Skip to main content Accessibility help
×
Hostname: page-component-848d4c4894-89wxm Total loading time: 0 Render date: 2024-07-07T16:04:21.646Z Has data issue: false hasContentIssue false

7 - Chemical reaction systems: large-scale systems simulation

Published online by Cambridge University Press:  05 June 2012

Daniel A. Beard
Affiliation:
Medical College of Wisconsin
Get access

Summary

Overview

So far in the examples of biochemical systems that we have studied, we have looked at systems of one or a handful of reactions. Yet the ultimate quest to understand (and simulate and predict) cellular function calls for the capability to synthesize many thousands of simultaneous chemical reaction and transport processes. Can we realistically expect to simulate cellular biochemistry with many important reactions accounted for at the level of rigor and detail of the examples in the previous two chapters? The answer is a qualified “yes,” because in principle there is no reason why realistic simulations of systems of hundreds or thousands of reactions cannot be constructed. One approach to doing to is to adopt a systematic approach based on the fundamentals developed in the previous two chapters. This approach is practical when data exist for building the necessary thermodynamic and kinetic models of the individual enzymes and transporters at the level of detail of the model of fumarase in Chapter 6. However, when that level of detail is either not possible or not practical, model-based simulations may still be developed.

This chapter describes examples of two contrasting approaches to simulation and analysis of large-scale systems – a simulation of the kinetics of a metabolic pathway based on detailed biochemical thermodynamics and kinetics, and a less biochemically rigorous analysis of gene expression data to identify regulatory network structure.

Type
Chapter
Information
Biosimulation
Simulation of Living Systems
, pp. 205 - 229
Publisher: Cambridge University Press
Print publication year: 2012

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

Save book to Kindle

To save this book to your Kindle, first ensure coreplatform@cambridge.org is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about saving to your Kindle.

Note you can select to save to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be saved to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

Find out more about the Kindle Personal Document Service.

Available formats
×

Save book to Dropbox

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Dropbox.

Available formats
×

Save book to Google Drive

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Google Drive.

Available formats
×