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Protein Based Computing - Biomatics.org

Protein Based Computing

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Developing the concept of biomachine computing whereby proteins or similar organic molecules play an integrated role in CPU function with traditional mechanical devices.
  

Much research has gone over recent years in exploring the computational potential of the DNA molecule.  This was spurred by Len Adelman's famous "computation in a test tube" discovery.  Recently it has been the central role of Histone proteins that have been investigated.  The "histone code" hypothesis demonstrates enormous computational potential, but is currently poorly understood by a biological community lacking in understanding of circuits and networks...the domain of computer scientists.  Thus the challenge is to characterize the dynamics of protein folding in such a way as to feasibly physically interface with silicon or whatever material is in fashion.

Given that proteins are capable of being described as finite state machines the challenge is to find some way of reading the state value (output bus).  Organic chemists could theoritically create standard proteins with known transition state tables.  The input could be in the form of methylation, acetylation, or ubiquitination, reactions.  The scaling advantages of single molecules replacing current gating technology would be invaluable in pursuit of Moore's law.

Rather than a simple NAND gate as the hub of the CPU would be a complex finite state machine. Therefore  the scaling would come as much from logical as spatial condensation.

Cayley Tables describe the behaviour of 1,2, or n dimensional machines which could act as fundamental building blocks of logic design.  The molecule could be fashioned after the Histone Protein with its modifiable tails.  For simplicity and tractabllity assume the synthetic molecule has only one tail with one input site.  What tricks could be taught to such a protein.  Could it be designed to be a two state, on/off device (a flip-flop)?  How about a sequential counting device?  What tricks could a molecule do if it had four modifiable tails all capable of multiple inputs?  Such is the  large repertoire of histone modifications, including lysine  and arginine  methylation, serine  and threonine phosphorylation, and lysine acetylation, ubiquitination, and sumoylation.

Thus not only is there a great number of inputs to the histone tails (approximately 26 currently known) but these are of different molecular weights ranging from single carbon atoms (methylation) to large proteins (ubiquitination).  The result is that as opposed to all-or-none input, the inputs are discretely graded.  In short as compared to a NAND gate with two binary inputs we have a device at each nucleosome  with at least twenty six inputs with a potentially great number of levels as determined by molecular weight (and possibly other chemical properties).

Can we generalize the logic design process (truth tables, Karnaugh maps, Quine-McCluskey algorithm) to this more complex situation? 

 

"Wayne State University’s Michael Conrad has defined his vision of a molecular computer in which proteins integrate multiple input modes to perform a functional output (Conrad, 1986). In addition to smaller size scale, protein based molecular computing offers different architectures and computing dimensions. Conrad suggests that “non-von Neumann, nonserial and non-silicon” computers will be “context dependent,” with input processed as dynamical physical structures, patterns, or analog symbols. Multidimensional conditions determine the conformational state of any one protein: temperature, pH, ionic concentrations, voltage, dipole moment, electroacoustical vibration, phosphorylation or hydrolysis state, conformational state of bound neighbor proteins, etc. Proteins integrate all this information to determine output. Thus each protein is a rudimentary computer and converts a complex analog input to an output state or conformation."  

(http://www.quantumconsciousness.org/pdfs/UltComp_v51.pdf)

Contents

Protein Qubits? (Penrose and Hameroff)

By changing their conformational shape, proteins are able to perform a wide variety of functions. The types of forces acting on proteins include charged interactions (such as covalent, ionic, electrostatic, and hydrogen bonds), hydrophobic interactions, and dipole interactions. The latter group, also known as van der Waals forces, encompasses three types of interactions:

  • permanent dipole - permanent dipole,
  • permanent dipole - induced dipole, and
  • induced dipole - induced dipole (London dispersion forces)

While induced dipole - induced dipole interactions, or London dispersion forces, are the weakest of the forces, they are also the most numerous and influential.  London force attraction between any two atoms is usually less than a few kilojoules; however, since thousands occur in each protein, they add up to thousands of kilojoules per mole, and cause changes in conformational structure. As London forces are instrumental in protein folding, protein conformation and folding may be quantum computations.

Quantum level n to 2**n conversion?

 

The circuit symbol for a multiplexer with inputs (A,B,C) is as follows:  

Multiplex.jpg

Quantum Multiplexing in microtubules?-


QuantumMultiplexer.jpg
 

Schematic of quantum computation of three tubulins which begin (left) in initial classical states, then enter isolated quantum superposition in which all possible states coexist. After reduction, one particular classical outcome state is chosen (right).




 

Quantum Control Group acting on Tubulin


*
0
A
B
C
AB
AC
BC
ABC
G0
G0
G1
G2
G3
G4
G5
G6
G7
G1
G1
G0
G4
G5
G2
G3
G7
G6
G2
G2
G4
G0
G6
G1
G7
G3
G5
G3
G3
G5
G6
G0
G7
G1
G2
G4
 G4
G4
G2
G1
G7
G0
G6
G5
G3
G5
G5
G3
G7
G1
G6
G0
G4
G2
G6
G6
G7
G3
G2
G5
G4
G0
G1
G7
G7
G6
G5
G4
G3
G2
G1
G0

 


 

Here we have the specification of a finite state machine model- eight states with state transitions specified for each possible input.


