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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
2020-05-01 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.
$ 15.443
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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
muath
Photography Lovers
2026-06-16 00:41
Promoted
🔥 Today we are showcasing very rare natural masterpieces of natural Yemeni agate: feast your eyes on this enchanting natural beauty!
Hello to the Hive community and gemstone enthusiasts, Sometimes, nature creates masterpieces that surpass the imagination of even the most skilled human artists. Today, I am delighted to share with you
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
2020-04-02 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
2019-02-10 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
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
shaidon
Silver Bloggers
2026-06-10 12:01
Promoted
Knuckle Down!
Knuckle Down! I have one last assignment due for this term. It’s due on Sunday 14th of June before 11:59pm. I have a shift at the Adelaide Oval on Saturday meaning that I really should finish it by Friday
dexterdev
steemstem
2018-12-24 10:09
Understanding Correlation measurements of Protein motions from MD trajectories
Today let us try understanding correlation maps. It is very common to see correlation maps of protein motions in molecular dynamics research papers. For example, see the figure below: A typical correlation
dexterdev
steemstem
2018-12-14 10:36
Why SER11 site was chosen as the phosphorylation site? : A frequent question which we encounter regarding our work
Hi friends... Recently I had written about our research work which got published in this August. Those who have not read that article can find it below: Phosphorylation promotes binding affinity of Rap-Raf
dexterdev
steemstem
2018-12-05 16:27
Phosphorylation promotes binding affinity of Rap-Raf complex [Original Research Work Summary]
Hello, my dear friends! Welcome to yet another science article from @dexterdev. Today I am going to write about something which I was thinking to do for the last few months. This is about my first research
dexterdev
steemstem
2018-12-01 13:40
Addendum to my previous post: PCA caveat + Tracking Ubiquitin in the Principal component space
This is an addendum to my previous post which you can see here: Repository PCA caveat From PCA plots it is possible to create normalized histograms or distribution plots based on the density of scatter
ismaelvarela
Sketchbook
2026-06-13 19:30
Promoted
❄️✨ The Beauty Hidden in Anime Eyes | Adobe Illustrator Artwork ✨❄️/ ❄️✨ La Belleza Oculta en los Ojos Anime | Ilustración en Adobe Illustrator ✨❄️
Today I want to share a digital manga illustration that I created entirely in Adobe Illustrator. ✨💻 This artwork focuses on one of my favorite elements in anime and manga design: the eyes. 👀💙 For this
dexterdev
steemstem
2018-11-28 09:45
Studying fluctuations in proteins from Molecular Dynamics trajectories
Hi friends... Welcome to yet another article from @dexterdev. Molecules are not stationary entities. Most of the molecules function via dancing in particular patterns. Their motions under different external
dexterdev
steemstem
2018-11-16 06:27
How to create infinite structures for Molecular Dynamics simulations?
Hello, my dear friends! @dexterdev is back after a long gap. Today I will discuss on creating infinite molecular structures for MD simulations!!! (Sounds impossible task... Right?) In MD(molecular dynamics)