentially all of said elements; and

concentration of at least one entity within said fluid, the concentration of said entity at a particular element being modeled by a second mathematical representation which is a function of flow as determined by said first mathematical representation, and of concentration of said entity in essentially all of said elements;

initializing said constructed simulation model;

executing said configured simulation model to obtain bio-transport dynamics data for one or more elements, wherein said bio-transport dynamics data comprises at least flow data of said fluid at a particular element, and concentration data of said entity in said fluid at a particular element; and

outputting information to a user based on at least a portion of said bio-transport dynamics data.

31. A computer system for simulating a transport system comprising:

a processor;

a user interface operatively connected to the processor for receiving input from and conveying output to a user; and

memory operatively connected to the processor and containing instructions for constructing and/or executing the simulation model;

wherein constructing said simulation model comprises

(a) receiving construction data characterizing a plurality of elements to represent a bio-transport system or a portion thereof;

(b) constructing one or more mathematical representations that model bio-transport dynamics for each element based on the data characterizing said element to form a configured simulation model, wherein said bio-transport dynamics include at least;

flow of a fluid in said bio-transport system, the flow at a particular element being modeled by a first mathematical representation which at least conserves momentum and conserves energy of essentially all of said elements; and

concentration of at least one entity within said fluid, the concentration of said entity at a particular element being modeled by a second mathematical representation which is a function of flow as determined by said first mathematical representation, and of concentration of said entity is essentially all of said elements; and

wherein executing said simulation model comprises (a) initialing said configured simulation model; and

(b) executing said configured simulation model to obtain bio-transport dynamic data for one or more elements, wherein said bio-transport dynamics data comprises at least flow data of said fluid at a particular element, and concentration data of said entity in said fluid at a particular element.

32. A computer-readable medium comprising:

instructions for enabling a computer-based system to construct and/or execute the simulation model;

wherein construction said simulation model comprises (a) receiving data characterizing a plurality of elements to represent a bio-transport system or a portion thereof;

(b) constructing one or more mathematical representations that model bio-transport dynamics for each element based on the data characterizing said elements to form a configured simulation model,

wherein said bio-transport dynamics include at least;

flow of a fluid in said bio-transport system, the flow at a particular element being modeled by a first mathematical representation which at least conserves momentum and conserves energy of essentially all of said elements; and

concentration of at least one entity within said fluid, the concentration of said entity at a particular element being modeled by a second mathematical representation which is a function of flow as determined by said first mathematical representation, and of concentration of said entity in essentially all of said elements; and

wherein executing said simulation model comprises (a) initialing said configured simulation model; and

(b) executing said configured simulation model to obtain bio-transport dynamic data for one or more elements, wherein said bio-transport dynamics data comprises at least flow data of said fluid at a particular element, and concentration data of said entity in said fluid at a particular element.