Using Physics to Model Medical/Biological Phenomena

[claytonh4]

Just out of curiosity, is physics (advanced or theoretical, not simple classical physics like thermodynamics or mechanical properties) ever used to model, solve, explain, or apply to medical or biological (human) systems? I know hemodynamics and neuroscience involves a lot of math based physical science, but has the overlap ever been made between these fields of medicine/biology and advanced physical disciplines such as microfluidics, condensed matter, plasma physics, laser physics, high energy, particle, and the like? This is probably kind of absurd (I'm still in high school so I don't know a whole lot about these subjects) and I know that a lot of these properties are not directly involved in biological areas, but I was curious if any have ever been adapted to mirror or model certain system properties.

 

[pgardn]

Just out of curiosity, is physics (advanced or theoretical, not simple classical physics like thermodynamics or mechanical properties) ever used to model, solve, explain, or apply to medical or biological (human) systems? I know hemodynamics and neuroscience involves a lot of math based physical science, but has the overlap ever been made between these fields of medicine/biology and advanced physical disciplines such as microfluidics, condensed matter, plasma physics, laser physics, high energy, particle, and the like? This is probably kind of absurd (I'm still in high school so I don't know a whole lot about these subjects) and I know that a lot of these properties are not directly involved in biological areas, but I was curious if any have ever been adapted to mirror or model certain system properties.

One example might be an MRI as a technological application.
But as models for biological phenomena... its going to have to be something awfully simple biologically or something very specific. Maybe what happens to the appropriate electrons in a central Mg atom in a molecule of chlorophyll when a photon of light strikes. I can "see" lots of stuff with visible light as it has the right amount of energy to get biological molecules "excited".

 

[claytonh4]

One example might be an MRI as a technological application.
But as models for biological phenomena... its going to have to be something awfully simple biologically or something very specific. Maybe what happens to the appropriate electrons in a central Mg atom in a molecule of chlorophyll when a photon of light strikes. I can "see" lots of stuff with visible light as it has the right amount of energy to get biological molecules "excited".

Thanks for the reply! Yeah I hadn't considered photosynthesis, but that's a good point about using light to excite bio-molecules, esp. in those kind of light dependent reactions.

 

[Studiot]

A famous phrase from history, attributed to Franklin and to Faraday, is

What use is a newborn baby?

Well medicine has since made much use of their baby, electricity.

It is not that long since the structure of DNA was unravelled. We are pushing on to complicated molecular manipulations for both DNA and other substances - Who knows how tomorrow's virus treatments will arise?

MRI, Xrays, Radiotherapy, isotope tracers and istopic dilution analysis would not be possible today without the pioneering work in atomic and nuclear physics/chemistry.

Buckeyballs are a very recent discovery. Uses and potential uses are still being evaluated. However it is known that other things can be encpasulated within the ball for delivery to required locations.

 

[atyy]

Compare the mathematics in http://neurotheory.columbia.edu/~larry/ToyoizumiPRE11.pdf and http://prb.aps.org/abstract/PRB/v25/i11/p6860_1 . The first is a paper modelling some aspects of the cortex, the second is a paper about spin glasses.

The basic connection is a similarity between the Feynman path integral in quantum mechanics and the path integral of Wiener to describe classical random processes, eg. Chapter 3 of http://www.cs.washington.edu/homes/etheodor/papers/TheodorouThesisCorrected.pdf .

Also interesting is http://keck.ucsf.edu/~surya/DynCompSense.pdf , http://keck.ucsf.edu/~surya/DynCompSenseSupp.pdf about memory in the brain, which you can compare with the work of Terry Tao, a mathematician http://terrytao.files.wordpress.com/2009/08/compressed-sensing1.pdf , .

 

[Number Nine]

I've been starting to get into the use of mean field methods (from mechanics) to study populations of neuron; an approach which is becoming not-uncommon.

 

[Monique]

Sure, here's one example http://celldynamics.org/celldynamics/people/munro/index.html

I have spent most of my scientific life trying to reconcile simultaneous passions for mathematics and biology.[..] For me, mathematics and computer models are the natural way to talk about and predict how these behaviors could emerge from the molecular details.

There are many more examples, I know many research groups that are using physics-based computer models to explain complex biological systems. The beauty is that the computer models generate new hypotheses that can be tested in the lab to confirm the model.

 

[pgardn]

Sure, here's one example http://celldynamics.org/celldynamics/people/munro/index.html There are many more examples, I know many research groups that are using physics-based computer models to explain complex biological systems. The beauty is that the computer models generate new hypotheses that can be tested in the lab to confirm the model.

