<?xml version="1.0" encoding="UTF-8"?><rss xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:content="http://purl.org/rss/1.0/modules/content/" xmlns:atom="http://www.w3.org/2005/Atom" version="2.0"><channel><title><![CDATA[RSS Feed]]></title><description><![CDATA[RSS Feed]]></description><link>http://direct.ecency.com</link><image><url>http://direct.ecency.com/logo512.png</url><title>RSS Feed</title><link>http://direct.ecency.com</link></image><generator>RSS for Node</generator><lastBuildDate>Tue, 21 Apr 2026 05:23:03 GMT</lastBuildDate><atom:link href="http://direct.ecency.com/created/biophysics/rss.xml" rel="self" type="application/rss+xml"/><item><title><![CDATA[The Cell Remembers 🧫]]></title><description><![CDATA[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]]></description><link>http://direct.ecency.com/hive-163521/@seki1/the-cell-remembers</link><guid isPermaLink="true">http://direct.ecency.com/hive-163521/@seki1/the-cell-remembers</guid><category><![CDATA[hive-163521]]></category><dc:creator><![CDATA[seki1]]></dc:creator><pubDate>Mon, 29 May 2023 20:17:09 GMT</pubDate><enclosure url="https://images.ecency.com/p/k75bsZMwYNu2L3iBMXq5y7xeiy1isFJsZxnMZSXuXEsxe4ee1cUkGyPr8g2zQkMeQKbwoCNpcM8wRc4m57v5hnWsgxeoBcwndFTWcyxYUrBa8bFkpFQCi7SzzGyXSs7SRH8ZpLqXs9omdyGGBQzyBgHejMVDJqQhC?format=match&amp;mode=fit" length="0" type="false"/></item><item><title><![CDATA[COOKE-DESERNO membrane patch forming cylinder!]]></title><description><![CDATA[This is a simulation I am currently doing. The model is described here:]]></description><link>http://direct.ecency.com/hive-196387/@dexterdev/cooke-deserno-membrane-patch-forming-cylinder</link><guid isPermaLink="true">http://direct.ecency.com/hive-196387/@dexterdev/cooke-deserno-membrane-patch-forming-cylinder</guid><category><![CDATA[hive-196387]]></category><dc:creator><![CDATA[dexterdev]]></dc:creator><pubDate>Tue, 09 Feb 2021 10:21:00 GMT</pubDate><enclosure url="https://images.ecency.com/p/S5Eokt4BcQdk7EHeT1aYjzebg2hC7hkthT45dvfJKFz1UAJBcCJN7eU9QbGnPsZD9dgSJYe?format=match&amp;mode=fit" length="0" type="false"/></item><item><title><![CDATA[KL divergence as a measure to quantify irreversibility in non-equilibrium systems]]></title><description><![CDATA[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]]></description><link>http://direct.ecency.com/hive-196387/@dexterdev/kl-divergence-as-a-measure-to-quantify-irreversibi-1589388735</link><guid isPermaLink="true">http://direct.ecency.com/hive-196387/@dexterdev/kl-divergence-as-a-measure-to-quantify-irreversibi-1589388735</guid><category><![CDATA[hive-196387]]></category><dc:creator><![CDATA[dexterdev]]></dc:creator><pubDate>Wed, 13 May 2020 16:52:15 GMT</pubDate><enclosure url="https://images.ecency.com/p/2bP4pJr4wVimqCWjYimXJe2cnCgn4V9fxiC74Afiq7c?format=match&amp;mode=fit" length="0" type="false"/></item><item><title><![CDATA[Creating a CG vesicle structure and coordinate file for simulations]]></title><description><![CDATA[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.]]></description><link>http://direct.ecency.com/hive-196387/@dexterdev/creating-a-cg-vesicle-structure-and-coordinate-file-for-simulations</link><guid isPermaLink="true">http://direct.ecency.com/hive-196387/@dexterdev/creating-a-cg-vesicle-structure-and-coordinate-file-for-simulations</guid><category><![CDATA[hive-196387]]></category><dc:creator><![CDATA[dexterdev]]></dc:creator><pubDate>Fri, 01 May 2020 16:08:51 GMT</pubDate><enclosure url="https://images.ecency.com/p/2bP4pJr4wVimqCWjYimXJe2cnCgnL5gmsP735dBGPpq?format=match&amp;mode=fit" length="0" type="false"/></item><item><title><![CDATA[Coarse-grained simulation of lipid vesicles using Farago