Hi,

I am working on exploring the configuration space of IDP ensembles.

I am curious if there are any complete resources that dive into theory and analysis of these ensembles, such as mechanical properties/solvent influence etc.

Would appreciate any resource that explores this.
Thanks

Biological Leverage In Humans and Animals' Self-Movement
SSRN physiology eJournal

Your feedback and comments are appreciated.

Thanks,

Recently, I started using stir bars during the solvent exchange between tetrahydrofuran and water to form micelles out of a polymer. I noticed after a few experiments that it has messed up the size the micelle form at. Normally I have micelles forming anywhere between 10-20 nm and a larger aggregate around `120 nm. However, I added stir bars during the solvent exchange portion and its caused the micelles to form at sizes larger than 200 nm.

I'm thinking that since the THF causes the polymer to be miscible, that then the stirring causes the polymers to aggregate more rapidly and with more polymer molecules once it begins to reach the critical micelle concentration.

This might be a wild thought. I'm curious to what all you think about what could be happening here. I'm switching back to no stir bar today, so I'll update you all then.

Hi,

Could anyone recommend any introductory textbooks on oncology/microbiology/cell biology for mathematicians lacking biological background? I am primarily interested in understanding the fundamental phenomena/problems in these areas of biology.

Thank you very much in advance.

For some context, I did my undergrad in math and master’s in theoretical physics at a good school. I now work in industry. But I’m still trying to find ways to be useful in the sciences as an amateur. And I wanted to get this subreddit’s thoughts on my notes below. Ideas are subject to change.

In my quest to be a semi-useful amateur physicist, I’m trying to figure out where the niche problems are in greenfield areas, like quantum bio, that other pro-academics might not have time to look at. I thought that attempting computations, and asking ‘hey, should it be this hard to do?’ might serve as a decent prompt to finding some ideas. I think as an outsider this approach is great because you don’t have the influence of other people telling you something should be easy. This post is about my difficult experience in simulation software for quantum bio experiments.

When I started to read papers on quantum biology, like on protein tunneling and enzymes, I found that a lot of the experiments were computational. And most relied on a cocktail of different pieces of code and different bits of computational biology software to get a result. And I’ve been struggling to replicate them. With so many independent parts that researchers do separately, I think that it is amazing that these computational experiments are replicable among different groups with all that config. Even more so due to the fact that everyone is using different computers. So I tried to have a stab at running simple toy quantum mechanics / molecular mechanics (QM / MM) simulation on a laptop to start with a program called VMD.

I realised trying to start a basic QM / MM simulation is just really hard. And I think quite a few people agree. I posted on reddit about it, and emailing certain academics in the field asking ‘hey don’t you think this is just really hard to setup?’. And everyone I’ve emailed thinks compilation and simulation set up is just a pain in the ass. Cloud based solutions didn’t seem that easy to use either. I am trying to train myself to notice interesting problems by just asking dumb questions, and I think this is one of them - but posting here to see if I’m actually correct.

The first thing that makes it hard is that a lot of computational chemistry software is just old-style and not that aesthetic, so its already intimidating to begin with. It doesn’t allow for the easy entrance of hobbyists. And as we know from the computing revolution, hobbyists play a huge role in developing the ecosystem.

And if something breaks, its hard to know where to go for help (since its a niche field). The use of different softwares make it hard to share simulation configuration, so you can’t easily get other people to replicate your problem, let alone run your simulation. Given the replicability crisis there are no easy ways, that I know of, to share simulation config amongst researchers.

What doesn’t make it easier is that there are no good guides to at least getting a decent home lab setup so that simulations run on the order of hours, and not days. And I think academics are confused about this too, they are surprised when I tell them that other labs use high powered desktop setups instead of national supercomputers. Perhaps no one really thinks about which simulations can actually be done without supercompute - and this is not clear at all.

It’s expensive to get started. Some tools in the landscape (Gaussian) are expensive. I don’t think it should be this way, and this just feels like a symptom that the field of computational chemistry is not mature enough. A lot of things are becoming free though, like PySCF, but these don’t seem geared to QBio. Everything is completely free if we look at other fields like machine learning and deep learning.