To me this is much more like using math to study the dynamics of populations. Its large scale modeling more like weather. Except you cannot setup large scale controlled experiments for weather. The future weather is the experiment. Very interesting stuff. I guess I was trying to get down to the nitty gritty of using a very particular biological phenomena that one would have to use QM to explain. Atomic level stuff. But then that becomes rather uncontrolled as the surrounding molecule, ex using chlorophyll, adds uncontrolled features.

 

[Andy Resnick]

Just out of curiosity, is physics (advanced or theoretical, not simple classical physics like thermodynamics or mechanical properties) ever used to model, solve, explain, or apply to medical or biological (human) systems? I know hemodynamics and neuroscience involves a lot of math based physical science, but has the overlap ever been made between these fields of medicine/biology and advanced physical disciplines such as microfluidics, condensed matter, plasma physics, laser physics, high energy, particle, and the like? This is probably kind of absurd (I'm still in high school so I don't know a whole lot about these subjects) and I know that a lot of these properties are not directly involved in biological areas, but I was curious if any have ever been adapted to mirror or model certain system properties.

There are several efforts to do this- mechanobiology, genomics/proteomics/*-omics, etc., in addition to the use of more advanced experimental techniques: high-throughput screening, surface plasmon resonance, improved NMR methods (TROSY, etc.), single-molecule studies (protein folding, motor proteins), structure-function studies of proteins, and increasingly advanced statistical methods applied to data analysis.

However, there is still a considerable gap between what physicists *think* biology is and what biologists consider important problems. Why do you think high energy particle physics should be applicable to biology (except for radiobiology)?

 

[Monique]

I guess I was trying to get down to the nitty gritty of using a very particular biological phenomena that one would have to use QM to explain. Atomic level stuff.

When 'only' studying a certain aspect the modeling is a lot 'simpler' (some mentioned in the post above, advanced stuff), but the challenge and the shift in the field is to be able to model complex systems.

Read the paper described in the following link, I think it will be very interesting to you: http://f1000.com/1047248
http://www.cell.com/cancer-cell/retrieve/pii/S1535610802001332

 

[atyy]

However, there is still a considerable gap between what physicists *think* biology is and what biologists consider important problems.

But is this still true nowadays? Aren't there enough people like you who are both physicists and biologists to demonstrate to make this statement false?

 

[hivesaeed4]

One of the most exciting applications of physics in the fields of biology and medicine is the area of nanotechnology. It can be used (I'm not sure if it is possible as of right now but in the future it definitely will be) for better drug-delivery, early identification of diseases, removal of tumors or cancerous organs and so forth. And nanotechnology is basically advanced physics as it is very difficult to make complex structures at the nanoscale level which actually do something useful.

 

[Ygggdrasil]

But is this still true nowadays? Aren't there enough people like you who are both physicists and biologists to demonstrate to make this statement false?

There plenty of physicists who do very interesting biology. There are also plenty of physicists who do very uninteresting biology.

 

[claytonh4]

There are several efforts to do this- mechanobiology, genomics/proteomics/*-omics, etc., in addition to the use of more advanced experimental techniques: high-throughput screening, surface plasmon resonance, improved NMR methods (TROSY, etc.), single-molecule studies (protein folding, motor proteins), structure-function studies of proteins, and increasingly advanced statistical methods applied to data analysis.

However, there is still a considerable gap between what physicists *think* biology is and what biologists consider important problems. Why do you think high energy particle physics should be applicable to biology (except for radiobiology)?

Thanks for your response. To clarify, I don't think it SHOULD necessarily, I was just curious whether some of these properties, theories, and behaviors of what has been considered strictly high energy physics (or something of the like) have ever been used to explain or inspire the explanation of complicated bio-systems. I know there are several physics studies and behaviors that are sort of weird if you will (e.g. many classical mechanics properties don't hold true at the quantum level and vise versa), just as there are some bio-fields that too are much more advanced and don't behave the way that is easiest to understand (e.g. neuroscience or certain aspects of genetics or even more in depth aspects of cardiology and hematology). Advanced mathematical theories also can exhibit these properties. Therefore I wondered whether or not, since these subfields are so unique to the other realms of their respective fields, if maybe some of these bizarre qualities could relate to the bizarre qualities of other (seemingly unrelated) disciplines. So far the answers I've received have been great and there's a lot more out there than I even thought. So in short, I didn't really expect particle physics to be relatable, I was just trying to make sure the difference was clear that I wasn't meaning classical mechanics that would be quite obvious in having a role in biology just as they would anywhere else.

 

[claytonh4]

Thank you very much, everyone, for your responses and all the links. They've really helped and have been very interesting aspects of biology (and physics/math).

 

[Mike H]

Kinda late here, but anyway...

OP - I think you might be underappreciating the role of classical (& statistical) mechanics and thermodynamics in understanding biological questions.