model]]></title><description><![CDATA[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]]></description><link>http://direct.ecency.com/hive-100421/@dexterdev/seihnvqh</link><guid isPermaLink="true">http://direct.ecency.com/hive-100421/@dexterdev/seihnvqh</guid><category><![CDATA[hive-100421]]></category><dc:creator><![CDATA[dexterdev]]></dc:creator><pubDate>Tue, 28 Apr 2020 06:59:15 GMT</pubDate><enclosure url="https://images.ecency.com/p/2HeX3Zi2vTf1hsWg5nYFdFyFDGZN1HWb4uWowTgoQbErXa3BVx3zoQdhZRmF3ZkK1Tit6?format=match&amp;mode=fit" length="0" type="false"/></item><item><title><![CDATA[Modelling a "water-free" coarse-grained lipid system]]></title><description><![CDATA[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]]></description><link>http://direct.ecency.com/hive-196387/@dexterdev/modelling-a-water-fr-1587907199</link><guid isPermaLink="true">http://direct.ecency.com/hive-196387/@dexterdev/modelling-a-water-fr-1587907199</guid><category><![CDATA[hive-196387]]></category><dc:creator><![CDATA[dexterdev]]></dc:creator><pubDate>Sun, 26 Apr 2020 13:20:00 GMT</pubDate><enclosure url="https://images.ecency.com/p/2bP4pJr4wVimqCWjYimXJe2cnCgnLsCPQGfXPD4bfxS?format=match&amp;mode=fit" length="0" type="false"/></item><item><title><![CDATA[Longer run of the LAMMPS code from previous post exhibits bilayer self assembly !]]></title><description><![CDATA[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]]></description><link>http://direct.ecency.com/steemstem/@dexterdev/longer-run-of-the-la-1586775972</link><guid isPermaLink="true">http://direct.ecency.com/steemstem/@dexterdev/longer-run-of-the-la-1586775972</guid><category><![CDATA[steemstem]]></category><dc:creator><![CDATA[dexterdev]]></dc:creator><pubDate>Mon, 13 Apr 2020 11:06:15 GMT</pubDate><enclosure url="https://images.ecency.com/p/S5Eokt4BcQdk7EHeT1aYjzebg2hC7hkthT45eQpnxGXuo9uSdwroFtmdLZLB4mGfKeDH3Kk?format=match&amp;mode=fit" length="0" type="false"/></item><item><title><![CDATA[A toy example of molecule aggregation to familiarize with LAMMPS software]]></title><description><![CDATA[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,]]></description><link>http://direct.ecency.com/steemstem/@dexterdev/a-toy-example-of-molecule-aggregation-to-familiarize-with-lammps-software</link><guid isPermaLink="true">http://direct.ecency.com/steemstem/@dexterdev/a-toy-example-of-molecule-aggregation-to-familiarize-with-lammps-software</guid><category><![CDATA[steemstem]]></category><dc:creator><![CDATA[dexterdev]]></dc:creator><pubDate>Mon, 06 Apr 2020 10:45:09 GMT</pubDate><enclosure url="https://images.ecency.com/p/S5Eokt4BcQdk7EHeT1aYjzebg2hC7hkthT45eKDLBakomEy4skqH1Repsq2DvNmwJUr8FUA?format=match&amp;mode=fit" length="0" type="false"/></item><item><title><![CDATA[A discord server for Biophysics learning and discussions!]]></title><description><![CDATA[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]]></description><link>http://direct.ecency.com/steemstem/@dexterdev/a-discord-server-for-1585836955</link><guid isPermaLink="true">http://direct.ecency.com/steemstem/@dexterdev/a-discord-server-for-1585836955</guid><category><![CDATA[steemstem]]></category><dc:creator><![CDATA[dexterdev]]></dc:creator><pubDate>Thu, 02 Apr 2020 14:15:57 GMT</pubDate></item><item><title><![CDATA[Reproduction of a coarse-grained MD paper: A nanoparticle-lipid membrane interaction]]></title><description><![CDATA[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]]></description><link>http://direct.ecency.com/steemstem/@dexterdev/reproduction-of-a-co-1563975484</link><guid isPermaLink="true">http://direct.ecency.com/steemstem/@dexterdev/reproduction-of-a-co-1563975484</guid><category><![CDATA[steemstem]]></category><dc:creator><![CDATA[dexterdev]]></dc:creator><pubDate>Wed, 24 Jul 2019 13:41:42 GMT</pubDate><enclosure url="https://images.ecency.com/p/3W72119s5BjWMGm4Xa2MvD5AT2bJsSA8F9WeC6rcqfGXTVuNZGUDHYaLp3h86MDEaT6XaoV9qF6DQbvvgjyoyHjqEgmq7FaNJYeKpA4MVFHD4hNFonAxaz?format=match&amp;mode=fit" length="0" type="false"/></item><item><title><![CDATA[A 2D lipid aggregate formation video!]]