I think something that might ease these issues is making a very, very simple and clear tutorial on how to get started. And this is something that I want to build. I am trying to think of a way to make a tutorial that I would actually use if I was starting out. I would like a tutorial to actually learn how QM/MM works bare bones, and what it gives that classical simulations don't. I would also like a tutorial with real bare bones cases. And also, include a section on getting a decent homelab with a budget.

For example (starting from the beginning), in a good tutorial I would expect that:

• What quantities do classical molecular dynamics simulations give us

• Where do classical simulations fail

• How do basic quantum simulations work

• Where do the basic quantum simulations fail

• How does QM/MM fix the failure

• What quantities does QM/MM give us

• What differences in magnitude can we expect from QM / MM vs classical simulations

Anyway, those are some of my thoughts. Feedback really appreciated.

With these technologies, most if not all the sensors may be based on measuring physical properties of the cells that the sensors are pressed against, but measuring amounts of 1 or more chemical may augment the automated decisions that these devices would make. Some of the measurements may be between physical and chemical when gauging the surface grip of specially selected molecules on cells.

https://www.reddit.com/r/nano/comments/1czpva1/chain_of_tiny_electric_actuators_that_are/

What biology-related subreddit would be better for this?

I had an apartment where some mixed amphetamine smoke had gotten into the walls.

In a pot of boiled peanuts, I placed the usual kitchen-sink type of spice blend, salt, and baking soda at the end.

Then the pot began to fizzle.

I guess that through the steamy room, since the particles of liquid have been made semi-gaseous due to the colloidal nature of steam, existed an avenue through which the mixed amphetamines in the walls could condense into the pot through the magnetic forces between the chemicals.

I added alcohol (a few shots of vodka) at the end, which merited me more fizzling.

I boil the peanuts for a long time before that, though. It takes at least 24 hours boiling to chef a good batch of boiled peanuts, and that was my original intention anyway.

These peanuts turned out bitter and inedible, but I think the broth may be laced with MDMA or other similar chemicals due to this method.

What do you think? 🧐🤣

I have to write report which is related with my interest, physics in biology class. I've been searching electrophysiology, quantum biology, biophysics but i can't find nice subject Could you guys give me some proper topics?

Hey guys! I'm in my final year ug biomedical science. I've decided to take up biophysics for my masters.

Can you please recommend some books? Because my basics in physics is pretty bad rn. And I wanted to know what topics/concepts to focus on and what I should know before joining Msc. Biophysics. So I wanted to start now since my final year is pretty free.

Hi everyone! I’m new to this sub but hoping for some help. I’d like to find an online course/resource to improve my scientific communication and power point skills. I don’t need someone to teach me the basic tools of ppt, more so I want to elevate my presentations so I can look like those people that get up with slides that appear to have been made by a graphic designer! You know the ones I’m talking about - the ones that just hit it out of the park at conferences. I’m finding lots of different options online but hoping for some feedback from anyone who has already gone through one. Thanks in advance!

When I started reading papers on quantum biology (I'm a beginner), a lot of the experiments were computational and involved the use of mixed quantum mechanics and molecular mechanics simulations. So, I tried to have a stab at running a simple toy QM / MM simulation to start (a QM simulation with a classical molecular mechanics 'background').

However, most starter tutorials / to do this I found were extremely hard to use for amateurs like me—I have a theoretical physics background. The only tutorial I’ve found that actually works, is really explicit, and runs in a reasonable time, on a Mac M1 chip (8) is the tutorial by UIUC, which does QM/MM on a calcium site.

http://www.ks.uiuc.edu/Research/qmmm/Tutorial/Tutorial.pdf

It took me a day to run the classical minimisation step, a day to run the classical annealing step, and, surprisingly, around ten minutes to run the QM/MM step.

Specs below:

• macOS Monterey Version 12.5

• Model Name: MacBook Air

• Model Identifier: MacBookAir10,1

• Chip: Apple M1

• Total Number of Cores: 8 (4 performance and 4 efficiency)

• Memory: 8 GB

Folding upon binding is mostly associated with a transition in secondary structure of a protein.Assuming a transition from coil-helix and vice-versa for a protein,is it possible to associate this characteristic with the existing models of Zimm-Bragg and Lifson-Roig Models?

