Hi!

I recently graduated with a BS in applied math and due to some family healthcare circumstances, I left my math PhD after a semester to return to San Francisco to better care for my brother. While I'm home, I decided to pursue a second BS in cell and molecular biology. The degree will require me to take two general (non-calculus) based physics courses. I am interested in studying biophysical interactions in gene expression.

I would take the calculus based physics course but unfortunately, due to scheduling conflicts, I cannot and can only take the algebra based physics course. Will my degree in applied math be able to make up for my relative lack of physics specific training?

Thank you so much!

Any ideas for some project work in biophysics?

Hi team, I work in protein spectroscopy part-time and am interested in discovering new niche research areas in biophysics. I also want to learn machine learning as a skill in its own right. I want - killing two birds with one stone - to take a look at areas that combine the two.

A broad question - would anyone have any suggestions on up-and-coming, niche topics and areas that are being ignored in biophysics? Protein structure prediction is a huge one - but I'm more interested in the nooks and crannies of relatively unknown research areas :)

I’m a nursing student with goals of being a PMHNP. I love physics and would love to somehow work with it. I assume a minor isn’t enough for much and it would have a lot of direct relation. Any advice?

Hello,

I had a question, I am very fascinated with Biophysics and am really invested in a doing a PhD in the subject. But I am a undergraduate who is going to graduate with a B.S in Microbiology, will this hold me back from getting into a PhD program? Thank you:)

I have a PhD in Physics, but my work was in biophysics. I developed some mathematical models of calcium signaling in the context of wound healing.

I am currently a post-doc in a biology lab developing a mathematical model of brush border formation. Unfortunately, I recently found out my appointment is ending by the end of the year because my project hasn't been progressing fast enough. I need to find a new job by then.

I think I'm realizing that I really enjoy collaborating with others on modeling projects where I am helping answer someone else's questions. I just don't have as much of a desire to engage in my own research. In other words, I am more driven my by solving problems rather than trying to discover the problems I need to solve, if that makes sense.

Are there any jobs that exist where I can engage in mathematical modeling without being the "main person" in charge? Any positions I'm finding involve leading entire research projects.

Electrically charged antimatter, like bare positron, anti-proton or even a molecule consisting of antimatter atoms might be convenient to store inside specially formed molecules. Biomolecules can be convenient to make by using mRNA methods (the same made famous by vaccines) in cows and then taking that substance from cow blood or from some organ. Use the molecules as is or as scaffolding for other atoms, from uranium to lithium.

There might be strange extra reason to use the biomolecules as is. If panpsychism and "soul" (if that is a correct word in this context?) interface with normal physics by having some biomolecules react to electric fields in ways that normal physics does not predict, that same property might happen to make biomolecules better for storing antimatter.

The storage needs to be able to withstand at least acceleration of Earth's gravity without the antimatter falling to touch the matter. Antimatter can be used in spacecraft propulsion. Yes, it is fantastically difficult to make antimatter in useful amounts, but that is a discussion for another day.

What if the antimatter and it's container molecule are made so cold that their quantum states start to overlap like with bosen-einstein condensate?

It seems like there is a lot of controversy around this years nobel prize in physics. But I thought it was cool to see a biophysicist (Hopfield) win a nobel prize for what is in my mind unambiguously theoretical biophysics work (Hopfield networks)! Any thoughts?

So I am a Ontario highschool senior right now and I think I have narrowed my dream programs to be either the Biophysics specialist or Biochem specialist both at University of Toronto. I love biology, chemisty, and physics equally but I did the best in physics and really enjoy and think I am pretty good at math. First I was just wondering if I would be able to get into those two courses with my high 80s low 90s marks. Also what jobs lead out of each program. From what I've seen biochem is more pharmacy type stuff while biophysics is more the mechanical type stuff like hospital equipment. Im still wondering if i should take a chem or physics major to. The main thing i want to know it what jobs lead out of which program.

