/r/Biophysics

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/r/Biophysics

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1

Gromacs in wsl

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?

0 Comments
2024/04/05
22:41 UTC

6

Biochemistry student dissapointed in their undergraduate degree

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!

5 Comments
2024/04/02
18:53 UTC

1

In the science fiction book Solis by A.A. Attanasio describes a future community on Mars in which people can be bioengineered in vats of inductor enzymes...

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

1 Comment
2024/04/02
10:09 UTC

6

Biophysics phd competition

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?

12 Comments
2024/03/30
17:07 UTC

6

Rant: computational Experimental

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?

2 Comments
2024/03/19
11:35 UTC

3

Diff EQ courses

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.

1 Comment
2024/03/06
16:10 UTC

2

Getting an error in the VMD extension Molefacture 2.0

0 Comments
2024/02/29
08:27 UTC

2

Need help with kinact/KI determination by fluorogenic assay

Hey guys!

I'm a 6th year biophysics PhD student working with a student who needs to determine kinact/KI by fluorogenic assay. We did a literature search, but found little methodical information and so figured we had to design the assay ourselves.

Our primary reference is: https://journals.sagepub.com/doi/pdf/10.1177/1087057116671509

This paper, and most others like it, use % occupancy graphs generated for every concentration of inhibitor at a given time point. These % occupancy graphs are hyperbolic, the actual graph you obtain by inhibiting the enzyme with varying concentrations of inhibitor over time is, of course, one of exponential decay. The point of this stage is to obtain the observed rate of inactivation, kobs, which we calculated directly from the exponential decay curve in Graphpad Prism with the nonlinear one-phase association function Y=Y0 + (Plateau-Y0)*(1-exp(-K*x)). K was taken as kobs, and graphed as a function of inhibitor concentration. This hyperbolic curve was fit to Y=(X/(Ki+X))*kinact.

Early on, we noticed that this curve did not really saturate, though it did slow at high concentrations of course as we reached our max rate of inactivation. We added progressively higher concentrations, up to 10µM (compound IC50 = 250nM at our sol-hMGL) and still did not achieve a steady max rate; it continued to increase.

All assays were performed in 96-well plates. Substrate was 4-methylumbelliferone butyrate, a butyrate ester of coumarin which is hydrolyzed by MGL (monoacylglycerol lipase) and generates a fluorescent signal. Compound CAY10499 (covalent MGL inhibitor) was diluted to step 1 concentrations yielding working concentrations of 1, 10, 100, 500, 1000, 2000, 5000, and 10000 nM. These were transferred into a 96 well plates in triplicate along with blank wells (5µL of DMSO instead of 5µL CAY10499 in DMSO) to obtain an apo curve for each run. concentrated MGL was diluted to 20x the working concentration of 10nM/well, and incubated in PBS pH 7.4 with 0.5% Triton X-100 and 1mM TCEP at 37ºC for 10 minutes. The experimental wells were brought to 195µL with PBS pH 7.4 and 5µL enzyme was added to begin the reaction. Plates were shaken at room temperature until they reached their pre-determined incubation time, at which point 5µL of substrate in DMSO was added for a final concentration of 25µM 4-Methylumbelliferone butyrate per well. The plate was immediately read and recorded.

As you can see, the kobs vs [I] curves we obtained from this compound, of which we have several now, all give a KI of between 3-5µM, and we know for a fact that it should be at least 10 and at most 20 times less, but as we add higher and higher concentrations to try and get this curve to "saturate," we just keep going and get higher and higher KI estimates. Are we doing something wrong, like in the step of exponential decay? Knowing that the KI is so off makes me wonder if I need to generate those percent occupancy graphs, but why do I have to if I can get kobs from the exponential decay? Please someone with more experience than me help us out if you can! :D

14 Comments
2024/02/29
00:14 UTC

1

Advice on a DIY bio-physics corce

My university doesnt offer an undergrad major in bio-physics only minor, but I want to focus on this area. My current plan is to DIY by adding a bio-chemistry and molecular biology minor? As well as a major in physics, would this cover enough knowelde to pursue bio-physics? Thanks

5 Comments
2024/02/28
13:10 UTC

1

Study Abroad

Hi! Do you guys know where you should go if you want to study abroad and take classes in biophysics? I am from the US, and I am looking for universities I should go to. Any advice would be helpful! Thank you.

9 Comments
2024/02/27
04:54 UTC

0

We’re looking for expert Biology tutors to join an AI research project training AI models ($35-50 per hour)

Hey! I wanted to share an opportunity with this Biophysics Group to participate in cutting edge AI research!

Our team at, Pareto.AI, a Silicon Valley based startup, is helping AI researchers at top companies like Character.AI, Imbue, and many more build high quality datasets to train bespoke AI models.

We’re looking to start paid trials before the end of this week! Folks can learn more and apply here: https://paretoai.typeform.com/tutoring

Appreciate if you could help us forward the opportunity!