Hello everyone, I’m looking for an advice regarding pursuing a degree in science. Recently I got accepted into a Bachelors studies for both Physics, specializing in Biophysics and “Applied Biochem and Biotechnology”.

I don’t really know what Biophysics nor Biochem is, but I wanted to study something with biology, while not directly being a biology degree, and I always loved physics classes in high school ( altough I was really bad at them, but to some degree I would blame the teachers on this one ). While I hated chemistry for the lack of interest by both parties in high school, I applied for Biochem just in case the phyics didnt work out.

I plan on studying a lot, getting PhD too ( preferably more of them but thats in the future ), my current career path is becoming a professor and a patent lawyer. I need a future where being in a wheelchair will not prohibit me from doing my job. I have an arthitis that fucked up my left knee, and it’s affecting other joints now, and that’s why I chose Biophysics, because I think it would offer me a solution to my problem ( I could focus on it as part of my job ) , since there is no cure yet.

The Biophysics specialization doesn’t offer much physics classes, except optics, quantum physics, mechanics, medical biophysics, physics of biopolymers, electricity & magnetism, basic biophysics and physical chem. There’s some microbiology thrown in there, along with quite a bit of chemistry, and 3 semesters worth of math.

Is this Biophysics degree worth it? Is it even what I should be aiming for, or should I go to biochem. Should I try to ask the Admission Board if I could maybe get rid of the specialization and do just straight Physics degree, and hope I’ll figure it out on the way?

I’m adding an english link to the university, it’s probably the 2nd most prestigious in Czechia, has a modern lab and library too! You can view the Courser under, well “Courses”

I was awarded with the DAAD scholarship for Masters in Germany. My undergrad was in biochem and Chem at Sydney University. I want to eventually work in molecular biophysics/structural bio but I want a strong foundation in physics (potentially considering theoretical/computational biophys). I was wondering if anyone has any opinions or experience with TU Dresdens Physics of Life course?

The word 'worm' is not exactly correct unless there is some self-powered bending instead of just bending with external forces.

Tiny device, that has even tinier integrated circuit in it, or is itself a tiny integrated circuit that is something other than a chip, can move to desired locations and destroy cancer cells there. What kind of sizes are we talking about? I think, devices 5 microns or more can be manufactured, but bigger is easier and also lesser number of them is enough. Larger number of them must be autonomous, and can not be remote controlled. They can be injected to a vein upstream from the tumor.

A mechanical / artificial worm might use a drilling mechanism similar to this to first gain access to the tumor and then shred it:

https://youtu.be/TDRxnEHq068?si=O2shiwHU5M2hkfZ9&t=28

(time code link)

It would probably be a MEMS device:

https://en.wikipedia.org/wiki/MEMS

Can anyone recommend some good quantum biology PhD or Master's research programs? Any country is welcome. I'm interested in quantum processes in DNA and genetics. I have a background in theoretical physics.

Hi, I am looking at doing biophysics and/or comp bio for grad school - I'd prefer to apply to the structural biology and biophysics programs because Im realizing it is easier to pick up coding and algorithms than biophysics. In undergrad I only took physics 1 (not E&M) and up through Calc 2. However, I did work in an NMR lab. I am getting an associates now in computer science and working as a lab tech in diagnostics.

Are the PhD programs going to be discouraged to admit me based on my lack of physics classes/minimal background? Will I be better off applying to the comp bio programs and taking the biophysics classes when I get there??

Is there a lot of memorisation in biophysics? It it more "physics" or more "biology"? Does it have a lot of calculations?

I rarely hear any mention of these experiments which relate to (and I previously assumed served as the foundations of) biophysics.

The authors showed that a cytopathic effect can induced in a cell culture by viruses and/ or toxic chemicals, can be “transferred” to another (recipient) cell culture, completely separated by everything but a glass window. ^(1)

Quartz blocked the cytopathic effect while glass allowed it to happen, suggesting a photonic mechanism of action.

This isn't just one "lucky" experiment, Kaznacheev himself replicated the results thousands of times, and dozens of other independent labs have done the same, something that is somewhat rare for biology.