></title><description><![CDATA[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]]></description><link>http://direct.ecency.com/steemstem/@dexterdev/a-2d-lipid-aggregate-1561211177</link><guid isPermaLink="true">http://direct.ecency.com/steemstem/@dexterdev/a-2d-lipid-aggregate-1561211177</guid><category><![CDATA[steemstem]]></category><dc:creator><![CDATA[dexterdev]]></dc:creator><pubDate>Sat, 22 Jun 2019 13:49:45 GMT</pubDate><enclosure url="https://images.ecency.com/p/S5Eokt4BcQdk7EHeT1aYjzebg2hC7hkthT45eQT5yDPz2UTXRcHEdHfdLaBkt9JrXpjSvmL?format=match&amp;mode=fit" length="0" type="false"/></item><item><title><![CDATA[Our new paper got published in the journal of membrane biology!]]></title><description><![CDATA[![]( 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]]></description><link>http://direct.ecency.com/steemstem/@dexterdev/our-new-paper-got-published-in-the-journal-of-membrane-biology</link><guid isPermaLink="true">http://direct.ecency.com/steemstem/@dexterdev/our-new-paper-got-published-in-the-journal-of-membrane-biology</guid><category><![CDATA[steemstem]]></category><dc:creator><![CDATA[dexterdev]]></dc:creator><pubDate>Wed, 12 Jun 2019 08:46:30 GMT</pubDate><enclosure url="https://images.ecency.com/p/ADdPNihJzmPbNuTnFsHRNDmCAkAgattd5LYTTLx968pDiT28mXE8cVQhVusTW3Qhg7AGi3A1f8rxAQzoih5mcqdXW?format=match&amp;mode=fit" length="0" type="false"/></item><item><title><![CDATA[Two great mailing lists (soft-matter physics & Machine-Learning)]]></title><description><![CDATA[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]]></description><link>http://direct.ecency.com/steemstem/@dexterdev/two-great-mailing-lists-soft-matter-physics-and-machine-learning</link><guid isPermaLink="true">http://direct.ecency.com/steemstem/@dexterdev/two-great-mailing-lists-soft-matter-physics-and-machine-learning</guid><category><![CDATA[steemstem]]></category><dc:creator><![CDATA[dexterdev]]></dc:creator><pubDate>Tue, 11 Jun 2019 13:05:54 GMT</pubDate></item><item><title><![CDATA[A: Should you climb stairs two steps at a time to save energy?]]></title><description><![CDATA[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]]></description><link>http://direct.ecency.com/stemq/@scienceblocks/a-should-you-climb-stairs-two-steps-at-a-time-to-save-energy1555430100517</link><guid isPermaLink="true">http://direct.ecency.com/stemq/@scienceblocks/a-should-you-climb-stairs-two-steps-at-a-time-to-save-energy1555430100517</guid><category><![CDATA[stemq]]></category><dc:creator><![CDATA[scienceblocks]]></dc:creator><pubDate>Tue, 16 Apr 2019 15:55:03 GMT</pubDate><enclosure url="https://images.ecency.com/p/2r8F9rTBenJQfQgENfxADE6EVYabczqmSF5KeWefV5WL9WNSbQS5ykGUDMDDuATRuNfvCR49a1iMtEFnh5sH3xKW3boEL2YrmDon4t7xPNZ6GKPzxrbzzMKnVRpMj6LvJ?format=match&amp;mode=fit" length="0" type="false"/></item><item><title><![CDATA[Decipher my science meme]]></title><link>http://direct.ecency.com/steemstem/@dexterdev/decipher-my-science--1550047093</link><guid isPermaLink="true">http://direct.ecency.com/steemstem/@dexterdev/decipher-my-science--1550047093</guid><category><![CDATA[steemstem]]></category><dc:creator><![CDATA[dexterdev]]></dc:creator><pubDate>Wed, 13 Feb 2019 08:41:12 GMT</pubDate><enclosure