Warmly,

Dobie Anne

1 Comment
2024/02/22
12:05 UTC

5

Genetic engineering and quantum mechanics

Im currently attending my first year in college and planning on transferring to UT Austin. I want to get into genetic engineering and so thought that maybe I should major in biochemistry to start with and choose a more in depth specialty in my graduate school. But lately I've been so obsessed with quantum physics and now i've become unsure. I'm willing to compromise and blend the two. Mostly im wondering what the best approach to integrate both of these fields. what should my speciality be? Which specialty focuses on both synthetic biology (Human/animal cells) and quantum mechanics? I have looked into biophysics but what speciality would y’all say is the must focus in blending these two fields.

3 Comments
2024/02/21
03:10 UTC

1

hello can someone help me with this question? Ive been stuck on it for an hour.

5 Comments
2024/02/20
15:11 UTC

11

QM and Thermo in the same semester?

Trying to plan out my next couple semesters and trying to decide if I would hate myself for taking these 2 together. Any advice is greatly appreciated.

8 Comments
2024/01/31
21:37 UTC

2

Vertex models

Is there any good open source sofware to implement vertex models,I am looking to simulate epithelial cell sheets.

1 Comment
2024/01/31
16:02 UTC

19

Intrinsically disordered proteins or IDP's.

Hello everyone,

I'm very interested in entering the field of research of intrinsically disordered proteins (IDPs) and I want to explore it from a biophysical standpoint. I'm particularly interested in how statistical mechanics, electrostatic interactions, and charge regulation play into the description and dynamics of IDPs. I'm from the theoretical and computational side of biophysics, I'm in search of comprehensive and up-to-date review papers that can provide a solid foundation in these areas.

Could anyone recommend literature that strikes a balance between thoroughness and accessibility? Especially for someone transitioning into this field? I'm looking forward to delving deeper into this topic and would greatly appreciate any pointers or insights from this community.

Thank you in advance for your help!

8 Comments
2024/01/26
20:03 UTC

7

Biophysics Wet/Dry lab

Would you say that Biophysics offers the opportunity to pursue WetLab aswell as drylab? And if so, what differs between the Wet Lab of a biotechnologist from the one of a bioPhysicist, and what differs between the drylab of a bioinformatich and the lab of a bioPhysicist?

5 Comments
2024/01/23
21:14 UTC

6

Importance of Specificity in Undergraduate Research

Hello,

I am a physics junior in the US interested in pursuing a PhD in biophysics/soft matter physics upon graduation. I recently transferred to a new university and once I got settled I started looking for a new lab to do research with. My university has a good reputation for biophysics, but it also has a really great engineering school, so in the interest of increasing my chances to get into a lab I contacted some biomedical engineering labs that focused more on materials stuff as well.

Well the only lab that ended up coming through was one such engineering lab. I have met with the professor in charge of the lab, as well as the graduate student who I would be working under, and I get along with both of them well enough to where I think working in the lab would be a positive experience overall.

The specific topic I would be working on is about nanomaterials and polymers and all that good stuff. My question is: is this too far removed from current "physics" research to be useful to me when grad school comes around? I really don't feel like I have the knowledge base to know what specific research topics I'm interested in, so I don't know what else I would specifically be interested in.

Additional context I suppose is that there are more labs I could reach out to that do biophysical research, I just worry about starting off another long search process and having downtime in my resume. At my prior university I did research for about 1.5 years in an astro group, mostly just being a computer jockey.

Any advice is extremely appreciated, thanks in advance!

TL:DR: How much do the topics you do undergrad research in actually matter?

4 Comments
2024/01/16
00:07 UTC

3

QM/MM Research Guidance

My story’s a little complicated but I’ll sum it up quickly. I’m essentially a premed physics major interested in MD/PhD programs and QM/MM research.

I am taking stat thermo and quantum physics 1 in the spring; graduate molecular QM 1, quantum physics 2, and intermediate mechanics in fall 2024; and graduate molecular QM 2, graduate statistical mechanics 1, biophysics, and chemical dynamics in spring 2025.

I have prior research experience in physics but not QM/MM related. I have been in contact with a QM/MM researcher at my university and he recommended the graduate chem classes and chemical dynamics and seems open to me joining given sufficient coursework.

Questions

  1. When do you think it would be possible for me to be accepted into a QM/MM lab just based on my coursework

  2. What would an undergraduate possibly actually do in a QM/MM lab as in what are possible roles

  3. I was also thinking about taking quantum computing, advanced computational chemistry, and/or graduate physical organic chemistry. Should I sub out any of these classes for the ones I’ve listed above? Or are there any classes that you recommend I take?

  4. The researcher I was in contact with suggested that I could possibly do my own project in the future. What are some examples of projects for QM/MM that an undergrad could do (with guidance of course)?

If you could answer any of these questions it would help me immensely, thanks :)

6 Comments
2024/01/08
17:21 UTC

1

Particle nature of photons and the eye

Another redditor commented about how the eye is able to convert visible light into the sense of sight.

They didn't go into a lot of detail, but mentioned that the opsin proteins are able to "transduce the kinetic energy of photons into biochemical energy and fire an neuronal signaling pathway."

