Category Archives: Systems Theory

Skynet Edges Closer

There is a fascinating article in science this week about the construction in hardware of a neural chip. This isn’t a new idea but scale and flexibility is novel. The chip is made by researchers from IBM and Cornell and can … Continue reading

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Reversibility and Product Inhibition

It is common in biochemistry to categorize reactions as either reversible or irreversible. What do we mean by these terms? Let’s look at a simple reaction such as:     where A is transformed to B. The rate of reaction … Continue reading

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Synthetic Biology: It’s an analog world

I significant paper on synthetic biology got published this week by an innovative group from MIT (Daniel et al). Read our News and Views article that discusses the importance of the paper.

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Linear Dynamics Application

There are a number of online apps that can show students the phase plane dynamics of a 2d system. Notable examples include: Phase Portrait Viewer from the d’Arbeloff Interactive Math Project – requires Java installed Wolfram Phase Portrait Viewer – … Continue reading

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Choke points, Load points, Hots spots and Key steps

Choke points, load points, hot spots, key steps and critical steps are some of the many phrases that have been coined to describe places in a biochemical network where perturbations are said to make a difference. Locating these places is … Continue reading

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Irreversible Bistability

Last week I was in need of an irreversible bistable switch to show my class. I remember seeing one in the well known review by Tyson et al, Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in … Continue reading

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Michael Savageau’s Book in Print Again

I’ve been meaning to mention this for some time but Michael Savageau book, ‘Biochemical Systems Analysis’ is available in print again in the form of a paperback from amazon for only $29.95. I grew up with this book as an … Continue reading

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Building an Analog Integrator

Something I’ve been wanting to do for a while was is to build a simple analog integrator. Here is my first attempt. I bread-boarded the circuit first to get it working then made it more permanent and stable by soldering … Continue reading

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Electronic Gene Circuit

The figure below shows a single unit from the Microryza gene network circuit project. The circuit models a transcription factor that acts as a repressor. The output from the circuit is the level of protein which can be fed into … Continue reading

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Misconceptions in Metabolism II

A week ago I wrote about some misconceptions in metabolism that arose from a trip to a systems biology workshop in Holland. This week I discovered that Nature is perpetrating similar misconceptions in their News and Views section. I came … Continue reading

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