url="https://images.ecency.com/p/3W72119s5BjWMGm4Xa2MvD5AT2bJsSA8F9WeC6rcqfGXTVuNZGUDHYaLp3h86MDEaT6XaoV9qEnnF3EYEf12fWh7NdAEzrv3sQZbh2nvx9u2DmJfX4ABjc?format=match&amp;mode=fit" length="0" type="false"/></item><item><title><![CDATA[Tracking Interdigitated lipids from MD simulations]]></title><description><![CDATA[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]]></description><link>http://direct.ecency.com/steemstem/@dexterdev/tracking-interdigita-1549802647</link><guid isPermaLink="true">http://direct.ecency.com/steemstem/@dexterdev/tracking-interdigita-1549802647</guid><category><![CDATA[steemstem]]></category><dc:creator><![CDATA[dexterdev]]></dc:creator><pubDate>Sun, 10 Feb 2019 12:47:03 GMT</pubDate><enclosure url="https://images.ecency.com/p/S5Eokt4BcQdk7EHeT1aYjzebg2hC7hkthT45e9Z3PGPS6PkGZMLic7omBJwxCWbyK4hYPMG?format=match&amp;mode=fit" length="0" type="false"/></item><item><title><![CDATA[Visualizing Lipid Defects in model membrane simulations]]></title><description><![CDATA[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]]></description><link>http://direct.ecency.com/steemstem/@dexterdev/visualizing-lipid-de-1549468204</link><guid isPermaLink="true">http://direct.ecency.com/steemstem/@dexterdev/visualizing-lipid-de-1549468204</guid><category><![CDATA[steemstem]]></category><dc:creator><![CDATA[dexterdev]]></dc:creator><pubDate>Wed, 06 Feb 2019 15:53:00 GMT</pubDate><enclosure url="https://images.ecency.com/p/2gsjgna1uruvUuS7ndh9YqVwYGPLVszbFLwwpAYXZAmoq2YafDGmFjbBt6mDN5JhNGRpfcYPMjPyRBVPxaVSb5NfaeCZwRmRAC8srNtqV1EXxZf15p?format=match&amp;mode=fit" length="0" type="false"/></item><item><title><![CDATA[Mutated Nogo66 protein all atom classical molecular dynamics simulation video (50ns)]]></title><description><![CDATA[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]]></description><link>http://direct.ecency.com/steemstem/@dexterdev/mutated-nogo66-prote</link><guid isPermaLink="true">http://direct.ecency.com/steemstem/@dexterdev/mutated-nogo66-prote</guid><category><![CDATA[steemstem]]></category><dc:creator><![CDATA[dexterdev]]></dc:creator><pubDate>Thu, 24 Jan 2019 11:35:57 GMT</pubDate><enclosure url="https://images.ecency.com/p/S5Eokt4BcQdk7EHeT1aYjzebg2hC7hkthT45dwsrfYBSt5Ni5sfm7fHMXn9ypQUxs8npCdk?format=match&amp;mode=fit" length="0" type="false"/></item><item><title><![CDATA[A glimpse from my current work]]></title><description><![CDATA[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]]></description><link>http://direct.ecency.com/steemstem/@dexterdev/a-glimpse-from-my-cu</link><guid isPermaLink="true">http://direct.ecency.com/steemstem/@dexterdev/a-glimpse-from-my-cu</guid><category><![CDATA[steemstem]]></category><dc:creator><![CDATA[dexterdev]]></dc:creator><pubDate>Sun, 20 Jan 2019 15:43:27 GMT</pubDate><enclosure url="https://images.ecency.com/p/S5Eokt4BcQdk7EHeT1aYjzebg2hC7hkthT45dvHRjDe7Juj48LaZdFS3XpAb9NsNBS7ABaW?format=match&amp;mode=fit" length="0" type="false"/></item><item><title><![CDATA[Why Did Nature Choose Life?]]></title><description><![CDATA[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]]></description><link>http://direct.ecency.com/stemq/@gokhan83kurt/q-how-can-ophrys-apifera-bee-orchid-plant-imitate-female-bees-apperance1546513384369</link><guid isPermaLink="true">http://direct.ecency.com/stemq/@gokhan83kurt/q-how-can-ophrys-apifera-bee-orchid-plant-imitate-female-bees-apperance1546513384369</guid><category><![CDATA[stemq]]></category><dc:creator><![CDATA[gokhan83kurt]]></dc:creator><pubDate>Thu, 03 Jan 2019 11:03:06 GMT</pubDate><enclosure url="https://images.ecency.com/p/C3TZR1g81UNaPs7vzNXHueW5ZM76DSHWEY7onmfLxcK2iNpQFwK3ZeWrsUJgoneb54sDLrRpU3Z2uaviCQCuKVQjzuSc2Y1d8kmjVBAu4pye1FQdiF8MXjU?format=match&amp;mode=fit" length="0" type="false"/></item></channel></rss>