While I understand what they meant, in this example, i'm struggling relating to the particle nature of the photon, especially since the eye is not responding to general energy on the EM spectrum, but a very narrow portion of wavelengths.

Can someone help me to think about this correctly?

2 Comments
2024/01/07
05:01 UTC

19

Mixing biochemistry, chemistry, physics and maths all together?

I just finished my undergraduate, I did a double major in biochemistry and chemistry with an honours in biochem. During my degree I also took a fair amount of physics and maths courses (although I would have liked to take more). Now I am trying to decide what to do going forwards. I really enjoy research and academia, but I just want to find the right field for me.

My honours was with a structural biology group working on chromatin post translational modifications and was mainly experimental work. I found it highly enjoyable, but I am not sure I want to continue a PhD at my current uni as I feel that there is a lot more I want to learn which I would not be exposed.

My interests are in fundamentals of molecular biochemistry: protein and RNA folding, abiogenesis as well as chromatin structure, gene regulation and post translational modifications. My passion is really to understand at the chemical level how biology works. I also really enjoy physics (especially quantum mechanics, statistical mechanics and thermo) as well as mathematics and chemistry (mainly organic, chemical bio and physical chem). I always found spectroscopic techniques fascinating as well as structural biology techniques (especially NMR) but I would also like to learn more about computational methods like MD. I feel like my ideal scenario would be one where I can use mathematics and physics concepts alongside biochemical techniques to study and develop theories about the basis of biological processes, like I reckon it'd be so cool if we could develop mathematical descriptions for biology. But I don't really know if that is just a sort of a wild dream? Also, I am a bit worried about not having a strong background in physics and mathematics.

I am currently looking at masters programs in Europe (and US) that will provide me with a rigorous coursework in biophysics, but I am a little unsure about my options. Any suggestions or advice would be much appreciated!

14 Comments
2023/12/31
16:19 UTC

1

Bioacoustics Education Survey ending soon

Hi Everyone,

A couple of months ago, I made a post with links to a set of online surveys designed to assess the educational backgrounds of professionals and students interested in bioacoustics. These surveys are part of an MSc project, and their results will help inform the creation of educational material for those who wish to enter the field. The survey ends at the beginning of the New Year (Eastern Standard Time). I wanted to advertise them again to catch potential respondents who missed them when they were first posted. I have the links attached below:

This first link is for the professional survey (https://cwu.co1.qualtrics.com/jfe/form/SV_doipAjq6WLEP66O)

This second link is for the student survey (https://cwu.co1.qualtrics.com/jfe/form/SV_08JXJxtrD7DpeVU).

Neither should take more than 15 minutes.

0 Comments
2023/12/22
17:47 UTC

3

Would a roadrunner be faster than a horse, if they were roughly the same size?

I am a fiction writer, not a biophysicist. In general, I would like to know if there is a scientific or theoretic formula that could calculate a healthy creature’s speed at different sizes. I have a thing for ordinary animals being extraordinary sizes (both bigger and smaller).

Techniques to make realistic animal statistics would be appreciated, but an answer to the base question is enough, if you can explain your answer.

Also, if biophysics is the wrong field to theorize about something like this, I apologize and would appreciate any suggestions on better suited reddit threads or reference sites.

Thank you for any help 🙏

8 Comments
2023/12/16
12:14 UTC

10

What programming languages should I learn?

The title pretty much says it all, I'm in my undergrad for biophysics right now and I'm about to finish a course on java. I want to learn some more languages I was curious to know which ones are more commonly used in application in the field. Thank you in advance for any assistance.

11 Comments
2023/12/10
19:33 UTC

2

How much weight could a white-tailed deer carry on its back?

The title explains it all, I know deer obviously can’t carry a lot but I want to know how many pounds they could carry hypothetically.

0 Comments
2023/11/29
14:21 UTC

3

Bioacoustics Research Surveys

Hi Everyone,

I am a masters student in CWU's Primate Behavior & Ecology Program. I am interested in Primate Bioacoustics******* and STEM education. I've noticed there can be quite a learning curve for undergraduates who are interested in joining the field. Unfortunately, there's not a lot of materials that are concise, really available, and easily accessible. My goal is to create such a resource. To do this, I have designed two surveys; one survey is to assess the educational backgrounds of students (both graduate and undergraduate) and their expectations regarding the field. The second survey is similar but is targeted towards established bioacoustics researchers. Using the results of these surveys, I hope to create the materials we so desperately need.

Would those who are interested in bioacoustics be willing to participate or tell me where the appropriate place to post these would be?

This first link is for the professional survey (https://cwu.co1.qualtrics.com/jfe/form/SV_doipAjq6WLEP66O)

This second link is for the student survey (https://cwu.co1.qualtrics.com/jfe/form/SV_08JXJxtrD7DpeVU).

Neither should take more than 15 minutes.

Thanks in advance!

***Bioacoustics is the study of how living things produce, receive, and react to sound. For example some might study the physiology underlying vocal development, while others might use passive acoustic monitoring for conservation purposes.

1 Comment
2023/11/17
20:27 UTC

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