Simulate cells with transistors

Using analog circuits, rather than digital ones, scientists can easily build simulation models of biological systems efficiently and accurately.

In the world of analog circuits, electrical engineers often think most in terms of quantity as the voltage is constantly meaning, that they can receive endless ranges of values. Currently, with digital IC integration technology , engineers think more simply, they tend to think more about 0 and 1, binary opposites of digital logic.

Since the completion of the Human Genome Project, two new, thriving sectors are: synthetic biology and system biology have emerged from the observation that in some ways, the sequence of reactions is Learning leads to protein production in cells just like in electronic circuits. In general, researchers in both areas tend to analyze binary opposition reactions: If a chemical is present, one thing will happen, if this chemical is absent, another thing happened again.

However, Rahul Sarpeshkar, an electrical engineering professor at MIT's Electronic Research Laboratory (RLE), thinks it's the wrong approach. "The signals in the cells are not 0 or 1 , " Sarpeshkar said. "It is an oversimplified abstract concept that is the first type, at the crude level, that calculates a useful approximation for what the cell does. But everyone knows it is wrong."

In the Conference on biomedical integrated systems and circuits taking place in San Diego USA, in November 2011, Professor Sarpeshkar: scientist Lorenzo Turicchia, Dr. Ramiz Daniel and research student Sung Sik Woo and all both members of MIT's Electronic Research Laboratory (RLE) will present a report: they use similar electronic circuits to build two different types of patterns of interaction between proteins and DNA in the cell. Similar electronic circuits will mimic cell behavior with considerable accuracy, but perhaps more importantly, researchers build those biological models with only a few transistors much less than love. Demand of digital models requires.

The results of the study have opened up new directions: not only manufacturing but also electronically simulating biological systems more accurately and efficiently. This also shows a new framework for the analysis and design of biochemical processes that govern cell behavior.

The transistor's operation is like an electrical switch: when the transistor is turned on, the transistor is electrically conductive. On a computer chip, these two states are represented by 2 bits: 0 and 1.

However, in switching between non-conductive states and conductive states, a transistor will pass through all states such as slightly conductive, moderately conductive, fairly conductive, like a car. be accelerated from 0 to 60, speed up in a smooth way. Because transistors in a computer chip are used to perform binary logic operations, they are designed to make the transient phases undetectable. But Prof Sarpeshkar and colleagues are trying to exploit these transitional phases.

"We say that a pancreas cell will produce insulin , " Sarpeshkar said. "Yes, when blood sugar levels rise, pancreatic cells will give more insulin. But it doesn't scratch. If blood sugar rises more, pancreatic cells will produce more insulin. a little less in the blood, pancreatic cells produce a little less insulin. That's sort of, this activity is not a logic gate. "

Treated as a similar device, a single transistor has an infinite range of conductivity possible, so it can model a limited range of chemical concentrations. However, acting as a binary switch, a transistor has only two possible states, so modeling a large but finite range of concentrations will require a bank of all transistors. For large circuits such as the model sequence of reactions within the cell, binary logic quickly becomes so complex that it cannot be controlled. However, similar circuits are not. Indeed, the analog circuit exploits physical phenomena, helping to build simulation models of biological systems efficiently and accurately.

"What do you think electronics are?" Professor Sarpeshkar said. "That is the movement of electrons. What is chemistry? Chemistry: electrons move from one atom or molecule to another or atom. Two concepts must be deeply connected: Both both talk about electronics ".

Researchers at MIT's Electronic Research Laboratory (RLE), which performs biological experiments, measure the gradual effect of increasing the concentration of two different proteins in the cell. Both proteins affect cells that start producing other proteins but in two different directions: the first: One of the new proteins is bound to the DNA sequence and makes the cell increase the production of one protein. In particular, the second direction: limiting protein production of cells.

Prof Sarpeshkar and colleagues were able to create models for both processes using similar circuit boards with only 8 transistors per circuit. Furthermore, for the same circuit board to form a mirror image of each other, which represents the difference between: activating direct protein production and turning off a protein restriction cell. And finally, create circuits that model the interaction of genes and proteins with considerable accuracy.

"The concept by using a single transistor to make an entire equation is done on a digital computer, it will take a few lines of code, and if you look inside the box, it will be millions of transistors - certainly only running one application " . According to Gert Cauwenberghs, a professor of biotechnology and biology at the University of California in San Diego, USA. "Extreme transformations in biological systems, and the fact that the system remains resilient against variations, will show that similar circuits, with some principles of physical thermodynamics equally and noise embedded in them, will be a good execution platform ".

Professor Cauwenberghs warns that: utility for biologists, a similar pattern of genetic circuits will get much more complicated that researchers at the Electronic Research Laboratory (RLE) of MIT described in their new article. Building such a model, he said, would require the collaborative work of many biologists in creating accurate data on the concentration of chemicals in the cell, as well as demanding skills of techniques. electrician But "there is certainly synergy between these two areas," Cauwenberghs added.