Interface between Biological Physics and Quantum Physics

[AryaKimiaghalam]

TL;DR

What are some unsolved problems/areas of study in the interface of Biological Physics and Quantum Physics?

Are there areas of studies which could be characterized as an interface of biological physics and quantum physics? Does such an interface even exist?

 

[anuttarasammyak]

Hi.　How about searching quantum biology, e.g. https://en.wikipedia.org/wiki/Quantum_biology ?

 

[AryaKimiaghalam]

Thanks for your recommendation.
I already read that page. I was looking for direct applications that lead to robust subfields of study in biophysics. Many of the things listed in that page are limited implications.
For example, would biological memory and the retainment of memory in biosystems relate to quantum mechanics?

 

[hutchphd]

Roger Penrose did some stuff I am still trying to get my brain around. I don't think it set the world afire but far be it from me to diss a truly inventive mind.

 

[anuttarasammyak]

For example, would biological memory and the retainment of memory in biosystems relate to quantum mechanics?

Brain scientists search neuro circuits and memory reservoir extensively as https://news.mit.edu/2017/neuroscientists-identify-brain-circuit-necessary-memory-formation-0406 tells an example. But as far as I know they have not yet found any symptons and needs of quantum physics like superposition or entanglement of states in their search.

 

[vanhees71]

I would simply ask Schrödinger's old question: "What is life"? Are the laws of (statistical) quantum physics valid for matter making up living organisms? There's a quite interesting paper about this issue in Physics Today:

https://physicstoday.scitation.org/doi/10.1063/PT.3.4546

 

[phase_space_kid]

A more "boring" but nevertheless extremely important area is the quantum chemistry of proteins, DNA, and other biochemically relevant molecules.

For instance, modelling protein physics is exceedingly difficult and presently in its infancy. Empirically fitted potentials and Hamiltonian dynamics are used extensively but with great issues. For numerical efficiency reasons quantum mechanical effects are exceedingly challenging to incorporate, leading to interesting problems such as mixed quantum classical modelling, where say the binding pocket of an enzyme is modeled using ab initio quantum molecular dynamics and the rest of the protein is modeled with Monte Carlo or semi-empirical molecular dynamics.

 

[Auto-Didact]

At a semi-popular level, both Schrödinger's little book and more recently the book by McFadden & Al Khalili, show that quantum biology is a floodgate waiting to be unleashed. Sadly however, unto this very day still relatively few STEM students choose to go into biophysics and then even less take up the challenge of quantum biology.

For instance, modelling protein physics is exceedingly difficult and presently in its infancy. Empirically fitted potentials and Hamiltonian dynamics are used extensively but with great issues. For numerical efficiency reasons quantum mechanical effects are exceedingly challenging to incorporate, leading to interesting problems such as mixed quantum classical modelling, where say the binding pocket of an enzyme is modeled using ab initio quantum molecular dynamics and the rest of the protein is modeled with Monte Carlo or semi-empirical molecular dynamics.

I've been closely following this problem since my college days. I remember about a decade ago when PC's and consoles using online connection at home was still relatively new that the Folding@Home project became public, which attempted to utilize unused processing power to help solve the problem of protein folding.

Since then there has been a very recent and quite significant breakthrough in this field utilizing machine learning by Google's DeepMind team: AlphaFold 2.

 

[hilbert2]

Here's something about quantum effects in biological systems, and this article seems to be cited by several others:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5454345/

With "quantum effects" in this context, I mostly mean that you can observe phenomena similar to the tunneling, entanglement, etc. that you can see when playing with individual elementary particles and performing measurements on them.

 

[TeethWhitener]

You’ll ultimately need to invoke quantum mechanics any time you have light absorption. So photosynthesis, visual transduction, etc. And of course if you want really accurate modeling of a biological system, you’ll eventually need to lean on QM (especially for bond making/breaking in enzyme catalysis). As far as “quantum weirdness” and things like entanglement showing up in biological systems, there’s no evidence that any of that stuff plays an important role in biology.