QuCayley.jpg


 



Introduction to Organic and Molecular Electronics

New Magnetic Organic Molecules May Herald Malleable Computer Memory

Latest News in Organic and Molecular Electronics

Tubulins and Microtubules

 



 

 

Development of ternary computers at Moscow State University

It is known that the ternary arithmetic has essential advantages as compared with the binary one that is used in present-day computers. In connection with this Donald Knuth assumed that the replacement of "flip-flop" for "flip-flap-flop" one  "good" day will nevertheless happen [1]. Now, when the binary computers predominate, it is hard to believe in a reality of such assumption, but if it would happen not only the computer arithmetic, but the informatics on the whole would become most simple and most perfect. The third value (Aristotle named it snmbebhkoV – attendant) that is very actual but hidden in binary logic, will become obvious and directly manipulated. Ternary logic has better accordance with  Nature and human informal thinking [2]. Unfortunately, the modern researches of the multivalued (non-binary) logic are formal and are not associated with practical requests.

A remarkable exclusion is the experience of creating the ternary computers "Setun" and "Setun 70" at Moscow State University [3,4,5,6]. This experience convincingly confirms practical preferences of ternary digital technique...

Ternary threshold logic elements as compared with  binary ones provide more speed and reliability, require less equipment and power. These were reasons to design a ternary computer....

"Setun" has a one-address architecture with one index-register. The contents of it, in dependence of value (+,0,-) of address modification trit, may be added to or subtracted from the address part of instruction ..

Simplicity, economy and elegance of computer architecture are the direct and practically very important consequence of the ternarity, more exactly – of representation of data and instructions by symmetrical (balanced) code, i.e. by code with digits 0, +1, -1. In opposite to binary code there is no difference between "signed" and "unsigned" number. As a result the amount of conditional instructions is decrease twice and it is possible to use them more easily; the arithmetic operations allow free variation of the length of operands and may be executed with different lengths; the ideal rounding is achieved simply by truncation, i.e. the truncation coincides with the rounding and there is the best approximation the rounding number by rounded.

In total there were produced 50 computers (including the specimens). The 30 ones were installed at universities and colleges, the rest – at research laboratories and plants. Geographically "Setun" were scattered all over the country – from Kaliningrad to Jakutsk and from Ashkhabad to Novosibirsk.

On the base of "Setun’s" positive experience it was designed and exhaustively determined in Algol-like programming language the architecture of other ternary computer [5]. This computer named "Setun 70" was introduced in 1970 [6]. In "Setun 70" the peculiarities of ternarity are embodied with more understanding and completeness: the ternary format for symbols encoding – "tryte" (analog of binary byte) consisting of 6 trits (~9.5 bits) is established; the instruction set is updated of auxiliary ternary logic and control instructions; arithmetic instructions now allow more variation of operand length – 1, 2 and 3 trytes and length of result may be up to 6 trytes.

... in "Setun 70" the traditional conception of computer instruction as a word does not exists. The program is a sequence of tryte-operations and tryte-addresses. The executed combinations of such trytes may be interpreted as virtual instructions. But there is no necessity for a programmer to think about this – he (she) constructs postfix expressions directly from the operands and operations by similar way as it is made in mathematics.

However "Setun 70" was the last "ternac". After it the research was stopped. Some details of our work is available in [15, 16].

http://www.computer-museum.ru/english/setun.htm
 

Circadian Clock Proteins

January 2008 Molecule of the Month
 David S. Goodsell
  Previous Features

Our cells contain tiny molecular clocks that measure out a 24-hour circadian rhythm. This clock decides when we get hungry and when we get sleepy. This clock can sense when the days are getting longer and shorter, and then trigger seasonal changes. Our major clock is housed in a small region of the brain, called the suprachiasmic nuclei. It acts as our central pacemaker, checking the cycles of light and dark outside, and then sending signals to synchronize clocks throughout the rest of the body.

Counting the Hours

Molecular processes occur so fast that is it difficult to imagine a 24-hour clock that works at the molecular level. But surprisingly, different organisms have evolved many different ways of doing this. Animal cells use a complex collection of proteins (with fanciful names like Clock, Cryptochrome, and Period) that are rhythmically synthesized and degraded each day. The 24-hour oscillation of the levels of these proteins is controlled by a series of interconnected feedback loops, where the levels of the proteins precisely regulate their own production. A much simpler system has been discovered in cyanobacteria. It is composed of three proteins, KaiA, KaiB and KaiC, that together form a circadian clock. At the beginning of the cycle, KaiA (at the top, PDB entry 1r8j) stimulates the large KaiC hexamer (center, PDB entry 2gbl), which then adds phosphate groups to itself. Then, as KaiC fills itself up with phosphates, it binds to KaiB (bottom, PDB entry 1r5p), which inactivates KaiA and allows the phosphates to be slowly removed. As the number of phosphates drops, KaiB falls off and KaiA can start the cycle again.

Synchronize Your Watches

These clocks have a period of about 24 hours, but as you can imagine, they are not exact. So cells have a way of synchronizing their clocks with the outside world. The clock in our brain is synchronized by exposure to light. Light is sensed by the retina, and signals are sent into the brain to modify the timing of the circadian oscillations. If you have traveled across several time zones, you have experienced this synchronization. For the first day or two, you experience jet lag because your clock is synchronized with the old schedule. But gradually, the bright light of day (blue light seems to work best) shifts your clock to bring you into alignment with the local time.

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