How tf do you do it? Like for example if your name was Theresa, how do you make a polypeptide chain based on that, idk if it is hard to understand but i really need to know

Hey! I am a graduating undergrad, and I am interested in biophysics. Well, in particular, I want get into programs that tackle with biophysics and biophysical chemistry (I am also interested in describing biological systems from a thermodynamic view) at the systems level. I've been recently looking up some PIs in various institutes offering PhD programs, but I can't seem to find the one that really aligns with my interests, yet. Does anyone know of PIs who work in this field? Thanks!

I'm taking a graduate course in condensed matter physics right now (pure theoretical physics track). And I think it's super cool. Right now we are working on models for electron behavior inside of periodic lattice structures. I'd be super interested in any cross over between these ideas and protein structures and biological machines such as ATP synthase. Naturally, biomolecules are not crystals. But I'm interested in the ideas for the quantum mechanics that lays the foundations for our biomolecular mechanisms. Is this a field or topic in biophysics? Would love to hear more!

I recently graduated with a double major in mathematics (with a focus in computer science) and physics, and only in my senior year realized that I was interested in biophysics and soft matter physics (leaning more towards the latter, but still interested in the former, so apologies if this isn't the right space!). While I did reasonably well in college (3.84 GPA), I didn't apply myself in terms of getting into research until my junior year, and as a result, spent only my senior year working in a lab (specializing in particle physics, since that's what I thought I was interested in at the time, with a computational focus). To compensate for that, I've been working in a soft matter physics lab since the beginning of the summer as a post-baccalaureate research assistant, and due to picking up on a project left behind by some previous researchers in the lab, should end up being an author on a paper. I plan on working in that lab for the rest of the academic year, going into the next summer, but I wanted to apply for PhD programs this year, and was wondering how high I should reasonably set my sights on as far as good grad school programs. I'm looking more at experimental labs, with a secondary interest in computational labs.

Thanks for any answers that can be provided.

Hi all!

I'm new to the reddit page and hoping to gain some insight from others more senior in their biophysics careers. Im heading into my final year of PhD and, up until recently, had a very clear goal of doing a postdoc, mayyyybe two, to gain experience on a particular computational approach then aim for a junior position at an R2+ university or institute position where I could both teach and conduct research on some specific research ideas I'd like to pursue. Although, recently Ive started to think that perhaps a reputable R3 or research-focused PUI might be right for me. I've been vocal about this for a long time and always received encouraging feedback from those in the field around me that this was a good plan and I had begun preparing for it well ahead of time. However, in recent talks with my advisor he brought it my attention that for my field a minimum of two 3+ year postdocs was typically necessary. In the past, he's always said that 1-2 years is all either side needs for a fair transfer of information so this was surprising to me but he reiterated that I should expect 3+ years in most postdoc positions. This now has me questioning my future goals, since ultimately I care more about my life outside of the lab than in it.

I know that it varies within subfields and between computational and experimental work, but I'd greatly appreciate hearing about others' postdoc experiences as well as others' career paths to better understand what I'm in for.

Also for context: I am based in the US, but many of the postdoc prospects for what I'd like to do are in Europe.

Thank you so much for sharing your exoeriences!

This is a simple question. What field of science delves into the creation of biological computers? Is it biophysics, biochemistry, molecular biology, computer science or electrical/biomedical engineering. I am currently a physics major, but don’t know if physics is the right path for this kind of stuff.

As the title suggests, I have a protein, where I want to modify some Cysteines to cysteic acid and generate a GROMACS topology.

I have generated the parameters for Cysteic acid from Antechamber.

I created an entry for Cysteic acid in the aminoacids.rtp directory of the force field I want to use.

I manually edited the cysteines to cysteic acids in Chimera.

But I am running into problems like GROMACS is not recognising the cysteic acids.

I want to ask the community that whethere there is a better way to do this ? Or am I going in the right direction?

I’ve acquired an old FluoroHub unit, but I don’t have the DataStation software to program it. Horiba won’t assist me since it’s an obsolete model. It came with its two DAQ PCI cards, PCI-6602 and TUMP-PCI (misspelled on purpose, wink wink). Could anyone help me out with this or provide any version of DataStation?

