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latest #biophysics created topics on internet
seki1
STEMGeeks
2023-05-29 20:17
The Cell Remembers 🧫
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
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dexterdev
StemSocial
2021-02-09 10:21
COOKE-DESERNO membrane patch forming cylinder!
This is a simulation I am currently doing. The model is described here:
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dexterdev
StemSocial
2020-05-13 16:52
KL divergence as a measure to quantify irreversibility in non-equilibrium systems
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
dexterdev
StemSocial
2020-05-01 16:08
Creating a CG vesicle structure and coordinate file for simulations
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.
ravenmus1c
Drumming
2026-06-28 09:37
Promoted
Building My New Dream Drum Setup | TAMA Club Jam, Mod-Bubinga Snare & Hand-Forged Agean Cymbals! 🥁😍
DEUTSCHE Version hier Hallo zusammen! 😊 Wie geht es euch? Mit der Gürtelrose wird es langsam besser. Sie sitzt zwar immer noch im Auge, aber ich kann schon viel besser sehen und konnte die Medikamente
dexterdev
Threespeak - OLD
2020-04-28 06:59
Coarse-grained simulation of lipid vesicles using Farago model
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
dexterdev
StemSocial
2020-04-26 13:20
Modelling a "water-free" coarse-grained lipid system
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
dexterdev
steemstem
2020-04-13 11:06
Longer run of the LAMMPS code from previous post exhibits bilayer self assembly !
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
dexterdev
steemstem
2020-04-06 10:45
A toy example of molecule aggregation to familiarize with LAMMPS software
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,
asterkame
YAF - Young Art Fair
2026-06-25 10:18
Promoted
Painting a Blossoming Tree under Moonlit Sky
Hello Everyone! I drew a landscape with the full moon yesterday. There are the full moon with flower branches in this picture. I drew the picture with watercolor. In the first step, I drew the moon with
dexterdev
steemstem
2020-04-02 14:15
A discord server for Biophysics learning and discussions!
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
dexterdev
steemstem
2019-07-24 13:41
Reproduction of a coarse-grained MD paper: A nanoparticle-lipid membrane interaction
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
dexterdev
steemstem
2019-06-22 13:49
A 2D lipid aggregate formation video!
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
dexterdev
steemstem
2019-06-12 08:46
Our new paper got published in the journal of membrane biology!

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
scienceblocks
stemq
2019-04-16 15:55
A: Should you climb stairs two steps at a time to save energy?
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
dexterdev
steemstem
2019-02-13 08:41
Decipher my science meme
dexterdev
steemstem
2019-02-10 12:47
Tracking Interdigitated lipids from MD simulations
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
darth-azrael
retrocomputing
2026-06-28 18:20
Promoted
Digital Archaeology: Floppy Disk #14 – DEPRESS.DOC
This post includes the contents of DEPRESS.DOC. This file is dated September 2nd, 1985 and is in a subdirectory called TELEPSYC.
dexterdev
steemstem
2019-02-06 15:53
Visualizing Lipid Defects in model membrane simulations
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
dexterdev
steemstem
2019-01-24 11:35
Mutated Nogo66 protein all atom classical molecular dynamics simulation video (50ns)
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
dexterdev
steemstem
2019-01-20 15:43
A glimpse from my current work
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
gokhan83kurt
stemq
2019-01-03 11:03
Why Did Nature Choose Life?
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