Similar works were performed by Budagovsky (2006) Kirkin (1981), and later by Nikolaev (Nikolaev, 2000; Beloussov et al., 2007), Burlakov (Burlakov et al., 2000), Beloussov (Beloussov et al., 1997, 2000), Trushin (2004) and others (we apologize to those not mentioned) (For recent reviews see, Trushin, 2003; Cifra et al., 2011; Scholkmann et al., 2013).

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4561347/

https://web.archive.org/web/20190429043749/http://www.photonics.su/files/article_pdf/5/article_5655_114.pdf

https://www.google.com/books/edition/Biophotonics_and_Coherent_Systems_in_Bio/u3KXRjq3qMAC?hl=en

https://pubmed.ncbi.nlm.nih.gov/11036668/

https://www.researchgate.net/publication/246928261_Distant_interactions_in_bacteria
https://pubmed.ncbi.nlm.nih.gov/20674588/

I’m an almost a highschool senior and biophysics pick my interest. I just wanted to know what types of jobs can you get with this type of degree?

Hello I am a current first year student at my university. I have taken Cell bio 1, gen chem 1 and 2, organic chemistry 1, and I am going to take physics 1 in this spring term. I want to start to learn biophysics on my own and I cannot currently take in university as I am taking multiple hard classes next year and do not want to take another one. What are the best resources for learning biophysics. I am very intruiged by this topic and have bought the "Biological Physics Student Edition: Energy, Information, Life" textbook as this is what my university uses. What resources should I use and do I have enough prerequisite knowledge to start learning? thank you

Hi! I’m a current high school senior majoring in biophysical chemistry at JMU next year :)

I would love some tips on how to succeed in the subject, as well as any advice on what I should study this summer to prepare. For context, I’m currently taking AP physics, AP calculus BC, and a research class where I’m studying drosophila neurology. I’m not super strong in math so I’m retaking calc in college and I also haven’t done chem in like 2 years (it also wasn’t AP, just regular).

I would be super grateful for any advice, thanks!!

Anybody have any idea how long atoms exist for in the human body before needing to be turned over? Like how long does a particular carbon atom exist in our body after being ingested and incorporated into amino acids for whatever protein or say cobalt atoms in cobalamin.

Just curious.

I've recently installed gromacs and everything necessary to run it through wsl but in doing the tutorial I keep encountering an error that says the chosen file can't be found when attempting to unzip the tutorial folder I'm sure I've just messed up either a path or haven't installed something properly but I can't seem to get passed this issue and I've followed all of the setup tutorials, does anyone have experience with setting up the software that may be able to assist me?

Hi, i live in the uk and i am a 2nd year undergraduate biochemistry student studying in london.

My degree falls under the biosciences department rather than the chemistry department which i have found leaves me unsatisfied with my course.

I feel as if i am going through tedious example after tedious example without learning anything new or without studying any new interesting concepts to get my head around.

Biophysics is something that has caught my eye (for quite some time now) and i wondered if anyone here knows how realistic it is for a biochemistry student to pivot towards a more physical science.

And if anyone has any resources i could use or subjects to start on in biophysics to learn more about the subject.

Thank you!

From what I can tell of how he describes the process someone enters the vat of aqua-green liquid and perhaps with molecular coding a strong EM field (from outside the pool) directs the enzymes for the manipulation or body rebuild desired. I'm wondering if something similar could be developed for just healing....   

The book at Archive.org,
https://archive.org/details/solis0000atta

Guys how difficult is biophysics PhD? I have major in bio and minor in physics,statistics. What do they look for and what schools to consider?Should physics department be considered or bio?

I have been applying in REU as major in biology and minor in physics and stats. In my institute lab I majorly do theoretical biology whereas through summers and course work I do wet lab and have worked with model organisms ,protein cloning etc.

However recently I am only being considered for computational roles and experimental biophysics labs are hesitant to take me. Though I am an undergrad student just learning to balance both.

Its very disappointing..given I want to balance both,will phd admission committees also see the same and deny positions in experimental labs?

I am back with more course questions, my university has 2 diff eq course options one teaches Laplace transform and the other does not so is learning Laplace transform going to be necessary? Thank you in advance for any assistance.