Hi everyone! I have recently started a newsletter about molecular machines and I would love some feedback and opinions. I mainly summarize a single paper, until now covering genome editing systems, DNA origami, protein design with AI, these kind of things. I would love to have some feedback and some opinions! 

Here the link: https://plentyofroom.beehiiv.com/

Hey guys! I have some inhibitors which appear to be mixed, and I would like to determine their alpha values. I have tried to apply the mixed inhibition model with prism, but even though I have relatively good curves, I keep getting an unstable alpha. Some of the curves don't have a great saturation plateau, and I know that is part of the problem, but I just need a general idea of these alpha values.

My first question is: is the Alpha in this formula in prism the same as alpha non-prime, meaning the value for substrate-free enzyme?

VmaxApp=Vmax/(1+I/(Alpha*Ki))

KmApp=Km*(1+I/Ki)/(1+I/(Alpha*Ki))

Y=VmaxApp*X/(KmApp + X)

^ this is what keeps giving my unstable values.

One additional option I discovered was to use my double reciprocal plots and apply the formula alpha = slope(km/vmax). I've verified that all my units are consistent, and yet the slopes are quite large, even at low concentrations, and since the slope is multiplied by the Km and then divided by a relatively small Vmax (again though, units being consistent with the double reciprocal being a pure reciprocal). So while I can get values with this method, the alpha values are massive, sometimes into the millions, and I have no experience with this.

Could someone perhaps point me to relevant literature, where I could find some methods containing alpha determination by michaelis mention and even double reciprocal plots? I'm having trouble finding anything that gives a decent explanation of the actual method.

Hi! I’m currently starting my 4th year as a physics undergrad.

I have a great interest in biophysics and have loosely researched the positional information of Drosophila embryos over the past year. Currently, I have some uncertainties about my future path:

1. Most of the papers I find seem to be more mathematical than biophysical, and I always feel like I’m lacking the mathematical skills to make progress. From what I understand, biophysics seems to be divided into several paths—some more focused on mechanics and others on biology. I feel like I don’t quite fit into either of them, and as a physics student, I haven’t learned anything particularly useful for the research topic I’m curious about. Is it possible to find a more “mathematical” path?

2. Am I really capable of studying biophysics? The books Nonlinear Dynamics and Chaos, Biophysics: Searching for Principles, and An Introduction to Systems Biology: Design Principles of Biological Circuits are all fascinating and drew me into biophysics, but over time, it’s become less interesting than I initially thought. It’s much harder to discover dynamical principles by just analyzing and modeling. I’ve also tried to self-teach some basic concepts of topological geometry and it's fun, but my teacher told me that doing research is more about creating new things rather than understanding what already exists. So I kinda wonder if I am just pursuing the fun of learning and lack of ability to do actual research.

This might be a messy post so big thanks for anyone who reply!

After speaking with authors and agreeing that pdb templates are poorly resolved, I predicted a protein~400aa in alphafold and remodelled disordered regions wrt to authors' notes and pdb, and further refined them.

In the SAVES server, it passes through errat 93, verify pass, and no errors in procheck However, in whatcheck, the Z score is in -30s.it has acceptable rmsd with deposited structure (with missing resids) How to resolve Z score? Should I put it in md, and will it explore conformational space and resolve on its own?

Edit: A similar score is noticed with the original pdb, too

Edit: I am interested in a protein with lots of missing residues so I predicted it from sequence with template and loop modelled/refined the disordered regions. Rmsd is less than 1 from initial em template, q means 0.75 prosa z score too within range however whatcheck z score is greatly negative and that is freaking me out

Hey I am working with a EPC-10 and Patchmaster. I use the digital outputs to trigger a laser. I want to record/export also the trigger pulse together with my recorded current measurements. I could not find anything in the manual.

Thank you in advance

Freshman physics major interested in biophysics. Been reading Physics of Proteins by frauenfelder. Also do research in computational protein dynamics. Does anyone know of top research groups doing cool stuff in computational/theoretical protein dynamics? Can't find much online so was wondering if ppl here would know

Im currently an undergraduate student majoring in Biophysics. What are the jobs that you can get with just a degree in biophysics?