Configurable bio-transport system simulator

• US 20020120431A1
• Filed: 01/22/2002
• Published: 08/29/2002
• Est. Priority Date: 07/13/1998
• Status: Abandoned Application

• Current Assignee: John A. Keane
• Original Assignee: John A. Keane
• Inventors: Keane, John A.
• Application Number:
  US10/054,492
• Publication Number:
  US 20020120431A1
• Time in Patent Office: Days
• 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 one or more elements to represent a bio-transport system of an organism or a portion thereof;

constructing one or more mathematical representations that model one or more bio-transport dynamics for each element based on the characterization of said elements to form a configured simulation model;

initializing said configured simulation model;

executing said configured simulation model to obtain bio-transport dynamics data for one or more elements; 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 as 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 one bio-transport dynamic is the flow of fluid within the bio-transport system.

10. The method of claim 9, wherein additional bio-transport dynamics are selected from the group consisting of mass transport and/or reactions of entities in the fluid;

heat transport in the fluid;

external dynamical and mechanical effects on the fluid;

effects at a distance; and

combinations of two or more thereof.

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

12. The method of claim 1, wherein at least one of said user-specified characteristics is 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 one bio-transport dynamic is fluid flow which 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.

29. The method of claim 28, wherein said data is provided by at least a first organ model modeling said first organ, and said solution is outputted to a second model modeling said second organ.

30. The method of claim 28, wherein said one or more solutions is generated by a relations processing engine.

31. The method of claim 28, wherein said relationships comprise a time delay to account for spacial separation effects between said first and second organs.

32. The method of claim 28, wherein one of said first or second organ is a heart.

33. The method of claim 28, wherein one of said first or second organ is a kidney.

24. A method of simulating a transport system comprising:

providing a constructed simulation model comprising;

one or more elements characterized to represent a bio-transport system or a portion thereof;

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

initializing said constructed simulation model;

executing said constructed simulation model to obtain bio-transport dynamics data for each element; and

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

25. 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 one or more elements to represent a bio-transport system 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 data characterizing said elements to form a configured simulation model; 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 each element.

26. A computer-readable medium comprising instructions for enabling a computer-based system to construct and/or execute the simulation model;

wherein constructing said simulation model comprises (a) receiving data characterizing one or more elements to represent a bio-transport system 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 data characterizing said elements to form a configured simulation model; 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 each element.

27. A process for simulating on a computer system a circulatory system, said process comprising the steps of:

inputting an ordered selection of channel elements and fluid characteristics into a computer system;

inputting data of initial and boundary conditions;

configuring a circulatory model resident within said computer system according to said selection to form a configured circulatory model, said configured circulatory model having at least one mathematical representation corresponding to said selection;

applying said data to the configured circulatory model; and

displaying on a user interface of said computer the results of applying data to said configured circulatory model.

28. A method of simulating the interaction of two or more organs over a circutlatory system, said method comprising:

constructing a matrix of one or more relationships between at least a first organ and a second organ over a circulatory system;

providing data relating to said first organ'"'"'s interaction with said circulatory system;

applying said data to said matrix and solving to generate at least one solution corresponding to the effect of said first organ on said second organ over said circulatory system; and

outputting said solution.