Simulating Sound Waves

[Mahesh Venkat]

Hello, 

I'd be thankful if anyone can offer any advice with regards to my research project. I am currently investigating a potential relationship between carcinogenic gene expression and acoustic vibrations and would like to computationally model this phenomenon. 

More specifically, I would like to ask if there are any ways to simulate the effect of sound waves on the cell (specifically its genetic expression).

I am a high school student and am resorting to computational simulations as I do not have access to a lab.

Any help is much appreciated.

[Robert Phair]

Mahesh-

Primary cancers of the eardrum are exceedingly rare.

The tympanic membrane has 3 layers, two of them cellular. If any body cells are subjected to acoustic vibrations that are not damped out by the time they reach nuclear DNA, these cells are the likeliest. But cancer is rare here.

There is also a wavelength issue. Seems like even a high-frequency sound wave would be sensed as "nothing happening" on a nanometer scale. I'm no expert on this. Could be totally wrong.

What led you to this hypothesis?

I just happened upon your question, and am writing as a long-time science fair judge.

Good luck with your work!

Regards,

Robert

Robert D Phair PhD  |  Chief Science Officer  |  Integrative Bioinformatics Inc
Mountain View, CA
www.integrativebioinformatics.com

ProcessDB: Mechanistic modeling for systems biology

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[Dan Kolis]

That's an ambitious project; good luck. This forum is really focused on a file-making standards making process, not this sort of thing, at all.

You might be better off asking around, etc here:

https://groups.google.com/g/diybio

The title etc is misleading. Of the 4K people, members are mostly 'real professionals' moonlighting for some other ideas. Lots of capable people there. Picking the 'right horse to ride", is big. you might CONSIDER a molecular dynamics kick at this big cat, a program like this.

https://github.com/lammps

For instance, the labor to get it to compile 'all the way' etc is a huge partial step.

Hmmm, whoever wrote "Ear stuff" is no doubt missing the wide swatch of possible considerations. The idea acoustical energy just does 'ear stuff', is bizarre. The field of radiation medicine of intervention ultrasound, busts up blood clots, fixes nerve damage, even executes abortions. Sound is energy !

Good luck !

What your attempting, is hard and you know it. Good for everyone, including you, to jump on it.

KEEP not good, but GREAT notes as you go !

Regards,

Dan

my ref: 11 Jul 2023, sbml-discuss

[Dan Kolis]

Edited slightly for privacy, etc. Rainer said:

I am on the SBML list since > 20 years, lot's of people there who could just think of "ear stuff", regarding the student's question. 

May I ask what you are involved in professionally? A mid-term plan is to get to know lammps, I wanted to use the existing coarse-grained models of supercoiled DNA to study local DNA structures at promoters ( bacterial ) and a specific hypothesis on DNA cruciform formation.

Dan says 'back':

Ahhh. Well, I'm a self employed science programmer, have been 'forever'. I'm writing an IDE for biotechnology, SBML is a feed in to that,  moderately important to it.

My interest in amping LAMMPS was/is to study interaction between Methlation and inhibiting / promoting DNA translation.

I think the molecular dynamics universe favors throwing in on LAMMPS more then the other more biology alleged associated projects. Esp support for Vector chips like support for NVIDIA core number crunchers.

Your guidance for the student(s) might be to excel at LaTeX and write up places in Jupyter and maybe even publish on  https://www.biorxiv.org/

I've returned an email privately too.  If you your student / associate(s) or other readers have a CLEAN, understood compile of LAMMPS perhaps you can return a lnote to me here.

We can move the BLOG continuity, with ease as opposed to redirecting some purposes here. That would be counterproductive, or simply undesirable, and/or a mild intrusion, possibly.

So you're studying bacteria, are you ? I hear there are a lot of them, and they tend to keep busy.

Regards,

Daniel B. Kolis

my ref: 12 Jul 2023, sbml-discuss, google list