One of the areas of biology where quantum mechanics shows up which fascinates me is in the photophysics of nucleic acid bases. If I remember correctly, the structure of the potential energy surfaces of all five common bases feature conical intersections, meaning that when a UV photon excites, e.g., an adenine, the energy is very quickly and efficiently dissipated as heat something like 99.9% of the time. This is in contrast with many molecules where bond breaking would typically occur. This mechanism makes DNA and RNA far more photostable than many other naturally occurring polymers, and it’s hypothesized that this advantage led to natural selection of nucleic acids for information storage in prebiotic systems.

 

[Auto-Didact]

Here's something about quantum effects in biological systems, and this article seems to be cited by several others:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5454345/

With "quantum effects" in this context, I mostly mean that you can observe phenomena similar to the tunneling, entanglement, etc. that you can see when playing with individual elementary particles and performing measurements on them.

This technical review by Brookes nicely summarizes all the points mentioned in McFadden & Al Khalili's non-technical book on quantum biology.

The most important finding by far is that the main argument against quantum biology, namely that proteins are unable to utilize quantum effects such as tunneling or entanglement for biological functions due to decoherence, is wrong. Environmentally induced decoherence seems to be dynamically negated in interacting open systems, i.e. in biological systems, as has been argued for many decades now in biophysics, probably starting with Herbert Fröhlich:

Arguably, one of the most astonishing, and common, inferences from this examination is, counterintuitively, that the environment (the protein) in the PPC does not hinder any of these processes, but actually that it may help.

This review particularly focuses on an environment modeled using normal modes (bosonic baths). This assumes anharmonic, large amplitude, and long time-scale motions are on irrelevant time scales (with respect to the rates described here). If it were otherwise any quantum superposition state carrying information would collapse. It is found that, actually, normal mode vibrations, at least, do not decohere, but rather support and/or accelerate rates. In §2 Enzymes, the possibility of tunnelling being ‘stabilized by phonon emission’ is first introduced. In §3 Olfaction, tunnelling is conjectured to be assisted by phonon emission by an odorant. In both, it is possible that a vibrational mode may accept and/or promote the rate. Of course, there may also be ‘demoting’ modes. In §4, it is shown that a weak perturbative regime can model the excitonic energy transfer observed, but it is likely that the protein motions and so the mixing of electronic and vibrational wave functions is important [95,96]. Thus, the analysis goes well beyond that of vibrational modes and any semi-classical version of the golden rule. There is much exciting work in this area [97] and it is fascinating to consider whether these more ‘quantum’ models may be useful in the analysis of olfaction and enzyme reaction rates. It is less obvious how environmental vibrations contribute in magnetoreception; however, it has been experimentally shown that the environment does not disguise any effect [91], and it is likely that the D/A pair that encode the field are held at relative orientations optimal for the effect transduction (figure 13) which is of course determined by the host protein. As is the nuclear environment (the nuclear spin) which is key to coupling to the D/A states (equation (13)) for the asymmetry in reaction rates.

Intriguingly, although protein environments (e.g. enzymes) are more often thought of as insulating barriers (e.g. figure 2) and as ‘wet and noisy’ environments though not to be any way conducive to the survival of any ‘quantum effect’, it has been seen that protein motion may serve to promote key quantized events such as charge and energy transfer. Typically, proteins can facilitate transfer by: (i) reducing the effective tunnelling mass by solvent exclusion, (ii) enabling crossing by equalization of energy states reactants and products (i.e. moving the Born–Oppenheimer surfaces closer together; figure 1), and (iii) by reducing barrier widths. Perhaps, the most exciting is the idea that protein motion may support the persistence of coherent oscillations, seen in figure 11, for example, at ambient temperatures. The phenomena of vibronic coupling emerging in photosynthesis suggests the protein nuclear motion supports the efficient energy transfer in photosynthesis, these coherent effects have been observed in charge separation in natural systems [75,76]. Of course, this is exciting with respect to understanding the fundamental nature of one of the most essential processes in life, but beyond this, knowing the importance of vibrations in proteins allows for the manipulation of the effect: this can be tested and exploited in artificial systems [77–79].

 

[DennisN]

There's a quite interesting paper about this issue in Physics Today:

https://physicstoday.scitation.org/doi/10.1063/PT.3.4546

Very interesting, thanks for posting!