For example, there's this "www.rpgroup.caltech.edu/publications/Garcia2011a.pdf" (PDF) on the applications of thermodynamics/equilibrium stat. mech., where they touch upon applications ranging from hemoglobin and ion channel function to signal transduction and gene regulation. In addition, "alumnus.caltech.edu/~callaway/AdProtChem.pdf" (also a PDF) discusses dynamics of multidomain proteins utilizing a fundamentally classical model. (Although, admittedly, using quasielastic neutron spectroscopy is hardly the most classical of methods...) And there's a rather substantial literature on using classical methods to establish constraints on organismal behavior and physiology (e.g., are there thresholds for certain behaviors that depend on size?).

Anyway...

 

[cepheid]

I heard a story on the radio about "quantum biology" in which it was being discussed how the standard "lock and key" picture of how enzymes fit into their receptors may be insufficient to fully explain what is going on. The idea was that, in addition to considering the shape or structure of the molecule, there was evidence that we have to take into account what sort of vibrational modes or resonances it had. I'm no biochemist, but it certainly sounded interesting.

 

[Ygggdrasil]

The story was probably referring to the following paper, published last year in the Proceedings of the National Academy of Sciences:

Franco et al. 2011. Molecular vibration-sensing component in Drosophila melanogaster olfaction. Proc Natl Acad Sci USA 108:3797. doi:10.1073/pnas.1012293108

A common explanation of molecular recognition by the olfactory system posits that receptors recognize the structure or shape of the odorant molecule. We performed a rigorous test of shape recognition by replacing hydrogen with deuterium in odorants and asking whether Drosophila melanogaster can distinguish these identically shaped isotopes. We report that flies not only differentiate between isotopic odorants, but can be conditioned to selectively avoid the common or the deuterated isotope. Furthermore, flies trained to discriminate against the normal or deuterated isotopes of a compound, selectively avoid the corresponding isotope of a different odorant. Finally, flies trained to avoid a deuterated compound exhibit selective aversion to an unrelated molecule with a vibrational mode in the energy range of the carbon–deuterium stretch. These findings are inconsistent with a shape-only model for smell, and instead support the existence of a molecular vibration-sensing component to olfactory reception.

This isn't really "quantum biology" how most people might think of quantum biology. The quantum claim really only holds true in that the vibrations of molecules are governed by quantum mechanics. Furthermore, although the ideas presented in the paper are very interesting, the idea that olfactory receptors may be sensing the vibrations of a molecule remains controversial, and we don't yet fully understand everything that is going on here (see the following correspondences over the paper published here and here).

 

[mazinse]

being able to detect difference in isotopes does throw a huge wrench into our current system of experiments. Isotopes are used for A LOT OF PURPOSES because we can detect them in experiments in place of the normal compounds.

 

[atyy]

Isotopic effects in chemistry were known quite a bit before last year, eg.
http://pipeline.corante.com/archives/2006/08/01/testosterone_carbon_isotopes_and_floyd_landis.php

 

[Andy Resnick]

But is this still true nowadays? Aren't there enough people like you who are both physicists and biologists to demonstrate to make this statement false?

Most people (biologists, physicists, chemists, engineers, etc) have told me that I don't know anything about anything :)

But yes, the situation is slowly improving over time- people follow money, and the research money is currently being given out to multi-disciplinary work.

 

[Ygggdrasil]

being able to detect difference in isotopes does throw a huge wrench into our current system of experiments. Isotopes are used for A LOT OF PURPOSES because we can detect them in experiments in place of the normal compounds.

Deuterium is a special case for isotopes because its mass is twice that of hydrogen-1. This has a number of effects on its chemical properties, for example, altering hydrogen bonding strengths and changing the rates of proton transfer reactions. Other isotopes (e.g. using ³²P instead of ³¹P) involves only a very small mass change and would not be expected to affect the chemistry of the phosphorus.

 

[Andy Resnick]

[...] underappreciating the role of classical (& statistical) mechanics and thermodynamics in understanding biological questions.

<snip>

I totally agree- biology provides some of the most sophisticated applications of thermodynamics.

Another aspect that hasn't yet been discussed is using biology to model physical systems- the 'converse' of the OP. For example:

http://en.wikipedia.org/wiki/DNA_computing
http://en.wikipedia.org/wiki/Directed_evolution

and some books:

https://www.amazon.com/dp/0387989927/?tag=pfamazon01-20
https://www.amazon.com/dp/0195079515/?tag=pfamazon01-20

 

[cepheid]

The story was probably referring to the following paper, published last year in the Proceedings of the National Academy of Sciences:

Franco et al. 2011. Molecular vibration-sensing component in Drosophila melanogaster olfaction. Proc Natl Acad Sci USA 108:3797. doi:10.1073/pnas.1012293108



This isn't really "quantum biology" how most people might think of quantum biology. The quantum claim really only holds true in that the vibrations of molecules are governed by quantum mechanics. Furthermore, although the ideas presented in the paper are very interesting, the idea that olfactory receptors may be sensing the vibrations of a molecule remains controversial, and we don't yet fully understand everything that is going on here (see the following correspondences over the paper published here and here).

