#biophysics

Well it's been quite long since I did an article here based on a topic I didn't see from my memes page. Clearly it's due to the lack of time cause of school work that I began my lazy science posts(and

This is a simulation I am currently doing. The model is described here:

Hello friends... @dexterdev is back with his new article. This one is not about coarse-grained simulations. For the past few days I was thinking about active matter systems, non-equilibrium statistical

Hello friends! I am back with my coarse-grained(CG) molecular dynamics(MD) simulation series. Today we will see how to create a vesicle coordinate file and assign it proper topology and structure information.

See my recent article for the model. This is an attempt to see if I can see the fusion event between two vesicles. Will report the results once I finish the entire simulation. :) ▶️ 3Speak

In the last article, we saw how to set-up a coarse-grained simulation using LAMMPS software. In today's article, I will discuss how to come up with a model to simulate a coarse-grained lipid system. In

I just wanted to update you guys with a longer run of LAMMPS code in my previous article. In my previous article, it seemed that we were observing micelle like structures. But on running it for a longer

Hello friends... Welcome to my new molecular dynamics post. As I mentioned in my previous post, I am going to start the new series on coarse-grained lipid models. As an opening article to this series,

Few of us wanted to create a discord server for Biophysics. What we intend is to begin a commonplace for discussions/numerical experiments. Also possibly document the results in the form of HIVE blogs(under

This is a reproduction of the Hongyan Yuan et al paper "One-particle-thick, solvent-free, coarse-grained model for biological and biomimetic fluid membranes".The simulation was done in LAMMPS and the parameter

This is a 2-dimensional toy problem I ran today. You can guess here hydrophobic(water-hating) green(the cyan particles are the solvent particles) particles hiding in 2D micelles and bilayer structures

![]( Hello Friends! Our new paper got accepted. It's my second paper. The link to the paper is below: Unfortunately, it is behind the SPRINGER paywall! I should write a summary of the paper soon here at

I have recently joined two very useful mailing lists. One mailing list is for those who work in the interface of biology and physics. Another one is for Machine learning. These both are great for those

StemQ Notice: The following is an answer to this question Interesting question @irelandscape. Let's see if we can figure out the answer. I remember going to this trek as a child. During the 14 km of trek

Decipher my science meme

When using softwares like VMD to visualize membranes where lipids exhibit interdigitation as in our case, it will very useful if you can sort out those lipids which specifically exhibit this

Recently we did some all-atom classical molecular dynamics simulations involving DMPC model membrane, Nogo66 membrane active protein, TIP3P water model and NaCl ions. We used CHARMM36 forcefield and ran

Below is a youtube video of 50 nanoseconds long trajectory of a recent all-atom molecular dynamics simulation which I did using NAMD software. The yellow dots are sodium ions and cyan dots are chloride

Below is a video of two 400ns long all-atom classical molecular dynamics trajectories of Rap:Raf complex. The "ice blue" and "orange" tubes are Rap:Raf complex with phosphorylated Serine

Is From Pixabay.com As far as we know, life on earth began approximately 4 billion years ago. The life that emerged as protozoa evolved over time. As a result, there are many complex and intelligent life