Is DNA a quantum computer?

 

Stuart Hameroff

July 4, 2010

 

Base pair qubits

A recent paper by Rieper, Anders and Vedral

(arxiv.org/abs/1006.4053: The Relevance Of Continuous Variable Entanglement In DNA) suggests

that quantum entanglement among base pairs in the DNA double helix stabilizes the molecule.

A summary of their paper is reported in MIT Technology Review

(http://www.technologyreview.com/blog/arxiv/25375/) is below

 

Rieper et al ascribe the entangling connections to van der Waals interactions among the pi electron clouds

of base pairs in the DNA double helix. Base pairs are composed of purines and pyrimadines, aromatic carbon

and nitrogen rings with several mobile pi electrons.

In single aromatic ring structures (purines, pyrimadines, but also amino acids tryptophan, phenylalanine,

tyrosine), pi electrons may 1) localize and occupy specific sites, or 2) remain fully delocalized above and

beneath the ring in an electron resonance cloud,i.e. in quantum superposition of possible locations.

However when two or more rings with pi electron clouds are precisely adjacent (near the van der Waals radius),

a third possibility ensues, involving a particular type of van der Waals force, the London force.

London forces arise when mobile electrons in one cloud repel electrons in the neighboring cloud, inducing

an electron cloud dipole which in turn induces a dipole in the first cloud. A pair of coupled dipoles (like tiny bar magnets) results, with a slight attractive force between them.If the clouds get pushed together closer than the van der Waals radius, a repulsive force comes into play, 100 time stronger than the attractive force, perhaps enabling nonlinear phonon couplings to conformational, or mechanical vibrations. (These types of effects apparently occur in certain proteins in which groups of aromatic amino acids (e.g. tryptophan, phenlyalanine) form non-polar pockets in which London forces couple to conformational states.Anesthetic gas molecules, binding by their own London forces, act in such pockets).

Reiper et al describe such interactions between adjacent base pairs (purines, pyrimadines)

along the vertical axis of the DNA double helix.

Figure 1. Rieper et al - van der Waals coupling between electron clouds of

adjacent base pairs in DNA.

 

However we should also consider sideways, or lateral interactions

between the two members of each base pair.

(Following drawings from R Hallick, University of Arizona)

 

Figure 2. DNA double helix, as in Figure 1.

The base pairs are always either Adenine (purine) and Thymine (pyrimidine, “A-T”),

or Guanine (purine) and Cytosine (pyrimidine, “G-C”).

Elecxtron resonance regions are shown in blue. Purines have a double ring structure,

with a 6 member ring fused to a 5 member ring, and 4 mobile pi electrons whereas pyrimidines

have a single 6 member ring with one pi electron.Both have mobile pi electrons (e.g. blue in

Figure 2). The complementary base pairs are held together by hydrogen bonds— 2 between

A and T, and 3 between G and C. Thus each base pair always consists of one 6/5 purine ring

with 4 pi electrons and one 6 pyrimidine ring with one pi electron.

Figure 3. Base pairs linked by hydrogen bonds (yellow) may also form

London force couplings due to pi electrons (blue).

If we assume the complementary base pair members are near the van der Waals

radius they will form van der Waals London force couplings

(in addition to hydrogen bonds) each A-T and G-C base pair also has van der Waals

couplings and dipoles which are London force due to mutually induced polarizations

between electron clouds of the purine and pyrimidine rings. At any particular time an electron

negative charge may be shifted either toward the purine ring, or toward the pyrimidine ring.

For the A-T base pair we can have negative charge more localized toward the

adenine purine ring, e.g. AT, or more toward the thymine pyrimidine ring AT

For the base pair G-C we can similarly have

GC, or GC

But as these dipole couplings are quantum mechanical they can exist in superposition

of both possibilities. So quantum mechanically we can have:

Both AT and AT which eventually collapse to either AT or AT

As well as

Both GC and GC which eventually collapse to either GC or GC

Using quantum nomenclature we can refer to the quantum superpositions of both

possible states | AT > + | AT >

And similarly

| GC > + | GC >

Such superpositions may be used in quantum computing as "qubits", bit states which can

exist in quantum superposition of, e.g. Both 1 AND 0.

DNA could function as a quantum computers with superpositions of base pair dipoles

acting as qubits. Entanglement among the qubits, necessary in quantum computation is

accounted for through quantum coherence in the pi stack where the quantum information is shared

Consider a string of three base pairs:

A-T

G-C

G-C

A-T can be either AT or AT, or quantum superposition of both | AT > + | AT >

G-C can be either GC or GC, or quantum superposition of both | GC > + | GC>

As each pair may be in two possible dipole states mediated by quantum mechanical interactions,

the 3 base pairs may be seen as a quantum superposition of 8 possible dipole states:

    1            2              3              4

AT     AT       AT       AT

GC    GC       GC      GC

GC    GC       GC      GC

   5              6             7              8

AT     AT       AT       AT

GC    GC       GC      GC

GC    GC       GC      GC

As each dipole differs slightly due to structural differences, so for example

AT and GC have slightly different dipoles though pointing in the same general direction

whereas AT and GC have more or less opposite dipoles.

