<?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>Fri, 17 Apr 2026 17:51:56 GMT</lastBuildDate><atom:link href="http://direct.ecency.com/created/computational-biophysics/rss.xml" rel="self" type="application/rss+xml"/><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[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 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[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[Understanding Correlation measurements of Protein motions from MD trajectories]]></title><description><![CDATA[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]]></description><link>http://direct.ecency.com/steemstem/@dexterdev/understanding-correlation-measurements-of-protein-motions-from-md-trajectories</link><guid isPermaLink="true">http://direct.ecency.com/steemstem/@dexterdev/understanding-correlation-measurements-of-protein-motions-from-md-trajectories</guid><category><![CDATA[steemstem]]></category><dc:creator><![CDATA[dexterdev]]></dc:creator><pubDate>Mon, 24 Dec 2018 10:09:12 GMT</pubDate><enclosure url="https://images.ecency.com/p/2bP4pJr4wVimqCWjYimXJe2cnCgn9R7fdFwCXX6RLT8?format=match&amp;mode=fit" length="0" type="false"/></item><item><title><![CDATA[Why SER11 site was chosen as the phosphorylation site? :  A frequent question which we encounter regarding our work]]></title><description><![CDATA[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]]></description><link>http://direct.ecency.com/steemstem/@dexterdev/why-ser11-site-was-chosen-as-the-phosphorylation-site-a-frequent-question-which-we-encounter-regarding-our-work</link><guid isPermaLink="true">http://direct.ecency.com/steemstem/@dexterdev/why-ser11-site-was-chosen-as-the-phosphorylation-site-a-frequent-question-which-we-encounter-regarding-our-work</guid><category><![CDATA[steemstem]]></category><dc:creator><![CDATA[dexterdev]]></dc:creator><pubDate>Fri, 14 Dec 2018 10:36:36 GMT</pubDate><enclosure url="https://images.ecency.com/p/ChYr1cJZCH5LGrxCNukYkfUg6HFWv7Devos1AknzPKT8BV6aBg6d3fuTdmbYu7C1Q8Tt4WcWwJD5zk9KdqXN52XnpJzEWg1uykctYXpUmXsZ1eSVRCMbrmvSCMRcyY4T6yBa3HpZ9t7bFm8UaBdoqu2GK75ZgX9o4B4594rLRHRcdu8sUJX1g6bZi8PxAa?format=match&amp;mode=fit" length="0" type="false"/></item><item><title><![CDATA[Phosphorylation promotes binding affinity of Rap-Raf complex [Original Research Work Summary]]]></title><description><![CDATA[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]]></description><link>http://direct.ecency.com/steemstem/@dexterdev/phosphorylation-promotes-binding-affinity-of-rap-raf-complex-original-research-work-summary</link><guid isPermaLink="true">http://direct.ecency.com/steemstem/@dexterdev/phosphorylation-promotes-binding-affinity-of-rap-raf-complex-original-research-work-summary</guid><category><![CDATA[steemstem]]></category><dc:creator><![CDATA[dexterdev]]></dc:creator><pubDate>Wed, 05 Dec 2018 16:27:06 GMT</pubDate><enclosure url="https://images.ecency.com/p/2bP4pJr4wVimqCWjYimXJe2cnCgn4z35GgfhNhCASoY?format=match&amp;mode=fit" length="0" type="false"/></item><item><title><![CDATA[Addendum to my previous post: PCA caveat + Tracking Ubiquitin in the Principal component space]]></title><description><![CDATA[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]]></description><link>http://direct.ecency.com/steemstem/@dexterdev/addendum-to-my-previous-post-pca-caveat-tracking-ubiquitin-in-the-principal-component-space</link><guid isPermaLink="true">http://direct.ecency.com/steemstem/@dexterdev/addendum-to-my-previous-post-pca-caveat-tracking-ubiquitin-in-the-principal-component-space</guid><category><![CDATA[steemstem]]></category><dc:creator><![CDATA[dexterdev]]></dc:creator><pubDate>Sat, 01 Dec 2018 13:40:33 GMT</pubDate><enclosure url="https://images.ecency.com/p/C3TZR1g81UNaPs7vzNXHueW5ZM76DSHWEY7onmfLxcK2iNuXfzCmccV7N2nUPgp2ag7owMKYczUGrTUmwrPimPTgRGj5pwwnUaVbdtTCcyfwBrk4WKMdFxS?format=match&amp;mode=fit" length="0" type="false"/></item><item><title><![CDATA[Studying fluctuations in proteins from Molecular Dynamics trajectories]]></title><description><![CDATA[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]]></description><link>http://direct.ecency.com/steemstem/@dexterdev/studying-global-motions-of-proteins-from-molecular-dynamics-trajectories</link><guid isPermaLink="true">http://direct.ecency.com/steemstem/@dexterdev/studying-global-motions-of-proteins-from-molecular-dynamics-trajectories</guid><category><![CDATA[steemstem]]></category><dc:creator><![CDATA[dexterdev]]></dc:creator><pubDate>Wed, 28 Nov 2018 09:45:09 GMT</pubDate><enclosure url="https://images.ecency.com/p/ChYr1cJZCH5LGrxCNukYkfUg6HFWv7Devos1AknzPKT8BV6aBg6d3fuTdmbYu7C1Q8Tt4WcWwJD5zk9KdqXN52XnpJzEWg1uykctYXpUmXsZ1eSVRCMbrmvSCMRcyY4T6yBa3HpZ9t7bFm8UaBdoqu2GK75ZgX9o4B4594rLRHRcdu8sUMn1RPdfnDXqaW?format=match&amp;mode=fit" length="0" type="false"/></item><item><title><![CDATA[How to create infinite structures for Molecular Dynamics simulations?]]></title><description><![CDATA[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)]]></description><link>http://direct.ecency.com/steemstem/@dexterdev/how-to-create-infinite-structures-in-molecular-dynamics-simulations</link><guid isPermaLink="true">http://direct.ecency.com/steemstem/@dexterdev/how-to-create-infinite-structures-in-molecular-dynamics-simulations</guid><category><![CDATA[steemstem]]></category><dc:creator><![CDATA[dexterdev]]></dc:creator><pubDate>Fri, 16 Nov 2018 06:27:48 GMT</pubDate><enclosure url="https://images.ecency.com/p/2bP4pJr4wVimqCWjYimXJe2cnCgn9xXxRMnMozVTocH?format=match&amp;mode=fit" length="0" type="false"/></item></channel></rss>