I don't think so. The radio show in question has a website with a webpage for each episode that has links for further information on each story. In this case, the story linked to these tw articles:

http://www.nature.com/news/2011/110615/full/474272a.html
http://www.wired.com/wiredscience/tag/quantum-biology/[/URL]

both of which are explicitly referred to as being about quantum biology. It also linked to the webpages of these scientists:

[url]http://meche.mit.edu/people/faculty/?id=55[/url]
http://www.chem.utoronto.ca/staff/SCHOLES/bio.html
[url]http://www.jenniferbrookes.org/[/url]

Now I remember...the third person was talking about whether quantum effects were important in olfaction, and that's where the whole thing about sensory receptors came in. The middle guy was talking about quantum effects in photosynthesis. I don't know what the first guy was talking about.

So I guess I didn't describe the content of the story very well the first time.

 

[Andy Resnick]

<snip>
Now I remember...the third person was talking about whether quantum effects were important in olfaction, and that's where the whole thing about sensory receptors came in.

I recall reading a few papers about this:

http://pubs.rsc.org/en/Content/ArticleLanding/2004/OB/b409802a

Which is related to the Drosophila papers Ygggdrasil mentioned. Speaking for myself, I draw a distinction between applying quantum mechanics to individual (bio)molecules and (bio)chemical reactions, where it clearly *does* apply, and trying to apply quantum mechanics to higher levels of organization (organelle, cell, tissue, organ, etc), where it likely does not. At least, there has not yet been a biological example that displays quantum effects at the macroscale, analogous to superconductivity.

 

[atyy]

Most people (biologists, physicists, chemists, engineers, etc) have told me that I don't know anything about anything :)

But yes, the situation is slowly improving over time- people follow money, and the research money is currently being given out to multi-disciplinary work.

I think biologists (in some to be unnamed fields ) do that to each other all the time, sounds like you've been accepted to the club!

To the OP: I do think it is fun to brainstorm and ask questions like "Is number theory useful in biology"? Sometimes you get unexpected answers. But a basic philosophy in physics is to "think physically", which is really the same thing as biologists' "think biologically" - so to start off with the phenomena that have been reliably observed and try to explain it. One doesn't care if the mathematics needed is simple or complex, in fact, the best thing is if you can provide a simple insight to what appears complex. OTOH, as Freeman Dyson said, say you want to make a bicycle - high energy physics is not useful for telling you how to do that. I believe, for example, our ability to cure cancer is still very much in the phase of trial and error. In neurobiology, we know clinically that stroke patients can be rehabilitated to some extent, and that this rehabilitation is in part due to synaptic plasticity. In the lab, the dynamics of synaptic plasticity have been worked out very well for some conditions. There remains a lot to do in understanding if and how the rules worked out for neurons in a dish carry over to the intact animal, and even more to do in using that to improve stroke rehabilitation. A spectacular example of an unintended success is deep brain stimulation for Parkinson's. There was a theory that Parkinson's was due to excessive "inhibition", so one might be able to alleviate it by reducing the "inhibition". Curiously, it was found that this didn't work, but instead *stimulating* the area that produced inhibition did! (Now, maybe the electrical stimulation is in fact reducing the inhibition, but I don't think there is a widely accepted theory of how deep brain stimulation works.)

Here are some videos about DBS
http://www.youtube.com/watch?v=a-8LW5GAlbc&feature=related

 

[mazinse]

dealing with quantum mechanics at the electron level for biology has been going on for decades, so it's not new. Every biochemists need to learn physical chem and that's where they get their knowledge. now at the nuclear level or even one level below which is the high energy one, that's a little different. Maybe in the areas of radiation cancer therapy that comes in.

 

[Ygggdrasil]

With regard to particle physics, one area of particle physics research that has directly impacted biology is the development of synchotron light sources. Synchotrons are a form of particle accelerator that propel particles along a circular path. As these particles inside the accelerator turn along the track, they release x-ray radiation that can be used in x-ray diffraction studies to determine the structures of biological molecules. Synchotron light sources are much better than conventional x-ray generators for biological XRD studies because they produce much more intense radiation (allowing the collection of higher-resolution data) and they generate a wide spectrum of x-ray frequencies, allowing biologists to select specific frequencies for certain sets of experiments (anomalous scattering experiments) that are helpful for determining new biomolecular structures. Nowadays, most of the really important work in this field relies on data collected at synchotron light sources.

Of course, new developments in x-ray lasers may make synchotron light sources obsolete in the next few decades.