If we consider the longitudinal quantum couplings as described by Rieper et al, the quantum states at each

level may be nonlocally entangtled with many other base pairs, perhaps all of them.

 

Whats's the point?

Gene expression as quantum computation

To what end? If we think of DNA as purely a repository of information, there is no need for

quantum computation. However gene expression is regulated by various external factors, both

directly and indirectly. These could include entanglement between a signalling factor with a particular

base pair, or group, as well as mechanical/conformational phonons of the DNA strand.

Net and complex dipoles within the pi stack may show emergent phenomena, in some cases

corresponding to loops, hairpins, dyads etc, each having specific properties. Superconductive DNA loops,

for example, could function in a way analogous to SQUIDs (superconductive quantum interference devices).

or serve as quantum antenna.

Perhaps gene expression involves a reduction of base pair dipole superpostion to particular dipole states.

For each base pair, the two possible altenatiive dipole states could correspond with ON or OFF, in terms of gene expression. The nornal state may be in superposition of both, till an interaction, or combination of interactions causes quantum state reduction - collapse of the wave function to one dipole state or the other, the proper one resulting in expression of that particular base pair genetic information.

 

(See Appendix 2 in chapter: Thats life! The geometry of pi electron resonance clouds

in Abbott, Davies, Patil, World Scientific, 2007

http://www.quantumconsciousness.org/documents/Hameroff_received-1-05-07.pdf

Also see see

http://www.quantumconsciousness.org/views/QuantumComputingInDNA.html

From MIT Tech Review

Quantum Entanglement Holds DNA Together, Say Physicists

A new theoretical model suggests that quantum entanglement helps prevent the molecules of life from breaking apart.

There was a time, not so long ago, when biologists swore black and blue that quantum mechanics could play no role in the hot, wet systems of life. Since then, the discipline of quantum biology has emerged as one of the most exciting new fields in science. It's beginning to look as if quantum effects are crucial in a number of biological processes, such as photosynthesis and avian navigation which we've looked at here and here.

Now a group of physicists say that the weird laws of quantum mechanics may be more important for life than biologists could ever have imagined. Their new idea is that DNA is held together by quantum entanglement.

That's worth picking apart in more detail. Entanglement is the weird quantum process in which a single wavefunction describes two separate objects. When this happens, these objects effectively share the same existence, no matter how far apart they might be.

The question that Elisabeth Rieper at the National University of Singapore and a couple of buddies have asked is what role might entanglement play in DNA. To find out, they've constructed a simplified theoretical model of DNA in which each nucleotide consists of a cloud of electrons around a central positive nucleus. This negative cloud can move relative to the nucleus, creating a dipole. And the movement of the cloud back and forth is a harmonic oscillator.

When the nucleotides bond to form a base, these clouds must oscillate in opposite directions to ensure the stability of the structure.

Rieper and co ask what happens to these oscillations, or phonons as physicists call them, when the base pairs are stacked in a double helix. Phonons are quantum objects, meaning they can exist in a superposition of states and become entangled, just like other quantum objects. To start with, Rieper and co imagine the helix without any effect from outside heat. "Clearly the chain of coupled harmonic oscillators is entangled at zero temperature," they say. They then go on to show that the entanglement can also exist at room temperature.

That's possible because phonons have a wavelength which is similar in size to a DNA helix and this allows standing waves to form, a phenomenon known as phonon trapping. When this happens, the phonons cannot easily escape. A similar kind of phonon trapping is known to cause problems in silicon structures of the same size.

That would be of little significance if it had no overall effect on the helix. But the model developed by Rieper and co suggests that the effect is profound.

Although each nucleotide in a base pair is oscillating in opposite directions, this occurs as a superposition of states, so that the overall movement of the helix is zero. In a purely classical model, however, this cannot happen, in which case the helix would vibrate and shake itself apart.

So in this sense, these quantum effects are responsible for holding DNA together.

The question of course is how to prove this. They say that one line of evidence is that a purely classical analysis of the energy required to hold DNA together does not add up. However, their quantum model plugs the gap. That's interesting but they'll need to come up with something experimentally convincing to persuade biologists of these ideas.

One tantalising suggestion at the end of their paper is that the entanglement may have an influence on the way that information is read off a strand of DNA and that it may be possible to exploit this experimentally. Just how, they don't say.

Speculative but potentially explosive work.

Ref: arxiv.org/abs/1006.4053: The Relevance Of Continuous Variable Entanglement In DNA

http://www.technologyreview.com/blog/arxiv/25375/

http://arxiv.org/abs/1006.4053