1. Introduction

The purpose of this document is to give XSIM users a jumpstart. It is presented as a series of events for typical simulation runs, parameter estimation by curve fitting, and advanced simulation and analysis using tools such as sensitivity analysis. Users should refer to the XSIM Interface and Reference manuals for details of XSIM functionalities. 

The following streaming video clips (ASF - Advanced Stream Format) are provided for people who want to take a preview of XSIM but don't have a machine running X-server:

1. Simple fluid displacement without dispersion

Consider the lowly pipe. Unless it is clogged or leaks, what comes in goes out. This is mass balance--nothing lost, nothing gained. Fig. 1 shows an idealized pipe, one that is frictionless so that the fluid does not stick to the walls. Sticking only to itself (internal viscosity) but not to walls allows a flat velocity profile. (A velocity profile is defined as the map of velocities across a cross section of the pipe.)

NOTE: XSIM is NO Longer supported!

• XSIM On-line Documents
• MMID4 User Guide
  • On-line User Guide (html)
• Fractal Physiology, a textbook on

1. Model Overview

The chemistry in biological organisms is fundamentally different from that in test tubes and in chemical engineering largely due to the unique roles played by enzymes. With the presence of enzymes as specific catalysts, biochemical reactions are greatly accelerated. The unique role of enzymes also makes the kinetic of such reactions significantly different from that of conventional chemical kinetics. This was frist realized by L. Michaelis and M.L. Menten in 1913, when they developed a quantitative theory for the enzyme kinetics.

1. TABLE OF CONTENTS

Parameters

Output Variables

Diagram

Equations

Model demonstrations with parameter sets

A set of nonlinear transmembrane transporters (tutorial available).

Comp2ode is a model which describes the passage of a single solute through a simple organ. Although not as fully developed as the models used by the NSR for scientific research, the model does have some elements in common with these more complex models. Flow entering the organ passes through three regions in series: arteries, capillaries, and veins. The arteries and veins are modeled as vascular operators, while the capillary and surrounding tissues are modeled as two well-stirred compartments.

Model: BTEX40, a single capillary 4-region 3-barrier blood-tissue exchange model

1. TABLE OF CONTENTS

See Parameters:

See Outputs:

See Diagram

See Model Demonstrations with parameter sets:

A multi-path, multi-indicator, four-region organ model (tutorial available).

A multi-path, multi-species, four-region organ model.