16-10-2012, 01:17 PM
Introduction to Digital Computers and Bio-molecular Computing
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Today the term “Computer Science” has a very broad meaning.
From the viewpoint of computing characteristic, “Computer Science” actually contains a digital computer [Turing 1937, von Neumann 1956], bio-molecular computing [Adleman 1994] and quantum computing [Deutsch 1985].
Because the discussion for quantum computing exceeds the scope of this book, thus, we do not introduce “quantum computing”.
For the purpose of this book, the phrase “bio-molecular computing” describes the in vitro (therefore outside living cell) manipulation of bio-molecules.
Those manipulations may be applied to finish various kinds of computations.
In this introductory chapter, we try to explain the behaviors of a digital computer and bio-molecular computing.
The Behaviors of a Digital Computer
If you are not concerned with the internal mechanism of a digital computer, you can simply denote it as a black box.
However, you still need to denote the tasks finished by a digital computer for distinguishing it from other types of black boxes.
We offer computational model of a digital computer.
Figure 1.1.1 is used to represent computational model of a digital computer.
The Behaviors of Bio-molecular Computing
For bio-molecular computing, if you are not concerned with the internal mechanism, it can simply be defined as another black box.
The black box for bio-molecular computing is shown in Figure 1.2.1.
In Figure 1.2.1, all operations with test tubes have to be carried out by the user.
A more advanced model is depicted in Figure 1.2.2, where some robotics or electronic computing is used to carry out automatically the majority of the operations with the test tubes without the intervention of the user.
The Introduction for a Digital Computer of the Von Neumann Architecture
The so-called von Neumann architecture is a model for a computing machine that uses a single storage structure to hold both the set of instructions on how to perform the computation and the data required or generated by the computation.
Today, each digital computer based on the von Neumann architecture contains four subsystems: memory, arithmetic logic unit, control unit and input/output devices.
A digital computer system of the von Neumann architecture is shown in Figure 1.3.1. From Figure 1.3.1, the input subsystem accepts input data and the digital program from outside the digital computer and the output subsystem sends the result of processing to the outside.
Memory is the main storage area in the inside of the digital computer system.
It is used to store data and digital programs during processing.
The Von Neumann Architecture for Bio-molecular Computing
In bio-molecular computing, data also are represented as binary patterns (a sequence of 0s and 1s).
Those binary patterns are encoded by sequences of bio-molecules and are stored in a tube.
This is to say that a tube is the only storage area in bio-molecular computing and is aslo the memory and the input/output subsystem of the von Neumann architecture.
Bio-molecular programs are made of a set of bio-molecular operations and are used to perform calculation and logical operations.
So, bio-molecular programs can be regarded as the arithmetic logic unit of the von Neumann architecture.
A robot is used to automatically control the operations of a tube (the memory and the input/output subsystem) and bio-molecular programs (the ALU).
This implies that the robot can be regarded as the control unit of the von Neumann architecture.