Quantum Microbiology

J. T. Trevors and L. Masson
Quantum Microbiology
Curr. Issues Mol. Biol. 13: 43-50, 2011

http://www.horizonpress.com/cimb/v/v13/43.pdf

A couple of sentence from the abstract to show what the paper is about.

“During his famous 1943 lecture series at Trinity College Dublin, the renown physicist Erwin Schrödinger discussed the failure and challenges of interpreting life by classical physics alone and that a new approach, rooted in Quantum principles, must be involved.”


“In this article we explore the role of quantum events in microbial processes and endeavor to show that after nearly 67 years, Schrödinger was prophetic and visionary in his view of quantum theory and its connection with some of the fundamental mechanisms of life.”

I should say that the paper is written quite well and I have enjoyed reading it. The paper urges us to employ quantum mechanics in microbiology but I am not sure if I understand what the authors mean. I am a chemist and for me a cell after all is some small chemical reactor, hence let me look at this from a viewpoint of quantum chemistry.

More than forty years ago, the professor who taught quantum chemistry at our department of chemistry used to tell us that chemistry is a part of physics. We have just to solve the Schrödinger equation, that’s it, all the answers are already there. Yet, even now the situation is far away from that ideal goal. Chemists learn quantum chemistry, no doubt, but quantum chemistry is just a a part of chemistry.  By the way, the best way to check whether chemistry is a part of physics is to take a physicist and to challenge him/her to develop a new drug or create a new material. Guess what happens.

As for the paper, in my view it would be useful to look what molecular simulation is. Ten years ago I took part in developing a course “Molecular Simulation for MST Engineers”

http://evgenii.rudnyi.ru/teaching.html#md

For the last ten years, the computer power has increased significantly but I believe that the situation expressed on my slides has changed not that dramatically. Molecular simulation starts with the the Schrödinger equation, either transient of stationary yet at the adiabatic approximation (movements of electrons are separated from movements of nuclei). So far, so good. The problem is however that there is no good way to solve it directly from the first principles even for relatively small molecules even at the adiabatic approximation. In real life one finds an eclectic mixture of methods from semi-physical to semi-empirical that solve not the Schrödinger equation but some simplified form of it. These methods scale much better than for example Hartree-Fock + Configuration Interaction but then the question is how do we know how good these methods are. During a seminar presenting a popular semi-empricial software, there was a good statement that when you use an experimental apparatus, you first have to calibrate it. Similarly when you use your quantum chemistry code, you first must calibrate it. Chemists are very good in this, but this is exactly the reason why physicists hate chemistry as well as chemists.

Well, even semi-emprichal quantum methods scale up to some level only and then one cannot use them as well. Chemists continue then without delay with molecular mechanics, that is, with empirical classical forces between atoms expressed as classical balls. On the other hand, the Schrödinger equation is not enough in chemistry as well as in microbiology. The Schrödinger equation is for temperature zero Kelvin and there is no life there. In order to treat systems at room temperatures, one need to include molecular dynamics or statistics by means of the Monte-Carlo method. The majority simulations in molecular dynamics or Monte-Carlo are done at molecular mechanics level but even here there are own limits. I am not sure if one can imagine molecular dynamics of the whole cell even at molecular mechanics level. Then try for example run molecular dynamics for DNA  at molecular mechanics level for 1 s and see what time is needed, as you must make small timesteps at some femtoseconds. The hot buzzword nowadays is “multiscale method” but there are problems, problems, and problems. In my view it would be very nice to extend molecular simulation to biological objects but the question is how. Well, biologists as newcomers may do it better than chemists. Good luck.

P.S. Quantum microbiology happens to be a trademark of Accelr8

http://www.accelr8.com/quantum_microbiology.php

P.P.S. On LinkedIn

http://www.linkedin.com/e/-gay7jh-gl6mtib5-50/vaq/46703264/54503/33919015/view_disc/

Vladimir Teif has made a link to

Vasily V Ogryzko
Erwin Schroedinger, Francis Crick and epigenetic stability
Biology Direct 2008, 3:15
http://www.biology-direct.com/content/3/1/15


Comments

3 responses to “Quantum Microbiology”

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  1. As long as my essay in ‘Biology Direct’ was brought up, I would like to direct your attention to this archive posting, where I suggest what kind of approximations to the ‘from the first principles’ quantum description we can use in order to describe intracellular processes:

    http://fr.arxiv.org/abs/0906.4279

    Obviously, there are huge technical difficulties ahead, but the potential implications for the biological organization and evolution could make these suggestions worthy of consideration.

  2. Thanks for link. When I have time, I will try to look at your paper.

  3. Vasiliy, I have written a small text on your paper:

    http://blog.rudnyi.ru/ru/2011/04/kvantovaya-mechanika-i-kletka.html

    Well, it is in Russian but I guess that this is not a problem for you.